Bioinformatics, Volume 36

Volume 36, Number 1, January 2020

Original Papers
Genome Analysis

• 
  Vahid Jalili, Enis Afgan, James Taylor, Jeremy Goecks:
  Cloud bursting galaxy: federated identity and access management. 1-9
• 
  Peng Xu, Timothy Kennell Jr., Min Gao, Human Genome Structural Variation Consortium, Robert P. Kimberly, Zechen Chong:
  MRLR: unraveling high-resolution meiotic recombination by linked reads. 10-16
• 
  Adam Kaplan, Eric F. Lock, Mark Fiecas, Alzheimer's Disease Neuroimaging Initiative:
  Bayesian GWAS with Structured and Non-Local Priors. 17-25

Sequence Analysis

• 
  Davoud Torkamaneh, Jérôme Laroche, Brian Boyle, François Belzile:
  DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing. 26-32
• 
  Rose Orenbuch, Ioan Filip, Devon Comito, Jeffrey Shaman, Itsik Pe'er, Raul Rabadan:
  arcasHLA: high-resolution HLA typing from RNAseq. 33-40
• 
  Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang:
  Protein contact prediction using metagenome sequence data and residual neural networks. 41-48
• 
  Chenwei Lou, Jian Zhao, Ruoyao Shi, Qian Wang, Wenyang Zhou, Yubo Wang, Guoqing Wang, Lan Huang, Xin Feng, Fengfeng Zhou:
  sefOri: selecting the best-engineered sequence features to predict DNA replication origins. 49-55
• 
  Castrense Savojardo, Niccolò Bruciaferri, Giacomo Tartari, Pier Luigi Martelli, Rita Casadio:
  DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks. 56-64
• 
  Li Xing, Mary Lesperance, Xuekui Zhang:
  Simultaneous prediction of multiple outcomes using revised stacking algorithms. 65-72
• 
  Mohamed Chaabane, Robert M. Williams, Austin T. Stephens, Juw Won Park:
  circDeep: deep learning approach for circular RNA classification from other long non-coding RNA. 73-80
• 
  Jakub M. Bartoszewicz, Anja Seidel, Robert Rentzsch, Bernhard Y. Renard:
  DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks. 81-89
• 
  Fabian Sievers, Desmond G. Higgins:
  QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction. 90-95

Structural Bioinformatics

• 
  Jinfang Zheng, Xu Hong, Juan Xie, Xiaoxue Tong, Shiyong Liu:
  P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking. 96-103
• 
  Shuichiro Makigaki, Takashi Ishida:
  Sequence alignment using machine learning for accurate template-based protein structure prediction. 104-111
• 
  Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant G. Honavar, Alexandre M. J. J. Bonvin, Li C. Xue:
  iScore: a novel graph kernel-based function for scoring protein-protein docking models. 112-121
• 
  Jelena Vucinic, David Simoncini, Manon Ruffini, Sophie Barbe, Thomas Schiex:
  Positive multistate protein design. 122-130
• 
  Jiyao Wang, Philippe Youkharibache, Dachuan Zhang, Christopher J. Lanczycki, Renata C. Geer, Thomas Madej, Lon Phan, Minghong Ward, Shennan Lu, Gabriele H. Marchler, Yanli Wang, Stephen H. Bryant, Lewis Y. Geer, Aron Marchler-Bauer:
  iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. 131-135
• 
  Peng Xiong, Xiuhong Hu, Bin Huang, Jiahai Zhang, Quan Chen, Haiyan Liu:
  Increasing the efficiency and accuracy of the ABACUS protein sequence design method. 136-144
• 
  Angela Serra, Serli Önlü, Paola Festa, Vittorio Fortino, Dario Greco:
  MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling. 145-153
• 
  Tomer Meirson, David Bomze, Liron Gat Kahlon, Hava Gil-Henn, Abraham O. Samson:
  A helical lock and key model of polyproline II conformation with SH3. 154-159
• 
  Melanie Schneider, Jean-Luc Pons, William Bourguet, Gilles Labesse:
  Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity. 160-168

Gene expression

• 
  Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi:
  A dynamic programing approach to integrate gene expression data and network information for pathway model generation. 169-176
• 
  John Ferguson, Joseph Chang:
  An empirical Bayesian ranking method, with applications to high throughput biology. 177-185
• 
  Erwan Bigan, Satish Sasidharan Nair, François-Xavier Lejeune, Hélissande Fragnaud, Frédéric Parmentier, Lucile Mégret, Marc Verny, Jeff Aaronson, Jim Rosinski, Christian Néri:
  Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington's disease mice synchronous to symptoms. 186-196
• 
  Xin Zhou, Xiaodong Cai:
  Inference of differential gene regulatory networks based on gene expression and genetic perturbation data. 197-204
• 
  Elizabeth Guruceaga, Alba Garín-Muga, Victor Segura:
  MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides. 205-211

Genetics and Population Analysis

• 
  Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette:
  Mycorrhiza: genotype assignment using phylogenetic networks. 212-220
• 
  Yasuhiro Kojima, Hirotaka Matsumoto, Hisanori Kiryu:
  Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations. 221-231

Systems Biology

• 
  Axel Theorell, Katharina Nöh:
  Reversible jump MCMC for multi-model inference in Metabolic Flux Analysis. 232-240
• 
  Rudolf Schill, Stefan Solbrig, Tilo Wettig, Rainer Spang:
  Modelling cancer progression using Mutual Hazard Networks. 241-249

Data and Text Mining

• 
  Trang T. Le, Weixuan Fu, Jason H. Moore:
  Scaling tree-based automated machine learning to biomedical big data with a feature set selector. 250-256
• 
  Qian Li, Kate Fisher, Wenjun Meng, Bin Fang, Eric A. Welsh, Eric B. Haura, John M. Koomen, Steven A. Eschrich, Brooke L. Fridley, Yian Ann Chen:
  GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. 257-263
• 
  Alexander Junge, Lars Juhl Jensen:
  CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision. 264-271
• 
  Hannah F. Löchel, Dominic Eger, Theodor Sperlea, Dominik Heider:
  Deep learning on chaos game representation for proteins. 272-279
• 
  John M. Giorgi, Gary D. Bader:
  Towards reliable named entity recognition in the biomedical domain. 280-286
• 
  Arne P. Raulf, Joshua Butke, Claus Küpper, Frederik Großerüschkamp, Klaus Gerwert, Axel Mosig:
  Deep representation learning for domain adaptable classification of infrared spectral imaging data. 287-294
• 
  Leon Weber, Jannes Münchmeyer, Tim Rocktäschel, Maryam Habibi, Ulf Leser:
  HUNER: improving biomedical NER with pretraining. 295-302
• 
  Guoxian Yu, Keyao Wang, Carlotta Domeniconi, Maozu Guo, Jun Wang:
  Isoform function prediction based on bi-random walks on a heterogeneous network. 303-310
• 
  Nezar Abdennur, Leonid A. Mirny:
  Cooler: scalable storage for Hi-C data and other genomically labeled arrays. 311-316

Bioimage Informatics

• 
  Vincent Briane, Myriam Vimond, Cesar Augusto Valades-Cruz, Antoine Salomon, Christian Wunder, Charles Kervrann:
  A sequential algorithm to detect diffusion switching along intracellular particle trajectories. 317-329

Erratum
Bioimage Informatics

• 
  Yan Zhao, Xing Chen, Jun Yin:
  Adaptive boosting-based computational model for predicting potential miRNA-disease associations. 330

Volume 36, Number 2, January 2020

Original Papers
Genome Analysis

• 
  William H. Majoros, Young-Sook Kim, Alejandro Barrera, Fan Li, Xingyan Wang, Sarah J. Cunningham, Graham D. Johnson, Cong Guo, William L. Lowe, Denise M. Scholtens, M. Geoffrey Hayes, Timothy E. Reddy, Andrew S. Allen:
  Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. 331-338
• 
  Ran Su, Jiahang Zhang, Xiaofeng Liu, Leyi Wei:
  Identification of expression signatures for non-small-cell lung carcinoma subtype classification. 339-346
• 
  Chan Wang, Jiyuan Hu, Martin J. Blaser, Huilin Li:
  Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data. 347-355
• 
  Terry Ma, Di Xiao, Xin Xing:
  MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies. 356-363
• 
  Sierra S. Nishizaki, Natalie Ng, Shengcheng Dong, Robert S. Porter, Cody Morterud, Colten Williams, Courtney Asman, Jessica A Switzenberg, Alan P. Boyle:
  Predicting the effects of SNPs on transcription factor binding affinity. 364-372
• 
  Patrick Sorn, Christoph Holtsträter, Martin Löwer, Ugur Sahin, David Weber:
  ArtiFuse - computational validation of fusion gene detection tools without relying on simulated reads. 373-379

Sequence Analysis

• 
  Alfredo Velasco II, Benjamin T. James, Vincent D. Wells, Hani Z. Girgis:
  Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models. 380-387
• 
  Cong Pian, Guang-Le Zhang, Fei Li, Xiaodan Fan:
  MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model. 388-392
• 
  Michele Berselli, Enrico Lavezzo, Stefano Toppo:
  QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable. 393-399
• 
  Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin:
  Haplotype-aware graph indexes. 400-407
• 
  Martin C. Frith:
  How sequence alignment scores correspond to probability models. 408-415
• 
  Chloé Dimeglio, Stéphanie Raymond, Nicolas Jeanne, Christelle Reynès, Romain Carcenac, Caroline Lefebvre, Michelle Cazabat, Florence Nicot, Pierre Delobel, Jacques Izopet:
  THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage. 416-421
• 
  Maxat Kulmanov, Robert Hoehndorf:
  DeepGOPlus: improved protein function prediction from sequence. 422-429

Phylogenetics

• 
  Roberto Del Amparo, Alberto Vicens, Miguel Arenas:
  The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation. 430-436

Structural Bioinformatics

• 
  Di Wang, Ling Geng, Yu-Jun Zhao, Yang Yang, Yan Huang, Yang Zhang, Hong-Bin Shen:
  Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. 437-448
• 
  Justin Chan, Jinhao Zou, Christopher Llynard Ortiz, Chi-Hong Chang Chien, Rong-Long Pan, Lee-Wei Yang:
  DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing. 449-461
• 
  Gregor Entzian, Martin Raden:
  pourRNA - a time- and memory-efficient approach for the guided exploration of RNA energy landscapes. 462-469
• 
  Badri Adhikari:
  DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout. 470-477
• 
  Zeyu Wen, Jiahua He, Sheng-You Huang:
  Topology-independent and global protein structure alignment through an FFT-based algorithm. 478-486

Gene expression

• 
  Adib Shafi, Tin Nguyen, Azam Peyvandi-Pour, Sorin Draghici:
  GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis. 487-495
• 
  Wanwen Zeng, Yong Wang, Rui Jiang:
  Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network. 496-503
• 
  Christelle Reynès, Guilhem Kister, Marine Rohmer, Tristan Bouschet, Annie Varrault, Emeric Dubois, Stéphanie Rialle, Laurent Journot, Robert Sabatier:
  ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses. 504-513
• 
  Taneli Pusa, Mariana Galvao Ferrarini, Ricardo Andrade, Arnaud Mary, Alberto Marchetti-Spaccamela, Leen Stougie, Marie-France Sagot:
  MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network. 514-523
• 
  Zhiguang Huo, Shaowu Tang, Yongseok Park, George C. Tseng:
  P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications. 524-532
• 
  Feiyang Ma, Matteo Pellegrini:
  ACTINN: automated identification of cell types in single cell RNA sequencing. 533-538
• 
  Li Chen, Feng Wang, Emily C. Bruggeman, Chao Li, Bing Yao:
  circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. 539-545
• 
  Kyungsoo Kim, Sunmo Yang, Sang-Jun Ha, Insuk Lee:
  VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data. 546-551

Genetics and Population Analysis

• 
  Lerato E. Magosi, Anuj Goel, Jemma C. Hopewell:
  Identifying small-effect genetic associations overlooked by the conventional fixed-effect model in a large-scale meta-analysis of coronary artery disease. 552-557

Systems Biology

• 
  Mikel Hernaez, Charles Blatti, Olivier Gevaert:
  Comparison of single and module-based methods for modeling gene regulatory networks. 558-567
• 
  Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha S. Dina, Xuequn Shang, David M. Kramer, Jin Chen:
  Identifying emerging phenomenon in long temporal phenotyping experiments. 568-577
• 
  Ning Shi, Zexuan Zhu, Ke Tang, David Parker, Shan He:
  ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics. 578-585
• 
  Boseung Choi, Yu-Yu Cheng, Selahattin Cinar, William Ott, Matthew R. Bennett, Kresimir Josic, Jae Kyoung Kim:
  Bayesian inference of distributed time delay in transcriptional and translational regulation. 586-593
• 
  Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl:
  Efficient parameterization of large-scale dynamic models based on relative measurements. 594-602
• 
  Sameh K. Mohamed, Vít Novácek, Aayah Nounu:
  Discovering protein drug targets using knowledge graph embeddings. 603-610

Data and Text Mining

• 
  Peiliang Lou, Antonio Jimeno-Yepes, Zai Zhang, Qinghua Zheng, Xiangrong Zhang, Chen Li:
  BioNorm: deep learning-based event normalization for the curation of reaction databases. 611-620
• 
  Siva Rajesh Kasa, Sakyajit Bhattacharya, Vaibhav Rajan:
  Gaussian mixture copulas for high-dimensional clustering and dependency-based subtyping. 621-628
• 
  Sami Tabib, Denis Larocque:
  Non-parametric individual treatment effect estimation for survival data with random forests. 629-636
• 
  Shankai Yan, Ka-Chun Wong:
  Context awareness and embedding for biomedical event extraction. 637-643

Applications Notes
Genome Analysis

• 
  Ricardo N. Ramirez, Karni Bedirian, Simon M. Gray, Alos Diallo:
  DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data. 644-646

Structural Bioinformatics

• 
  Grace Meng, Marva Tariq, Swati Jain, Shereef Elmetwaly, Tamar Schlick:
  RAG-Web: RNA structure prediction/design using RNA-As-Graphs. 647-648

Data and Text Mining

• 
  Ramiro Magno, Ana-Teresa Maia:
  gwasrapidd: an R package to query, download and wrangle GWAS catalog data. 649-650

Corrigendum
Data and Text Mining

• 
  Antoine Limasset, Jean-François Flot, Pierre Peterlongo:
  Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. 651

Volume 36, Number 3, February 2020

Original Papers
Genome Analysis

• 
  Ya Wang, Min Qian, Deliang Tang, Julie Herbstman, Frederica Perera, Shuang Wang:
  A powerful and flexible weighted distance-based method incorporating interactions between DNA methylation and environmental factors on health outcomes. 653-659
• 
  Ren-Hua Chung, Chen-Yu Kang:
  pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions. 660-665
• 
  Yaqiang Cao, Zhaoxiong Chen, Xingwei Chen, Daosheng Ai, Guoyu Chen, Joseph McDermott, Yi Huang, Xiaoxiao Guo, Jing-Dong J. Han:
  Accurate loop calling for 3D genomic data with cLoops. 666-675
• 
  Joshua Millstein, Francesca Battaglin, Malcolm Barrett, Shu Cao, Wu Zhang, Sebastian Stintzing, Volker Heinemann, Heinz-Josef Lenz:
  Partition: a surjective mapping approach for dimensionality reduction. 676-681
• 
  Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher:
  Fast and accurate correction of optical mapping data via spaced seeds. 682-689
• 
  Tianlei Xu, Peng Jin, Zhaohui S. Qin:
  Regulatory annotation of genomic intervals based on tissue-specific expression QTLs. 690-697
• 
  Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese, Bastian Fromm, Jason Sydes, Ernesto Aparicio-Puerta, Víctor Barrera, Roderic Espín, Florian Thibord, Xavier Bofill-De Ros, Eric Londin, Aristeidis G. Telonis, Elisa Ficarra, Marc R. Friedländer, John H. Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S. Vlachos, Marc K. Halushka, Lorena Pantano:
  Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. 698-703

Sequence Analysis

• 
  Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, Zongyuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song:
  PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. 704-712
• 
  Mary A Wood, Austin Nguyen, Adam J. Struck, Kyle Ellrott, Abhinav Nellore, Reid F. Thompson:
  neoepiscope improves neoepitope prediction with multivariant phasing. 713-720
• 
  Robert S. Harris, Paul Medvedev:
  Improved representation of sequence bloom trees. 721-727
• 
  Timothy J. Hackmann:
  Accurate estimation of microbial sequence diversity with Distanced. 728-734
• 
  M. B. B. Gutierres, C. B. C. Bonorino, Maurício Menegatti Rigo:
  ChaperISM: improved chaperone binding prediction using position-independent scoring matrices. 735-741

Phylogenetics

• 
  Yufeng Wu:
  Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach. 742-750

Structural Bioinformatics

• 
  Sweta Vangaveti, Thom Vreven, Yang Zhang, Zhiping Weng:
  Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. 751-757
• 
  Fergus Boyles, Charlotte M. Deane, Garrett M. Morris:
  Learning from the ligand: using ligand-based features to improve binding affinity prediction. 758-764
• 
  Erney Ramírez-Aportela, Jose Luis Vilas, Alisa Glukhova, Roberto Melero, Pablo Conesa, Marta Martínez, David Maluenda, Javier Mota, Amaya Jiménez, Javier Vargas, Roberto Marabini, Patrick M. Sexton, José María Carazo, Carlos Oscar Sánchez Sorzano:
  Automatic local resolution-based sharpening of cryo-EM maps. 765-772

Gene expression

• 
  Hannah De Los Santos, Emily J. Collins, Catherine Mann, April W. Sagan, Meaghan S. Jankowski, Kristin P. Bennett, Jennifer M. Hurley:
  ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output. 773-781
• 
  Jiebiao Wang, Bernie Devlin, Kathryn Roeder:
  Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression. 782-788
• 
  Pengchao Ye, Wenbin Ye, Congting Ye, Shuchao Li, Lishan Ye, Guoli Ji, Xiaohui Wu:
  scHinter: imputing dropout events for single-cell RNA-seq data with limited sample size. 789-797
• 
  Priyam Das, Christine B. Peterson, Kim-Anh Do, Rehan Akbani, Veerabhadran Baladandayuthapani:
  NExUS: Bayesian simultaneous network estimation across unequal sample sizes. 798-804
• 
  Wenjiang Deng, Tian Mou, Krishna R. Kalari, Nifang Niu, Liewei Wang, Yudi Pawitan, Trung-Nghia Vu:
  Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data. 805-812
• 
  Godwin Woo, Michael Fernández, Michael Hsing, Nathan A. Lack, Ayse Derya Cavga, Artem Cherkasov:
  DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules. 813-818
• 
  Ziyi Chen, Chengyang Ji, Qin Shen, Wei Liu, F. Xiao-Feng Qin, Aiping Wu:
  Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes. 819-827

Genetics and Population Analysis

• 
  José Víctor Moreno-Mayar, Thorfinn Sand Korneliussen, Jyoti Dalal, Gabriel Renaud, Anders Albrechtsen, Rasmus Nielsen, Anna-Sapfo Malaspinas:
  A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data. 828-841
• 
  Cheng Peng, Jun Wang, Isaac Asante, Stan Louie, Ran Jin, Lida Chatzi, Graham Casey, Duncan C. Thomas, David V. Conti:
  A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits. 842-850

Systems Biology

• 
  Yu-An Huang, Pengwei Hu, Keith C. C. Chan, Zhu-Hong You:
  Graph convolution for predicting associations between miRNA and drug resistance. 851-858
• 
  Hongyang Li, Yuanfang Guan:
  Machine learning empowers phosphoproteome prediction in cancers. 859-864
• 
  Noemi Di Nanni, Matteo Gnocchi, Marco Moscatelli, Luciano Milanesi, Ettore Mosca:
  Gene relevance based on multiple evidences in complex networks. 865-871
• 
  Rafsan Ahmed, Ilyes Baali, Cesim Erten, Evis Hoxha, Hilal Kazan:
  MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules. 872-879
• 
  Ashwani Kumar, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Sunyoung Kim, Khaled A Aly, Sandra Zilles, Mohan Babu:
  A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli. 880-889

Data and Text Mining

• 
  Xavier Farré, Nino Spataro, Frédéric Haziza, Jordi Rambla, Arcadi Navarro:
  Genome-phenome explorer (GePhEx): a tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence. 890-896

Databases and Ontologies

• 
  Wei Zhang, Longlong Wang, Ke Liu, Xiaofeng Wei, Kai Yang, Wensi Du, Shiyu Wang, Nannan Guo, Chuanchuan Ma, Lihua Luo, Jinghua Wu, Liya Lin, Fan Yang, Fei Gao, Xie Wang, Tao Li, Ruifang Zhang, Nitin K. Saksena, Huanming Yang, Jian Wang, Lin Fang, Yong Hou, Xun Xu, Xiao Liu:
  PIRD: Pan Immune Repertoire Database. 897-903
• 
  Gen Li, Yu Su, Yu-Hang Yan, Jiayi Peng, Qing-Qing Dai, Xiang-Li Ning, Cheng-Long Zhu, Chen Fu, Michael A. McDonough, Christopher J. Schofield, Cheng Huang, Guo-Bo Li:
  MeLAD: an integrated resource for metalloenzyme-ligand associations. 904-909

Bioimage Informatics

• 
  Blair J. Rossetti, Steven A. Wilbert, Jessica L. Mark Welch, Gary G. Borisy, James G. Nagy:
  Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs. 910-917

Applications note
Genome Analysis

• 
  Endre Bakken Stovner, Pål Sætrom:
  PyRanges: efficient comparison of genomic intervals in Python. 918-919
• 
  Tao Li, Shaokai Wang, Feng Luo, Fang-Xiang Wu, Jianxin Wang:
  MultiGuideScan: a multi-processing tool for designing CRISPR guide RNA libraries. 920-921
• 
  Oscar L. Rodriguez, Anna M. Ritz, Andrew J. Sharp, Ali Bashir:
  MsPAC: a tool for haplotype-phased structural variant detection. 922-924
• 
  Hrant Hovhannisyan, Ahmed Ibrahem Hafez, Carlos Lloréns, Toni Gabaldón:
  CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies. 925-927
• 
  Xin Guo, Bo Zhang, Wenqi Zeng, Shuting Zhao, Dongliang Ge:
  G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram. 928-929
• 
  Max Lam, Swapnil Awasthi, Hunna J. Watson, Jackie Goldstein, Georgia Panagiotaropoulou, Vassily Trubetskoy, Robert Karlsson, Oleksander Frei, Chun-Chieh Fan, Ward De Witte, Nina R. Mota, Niamh Mullins, Kim Brügger, Sang Hong Lee, Naomi R. Wray, Nora Skarabis, Hailiang Huang, Benjamin M. Neale, Mark J. Daly, Manuel Mattheisen, Raymond Walters, Stephan Ripke:
  RICOPILI: Rapid Imputation for COnsortias PIpeLIne. 930-933
• 
  Tomasz J. Kurowski, Fady R. Mohareb:
  Tersect: a set theoretical utility for exploring sequence variant data. 934-935
• 
  Eric Hugoson, Wai Tin Lam, Lionel Guy:
  miComplete: weighted quality evaluation of assembled microbial genomes. 936-937

Sequence Analysis

• 
  Harry J. Whitwell, Peter A. DiMaggio Jr.:
  HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs. 938-939
• 
  Riccardo Delli Ponti, Alexandros Armaos, Andrea Vandelli, Gian Gaetano Tartaglia:
  CROSSalive: a web server for predicting the in vivo structure of RNA molecules. 940-941
• 
  Tingyang Li, Ashootosh Tripathi, Fengan Yu, David H. Sherman, Arvind Rao:
  DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases. 942-944

Phylogenetics

• 
  Adriano de Bernardi Schneider, Colby T. Ford, Reilly Hostager, John Williams, Michael Cioce, Ümit V. Çatalyürek, Joel O. Wertheim, Daniel Janies:
  StrainHub: a phylogenetic tool to construct pathogen transmission networks. 945-947

Structural Bioinformatics

• 
  Reshmi Ramakrishnan, Bert Houben, Lukasz Kreft, Alexander Botzki, Joost Schymkowitz, Frederic Rousseau:
  Protein Homeostasis Database: protein quality control in E.coli. 948-949
• 
  Jorge Roel-Touris, Alexandre M. J. J. Bonvin, Brian Jiménez-García:
  LightDock goes information-driven. 950-952
• 
  Aleksandra I. Jarmolinska, Anna Gambin, Joanna I. Sulkowska:
  Knot_pull - python package for biopolymer smoothing and knot detection. 953-955
• 
  Iñigo Marcos-Alcalde, Eduardo López-Viñas, Paulino Gómez-Puertas:
  MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces. 956-958
• 
  Aeri Lee, Dongsup Kim:
  CRDS: Consensus Reverse Docking System for target fishing. 959-960
• 
  Yoonji Lee, Jordan M. Baumhardt, Jimin Pei, Yuh Min Chook, Nick V. Grishin:
  pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes. 961-963

Gene expression

• 
  Krzysztof Polanski, Matthew D. Young, Zhichao Miao, Kerstin B. Meyer, Sarah A. Teichmann, Jong-Eun Park:
  BBKNN: fast batch alignment of single cell transcriptomes. 964-965
• 
  A Ozuna, D. Liberto, R. M. Joyce, K. B. Arnvig, Irene Nobeli:
  baerhunter: an R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data. 966-969
• 
  Mickaël Canouil, Gerard A. Bouland, Amélie Bonnefond, Philippe Froguel, Leen M. 't Hart, Roderick C. Slieker:
  NACHO: an R package for quality control of NanoString nCounter data. 970-971

Genetics and Population Analysis

• 
  Vinícius da Silva, Marcel Ramos, Martien Groenen, Richard Crooijmans, Anna Johansson, Luciana C. A. Regitano, Luiz Coutinho, Ralf Zimmer, Levi Waldron, Ludwig Geistlinger:
  CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. 972-973
• 
  Zheng Gao, Jonathan Terhorst, Cristopher V. Van Hout, Stilian Stoev:
  U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies. 974-975

Systems Biology

• 
  Jordi Bartolomé, Rui Alves, Francesc Solsona, Ivan Teixido:
  EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology. 976-977

Data and Text Mining

• 
  Leonid A. Stolbov, Dmitry S. Druzhilovskiy, Anastasia V. Rudik, Dmitry Filimonov, Vladimir Poroikov, Marc C. Nicklaus:
  AntiHIV-Pred: web-resource for in silico prediction of anti-HIV/AIDS activity. 978-979

Databases and Ontologies

• 
  Rafal Cylwa, Kornel Kielczewski, Marta Machnik, Urszula Oleksiewicz, Przemyslaw Biecek:
  KRAB ZNF explorer - the online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas. 980-981
• 
  Thoba Lose, Peter van Heusden, Alan Christoffels:
  COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies. 982-983

Volume 36, Number 4, February 2020

Discovery Notes
Genome Analysis

• 
  Galo A. Goig, Manuela Torres-Puente, Carla Mariner-Llicer, Luis M. Villamayor, Álvaro Chiner-Oms, Ana Gil-Brusola, Rafael Borrás, Iñaki Comas Espadas:
  Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics. 985-989

Sequence Analysis

• 
  Luis Sánchez-Pulido, Chris P. Ponting:
  Hexa-Longin domain scaffolds for inter-Rab signalling. 990-993

Gene expression

• 
  Qian Zhu, Xavier Tekpli, Olga G. Troyanskaya, Vessela N. Kristensen:
  Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations. 994-999

Original Papers
Genome Analysis

• 
  Kang Jin Kim, Jaehyun Park, Sang-Chul Park, Sungho Won:
  Phylogenetic tree-based microbiome association test. 1000-1006
• 
  Gaia Ceddia, Liuba Nausicaa Martino, Alice C. L. Parodi, Piercesare Secchi, Stefano Campaner, Marco Masseroli:
  Association rule mining to identify transcription factor interactions in genomic regions. 1007-1013
• 
  Arif Ozgun Harmanci, Akdes Serin Harmanci, Jyothishmathi Swaminathan, Vidya Gopalakrishnan:
  EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements. 1014-1021
• 
  Deepank R. Korandla, Jacob M. Wozniak, Anaamika Campeau, David J. Gonzalez, Erik Scott Wright:
  AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions. 1022-1029
• 
  Ziwei Li, Bo He, Weixing Feng:
  Evaluation of bottom-up and top-down mass spectrum identifications with different customized protein sequences databases. 1030-1036

Sequence Analysis

• 
  Zengyan Hong, Xiangxiang Zeng, Leyi Wei, Xiangrong Liu:
  Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism. 1037-1043
• 
  Yichao Li, Yating Liu, David Juedes, Frank Drews, Razvan C. Bunescu, Lonnie R. Welch:
  Set cover-based methods for motif selection. 1044-1051
• 
  Xue Qing, Meng Wang, Gerrit Karssen, Patricia Bucki, Wim Bert, Sigal Braun-Miyara:
  PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes. 1052-1056
• 
  Fuyi Li, Jinxiang Chen, André Leier, Tatiana T. Marquez-Lago, Quanzhong Liu, Yanze Wang, Jerico Nico De Leon Revote, Alexander Ian Smith, Tatsuya Akutsu, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song:
  DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. 1057-1065
• 
  Sen Liu, Yuping Wang, Wuning Tong, Shiwei Wei:
  A fast and memory efficient MLCS algorithm by character merging for DNA sequences alignment. 1066-1073
• 
  Bin Yu, Wenying Qiu, Cheng Chen, Anjun Ma, Jing Jiang, Hongyan Zhou, Qin Ma:
  SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting. 1074-1081

Phylogenetics

• 
  Camir Ricketts, Daniel Seidman, Victoria Popic, Fereydoun Hormozdiari, Serafim Batzoglou, Iman Hajirasouliha:
  Meltos: multi-sample tumor phylogeny reconstruction for structural variants. 1082-1090

Structural Bioinformatics

• 
  Tianqi Wu, Jie Hou, Badri Adhikari, Jianlin Cheng:
  Analysis of several key factors influencing deep learning-based inter-residue contact prediction. 1091-1098
• 
  Amélie Barozet, Kevin Molloy, Marc Vaisset, Thierry Siméon, Juan Cortés:
  A reinforcement-learning-based approach to enhance exhaustive protein loop sampling. 1099-1106
• 
  Jack Hanson, Thomas Litfin, Kuldip K. Paliwal, Yaoqi Zhou:
  Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning. 1107-1113
• 
  Min Zeng, Fuhao Zhang, Fang-Xiang Wu, Yaohang Li, Jianxin Wang, Min Li:
  Protein-protein interaction site prediction through combining local and global features with deep neural networks. 1114-1120
• 
  Tanvir Alam, Meshari Alazmi, Rayan Naser, Franceline Huser, Afaque A. Momin, Veronica Astro, SeungBeom Hong, Katarzyna W. Walkiewicz, Christian G. Canlas, Raphaël Huser, Amal J. Ali, Jasmeen Merzaban, Antonio Adamo, Mariusz Jaremko, Lukasz Jaremko, Vladimir B. Bajic, Xin Gao, Stefan T. Arold:
  Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs. 1121-1128
• 
  Mariusz Popenda, Joanna Miskiewicz, Joanna Sarzynska, Tomasz Zok, Marta Szachniuk:
  Topology-based classification of tetrads and quadruplex structures. 1129-1134
• 
  Xiaoqiang Huang, Robin Pearce, Yang Zhang:
  EvoEF2: accurate and fast energy function for computational protein design. 1135-1142

Gene expression

• 
  Juan Xie, Anjun Ma, Yu Zhang, Bingqiang Liu, Sha Cao, Cankun Wang, Jennifer Xu, Chi Zhang, Qin Ma:
  QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data. 1143-1149
• 
  Abha S. Bais, Dennis Kostka:
  scds: computational annotation of doublets in single-cell RNA sequencing data. 1150-1158
• 
  Christopher R. John, David S. Watson, Michael R. Barnes, Costantino Pitzalis, Myles J. Lewis:
  Spectrum: fast density-aware spectral clustering for single and multi-omic data. 1159-1166
• 
  Wilson H. McKerrow, David Fenyö:
  L1EM: a tool for accurate locus specific LINE-1 RNA quantification. 1167-1173
• 
  Wenhao Tang, François Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei:
  bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data. 1174-1181
• 
  Stavros Makrodimitris, Marcel J. T. Reinders, Roeland C. H. J. van Ham:
  Metric learning on expression data for gene function prediction. 1182-1190

Genetics and Population Analysis

• 
  María Bogaerts-Márquez, Maite G. Barrón, Anna-Sophie Fiston-Lavier, Pol Vendrell-Mir, Raúl Castanera, Josep M. Casacuberta, Josefa González:
  T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data. 1191-1197

Systems Biology

• 
  Mahdi Shafiee Kamalabad, Marco Grzegorczyk:
  Non-homogeneous dynamic Bayesian networks with edge-wise sequentially coupled parameters. 1198-1207
• 
  Rex Parsons, Richard Parsons, Nicholas Garner, Henrik Oster, Oliver Rawashdeh:
  CircaCompare: a method to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms. 1208-1212
• 
  Yuanyue Li, Michael Kuhn, Anne-Claude Gavin, Peer Bork:
  Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features. 1213-1218
• 
  Saman Salike, Nirav Bhatt:
  Thermodynamically consistent estimation of Gibbs free energy from data: data reconciliation approach. 1219-1225

Data and Text Mining

• 
  Ginger Tsueng, Max Nanis, Jennifer T. Fouquier, Michael Mayers, Benjamin M. Good, Andrew I. Su:
  Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts. 1226-1233
• 
  Jinhyuk Lee, Wonjin Yoon, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, Jaewoo Kang:
  BioBERT: a pre-trained biomedical language representation model for biomedical text mining. 1234-1240
• 
  Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang, Huan Sun:
  Graph embedding on biomedical networks: methods, applications and evaluations. 1241-1251

Bioimage Informatics

• 
  Ruijie Yao, Jiaqiang Qian, Qiang Huang:
  Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules. 1252-1259

Applications Notes
Genome Analysis

• 
  David Porubsky, Ashley D. Sanders, Aaron Taudt, Maria Colomé-Tatché, Peter M. Lansdorp, Victor Guryev:
  breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data. 1260-1261
• 
  Congting Ye, Qian Zhou, Xiaohui Wu, Chen Yu, Guoli Ji, Daniel R. Saban, Qingshun Quinn Li:
  scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. 1262-1264
• 
  Marina Marcet-Houben, Toni Gabaldón:
  EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes. 1265-1266
• 
  Davide Bolognini, Ashley D. Sanders, Jan O. Korbel, Alberto Magi, Vladimir Benes, Tobias Rausch:
  VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing. 1267-1269
• 
  Hongjian Jin, Lawryn H. Kasper, Jon D. Larson, Gang Wu, Suzanne J. Baker, Jinghui Zhang, Yiping Fan:
  ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in. 1270-1272
• 
  Ignacio Ferrés, Pablo Fresia, Gregorio Iraola:
  simurg: simulate bacterial pangenomes in R. 1273-1274

Sequence Analysis

• 
  Gaëtan Benoit, Mahendra Mariadassou, Stéphane Robin, Sophie Schbath, Pierre Peterlongo, Claire Lemaitre:
  SimkaMin: fast and resource frugal de novo comparative metagenomics. 1275-1276
• 
  Jun Wang, Pu-Feng Du, Xin-Yu Xue, Guang-Ping Li, Yuan-Ke Zhou, Wei Zhao, Hao Lin, Wei Chen:
  VisFeature: a stand-alone program for visualizing and analyzing statistical features of biological sequences. 1277-1278
• 
  Guillermo Serrano, Elizabeth Guruceaga, Victor Segura:
  DeepMSPeptide: peptide detectability prediction using deep learning. 1279-1280
• 
  Zhenhua Yu, Fang Du, Xuehong Sun, Ao Li:
  SCSsim: an integrated tool for simulating single-cell genome sequencing data. 1281-1282
• 
  Zeynep Baskurt, Scott Mastromatteo, Jiafen Gong, Richard F. Wintle, Stephen W. Scherer, Lisa J. Strug:
  VikNGS: a C++ variant integration kit for next generation sequencing association analysis. 1283-1285

Phylogenetics

• 
  Adrián A. Davín, Théo Tricou, Eric Tannier, Damien M. de Vienne, Gergely J. Szöllosi:
  Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages. 1286-1288
• 
  Patrick H. Bradley, Katherine S. Pollard:
  phylogenize: correcting for phylogeny reveals genes associated with microbial distributions. 1289-1290

Structural Bioinformatics

• 
  Conrad Stork, Gerd Embruch, Martin Sícho, Christina de Bruyn Kops, Ya Chen, Daniel Svozil, Johannes Kirchmair:
  NERDD: a web portal providing access to in silico tools for drug discovery. 1291-1292
• 
  Chao Fang, Zhaoyu Li, Dong Xu, Yi Shang:
  MUFold-SSW: a new web server for predicting protein secondary structures, torsion angles and turns. 1293-1295
• 
  Julian Bender, Carla Schmidt:
  The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments. 1296-1297

Gene expression

• 
  António Cruz, Penousal Machado, Joel P. Arrais:
  CroP - Coordinated Panel visualization for biological networks analysis. 1298-1299
• 
  A. Trullo, J. Dufourt, Mounia Lagha:
  MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos. 1300-1302

Genetics and Population Analysis

• 
  Florian P. Breitwieser, Steven L. Salzberg:
  Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification. 1303-1304

Data and Text Mining

• 
  Grégoire Versmée, Laura Versmée, Mikaël Dusenne, Niloofar Jalali, Paul Avillach:
  dbgap2x: an R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP). 1305-1306
• 
  Anthony Federico, Stefano Monti:
  hypeR: an R package for geneset enrichment workflows. 1307-1308
• 
  Kevin McDonnell, Nicholas Waters, Enda Howley, Florence Abram:
  Chordomics: a visualization tool for linking function to phylogeny in microbiomes. 1309-1310

Databases and Ontologies

• 
  Marcela Aguilera Flores, Iulia M. Lazar:
  XMAn v2 - a database of Homo sapiens mutated peptides. 1311-1313

Bioimage Informatics

• 
  Pablo Vicente-Munuera, Pedro Gómez-Gálvez, Robert J. Tetley, Cristina Forja, Antonio Tagua, Marta Letrán, Melda Tozluoglu, Yanlan Mao, Luis M. Escudero:
  EpiGraph: an open-source platform to quantify epithelial organization. 1314-1316

Volume 36, Number 5, March 2020

Review
Bioimage Informatics

• 
  Sandeep Manandhar, Patrick Bouthemy, Erik Welf, Gaudenz Danuser, Philippe Roudot, Charles Kervrann:
  3D flow field estimation and assessment for live cell fluorescence microscopy. 1317-1325

Discovery note
Systems Biology

• 
  Victoria A. Sleight, Philipp Antczak, Francesco Falciani, Melody S. Clark:
  Computationally predicted gene regulatory networks in molluscan biomineralization identify extracellular matrix production and ion transportation pathways. 1326-1332

Original Papers
Genome Analysis

• 
  Renmin Han, Sheng Wang, Xin Gao:
  Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing. 1333-1343
• 
  Daiwei Tang, Seyoung Park, Hongyu Zhao:
  NITUMID: Nonnegative matrix factorization-based Immune-TUmor MIcroenvironment Deconvolution. 1344-1350
• 
  Liam F. Spurr, Nawaf Alomran, Pavlos Bousounis, Dacian Reece-Stremtan, N. M. Prashant, Hongyu Liu, Piotr Slowinski, Muzi Li, Qianqian Zhang, Justin Sein, Gabriel Asher, Keith A. Crandall, Krasimira Tsaneva-Atanasova, Anelia Horvath:
  ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data. 1351-1359
• 
  Bong-Hyun Kim, Kijin Yu, Peter C. W. Lee:
  Cancer classification of single-cell gene expression data by neural network. 1360-1366
• 
  Raphaël Mourad:
  Studying 3D genome evolution using genomic sequence. 1367-1373

Sequence Analysis

• 
  Antoine Limasset, Jean-François Flot, Pierre Peterlongo:
  Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. 1374-1381
• 
  Kohei Hagiwara, Liang Ding, Michael N. Edmonson, Stephen V. Rice, Scott Newman, John Easton, Juncheng Dai, Soheil Meshinchi, Rhonda E. Ries, Michael Rusch, Jinghui Zhang:
  RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. 1382-1390
• 
  Jian-Peng Zhou, Lei Chen, Zi-Han Guo:
  iATC-NRAKEL: an efficient multi-label classifier for recognizing anatomical therapeutic chemical classes of drugs. 1391-1396
• 
  Chencheng Xu, Qiao Liu, Jianyu Zhou, Minzhu Xie, Jianxing Feng, Tao Jiang:
  Quantifying functional impact of non-coding variants with multi-task Bayesian neural network. 1397-1404
• 
  Xiao Luo, Xinming Tu, Yang Ding, Ge Gao, Minghua Deng:
  Expectation pooling: an effective and interpretable pooling method for predicting DNA-protein binding. 1405-1412
• 
  Thomas Büchler, Enno Ohlebusch:
  An improved encoding of genetic variation in a Burrows-Wheeler transform. 1413-1419

Structural Bioinformatics

• 
  David Becerra, Alexander Butyaev, Jérôme Waldispühl:
  Fast and flexible coarse-grained prediction of protein folding routes using ensemble modeling and evolutionary sequence variation. 1420-1428
• 
  Abdurrahman Elbasir, Raghvendra Mall, Khalid Kunji, Reda Rawi, Zeyaul Islam, Gwo-Yu Chuang, Prasanna R. Kolatkar, Halima Bensmail:
  BCrystal: an interpretable sequence-based protein crystallization predictor. 1429-1438
• 
  Puneet Rawat, R. Prabakaran, Sandeep Kumar, M. Michael Gromiha:
  AggreRATE-Pred: a mathematical model for the prediction of change in aggregation rate upon point mutation. 1439-1444
• 
  Qingzhen Hou, Jean Marc Kwasigroch, Marianne Rooman, Fabrizio Pucci:
  SOLart: a structure-based method to predict protein solubility and aggregation. 1445-1452
• 
  Yoochan Myung, Carlos H. M. Rodrigues, David B. Ascher, Douglas E. V. Pires:
  mCSM-AB2: guiding rational antibody design using graph-based signatures. 1453-1459
• 
  Amir Vajdi, Kourosh Zarringhalam, Nurit Haspel:
  Patch-DCA: improved protein interface prediction by utilizing structural information and clustering DCA scores. 1460-1467

Gene expression

• 
  Giacomo Baruzzo, Ilaria Patuzzi, Barbara Di Camillo:
  SPARSim single cell: a count data simulator for scRNA-seq data. 1468-1475
• 
  Runpu Chen, Le Yang, Steve Goodison, Yijun Sun:
  Deep-learning approach to identifying cancer subtypes using high-dimensional genomic data. 1476-1483
• 
  Magdalena E. Strauß, Paul D. W. Kirk, John E. Reid, Lorenz Wernisch:
  GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution. 1484-1491

Genetics and Population Analysis

• 
  Hamed Haselimashhadi, Jeremy C. Mason, Violeta Muñoz-Fuentes, Federico López-Gómez, Kolawole O. Babalola, Elif F. Acar, Vivek Kumar, Jacqui White, Ann M. Flenniken, Ruairidh King, Ewan Straiton, John Richard Seavitt, Angelina Gaspero, Arturo Garza, Audrey E. Christianson, Chih-Wei Hsu, Corey L. Reynolds, Denise G. Lanza, Isabel Lorenzo, Jennie R. Green, Juan J. Gallegos, Ritu Bohat, Rodney C. Samaco, Surabi Veeraragavan, Jong Kyoung Kim, Gregor Miller, Helmut Fuchs, Lillian Garrett, Lore Becker, Yeon Kyung Kang, David Clary, Soo Young Cho, Masaru Tamura, Nobuhiko Tanaka, Kyung Dong Soo, Alexandr Bezginov, Ghina Bou About, Marie-France Champy, Laurent Vasseur, Sophie Leblanc, Hamid Meziane, Mohammed Selloum, Patrick T. Reilly, Nadine Spielmann, Holger Maier, Valérie Gailus-Durner, Tania Sorg, Hiroshi Masuya, Yuichi Obata, Jason D. Heaney, Mary E. Dickinson, Wolfgang Wurst, Glauco P. Tocchini-Valentini, Kevin C. Kent Lloyd, Colin McKerlie, Je Kyung Seong, Yann Herault, Martin Hrabé de Angelis, Steve D. M. Brown, Damian Smedley, Paul Flicek, Ann-Marie Mallon, Helen E. Parkinson, Terrence F. Meehan:
  Soft windowing application to improve analysis of high-throughput phenotyping data. 1492-1500
• 
  Jia Zhao, Jingsi Ming, Xianghong Hu, Gang Chen, Jin Liu, Can Yang:
  Bayesian weighted Mendelian randomization for causal inference based on summary statistics. 1501-1508
• 
  Andrew W. George, Arunas Verbyla, Joshua Bowden:
  Eagle: multi-locus association mapping on a genome-wide scale made routine. 1509-1516
• 
  Leilei Cui, Bin Yang, Nikolas Pontikos, Richard Mott, Lusheng Huang:
  ADDO: a comprehensive toolkit to detect, classify and visualize additive and non-additive quantitative trait loci. 1517-1521

Systems Biology

• 
  Rui Liu, Pei Chen, Luonan Chen:
  Single-sample landscape entropy reveals the imminent phase transition during disease progression. 1522-1532

Data and Text Mining

• 
  Suyang Dai, Ronghui You, Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu:
  FullMeSH: improving large-scale MeSH indexing with full text. 1533-1541
• 
  Zheng Chen, Meng Pang, Zixin Zhao, Shuainan Li, Rui Miao, Yifan Zhang, Xiaoyue Feng, Xin Feng, Yexian Zhang, Meiyu Duan, Lan Huang, Fengfeng Zhou:
  Feature selection may improve deep neural networks for the bioinformatics problems. 1542-1552
• 
  Paolo Mignone, Gianvito Pio, Domenica D'Elia, Michelangelo Ceci:
  Exploiting transfer learning for the reconstruction of the human gene regulatory network. 1553-1561
• 
  Antonino Lauria, Salvatore Mannino, Carla Gentile, Giuseppe Mannino, Annamaria Martorana, Daniele Peri:
  DRUDIT: web-based DRUgs DIscovery Tools to design small molecules as modulators of biological targets. 1562-1569
• 
  Nooshin Shomal Zadeh, Sangdi Lin, George C. Runger:
  Matched Forest: supervised learning for high-dimensional matched case-control studies. 1570-1576
• 
  Yu Liu, Paul W. Bible, Bin Zou, Qiaoxing Liang, Cong Dong, Xiaofeng Wen, Yan Li, Xiaofei Ge, Xifang Li, Xiuli Deng, Rong Ma, Shixin Guo, Juanran Liang, Tingting Chen, Wenliang Pan, Lixin Liu, Wei Chen, Xueqin Wang, Lai Wei:
  CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples. 1577-1583

Databases and Ontologies

• 
  Eiru Kim, Dasom Bae, Sunmo Yang, Gunhwan Ko, Sungho Lee, Byungwook Lee, Insuk Lee:
  BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genome. 1584-1589

Bioimage Informatics

• 
  Daniel Jimenez-Carretero, Mikel Ariz, José Mário T. Morgado, Iván Cortés-Domínguez, Carlos Ortiz-de-Solórzano:
  NMF-RI: blind spectral unmixing of highly mixed multispectral flow and image cytometry data. 1590-1598
• 
  Yizhi Wang, Congchao Wang, Petter Ranefall, Gerard Broussard, Yinxue Wang, Guilai Shi, Boyu Lyu, Chiung-Ting Wu, Yue Wang, Lin Tian, Guoqiang Yu:
  SynQuant: an automatic tool to quantify synapses from microscopy images. 1599-1606
• 
  Joseph Boyd, Alice Pinheiro, Elaine Del Nery, Fabien Reyal, Thomas Walter:
  Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen. 1607-1613
• 
  Jeremy A. Pike, Abdullah O. Khan, Chiara Pallini, Steven G. Thomas, Markus Mund, Jonas Ries, Natalie S. Poulter, Iain B. Styles:
  Topological data analysis quantifies biological nano-structure from single molecule localization microscopy. 1614-1621

Applications note
Genome Analysis

• 
  Andrea Calabria, Stefano Beretta, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Yuri Pirola, Fabrizio Benedicenti, Erika Tenderini, Paola Bonizzoni, Luciano Milanesi, Eugenio Montini:
  γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites. 1622-1624
• 
  Cheng Yee Tang, Rick Twee-Hee Ong:
  MIRUReader: MIRU-VNTR typing directly from long sequencing reads. 1625-1626
• 
  Christopher N. Larsen, Guangyu Sun, Xiaomei Li, Sam Zaremba, Hongtao Zhao, Sherry He, Liwei Zhou, Sanjeev Kumar, Vincent Desborough, Edward B. Klem:
  Mat_peptide: comprehensive annotation of mature peptides from polyproteins in five virus families. 1627-1628

Sequence Analysis

• 
  Catherine Badel, Violette Da Cunha, Ryan Catchpole, Patrick Forterre, Jacques Oberto:
  WASPS: web-assisted symbolic plasmid synteny server. 1629-1631
• 
  Adam T. Lafontaine, Bruce J. Mayer, Kazuya Machida:
  Dynalogo: an interactive sequence logo with dynamic thresholding of matched quantitative proteomic data. 1632-1633

Gene expression

• 
  Raphaël Leman, Valentin Harter, Alexandre Atkinson, Grégoire Davy, Antoine Rousselin, Etienne Muller, Laurent Castéra, Frédéric Lemoine, Pierre de la Grange, Marine Guillaud-Bataille, Dominique Vaur, Sophie Krieger:
  SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data. 1634-1636
• 
  Simon Steffens, Xiuling Fu, Fangfang He, Yuhao Li, Isaac A. Babarinde, Andrew Paul Hutchins:
  DPre: computational identification of differentiation bias and genes underlying cell type conversions. 1637-1639

Systems Biology

• 
  Pencho Yordanov, Jörg Stelling, Irene Otero-Muras:
  BioSwitch: a tool for the detection of bistability and multi-steady state behaviour in signalling and gene regulatory networks. 1640-1641
• 
  Yu Tian, Ling Wu, Le Yuan, Shaozhen Ding, Fu Chen, Tong Zhang, Ailin Ren, Dachuan Zhang, Weizhong Tu, Junni Chen, Qian-Nan Hu:
  BCSExplorer: a customized biosynthetic chemical space explorer with multifunctional objective function analysis. 1642-1643
• 
  Nikolay Martyushenko, Eivind Almaas:
  ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models. 1644-1646
• 
  Bilal Wajid, Hasan Iqbal, Momina Jamil, Hafsa Rafique, Faria Anwar:
  MetumpX - a metabolomics support package for untargeted mass spectrometry. 1647-1648

Databases and Ontologies

• 
  Moli Huang, Yunpeng Wang, Manqiu Yang, Jun Yan, Henry Yang, Wenzhuo Zhuang, Ying Xu, H. Phillip Koeffler, De-Chen Lin, Xi Chen:
  dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq. 1649-1651
• 
  David Sánchez, Sergio Martínez, Josep Domingo-Ferrer, Jordi Soria-Comas, Montserrat Batet:
  µ-ANT: semantic microaggregation-based anonymization tool. 1652-1653

Volume 36, Number 6, March 2020

Review
Sequence Analysis

• 
  Nina Baumgarten, Florian Schmidt, Marcel H. Schulz:
  Improved linking of motifs to their TFs using domain information. 1655-1662

Discovery note
Genome Analysis

• 
  Qingsu Cheng, Mina Khoshdeli, Bradley S. Ferguson, Kosar Jabbari, Chongzhi Zang, Bahram Parvin:
  YY1 is a cis-regulator in the organoid models of high mammographic density. 1663-1667

Sequence Analysis

• 
  Sergey V. Tarlachkov, Taras V. Shevchuk, Maria del Carmen Montero-Calasanz, Irina P. Starodumova:
  Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments. 1668-1672

Original Papers
Genome Analysis

• 
  Judith Bergadà-Pijuan, Carlos Pulido-Quetglas, Adrienne Vancura, Rory Johnson:
  CASPR, an analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target selection for long non-coding RNAs. 1673-1680
• 
  Joel A. Southgate, Matthew J. Bull, Clare M. Brown, Joanne Watkins, Sally Corden, Benjamin Southgate, Catherine Moore, Thomas R. Connor:
  Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications. 1681-1688
• 
  Abhay Hukku, Corbin Quick, Francesca Luca, Roger Pique-Regi, Xiaoquan Wen:
  BAGSE: a Bayesian hierarchical model approach for gene set enrichment analysis. 1689-1695
• 
  Nour Almadhoun, Erman Ayday, Özgür Ulusoy:
  Differential privacy under dependent tuples - the case of genomic privacy. 1696-1703
• 
  Artur Tomasz Jaroszewicz, Jason Ernst:
  An integrative approach for fine-mapping chromatin interactions. 1704-1711
• 
  Pramod Chandrashekar, Navid Ahmadinejad, Junwen Wang, Aleksandar Sekulic, Jan B. Egan, Yan W. Asmann, Sudhir Kumar, Carlo Maley, Li Liu:
  Somatic selection distinguishes oncogenes and tumor suppressor genes. 1712-1717

Sequence Analysis

• 
  Max E. Schön, Laura Eme, Thijs J. G. Ettema:
  PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics. 1718-1724
• 
  Sherlyn Jemimah, Masakazu Sekijima, M. Michael Gromiha:
  ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification. 1725-1730
• 
  Erand Smakaj, Lmar Babrak, Mats Ohlin, Mikhail Shugay, Bryan S. Briney, Deniz Tosoni, Christopher Galli, Vendi Grobelsek, Igor D'Angelo, Branden J. Olson, Sai T. Reddy, Victor Greiff, Johannes Trück, Susanna Marquez, William D. Lees, Enkelejda Miho:
  Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. 1731-1739

Structural Bioinformatics

• 
  Raphael Eguchi, Po-Ssu Huang:
  Multi-scale structural analysis of proteins by deep semantic segmentation. 1740-1749
• 
  Mark Chonofsky, Saulo Henrique Pires de Oliveira, Konrad Krawczyk, Charlotte M. Deane:
  The evolution of contact prediction: evidence that contact selection in statistical contact prediction is changing. 1750-1756
• 
  Saida S. Mohamed, Gennaro Esposito, Giuseppe Serra, Federico Fogolari:
  Generalized Born radii computation using linear models and neural networks. 1757-1764
• 
  Gabriel Studer, Christine Rempfer, Andrew Waterhouse, Rafal Gumienny, Jürgen Haas, Torsten Schwede:
  QMEANDisCo - distance constraints applied on model quality estimation. 1765-1771

Gene expression

• 
  Alena Orlenko, Daniel Kofink, Leo-Pekka Lyytikäinen, Kjell Nikus, Pashupati P. Mishra, Pekka Kuukasjärvi, Pekka J. Karhunen, Mika Kähönen, Jari O. Laurikka, Terho Lehtimäki, Folkert W. Asselbergs, Jason H. Moore:
  Model selection for metabolomics: predicting diagnosis of coronary artery disease using automated machine learning. 1772-1778
• 
  Chuanqi Wang, Jun Li:
  SINC: a scale-invariant deep-neural-network classifier for bulk and single-cell RNA-seq data. 1779-1784

Genetics and Population Analysis

• 
  Jun Li, Qing Lu, Yalu Wen:
  Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data. 1785-1794
• 
  David Gerard, Luís Felipe Ventorim Ferrão:
  Priors for genotyping polyploids. 1795-1800

Systems Biology

• 
  Maureen Kachman, Hani Habra, William Duren, Janis E. Wigginton, Peter Sajjakulnukit, George Michailidis, Charles F. Burant, Alla Karnovsky:
  Deep annotation of untargeted LC-MS metabolomics data with Binner. 1801-1806
• 
  Pau Erola, Johan Björkegren, Tom Michoel:
  Model-based clustering of multi-tissue gene expression data. 1807-1813
• 
  Zhibo Wang, Zhezhi He, Milan Shah, Teng Zhang, Deliang Fan, Wei Zhang:
  Network-based multi-task learning models for biomarker selection and cancer outcome prediction. 1814-1822
• 
  Wai Kit Ong, Peter E. Midford, Peter D. Karp:
  Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models. 1823-1830
• 
  Gal Dinstag, Ron Shamir:
  PRODIGY: personalized prioritization of driver genes. 1831-1839
• 
  Kevin McGregor, Aurélie Labbe, Celia M. T. Greenwood:
  MDiNE: a model to estimate differential co-occurrence networks in microbiome studies. 1840-1847
• 
  Adrian L. Hauber, Raphael Engesser, Joep Vanlier, Jens Timmer:
  Estimating chain length for time delays in dynamical systems using profile likelihood. 1848-1854

Data and Text Mining

• 
  Jianing Xi, Xiguo Yuan, Minghui Wang, Ao Li, Xuelong Li, Qinghua Huang:
  Inferring subgroup-specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication. 1855-1863
• 
  Keyao Wang, Jun Wang, Carlotta Domeniconi, Xiangliang Zhang, Guoxian Yu:
  Differentiating isoform functions with collaborative matrix factorization. 1864-1871
• 
  Naiara Pérez, Pablo Accuosto, Àlex Bravo, Montse Cuadros, Eva Martínez Garcia, Horacio Saggion, German Rigau:
  Cross-lingual semantic annotation of biomedical literature: experiments in Spanish and English. 1872-1880
• 
  Minh Pham, Stephen J. Wilson, Harikumar Govindarajan, Chih-Hsu Lin, Olivier Lichtarge:
  Discovery of disease- and drug-specific pathways through community structures of a literature network. 1881-1888

Databases and Ontologies

• 
  Sergio Castillo-Lara, E. Pascual-Carreras, Josep F. Abril:
  PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources. 1889-1895
• 
  Anne Morgat, Thierry Lombardot, Elisabeth Coudert, Kristian B. Axelsen, Teresa Batista Neto, Sebastien Gehant, Parit Bansal, Jerven T. Bolleman, Elisabeth Gasteiger, Edouard De Castro, Delphine Baratin, Monica Pozzato, Ioannis Xenarios, Sylvain Poux, Nicole Redaschi, Alan J. Bridge, The UniProt Consortium:
  Enzyme annotation in UniProtKB using Rhea. 1896-1901
• 
  J. Bradley Holmes, Eric Moyer, Lon Phan, Donna R. Maglott, Brandi L. Kattman:
  SPDI: data model for variants and applications at NCBI. 1902-1907

Bioimage Informatics

• 
  Ying-Ying Xu, Hong-Bin Shen, Robert F. Murphy:
  Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images. 1908-1914

Applications note
Genome Analysis

• 
  Frédéric Escudié, Charles Van Goethem, David Grand, Julie Vendrell, Anna Vigier, Pierre Brousset, Solène M. Evrard, Jérôme Solassol, Janick Selves:
  MIAmS: microsatellite instability detection on NGS amplicons data. 1915-1916
• 
  Koustav Pal, Ilario Tagliaferri, Carmen Maria Livi, Francesco Ferrari:
  HiCBricks: building blocks for efficient handling of large Hi-C datasets. 1917-1919
• 
  Quentin Ferré, Guillaume Charbonnier, N. Sadouni, Frédéric Lopez, Yasmina Kermezli, Salvatore Spicuglia, Cécile Capponi, Badih Ghattas, Denis Puthier:
  OLOGRAM: determining significance of total overlap length between genomic regions sets. 1920-1922
• 
  Yu Jiang, Hongmei Zhang, Shan V. Andrews, Hasan Arshad, Susan Ewart, John W. Holloway, M. Daniele Fallin, Kelly M. Bakulski, Wilfried Karmaus:
  Estimation of eosinophil cells in cord blood with references based on blood in adults via Bayesian measurement error modeling. 1923-1924
• 
  Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks:
  GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. 1925-1927

Sequence Analysis

• 
  Timo Lassmann:
  Kalign 3: multiple sequence alignment of large datasets. 1928-1929
• 
  Martijn Cordes, Karin Pike-Overzet, Marja van Eggermond, Sandra Vloemans, Miranda R. Baert, Laura Garcia-Perez, Frank J. T. Staal, Marcel J. T. Reinders, Erik van den Akker:
  ImSpectR: R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data. 1930-1932
• 
  Xiangfu Zhong, Albert Pla, Simon Rayner:
  Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq data. 1933-1936
• 
  Yuhan Fei, Yiyang Mao, Chengji Shen, Rui Wang, Hongsheng Zhang, Ji Huang:
  WPMIAS: Whole-degradome-based Plant MicroRNA-target Interaction Analysis Server. 1937-1939
• 
  Nicolaas C. Kist, Robert A. Power, Andrew Skelton, Seth D. Seegobin, Moira Verbelen, Bushan Bonde, Karim Malki:
  RNASeq_similarity_matrix: visually identify sample mix-ups in RNASeq data using a 'genomic' sequence similarity matrix. 1940-1941

Structural Bioinformatics

• 
  Kai Cheng, Gabrielle Pawlowski, Xinheng Yu, Yusen Zhou, Sriram Neelamegham:
  DrawGlycan-SNFG and gpAnnotate: rendering glycans and annotating glycopeptide mass spectra. 1942-1943

Gene expression

• 
  Francesco Napolitano, Diego Carrella, Xin Gao, Diego di Bernardo:
  gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles. 1944-1945
• 
  Debajyoti Sinha, Pradyumn Sinha, Ritwik Saha, Sanghamitra Bandyopadhyay, Debarka Sengupta:
  Improved dropClust R package with integrative analysis support for scRNA-seq data. 1946-1947
• 
  James J. Cai:
  scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. 1948-1949
• 
  Shijie C. Zheng, Charles E. Breeze, Stephan Beck, Danyue Dong, Tianyu Zhu, Liang-Xiao Ma, Wei Ye, Guoqing Zhang, Andrew E. Teschendorff:
  EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI. 1950-1951
• 
  Matthew Carlucci, Algimantas Krisciunas, Haohan Li, Povilas Gibas, Karolis Koncevicius, Art Petronis, Gabriel Oh:
  DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity. 1952-1954
• 
  Carlos Prieto, David Barrios:
  RaNA-Seq: interactive RNA-Seq analysis from FASTQ files to functional analysis. 1955-1956

Genetics and Population Analysis

• 
  Alencar Xavier, William M. Muir, Katy Martin Rainey:
  bWGR: Bayesian whole-genome regression. 1957-1959
• 
  Laura A. Esteban, Lyubov R. Lonishin, Daniil M. Bobrovskiy, Gregory Leleytner, Natalya S. Bogatyreva, Fyodor A. Kondrashov, Dmitry N. Ivankov:
  HypercubeME: two hundred million combinatorially complete datasets from a single experiment. 1960-1962

Systems Biology

• 
  Srikanth Ravichandran, András Hartmann, Antonio del Sol:
  SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies. 1963-1965
• 
  Stian Holmås, Rafel Riudavets Puig, Marcio Luis Acencio, Vladimir Mironov, Martin Kuiper:
  The Cytoscape BioGateway App: explorative network building from an RDF store. 1966-1967
• 
  Maciej Dobrzynski, Marc-Antoine Jacques, Olivier Pertz:
  Mining single-cell time-series datasets with Time Course Inspector. 1968-1969

Data and Text Mining

• 
  Deeptanshu Jha, Rahul Singh:
  SMARTS: the social media-based addiction recovery and intervention targeting server. 1970-1972
• 
  Jia-Hong Wang, Ling-Feng Zhao, Hua-Feng Wang, Yue-Ting Wen, Kui-Kui Jiang, Xiang-Ming Mao, Zi-Ying Zhou, Kai-Tai Yao, Qing-Shan Geng, Dan Guo, Zhong-Xi Huang:
  GenCLiP 3: mining human genes' functions and regulatory networks from PubMed based on co-occurrences and natural language processing. 1973-1975
• 
  Sebastian J. Teran Hidalgo, Mengyun Wu, Shuangge Ma:
  NCutYX: a package for clustering analysis of multilayer omics data. 1976-1977
• 
  Pieter Moris, Danh Bui Thi, Kris Laukens, Pieter Meysman:
  MILES: a Java tool to extract node-specific enriched subgraphs in biomolecular networks. 1978-1980

Databases and Ontologies

• 
  Radoslav Davidovic, Vladimir Perovic, Branislava Gemovic, Nevena Veljkovic:
  DiNGO: standalone application for Gene Ontology and Human Phenotype Ontology term enrichment analysis. 1981-1982
• 
  Manuel Holtgrewe, Clemens Messerschmidt, Mikko Nieminen, Dieter Beule:
  DigestiFlow: from BCL to FASTQ with ease. 1983-1985

Letter to the Editor
Systems Biology

• 
  Miguel Ponce de Leon, Iñigo Apaolaza, Alfonso Valencia, Francisco J. Planes:
  On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models. 1986-1988

Volume 36, Number 7, April 2020

• 
  Qingsu Cheng, Bahram Parvin:
  Organoid model of mammographic density displays a higher frequency of aberrant colony formations with radiation exposure. 1989-1993
• 
  Kevin R. Amses, William J. Davis, Timothy Y. James:
  SCGid: a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries of uncultured eukaryotes. 1994-2000
• 
  Samuele Cancellieri, Matthew C. Canver, Nicola Bombieri, Rosalba Giugno, Luca Pinello:
  CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing. 2001-2008
• 
  Yi Yang, Xingjie Shi, Yuling Jiao, Jian Huang, Min Chen, Xiang Zhou, Lei Sun, Xinyi Lin, Can Yang, Jin Liu:
  CoMM-S2: a collaborative mixed model using summary statistics in transcriptome-wide association studies. 2009-2016
• 
  Weiwei Zhang, Ziyi Li, Nana Wei, Hua-Jun Wu, Xiaoqi Zheng:
  Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities. 2017-2024
• 
  Yuwei Zhang, Tianfei Yi, Huihui Ji, Guofang Zhao, Yang Xi, Changzheng Dong, Lina Zhang, Xiaohong Zhang, Jinshun Zhao, Qi Liao:
  Designing a general method for predicting the regulatory relationships between long noncoding RNAs and protein-coding genes based on multi-omics characteristics. 2025-2032
• 
  Junfeng Liu, Ziyang An, Jianjun Luo, Jing Li, Feifei Li, Zhihua Zhang:
  Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite. 2033-2039
• 
  Fabian Klötzl, Bernhard Haubold:
  Phylonium: fast estimation of evolutionary distances from large samples of similar genomes. 2040-2046
• 
  Ha Young Kim, Dongsup Kim:
  Prediction of mutation effects using a deep temporal convolutional network. 2047-2052
• 
  Saket Choudhary, Wenzheng Li, Andrew D. Smith:
  Accurate detection of short and long active ORFs using Ribo-seq data. 2053-2059
• 
  Sam Friedman, Laura D. Gauthier, Yossi Farjoun, Eric Banks:
  Lean and deep models for more accurate filtering of SNP and INDEL variant calls. 2060-2067
• 
  Jing Xu, Han Zhang, Jinfang Zheng, Philippe Dovoedo, Yanbin Yin:
  eCAMI: simultaneous classification and motif identification for enzyme annotation. 2068-2075
• 
  Gabriele Orlando, Alexandra Silva, Sandra Macedo-Ribeiro, Daniele Raimondi, Wim F. Vranken:
  Accurate prediction of protein beta-aggregation with generalized statistical potentials. 2076-2081
• 
  Tomasz Marek Kowalski, Szymon Grabowski:
  PgRC: pseudogenome-based read compressor. 2082-2089
• 
  Zach Dinardo, Kiran Tomlinson, Anna M. Ritz, Layla Oesper:
  Distance measures for tumor evolutionary trees. 2090-2097
• 
  Simon Dellicour, Philippe Lemey, Jean Artois, Tommy T. Lam, Alice Fusaro, Isabella Monne, Giovanni Cattoli, Dmitry Kuznetsov, Ioannis Xenarios, Gwenaelle Dauphin, Wantanee Kalpravidh, Sophie von Dobschütz, Filip Claes, Scott H. Newman, Marc A. Suchard, Guy Baele, Marius Gilbert:
  Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region. 2098-2104
• 
  Chengxin Zhang, Wei Zheng, S. M. Mortuza, Yang Li, Yang Zhang:
  DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. 2105-2112
• 
  Xiao Wang, Genki Terashi, Charles Christoffer, Mengmeng Zhu, Daisuke Kihara:
  Protein docking model evaluation by 3D deep convolutional neural networks. 2113-2118
• 
  Zongyang Du, Shuo Pan, Qi Wu, Zhenling Peng, Jianyi Yang:
  CATHER: a novel threading algorithm with predicted contacts. 2119-2125
• 
  Ge Liu, Haoyang Zeng, Jonas Mueller, Brandon Carter, Ziheng Wang, Jonas Schilz, Geraldine Horny, Michael E. Birnbaum, Stefan Ewert, David K. Gifford:
  Antibody complementarity determining region design using high-capacity machine learning. 2126-2133
• 
  Carlos Martí-Gómez, Enrique Lara Pezzi, Fátima Sánchez-Cabo:
  dSreg: a Bayesian model to integrate changes in splicing and RNA-binding protein activity. 2134-2141
• 
  Annika Jacobsen, Olga Ivanova, Saman Amini, Jaap Heringa, Patrick Kemmeren, K. Anton Feenstra:
  A framework for exhaustive modelling of genetic interaction patterns using Petri nets. 2142-2149
• 
  Likun Huang, Weiqi Tang, Suhong Bu, Weiren Wu:
  BRM: a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing. 2150-2156
• 
  Estelle Geffard, Sophie Limou, Alexandre Walencik, Michelle Daya, Harold Watson, Dara Torgerson, Kathleen C. Barnes, Anne Cesbron Gautier, Pierre-Antoine Gourraud, Nicolas Vince:
  Easy-HLA: a validated web application suite to reveal the full details of HLA typing. 2157-2164
• 
  Filippo Maggioli, Toni Mancini, Enrico Tronci:
  SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems. 2165-2172
• 
  Jui Wan Loh, Caitlin Guccione, Frances Di Clemente, Gregory M. Riedlinger, Shridar Ganesan, Hossein Khiabanian:
  All-FIT: allele-frequency-based imputation of tumor purity from high-depth sequencing data. 2173-2180
• 
  Marco S. Nobile, Giuseppina Votta, Roberta Palorini, Simone Spolaor, Humberto De Vitto, Paolo Cazzaniga, Francesca Ricciardiello, Giancarlo Mauri, Lilia Alberghina, Ferdinando Chiaradonna, Daniela Besozzi:
  Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells. 2181-2188
• 
  Lars Thielecke, Kerstin Cornils, Ingmar Glauche:
  genBaRcode: a comprehensive R-package for genetic barcode analysis. 2189-2194
• 
  Zhe Cui, Jayaram Kancherla, Kyle W. Chang, Niklas Elmqvist, Héctor Corrada Bravo:
  Proactive visual and statistical analysis of genomic data in Epiviz. 2195-2201
• 
  Fabio Fabris, Daniel Palmer, Khalid M. Salama, João Pedro de Magalhães, Alex Alves Freitas:
  Using deep learning to associate human genes with age-related diseases. 2202-2208
• 
  Herty Liany, Anand Jeyasekharan, Vaibhav Rajan:
  Predicting synthetic lethal interactions using heterogeneous data sources. 2209-2216
• 
  Kathryn A. McGurk, Arianna Dagliati, Davide Chiasserini, Dave Lee, Darren Plant, Ivona Baricevic-Jones, Janet Kelsall, Rachael Eineman, Rachel Reed, Bethany Geary, Richard D. Unwin, Anna Nicolaou, Bernard D. Keavney, Anne Barton, Anthony D. Whetton, Nophar Geifman:
  The use of missing values in proteomic data-independent acquisition mass spectrometry to enable disease activity discrimination. 2217-2223
• 
  Raul Rodriguez-Esteban:
  Semantic persistence of ambiguous biomedical names in the citation network. 2224-2228
• 
  Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
  Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. 2229-2236
• 
  Cyril F. Reboul, Simon Kiesewetter, Dominika Elmlund, Hans Elmlund:
  Point-group symmetry detection in three-dimensional charge density of biomolecules. 2237-2243
• 
  Wei Long, Yang Yang, Hong-Bin Shen:
  ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images. 2244-2250
• 
  Takuya Aramaki, Romain Blanc-Mathieu, Hisashi Endo, Koichi Ohkubo, Minoru Kanehisa, Susumu Goto, Hiroyuki Ogata:
  KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. 2251-2252
• 
  Jiang Hu, Junpeng Fan, Zongyi Sun, Shanlin Liu:
  NextPolish: a fast and efficient genome polishing tool for long-read assembly. 2253-2255
• 
  Readman Chiu, Ka Ming Nip, Inanç Birol:
  Fusion-Bloom: fusion detection in assembled transcriptomes. 2256-2257
• 
  Gurjit S. Randhawa, Kathleen A. Hill, Lila Kari:
  MLDSP-GUI: an alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis. 2258-2259
• 
  Georgios Fotakis, Dietmar Rieder, Marlene Haider, Zlatko Trajanoski, Francesca Finotello:
  NeoFuse: predicting fusion neoantigens from RNA sequencing data. 2260-2261
• 
  Ahmed A. Quadeer, David Morales-Jiménez, Matthew R. McKay:
  RocaSec: a standalone GUI-based package for robust co-evolutionary analysis of proteins. 2262-2263
• 
  Mehari B. Zerihun, Fabrizio Pucci, Emanuel K. Peter, Alexander Schug:
  pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences. 2264-2265
• 
  Jimmy Caroli, Mattia Forcato, Silvio Bicciato:
  APTANI2: update of aptamer selection through sequence-structure analysis. 2266-2268
• 
  Snædís Kristmundsdóttir, Hannes P. Eggertsson, Gudny A. Arnadottir, Bjarni V. Halldórsson:
  popSTR2 enables clinical and population-scale genotyping of microsatellites. 2269-2271
• 
  Ammar Tareen, Justin B. Kinney:
  Logomaker: beautiful sequence logos in Python. 2272-2274
• 
  Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S. Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez:
  GABAC: an arithmetic coding solution for genomic data. 2275-2277
• 
  Ahmed A. Quadeer, Matthew R. McKay, John P. Barton, Raymond H. Y. Louie:
  MPF-BML: a standalone GUI-based package for maximum entropy model inference. 2278-2279
• 
  Sarah Lutteropp, Alexey M. Kozlov, Alexandros Stamatakis:
  A fast and memory-efficient implementation of the transfer bootstrap. 2280-2281
• 
  Jacques Ducasse, Visotheary Ung, Guillaume Lecointre, Aurélien Miralles:
  LIMES: a tool for comparing species partition. 2282-2283
• 
  Miguel Romero-Durana, Brian Jiménez-García, Juan Fernández-Recio:
  pyDockEneRes: per-residue decomposition of protein-protein docking energy. 2284-2285
• 
  Krisztian Adam, Zoltan Gyorgypal, Zoltan Hegedus:
  DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments. 2286-2287
• 
  Shian Su, Luyi Tian, Xueyi Dong, Peter F. Hickey, Saskia Freytag, Matthew E. Ritchie:
  CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods. 2288-2290
• 
  Saskia Freytag, Ryan Lister:
  schex avoids overplotting for large single-cell RNA-sequencing datasets. 2291-2292
• 
  Xiao Tan, Andrew Su, Minh Tran, Quan Nguyen:
  SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells. 2293-2294
• 
  Christina Nieuwoudt, Angela Brooks-Wilson, Jinko Graham:
  SimRVSequences: an R package to simulate genetic sequence data for pedigrees. 2295-2297
• 
  Laura M. Zingaretti, Gilles Renand, Diego P. Morgavi, Yuliaxis Ramayo-Caldas:
  Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities. 2298-2299
• 
  Maryam Nazarieh, Mohamed Hamed, Christian Spaniol, Thorsten Will, Volkhard Helms:
  TFmiR2: constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks. 2300-2302
• 
  Junwei Han, Xudong Han, Qingfei Kong, Liang Cheng:
  psSubpathway: a software package for flexible identification of phenotype-specific subpathways in cancer progression. 2303-2305
• 
  Sergii Domanskyi, Carlo Piermarocchi, George Mias:
  PyIOmica: longitudinal omics analysis and trend identification. 2306-2307
• 
  Gongchao Jing, Yufeng Zhang, Ming Yang, Lu Liu, Jian Xu, Xiaoquan Su:
  Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level. 2308-2310
• 
  Roman Hillje, Pier Giuseppe Pelicci, Lucilla Luzi:
  Cerebro: interactive visualization of scRNA-seq data. 2311-2313
• 
  Jacobo de la Cuesta-Zuluaga, Ruth E. Ley, Nicholas D. Youngblut:
  Struo: a pipeline for building custom databases for common metagenome profilers. 2314-2315
• 
  Bilge Sürün, Charlotta P. I. Schärfe, Mathew R. Divine, Julian Heinrich, Nora C. Toussaint, Lukas Zimmermann, Janina Beha, Oliver Kohlbacher:
  ClinVAP: a reporting strategy from variants to therapeutic options. 2316-2317

Volume 36, Number 8, April 2020

• 
  Jonathan Raad, Georgina Stegmayer, Diego H. Milone:
  Complexity measures of the mature miRNA for improving pre-miRNAs prediction. 2319-2327
• 
  Chuanyi Zhang, Idoia Ochoa:
  VEF: a variant filtering tool based on ensemble methods. 2328-2336
• 
  Gleb Goussarov, Ilse Cleenwerck, Mohamed Mysara, Natalie Leys, Pieter Monsieurs, Guillaume Tahon, Aurélien Carlier, Peter Vandamme, Rob Van Houdt:
  PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing. 2337-2344
• 
  Xinyan Zhang, Nengjun Yi:
  Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data. 2345-2351
• 
  Guodong Yang, Aiqun Ma, Zhaohui S. Qin, Li Chen:
  Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules. 2352-2358
• 
  Pasi Rastas:
  Lep-Anchor: automated construction of linkage map anchored haploid genomes. 2359-2364
• 
  Xiaqiong Wang, Yalu Wen:
  A U-statistics for integrative analysis of multilayer omics data. 2365-2374
• 
  Akhilesh Mishra, Sahil Dhanda, Priyanka Siwach, Shruti Aggarwal, B. Jayaram:
  A novel method SEProm for prokaryotic promoter prediction based on DNA structure and energetics. 2375-2384
• 
  Shilpa Garg, John Aach, Heng Li, Isaac Sebenius, Richard Durbin, George M. Church:
  A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. 2385-2392
• 
  Haitao Yu, Zhiming Dai:
  SANPolyA: a deep learning method for identifying Poly(A) signals. 2393-2400
• 
  Nils Strodthoff, Patrick Wagner, Markus Wenzel, Wojciech Samek:
  UDSMProt: universal deep sequence models for protein classification. 2401-2409
• 
  Thomas Bradley, Simon Moxon:
  FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals. 2410-2416
• 
  Tobias Brinkjost, Christiane Ehrt, Oliver Koch, Petra Mutzel:
  SCOT: Rethinking the classification of secondary structure elements. 2417-2428
• 
  Xiaoqiang Huang, Wei Zheng, Robin Pearce, Yang Zhang:
  SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. 2429-2437
• 
  Yiwei Cao, Sang-Jun Park, Akul Y. Mehta, Richard D. Cummings, Wonpil Im:
  GlyMDB: Glycan Microarray Database and analysis toolset. 2438-2442
• 
  Jun Liu, Xiao-Gen Zhou, Yang Zhang, Gui-Jun Zhang:
  CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. 2443-2450
• 
  Louis Becquey, Eric Angel, Fariza Tahi:
  BiORSEO: a bi-objective method to predict RNA secondary structures with pseudoknots using RNA 3D modules. 2451-2457
• 
  Isak Johansson-Åkhe, Claudio Mirabello, Björn Wallner:
  InterPep2: global peptide-protein docking using interaction surface templates. 2458-2465
• 
  Jiao Sun, Jae-Woong Chang, Teng Zhang, Jeongsik Yong, Rui Kuang, Wei Zhang:
  Platform-integrated mRNA isoform quantification. 2466-2473
• 
  Zhan-Ying Feng, Xianwen Ren, Yuan Fang, Yining Yin, Chutian Huang, Yimin Zhao, Yong Wang:
  scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization. 2474-2485
• 
  Serin Zhang, Jiang Shao, Disa Yu, Xing Qiu, Jinfeng Zhang:
  MatchMixeR: a cross-platform normalization method for gene expression data integration. 2486-2491
• 
  Yifan Ji, Chang Yu, Hong Zhang:
  contamDE-lm: linear model-based differential gene expression analysis using next-generation RNA-seq data from contaminated tumor samples. 2492-2499
• 
  Gittu George, Sushrima Gan, Yu Huang, Philip Appleby, A. S. Nar, Radha Venkatesan, Viswanathan Mohan, Colin N. A. Palmer, Alex S. F. Doney:
  PheGWAS: a new dimension to visualize GWAS across multiple phenotypes. 2500-2505
• 
  Jingsi Ming, Tao Wang, Can Yang:
  LPM: a latent probit model to characterize the relationship among complex traits using summary statistics from multiple GWASs and functional annotations. 2506-2514
• 
  Kristina Buschur, Maria Chikina, Panayiotis V. Benos:
  Causal network perturbations for instance-specific analysis of single cell and disease samples. 2515-2521
• 
  Rasmus Magnusson, Mika Gustafsson:
  LiPLike: towards gene regulatory network predictions of high certainty. 2522-2529
• 
  Hui-Zeng Sun, Mi Zhou, Ou Wang, Yanhong Chen, Jian-Xin Liu, Le Luo Guan:
  Multi-omics reveals functional genomic and metabolic mechanisms of milk production and quality in dairy cows. 2530-2537
• 
  Jin Li, Sai Zhang, Tao Liu, Chenxi Ning, Zhuoxuan Zhang, Wei Zhou:
  Neural inductive matrix completion with graph convolutional networks for miRNA-disease association prediction. 2538-2546
• 
  Mayank Baranwal, Abram Magner, Paolo Elvati, Jacob Saldinger, Angela Violi, Alfred O. Hero III:
  A deep learning architecture for metabolic pathway prediction. 2547-2553
• 
  Xiaohui Yao, Shan Cong, Jingwen Yan, Shannon L. Risacher, Andrew J. Saykin, Jason H. Moore, Li Shen:
  Regional imaging genetic enrichment analysis. 2554-2560
• 
  Xia-an Bi, Yingchao Liu, Yiming Xie, Xi Hu, Qinghua Jiang:
  Morbigenous brain region and gene detection with a genetically evolved random neural network cluster approach in late mild cognitive impairment. 2561-2568
• 
  Cinta Pegueroles, Verónica Mixão, Laia Carreté, Manuel Molina, Toni Gabaldón:
  HaploTypo: a variant-calling pipeline for phased genomes. 2569-2571
• 
  Soumitra Pal, Teresa M. Przytycka:
  Bioinformatics pipeline using JUDI: Just Do It! 2572-2574
• 
  Swadha Anand, Bhusan K. Kuntal, Anwesha Mohapatra, Vineet Bhatt, Sharmila S. Mande:
  FunGeCo: a web-based tool for estimation of functional potential of bacterial genomes and microbiomes using gene context information. 2575-2577
• 
  Yu Li, Sheng Wang, Chongwei Bi, Zhaowen Qiu, Mo Li, Xin Gao:
  DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing. 2578-2580
• 
  Sophia C. Tintori, Patrick Golden, Bob Goldstein:
  Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets. 2581-2583
• 
  Dominika Labudová, Jirí Hon, Matej Lexa:
  pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. 2584-2586
• 
  Christopher M. Ward, Thu-Hien To, Stephen M. Pederson:
  ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files. 2587-2588
• 
  Lorraine A. K. Ayad, Panagiotis Charalampopoulos, Solon P. Pissis:
  SMART: SuperMaximal approximate repeats tool. 2589-2591
• 
  Deren A. R. Eaton, Isaac Overcast:
  ipyrad: Interactive assembly and analysis of RADseq datasets. 2592-2594
• 
  Bianka Farkas, Georgina Csizmadia, Eszter Katona, Gábor E. Tusnády, Tamás Hegedüs:
  MemBlob database and server for identifying transmembrane regions using cryo-EM maps. 2595-2598
• 
  Tomasz Magdziarz, Karolina Mitusinska, Maria Bzówka, Agata Raczynska, Agnieszka Stanczak, Michal Banas, Weronika Bagrowska, Artur Góra:
  AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective. 2599-2601
• 
  Evangelos Karatzas, Juan Eiros Zamora, Emmanouil Athanasiadis, Dimitris Dellis, Zoe Cournia, George M. Spyrou:
  ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing. 2602-2604
• 
  Gui-Yan Xie, Meng-Xuan Xia, Ya-Ru Miao, Mei Luo, Qiong Zhang, An-Yuan Guo:
  FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human. 2605-2607
• 
  Aritro Nath, Jeremy Chang, Rong Stephanie Huang:
  iMIRAGE: an R package to impute microRNA expression using protein-coding genes. 2608-2610
• 
  Thang Viet Pham, Alex A. Henneman, Connie R. Jimenez:
  iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics. 2611-2613
• 
  Palle Duun Rohde, Izel Fourie Sørensen, Peter Sørensen:
  qgg: an R package for large-scale quantitative genetic analyses. 2614-2615
• 
  Andre Schultz, Rehan Akbani:
  SAMMI: a semi-automated tool for the visualization of metabolic networks. 2616-2617
• 
  César Parra-Rojas, Esteban A. Hernández-Vargas:
  PDEparams: parameter fitting toolbox for partial differential equations in python. 2618-2619
• 
  Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev:
  cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. 2620-2622
• 
  Thomas C. Keaty, Paul A. Jensen:
  Gapsplit: efficient random sampling for non-convex constraint-based models. 2623-2625
• 
  Corentin Molitor, Matt Brember, Fady R. Mohareb:
  VarGen: an R package for disease-associated variant discovery and annotation. 2626-2627
• 
  Steven X. Ge, Dongmin Jung, Runan Yao:
  ShinyGO: a graphical gene-set enrichment tool for animals and plants. 2628-2629
• 
  Alexander Keller, Sonja Hohlfeld, Andreas Kolter, Jörg Schultz, Birgit Gemeinholzer, Markus J. Ankenbrand:
  BCdatabaser: on-the-fly reference database creation for (meta-)barcoding. 2630-2631
• 
  Francesco Ceccarelli, Dénes Türei, Attila Gábor, Julio Saez-Rodriguez:
  Bringing data from curated pathway resources to Cytoscape with OmniPath. 2632-2633
• 
  Sébastien Tosi, Lídia Bardia, Maria Jose Filgueira, Alexandre Calon, Julien Colombelli:
  LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data. 2634-2635
• 
  Rachel Drysdale, Charles E. Cook, Robert Petryszak, Vivienne Baillie Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl, Jürgen Haas, Jerry Lanfear, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Alex Bateman, Alan J. Bridge, Guy Cochrane, Robert D. Finn, Frank Oliver Glöckner, Marc Hanauer, Thomas M. Keane, Andrew Leach, Luana Licata, Per Oksvold, Sandra E. Orchard, Christine A. Orengo, Helen E. Parkinson, Bengt Persson, Pablo Porras, Jordi Rambla, Ana Rath, Charlotte Rodwell, Ugis Sarkans, Dietmar Schomburg, Ian Sillitoe, J. Dylan Spalding, Mathias Uhlén, Sameer Velankar, Juan Antonio Vizcaíno, Kalle von Feilitzen, Christian von Mering, Andrew D. Yates, Niklas Blomberg, Christine Durinx, Johanna R. McEntyre:
  The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. 2636-2642
• 
  Nils Koelling, Marie Bernkopf, Eduardo Calpena, Geoffrey J. Maher, Kerry A. Miller, Hannah K. Ralph, Anne Goriely, Andrew O. M. Wilkie:
  amplimap: a versatile tool to process and analyze targeted NGS data. 2643
• 
  Rui Liu, Pei Chen, Luonan Chen:
  Corrigendum to: Single-sample landscape entropy reveals the imminent phase transition during disease progression. 2644
• 
  Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang:
  SynergyFinder: a web application for analyzing drug combination dose-response matrix data. 2645
• 
  Sergey V. Tarlachkov, Taras V. Shevchuk, Maria del Carmen Montero-Calasanz, Irina P. Starodumova:
  Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments. 2646
• 
  Gabriel Studer, Christine Rempfer, Andrew Waterhouse, Rafal Gumienny, Juergen Haas, Torsten Schwede:
  QMEANDisCo - distance constraints applied on model quality estimation. 2647

Volume 36, Number 9, May 2020

• 
  Dinh Van Tran, Alessandro Sperduti, Rolf Backofen, Fabrizio Costa:
  Heterogeneous networks integration for disease-gene prioritization with node kernels. 2649-2656
• 
  Md Amanullah, Mengqian Yu, Xiwei Sun, Aoran Luo, Qing Zhou, Liyuan Zhou, Ling Hou, Wei Wang, Weiguo Lu, Pengyuan Liu, Yan Lu:
  MDEHT: a multivariate approach for detecting differential expression of microRNA isoform data in RNA-sequencing studies. 2657-2664
• 
  Nicola Casiraghi, Francesco Orlando, Yari Ciani, Jenny Xiang, Andrea Sboner, Olivier Elemento, Gerhardt Attard, Himisha Beltran, Francesca Demichelis, Alessandro Romanel:
  ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA. 2665-2674
• 
  Evan Gatev, Nicole Gladish, Sara Mostafavi, Michael S. Kobor:
  CoMeBack: DNA methylation array data analysis for co-methylated regions. 2675-2683
• 
  Kasidet Hiranniramol, Yuhao Chen, Weijun Liu, Xiaowei Wang:
  Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency. 2684-2689
• 
  Jarkko Toivonen, Pratyush K. Das, Jussi Taipale, Esko Ukkonen:
  MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs. 2690-2696
• 
  Rui Yin, Emil Luusua, Jan Dabrowski, Yu Zhang, Chee Keong Kwoh:
  Tempel: time-series mutation prediction of influenza A viruses via attention-based recurrent neural networks. 2697-2704
• 
  Gianvito Urgese, Emanuele Parisi, Orazio M. Scicolone, Santa Di Cataldo, Elisa Ficarra:
  BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis. 2705-2711
• 
  Ting Yu, Juntao Liu, Xin Gao, Guojun Li:
  iPAC: a genome-guided assembler of isoforms via phasing and combing paths. 2712-2717
• 
  Vincent Sater, Pierre-Julien Viailly, Thierry Lecroq, Élise Prieur-Gaston, Élodie Bohers, Mathieu Viennot, Philippe Ruminy, Hélène Dauchel, Pierre Vera, Fabrice Jardin:
  UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries. 2718-2724
• 
  Keisuke Shimmura, Yuki Kato, Yukio Kawahara:
  Bivartect: accurate and memory-saving breakpoint detection by direct read comparison. 2725-2730
• 
  Anastasia A. Gulyaeva, Andrey I Sigorskih, Elena S. Ocheredko, Dmitry V. Samborskiy, Alexander E. Gorbalenya:
  LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins. 2731-2739
• 
  Henry Xing, Steven W. Kembel, Vladimir Makarenkov:
  Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks. 2740-2749
• 
  Sam M. Ireland, Andrew C. R. Martin:
  atomium - a Python structure parser. 2750-2754
• 
  Jia-Juan Tu, Le Ou-Yang, Hong Yan, Xiao-Fei Zhang, Hong Qin:
  Joint reconstruction of multiple gene networks by simultaneously capturing inter-tumor and intra-tumor heterogeneity. 2755-2762
• 
  Jie-Huei Wang, Yi-Hau Chen:
  Interaction screening by Kendall's partial correlation for ultrahigh-dimensional data with survival trait. 2763-2769
• 
  Trang T. Le, Bryan A. Dawkins, Brett A. McKinney:
  Nearest-neighbor Projected-Distance Regression (NPDR) for detecting network interactions with adjustments for multiple tests and confounding. 2770-2777
• 
  Shobana V. Stassen, Dickson M. D. Siu, Kelvin C. M. Lee, Joshua W. K. Ho, Hayden K. H. So, Kevin K. Tsia:
  PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells. 2778-2786
• 
  Yue Qiu, Tianhuan Lu, Hansaim Lim, Lei Xie:
  A Bayesian approach to accurate and robust signature detection on LINCS L1000 data. 2787-2795
• 
  Stephen S. Tran, Qing Zhou, Xinshu Xiao:
  Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling. 2796-2804
• 
  Xiangxiang Zeng, Siyi Zhu, Yuan Hou, Pengyue Zhang, Lang Li, Jing Li, L. Frank Huang, Stephen J. Lewis, Ruth Nussinov, Feixiong Cheng:
  Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest. 2805-2812
• 
  N. Suhas Jagannathan, Mario O. Ihsan, Xiao Xuan Kin, Roy E. Welsch, Marie-Véronique Clément, Lisa Tucker-Kellogg:
  Transcompp: understanding phenotypic plasticity by estimating Markov transition rates for cell state transitions. 2813-2820
• 
  Omer Basha, Chanan M. Argov, Raviv Artzy, Yazeed Zoabi, Idan Hekselman, Liad Alfandari, Vered Chalifa-Caspi, Esti Yeger Lotem:
  Differential network analysis of multiple human tissue interactomes highlights tissue-selective processes and genetic disorder genes. 2821-2828
• 
  So Nakashima, Yuki Sughiyama, Tetsuya J. Kobayashi:
  Lineage EM algorithm for inferring latent states from cellular lineage trees. 2829-2838
• 
  Wenjuan Zhang, Hunan Xu, Xiaozhong Li, Qiang Gao, Lin Wang:
  DRIMC: an improved drug repositioning approach using Bayesian inductive matrix completion. 2839-2847
• 
  Lingwei Xie, Song He, Zhongnan Zhang, Kunhui Lin, Xiaochen Bo, Shu Yang, Boyuan Feng, Kun Wan, Kang Yang, Jie Yang, Yufei Ding:
  Domain-adversarial multi-task framework for novel therapeutic property prediction of compounds. 2848-2855
• 
  Gabriel E. Hoffman, Jaroslav Bendl, Kiran Girdhar, Panos Roussos:
  decorate: differential epigenetic correlation test. 2856-2861
• 
  Chiung-Ting Wu, Yizhi Wang, Yinxue Wang, Timothy M. D. Ebbels, Ibrahim Karaman, Gonçalo Graça, Rui Pinto, David M. Herrington, Yue Wang, Guoqiang Yu:
  Targeted realignment of LC-MS profiles by neighbor-wise compound-specific graphical time warping with misalignment detection. 2862-2871
• 
  Rong Ma, Yi Li, Chenxing Li, Fangping Wan, Hailin Hu, Wei Xu, Jianyang Zeng:
  Secure multiparty computation for privacy-preserving drug discovery. 2872-2880
• 
  Joy Roy, Eric Cheung, Junaid Bhatti, Abraar Muneem, Daniel Lobo:
  Curation and annotation of planarian gene expression patterns with segmented reference morphologies. 2881-2887
• 
  Zhenyuan Ning, Weihao Pan, Yuting Chen, Qing Xiao, Xinsen Zhang, Jiaxiu Luo, Jian Wang, Yu Zhang:
  Integrative analysis of cross-modal features for the prognosis prediction of clear cell renal cell carcinoma. 2888-2895
• 
  Dengfeng Guan, Shane A. McCarthy, Jonathan Wood, Kerstin Howe, Yadong Wang, Richard Durbin:
  Identifying and removing haplotypic duplication in primary genome assemblies. 2896-2898
• 
  Quanhu Sheng, Hui Yu, Olufunmilola Oyebamiji, Jiandong Wang, Danqian Chen, Scott Ness, Ying-Yong Zhao, Yan Guo:
  AnnoGen: annotating genome-wide pragmatic features. 2899-2901
• 
  Connor A. Horton, Burak Han Alver, Peter J. Park:
  GiniQC: a measure for quantifying noise in single-cell Hi-C data. 2902-2904
• 
  Kevin R. Shieh, Christina Kratschmer, Keith E. Maier, John M. Greally, Matthew Levy, Aaron Golden:
  AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX. 2905-2906
• 
  Stilianos Louca:
  Simulating trees with millions of species. 2907-2908
• 
  Gianluca Tomasello, Ilaria Armenia, Gianluca Molla:
  The Protein Imager: a full-featured online molecular viewer interface with server-side HQ-rendering capabilities. 2909-2911
• 
  José Luis Velázquez-Libera, Fabio Durán-Verdugo, Alejandro Valdés-Jiménez, Gabriel Núñez-Vivanco, Julio Caballero:
  LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking. 2912-2914
• 
  Daniel K. Weber, Songlin Wang, John L. Markley, Gianluigi Veglia, Woonghee Lee:
  PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. 2915-2916
• 
  Christopher W. Wood, Amaurys Ávila Ibarra, Gail J. Bartlett, Andrew J. Wilson, Derek N. Woolfson, Richard B. Sessions:
  BAlaS: fast, interactive and accessible computational alanine-scanning using BudeAlaScan. 2917-2919
• 
  Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, Danny Barash:
  incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. 2920-2922
• 
  Tomás Tokár, Chiara Pastrello, Igor Jurisica:
  GSOAP: a tool for visualization of gene set over-representation analysis. 2923-2925
• 
  Warren D. Anderson, Fabiana M. Duarte, Mete Civelek, Michael J. Guertin:
  Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R. 2926-2928
• 
  Hakan Özadam, Michael Geng, Can Cenik:
  RiboFlow, RiboR and RiboPy: an ecosystem for analyzing ribosome profiling data at read length resolution. 2929-2931
• 
  Angela Serra, Laura Aliisa Saarimäki, Michele Fratello, Veer Singh Marwah, Dario Greco:
  BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data. 2932-2933
• 
  Yi Zheng, Fangqing Zhao:
  Visualization of circular RNAs and their internal splicing events from transcriptomic data. 2934-2935
• 
  Gareth Peat, William Jones, Michael Nuhn, José Carlos Marugán, William Newell, Ian Dunham, Daniel R. Zerbino:
  The open targets post-GWAS analysis pipeline. 2936-2937
• 
  Olivia Angelin-Bonnet, Patrick J. Biggs, Samantha J. Baldwin, Susan Thomson, Matthieu Vignes:
  sismonr: simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R. 2938-2940
• 
  Stepán Kouril, Julie de Sousa, Jan Václavík, David Friedecký, Tomás Adam:
  CROP: correlation-based reduction of feature multiplicities in untargeted metabolomic data. 2941-2942
• 
  Francisco Madrid-Gambin, Sergio Oller-Moreno, Luis Fernández Romero, Simona Bartova, Maria Pilar Giner, Christopher Joyce, Francesco Ferraro, Ivan Montoliu, Sofia Moco, Santiago Marco:
  AlpsNMR: an R package for signal processing of fully untargeted NMR-based metabolomics. 2943-2945
• 
  Xingxiang Cheng, Dandan Sun, Dachuan Zhang, Yu Tian, Shaozhen Ding, Pengli Cai, Qian-Nan Hu:
  RxnBLAST: molecular scaffold and reactive chemical environment feature extractor for biochemical reactions. 2946-2947
• 
  Ervin A. Tasnádi, Timea Toth, Maria Kovacs, Akos Diosdi, Francesco Pampaloni, József Molnár, Filippo Piccinini, Péter Horváth:
  3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images. 2948-2949
• 
  Jacqueline Nowak, Kristin Gennermann, Staffan Persson, Zoran Nikoloski:
  CytoSeg 2.0: automated extraction of actin filaments. 2950-2951
• 
  Luciano A. Abriata, Rosalba Lepore, Matteo Dal Peraro:
  About the need to make computational models of biological macromolecules available and discoverable. 2952-2954
• 
  Jacopo Di Iorio, Francesca Chiaromonte, Marzia A. Cremona:
  On the bias of H-scores for comparing biclusters, and how to correct it. 2955-2957
• 
  Jayvardan S. Naidu, Justin Delano, Scott Mathews, Predrag Radivojac:
  An examination of citation-based impact of the computational biology conferences. 2958-2962
• 
  Anastasia Chasapi, Vasilis J. Promponas, Christos A. Ouzounis:
  The bioinformatics wealth of nations. 2963-2965
• 
  Gustavo A. Arango-Argoty, G. K. P. Guron, Emily Garner, M. V. Riquelme, Lenwood S. Heath, Amy Pruden, Peter J. Vikesland, Liqing Zhang:
  ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes. 2966-2973
• 
  Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher:
  Fast and accurate correction of optical mapping data via spaced seeds. 2974

Volume 36, Number 10, May 2020

• 
  Zheng Zhang, Fen Yu, Yuanqiang Zou, Ye Qiu, Aiping Wu, Taijiao Jiang, Yousong Peng:
  Phage protein receptors have multiple interaction partners and high expressions. 2975-2979
• 
  Ilya M. Flyamer, Robert S. Illingworth, Wendy A. Bickmore:
  Coolpup.py: versatile pile-up analysis of Hi-C data. 2980-2985
• 
  Qiang Kang, Jun Meng, Jun Cui, Yushi Luan, Ming Chen:
  PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA-lncRNA interaction prediction. 2986-2992
• 
  Pavel Avdeyev, Nikita Alexeev, Yongwu Rong, Max A. Alekseyev:
  A unified ILP framework for core ancestral genome reconstruction problems. 2993-3003
• 
  Huang Xu, Xiang Li, Yaning Yang, Yi Li, Jose Pinheiro, Kate Sasser, Hisham Hamadeh, Xu Steven, Min Yuan:
  High-throughput and efficient multilocus genome-wide association study on longitudinal outcomes. 3004-3010
• 
  Olga Mineeva, Mateo Rojas-Carulla, Ruth E. Ley, Bernhard Schölkopf, Nicholas D. Youngblut:
  DeepMAsED: evaluating the quality of metagenomic assemblies. 3011-3017
• 
  Chun-Qiu Xia, Xiaoyong Pan, Hong-Bin Shen:
  Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data. 3018-3027
• 
  Xiangzheng Fu, Lijun Cai, Xiangxiang Zeng, Quan Zou:
  StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency. 3028-3034
• 
  Shiwei Wei, Yuping Wang, Yuanchao Yang, Sen Liu:
  A path recorder algorithm for Multiple Longest Common Subsequences (MLCS) problems. 3035-3042
• 
  Michael A. Peabody, Wing Yin Venus Lau, Gemma Hoad, Baofeng Jia, Finlay Maguire, Kristen L. Gray, Robert G. Beiko, Fiona S. L. Brinkman:
  PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data. 3043-3048
• 
  Jae Yong Ryu, Mi Young Lee, Jeong Hyun Lee, Byung Ho Lee, Kwang-Seok Oh:
  DeepHIT: a deep learning framework for prediction of hERG-induced cardiotoxicity. 3049-3055
• 
  Yuan Zhang, Xing Sui, Scott Stagg, Jinfeng Zhang:
  FTIP: an accurate and efficient method for global protein surface comparison. 3056-3063
• 
  Rostislav K. Skitchenko, Dmitrii Usoltsev, Mayya Uspenskaya, Andrey V. Kajava, Albert Guskov:
  Census of halide-binding sites in protein structures. 3064-3071
• 
  Elena Rivas, Jody Clements, Sean R. Eddy:
  Estimating the power of sequence covariation for detecting conserved RNA structure. 3072-3076
• 
  Wentao Shi, Jeffrey Mitchell Lemoine, Abd-El-Monsif A. Shawky, Manali Singha, Limeng Pu, Shuangyan Yang, J. Ramanujam, Michal Brylinski:
  BionoiNet: ligand-binding site classification with off-the-shelf deep neural network. 3077-3083
• 
  Luca Ponzoni, Daniel A. Peñaherrera, Zoltán N. Oltvai, Ivet Bahar:
  Rhapsody: predicting the pathogenicity of human missense variants. 3084-3092
• 
  Saeid Parvandeh, Hung-Wen Yeh, Martin P. Paulus, Brett A. McKinney:
  Consensus features nested cross-validation. 3093-3098
• 
  Burim Ramosaj, Lubna Amro, Markus Pauly:
  A cautionary tale on using imputation methods for inference in matched-pairs design. 3099-3106
• 
  Neo Christopher Chung:
  Statistical significance of cluster membership for unsupervised evaluation of cell identities. 3107-3114
• 
  Teng Fei, Tianwei Yu:
  scBatch: batch-effect correction of RNA-seq data through sample distance matrix adjustment. 3115-3123
• 
  Wenfei Zhang, Ying Wei, Donghui Zhang, Ethan Y. Xu:
  ZIAQ: a quantile regression method for differential expression analysis of single-cell RNA-seq data. 3124-3130
• 
  Ke Jin, Le Ou-Yang, Xing-Ming Zhao, Hong Yan, Xiao-Fei Zhang:
  scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation. 3131-3138
• 
  Junlin Xu, Lijun Cai, Bo Liao, Wen Zhu, Jialiang Yang:
  CMF-Impute: an accurate imputation tool for single-cell RNA-seq data. 3139-3147
• 
  David Bouyssié, Anne-Marie Hesse, Emmanuelle Mouton-Barbosa, Magali Rompais, Charlotte Macron, Christine Carapito, Anne Gonzalez de Peredo, Yohann Couté, Véronique Dupierris, Alexandre Burel, Jean-Philippe Menetrey, Andrea Kalaitzakis, Julie Poisat, Aymen Romdhani, Odile Burlet-Schiltz, Sarah Cianférani, Jerome Garin, Christophe Bruley:
  Proline: an efficient and user-friendly software suite for large-scale proteomics. 3148-3155
• 
  Chong Chen, Changjing Wu, Linjie Wu, Xiaochen Wang, Minghua Deng, Ruibin Xi:
  scRMD: imputation for single cell RNA-seq data via robust matrix decomposition. 3156-3161
• 
  Hong Zhang, Ni Zhao, Devan V. Mehrotra, Judong Shen:
  Composite Kernel Association Test (CKAT) for SNP-set joint assessment of genotype and genotype-by-treatment interaction in Pharmacogenetics studies. 3162-3168
• 
  Akio Onogi:
  Connecting mathematical models to genomes: joint estimation of model parameters and genome-wide marker effects on these parameters. 3169-3176
• 
  Eshan D. Mitra, William S. Hlavacek:
  Bayesian inference using qualitative observations of underlying continuous variables. 3177-3184
• 
  Edison Ong, Haihe Wang, Mei U. Wong, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He:
  Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. 3185-3191
• 
  Stephen Kotiang, Ali Eslami:
  A probabilistic graphical model for system-wide analysis of gene regulatory networks. 3192-3199
• 
  Kavishwar B. Wagholikar, Hossein Estiri, Marykate Murphy, Shawn N. Murphy:
  Polar labeling: silver standard algorithm for training disease classifiers. 3200-3206
• 
  Rashmie Abeysinghe, Eugene W. Hinderer, Hunter N. B. Moseley, Licong Cui:
  SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology. 3207-3214
• 
  Katja Ovchinnikova, Lachlan Stuart, Alexander Rakhlin, Sergey I. Nikolenko, Theodore Alexandrov:
  ColocML: machine learning quantifies co-localization between mass spectrometry images. 3215-3224
• 
  Jie Shu, Jingxin Liu, Yongmei Zhang, Hao Fu, Mohammad Ilyas, Giuseppe Faraci, Vincenzo Della Mea, Bozhi Liu, Guoping Qiu:
  Marker controlled superpixel nuclei segmentation and automatic counting on immunohistochemistry staining images. 3225-3233
• 
  Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan:
  pyBedGraph: a python package for fast operations on 1D genomic signal tracks. 3234-3235
• 
  Wouter De Coster, Endre Bakken Stovner, Mojca Strazisar:
  Methplotlib: analysis of modified nucleotides from nanopore sequencing. 3236-3238
• 
  Zhencheng Fang, Jie Tan, Shufang Wu, Mo Li, Chunhui Wang, Yongchu Liu, Huaiqiu Zhu:
  PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning. 3239-3241
• 
  Samuel O'donnell, Gilles Fischer:
  MUM&Co: accurate detection of all SV types through whole-genome alignment. 3242-3243
• 
  Lisanna Paladin, Mathieu Schaeffer, Pascale Gaudet, Monique Zahn-Zabal, Pierre-André Michel, Damiano Piovesan, Silvio C. E. Tosatto, Amos Bairoch:
  The Feature-Viewer: a visualization tool for positional annotations on a sequence. 3244-3245
• 
  Václav Brázda, Jan Kolomazník, Jean-Louis Mergny, Jiri Stastny:
  G4Killer web application: a tool to design G-quadruplex mutations. 3246-3247
• 
  Marta Lovino, Maria Serena Ciaburri, Gianvito Urgese, Santa Di Cataldo, Elisa Ficarra:
  DEEPrior: a deep learning tool for the prioritization of gene fusions. 3248-3250
• 
  Congyu Lu, Zena Cai, Yuanqiang Zou, Zheng Zhang, Wenjun Chen, Lizong Deng, Xiangjun Du, Aiping Wu, Lei Yang, Dayan Wang, Yuelong Shu, Taijiao Jiang, Yousong Peng:
  FluPhenotype - a one-stop platform for early warnings of the influenza A virus. 3251-3253
• 
  Hang Dai, Yongtao Guan:
  Nubeam-dedup: a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping. 3254-3256
• 
  Hao-Dong Xu, Ruifeng Hu, Peilin Jia, Zhongming Zhao:
  6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes. 3257-3259
• 
  Vladimir Perovic, Jeremy Y. Leclercq, Neven Sumonja, François D. Richard, Nevena Veljkovic, Andrey V. Kajava:
  Tally-2.0: upgraded validator of tandem repeat detection in protein sequences. 3260-3262
• 
  Lucas Czech, Pierre Barbera, Alexandros Stamatakis:
  Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data. 3263-3265
• 
  Claudio Mirabello, Björn Wallner:
  InterLig: improved ligand-based virtual screening using topologically independent structural alignments. 3266-3267
• 
  Matteo P. Ferla, Alistair T. Pagnamenta, David R. Damerell, Jenny C. Taylor, Brian D. Marsden:
  MichelaNglo: sculpting protein views on web pages without coding. 3268-3270
• 
  Adrián García-Recio, Gemma Navarro, Rafael Franco, Mireia Olivella, Ramon Guixà-González, Arnau Cordomí:
  DIMERBOW: exploring possible GPCR dimer interfaces. 3271-3272
• 
  Elaine Y. Cao, John F. Ouyang, Owen J. L. Rackham:
  GeneSwitches: ordering gene expression and functional events in single-cell experiments. 3273-3275
• 
  Alemu Takele Assefa, Jo Vandesompele, Olivier Thas:
  SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data. 3276-3278
• 
  Arnaud Becheler, L. Lacey Knowles:
  Occupancy spectrum distribution: application for coalescence simulation with generic mergers. 3279-3280
• 
  Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi:
  GEMtractor: extracting views into genome-scale metabolic models. 3281-3282
• 
  Jinhwan Kim, Sora Yoon, Dougu Nam:
  netGO: R-Shiny package for network-integrated pathway enrichment analysis. 3283-3285
• 
  Evgeny Tankhilevich, Jonathan Ish-Horowicz, Tara Hameed, Elisabeth Roesch, Istvan T. Kleijn, Michael P. H. Stumpf, Fei He:
  GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation. 3286-3287
• 
  Miroslav Kratochvíl, David Bednárek, Tomás Sieger, Karel Fiser, Jirí Vondrásek:
  ShinySOM: graphical SOM-based analysis of single-cell cytometry data. 3288-3289
• 
  Niall Beard, Finn Bacall, Aleksandra Nenadic, Milo Thurston, Carole A. Goble, Susanna-Assunta Sansone, Teresa K. Attwood:
  TeSS: a platform for discovering life-science training opportunities. 3290-3291
• 
  Zaki Hasnain, Andrew K. Fraser, Dan Georgess, Alex Choi, Paul Macklin, Joel S. Bader, Shelly R. Peyton, Andrew J. Ewald, Paul K. Newton:
  OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics. 3292-3294

Volume 36, Number 11, June 2020

• 
  Sen Liu, Qiang Zheng, Zhiying Wang:
  Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus. 3295-3298
• 
  Ziwei Chen, Fuzhou Gong, Lin Wan, Liang Ma:
  RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data. 3299-3306
• 
  Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin:
  GraphBin: refined binning of metagenomic contigs using assembly graphs. 3307-3313
• 
  Clemens Kreutz, Nilay S. Can, Ralf Schulze Bruening, Rabea Meyberg, Zsuzsanna Mérai, Noé Fernández-Pozo, Stefan A. Rensing:
  A blind and independent benchmark study for detecting differentially methylated regions in plants. 3314-3321
• 
  Michael Schwarz, Marius Welzel, Tolganay Kabdullayeva, Anke Becker, Bernd Freisleben, Dominik Heider:
  MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors. 3322-3326
• 
  Qiang Tang, Juanjuan Kang, Jiaqing Yuan, Hua Tang, Xianhai Li, Hao Lin, Jian Huang, Wei Chen:
  DNA4mC-LIP: a linear integration method to identify N4-methylcytosine site in multiple species. 3327-3335
• 
  Kewei Liu, Wei Chen:
  iMRM: a platform for simultaneously identifying multiple kinds of RNA modifications. 3336-3342
• 
  Manaz Kaleel, Yandan Zheng, Jialiang Chen, Xuanming Feng, Jeremy C. Simpson, Gianluca Pollastri, Catherine Mooney:
  SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks. 3343-3349
• 
  Md. Mehedi Hasan, Nalini Schaduangrat, Shaherin Basith, Gwang Lee, Watshara Shoombuatong, Balachandran Manavalan:
  HLPpred-Fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation. 3350-3356
• 
  Tyler Shimko, Polly Fordyce, Yaron Orenstein:
  DeCoDe: degenerate codon design for complete protein-coding DNA libraries. 3357-3364
• 
  Yaxin Xue, Anders Lanzén, Inge Jonassen:
  Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data. 3365-3371
• 
  Alexander Greß, Olga V. Kalinina:
  SphereCon - a method for precise estimation of residue relative solvent accessible area from limited structural information. 3372-3378
• 
  Adrien H. Cerdan, Marion Sisquellas, Gilberto Pereira, Diego Enry Barreto Gomes, Jean-Pierre Changeux, Marco Cecchini:
  The Glycine Receptor Allosteric Ligands Library (GRALL). 3379-3384
• 
  Zi-Lin Liu, Jing-Hao Hu, Fan Jiang, Yun-Dong Wu:
  CRiSP: accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning. 3385-3392
• 
  Vittorio Fortino, Giovanni Scala, Dario Greco:
  Feature set optimization in biomarker discovery from genome-scale data. 3393-3400
• 
  Shen Yin, Xinlei Wang, Gaoxiang Jia, Yang Xie:
  MIXnorm: normalizing RNA-seq data from formalin-fixed paraffin-embedded samples. 3401-3408
• 
  Lauren Spirko-Burns, Karthik Devarajan:
  Unified methods for feature selection in large-scale genomic studies with censored survival outcomes. 3409-3417
• 
  Valentine Svensson, Adam Gayoso, Nir Yosef, Lior Pachter:
  Interpretable factor models of single-cell RNA-seq via variational autoencoders. 3418-3421
• 
  Philippe Boileau, Nima S. Hejazi, Sandrine Dudoit:
  Exploring high-dimensional biological data with sparse contrastive principal component analysis. 3422-3430
• 
  Ziyi Li, Zhenxing Guo, Ying Cheng, Peng Jin, Hao Wu:
  Robust partial reference-free cell composition estimation from tissue expression. 3431-3438
• 
  Daiwei Zhang, Rounak Dey, Seunggeun Lee:
  Fast and robust ancestry prediction using principal component analysis. 3439-3446
• 
  Matthew Waas, Shana T. Snarrenberg, Jack Littrell, Rachel A. Jones Lipinski, Polly A. Hansen, John A. Corbett, Rebekah L. Gundry, Janet Kelso:
  SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates. 3447-3456
• 
  Renming Liu, Christopher A. Mancuso, Anna Yannakopoulos, Kayla A. Johnson, Arjun Krishnan:
  Supervised learning is an accurate method for network-based gene classification. 3457-3465
• 
  Maya Levy, Amit Frishberg, Irit Gat-Viks:
  Inferring cellular heterogeneity of associations from single cell genomics. 3466-3473
• 
  Zi-Chao Zhang, Xiao-Fei Zhang, Min Wu, Le Ou-Yang, Xing-Ming Zhao, Xiaoli Li:
  A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks. 3474-3481
• 
  Shouyong Jiang, Yong Wang, Marcus Kaiser, Natalio Krasnogor:
  NIHBA: a network interdiction approach for metabolic engineering design. 3482-3492
• 
  Yan Ni, Gang Yu, Huan Chen, Yongqiong Deng, Philippa M. Wells, Claire J. Steves, Feng Ju, Junfen Fu:
  M2IA: a web server for microbiome and metabolome integrative analysis. 3493-3498
• 
  Leandro A Bugnon, Cristian A. Yones, Jonathan Raad, Matias Gerard, Mariano Rubiolo, Gabriela Alejandra Merino, Milton Pividori, Leandro E. Di Persia, Diego H. Milone, Georgina Stegmayer:
  DL4papers: a deep learning approach for the automatic interpretation of scientific articles. 3499-3506
• 
  Yunchuan Kong, Tianwei Yu:
  forgeNet: a graph deep neural network model using tree-based ensemble classifiers for feature graph construction. 3507-3515
• 
  Lixiang Zhang, Lin Lin, Jia Li:
  CPS analysis: self-contained validation of biomedical data clustering. 3516-3521
• 
  Emanuele Aliverti, Jeffrey L. Tilson, Dayne L. Filer, Benjamin Babcock, Alejandro Colaneri, Jennifer Ocasio, Timothy R. Gershon, Kirk C. Wilhelmsen, David B. Dunson:
  Projected t-SNE for batch correction. 3522-3527
• 
  Bowen Song, Yujiao Tang, Kunqi Chen, Zhen Wei, Rong Rong, Zhiliang Lu, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng:
  m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. 3528-3536
• 
  Nova F. Smedley, Suzie El-Saden, William Hsu:
  Discovering and interpreting transcriptomic drivers of imaging traits using neural networks. 3537-3548
• 
  Eddie Ip, Clinton Hadinata, Joshua Wing Kei Ho, Eleni Giannoulatou:
  dv-trio: a family-based variant calling pipeline using DeepVariant. 3549-3551
• 
  Sara Cleemput, Wim Dumon, Vagner Fonseca, Wasim Abdool Karim, Marta Giovanetti, Luiz Carlos Alcantara, Koen Deforche, Tulio de Oliveira:
  Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes. 3552-3555
• 
  Maria Anastasiadi, E. Bragin, P. Biojoux, Alisha Ahamed, Josephine Burgin, K. de Castro Cogle, Sergio-Llaneza Lago, R. Muvunyi, M. Scislak, I Aktan, Corentin Molitor, Tomasz J. Kurowski, Fady R. Mohareb:
  CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances. 3556-3557
• 
  Emmanuel L. P. Dumont, Benjamin Tycko, Catherine Do:
  CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation. 3558-3560
• 
  Kun Sun:
  Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data. 3561-3562
• 
  Li Chen:
  powmic: an R package for power assessment in microbiome case-control studies. 3563-3565
• 
  Sinisa Bidin, Ivan Vujaklija, Tina Paradzik, Ana Bielen, Dusica Vujaklija:
  Leitmotif: protein motif scanning 2.0. 3566-3567
• 
  Jian-Peng Zhou, Lei Chen, Tianyun Wang, Min Liu:
  iATC-FRAKEL: a simple multi-label web server for recognizing anatomical therapeutic chemical classes of drugs with their fingerprints only. 3568-3569
• 
  Mindaugas Margelevicius:
  COMER2: GPU-accelerated sensitive and specific homology searches. 3570-3572
• 
  Henry E. Pratt, Zhiping Weng:
  LogoJS: a Javascript package for creating sequence logos and embedding them in web applications. 3573-3575
• 
  Marcelo Depólo Polêto, Bruno Iochins Grisci, Márcio Dorn, Hugo Verli:
  ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories. 3576-3577
• 
  Michela Quadrini, Luca Tesei, Emanuela Merelli:
  ASPRAlign: a tool for the alignment of RNA secondary structures with arbitrary pseudoknots. 3578-3579
• 
  Wing Ki Wong, Claire Marks, Jinwoo Leem, Alan P. Lewis, Jiye Shi, Charlotte M. Deane:
  TCRBuilder: multi-state T-cell receptor structure prediction. 3580-3581
• 
  Nathan Lawlor, Eladio J. Márquez, Donghyung Lee, Duygu Ucar:
  V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single-cell RNA-seq data. 3582-3584
• 
  Lin Wang, Francisca Catalan, Karin Shamardani, Husam Babikir, Aaron Diaz:
  Ensemble learning for classifying single-cell data and projection across reference atlases. 3585-3587
• 
  Kaiyi Zhu, Dimitris Anastassiou:
  2DImpute: imputation in single-cell RNA-seq data from correlations in two dimensions. 3588-3589
• 
  Simo Kitanovski, Daniel Hoffmann:
  IgGeneUsage: differential gene usage in immune repertoires. 3590-3591
• 
  Gaurav Sharma, Carlo Colantuoni, Loyal A. Goff, Elana J. Fertig, Genevieve L. Stein-O'Brien:
  projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering. 3592-3593
• 
  Cédric R. Weber, Rahmad Akbar, Alexander Yermanos, Milena Pavlovic, Igor Snapkov, Geir Kjetil Sandve, Sai T. Reddy, Victor Greiff:
  immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking. 3594-3596
• 
  Iurii S. Nagornov, Mamoru Kato:
  tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes. 3597-3599
• 
  Tong Zhang, Yu Tian, Le Yuan, Fu Chen, Ailin Ren, Qian-Nan Hu:
  Bio2Rxn: sequence-based enzymatic reaction predictions by a consensus strategy. 3600-3601
• 
  Potdar Swapnil, Aleksandr Ianevski, John-Patrick Mpindi, Dmitrii Bychkov, Clément Fiere, Philipp Ianevski, Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio, Olli-P. Kallioniemi, Saarela Jani, Päivi Östling:
  Breeze: an integrated quality control and data analysis application for high-throughput drug screening. 3602-3604
• 
  Pumin Li, Qi Xu, Xu Hua, Zhongwei Xie, Jie Li, Jin Wang:
  primirTSS: an R package for identifying cell-specific microRNA transcription start sites. 3605-3606
• 
  Louis J. Taylor, Arwa Abbas, Frederic D. Bushman:
  grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories. 3607-3609
• 
  Qingyang Ding, Siyu Hou, Songpeng Zu, Yonghui Zhang, Shao Li:
  VISAR: an interactive tool for dissecting chemical features learned by deep neural network QSAR models. 3610-3612
• 
  Akul Y. Mehta, Richard D. Cummings:
  GlycoGlyph: a glycan visualizing, drawing and naming application. 3613-3614
• 
  N. R. Siva Shanmugam, J. Jino Blessy, K. Veluraja, M. Michael Gromiha:
  ProCaff: protein-carbohydrate complex binding affinity database. 3615-3617
• 
  Pere Ràfols, Bram Heijs, Esteban del Castillo, Oscar Yanes, Liam A. McDonnell, Jesús Brezmes, Iara Pérez-Taboada, Mario Vallejo, María García-Altares, Xavier Correig:
  rMSIproc: an R package for mass spectrometry imaging data processing. 3618-3619
• 
  Alexander Auer, Maximilian T. Strauss, Sebastian Strauss, Ralf Jungmann:
  nanoTRON: a Picasso module for MLP-based classification of super-resolution data. 3620-3622
• 
  Minh Pham, Stephen J. Wilson, Harikumar Govindarajan, Chih-Hsu Lin, Olivier Lichtarge:
  Discovery of disease- and drug-specific pathways through community structures of a literature network. 3623

Volume 36, Number 12, June 2020

• 
  Chenfu Shi, Magnus Rattray, Gisela Orozco:
  HiChIP-Peaks: a HiChIP peak calling algorithm. 3625-3631
• 
  Weibo Zheng, Jing Chen, Thomas G. Doak, Weibo Song, Ying Yan:
  ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data. 3632-3636
• 
  Mark F. Rogers, Tom R. Gaunt, Colin Campbell:
  CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome. 3637-3644
• 
  Lyam Baudry, Gaël A. Millot, Agnes Thierry, Romain Koszul, Vittore F. Scolari:
  Serpentine: a flexible 2D binning method for differential Hi-C analysis. 3645-3651
• 
  Iman Deznabi, Busra Arabaci, Mehmet Koyutürk, Öznur Tastan:
  DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving understudied kinases. 3652-3661
• 
  Etminan Naznooshsadat, Elham Parvinnia, Ali Sharifi-Zarchi:
  FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots. 3662-3668
• 
  Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu:
  Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. 3669-3679
• 
  Amlan Talukder, Xiaoman Li, Haiyan Hu:
  Position-wise binding preference is important for miRNA target site prediction. 3680-3686
• 
  Christopher Pockrandt, Mai Alzamel, Costas S. Iliopoulos, Knut Reinert:
  GenMap: ultra-fast computation of genome mappability. 3687-3692
• 
  Dandan Zheng, Guansong Pang, Bo Liu, Lihong Chen, Jian Yang:
  Learning transferable deep convolutional neural networks for the classification of bacterial virulence factors. 3693-3702
• 
  Hossein Asghari, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, Faraz Hach:
  CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme. 3703-3711
• 
  Charlotte A. Darby, Ravi Gaddipati, Michael C. Schatz, Ben Langmead:
  Vargas: heuristic-free alignment for assessing linear and graph read aligners. 3712-3718
• 
  Simon J. Hickinbotham, Sarah Fiddyment, Timothy L. Stinson, Matthew J. Collins:
  How to get your goat: automated identification of species from MALDI-ToF spectra. 3719-3725
• 
  Tomer Meirson, David Bomze, Gal Markel, Abraham O. Samson:
  κ-helix and the helical lock and key model: a pivotal way of looking at polyproline II. 3726-3732
• 
  Tomer Sidi, Chen Keasar:
  Redundancy-weighting the PDB for detailed secondary structure prediction using deep-learning models. 3733-3738
• 
  Abhilesh S. Dhawanjewar, Ankit A. Roy, Mallur S. Madhusudhan:
  A knowledge-based scoring function to assess quaternary associations of proteins. 3739-3748
• 
  Wei Zheng, Xiaogen Zhou, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang:
  FUpred: detecting protein domains through deep-learning-based contact map prediction. 3749-3757
• 
  Xiaoqiang Huang, Robin Pearce, Yang Zhang:
  FASPR: an open-source tool for fast and accurate protein side-chain packing. 3758-3765
• 
  Arezou Rahimi, Mehmet Gönen:
  A multitask multiple kernel learning formulation for discriminating early- and late-stage cancers. 3766-3772
• 
  Meenakshi Venkatasubramanian, Kashish Chetal, Daniel J. Schnell, Gowtham Atluri, Nathan Salomonis:
  Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF. 3773-3780
• 
  Pavel Sulimov, Anastasia Voronkova, Attila Kertész-Farkas:
  Annotation of tandem mass spectrometry data using stochastic neural networks in shotgun proteomics. 3781-3787
• 
  Wenjian Xu, Xuanshi Liu, Fei Leng, Wei Li:
  Blood-based multi-tissue gene expression inference with Bayesian ridge regression. 3788-3794
• 
  Arttu Arjas, Andreas Hauptmann, Mikko J. Sillanpää:
  Estimation of dynamic SNP-heritability with Bayesian Gaussian process models. 3795-3802
• 
  Jia Wen, Colby T. Ford, Daniel Janies, Xinghua Shi:
  A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models. 3803-3810
• 
  Songshan Yang, Jiawei Wen, Scott T. Eckert, Yaqun Wang, Dajiang J. Liu, Rongling Wu, Runze Li, Xiang Zhan:
  Prioritizing genetic variants in GWAS with lasso using permutation-assisted tuning. 3811-3817
• 
  Sangseon Lee, Sangsoo Lim, Taeheon Lee, Inyoung Sung, Sun Kim:
  Cancer subtype classification and modeling by pathway attention and propagation. 3818-3824
• 
  Wenming Wu, Xiaoke Ma:
  Joint learning dimension reduction and clustering of single-cell RNA-sequencing data. 3825-3832
• 
  Ming-Ju Tsai, Jyun-Rong Wang, Shinn-Jang Ho, Li-Sun Shu, Wen-Lin Huang, Shinn-Ying Ho:
  GREMA: modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem. 3833-3840
• 
  Michael Gruenstaeudl:
  annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA. 3841-3848
• 
  Jakob Raymaekers, Ruben H. Zamar:
  Pooled variable scaling for cluster analysis. 3849-3855
• 
  Di Jin, Peter Szolovits:
  Advancing PICO element detection in biomedical text via deep neural networks. 3856-3862
• 
  Mischa Schwendy, Ronald E. Unger, Sapun H. Parekh:
  EVICAN - a balanced dataset for algorithm development in cell and nucleus segmentation. 3863-3870
• 
  Xiangyang Li, Fang Chen, Yunpeng Chen:
  Gcluster: a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes. 3871-3873
• 
  Sergio Arredondo-Alonso, Martin Bootsma, Yaïr Hein, Malbert R. C. Rogers, Jukka Corander, Rob J. L. Willems, Anita C. Schürch:
  gplas: a comprehensive tool for plasmid analysis using short-read graphs. 3874-3876
• 
  Mark Grivainis, Zuojian Tang, David Fenyö:
  TranspoScope: interactive visualization of retrotransposon insertions. 3877-3878
• 
  Pavel P. Kuksa, Chien-Yueh Lee, Alexandre Amlie-Wolf, Prabhakaran Gangadharan, Elizabeth E. Mlynarski, Yi-Fan Chou, Han-Jen Lin, Heather Issen, Emily Greenfest-Allen, Otto Valladares, Yuk Yee Leung, Li-San Wang:
  SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants. 3879-3881
• 
  Elizaveta V. Starikova, Polina O. Tikhonova, Nikita A. Prianichnikov, Chris M. Rands, Evgeny M. Zdobnov, Elena N. Ilina, Vadim M. Govorun:
  Phigaro: high-throughput prophage sequence annotation. 3882-3884
• 
  Lauren Coombe, Vladimir Nikolic, Justin Chu, Inanç Birol, René L. Warren:
  ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs. 3885-3887
• 
  Alexandre Eeckhoutte, Alexandre Houy, Elodie Manié, Manon Reverdy, Ivan Bièche, Elisabetta Marangoni, Oumou Goundiam, Anne Vincent-Salomon, Dominique Stoppa-Lyonnet, François-Clément Bidard, Marc-Henri Stern, Tatiana G. Popova:
  ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing. 3888-3889
• 
  Linjie Wu, Han Wang, Yuchao Xia, Ruibin Xi:
  CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome. 3890-3891
• 
  Antonio Benítez-Hidalgo, Antonio J. Nebro, José Francisco Aldana Montes:
  Sequoya: multiobjective multiple sequence alignment in Python. 3892-3893
• 
  Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré:
  yacrd and fpa: upstream tools for long-read genome assembly. 3894-3896
• 
  Mirko Torrisi, Gianluca Pollastri:
  Brewery: deep learning and deeper profiles for the prediction of 1D protein structure annotations. 3897-3898
• 
  Bilal El Houdaigui, Sam Meyer:
  TwisTranscripT: stochastic simulation of the transcription-supercoiling coupling. 3899-3901
• 
  Timothy O'Connor, Charles E. Grant, Mikael Bodén, Timothy L. Bailey:
  T-Gene: improved target gene prediction. 3902-3904
• 
  Charlotte A. Darby, Michael J. T. Stubbington, Patrick J. Marks, Álvaro Martínez Barrio, Ian T. Fiddes:
  scHLAcount: allele-specific HLA expression from single-cell gene expression data. 3905-3906
• 
  Ruijia Wang, Bin Tian:
  APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms. 3907-3909
• 
  Oscar Franzén, Johan L. M. Björkegren:
  alona: a web server for single-cell RNA-seq analysis. 3910-3912
• 
  Hemi Luan, Xingen Jiang, Fenfen Ji, Zhangzhang Lan, Zongwei Cai, Wenyong Zhang:
  CPVA: a web-based metabolomic tool for chromatographic peak visualization and annotation. 3913-3915
• 
  Daniele Mercatelli, Gonzalo Lopez-Garcia, Federico M. Giorgi:
  corto: a lightweight R package for gene network inference and master regulator analysis. 3916-3917
• 
  Hendrik A. de Weerd, Tejaswi V. S. Badam, David Martínez-Enguita, Julia Åkesson, Daniel Muthas, Mika Gustafsson, Zelmina Lubovac-Pilav:
  MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks. 3918-3919
• 
  Mattia Tomasoni, Sergio Gómez, Jake Crawford, Weijia Zhang, Sarvenaz Choobdar, Daniel Marbach, Sven Bergmann:
  MONET: a toolbox integrating top-performing methods for network modularization. 3920-3921
• 
  Brandon Reyes, Irene Otero-Muras, Michael T. Shuen, Alexandre M. Tartakovsky, Vladislav A. Petyuk:
  CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks. 3922-3924
• 
  Christian-Alexander Dudek, Carsten Reuse, Regine Fuchs, Janneke Hendriks, Veronique Starck, Karsten Hiller:
  MIAMI--a tool for non-targeted detection of metabolic flux changes for mode of action identification. 3925-3926
• 
  Lulu Chen, Chiung-Ting Wu, Niya Wang, David M. Herrington, Robert Clarke, Yue Wang:
  debCAM: a bioconductor R package for fully unsupervised deconvolution of complex tissues. 3927-3929
• 
  Oliver B. Scott, A. W. Edith Chan:
  ScaffoldGraph: an open-source library for the generation and analysis of molecular scaffold networks and scaffold trees. 3930-3931
• 
  Alon Bartal, Alexander Lachmann, Daniel J. B. Clarke, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma'ayan:
  EnrichrBot: Twitter bot tracking tweets about human genes. 3932-3934
• 
  Hongchun Li, Fen Pei, D. Lansing Taylor, Ivet Bahar:
  QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics. 3935-3937
• 
  Da Kuang, Jochen Weile, Roujia Li, Tom W. Ouellette, Jarry A. Barber, Frederick P. Roth:
  MaveQuest: a web resource for planning experimental tests of human variant effects. 3938-3940
• 
  Robel Y. Kahsay, Jeet Vora, Rahi Navelkar, Reza Mousavi, Brian C. Fochtman, Xavier Holmes, Nagarajan Pattabiraman, René Ranzinger, Rupali Mahadik, Tatiana Williamson, Sujeet Kulkarni, Gaurav Agarwal, Maria Jesus Martin, Preethi Vasudev, Leyla J. García, Nathan Edwards, Wenjin Zhang, Darren A. Natale, Karen Ross, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, William S. York, Raja Mazumder:
  GlyGen data model and processing workflow. 3941-3943
• 
  Shanyu Chen, Xiaoyu He, Ruilin Li, Xiaohong Duan, Beifang Niu:
  HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures. 3944-3946
• 
  José-Jesús Fernández, Teobaldo E. Torres, Eva Martin-Solana, Gerardo F. Goya, Maria-Rosario Fernandez-Fernandez:
  PolishEM: image enhancement in FIB-SEM. 3947-3948
• 
  Illia Ziamtsov, Saket Navlakha:
  Plant 3D (P3D): a plant phenotyping toolkit for 3D point clouds. 3949-3950

Volume 36, Number 13, July 2020

• 
  Arnab Kumar Maity, Sang Chan Lee, Bani K. Mallick, Tapasree Roy Sarkar:
  Bayesian structural equation modeling in multiple omics data with application to circadian genes. 3951-3958
• 
  Yuanjing Ma, Yuan Luo, Hongmei Jiang:
  A novel normalization and differential abundance test framework for microbiome data. 3959-3965
• 
  Ryo Nakabayashi, Shinichi Morishita:
  HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C. 3966-3974
• 
  Laurent David, Riccardo Vicedomini, Hugues Richard, Alessandra Carbone:
  Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A. 3975-3981
• 
  Yu P. Zhang, Quan Zou:
  PPTPP: a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning. 3982-3987
• 
  Pablo A. Goloboff, Martín E. Morales:
  A phylogenetic C interpreter for TNT. 3988-3995
• 
  Srivamshi Pittala, Chris Bailey-Kellogg:
  Learning context-aware structural representations to predict antigen and antibody binding interfaces. 3996-4003
• 
  Kai Wang, Nan Lyu, Hongjuan Diao, Shujuan Jin, Tao Zeng, Yaoqi Zhou, Ruibo Wu:
  GM-DockZn: a geometry matching-based docking algorithm for zinc proteins. 4004-4011
• 
  Alper Sen, Kamyar Kargar, Esma Akgün, Mustafa Ç. Pinar:
  Codon optimization: a mathematical programing approach. 4012-4020
• 
  Hyundoo Jeong, Zhandong Liu:
  PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing. 4021-4029
• 
  Lifan Liang, Kunju Zhu, Songjian Lu:
  BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization. 4030-4037
• 
  Lei Wang, Zhu-Hong You, Yu-An Huang, De-Shuang Huang, Keith C. C. Chan:
  An efficient approach based on multi-sources information to predict circRNA-disease associations using deep convolutional neural network. 4038-4046
• 
  Luke A. D. Hutchison, Bonnie Berger, Isaac S. Kohane:
  Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation. 4047-4057
• 
  Jie Hu, Huihui Qin, Xiaodan Fan:
  Can ODE gene regulatory models neglect time lag or measurement scaling? 4058-4064
• 
  Abdul Arif Khan, Zakir Khan:
  COVID-2019-associated overexpressed Prevotella proteins mediated host-pathogen interactions and their role in coronavirus outbreak. 4065-4069
• 
  Evangelos Karatzas, Margarita Zachariou, Marilena M. Bourdakou, George Minadakis, Anastasis Oulas, George Kolios, Alex Delis, George M. Spyrou:
  PathWalks: identifying pathway communities using a disease-related map of integrated information. 4070-4079
• 
  Paul D. Tar, Neil A. Thacker, Somrudee Deepaisarn, J. P. B. O'Connor, A. W. McMahon:
  A reformulation of pLSA for uncertainty estimation and hypothesis testing in bio-imaging. 4080-4087
• 
  Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Rob Knight, Dan Knight:
  SHOGUN: a modular, accurate and scalable framework for microbiome quantification. 4088-4090
• 
  Divon Lan, Raymond Tobler, Yassine Souilmi, Bastien Llamas:
  genozip: a fast and efficient compression tool for VCF files. 4091-4092
• 
  Robin Winter, Joren Retel, Frank Noé, Djork-Arné Clevert, Andreas Steffen:
  grünifai: interactive multiparameter optimization of molecules in a continuous vector space. 4093-4094
• 
  Matteo Ciciani, Thomas Cantore, Mario Lauria, Janet Kelso:
  rScudo: an R package for classification of molecular profiles using rank-based signatures. 4095-4096
• 
  Anna Breit, Simon Ott, Asan Agibetov, Matthias Samwald:
  OpenBioLink: a benchmarking framework for large-scale biomedical link prediction. 4097-4098
• 
  Yushu Shi, Liangliang Zhang, Kim-Anh Do, Christine B. Peterson, Robert R. Jenq:
  aPCoA: covariate adjusted principal coordinates analysis. 4099-4101

Volume 36, Number Supplement-1, July 2020

• 
  Nadia El-Mabrouk, Donna K. Slonim:
  ISMB 2020 proceedings. i1-i2
• 
  Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan, Yu Lin:
  MetaBCC-LR: metagenomics binning by coverage and composition for long reads. i3-i11
• 
  Vitor Piro, Temesgen Hailemariam Dadi, Enrico Seiler, Knut Reinert, Bernhard Y. Renard:
  ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. i12-i20
• 
  Dina Svetlitsky, Tal Dagan, Michal Ziv-Ukelson:
  Discovery of multi-operon colinear syntenic blocks in microbial genomes. i21-i29
• 
  Caroline Weis, Max Horn, Bastian Rieck, Aline Cuénod, Adrian Egli, Karsten M. Borgwardt:
  Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra. i30-i38
• 
  Mohammad Arifur Rahman, Huzefa Rangwala:
  IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data. i39-i47
• 
  Kai Cao, Xiangqi Bai, Yiguang Hong, Lin Wan:
  Unsupervised topological alignment for single-cell multi-omics integration. i48-i56
• 
  Erin K. Molloy, Tandy J. Warnow:
  FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. i57-i65
• 
  Helena Todorov, Robrecht Cannoodt, Wouter Saelens, Yvan Saeys:
  TinGa: fast and flexible trajectory inference with Growing Neural Gas. i66-i74
• 
  Alla Mikheenko, Andrey V. Bzikadze, Alexey A. Gurevich, Karen H. Miga, Pavel A. Pevzner:
  TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. i75-i83
• 
  Zeyang Shen, Marten A. Hoeksema, Zhengyu Ouyang, Christopher Benner, Christopher K. Glass:
  MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function. i84-i92
• 
  Tatiana Dvorkina, Andrey V. Bzikadze, Pavel A. Pevzner:
  The string decomposition problem and its applications to centromere analysis and assembly. i93-i101
• 
  Hirak Sarkar, Avi Srivastava, Héctor Corrada Bravo, Michael I. Love, Rob Patro:
  Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data. i102-i110
• 
  Chirag Jain, Arang Rhie, Haowen Zhang, Claudia Chu, Brian Walenz, Sergey Koren, Adam M. Phillippy:
  Weighted minimizer sampling improves long read mapping. i111-i118
• 
  Hongyu Zheng, Carl Kingsford, Guillaume Marçais:
  Improved design and analysis of practical minimizers. i119-i127
• 
  Rui Zhu, Chao Jiang, Xiaofeng Wang, Shuang Wang, Hao Zheng, Haixu Tang:
  Privacy-preserving construction of generalized linear mixed model for biomedical computation. i128-i135
• 
  Nour Almadhoun, Erman Ayday, Özgür Ulusoy:
  Inference attacks against differentially private query results from genomic datasets including dependent tuples. i136-i145
• 
  Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Sirén, Benedict Paten:
  Distance indexing and seed clustering in sequence graphs. i146-i153
• 
  Xinrui Lyu, Jean Garret, Gunnar Rätsch, Kjong-Van Lehmann:
  Mutational signature learning with supervised negative binomial non-negative matrix factorization. i154-i160
• 
  Jiaqi Wu, Mohammed El-Kebir:
  ClonArch: visualizing the spatial clonal architecture of tumors. i161-i168
• 
  Erfan Sadeqi Azer, Farid Rashidi Mehrabadi, Salem Malikic, Xuan Cindy Li, Osnat Bartok, Kevin Litchfield, Ronen Levy, Yardena Samuels, Alejandro A. Schäffer, E. Michael Gertz, Chi-Ping Day, Eva Pérez-Guijarro, Kerrie Marie, Maxwell P. Lee, Glenn Merlino, Funda Ergün, Süleyman Cenk Sahinalp:
  PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem. i169-i176
• 
  Camille Marchet, Zamin Iqbal, Daniel Gautheret, Mikaël Salson, Rayan Chikhi:
  REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets. i177-i185
• 
  Matthew A. Myers, Simone Zaccaria, Benjamin J. Raphael:
  Identifying tumor clones in sparse single-cell mutation data. i186-i193
• 
  Berk A. Alpay, Pinar Demetci, Sorin Istrail, Derek Aguiar:
  Combinatorial and statistical prediction of gene expression from haplotype sequence. i194-i202
• 
  Seung-Hyuk Choi, Eunok Paek:
  MutCombinator: identification of mutated peptides allowing combinatorial mutations using nucleotide-based graph search. i203-i209
• 
  Alex Warwick Vesztrocy, Christophe Dessimoz:
  Benchmarking gene ontology function predictions using negative annotations. i210-i218
• 
  Moses Stamboulian, Rafael F. Guerrero, Matthew W. Hahn, Predrag Radivojac:
  The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. i219-i226
• 
  Hiroki Takizawa, Junichi Iwakiri, Goro Terai, Kiyoshi Asai:
  Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model. i227-i235
• 
  Benjamin Demeo, Bonnie Berger:
  Hopper: a mathematically optimal algorithm for sketching biological data. i236-i241
• 
  Teresa Müller, Milad Miladi, Frank Hutter, Ivo L. Hofacker, Sebastian Will, Rolf Backofen:
  The locality dilemma of Sankoff-like RNA alignments. i242-i250
• 
  Kerem Wainer-Katsir, Michal Linial:
  BIRD: identifying cell doublets via biallelic expression from single cells. i251-i257
• 
  He Zhang, Liang Zhang, David H. Mathews, Liang Huang:
  LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities. i258-i267
• 
  Jeffrey A. Ruffolo, Carlos Guerra, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray:
  Geometric potentials from deep learning improve prediction of CDR H3 loop structures. i268-i275
• 
  Zichao Yan, William L. Hamilton, Mathieu Blanchette:
  Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions. i276-i284
• 
  Md Hossain Shuvo, Sutanu Bhattacharya, Debswapna Bhattacharya:
  QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks. i285-i291
• 
  Avi Srivastava, Laraib Malik, Hirak Sarkar, Rob Patro:
  A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification. i292-i299
• 
  Dan Guo, Melanie Christine Föll, Veronika Volkmann, Kathrin Enderle-Ammour, Peter Bronsert, Oliver Schilling, Olga Vitek:
  Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations. i300-i308
• 
  Yang Zhang, Yunxuan Xiao, Muyu Yang, Jian Ma:
  Cancer mutational signatures representation by large-scale context embedding. i309-i316
• 
  Spencer Krieger, John D. Kececioglu:
  Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization. i317-i325
• 
  Yufeng Wu:
  Inference of population admixture network from local gene genealogies: a coalescent-based maximum likelihood approach. i326-i334
• 
  Metin Balaban, Siavash Mirarab:
  Phylogenetic double placement of mixed samples. i335-i343
• 
  Ron Zeira, Benjamin J. Raphael:
  Copy number evolution with weighted aberrations in cancer. i344-i352
• 
  Dongjoon Lim, Mathieu Blanchette:
  EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM. i353-i361
• 
  Palash Sashittal, Mohammed El-Kebir:
  Sampling and summarizing transmission trees with multi-strain infections. i362-i370
• 
  Lei Du, Fang Liu, Kefei Liu, Xiaohui Yao, Shannon L. Risacher, Junwei Han, Lei Guo, Andrew J. Saykin, Li Shen:
  Identifying diagnosis-specific genotype-phenotype associations via joint multitask sparse canonical correlation analysis and classification. i371-i379
• 
  Hossein Sharifi-Noghabi, Shuman Peng, Olga I. Zolotareva, Colin C. Collins, Martin Ester:
  AITL: Adversarial Inductive Transfer Learning with input and output space adaptation for pharmacogenomics. i380-i388
• 
  Sunkyu Kim, Keonwoo Kim, Junseok Choe, Inggeol Lee, Jaewoo Kang:
  Improved survival analysis by learning shared genomic information from pan-cancer data. i389-i398
• 
  Gopalakrishnan Venkatesh, Aayush Grover, G. Srinivasaraghavan, Shrisha Rao:
  MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model. i399-i406
• 
  Yifeng Tao, Haoyun Lei, Xuecong Fu, Adrian V. Lee, Jian Ma, Russell Schwartz:
  Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis. i407-i416
• 
  Assya Trofimov, Joseph Paul Cohen, Yoshua Bengio, Claude Perreault, Sébastien Lemieux:
  Factorized embeddings learns rich and biologically meaningful embedding spaces using factorized tensor decomposition. i417-i426
• 
  Ermin Hodzic, Raunak Shrestha, Salem Malikic, Colin C. Collins, Kevin Litchfield, Samra Turajlic, Süleyman Cenk Sahinalp:
  Identification of conserved evolutionary trajectories in tumors. i427-i435
• 
  Mengshi Zhou, Chunlei Zheng, Rong Xu:
  Combining phenome-driven drug-target interaction prediction with patients' electronic health records-based clinical corroboration toward drug discovery. i436-i444
• 
  Mostafa Karimi, Arman Hasanzadeh, Yang Shen:
  Network-principled deep generative models for designing drug combinations as graph sets. i445-i454
• 
  Noël Malod-Dognin, Vera Pancaldi, Alfonso Valencia, Natasa Przulj:
  Chromatin network markers of leukemia. i455-i463
• 
  Kapil Devkota, James M. Murphy, Lenore J. Cowen:
  GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks. i464-i473
• 
  Shaoke Lou, Tianxiao Li, Xiangmeng Kong, Jing Zhang, Jason Liu, Donghoon Lee, Mark Gerstein:
  TopicNet: a framework for measuring transcriptional regulatory network change. i474-i481
• 
  Torsten Gross, Nils Blüthgen:
  Identifiability and experimental design in perturbation studies. i482-i489
• 
  Leon Weber, Kirsten Thobe, Oscar Arturo Migueles Lozano, Jana Wolf, Ulf Leser:
  PEDL: extracting protein-protein associations using deep language models and distant supervision. i490-i498
• 
  Yi Liu, Kenneth Barr, John Reinitz:
  Fully interpretable deep learning model of transcriptional control. i499-i507
• 
  Anja C. Gumpinger, Kasper Lage, Heiko Horn, Karsten M. Borgwardt:
  Prediction of cancer driver genes through network-based moment propagation of mutation scores. i508-i515
• 
  Midori Iida, Michio Iwata, Yoshihiro Yamanishi:
  Network-based characterization of disease-disease relationships in terms of drugs and therapeutic targets. i516-i524
• 
  Zichen Wang, Mu Zhou, Corey W. Arnold:
  Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing. i525-i533
• 
  Marwan Abdellah, Nadir Román Guerrero, Samuel Lapere, Jay S. Coggan, Daniel Keller, Benoit Coste, Snigdha Dagar, Jean-Denis Courcol, Henry Markram, Felix Schürmann:
  Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis. i534-i541
• 
  Qiuyu Lian, Hongyi Xin, Jianzhu Ma, Liza Konnikova, Wei Chen, Jin Gu, Kong Chen:
  Artificial-cell-type aware cell-type classification in CITE-seq. i542-i550
• 
  Yannik Schälte, Jan Hasenauer:
  Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation. i551-i559
• 
  Amirali Aghazadeh, Orhan Ocal, Kannan Ramchandran:
  CRISPRL and: Interpretable large-scale inference of DNA repair landscape based on a spectral approach. i560-i568

Volume 36, Number 14, August 2020

• 
  Jiali Yang, Kun Lang, Guang-Le Zhang, Xiaodan Fan, Yuanyuan Chen, Cong Pian:
  SOMM4mC: a second-order Markov model for DNA N4-methylcytosine site prediction in six species. 4103-4105
• 
  Yi-Juan Hu, Glen A. Satten:
  Testing hypotheses about the microbiome using the linear decomposition model (LDM). 4106-4115
• 
  Idit Bloch, Dana Sherill-Rofe, Doron Stupp, Irene Unterman, Hodaya Beer, Elad Sharon, Yuval Tabach:
  Optimization of co-evolution analysis through phylogenetic profiling reveals pathway-specific signals. 4116-4125
• 
  Dmitry Antipov, Mikhail Raiko, Alla L. Lapidus, Pavel A. Pevzner:
  Metaviral SPAdes: assembly of viruses from metagenomic data. 4126-4129
• 
  David J. Burks, Rajeev K. Azad:
  Higher-order Markov models for metagenomic sequence classification. 4130-4136
• 
  Hani Jieun Kim, Yingxin Lin, Thomas Andrew Geddes, Jean Yee Hwa Yang, Pengyi Yang:
  CiteFuse enables multi-modal analysis of CITE-seq data. 4137-4143
• 
  Jack LeBien, Gerald McCollam, Joel Atallah:
  An in silico model of LINE-1-mediated neoplastic evolution. 4144-4153
• 
  Meiyue Wang, Ruidong Li, Shizhong Xu:
  Deshrinking ridge regression for genome-wide association studies. 4154-4162
• 
  Francisco Guil, José F. Hidalgo, José M. García:
  Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach. 4163-4170
• 
  Caitlin M. A. Simopoulos, Zhibin Ning, Xu Zhang, Leyuan Li, Krystal Walker, Mathieu Lavallée-Adam, Daniel Figeys:
  pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies. 4171-4179
• 
  Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu:
  HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank. 4180-4188
• 
  Yang Liu, Vinod Kumar Singh, Deyou Zheng:
  Stereo3D: using stereo images to enrich 3D visualization. 4189-4190
• 
  Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar:
  DeepNano-blitz: a fast base caller for MinION nanopore sequencers. 4191-4192
• 
  Patrick F. McKenzie, Deren A. R. Eaton:
  ipcoal: an interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network. 4193-4196
• 
  Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri:
  Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions. 4197-4199
• 
  Douglas E. V. Pires, Wandré N. P. Veloso, Yoochan Myung, Carlos H. M. Rodrigues, Michael Silk, Pâmela M. Rezende, Francislon Silva, Joicymara S. Xavier, João P. L. Velloso, Carlos Henrique da Silveira, David B. Ascher:
  EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening. 4200-4202
• 
  Eugenia Ulzurrun, Yorley Duarte, Esteban Pérez-Wohlfeil, Fernando D. González Nilo, Oswaldo Trelles:
  PLIDflow: an open-source workflow for the online analysis of protein-ligand docking using galaxy. 4203-4205
• 
  Joe G. Greener, Joel Selvaraj, Ben J. Ward:
  BioStructures.jl: read, write and manipulate macromolecular structures in Julia. 4206-4207
• 
  Damiano Cianferoni, Leandro G. Radusky, Sarah A. Head, Luis Serrano, Javier Delgado:
  ProteinFishing: a protein complex generator within the ModelX toolsuite. 4208-4210
• 
  Xiao Wang, Haidong Yi, Jia Wang, Zhandong Liu, Yanbin Yin, Han Zhang:
  GDASC: a GPU parallel-based web server for detecting hidden batch factors. 4211-4213
• 
  Mario Failli, Jussi Paananen, Vittorio Fortino:
  ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery. 4214-4216
• 
  Yan Zhang, Yaru Zhang, Jun Hu, Ji Zhang, Fangjie Guo, Meng Zhou, Guijun Zhang, Fulong Yu, Jianzhong Su:
  scTPA: a web tool for single-cell transcriptome analysis of pathway activation signatures. 4217-4219
• 
  Pieter Verschaffelt, Philippe Van Thienen, Tim Van Den Bossche, Felix Van der Jeugt, Caroline De Tender, Lennart Martens, Peter Dawyndt, Bart Mesuere:
  Unipept CLI 2.0: adding support for visualizations and functional annotations. 4220-4221
• 
  Zhong Wang, Nating Wang, Zilu Wang, Libo Jiang, Yaqun Wang, Jiahan Li, Rongling Wu, Janet Kelso:
  HiGwas: how to compute longitudinal GWAS data in population designs. 4222-4224
• 
  Ludovic Chaput, Valentin Guillaume, Natesh Singh, Benoit Deprez, Bruno O. Villoutreix:
  FastTargetPred: a program enabling the fast prediction of putative protein targets for input chemical databases. 4225-4226
• 
  Ataberk Donmez, Ahmet Süreyya Rifaioglu, Aybar C. Acar, Tunca Dogan, Rengül Çetin-Atalay, Volkan Atalay, Wren Jonathan:
  iBioProVis: interactive visualization and analysis of compound bioactivity space. 4227-4230
• 
  Kohei Hagiwara, Liang Ding, Michael N. Edmonson, Stephen V. Rice, Scott Newman, John Easton, Juncheng Dai, Soheil Meshinchi, Rhonda E. Ries, Michael Rusch, Jinghui Zhang:
  RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. 4231

Volume 36, Number 15, August 2020

• 
  Di Ran, Shanshan Zhang, Nicholas Lytal, Lingling An:
  scDoc: correcting drop-out events in single-cell RNA-seq data. 4233-4239
• 
  Rohan Shah, Gabriel Keeble-Gagnère, Alex Whan:
  Accurate calling of homeoallelic genotypes of iSelect markers using inbred structured populations. 4240-4247
• 
  Nazia Fatima, Luis Rueda:
  iSOM-GSN: an integrative approach for transforming multi-omic data into gene similarity networks via self-organizing maps. 4248-4254
• 
  Si-Yi Chen, Chun-Jie Liu, Qiong Zhang, An-Yuan Guo:
  An ultra-sensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data. 4255-4262
• 
  Zijie Shen, Quan Zou:
  Basic polar and hydrophobic properties are the main characteristics that affect the binding of transcription factors to methylation sites. 4263-4268
• 
  Haidong Yan, Aureliano Bombarely, Song Li:
  DeepTE: a computational method for de novo classification of transposons with convolutional neural network. 4269-4275
• 
  Cangzhi Jia, Yue Bi, Jinxiang Chen, André Leier, Fuyi Li, Jiangning Song:
  PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs. 4276-4282
• 
  Jiajing Xie, Yang Xu, Haifeng Chen, Meirong Chi, Jun He, Meifeng Li, Hui Liu, Jie Xia, Qingzhou Guan, Zheng Guo, Haidan Yan:
  Identification of population-level differentially expressed genes in one-phenotype data. 4283-4290
• 
  Philipp Angerer, David S. Fischer, Fabian J. Theis, Antonio Scialdone, Carsten Marr:
  Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data. 4291-4295
• 
  Maria Solovey, Antonio Scialdone:
  COMUNET: a tool to explore and visualize intercellular communication. 4296-4300
• 
  Stephan Seifert, Sven Gundlach, Olaf Junge, Silke Szymczak, Luigi Martelli:
  Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study. 4301-4308
• 
  Gayathri Sambamoorthy, Karthik Raman:
  MinReact: a systematic approach for identifying minimal metabolic networks. 4309-4315
• 
  Yifan Deng, Xinran Xu, Yang Qiu, Jingbo Xia, Wen Zhang, Shichao Liu:
  A multimodal deep learning framework for predicting drug-drug interaction events. 4316-4322
• 
  Cong Sun, Zhihao Yang, Leilei Su, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang:
  Chemical-protein interaction extraction via Gaussian probability distribution and external biomedical knowledge. 4323-4330
• 
  Mei Zuo, Yang Zhang:
  Dataset-aware multi-task learning approaches for biomedical named entity recognition. 4331-4338
• 
  Xiaoyu Zhang, Irene M. Kaplow, Morgan Wirthlin, Tae Yoon Park, Andreas R. Pfenning:
  HALPER facilitates the identification of regulatory element orthologs across species. 4339-4340
• 
  Christopher J. Neely, Elaina D. Graham, Benjamin J. Tully:
  MetaSanity: an integrated microbial genome evaluation and annotation pipeline. 4341-4344
• 
  Loïc Meunier, Pierre Tocquin, Luc Cornet, Damien Sirjacobs, Valérie Leclère, Maude Pupin, Philippe Jacques, Denis Baurain:
  Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects. 4345-4347
• 
  Jett Crowdis, Meng Xiao He, Brendan Reardon, Eliezer M. Van Allen:
  CoMut: visualizing integrated molecular information with comutation plots. 4348-4349
• 
  Valentin Zulkower, Susan Rosser:
  DNA Features Viewer: a sequence annotation formatting and plotting library for Python. 4350-4352
• 
  Pushkala Jayaraman, Timothy Mosbruger, Taishan Hu, Nikolaos G. Tairis, Chao Wu, Peter M. Clark, Monica D'arcy, Deborah Ferriola, Katarzyna Mackiewicz, Xiaowu Gai, Dimitrios Monos, Mahdi Sarmady:
  AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies. 4353-4356
• 
  Richard A. Schäfer, Steffen Lott, Jens Georg, Björn A. Grüning, Wolfgang R. Hess, Björn Voß:
  GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs. 4357-4359
• 
  Mayya Sedova, Lukasz Jaroszewski, Arghavan Alisoltani, Adam Godzik:
  Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence. 4360-4362
• 
  Leslie Solorzano, Gabriele Partel, Carolina Wählby:
  TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data. 4363-4365
• 
  Tobias Rohde, Rita Chupalov, Nicholas Shulman, Vagisha Sharma, Josh Eckels, Brian S. Pratt, Michael J. MacCoss, Brendan MacLean:
  Audit logs to enforce document integrity in Skyline and Panorama. 4366-4368
• 
  Andrew Whalen, Gregor Gorjanc, John M. Hickey:
  AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data. 4369-4371
• 
  James P. Roney, Jeremy Ferlic, Franziska Michor, Thomas O. McDonald:
  ESTIpop: a computational tool to simulate and estimate parameters for continuous-time Markov branching processes. 4372-4373
• 
  Ninon Mounier, Zoltán Kutalik:
  bGWAS: an R package to perform Bayesian genome wide association studies. 4374-4376
• 
  Giuseppe Agapito, Chiara Pastrello, Pietro Hiram Guzzi, Igor Jurisica, Mario Cannataro:
  BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways. 4377-4378
• 
  Florence Jornod, Marylène Rugard, Luc Tamisier, Xavier Coumoul, Helle R. Andersen, Robert Barouki, Karine Audouze:
  AOP4EUpest: mapping of pesticides in adverse outcome pathways using a text mining tool. 4379-4381

Volume 36, Number 16, August 2020

• 
  Xiaoqiong Wei, Chengxin Zhang, Peter L. Freddolino, Yang Zhang, Zhiyong Lu:
  Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. 4383-4388
• 
  Shouheng Tuo, Haiyan Liu, Hao Chen:
  Multipopulation harmony search algorithm for the detection of high-order SNP interactions. 4389-4398
• 
  Marco Oliva, Franco Milicchio, Kaden King, Grace Benson, Christina Boucher, Mattia Prosperi, Inanç Birol:
  Portable nanopore analytics: are we there yet? 4399-4405
• 
  Lifan Chen, Xiaoqin Tan, Dingyan Wang, Feisheng Zhong, Xiaohong Liu, Tianbiao Yang, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, Mingyue Zheng, Arne Elofsson:
  TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments. 4406-4414
• 
  Christopher Heje Grønbech, Maximillian Fornitz Vording, Pascal N. Timshel, Casper Kaae Sønderby, Tune H. Pers, Ole Winther, Bonnie Berger:
  scVAE: variational auto-encoders for single-cell gene expression data. 4415-4422
• 
  Wenbo Xu, Yan Tian, Siye Wang, Yupeng Cui, Pier Luigi Martelli:
  Feature selection and classification of noisy proteomics mass spectrometry data based on one-bit perturbed compressed sensing. 4423-4431
• 
  Yet Nguyen, Dan Nettleton:
  rmRNAseq: differential expression analysis for repeated-measures RNA-seq data. 4432-4439
• 
  Zhenqin Wu, Nilah M. Ioannidis, James Zou, Russell Schwartz:
  Predicting target genes of non-coding regulatory variants with IRT. 4440-4448
• 
  Florian Privé, Keurcien Luu, Michael G. B. Blum, John J. McGrath, Bjarni J. Vilhjálmsson, Russell Schwartz:
  Efficient toolkit implementing best practices for principal component analysis of population genetic data. 4449-4457
• 
  Ruichu Cai, Xuexin Chen, Yuan Fang, Min Wu, Yuexing Hao, Jonathan D. Wren:
  Dual-dropout graph convolutional network for predicting synthetic lethality in human cancers. 4458-4465
• 
  Tianyi Zhao, Yang Hu, Jiajie Peng, Liang Cheng, Pier Luigi Martelli:
  DeepLGP: a novel deep learning method for prioritizing lncRNA target genes. 4466-4472
• 
  Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomás Helikar, Sylvain Soliman, Anna Niarakis, Jinbo Xu:
  Automated inference of Boolean models from molecular interaction maps using CaSQ. 4473-4482
• 
  Zexuan Sun, Shujun Huang, Peiran Jiang, Pingzhao Hu, Zhiyong Lu:
  DTF: Deep Tensor Factorization for predicting anticancer drug synergy. 4483-4489
• 
  Siqi Liang, Haiyuan Yu, Jonathan D. Wren:
  Revealing new therapeutic opportunities through drug target prediction: a class imbalance-tolerant machine learning approach. 4490-4497
• 
  Sen Li, Qi Yang, Hao Jiang, Jesús A. Cortés-Vecino, Yang Zhang, Alfonso Valencia:
  Parasitologist-level classification of apicomplexan parasites and host cell with deep cycle transfer learning (DCTL). 4498-4505
• 
  Guillermo Dufort y Álvarez, Gadiel Seroussi, Pablo Smircich, José Sotelo, Idoia Ochoa, Álvaro Martín, Inanç Birol:
  ENANO: Encoder for NANOpore FASTQ files. 4506-4507
• 
  Valentin Zulkower, Susan Rosser, Yann Ponty:
  DNA Chisel, a versatile sequence optimizer. 4508-4509
• 
  Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra M. Walczak, Thierry Mora:
  SOS: online probability estimation and generation of T-and B-cell receptors. 4510-4512
• 
  Yuri Kochnev, Erich Hellemann, Kevin C. Cassidy, Jacob D. Durrant, Yann Ponty:
  Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser. 4513-4515
• 
  Weronika Puchala, Michal Burdukiewicz, Michal Kistowski, Katarzyna A. Dabrowska, Aleksandra E. Badaczewska-Dawid, Dominik Cysewski, Michal Dadlez, Yann Ponty:
  HaDeX: an R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments. 4516-4518
• 
  Ying Zhou, Sharon R. Browning, Brian L. Browning, Russell Schwartz:
  IBDkin: fast estimation of kinship coefficients from identity by descent segments. 4519-4520
• 
  Ilja M. Nolte, Russell Schwartz:
  Metasubtract: an R-package to analytically produce leave-one-out meta-analysis GWAS summary statistics. 4521-4522
• 
  Enio Gjerga, Panuwat Trairatphisan, Attila Gábor, Hermann Koch, Céline Chevalier, Franceco Ceccarelli, Aurélien Dugourd, Alexander Mitsos, Julio Saez-Rodriguez, Jonathan D. Wren:
  Converting networks to predictive logic models from perturbation signalling data with CellNOpt. 4523-4524
• 
  Oriol Canela-Xandri, Samira Anbari, Javier Buceta, Alfonso Valencia:
  TiFoSi: an efficient tool for mechanobiology simulations of epithelia. 4525-4526
• 
  Ales Saska, David Tichy, Robert Moore, Achilles Rasquinha, Caner Akdas, Xiaodong Zhao, Renato Fabbri, Ana Jelicic, Gaurav Grover, Himanshu Jotwani, Mohamed Shadab, Resa M. K. Helikar, Tomás Helikar, Jonathan D. Wren:
  ccNetViz: a WebGL-based JavaScript library for visualization of large networks. 4527-4529
• 
  Charles E. Vejnar, Antonio J. Giraldez, Pier Luigi Martelli:
  LabxDB: versatile databases for genomic sequencing and lab management. 4530-4531
• 
  Joselyn Chávez, Carmina Barberena-Jonas, Jesus E. Sotelo-Fonseca, José Alquicira-Hernández, Heladia Salgado, Leonardo Collado-Torres, Alejandro Reyes:
  Programmatic access to bacterial regulatory networks with regutools. 4532-4534

Volume 36, Number 17, September 2020

• 
  Viivi Halla-aho, Harri Lähdesmäki:
  LuxUS: DNA methylation analysis using generalized linear mixed model with spatial correlation. 4535-4543
• 
  Divya Sharma, Andrew D. Paterson, Wei Xu:
  TaxoNN: ensemble of neural networks on stratified microbiome data for disease prediction. 4544-4550
• 
  Rongshan Yu, Wenxian Yang:
  ScaleQC: a scalable lossy to lossless solution for NGS data compression. 4551-4559
• 
  Mikhail D. Magnitov, Veronika S. Kuznetsova, Sergey V. Ulianov, Sergey V. Razin, Alexander V. Tyakht:
  Benchmark of software tools for prokaryotic chromosomal interaction domain identification. 4560-4567
• 
  Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre:
  SVJedi: genotyping structural variations with long reads. 4568-4575
• 
  Yaobin Ke, Jiahua Rao, Huiying Zhao, Yutong Lu, Nong Xiao, Yuedong Yang:
  Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting. 4576-4582
• 
  Safyan Aman Memon, Kinaan Aamir Khan, Hammad Naveed:
  HECNet: a hierarchical approach to enzyme function classification using a Siamese Triplet Network. 4583-4589
• 
  Robert Page, Ruriko Yoshida, Leon Zhang:
  Tropical principal component analysis on the space of phylogenetic trees. 4590-4598
• 
  Mostofa Rafid Uddin, Sazan Mahbub, Mohammad Saifur Rahman, Md. Shamsuzzoha Bayzid:
  SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction. 4599-4608
• 
  W. Garrett Jenkinson, Yang I Li, Shubham Basu, Margot A. Cousin, Gavin R. Oliver, Eric W. Klee:
  LeafCutterMD: an algorithm for outlier splicing detection in rare diseases. 4609-4615
• 
  Theodoulos Rodosthenous, Vahid Shahrezaei, Marina Evangelou:
  Integrating multi-OMICS data through sparse canonical correlation analysis for the prediction of complex traits: a comparison study. 4616-4625
• 
  Yonglin Peng, Meng Yuan, Juncai Xin, Xinhua Liu, Ju Wang:
  Screening novel drug candidates for Alzheimer's disease by an integrated network and transcriptome analysis. 4626-4632
• 
  Karim Abbasi, Parvin Razzaghi, Antti Poso, Massoud Amanlou, Jahan B. Ghasemi, Ali Masoudi-Nejad:
  DeepCDA: deep cross-domain compound-protein affinity prediction through LSTM and convolutional neural networks. 4633-4642
• 
  Mihai Glont, Chinmay Arankalle, Krishan K. Tiwari, Tung V. N. Nguyen, Henning Hermjakob, Rahuman S. Malik-Sheriff:
  BioModels Parameters: a treasure trove of parameter values from published systems biology models. 4649-4654
• 
  Marianne L. Slaten, Yen On Chan, Vivek Shrestha, Alexander E. Lipka, Ruthie Angelovici:
  HAPPI GWAS: Holistic Analysis with Pre- and Post-Integration GWAS. 4655-4657
• 
  César Piñeiro, José Manuel Abuín, Juan Carlos Pichel:
  Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies. 4658-4659
• 
  Milosz Wieczór, Adam Hospital, Genis Bayarri, Jacek Czub, Modesto Orozco:
  Molywood: streamlining the design and rendering of molecular movies. 4660-4661
• 
  Colin Farrell, Sagi Snir, Matteo Pellegrini:
  The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework. 4662-4663
• 
  Erika Gardini, Federico M. Giorgi, Sergio Decherchi, Andrea Cavalli:
  Spathial: an R package for the evolutionary analysis of biological data. 4664-4667
• 
  Tim Scherr, Karolin Streule, Andreas Bartschat, Moritz Böhland, Johannes Stegmaier, Markus Reischl, Véronique Orian-Rousseau, Ralf Mikut:
  BeadNet: deep learning-based bead detection and counting in low-resolution microscopy images. 4668-4670
• 
  Alex J. Cornish, Daniel Chubb, Anna Frangou, Phuc H. Hoang, Martin Kaiser, David C. Wedge, Richard S. Houlston:
  Reference bias in the Illumina Isaac aligner. 4671-4672
• 
  Clemens Kreutz, Nilay S. Can, Ralf Schulze Bruening, Rabea Meyberg, Zsuzsanna Mérai, Noé Fernández-Pozo, Stefan A. Rensing:
  A Blind and Independent Benchmark Study for Detecting Differentially Methylated Regions in Plants. 4673
• 
  Ataberk Donmez, Ahmet Süreyya Rifaioglu, Aybar C. Acar, Tunca Dogan, Rengül Çetin-Atalay, Volkan Atalay:
  iBioProVis: interactive visualization and analysis of compound bioactivity space. 4674

Volume 36, Number 18, September 2020

• 
  Yuansheng Liu, Limsoon Wong, Jinyan Li:
  Allowing mutations in maximal matches boosts genome compression performance. 4675-4681
• 
  Jayaram Kancherla, Yifan Yang, Hyeyun Chae, Héctor Corrada Bravo:
  Epiviz File Server: Query, transform and interactively explore data from indexed genomic files. 4682-4690
• 
  Bikash K. Bhandari, Paul P. Gardner, Chun Shen Lim:
  Solubility-Weighted Index: fast and accurate prediction of protein solubility. 4691-4698
• 
  Hamid Bagheri, Andrew J. Severin, Hridesh Rajan:
  Detecting and correcting misclassified sequences in the large-scale public databases. 4699-4705
• 
  Connor Morgan-Lang, Ryan J. McLaughlin, Zachary Armstrong, Grace Zhang, Kevin Chan, Steven J. Hallam:
  TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler. 4706-4713
• 
  Farzin Sohraby, Mostafa Javaheri Moghadam, Masoud Aliyar, Hassan Aryapour:
  A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: probing the binding pathway of dasatinib to Src-kinase. 4714-4720
• 
  Jike Wang, Dong-Sheng Cao, Cunchen Tang, Xi Chen, Huiyong Sun, Tingjun Hou:
  Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning. 4721-4728
• 
  Jian Zhang, Sina Ghadermarzi, Lukasz A. Kurgan:
  Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes versus disordered proteins. 4729-4738
• 
  Jia-Bin Chen, Shan-Shan Dong, Shi Yao, Yuan-Yuan Duan, Wei-Xin Hu, Hao Chen, Nai-Ning Wang, Xiao-Feng Chen, Ruo-Han Hao, Hlaing Nwe Thynn, Ming-Rui Guo, Yu-Jie Zhang, Yu Rong, Yi-Xiao Chen, Fu-Ling Zhou, Yan Guo, Tie-Lin Yang:
  Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression. 4739-4748
• 
  Alexey A. Shadrin, Oleksandr Frei, Olav B. Smeland, Francesco Bettella, Kevin S. O'Connell, Osman Gani, Shahram Bahrami, Tea K. E. Uggen, Srdjan Djurovic, Dominic Holland, Ole A. Andreassen, Anders M. Dale:
  Phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories revealed by AI-MiXeR. 4749-4756
• 
  Liran Juan, Yongtian Wang, Jingyi Jiang, Qi Yang, Guohua Wang, Yadong Wang:
  Evaluating individual genome similarity with a topic model. 4757-4764
• 
  Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass:
  PUMA: PANDA Using MicroRNA Associations. 4765-4773
• 
  Pierre-Cyril Aubin-Frankowski, Jean-Philippe Vert:
  Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference. 4774-4780
• 
  Yan Ren, Siva Sivaganesan, Nicholas A. Clark, Lixia Zhang, Jacek Biesiada, Wen Niu, David R. Plas, Mario Medvedovic:
  Predicting mechanism of action of cellular perturbations with pathway activity signatures. 4781-4788
• 
  Alessandra Cabassi, Paul D. W. Kirk:
  Multiple kernel learning for integrative consensus clustering of omic datasets. 4789-4796
• 
  Shu Yang, Xiaoxi Liu, Raymond T. Ng:
  ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins. 4797-4804
• 
  Kieran Walsh, Mircea A. Voineagu, Fatemeh Vafaee, Irina Voineagu:
  TDAview: an online visualization tool for topological data analysis. 4805-4809
• 
  Qingxi Meng, Idoia Ochoa, Mikel Hernaez:
  GPress: a framework for querying general feature format (GFF) files and expression files in a compressed form. 4810-4812
• 
  Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Atsushi Niida, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto:
  Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens. 4813-4816
• 
  Gregor Sturm, Tamás Szabó, Georgios Fotakis, Marlene Haider, Dietmar Rieder, Zlatko Trajanoski, Francesca Finotello:
  Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. 4817-4818
• 
  Anastasiia Kim, James H. Degnan:
  PRANC: ML species tree estimation from the ranked gene trees under coalescence. 4819-4821
• 
  Nicolas Comte, Benoit Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin, Simon Penel, Céline Scornavacca, Manolo Gouy, Alexandros Stamatakis, Eric Tannier, David P. Parsons:
  Treerecs: an integrated phylogenetic tool, from sequences to reconciliations. 4822-4824
• 
  Vo Hong Thanh:
  RSSALib: a library for stochastic simulation of complex biochemical reactions. 4825-4826

Volume 36, Number 19, December 2020

• 
  C. S. Casimiro-Soriguer, M. M. Rigual, Ana M. Brokate-Llanos, Manuel J. Muñoz, Andrés Garzón, Antonio J. Pérez-Pulido, Juan Jiménez:
  Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome. 4827-4832
• 
  Dan Wang, Hui Tang, Jianfeng Liu, Shizhong Xu, Qin Zhang, Chao Ning:
  Rapid epistatic mixed-model association studies by controlling multiple polygenic effects. 4833-4837
• 
  Yan Song, Haixu Tang, Haoyu Zhang, Qin Zhang:
  Overlap detection on long, error-prone sequencing reads via smooth q-gram. 4838-4845
• 
  Yan Wang, Miguel Correa Marrero, Marnix H. Medema, Aalt D. J. van Dijk:
  Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines. 4846-4853
• 
  Nico Borgsmüller, José Bonet, Francesco Marass, Abel Gonzalez-Perez, Núria López-Bigas, Niko Beerenwinkel:
  BnpC: Bayesian non-parametric clustering of single-cell mutation profiles. 4854-4859
• 
  Kenong Su, Zhijin Wu, Hao Wu:
  Simulation, power evaluation and sample size recommendation for single-cell RNA-seq. 4860-4868
• 
  Ruhul Amin, Chowdhury Rafeed Rahman, Sajid Ahmed, Md. Habibur Rahman Sifat, Md Nazmul Khan Liton, Md. Moshiur Rahman, Md Zahid Hossain Khan, Swakkhar Shatabda:
  iPromoter-BnCNN: a novel branched CNN-based predictor for identifying and classifying sigma promoters. 4869-4875
• 
  Khalique Newaz, Gabriel Wright, Jacob Piland, Jun Li, Patricia L. Clark, Scott J. Emrich, Tijana Milenkovic:
  Network analysis of synonymous codon usage. 4876-4884
• 
  Baoshan Ma, Mingkun Fang, Xiangtian Jiao:
  Inference of gene regulatory networks based on nonlinear ordinary differential equations. 4885-4893
• 
  Yi Shi, Zehua Guo, Xianbin Su, Luming Meng, Mingxuan Zhang, Jing Sun, Chao Wu, Minhua Zheng, Xueyin Shang, Xin Zou, Wangqiu Cheng, Yaoliang Yu, Yujia Cai, Chaoyi Zhang, Weidong Cai, Lin-Tai Da, Guang He, Zeguang Han:
  DeepAntigen: a novel method for neoantigen prioritization via 3D genome and deep sparse learning. 4894-4901
• 
  Peifeng Ruan, Shuang Wang, Hua Liang:
  mirPLS: a partial linear structure identifier method for cancer subtyping using microRNAs. 4902-4909
• 
  Hai-Long Trieu, Thy Thy Tran, Anh-Khoa Duong Nguyen, Anh Nguyen, Makoto Miwa, Sophia Ananiadou:
  DeepEventMine: end-to-end neural nested event extraction from biomedical texts. 4910-4917
• 
  Yahui Long, Min Wu, Chee Keong Kwoh, Jiawei Luo, Xiaoli Li:
  Predicting human microbe-drug associations via graph convolutional network with conditional random field. 4918-4927
• 
  Hongxu Ding, Andrew D. Bailey, Miten Jain, Hugh E. Olsen, Benedict Paten:
  Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts. 4928-4934
• 
  Yao Yao, Ihor Smal, Ilya Grigoriev, Anna Akhmanova, Erik Meijering:
  Deep-learning method for data association in particle tracking. 4935-4941
• 
  Canhong Wen, Yuhui Yang, Quan Xiao, Meiyan Huang, Wenliang Pan:
  Genome-wide association studies of brain imaging data via weighted distance correlation. 4942-4950
• 
  Lina Yang, Shuang Jiang, Bibo Jiang, Dajiang J. Liu, Xiaowei Zhan:
  Seqminer2: an efficient tool to query and retrieve genotypes for statistical genetics analyses from biobank scale sequence dataset. 4951-4954
• 
  Lili Dong, Jianan Wang, Guohua Wang:
  BYASE: a Python library for estimating gene and isoform level allele-specific expression. 4955-4956
• 
  David B. Blumenthal, Lorenzo Viola, Markus List, Jan Baumbach, Paolo Tieri, Tim Kacprowski:
  EpiGEN: an epistasis simulation pipeline. 4957-4959
• 
  Lauren Marazzi, Andrew Gainer-Dewar, Paola Vera-Licona:
  OCSANA+: optimal control and simulation of signaling networks from network analysis. 4960-4962
• 
  Mahiar Mahjoub, Daphne Ezer:
  PAFway: pairwise associations between functional annotations in biological networks and pathways. 4963-4964
• 
  James Luke Gallant, Tiaan Heunis, Samantha Leigh Sampson, Wilbert Bitter:
  ProVision: a web-based platform for rapid analysis of proteomics data processed by MaxQuant. 4965-4967
• 
  Zhicheng Zhang, Xiaokun Liang, Wenjian Qin, Shaode Yu, Yaoqin Xie:
  matFR: a MATLAB toolbox for feature ranking. 4968-4969
• 
  Gonzalo Neira, Diego Cortez, Joaquin Jil, David S. Holmes:
  AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata. 4970-4971
• 
  Janel L. Davis, Brian Soetikno, Ki-Hee Song, Yang Zhang, Cheng Sun, Hao F. Zhang:
  RainbowSTORM: an open-source ImageJ plug-in for spectroscopic single-molecule localization microscopy (sSMLM) data analysis and image reconstruction. 4972-4974
• 
  Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev:
  cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. 4975

Volume 36, Number 20, December 2020

• 
  Jing-Bo Zhou, Yao Xiong, Ke An, Zhi-Qiang Ye, Yun-Dong Wu:
  IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions. 4977-4983
• 
  Prateek Gupta, Pankaj Singh Dholaniya, Sameera Devulapalli, Nilesh R. Tawari, Yellamaraju Sreelakshmi, Rameshwar Sharma:
  Reanalysis of genome sequences of tomato accessions and its wild relatives: development of Tomato Genomic Variation (TGV) database integrating SNPs and INDELs polymorphisms. 4984-4990
• 
  Matej Lexa, Pavel Jedlicka, Ivan Vanat, Michal Cervenanský, Eduard Kejnovský:
  TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting. 4991-4999
• 
  Lucile Broseus, Aubin Thomas, Andrew J. Oldfield, Dany Severac, Emeric Dubois, William Ritchie:
  TALC: Transcript-level Aware Long-read Correction. 5000-5006
• 
  Martin R. Smith:
  Information theoretic generalized Robinson-Foulds metrics for comparing phylogenetic trees. 5007-5013
• 
  Nina I Ilieva, Nicola Galvanetto, Michele Allegra, Marco Brucale, Alessandro Laio:
  Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples. 5014-5020
• 
  Gang Xu, Qinghua Wang, Jianpeng Ma:
  OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks. 5021-5026
• 
  Mingzhou Song, Hua Zhong:
  Efficient weighted univariate clustering maps outstanding dysregulated genomic zones in human cancers. 5027-5036
• 
  Martin E. Guerrero-Gimenez, J. M. Fernandez-Muñoz, B. J. Lang, K. M. Holton, D. R. Ciocca, C. A. Catania, F. C. M. Zoppino:
  Galgo: a bi-objective evolutionary meta-heuristic identifies robust transcriptomic classifiers associated with patient outcome across multiple cancer types. 5037-5044
• 
  Moritz Hess, Maren Hackenberg, Harald Binder:
  Exploring generative deep learning for omics data using log-linear models. 5045-5053
• 
  Xiangyu Liu, Di Li, Juntao Liu, Zhengchang Su, Guojun Li:
  RecBic: a fast and accurate algorithm recognizing trend-preserving biclusters. 5054-5060
• 
  Ali Akbar Jamali, Anthony J. Kusalik, Fang-Xiang Wu:
  MDIPA: a microRNA-drug interaction prediction approach based on non-negative matrix factorization. 5061-5067
• 
  Yue Wu, Michael T. Judge, Jonathan P. Arnold, Suchendra M. Bhandarkar, Arthur Edison:
  RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking. 5068-5075
• 
  Nikolay Russkikh, Denis V. Antonets, Dmitry Shtokalo, Alexander Makarov, Yuri Vyatkin, Alexey Zakharov, Evgeny Terentyev:
  Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis. 5076-5085
• 
  Antti Häkkinen, Juha Koiranen, Julia Casado, Katja Kaipio, Oskari Lehtonen, Eleonora Petrucci, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Luca Pasquini, Mauro Biffoni, Rainer Lehtonen, Sampsa Hautaniemi:
  qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets. 5086-5092
• 
  Mark Kittisopikul, Amir Vahabikashi, Takeshi Shimi, Robert D. Goldman, Khuloud Jaqaman:
  Adaptive multiorientation resolution analysis of complex filamentous network images. 5093-5103
• 
  Kirill Zinovjev, Marc van der Kamp:
  Enlighten2: molecular dynamics simulations of protein-ligand systems made accessible. 5104-5106
• 
  Francesco Ambrosetti, Tobias Hegelund Olsen, Pier Paolo Olimpieri, Brian Jiménez-García, Edoardo Milanetti, Paolo Marcatili, Alexandre M. J. J. Bonvin:
  proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking. 5107-5108
• 
  Ren Kong, Guangbo Yang, Rui Xue, Ming Liu, Feng Wang, Jianping Hu, Xiaoqiang Guo, Shan Chang:
  COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19. 5109-5111
• 
  Max Hebditch, Jim Warwicker:
  Protein-sol pKa: prediction of electrostatic frustration, with application to coronaviruses. 5112-5114
• 
  August E. Woerner, Jennifer Churchill Cihlar, Utpal Smart, Bruce Budowle:
  Numt identification and removal with RtN! 5115-5116
• 
  Amel Bekkar, Anita Nasrallah, Nicolas Guex, Lluis Fajas, Ioannis Xenarios, Isabel C. Lopez-Mejia:
  PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling. 5117-5119
• 
  Arjun Magge, Davy Weissenbacher, Karen O'Connor, Tasnia Tahsin, Graciela Gonzalez-Hernandez, Matthew Scotch:
  GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography. 5120-5121
• 
  Christiana N. Fogg, Ron Shamir, Diane E. Kovats:
  Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient. 5122-5123
• 
  Christiana N. Fogg, Ron Shamir, Diane E. Kovats:
  2019 ISCB Overton Prize: Christophe Dessimoz. 5124-5125
• 
  Christiana N. Fogg, Ron Shamir, Diane E. Kovats:
  2019 Outstanding Contributions to ISCB Awarded to Barb Bryant. 5126
• 
  Christiana N. Fogg, Ron Shamir, Diane E. Kovats:
  2019 ISCB Innovator Award Recognizes William Stafford Noble. 5127-5128

Volume 36, Number 21, January 2021

• 
  Diogo Pratas, Jorge Miguel Silva:
  Persistent minimal sequences of SARS-CoV-2. 5129-5132
• 
  Shijie Qin, Xinyi Xia, Xuejia Shi, Xinglai Ji, Fei Ma, Liming Chen:
  Mechanistic insights into SARS-CoV-2 epidemic via revealing the features of SARS-CoV-2 coding proteins and host responses upon its infection. 5133-5138
• 
  Jordan M. Eizenga, Adam M. Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos, Glenn Hickey, Vincenza Colonna, Benedict Paten, Erik Garrison:
  Efficient dynamic variation graphs. 5139-5144
• 
  Gamze Gürsoy, Charlotte M. Brannon, Fabio C. P. Navarro, Mark Gerstein:
  FANCY: fast estimation of privacy risk in functional genomics data. 5145-5150
• 
  Xiyu Peng, Karin S. Dorman:
  AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data. 5151-5158
• 
  Xiaoyong Pan, Jasper Zuallaert, Xi Wang, Hong-Bin Shen, Elda Posada Campos, Denys O. Marushchak, Wesley De Neve:
  ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity. 5159-5168
• 
  Anil Kumar Hanumanthappa, Jaswinder Singh, Kuldip K. Paliwal, Jaspreet Singh, Yaoqi Zhou:
  Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network. 5169-5176
• 
  Yi-Jun Tang, Yihe Pang, Bin Liu:
  IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning. 5177-5186
• 
  Gourab Ghosh Roy, Nicholas Geard, Karin Verspoor, Shan He:
  PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data. 5187-5193
• 
  Dimitris V. Manatakis, Aaron Vandevender, Elias S. Manolakos:
  An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures. 5194-5204
• 
  Mete Akgün, Ali Burak Ünal, Bekir Ergüner, Nico Pfeifer, Oliver Kohlbacher:
  Identifying disease-causing mutations with privacy protection. 5205-5213
• 
  Canhong Wen, Hailong Ba, Wenliang Pan, Meiyan Huang:
  Co-sparse reduced-rank regression for association analysis between imaging phenotypes and genetic variants. 5214-5222
• 
  Tianzhong Yang, Peng Wei, Wei Pan:
  Integrative analysis of multi-omics data for discovering low-frequency variants associated with low-density lipoprotein cholesterol levels. 5223-5228
• 
  Ruey Leng Loo, Queenie Chan, Henrik Antti, Jia V. Li, Hutan Ashrafian, Paul Elliott, Jeremiah Stamler, Jeremy K. Nicholson, Elaine Holmes, Julien Wist:
  Strategy for improved characterization of human metabolic phenotypes using a COmbined Multi-block Principal components Analysis with Statistical Spectroscopy (COMPASS). 5229-5236
• 
  Yasin Ilkagan Tepeli, Ali Burak Ünal, Furkan Mustafa Akdemir, Öznur Tastan:
  PAMOGK: a pathway graph kernel-based multiomics approach for patient clustering. 5237-5246
• 
  James H. Joly, William E. Lowry, Nicholas A. Graham:
  Differential Gene Set Enrichment Analysis: a statistical approach to quantify the relative enrichment of two gene sets. 5247-5254
• 
  Keno K. Bressem, Lisa C. Adams, Robert A. Gaudin, Daniel Tröltzsch, Bernd Hamm, Marcus R. Makowski, Chan-Yong Schüle, Janis Lucas Vahldiek, Stefan Markus Niehues:
  Highly accurate classification of chest radiographic reports using a deep learning natural language model pre-trained on 3.8 million text reports. 5255-5261
• 
  Legana C. H. W. Fingerhut, David J. Miller, Jan M. Strugnell, Norelle L. Daly, Ira Cooke:
  ampir: an R package for fast genome-wide prediction of antimicrobial peptides. 5262-5263
• 
  Benjamin Linard, Nikolai Romashchenko, Fabio Pardi, Eric Rivals:
  PEWO: a collection of workflows to benchmark phylogenetic placement. 5264-5266
• 
  Jon D. Hill:
  Gene Teller: an extensible Alexa Skill for gene-relevant databases. 5267-5268
• 
  Dongliang Liu, Mengying Han, Yu Tian, Linlin Gong, Cancan Jia, Pengli Cai, Weizhong Tu, Junni Chen, Qian-Nan Hu:
  Cell2Chem: mining explored and unexplored biosynthetic chemical spaces. 5269-5270
• 
  René L. Warren, Inanç Birol:
  HLA predictions from the bronchoalveolar lavage fluid and blood samples of eight COVID-19 patients at the pandemic onset. 5271-5273

Volume 36, Numbers 22-23, April 2021

• 
  Jingwen Guo, David Starr, Huazhang Guo:
  Classification and review of free PCR primer design software. 5263-5268
• 
  Uriel Singer, Kira Radinsky, Eric Horvitz:
  On biases of attention in scientific discovery. 5269-5274
• 
  Bahar Alipanahi, Martin D. Muggli, Musa Jundi, Noelle R. Noyes, Christina Boucher:
  Metagenome SNP calling via read-colored de Bruijn graphs. 5275-5281
• 
  Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu:
  SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs. 5282-5290
• 
  Felix Stiehler, Marvin Steinborn, Stephan Scholz, Daniela Dey, Andreas P. M. Weber, Alisandra K. Denton:
  Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning. 5291-5298
• 
  Xiaohua Douglas Zhang, Dandan Wang, Shixue Sun, Heping Zhang:
  Issues of Z-factor and an approach to avoid them for quality control in high-throughput screening studies. 5299-5303
• 
  Roman Feldbauer, Lukas Gosch, Lukas Lüftinger, Patrick Hyden, Arthur Flexer, Thomas Rattei:
  DeepNOG: fast and accurate protein orthologous group assignment. 5304-5312
• 
  Shubham Chandak, Kedar Tatwawadi, Srivatsan Sridhar, Tsachy Weissman:
  Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy. 5313-5321
• 
  Daniel Munro, Mona Singh:
  DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction. 5322-5329
• 
  Stefan Schulze, Anne Oltmanns, Christian Fufezan, Julia Krägenbring, Michael Mormann, Mechthild Pohlschröder, Michael Hippler:
  SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides. 5330-5336
• 
  Lennart Langouche, April Joy C. Aralar, Mridu Sinha, Shelley M. Lawrence, Stephanie I Fraley, Todd P. Coleman:
  Data-driven noise modeling of digital DNA melting analysis enables prediction of sequence discriminating power. 5337-5343
• 
  Martin C. Frith, Laurent Noé, Gregory Kucherov:
  Minimally overlapping words for sequence similarity search. 5344-5350
• 
  Guillaume E. Scholz, Benjamin Linard, Nikolai Romashchenko, Eric Rivals, Fabio Pardi:
  Rapid screening and detection of inter-type viral recombinants using phylo-k-mers. 5351-5360
• 
  Xiaoyang Jing, Jinbo Xu:
  Improved protein model quality assessment by integrating sequential and pairwise features using deep learning. 5361-5367
• 
  Krzysztof Szczepaniak, Adriana Bukala, Antonio Marinho da Silva Neto, Jan Ludwiczak, Stanislaw Dunin-Horkawicz:
  A library of coiled-coil domains: from regular bundles to peculiar twists. 5368-5376
• 
  Tyler Borrman, Brian G. Pierce, Thom Vreven, Brian M. Baker, Zhiping Weng:
  High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. 5377-5385
• 
  Benjamin Hsu, Valeriia Sherina, Matthew N. McCall:
  Autoregressive modeling and diagnostics for qPCR amplification. 5386-5391
• 
  Markus Ekvall, Michael Höhle, Lukas Käll:
  Parallelized calculation of permutation tests. 5392-5397
• 
  Shaked Bergman, Alon Diament, Tamir Tuller:
  New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region. 5398-5404
• 
  Wei Wang, Wei Liu:
  Integration of gene interaction information into a reweighted Lasso-Cox model for accurate survival prediction. 5405-5414
• 
  Yang Hai, Yalu Wen:
  A Bayesian linear mixed model for prediction of complex traits. 5415-5423
• 
  Florian Privé, Julyan Arbel, Bjarni J. Vilhjálmsson:
  LDpred2: better, faster, stronger. 5424-5431
• 
  Julian Hecker, F. William Townes, Priyadarshini Kachroo, Cecelia A. Laurie, Jessica Lasky-Su, John Ziniti, Michael H. Cho, Scott T. Weiss, Nan M. Laird, Christoph Lange:
  A unifying framework for rare variant association testing in family-based designs, including higher criticism approaches, SKATs, and burden tests. 5432-5438
• 
  Ziqiao Wang, Peng Wei:
  IMIX: a multivariate mixture model approach to association analysis through multi-omics data integration. 5439-5447
• 
  Da Kuang, Rebecca Truty, Jochen Weile, Britt Johnson, Keith Nykamp, Carlos Araya, Robert L. Nussbaum, Frederick P. Roth:
  Prioritizing genes for systematic variant effect mapping. 5448-5455
• 
  Mengyun Yang, Lan Huang, Yunpei Xu, Chengqian Lu, Jianxin Wang:
  Heterogeneous graph inference with matrix completion for computational drug repositioning. 5456-5464
• 
  Stefano Sinisi, Vadim Alimguzhin, Toni Mancini, Enrico Tronci, Brigitte Leeners:
  Complete populations of virtual patients for in silico clinical trials. 5465-5472
• 
  Rodrigo Santibañez, Daniel Garrido, Alberto J. M. Martin:
  Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages. 5473-5480
• 
  Cong Shen, Jiawei Luo, Wenjue Ouyang, Pingjian Ding, Xiangtao Chen:
  IDDkin: network-based influence deep diffusion model for enhancing prediction of kinase inhibitors. 5481-5491
• 
  Shaoqi Chen, Dongyu Xue, Guohui Chuai, Qiang Yang, Qi Liu:
  FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery. 5492-5498
• 
  Shuai Wang, Yiqi Jiang, Shuai Cheng Li:
  PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data. 5499-5506
• 
  Mateusz Kudla, Kaja Gutowska, Jaroslaw Synak, Mirko Weber, Katrin Sophie Bohnsack, Piotr Lukasiak, Thomas Villmann, Jacek Blazewicz, Marta Szachniuk:
  Virxicon: a lexicon of viral sequences. 5507-5513
• 
  Roman Martin, Thomas Hackl, Georges Hattab, Matthias G. Fischer, Dominik Heider:
  MOSGA: Modular Open-Source Genome Annotator. 5514-5515
• 
  Fábio K. Mendes, Dan Vanderpool, Ben Fulton, Matthew W. Hahn:
  CAFE 5 models variation in evolutionary rates among gene families. 5516-5518
• 
  David Heller, Martin Vingron:
  SVIM-asm: structural variant detection from haploid and diploid genome assemblies. 5519-5521
• 
  Matteo Chiara, Federico Zambelli, Marco Antonio Tangaro, Pietro Mandreoli, David Stephen Horner, Graziano Pesole:
  CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes. 5522-5523
• 
  Anand Mayakonda, Maximilian Schönung, Joschka Hey, Rajbir Nath Batra, Clarissa Feuerstein-Akgoz, Kristin Köhler, Daniel B. Lipka, Rocio Sotillo, Christoph Plass, Pavlo Lutsik, Reka Toth:
  Methrix: an R/Bioconductor package for systematic aggregation and analysis of bisulfite sequencing data. 5524-5525
• 
  Joan Segura, Yana Rose, John D. Westbrook, Stephen K. Burley, Jose M. Duarte:
  RCSB Protein Data Bank 1D tools and services. 5526-5527
• 
  Arthur Ecoffet, Frédéric Poitevin, Khanh Dao Duc:
  MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX. 5528-5529
• 
  Emma H. Gail, Anup D. Shah, Ralf B. Schittenhelm, Chen Davidovich:
  crisscrosslinkeR: identification and visualization of protein-RNA and protein-protein interactions from crosslinking mass spectrometry. 5530-5532
• 
  Marco Necci, Damiano Piovesan, Damiano Clementel, Zsuzsanna Dosztányi, Silvio C. E. Tosatto:
  MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins. 5533-5534
• 
  Daniel G. Bunis, Jared M. Andrews, Gabriela K. Fragiadakis, Trevor D. Burt, Marina Sirota:
  dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit. 5535-5536
• 
  Michael F. Lin, Xiaodong Bai, William J. Salerno, Jeffrey G. Reid:
  Sparse Project VCF: efficient encoding of population genotype matrices. 5537-5538
• 
  Xiaofan Lu, Jialin Meng, Yujie Zhou, Liyun Jiang, Fangrong Yan:
  MOVICS: an R package for multi-omics integration and visualization in cancer subtyping. 5539-5541
• 
  Jeffrey West, Yongqian Ma, Artem Kaznatcheev, Alexander R. A. Anderson:
  IsoMaTrix: a framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations. 5542-5544
• 
  Kexin Huang, Tianfan Fu, Lucas M. Glass, Marinka Zitnik, Cao Xiao, Jimeng Sun:
  DeepPurpose: a deep learning library for drug-target interaction prediction. 5545-5547
• 
  Jan P. Buchmann, Edward C. Holmes:
  Collecting and managing taxonomic data with NCBI-taxonomist. 5548-5550
• 
  Gavin Rhys Lloyd, Andris Jankevics, Ralf J. M. Weber:
  struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond. 5551-5552
• 
  Giuseppe Sgroi, Giulia Russo, Francesco Pappalardo:
  PETAL: a Python tool for deep analysis of biological pathways. 5553-5555
• 
  Michael Milton, Natalie Thorne:
  aCLImatise: automated generation of tool definitions for bioinformatics workflows. 5556-5557
• 
  Michiel Van Bel, Klaas Vandepoele:
  Comment on 'Hayai-Annotation Plants: an ultrafast and comprehensive functional gene annotation system in plants': the importance of taking the GO graph structure into account. 5558-5560
• 
  Corrigendum to: HALPER facilitates the identification of regulatory element orthologs across species. 5561
• 
  Alistair MacDougall, Vladimir Volynkin, Rabie Saidi, Diego Poggioli, Hermann Zellner, Emma Hatton-Ellis, Vishal Joshi, Claire O'Donovan, Sandra E. Orchard, Andrea H. Auchincloss, Delphine Baratin, Jerven T. Bolleman, Elisabeth Coudert, Edouard De Castro, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Cecilia N. Arighi, Qinghua Wang, Chuming Chen, Hongzhan Huang, John Garavelli, C. R. Vinayaka, Lai-Su Yeh, Darren A. Natale, Kati Laiho, Maria Jesus Martin, Alexandre Renaux, Klemens Pichler:
  UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. 5562
• 
  Junlin Xu, Lijun Cai, Bo Liao, Wen Zhu, Jialiang Yang:
  CMF-Impute: an accurate imputation tool for single cell RNA-seq data. 5563-5564
• 
  Neha Warikoo, Yung-Chun Chang, Wen-Lian Hsu:
  LBERT: Lexically-aware Transformers based Bidirectional Encoder Representation model for learning Universal Bio-Entity Relations. 5565
• 
  LFQC: A lossless compression algorithm for FASTQ files. 5566

Volume 36, Number 24, April 2021

• 
  Kyuto Sonehara, Yukinori Okada:
  Obelisc: an identical-by-descent mapping tool based on SNP streak. 5567-5570
• 
  Gabriela Alejandra Merino, Jonathan Raad, Leandro A Bugnon, Cristian A. Yones, Laura Kamenetzky, Juan Claus, Federico Ariel, Diego H. Milone, Georgina Stegmayer:
  Novel SARS-CoV-2 encoded small RNAs in the passage to humans. 5571-5581
• 
  Taedong Yun, Helen Li, Pi-Chuan Chang, Michael F. Lin, Andrew Carroll, Cory Y. McLean:
  Accurate, scalable cohort variant calls using DeepVariant and GLnexus. 5582-5589
• 
  Matteo Chiara, Pietro Mandreoli, Marco Antonio Tangaro, Anna Maria D'Erchia, Sandro Sorrentino, Cinzia Forleo, David Stephen Horner, Federico Zambelli, Graziano Pesole:
  VINYL: Variant prIoritizatioN bY survivaL analysis. 5590-5599
• 
  Zhibin Lv, Pingping Wang, Quan Zou, Qinghua Jiang:
  Identification of sub-Golgi protein localization by use of deep representation learning features. 5600-5609
• 
  Dipankar Ranjan Baisya, Stefano Lonardi:
  Prediction of histone post-translational modifications using deep learning. 5610-5617
• 
  Joana Pereira, Andrei N. Lupas:
  The VCBS superfamily forms a third supercluster of β-propellers that includes tachylectin and integrins. 5618-5622
• 
  Maryam Rabiee, Siavash Mirarab:
  SODA: multi-locus species delimitation using quartet frequencies. 5623-5631
• 
  Matthew Kerin, Jonathan Marchini:
  A non-linear regression method for estimation of gene-environment heritability. 5632-5639
• 
  Arunabha Majumdar, Kathryn S. Burch, Tanushree Haldar, Sriram Sankararaman, Bogdan Pasaniuc, W. James Gauderman, John S. Witte:
  A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes. 5640-5648
• 
  Jingyi Cai, Tianwei Tan, Siu Hung Joshua Chan:
  Predicting Nash equilibria for microbial metabolic interactions. 5649-5655
• 
  Chengqian Lu, Min Zeng, Fang-Xiang Wu, Min Li, Jianxin Wang:
  Improving circRNA-disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks. 5656-5664
• 
  Yuanjing Ma, Hongmei Jiang:
  NinimHMDA: neural integration of neighborhood information on a multiplex heterogeneous network for multiple types of human Microbe-Disease association. 5665-5671
• 
  Lili Zhao:
  Deep neural networks for predicting restricted mean survival times. 5672-5677
• 
  Po-Ting Lai, Zhiyong Lu:
  BERT-GT: cross-sentence n-ary relation extraction with BERT and Graph Transformer. 5678-5685
• 
  Marne C. Hagemeijer, Annelotte M. Vonk, Nikhil T. Awatade, Iris A. L. Silva, Christian Tischer, Volker Hilsenstein, Jeffrey M. Beekman, Margarida D. Amaral, Hugo M. Botelho:
  An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay. 5686-5694
• 
  Taylor Jones, Samuel B. Day, Luke Myers, James E. Crowe Jr., Cinque S. Soto:
  ClonoMatch: a tool for identifying homologous immunoglobulin and T-cell receptor sequences in large databases. 5695-5697
• 
  Georgios Iakovou, Mousa Alhazzazi, Steven Hayward, Stephen D. Laycock:
  DockIT: a tool for interactive molecular docking and molecular complex construction. 5698-5700
• 
  Constantin Ahlmann-Eltze, Wolfgang Huber:
  glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data. 5701-5702
• 
  Astghik Sargsyan, Alpha Tom Kodamullil, Shounak Baksi, Johannes Darms, Sumit Madan, Stephan Gebel, Oliver Keminer, Geena Mariya Jose, Helena Balabin, Lauren Nicole Delong, Manfred Kohler, Marc Jacobs, Martin Hofmann-Apitius:
  The COVID-19 Ontology. 5703-5705
• 
  Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller:
  cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data. 5706-5708
• 
  Silvia Benevenuta, Emidio Capriotti, Piero Fariselli:
  Calibrating variant-scoring methods for clinical decision making. 5709-5711
• 
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