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Bioinformatics, Volume 37
Volume 37, Number 1, April 2021
- M. K. Sobczyk
, Tom R. Gaunt
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. 1-8 - Aditya Gorla
xGAP: a python based efficient, modular, extensible and fault tolerant genomic analysis pipeline for variant discovery. 9-16 - Benjamin J. M. Tremblay
PhyloCorrelate: inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling. 17-22 - Jirí Hon
SoluProt: prediction of soluble protein expression in Escherichia coli. 23-28 - Jordi Silvestre-Ryan
Machine Boss: rapid prototyping of bioinformatic automata. 29-35 - Hong Su, Zhenling Peng, Jianyi Yang
Recognition of small molecule-RNA binding sites using RNA sequence and structure. 36-42 - Zhengyang Dong
netAE: semi-supervised dimensionality reduction of single-cell RNA sequencing to facilitate cell labeling. 43-49 - Meiling Liu
A method for subtype analysis with somatic mutations. 50-56 - Anja C. Gumpinger
Network-guided search for genetic heterogeneity between gene pairs. 57-65 - Cunmei Ji
AEMDA: inferring miRNA-disease associations based on deep autoencoder. 66-72 - Sara Omranian
PC2P: parameter-free network-based prediction of protein complexes. 73-81 - Chuang Liu, Zhen Han, Zi-Ke Zhang, Ruth Nussinov
A network-based deep learning methodology for stratification of tumor mutations. 82-88 - Rachel Torchet, Karen Druart
The iPPI-DB initiative: a community-centered database of protein-protein interaction modulators. 89-96 - Afshin Khadangi
EM-stellar: benchmarking deep learning for electron microscopy image segmentation. 97-106 - Renmin Han
Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints. 107-117 - Jianglin Feng, Nathan C. Sheffield
IGD: high-performance search for large-scale genomic interval datasets. 118-120 - Anna Abramova
CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data. 121-122 - Jonathan Jacob Weinstein
PROSS 2: a new server for the design of stable and highly expressed protein variants. 123-125 - A. K. M. Firoj Mahmud
ProkSeq for complete analysis of RNA-Seq data from prokaryotes. 126-128 - Alireza Ani
GWASinspector: comprehensive quality control of genome-wide association study results. 129-130 - Maria Suprun
bbeaR: an R package and framework for epitope-specific antibody profiling. 131-133 - Wei He
GuidePro: a multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts. 134-136 - Josep Marín-Llaó, Sarah Mubeen
MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms. 137-139 - Evgeny S. Zhvansky
The software for interactive evaluation of mass spectra stability and reproducibility. 140-142 - John Zobolas
UniBioDicts: Unified access to Biological Dictionaries. 143-144 - Georgios N. Dimitrakopoulos
PICKLE 3.0: enriching the human meta-database with the mouse protein interactome extended via mouse-human orthology. 145-146
Volume 37, Number 2, April 2021
- Dimitrios V. Vavoulis
A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data. 147-154 - Yang Young Lu, Jiaxing Bai, Yiwen Wang, Ying Wang
CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase. 155-161 - Amelia Villegas-Morcillo
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function. 162-170 - Dan Zhang, Zhao-Chun Xu
iCarPS: a computational tool for identifying protein carbonylation sites by novel encoded features. 171-177 - Simone Ciccolella
Triplet-based similarity score for fully multilabeled trees with poly-occurring labels. 178-184 - Liangyong Yu, Ran Li, Xiangrui Zeng, Hongyi Wang, Jie Jin, Ge Yang, Rui Jiang, Min Xu
Few shot domain adaptation for in situ macromolecule structural classification in cryoelectron tomograms. 185-191 - Gabriel E. Hoffman
Dream: powerful differential expression analysis for repeated measures designs. 192-201 - Samuel Melton, Sharad Ramanathan:
Discovering a sparse set of pairwise discriminating features in high-dimensional data. 202-212 - Saptarshi Sinha
Network approach to mutagenesis sheds insight on phage resistance in mycobacteria. 213-220 - Marzieh Ayati
Co-phosphorylation networks reveal subtype-specific signaling modules in breast cancer. 221-228 - Gustavo Hernandez-Mejia, Esteban A. Hernández-Vargas
Uncovering antibody cross-reaction dynamics in influenza A infections. 229-235 - Mario Sänger
Large-scale entity representation learning for biomedical relationship extraction. 236-242 - Elena Tutubalina
The Russian Drug Reaction Corpus and neural models for drug reactions and effectiveness detection in user reviews. 243-249 - William G. La Cava
Evaluating recommender systems for AI-driven biomedical informatics. 250-256 - Octavio Morante-Palacios
shinyÉPICo: a graphical pipeline to analyze Illumina DNA methylation arrays. 257-259 - Lifen Liu, Ge Zhang, Shoupeng He, Xuehai Hu
TSPTFBS: a Docker image for trans-species prediction of transcription factor binding sites in plants. 260-262 - Minseok Kwon, Soohyun Lee
BamSnap: a lightweight viewer for sequencing reads in BAM files. 263-264 - Chenxin Li, Mingxuan Gao, Wenxian Yang
Diamond: a multi-modal DIA mass spectrometry data processing pipeline. 265-267 - Jordan Douglas
UglyTrees: a browser-based multispecies coalescent tree visualizer. 268-269 - Andy M. C. Lau
Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry. 270-272 - Tiansheng Zhu
ProteomeExpert: a Docker image-based web server for exploring, modeling, visualizing and mining quantitative proteomic datasets. 273-275 - Daniel Sumner Magruder
Interactive gene networks with KNIT. 276-278 - Prashant Singh, Fredrik Wrede, Andreas Hellander:
Scalable machine learning-assisted model exploration and inference using Sciope. 279-281 - Trang T. Le
treeheatr: an R package for interpretable decision tree visualizations. 282-284 - Tao Hu, Shixiong Xu, Lei Wei, Xuegong Zhang
CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images. 285-287 - Yi Liu
Erratum to: EpiGraphDB: a database and data mining platform for health data science. 288
Volume 37, Number 3, April 2021
- Luyu Xie
PDR: a new genome assembly evaluation metric based on genetics concerns. 289-295 - Yue Fan, Huanhuan Zhu, Yanyi Song, Qinke Peng, Xiang Zhou:
Efficient and effective control of confounding in eQTL mapping studies through joint differential expression and Mendelian randomization analyses. 296-302 - Shani Cohen
minMLST: machine learning for optimization of bacterial strain typing. 303-311 - Xizhi Luo, Fei Qin, Guoshuai Cai, Feifei Xiao:
Integrating genomic correlation structure improves copy number variations detection. 312-317 - Florian Mock
VIDHOP, viral host prediction with deep learning. 318-325 - Simone Ciccolella
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. 326-333 - Pep Amengual-Rigo
UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes. 334-341 - Oliver P. Watson, Isidro Cortes-Ciriano
A semi-supervised learning framework for quantitative structure-activity regression modelling. 342-350 - Joshua M. Toth
ResiRole: residue-level functional site predictions to gauge the accuracies of protein structure prediction techniques. 351-359 - Federico Baldassarre
GraphQA: protein model quality assessment using graph convolutional networks. 360-366 - Andrew J. Bass
The optimal discovery procedure for significance analysis of general gene expression studies. 367-374 - Rajinder Gupta
FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts. 375-381 - Liya Wang
BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations. 382-387 - Woosub Shin, Joseph L. Hellerstein:
Isolating structural errors in reaction networks in systems biology. 388-395 - Shuzhen Kuang, Yanzhang Wei, Liangjiang Wang
Expression-based prediction of human essential genes and candidate lncRNAs in cancer cells. 396-403 - Neha Warikoo
LBERT: Lexically aware Transformer-based Bidirectional Encoder Representation model for learning universal bio-entity relations. 404-412 - Maria Nattestad, Robert Aboukhalil, Chen-Shan Chin, Michael C. Schatz
Ribbon: intuitive visualization for complex genomic variation. 413-415 - Wanson Choi
HATK: HLA analysis toolkit. 416-418 - Thiago L. A. Miller
sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies. 419-421 - Lucille Lopez-Delisle
pyGenomeTracks: reproducible plots for multivariate genomic datasets. 422-423 - Konrad Diedrich
GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank. 424-425 - Silver A. Wolf, Lennard Epping, Sandro Andreotti
SCORE: Smart Consensus Of RNA Expression - a consensus tool for detecting differentially expressed genes in bacteria. 426-428 - Quanxue Li, Wentao Dai, Jixiang Liu, Qingqing Sang, Yi-Xue Li, Yuan-Yuan Li:
DysRegSig: an R package for identifying gene dysregulations and building mechanistic signatures in cancer. 429-430 - Nils Kurzawa
Rtpca: an R package for differential thermal proximity coaggregation analysis. 431-433 - Ailin Ren, Dachuan Zhang
Transcriptor: a comprehensive platform for annotation of the enzymatic functions of transcripts. 434-435 - Sarah E. I. Perez, Aria S. Hahn
Hive Panel Explorer: an interactive network visualization tool. 436-437
Volume 37, Number 4, May 2021
- Jacob M. Schreiber, Jeffrey A. Bilmes, William Stafford Noble
Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data. 439-447 - Maximilian Collatz, Florian Mock
EpiDope: a deep neural network for linear B-cell epitope prediction. 448-455 - Luca Denti
Shark: fishing relevant reads in an RNA-Seq sample. 464-472 - Borja Freire, Susana Ladra
Inference of viral quasispecies with a paired de Bruijn graph. 473-481 - Vyacheslav Tretyachenko
CoLiDe: Combinatorial Library Design tool for probing protein sequence space. 482-489 - Mu Gao
A novel sequence alignment algorithm based on deep learning of the protein folding code. 490-496 - Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser:
Text mining for modeling of protein complexes enhanced by machine learning. 497-505 - Pietro Di Lena
Fold recognition by scoring protein maps using the congruence coefficient. 506-513 - Chubing Zeng
Incorporating prior knowledge into regularized regression. 514-521 - Hong-Dong Li
IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation. 522-530 - Christopher N. Foley
MR-Clust: clustering of genetic variants in Mendelian randomization with similar causal estimates. 531-541 - Lun Hu
HiSCF: leveraging higher-order structures for clustering analysis in biological networks. 542-550 - Arthur M. Lesk
Neighbourhoods in the yeast regulatory network in different physiological states. 551-558 - Heeva Baharlou
AFid: a tool for automated identification and exclusion of autofluorescent objects from microscopy images. 559-567 - M. A. Kühl, B. Stich
Mutation-Simulator: fine-grained simulation of random mutations in any genome. 568-569 - Anuradha Jagadeesan
HaploGrouper: a generalized approach to haplogroup classification. 570-572 - Zekun Yin
RabbitQC: high-speed scalable quality control for sequencing data. 573-574 - Xin Li, Haiyan Hu, Xiaoman Li:
mixtureS: a novel tool for bacterial strain genome reconstruction from reads. 575-577 - Kevin Troulé, Hugo López-Fernández
DREIMT: a drug repositioning database and prioritization tool for immunomodulation. 578-579 - Sunil Nagpal
NetSets.js: a JavaScript framework for compositional assessment and comparison of biological networks through Venn-integrated network diagrams. 580-582 - Benjamin L. Elsworth
MELODI Presto: a fast and agile tool to explore semantic triples derived from biomedical literature. 583-585 - Daniel Robert Korn, Tesia M. Bobrowski
COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database. 586-587
Volume 37, Number 5, May 2021
- Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. 589-595 - Michael Menzel, Sabine Hurka
NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling. 596-602 - Priyesh Agrawal, Debasisa Mohanty
A machine learning-based method for prediction of macrocyclization patterns of polyketides and non-ribosomal peptides. 603-611 - Shinichi Morishita
Finding long tandem repeats in long noisy reads. 612-621 - Cristian D. Loaiza, Rakesh Kaundal:
PredHPI: an integrated web server platform for the detection and visualization of host-pathogen interactions using sequence-based methods. 622-624 - Dhaivat Joshi, Shunfu Mao, Sreeram Kannan, Suhas N. Diggavi:
QAlign: aligning nanopore reads accurately using current-level modeling. 625-633 - Ruoyi Cai, Cécile Ané
Assessing the fit of the multi-species network coalescent to multi-locus data. 634-641 - Shijia Wang
Particle Gibbs sampling for Bayesian phylogenetic inference. 642-649 - Xu Shi
IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles. 650-658 - Frédéric Bertrand
selectBoost: a general algorithm to enhance the performance of variable selection methods. 659-668 - Juan Pablo Prada, Gaby Wangorsch, Kirstin Kucka, Isabell Lang
A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2. 669-676 - Gabriel J. Kowalczyk
dNEMO: a tool for quantification of mRNA and punctate structures in time-lapse images of single cells. 677-683 - Ronghui You, Yuxuan Liu, Hiroshi Mamitsuka
BERTMeSH: deep contextual representation learning for large-scale high-performance MeSH indexing with full text. 684-692 - Ahmet Süreyya Rifaioglu
MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery. 693-704 - Rosa L. Allesøe, Camilla K. Lemvigh, My V. T. Phan
Automated download and clean-up of family-specific databases for kmer-based virus identification. 705-710 - Zongli Xu
ipDMR: identification of differentially methylated regions with interval P-values. 711-713 - Niema Moshiri
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes. 714-716 - Michaela Frye
CONCUR: quick and robust calculation of codon usage from ribosome profiling data. 717-719 - Omer Sabary, Yoav Orlev, Roy Shafir, Leon Anavy, Eitan Yaakobi, Zohar Yakhini
SOLQC: Synthetic Oligo Library Quality Control tool. 720-722 - Emanuela Iovino
unCOVERApp: an interactive graphical application for clinical assessment of sequence coverage at the base-pair level. 723-725 - Markku Kuismin
MCPeSe: Monte Carlo penalty selection for graphical lasso. 726-727 - Xiuwen Zheng
SAIGEgds - an efficient statistical tool for large-scale PheWAS with mixed models. 728-730 - Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek
TRTools: a toolkit for genome-wide analysis of tandem repeats. 731-733 - Matthew I. J. Raybould
CoV-AbDab: the coronavirus antibody database. 734-735
Volume 37, Number 6, May 2021
- Rui Yin
VirPreNet: a weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all eight segments. 737-743 - Melanie Kirsche
Sapling: accelerating suffix array queries with learned data models. 744-749 - Runbin Tang, Zuguo Yu, Yuanlin Ma, Yaoqun Wu, Yi-Ping Phoebe Chen
Genetic source completeness of HIV-1 circulating recombinant forms (CRFs) predicted by multi-label learning. 750-758 - Xin Bai
KIMI: Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate. 759-766 - Hannah De Los Santos, Kristin P. Bennett, Jennifer M. Hurley:
MOSAIC: a joint modeling methodology for combined circadian and non-circadian analysis of multi-omics data. 767-774 - Liang Chen, Qiuyan He, Yuyao Zhai, Minghua Deng
Single-cell RNA-seq data semi-supervised clustering and annotation via structural regularized domain adaptation. 775-784 - Mingming Gong, Peng Liu, Frank C. Sciurba
Unpaired data empowers association tests. 785-792 - Julie Jiang
Learning graph representations of biochemical networks and its application to enzymatic link prediction. 793-799 - Jeffrey N. Law
Accurate and efficient gene function prediction using a multi-bacterial network. 800-806 - Andres M. Cifuentes-Bernal
A pseudotemporal causality approach to identifying miRNA-mRNA interactions during biological processes. 807-814 - Meng Wang, Lihua Jiang, Ruiqi Jian, Joanne Y. Chan, Qing Liu, Michael Snyder
RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data. 815-821 - Abdur Rahman Mohd Abul Basher, Steven J. Hallam:
Leveraging heterogeneous network embedding for metabolic pathway prediction. 822-829 - Kexin Huang
MolTrans: Molecular Interaction Transformer for drug-target interaction prediction. 830-836 - Ahmad Borzou
A novel estimator of the interaction matrix in Graphical Gaussian Model of omics data using the entropy of non-equilibrium systems. 837-844 - Sergio Picart-Armada
The effect of statistical normalization on network propagation scores. 845-852 - Jun Chen
Predicting candidate genes from phenotypes, functions and anatomical site of expression. 853-860 - Paula A. Marin Zapata
Self-supervised feature extraction from image time series in plant phenotyping using triplet networks. 861-867 - Heather Manching
SPEARS: Standard Performance Evaluation of Ancestral haplotype Reconstruction through Simulation. 868-870 - Russell Lewis McLaughlin
REscan: inferring repeat expansions and structural variation in paired-end short read sequencing data. 871-872 - Zekun Yin
RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures. 873-875 - Thomas Peacock, James M. Heather
Decombinator V4: an improved AIRR compliant-software package for T-cell receptor sequence annotation? 876-878 - Cui Su
CABEAN: a software for the control of asynchronous Boolean networks. 879-881 - Massimo Andreatta
STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data. 882-884 - Blaz Skrlj, Nika Erzen, Nada Lavrac
CaNDis: a web server for investigation of causal relationships between diseases, drugs and drug targets. 885-887
Volume 37, Number 7, May 2021
- Felix Kallenborn
CARE: context-aware sequencing read error correction. 889-895 - Yiwei Li, Geoffrey Brian Golding, Lucian Ilie
DELPHI: accurate deep ensemble model for protein interaction sites prediction. 896-904 - Marleen Balvert
OGRE: Overlap Graph-based metagenomic Read clustEring. 905-912 - Xiaopeng Jin, Qing Liao, Hang Wei
SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection. 913-920 - Sylvain Träger, Giorgio Tamò, Deniz Aydin
CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles. 921-928 - Tomer Meirson
Structural basis of SARS-CoV-2 spike protein induced by ACE2. 929-936 - Yang Liu, Weikang Gong, Yanpeng Zhao, Xueqing Deng, Shan Zhang, Chunhua Li:
aPRBind: protein-RNA interface prediction by combining sequence and I-TASSER model-based structural features learned with convolutional neural networks. 937-942 - Maria Kadukova
KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions. 943-950 - Stephen Todd, Peter Todd, Simon J. McGowan
CSynth: an interactive modelling and visualization tool for 3D chromatin structure. 951-955 - Alan Zammit, Leon S. Helwerda
A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions. 956-962 - Daniel Osório
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control. 963-967 - Dongshunyi Li
Identifying signaling genes in spatial single-cell expression data. 968-975 - Tao Jiang, Yuanyuan Li, Alison A. Motsinger-Reif
Knockoff boosted tree for model-free variable selection. 976-983 - Weiguang Mao, Javad Rahimikollu, Ryan Hausler, Maria Chikina:
DataRemix: a universal data transformation for optimal inference from gene expression datasets. 984-991 - Gen Li
SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity. 992-999 - Jose Lugo-Martinez
Classification in biological networks with hypergraphlet kernels. 1000-1007 - Jinmyung Jung
Characterizing therapeutic signatures of transcription factors in cancer by incorporating profiles in compound treated cells. 1008-1014 - Quang Tran, Alexej Abyzov
LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads. 1015-1017 - Martin Hölzer, Manja Marz
PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection. 1018-1020 - Shixu He
SOAPMetaS: profiling large metagenome datasets efficiently on distributed clusters. 1021-1023 - Po-E Li
A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays. 1024-1025 - Néli J. Fonseca-Júnior, Marcelo Q. L. Afonso, Lucas Carrijo de Oliveira, Lucas Bleicher
CONAN: a web application to detect specificity determinants and functional sites by amino acids co-variation network analysis. 1026-1028 - Kui Xu
VRmol: an integrative web-based virtual reality system to explore macromolecular structure. 1029-1031 - Jan Niclas Wolf
PTGL: extension to graph-based topologies of cryo-EM data for large protein structures. 1032-1034 - Jessica Ewald
FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data. 1035-1036 - Quan Do, Bich Hai Ho, Pierre Larmande
PyRice: a Python package for querying Oryza sativa databases. 1037-1038
Volume 37, Number 8, May 2021
- Nan Hao, Huawei Xin, Xiaowei Shi, Jie Xin, Haijuan Zhang, Shaofen Guo, Zhen Wang, Chunxiang Hao
Paternal reprogramming-escape histone H3K4me3 marks located within promoters of RNA splicing genes. 1039-1044 - Dhawal Jain, Chong Chu, Burak Han Alver
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data. 1045-1051 - Weiwei Zhang, Hao Wu
Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach. 1052-1059 - Lijun Cai, Xuanbai Ren, Xiangzheng Fu
iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor. 1060-1067 - Babak Saremi
Measuring reproducibility of virus metagenomics analyses using bootstrap samples from FASTQ-files. 1068-1075 - Borja Pitarch, Juan A. G. Ranea
Protein residues determining interaction specificity in paralogous families. 1076-1082 - Vaibhav Rajan
Maximum likelihood reconstruction of ancestral networks by integer linear programming. 1083-1092 - Saisai Sun, Wenkai Wang
RNA inter-nucleotide 3D closeness prediction by deep residual neural networks. 1093-1098 - Sayoni Das, Harry M. Scholes
CATH functional families predict functional sites in proteins. 1099-1106 - Johannes Smolander
ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq data. 1107-1114 - Ting Jin
ECMarker: interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages. 1115-1124 - Li Liu
TreeMap: a structured approach to fine mapping of eQTL variants. 1125-1134 - Bilal Shaker, Myeong-Sang Yu, Jin Sook Song, Sunjoo Ahn, Jae Yong Ryu, Kwang-Seok Oh
LightBBB: computational prediction model of blood-brain-barrier penetration based on LightGBM. 1135-1139 - Thin Nguyen
GraphDTA: predicting drug-target binding affinity with graph neural networks. 1140-1147 - Julio Aracena, Luis Cabrera-Crot, Lilian Salinas
Finding the fixed points of a Boolean network from a positive feedback vertex set. 1148-1155 - Peiliang Lou
A representation model for biological entities by fusing structured axioms with unstructured texts. 1156-1163 - Raghu Chandramohan, Nipun Kakkar, Angshumoy Roy, D. Williams Parsons:
reconCNV: interactive visualization of copy number data from high-throughput sequencing. 1164-1167 - Arnav Moudgil
The qBED track: a novel genome browser visualization for point processes. 1168-1170 - Xiaolei Zhang
Annotating high-impact 5′untranslated region variants with the UTRannotator. 1171-1173 - Alessandro Pedretti
The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects. 1174-1175 - Hongzhao Shao, Stephen Boulton
CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery. 1176-1177 - Derek W. Brown
PCAmatchR: a flexible R package for optimal case-control matching using weighted principal components. 1178-1181 - Dachuan Zhang
SARS2020: an integrated platform for identification of novel coronavirus by a consensus sequence-function model. 1182-1183 - Lu-Chi Liu, Ming-Yang Ho
PanGPCR: predictions for multiple targets, repurposing and side effects. 1184-1186 - Maxat Kulmanov
DeepGOPlus: improved protein function prediction from sequence. 1187
Volume 37, Number 9, June 2021
- Sisheng Liu
MEScan: a powerful statistical framework for genome-scale mutual exclusivity analysis of cancer mutations. 1189-1197 - Peter Ebert
Fast detection of differential chromatin domains with SCIDDO. 1198-1205 - Arnab Mallik, Lucian Ilie
ALeS: adaptive-length spaced-seed design. 1206-1210 - Hiroki Konishi, Rui Yamaguchi, Kiyoshi Yamaguchi, Yoichi Furukawa, Seiya Imoto
Halcyon: an accurate basecaller exploiting an encoder-decoder model with monotonic attention. 1211-1217 - Louis Becquey, Eric Angel, Fariza Tahi:
RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures. 1218-1224 - Yidan Eden Sun
Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species. 1225-1233 - Cynthia Z. Ma
Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data. 1234-1245 - Laura Baumgartner
Simulating intervertebral disc cell behaviour within 3D multifactorial environments. 1246-1253 - Narmada Sambaturu
PathExt: a general framework for path-based mining of omics-integrated biological networks. 1254-1262 - Julia Casado
Agile workflow for interactive analysis of mass cytometry data. 1263-1268 - Giulia Simoni, Chanchala Kaddi, Mengdi Tao, Federico Reali
A robust computational pipeline for model-based and data-driven phenotype clustering. 1269-1277 - Victor Barreto Mesquita, Florêncio Mendes Oliveira Filho, Paulo Canas Rodrigues
Detection of crossover points in detrended fluctuation analysis: an application to EEG signals of patients with epilepsy. 1278-1284 - Yue Wang
MetaTX: deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis. 1285-1291 - Anthony Westbrook
RepeatFS: a file system providing reproducibility through provenance and automation. 1292-1296 - Santiago Codesido, Mohamed Hanafi, Yoric Gagnebin, Víctor González-Ruiz
Network principal component analysis: a versatile tool for the investigation of multigroup and multiblock datasets. 1297-1303 - Yi Liu
EpiGraphDB: a database and data mining platform for health data science. 1304-1311 - Chayan Kumar Saha
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation. 1312-1314 - Heng Li
Bedtk: finding interval overlap with implicit interval tree. 1315-1316 - Janina Reeder, Mo Huang, Joshua S. Kaminker, Joseph N. Paulson
MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities. 1317-1318 - Shanwen Sun
BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method. 1319-1321 - Fairlie Reese
Swan: a library for the analysis and visualization of long-read transcriptomes. 1322-1323 - Wei Huang, Ping Zheng, Zhenhai Cui, Zhuo Li, Yifeng Gao, Helong Yu, You Tang, Xiaohui Yuan, Zhiwu Zhang
MMAP: a cloud computing platform for mining the maximum accuracy of predicting phenotypes from genotypes. 1324-1326 - Vivek Kohar
Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. 1327-1329 - Tobias Newmiwaka, Benjamin Engelhardt, Philipp Wendland
SEEDS: data driven inference of structural model errors and unknown inputs for dynamic systems biology. 1330-1331 - Daniel Domingo-Fernández
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology. 1332-1334 - Loane Danès, Nicolas Tchitchek, Christophe Bécavin
Bacnet: a user-friendly platform for building multi-omics websites. 1335-1336 - Joachim Wolff
Scool: a new data storage format for single-cell Hi-C data. 1337 - Johan Nyström-Persson, Gabriel Keeble-Gagnère, Niamat Zawad:
Compact and evenly distributed k-mer binning for genomic sequences. 1338
Volume 37, Number 10, June 2021
- Xiang-He Meng
Combining artificial intelligence: deep learning with Hi-C data to predict the functional effects of non-coding variants. 1339-1344 - Mojtaba Bahrami
Deep feature extraction of single-cell transcriptomes by generative adversarial network. 1345-1351 - Victor Alexandre Padilha, Omer S. Alkhnbashi
Casboundary: automated definition of integral Cas cassettes. 1352-1359 - Samuel M. Nicholls
On the complexity of haplotyping a microbial community. 1360-1366 - Swarnendu Tripathi, Nikita R. Dsouza, Raul Urrutia, Michael T. Zimmermann
Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations. 1367-1375 - Norberto Sánchez-Cruz
Extended connectivity interaction features: improving binding affinity prediction through chemical description. 1376-1382 - Tiago Olivoto
MGIDI: toward an effective multivariate selection in biological experiments. 1383-1389 - Xiaofeng Zhu, Xiaoyin Li, Rong Xu, Tao Wang:
An iterative approach to detect pleiotropy and perform Mendelian Randomization analysis using GWAS summary statistics. 1390-1400 - Hyun-Myung Woo
MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes. 1401-1410 - Francesco Bardozzo
Signal metrics analysis of oscillatory patterns in bacterial multi-omic networks. 1411-1419 - Antonio de Falco, Zoltán Dezsö, Francesco Ceccarelli
Adaptive one-class Gaussian processes allow accurate prioritization of oncology drug targets. 1420-1427 - Robert W. Gregg
Agent-based modeling reveals benefits of heterogeneous and stochastic cell populations during cGAS-mediated IFNβ production. 1428-1434 - Alexia Giannoula, Emilio Centeno, Miguel Angel Mayer
A system-level analysis of patient disease trajectories based on clinical, phenotypic and molecular similarities. 1435-1443 - Beatriz García Jiménez
Predicting microbiomes through a deep latent space. 1444-1451 - Inna Chervoneva
Quantification of spatial tumor heterogeneity in immunohistochemistry staining images. 1452-1460 - Krzysztof J. Szkop
flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data. 1461-1464 - Yoshiaki Yasumizu
VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data. 1465-1467 - Mujtahid Akon, Muntashir Akon, Mohimenul Kabir, Mohammad Saifur Rahman, M. Sohel Rahman
ADACT: a tool for analysing (dis)similarity among nucleotide and protein sequences using minimal and relative absent words. 1468-1470 - Giacomo Janson
PyMod 3: a complete suite for structural bioinformatics in PyMOL. 1471-1472 - David J. Wooten
synergy: a Python library for calculating, analyzing and visualizing drug combination synergy. 1473-1474 - Hasan Balci, Metin Can Siper, Nasim Saleh, Ilkin Safarli, Ludovic Roy, Merve Kilicarslan, Rumeysa Ozaydin, Alexander Mazein
Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. 1475-1477 - Jorge Álvarez-Jarreta
LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications. 1478-1479 - Juan Saez Hidalgo, Karen Y. Oróstica
BEST: a Shiny/R web-based application to easily retrieve cross-related enzyme functional parameters and information from BRENDA. 1480-1481 - Romain Fernandez
Fijiyama: a registration tool for 3D multimodal time-lapse imaging. 1482-1484 - Gabriel Landini
Colour deconvolution: stain unmixing in histological imaging. 1485-1487
Volume 37, Number 11, July 2021
- Ron Zeira, Ron Shamir:
Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions. 1489-1496 - Ramesh Rajaby
SurVIndel: improving CNV calling from high-throughput sequencing data through statistical testing. 1497-1505 - Jia-Ming Chang
Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability. 1506-1514 - Baldomero Imbernón, Antonio Serrano, Andrés Bueno-Crespo
METADOCK 2: a high-throughput parallel metaheuristic scheme for molecular docking. 1515-1520 - Yuqing Zhang, Prasad Patil, W. Evan Johnson
Robustifying genomic classifiers to batch effects via ensemble learning. 1521-1527 - Andrew E. Teschendorff, Alok K. Maity, Xue Hu, Weiyan Chen
Ultra-fast scalable estimation of single-cell differentiation potency from scRNA-Seq data. 1528-1534 - Sabrina Rashid, Sohrab Shah, Ziv Bar-Joseph, Ravi Pandya:
Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data. 1535-1543 - Hyejin Kang, Hongryul Ahn
mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering. 1544-1553 - Le Zhang
Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model. 1554-1561 - Byunghan Lee, Hyeyoung Min, Sungroh Yoon
MUGAN: multi-GPU accelerated AmpliconNoise server for rapid microbial diversity assessment. 1562-1570 - Ignacio Díaz Blanco
Morphing projections: a new visual technique for fast and interactive large-scale analysis of biomedical datasets. 1571-1580 - Hao Fei, Yue Zhang, Yafeng Ren, Donghong Ji:
A span-graph neural model for overlapping entity relation extraction in biomedical texts. 1581-1589 - Shixiang Wang, Ziyu Tao
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis. 1590-1592 - Etienne Routhier, Ayman Bin Kamruddin
keras_dna: a wrapper for fast implementation of deep learning models in genomics. 1593-1594 - Nehemiah Wilson, Ni Zhao
MiRKAT: kernel machine regression-based global association tests for the microbiome. 1595-1597 - Ting Wei, Jinfu J. Nie, Nicholas B. Larson
CpGtools: a python package for DNA methylation analysis. 1598-1599 - Héctor Rodríguez-Pérez, Laura Ciuffreda, Carlos Flores
NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data. 1600-1601 - Carlos Pintado
SolupHred: a server to predict the pH-dependent aggregation of intrinsically disordered proteins. 1602-1603 - Yuansheng Liu
Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers. 1604-1606 - Aziz Khan
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences. 1607-1609 - Ahmed Ibrahem Hafez
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files. 1610-1612 - Pawel Krupa
UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations. 1613-1615 - Renmin Han
A novel constrained reconstruction model towards high-resolution subtomogram averaging. 1616-1626 - Anhui Huang, Dianting Liu:
EBglmnet: a comprehensive R package for sparse generalized linear regression models. 1627-1629 - Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2020 ISCB Overton Prize: Jian Peng. 1630-1631 - Kodai Minoura
CYBERTRACK2.0: zero-inflated model-based cell clustering and population tracking method for longitudinal mass cytometry data. 1632-1634 - Michael G. Leeming
Phosphomatics: interactive interrogation of substrate-kinase networks in global phosphoproteomics datasets. 1635-1636 - Sage Hahn
Brain Predictability toolbox: a Python library for neuroimaging-based machine learning. 1637-1638
Volume 37, Number 12, July 2021
- Alaina Shumate
Liftoff: accurate mapping of gene annotations. 1639-1643 - Sylwester Swat
Genome-scale de novo assembly using ALGA. 1644-1651 - Yi-Juan Hu
A rarefaction-based extension of the LDM for testing presence-absence associations in the microbiome. 1652-1657 - Umberto Ferraro Petrillo
Alignment-free Genomic Analysis via a Big Data Spark Platform. 1658-1665 - Vladimir Smirnov
MAGUS: Multiple sequence Alignment using Graph clUStering. 1666-1672 - Susana Posada-Céspedes
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. 1673-1680 - Stelios K. Mylonas
DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins. 1681-1690 - Olga I. Zolotareva
Identification of differentially expressed gene modules in heterogeneous diseases. 1691-1698 - Scott Van Buren, Hirak Sarkar
Compression of quantification uncertainty for scRNA-seq counts. 1699-1707 - Zahra Razaghi-Moghadam
GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level. 1717-1723 - Eric Bach
Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification. 1724-1731 - Alexey Ovchinnikov, Isabel Cristina Pérez-Verona, Gleb Pogudin
CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations. 1732-1738 - Masaki Asada
Using drug descriptions and molecular structures for drug-drug interaction extraction from literature. 1739-1746 - Lianne Abrahams
Single-cell systems analysis: decision geometry in outliers. 1747-1755 - Dolors Pelegí-Sisó
methylclock: a Bioconductor package to estimate DNA methylation age. 1759-1760 - Frédéric Lemoine
COVID-Align: accurate online alignment of hCoV-19 genomes using a profile HMM. 1761-1762 - Nuwan Goonasekera
GalaxyCloudRunner: enhancing scalable computing for Galaxy. 1763-1765 - John A. Rhodes
MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R. 1766-1768 - Anku Gupta, Mohit Choudhary, Sanjay Kumar Mohanty
Machine-OlF-Action: a unified framework for developing and interpreting machine-learning models for chemosensory research. 1769-1771 - Nam D. Nguyen
Varmole: a biologically drop-connect deep neural network model for prioritizing disease risk variants and genes. 1772-1775 - Johann F. Jadebeck
HOPS: high-performance library for (non-)uniform sampling of convex-constrained models. 1776-1777 - Nick Strayer
PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS. 1778-1780 - Manuel Bernal Llinares
Identifiers.org: Compact Identifier services in the cloud. 1781-1782 - Estefania Mancini, Andres Rabinovich, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz:
Corrigendum to: ASpli: Integrative analysis of splicing landscapes through RNA-Seq assays. 1783 - Maximilian Collatz, Florian Mock, Emanuel Barth
EpiDope: a deep neural network for linear B-cell epitope prediction. 1784
Volume 37, Number 13, July 2021
- Tony Robinson
Hardware acceleration of genomics data analysis: challenges and opportunities. 1785-1795 - Michaela Areti Zervou
Structural classification of proteins based on the computationally efficient recurrence quantification analysis and horizontal visibility graphs. 1796-1804 - Joan Carles Pons
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. 1805-1813 - Jianxiong Tang
CaMelia: imputation in single-cell methylomes based on local similarities between cells. 1814-1820 - Xi Zeng
HIVID2: an accurate tool to detect virus integrations in the host genome. 1821-1827 - Phillipe Loher, Nestoras Karathanasis, Eric Londin
IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets. 1828-1838 - Nidhi Shah
TIPP2: metagenomic taxonomic profiling using phylogenetic markers. 1839-1845 - Ting-Hsuan Wang, Cheng-Ching Huang, Jui-Hung Hung
EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences. 1846-1852 - Daniel A. Nissley
Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains. 1853-1859 - Juho Timonen
lgpr: an interpretable non-parametric method for inferring covariate effects from longitudinal data. 1860-1867 - Jonas Meisner
Large-scale inference of population structure in presence of missingness using PCA. 1868-1875 - Ksenia Lavrichenko, Øyvind Helgeland, Pål R. Njølstad, Inge Jonassen, Stefan Johansson
SeeCiTe: a method to assess CNV calls from SNP arrays using trio data. 1876-1883 - Ling Luo
PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology. 1884-1890 - Weizhong Zhao
Efficient multiple biomedical events extraction via reinforcement learning. 1891-1899 - Yassene Mohammed
Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays. 1900-1908 - Edith M. Ross
Allele-specific multi-sample copy number segmentation in ASCAT. 1909-1911 - Gonzalo López
svpluscnv: analysis and visualization of complex structural variation data. 1912-1914 - Dandan Huang, Zhao Wang, Yao Zhou, Qian Liang, Pak Chung Sham, Hongcheng Yao, Mulin Jun Li
vSampler: fast and annotation-based matched variant sampling tool. 1915-1917 - Rajeeva Musunuri
Somatic variant analysis of linked-reads sequencing data with Lancet. 1918-1919 - Esaie Kuitche, Yanchun Qi, Nadia Tahiri
DoubleRecViz: a web-based tool for visualizing transcript-gene-species tree reconciliation. 1920-1922 - Richard H. Adams, Todd A. Castoe, Michael Degiorgio:
PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments. 1923-1925 - Naifu Zhang, Xiaohe Yu
HD-eXplosion: visualization of hydrogen-deuterium exchange data as chiclet and volcano plots with statistical filtering. 1926-1927 - Lyuba V. Bozhilova
COGENT: evaluating the consistency of gene co-expression networks. 1928-1929 - R. Pinto-Cámara, Alejandro Linares
FCSlib: an open-source tool for fluorescence fluctuation spectroscopy analysis for mobility, number and molecular brightness in R. 1930-1931
Volume 37, Number 14, August 2021
- Javier Pardo-Diaz
Robust gene coexpression networks using signed distance correlation. 1982-1989 - Armin Rauschenberger
Predictive and interpretable models via the stacked elastic net. 2012-2016 - Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi
Succinct dynamic de Bruijn graphs. 1946-1952 - Yang Zhang
Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis. 2025-2032 - Martin R. Smith:
Information theoretic generalized Robinson-Foulds metrics for comparing phylogenetic trees. 2077-2078 - Corrigendum to: HRIBO: high-throughput analysis of bacterial ribosome profiling data. 2079
- Jennifer L. Harrow
ELIXIR: providing a sustainable infrastructure for life science data at European scale. 2506-2511 - Dimitris V. Manatakis
Erratum to: An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures. 2512
Volume 37, Number 15, August 2021
- Bernhard Haubold
Fur: Find unique genomic regions for diagnostic PCR. 2081-2087 - Stefano Franzini, Marco Di Stefano
essHi-C: essential component analysis of Hi-C matrices. 2088-2094 - Mengyang Xu
Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios. 2095-2102 - Yanrong Ji, Zhihan Zhou, Han Liu, Ramana V. Davuluri
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome. 2112-2120 - Emmanuel Sapin
Novel approach for parallelizing pairwise comparison problems as applied to detecting segments identical by decent in whole-genome data. 2121-2125 - Gregor Entzian, Ivo L. Hofacker
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes. 2126-2133 - Fergus Imrie
Generating property-matched decoy molecules using deep learning. 2134-2141 - Peter Hettegger
Random rotation for identifying differentially expressed genes with linear models following batch effect correction. 2142-2149 - Jie-Huei Wang
Network-adjusted Kendall's Tau Measure for Feature Screening with Application to High-dimensional Survival Genomic Data. 2150-2156 - Hao Wang
eHSCPr discriminating the cell identity involved in endothelial to hematopoietic transition. 2157-2164 - Jean-Michel Nguyen, Pascal Jézéquel, Pierre Gillois, Luisa Silva, Faouda Ben Azzouz, Sophie Lambert-Lacroix, Philippe P. Juin
Random forest of perfect trees: concept, performance, applications and perspectives. 2165-2174 - Luca Cardelli, Isabel Cristina Pérez-Verona, Mirco Tribastone
Exact maximal reduction of stochastic reaction networks by species lumping. 2175-2182 - Yuanyuan Han, Lan Huang, Fengfeng Zhou
A dynamic recursive feature elimination framework (dRFE) to further refine a set of OMIC biomarkers. 2183-2189 - Kishlay Jha
Continual representation learning for evolving biomedical bipartite networks. 2190-2197 - Phuc-Loi Luu
MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection. 2198-2200 - Jiannan Liu, Chuanpeng Dong, Yunlong Liu, Huanmei Wu
CGPE: an integrated online server for Cancer Gene and Pathway Exploration. 2201-2202 - Markus Hiltunen
ARBitR: an overlap-aware genome assembly scaffolder for linked reads. 2203-2205 - Diogo B. Lima
ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment. 2206-2208 - Yan Gao
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band. 2209-2211 - Ming Tang, Yasin Kaymaz
Evaluating single-cell cluster stability using the Jaccard similarity index. 2212-2214 - Hannes P. Eggertsson, Bjarni V. Halldórsson
read_haps: using read haplotypes to detect same species contamination in DNA sequences. 2215-2217 - Carl Beuchel, Holger Kirsten
Metabolite-Investigator: an integrated user-friendly workflow for metabolomics multi-study analysis. 2218-2220 - Zhuohang Yu, Zengrui Wu
MetaADEDB 2.0: a comprehensive database on adverse drug events. 2221-2222 - A. Sina Booeshaghi
Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x). 2223-2224
Volume 37, Number 16, August 2021
- Divon Lan
Genozip: a universal extensible genomic data compressor. 2225-2230 - Hai Yang
Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data. 2231-2237 - Wencan Zhu
A variable selection approach for highly correlated predictors in high-dimensional genomic data. 2238-2244 - Zachary F. Gerring
E-MAGMA: an eQTL-informed method to identify risk genes using genome-wide association study summary statistics. 2245-2249 - Balaram Bhattacharyya
Tandem repeat interval pattern identifies animal taxa. 2250-2258 - Sheng-Mao Chang
Gene-set integrative analysis of multi-omics data using tensor-based association test. 2259-2265 - Tizian Schulz
Detecting high-scoring local alignments in pangenome graphs. 2266-2274 - Daniele Raimondi
A novel method for data fusion over entity-relation graphs and its application to protein-protein interaction prediction. 2275-2281 - Denisa Bojkova
Differentially conserved amino acid positions may reflect differences in SARS-CoV-2 and SARS-CoV behaviour. 2282-2288 - Bennett J. Kapili
PPIT: an R package for inferring microbial taxonomy from nifH sequences. 2289-2298 - Jérémy Charlier, Robert Nadon, Vladimir Makarenkov
Accurate deep learning off-target prediction with novel sgRNA-DNA sequence encoding in CRISPR-Cas9 gene editing. 2299-2307 - Yang Lin
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning. 2308-2316 - Payam Dibaeinia, Shayan Tabe-Bordbar, Tandy J. Warnow
FASTRAL: improving scalability of phylogenomic analysis. 2317-2324 - Jacob L. Steenwyk
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. 2325-2331 - Ilia Igashov
VoroCNN: deep convolutional neural network built on 3D Voronoi tessellation of protein structures. 2332-2339 - Xuefeng Du, Haohan Wang, Zhenxi Zhu, Xiangrui Zeng, Yi-Wei Chang
Active learning to classify macromolecular structures in situ for less supervision in cryo-electron tomography. 2340-2346 - Ashleigh C. Myall
An OMICs-based meta-analysis to support infection state stratification. 2347-2355 - Davide Risso
Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles. 2356-2364 - Valentin Junet
CuBlock: a cross-platform normalization method for gene-expression microarrays. 2365-2373 - Jinjin Tian
ESCO: single cell expression simulation incorporating gene co-expression. 2374-2381 - Darawan Rinchai
BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R. 2382-2389 - Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
d-PBWT: dynamic positional Burrows-Wheeler transform. 2390-2397 - Olga Lazareva, Stefan Canzar
BiCoN: network-constrained biclustering of patients and omics data. 2398-2404 - So Yeon Kim, Eun Kyung Choe, Manu K. Shivakumar
Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer. 2405-2413 - Meet Barot
NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity. 2414-2422 - Yahui Long
Graph contextualized attention network for predicting synthetic lethality in human cancers. 2432-2440 - Martin Pirkl
Inferring perturbation profiles of cancer samples. 2441-2449 - Sachin Heerah
Granger-causal testing for irregularly sampled time series with application to nitrogen signalling in Arabidopsis. 2450-2460 - Liam F. Spurr
Quantification of aneuploidy in targeted sequencing data using ASCETS. 2461-2463 - Travis N. Mavrich, Christian Gauthier
pdm_utils: a SEA-PHAGES MySQL phage database management toolkit. 2464-2466 - Hue V. Reardon
AVIA 3.0: interactive portal for genomic variant and sample level analysis. 2467-2469 - Wenbin Ye
movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples. 2470-2472 - Cameron L. M. Gilchrist
clinker & clustermap.js: automatic generation of gene cluster comparison figures. 2473-2475 - Mikko Rautiainen
MBG: Minimizer-based sparse de Bruijn Graph construction. 2476-2478 - Benjamin Crysup
ProDerAl: reference position dependent alignment. 2479-2480 - Santi Santichaivekin, Qing Yang, Jingyi Liu
eMPRess: a systematic cophylogeny reconciliation tool. 2481-2482 - Bruck Taddese
Bios2cor: an R package integrating dynamic and evolutionary correlations to identify functionally important residues in proteins. 2483-2484 - José Alquicira-Hernández
Nebulosa recovers single-cell gene expression signals by kernel density estimation. 2485-2487 - Julia Yan, Nick Patterson, Vagheesh Narasimhan
miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization. 2488-2490 - Xudong Han
SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs. 2491-2493 - Vitor Pereira
MEWpy: a computational strain optimization workbench in Python. 2494-2496 - Xiaoyu Liang
i2d: an R package for simulating data from images and the implications in biomedical research. 2497-2498 - Abeed Sarker
LexExp: a system for automatically expanding concept lexicons for noisy biomedical texts. 2499-2501 - Haizi Zheng
FinaleDB: a browser and database of cell-free DNA fragmentation patterns. 2502-2503 - Gubbi Vani HarshaRani, S. Moza
SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches. 2504-2505
Volume 37, Number Supplement 1, August 2021
- Christiana N. Fogg, Diane E. Kovats, Martin Vingron:
ISCB Honors 2021 Award Recipients Peer Bork, Barbara Engelhardt, Ben Raphael, Teresa Attwood. 1-6 - Christophe Dessimoz
ISMB/ECCB 2021 proceedings. 7-8 - Sanna Abrahamsson
Comparison of online learning designs during the COVID-19 pandemic within bioinformatics courses in higher education. 9-15 - Shion Hosoda
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model. 16-24 - Jiayu Shang
Bacteriophage classification for assembled contigs using graph convolutional network. 25-33 - Yancong Zhang
Statistical approaches for differential expression analysis in metatranscriptomics. 34-41 - Omid Bazgir, Souparno Ghosh, Ranadip Pal
Investigation of REFINED CNN ensemble learning for anti-cancer drug sensitivity prediction. 42-50 - Ziyang Wei, Shuqin Zhang
CALLR: a semi-supervised cell-type annotation method for single-cell RNA sequencing data. 51-66 - Dillon Aberasturi, Nima Pouladi, Samir Rachid Zaim
'Single-subject studies'-derived analyses unveil altered biomechanisms between very small cohorts: implications for rare diseases. 67-75 - Rafael Peres da Silva, Chayaporn Suphavilai, Niranjan Nagarajan
TUGDA: task uncertainty guided domain adaptation for robust generalization of cancer drug response prediction from in vitro to in vivo settings. 76-83 - Tiago Pereira
Optimizing blood-brain barrier permeation through deep reinforcement learning for de novo drug design. 84-92 - Tianduanyi Wang, Sándor Szedmák
Modeling drug combination effects via latent tensor reconstruction. 93-101 - Qiqing Tao, Jose Barba-Montoya, Sudhir Kumar
Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies. 102-110 - Wei Wang
Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited. 111-119 - Yoann Anselmetti, Nadia El-Mabrouk, Manuel Lafond, Aïda Ouangraoua:
Gene tree and species tree reconciliation with endosymbiotic gene transfer. 120-132 - Chaitanya Aluru, Mona Singh
Improved inference of tandem domain duplications. 133-141 - Erin K. Molloy
Advancing admixture graph estimation via maximum likelihood network orientation. 142-150 - Ziye Tao, Griffin M. Weber
Expected 10-anonymity of HyperLogLog sketches for federated queries of clinical data repositories. 151-160 - Diyue Bu, XiaoFeng Wang, Haixu Tang:
Haplotype-based membership inference from summary genomic data. 161-168 - Daniel Danciu, Mikhail Karasikov, Harun Mustafa
Topology-based sparsification of graph annotations. 169-176 - Jamshed Khan
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections. 177-186 - Hongyu Zheng, Carl Kingsford, Guillaume Marçais:
Sequence-specific minimizers via polar sets. 187-195 - Tatiana Dvorkina, Olga Kunyavskaya, Andrey V. Bzikadze, Ivan V. Alexandrov, Pavel A. Pevzner:
CentromereArchitect: inference and analysis of the architecture of centromeres. 196-204 - Yutong Qiu
Constructing small genome graphs via string compression. 205-213 - Leah L. Weber
doubletD: detecting doublets in single-cell DNA sequencing data. 214-221 - Daiyun Huang
Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data. 222-230 - Zeyuan Zuo, Liu Cao
MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition. 231-236 - Anna Weber
TITAN: T-cell receptor specificity prediction with bimodal attention networks. 237-244 - Joris Cadow
On the feasibility of deep learning applications using raw mass spectrometry data. 245-253 - Peiyuan Feng, Jianyang Zeng, Jianzhu Ma:
Predicting MHC-peptide binding affinity by differential boundary tree. 254-261 - Ronghui You, Shuwei Yao, Hiroshi Mamitsuka
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. 262-271 - Yangyang Hu, Wenxiu Ma
EnHiC: learning fine-resolution Hi-C contact maps using a generative adversarial framework. 272-279 - Zhanlin Chen, Jing Zhang, Jason Liu
DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays. 280-288 - Jyun-Yu Jiang, Chelsea J.-T. Ju, Junheng Hao, Muhao Chen
JEDI: circular RNA prediction based on junction encoders and deep interaction among splice sites. 289-298 - Shengquan Chen
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. 299-307 - Salma Sohrabi-Jahromi, Johannes Söding:
Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins. 308-316 - Yingxin Cao, Laiyi Fu
SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration. 317-326 - Sapir Margalit, Yotam Abramson, Hila Sharim, Zohar Manber, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Hayk Barseghyan, Ran Elkon, Roded Sharan, Yuval Ebenstein:
Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution. 327-333 - Laura H. Tung, Carl Kingsford:
Practical selection of representative sets of RNA-seq samples using a hierarchical approach. 334-341 - Victoria R. Li, Zijun Zhang, Olga G. Troyanskaya
CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes. 342-348 - Alexander P. Wu, Jian Peng, Bonnie Berger
Bayesian information sharing enhances detection of regulatory associations in rare cell types. 349-357 - Dongyuan Song, Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li:
scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling. 358-366 - Anushua Biswas, Leelavati Narlikar:
Resolving diverse protein-DNA footprints from exonuclease-based ChIP experiments. 367-375 - Gwanghoon Jang, Sungjoon Park, Sanghoon Lee, Sunkyu Kim
Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding. 376-382 - Hung-Cuong Trinh, Yung-Keun Kwon:
A novel constrained genetic algorithm-based Boolean network inference method from steady-state gene expression data. 383-391 - Jakob L. Andersen
Graph transformation for enzymatic mechanisms. 392-400 - Julien Martinelli, Sandrine Dulong, Xiao-Mei Li, Michèle Teboul, Sylvain Soliman, Francis Lévi, François Fages, Annabelle Ballesta:
Model learning to identify systemic regulators of the peripheral circadian clock. 401-409 - Juan Shu, Yu Li, Sheng Wang, Bowei Xi, Jianzhu Ma:
Disease gene prediction with privileged information and heteroscedastic dropout. 410-417 - Shike Wang, Fan Xu, Yunyang Li
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers. 418-425 - Marwan Abdellah, Alessandro Foni, Eleftherios Zisis
Metaball skinning of synthetic astroglial morphologies into realistic mesh models for in silico simulations and visual analytics. 426-433 - Yang Young Lu, Jeff A. Bilmes, Ricard A. Rodriguez-Mias, Judit Villén, William Stafford Noble:
DIAmeter: matching peptides to data-independent acquisition mass spectrometry data. 434-432 - Jung Hun Oh
PathCNN: interpretable convolutional neural networks for survival prediction and pathway analysis applied to glioblastoma. 443-450 - Trevor S. Frisby
Asynchronous parallel Bayesian optimization for AI-driven cloud laboratories. 451-459 - Chirag Jain, Neda Tavakoli, Srinivas Aluru:
A variant selection framework for genome graphs. 460-467 - Pengyuan Li
Utilizing image and caption information for biomedical document classification. 468-476 - Haowen Zhang
Real-time mapping of nanopore raw signals. 477-483
Volume 37, Number 17, September 2021
- Fan Yang, Kevin J. Gleason
CCmed: cross-condition mediation analysis for identifying replicable trans-associations mediated by cis-gene expression. 2513-2520 - Mandar S. Chaudhary
NIBNA: a network-based node importance approach for identifying breast cancer drivers. 2521-2528 - Manisha Panta, Avdesh Mishra, Md. Tamjidul Hoque
ClassifyTE: a stacking-based prediction of hierarchical classification of transposable elements. 2529-2536 - Amir Bahmani
Hummingbird: efficient performance prediction for executing genomic applications in the cloud. 2537-2543 - Raghvendra Mall
A modeling framework for embedding-based predictions for compound-viral protein activity. 2544-2555 - Phasit Charoenkwan, Chanin Nantasenamat, Md. Mehedi Hasan
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides. 2556-2562 - Johan Nyström-Persson, Gabriel Keeble-Gagnère, Niamat Zawad:
Compact and evenly distributed k-mer binning for genomic sequences. 2563-2569 - Debby Dan Wang
Proteo-chemometrics interaction fingerprints of protein-ligand complexes predict binding affinity. 2570-2579 - Bowen Dai, Chris Bailey-Kellogg
Protein interaction interface region prediction by geometric deep learning. 2580-2588 - Jaswinder Singh
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning. 2589-2600 - Isabelle Bichindaritz, Guanghui Liu
Integrative survival analysis of breast cancer with gene expression and DNA methylation data. 2601-2608 - Estefania Mancini
ASpli: integrative analysis of splicing landscapes through RNA-Seq assays. 2609-2616 - Calvin Chi
Bipartite graph-based approach for clustering of cell lines by gene expression-drug response associations. 2617-2626 - Zihan Cui, Yuhang Liu, Jinfeng Zhang
Super-delta2: an enhanced differential expression analysis procedure for multi-group comparisons of RNA-seq data. 2627-2636 - Zihao Zheng
MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing. 2637-2643 - Alma Andersson, Joakim Lundeberg:
sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling. 2644-2650 - Yujie Chen, Tengfei Ma, Xixi Yang, Jianmin Wang
MUFFIN: multi-scale feature fusion for drug-drug interaction prediction. 2651-2658 - Ferhat Alkan
Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq. 2659-2667 - Abdullah Çaglar Öksüz, Erman Ayday, Ugur Güdükbay:
Privacy-preserving and robust watermarking on sequential genome data using belief propagation and local differential privacy. 2668-2674 - Chih-Hsu Lin
Using interpretable deep learning to model cancer dependencies. 2675-2681 - Wen Liu, Xiang Li, Hong Qi, Yuning Wu, Jing Qu, Zhiyong Yin, Xuejuan Gao, Aidong Han, Jianwei Shuai
Biphasic regulation of transcriptional surge generated by the gene feedback loop in a two-component system. 2682-2690 - Sorin Draghici
COVID-19: disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases. 2691-2698 - Yufei Li
Knowledge enhanced LSTM for coreference resolution on biomedical texts. 2699-2705 - Régis Ongaro-Carcy, Marie-Pier Scott-Boyer, Adrien Dessemond, François Belleau, Mickaël Leclercq, Olivier Périn, Arnaud Droit
KibioR & Kibio: a new architecture for next-generation data querying and sharing in big biology. 2706-2713 - Cansu Alakus, Denis Larocque
Conditional canonical correlation estimation based on covariates with random forests. 2714-2721 - Wang Liu-Wei
DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes. 2722-2729 - Lekha Patel
Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM). 2730-2737 - Alexis Hardy, Mélody Matelot, Amandine Touzeau, Christophe Klopp, Céline Lopez-Roques
DNAModAnnot: a R toolbox for DNA modification filtering and annotation. 2738-2740 - Yixin Guo, Ziwei Xue
RAD: a web application to identify region associated differentially expressed genes. 2741-2743 - Chen Cao
WgLink: reconstructing whole-genome viral haplotypes using L0+L1-regularization. 2744-2746 - Sandra Dérozier
Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations. 2747-2749 - Benjamin Hepp, Violette Da Cunha
BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence. 2750-2752 - Alexander Senf
Crypt4GH: a file format standard enabling native access to encrypted data. 2753-2754 - Marek Schwarz, Jirí Vohradský, Josef Pánek:
rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output. 2755-2756 - Kang Hu, Neng Huang, You Zou, Xingyu Liao
MultiNanopolish: refined grouping method for reducing redundant calculations in Nanopolish. 2757-2760 - David Roura Padrosa
CapiPy: python-based GUI-application to assist in protein immobilization. 2761-2762 - Filomeno Sánchez Rodríguez
ConPlot: web-based application for the visualization of protein contact maps integrated with other data. 2763-2765 - Tomasz Zok
BioCommons: a robust java library for RNA structural bioinformatics. 2766-2767 - Rob Marissen
mzRecal: universal MS1 recalibration in mzML using identified peptides in mzIdentML as internal calibrants. 2768-2769 - Hélène Borges
Well Plate Maker: a user-friendly randomized block design application to limit batch effects in large-scale biomedical studies. 2770-2771 - Di Wang, Zheng Jing
Cox-nnet v2.0: improved neural-network-based survival prediction extended to large-scale EMR data. 2772-2774 - Michael A. Skinnider, Charley Cai, R. Greg Stacey
PrInCE: an R/Bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data. 2775-2777 - Jonas Förster
CoRC: the COPASI R Connector. 2778-2779 - Zachary B. Abrams
Mercator: a pipeline for multi-method, unsupervised visualization and distance generation. 2780-2781 - Tobias Pietzsch, Lorenzo Duso
Compartor: a toolbox for the automatic generation of moment equations for dynamic compartment populations. 2782-2784 - Ewelina Weglarz-Tomczak
M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models. 2785-2786 - Richard M. Jiang, Bruno Jacob
Epidemiological modeling in StochSS Live! 2787-2788 - Raphael Sonabend
mlr3proba: an R package for machine learning in survival analysis. 2789-2791 - Leon Weber, Mario Sänger
HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition. 2792-2794 - Shih-Chi Su, James E. Galvin, Shun-Fa Yang, Wen-Hung Chung, Lun-Ching Chang
wiSDOM: a visual and statistical analytics for interrogating microbiome. 2795-2797 - Quentin Lamy-Besnier
Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions. 2798-2801
Volume 37, Number 18, September 2021
- Cédric Arisdakessian
CoCoNet: an efficient deep learning tool for viral metagenome binning. 2803-2810 - Mihai Lefter
Mutalyzer 2: next generation HGVS nomenclature checker. 2811-2817 - Zhenxing Guo, Andrew M. Shafik
Detecting m6A methylation regions from Methylated RNA Immunoprecipitation Sequencing. 2818-2824 - Yue Cao, Yang Shen
TALE: Transformer-based protein function Annotation with joint sequence-Label Embedding. 2825-2833 - Timothy L. Bailey
STREME: accurate and versatile sequence motif discovery. 2834-2840 - Haochen Zhao
A convolutional neural network and graph convolutional network-based method for predicting the classification of anatomical therapeutic chemicals. 2841-2847 - Seth Commichaux
A critical assessment of gene catalogs for metagenomic analysis. 2848-2857 - Camille Marchet
BLight: efficient exact associative structure for k-mers. 2858-2865 - Victor Rossier
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. 2866-2873 - Filip Ljung
ZEAL: protein structure alignment based on shape similarity. 2874-2881 - Antti Häkkinen
PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples. 2882-2888 - Andrea Blasco, Ted Natoli, Michael G. Endres
Improving deconvolution methods in biology through open innovation competitions: an application to the connectivity map. 2889-2895 - Alain J. Mbebi
L2, 1-norm regularized multivariate regression model with applications to genomic prediction. 2896-2904 - Juan A. Sánchez, Ana L. Gil-Martinez, Alejandro Cisterna
Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights. 2905-2911 - Sylwester Kloska
Queueing theory model of Krebs cycle. 2912-2919 - Junliang Shang
Multiscale part mutual information for quantifying nonlinear direct associations in networks. 2920-2929 - Chen Cui, Xiaoyu Ding, Dingyan Wang, Lifan Chen
Drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug-drug links based on graph neural network. 2930-2937 - Mattia G. Gollub
Probabilistic thermodynamic analysis of metabolic networks. 2938-2945 - Joel Dokmegang
Quantification of cell behaviors and computational modeling show that cell directional behaviors drive zebrafish pectoral fin morphogenesis. 2946-2954 - Sunjoo Bang
Polypharmacy side-effect prediction with enhanced interpretability based on graph feature attention network. 2955-2962 - Zhiqin Wang
GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction. 2963-2970 - Jaesik Kim
HiG2Vec: hierarchical representations of Gene Ontology and genes in the Poincaré ball. 2971-2980 - Ziqiao Zhang, Jihong Guan, Shuigeng Zhou
FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction. 2981-2987 - Yue Yu, Kexin Huang
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization. 2988-2995 - Dejun Lin, Justin Sanders, William Stafford Noble
HiCRep.py: fast comparison of Hi-C contact matrices in Python. 2996-2997 - Shaoke Lou, Tianxiao Li
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization. 2998-3000 - Jun-Yu Li, Wei-Xuan Li
MitoFlex: an efficient, high-performance toolkit for animal mitogenome assembly, annotation and visualization. 3001-3003 - Kimberly E. Taylor
PICS2: next-generation fine mapping via probabilistic identification of causal SNPs. 3004-3007 - Quirin Manz
ASimulatoR: splice-aware RNA-Seq data simulation. 3008-3010 - Guanjue Xiang
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. 3011-3013 - Christopher Wilks
Megadepth: efficient coverage quantification for BigWigs and BAMs. 3014-3016 - Andrew P. Boughton
LocusZoom.js: interactive and embeddable visualization of genetic association study results. 3017-3018 - Urminder Singh
orfipy: a fast and flexible tool for extracting ORFs. 3019-3020 - Sung-Joon Park
OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data. 3021-3022 - Xavier Bofill-De Ros
Tumor IsomiR Encyclopedia (TIE): a pan-cancer database of miRNA isoforms. 3023-3025 - Chi Song, Shih-Chi Su, Zhiguang Huo, Suleyman Vural, James E. Galvin, Lun-Ching Chang
HCMMCNVs: hierarchical clustering mixture model of copy number variants detection using whole exome sequencing technology. 3026-3028 - Milot Mirdita
Fast and sensitive taxonomic assignment to metagenomic contigs. 3029-3031 - Benjamin D. Redelings
Bali-Phy version 3: model-based co-estimation of alignment and phylogeny. 3032-3034 - Louise U. Kurt
Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition. 3035-3037 - Atilio O. Rausch
FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations. 3038-3040 - Woonghee Lee
POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules. 3041-3042 - Nour-al-dain Marzouka
multiclassPairs: an R package to train multiclass pair-based classifier. 3043-3044 - Yuzhou Chang
IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis. 3045-3047 - Aaron Graubert
RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts. 3048-3050 - Lucy Sinke
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies. 3051-3052 - William Goh, Marek Mutwil
LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life. 3053-3055 - Christopher Jürges
Integrative transcription start site identification with iTiSS. 3056-3057 - Irzam Sarfraz
ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects. 3058-3060 - Nora Scherer
pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS. 3061-3063 - Vishnuvardhan Mahamkali, Tim McCubbin
multiTFA: a Python package for multi-variate thermodynamics-based flux analysis. 3064-3066 - Anastasiya Belyaeva
DCI: learning causal differences between gene regulatory networks. 3067-3069 - Siddharth Annaldasula, Martyna Gajos
IsoTV: processing and visualizing functional features of translated transcript isoforms. 3070-3072 - Mingyang Ren
HeteroGGM: an R package for Gaussian graphical model-based heterogeneity analysis. 3073-3074 - Zhenjia Wang, Yifan Zhang, Chongzhi Zang
BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data. 3075-3078 - Christian Tischer, Ashis Ravindran, Sabine Reither
BigDataProcessor2: a free and open-source Fiji plugin for inspection and processing of TB sized image data. 3079-3081 - Callum Arthurs
QuArray: an application for tissue array whole slide image export and signal analysis. 3082-3083 - Garrett Winkelmaier, Bahram Parvin:
An enhanced loss function simplifies the deep learning model for characterizing the 3D organoid models. 3084-3085 - Qingjie Zhu, Yi Shao, Zhicheng Wang, Xingjun Chen, Chunqiong Li, Zihan Liang, Mingyue Jia, Qingchun Guo, Hu Zhao
DeepS: a web server for image optical sectioning and super resolution microscopy based on a deep learning framework. 3086-3087 - Friedrich Preusser
FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids. 3088-3090
Volume 37, Number 19, October 2021
- Ciara Frances Loughrey
The topology of data: opportunities for cancer research. 3091-3098 - Linjing Liu
Early cancer detection from genome-wide cell-free DNA fragmentation via shuffled frog leaping algorithm and support vector machine. 3099-3105 - Shenghua He, Chunfeng Lian, Wade Thorstad, Hiram Gay, Yujie Zhao, Su Ruan, Xiaowei Wang
A novel systematic approach for cancer treatment prognosis and its applications in oropharyngeal cancer with microRNA biomarkers. 3106-3114 - Daniel Cameron
VIRUSBreakend: Viral Integration Recognition Using Single Breakends. 3115-3119 - Neng Huang, Fan Nie, Peng Ni, Feng Luo
NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks. 3120-3127 - Julia Markowski
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. 3128-3135 - Jaeho Jeong
Cooperative sequence clustering and decoding for DNA storage system with fountain codes. 3136-3143 - Michael Apostolides
MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates. 3144-3151 - Fengyuan Hu
ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes. 3152-3159 - Zheng Dai, Brooke D. Huisman, Haoyang Zeng, Brandon Carter, Siddhartha Jain, Michael E. Birnbaum
Machine learning optimization of peptides for presentation by class II MHCs. 3160-3167 - Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Aashish Jain, Yuki Kagaya, Daisuke Kihara
Protein contact map refinement for improving structure prediction using generative adversarial networks. 3168-3174 - Chloé Quignot, Pierre Granger, Pablo Chacón
Atomic-level evolutionary information improves protein-protein interface scoring. 3175-3181 - Noelia Ferruz
Protlego: a Python package for the analysis and design of chimeric proteins. 3182-3189 - Zhiye Guo, Tianqi Wu
Improving deep learning-based protein distance prediction in CASP14. 3190-3196 - Jin Li, Jinbo Xu
Study of real-valued distance prediction for protein structure prediction with deep learning. 3197-3203 - Roman Schefzik, Julian Flesch, Ângela Gonçalves:
Fast identification of differential distributions in single-cell RNA-sequencing data with waddR. 3204-3211 - Shahin Boluki
Optimal Bayesian supervised domain adaptation for RNA sequencing data. 3212-3219 - Alexander Gerniers
MicroCellClust: mining rare and highly specific subpopulations from single-cell expression data. 3220-3227 - Yixuan Qiu
Identification of cell-type-specific marker genes from co-expression patterns in tissue samples. 3228-3234 - Qinglin Mei, Guojun Li
Clustering single-cell RNA-seq data by rank constrained similarity learning. 3235-3242 - Andrew L. Thurman
Differential gene expression analysis for multi-subject single-cell RNA-sequencing studies with aggregateBioVar. 3243-3251 - Raktim Mitra
RVAgene: generative modeling of gene expression time series data. 3252-3262 - Jinglong Zhang
MAT2: manifold alignment of single-cell transcriptomes with cell triplets. 3263-3269 - Ziyang Ma, Jeongyoun Ahn
Feature-weighted ordinal classification for predicting drug response in multiple myeloma. 3270-3276 - Anastasia Ignatieva
KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation. 3277-3284 - Vu Viet Hoang Pham
pDriver: a novel method for unravelling personalized coding and miRNA cancer drivers. 3285-3292 - Ruby Sharma, Sajal Kumar
Fundamental gene network rewiring at the second order within and across mammalian systems. 3293-3301 - Hang Wei
iCircDA-LTR: identification of circRNA-disease associations based on Learning to Rank. 3302-3310 - Vinay Srinivas Bharadhwaj, Mehdi Ali
CLEP: a hybrid data- and knowledge-driven framework for generating patient representations. 3311-3318 - Saifur Rahaman
CancerEMC: frontline non-invasive cancer screening from circulating protein biomarkers and mutations in cell-free DNA. 3319-3327 - Lizhi Liu
HPOFiller: identifying missing protein-phenotype associations by graph convolutional network. 3328-3336 - Bill Lee
Alignment free sequence comparison methods and reservoir host prediction. 3337-3342 - Benjamin M. Good, Kimberly Van Auken, David P. Hill, Huaiyu Mi, Seth Carbon, James P. Balhoff, Laurent-Philippe Albou
Reactome and the Gene Ontology: digital convergence of data resources. 3343-3348 - Pavel Beran
KEC: unique sequence search by K-mer exclusion. 3349-3350 - Qiang Hu, Alan David Hutson, Song Liu, Martin Morgan, Qian Liu:
Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines. 3351-3352 - Alejandra Cervera
FUNGI: FUsioN Gene Integration toolset. 3353-3355 - Christina Gros
ASHLEYS: automated quality control for single-cell Strand-seq data. 3356-3357 - Sebastian Deorowicz
VCFShark: how to squeeze a VCF file. 3358-3360 - Xiaolong Cao, Jinchuan Xing
PrecisionProDB: improving the proteomics performance for precision medicine. 3361-3363 - Ruoshi Zhang
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. 3364-3366 - Justine C. Williams, Subha Kalyaanamoorthy
PoseFilter: a PyMOL plugin for filtering and analyzing small molecule docking in symmetric binding sites. 3367-3368 - Olivier Mailhot
The NRGTEN Python package: an extensible toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules and their complexes. 3369-3371 - Ruhollah Shemirani
EPS: automated feature selection in case-control studies using extreme pseudo-sampling. 3372-3373 - John F. Ouyang
ShinyCell: simple and sharable visualization of single-cell gene expression data. 3374-3376 - Renming Liu, Arjun Krishnan
PecanPy: a fast, efficient and parallelized Python implementation of node2vec. 3377-3379 - Imran Shah
Generalized Read-Across prediction using genra-py. 3380-3381 - Da Kuang
MaveRegistry: a collaboration platform for multiplexed assays of variant effect. 3382-3383 - Yan Gao
Erratum to: abPOA: an SIMD-based C library for fast partial order alignment using adaptive band. 3384 - Alexey Ovchinnikov, Isabel Cristina Pérez-Verona, Gleb Pogudin, Mirco Tribastone:
CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations. 3385 - Jia-Bin Chen, Shan-Shan Dong, Shi Yao
Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression. 3386 - Valentine U. Nlebedim
Corrigendum to: Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries. 3387 - Anton Pirogov, Peter Pfaffelhuber, Angelika Börsch-Haubold, Bernhard Haubold:
High-complexity regions in mammalian genomes are enriched for developmental genes. 3388 - Pengyuan Li
Corrigendum to: Utilizing image and caption information for biomedical document classification. 3389
Volume 37, Number 20, October 2021
- Michal Vasinek
Determining optical mapping errors by simulations. 3391-3397 - Jakub Savara
Comparison of structural variants detected by optical mapping with long-read next-generation sequencing. 3398-3404 - Jiuxing Liang, Zifeng Cui, Canbiao Wu
DeepEBV: a deep learning model to predict Epstein-Barr virus (EBV) integration sites. 3405-3411 - Abhijit Chakraborty, Ferhat Ay
ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs. 3412-3420 - Qingzhen Hou
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes. 3421-3427 - QHwan Kim, Joon-Hyuk Ko, Sunghoon Kim
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction. 3428-3435 - Jianwei Hong, Ruitian Gao, Yang Yang
CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks. 3436-3443 - Felix Mölder
Rapid T-cell receptor interaction grouping with ting. 3444-3448 - Maria Littmann
Clustering FunFams using sequence embeddings improves EC purity. 3449-3455 - Andrew F. Neuwald
eCOMPASS: evaluative comparison of multiple protein alignments by statistical score. 3456-3463 - Jaspreet Singh
SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning. 3464-3472 - Daniele Raimondi
In silico prediction of in vitro protein liquid-liquid phase separation experiments outcomes with multi-head neural attention. 3473-3479 - Jiahua He
Full-length de novo protein structure determination from cryo-EM maps using deep learning. 3480-3490 - Martin Rydén
ProteoMill: efficient network-based functional analysis portal for proteomics data. 3491-3493 - Tongchuan Zhang
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis. 3494-3500 - Jon E. T. Jakobsson
scConnect: a method for exploratory analysis of cell-cell communication based on single-cell RNA-sequencing data. 3501-3508 - Guangzheng Weng
VeTra: a tool for trajectory inference based on RNA velocity. 3509-3513 - Kenneth E. Westerman, Duy T. Pham, Liang Hong, Ye Chen
GEM: scalable and flexible gene-environment interaction analysis in millions of samples. 3514-3520 - Sahar Ghasemi, Alexander Teumer
Assessment of significance of conditionally independent GWAS signals. 3521-3529 - Felix M. Weidner
Capturing dynamic relevance in Boolean networks using graph theoretical measures. 3530-3537 - Huangqingbo Sun
Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery. 3538-3545 - Giuseppe Magazzù, Guido Zampieri
Multimodal regularized linear models with flux balance analysis for mechanistic integration of omics data. 3546-3552 - Deniz Seçilmis
Inferring the experimental design for accurate gene regulatory network inference. 3553-3559 - Jasmin Hafner
NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs. 3560-3568 - Maidi Liu
MANIEA: a microbial association network inference method based on improved Eclat association rule mining algorithm. 3569-3578 - Yang Li
Evaluating disease similarity based on gene network reconstruction and representation. 3579-3587 - Ali Rahnavard
Omics community detection using multi-resolution clustering. 3588-3594 - Cesaré Ovando-Vázquez, Daniel Cázarez-García, Robert Winkler
Target-Decoy MineR for determining the biological relevance of variables in noisy datasets. 3595-3603 - Krutik Patel
TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis. 3604-3609 - Ming Liang
A combined recall and rank framework with online negative sampling for Chinese procedure terminology normalization. 3610-3617 - Chang Sun
Autoencoder-based drug-target interaction prediction by preserving the consistency of chemical properties and functions of drugs. 3618-3625 - Michelle Saul
Family Rank: a graphical domain knowledge informed feature ranking algorithm. 3626-3631 - Dominik Stallmann
Towards an automatic analysis of CHO-K1 suspension growth in microfluidic single-cell cultivation. 3632-3639 - Aojie Lian, James Guevara, Kun Xia, Jonathan Sebat:
Customized de novo mutation detection for any variant calling pipeline: SynthDNM. 3640-3641 - Zhe Cui
interacCircos: an R package based on JavaScript libraries for the generation of interactive circos plots. 3642-3644 - Zhemin Zhou
HierCC: a multi-level clustering scheme for population assignments based on core genome MLST. 3645-3646 - Yadong Liu
SKSV: ultrafast structural variation detection from circular consensus sequencing reads. 3647-3649 - Ales Varabyou
TieBrush: an efficient method for aggregating and summarizing mapped reads across large datasets. 3650-3651 - Judith Neukamm
DamageProfiler: fast damage pattern calculation for ancient DNA. 3652-3653 - Travis J. Lawrence
tSFM 1.0: tRNA Structure-Function Mapper. 3654-3656 - She Zhang
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python. 3657-3659 - Maxie Dion Schmidt, Anna Kirkpatrick, Christine E. Heitsch
RNAStructViz: graphical base pairing analysis. 3660-3661 - Justyna Krys
VisuaLife: library for interactive visualization in rich web applications. 3662-3663 - Kieran Walsh, Akira Gokool
NeuroCirc: an integrative resource of circular RNA expression in the human brain. 3664-3666 - Haidong Yi
COBRAC: a fast implementation of convex biclustering with compression. 3667-3669 - Benbo Gao, Jing Zhu
Quickomics: exploring omics data in an intuitive, interactive and informative manner. 3670-3672 - Thimothée Virgoulay
GSpace: an exact coalescence simulator of recombining genomes under isolation by distance. 3673-3675 - Fabian Fröhlich
AMICI: high-performance sensitivity analysis for large ordinary differential equation models. 3676-3677 - Yasin El Abiead
mzRAPP: a tool for reliability assessment of data pre-processing in non-targeted metabolomics. 3678-3680 - Mengyu Xie, Kyubum Lee
TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures. 3681-3683 - Eliot Ragueneau
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis. 3684-3685 - Dong Xu, Zhuchou Lu, Kangming Jin, Wenmin Qiu, Guirong Qiao, Xiaojiao Han, Renying Zhuo
SPDE: a multi-functional software for sequence processing and data extraction. 3686-3687 - Vishnu Shankar
MassExplorer: a computational tool for analyzing desorption electrospray ionization mass spectrometry data. 3688-3690 - Mengyun Wu, Xing Qin, Shuangge Ma
GEInter: an R package for robust gene-environment interaction analysis. 3691-3692 - Momo Langenstein
A decoupled, modular and scriptable architecture for tools to curate data platforms. 3693-3694 - Mikolaj Rogalski
FPM app: an open-source MATLAB application for simple and intuitive Fourier ptychographic reconstruction. 3695-3696
Volume 37, Number 21, November 2021
- Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2020 ISCB Innovatory Award: Xiaole Shirley Liu. 3697-3698 - Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2020 ISCB accomplishments by a Senior Scientist Award: Steven Salzberg. 3699-3700 - Christiana N. Fogg, Diane E. Kovats, Ron Shamir:
2020 Outstanding contributions to ISCB award: Judith Blake. 3701 - Andreas Dräger
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. 3702-3706 - Divya Sharma
phyLoSTM: a novel deep learning model on disease prediction from longitudinal microbiome data. 3707-3714 - Bo Yang
Deep Subspace Mutual Learning for cancer subtypes prediction. 3715-3722 - Benjamin R. Weeder
pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification. 3723-3733 - Mahim Mahbub, Zahin Wahab, Rezwana Reaz, Mohammad Saifur Rahman
wQFM: highly accurate genome-scale species tree estimation from weighted quartets. 3734-3743 - Lewis Moffat
Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework. 3744-3751 - Lisha Ye, Peikun Wu, Zhenling Peng
Improved estimation of model quality using predicted inter-residue distance. 3752-3759 - Gen Li
SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions. 3760-3765 - Guilherme F. Bottino
Structural discrimination analysis for constraint selection in protein modeling. 3766-3773 - Chengchen Zhao
CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data. 3774-3780 - Tobias Tekath
Differential transcript usage analysis of bulk and single-cell RNA-seq data with DTUrtle. 3781-3787 - Nuha Bintayyash
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments. 3788-3795 - Alona Levy-Jurgenson
Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging. 3796-3804 - Gianna Serafina Monti
Sparse least trimmed squares regression with compositional covariates for high-dimensional data. 3805-3814 - Haixiang Zhang, Yinan Zheng, Lifang Hou, Cheng Zheng
Mediation analysis for survival data with high-dimensional mediators. 3815-3821 - Peter M. Bourke
Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR. 3822-3829 - Phorutai Pearngam
MHCVision: estimation of global and local false discovery rate for MHC class I peptide binding prediction. 3830-3838 - Alexandros Xenos
Linear functional organization of the omic embedding space. 3839-3847 - Rudan Xu, Zahra Razaghi-Moghadam
Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli. 3848-3855 - Zulfat Miftahutdinov, Artur Kadurin
Medical concept normalization in clinical trials with drug and disease representation learning. 3856-3864 - Jeremy J. Yang
TIGA: target illumination GWAS analytics. 3865-3873 - Jiaxuan Wangwu
scAMACE: model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation. 3874-3880 - Kerstin Lenhof
MERIDA: a novel Boolean logic-based integer linear program for personalized cancer therapy. 3881-3888 - Armin Rauschenberger
Predicting correlated outcomes from molecular data. 3889-3895 - Maxime Delmas
FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. 3896-3904 - Hongyi Duanmu
Foveal blur-boosted segmentation of nuclei in histopathology images with shape prior knowledge and probability map constraints. 3905-3913 - Elliot A. Hershberg
JBrowseR: an R interface to the JBrowse 2 genome browser. 3914-3915 - Sebastian Hollizeck
Custom workflows to improve joint variant calling from multiple related tumour samples: FreeBayesSomatic and Strelka2Pass. 3916-3919 - Evin M. Padhi, Jeffrey K. Ng, Elvisa Mehinovic, Eleanor I Sams, Tychele Turner
ACES: Analysis of Conservation with an Extensive list of Species. 3920-3922 - Felix Hanau
mspack: efficient lossless and lossy mass spectrometry data compression. 3923-3925 - Yating Liu
utr.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation. 3926-3928 - Brandon K. B. Seah
BleTIES: annotation of natural genome editing in ciliates using long read sequencing. 3929-3931 - David Sundell
FlexTaxD: flexible modification of taxonomy databases for improved sequence classification. 3932-3933 - Sara Hetzel
RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data. 3934-3935 - Simon Lee
Prowler: a novel trimming algorithm for Oxford Nanopore sequence data. 3936-3937 - Anja Mösch
TCRpair: prediction of functional pairing between HLA-A*02: 01-restricted T-cell receptor α and β chains. 3938-3940 - Julian A. Liber
CONSTAX2: improved taxonomic classification of environmental DNA markers. 3941-3943 - Hiroshi Mori
PZLAST: an ultra-fast amino acid sequence similarity search server against public metagenomes. 3944-3946 - Thomas Haschka
MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences. 3947-3949 - Sreenath Nair
PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data. 3950-3952 - Fabio D. Steffen
FRETraj: integrating single-molecule spectroscopy with molecular dynamics. 3953-3955 - Burak T. Kaynak
ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution. 3956-3958 - John Lamb
pyconsFold: a fast and easy tool for modeling and docking using distance predictions. 3959-3960 - Dylan Kotliar
Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment. 3961-3963 - Ziheng Zou
HGC: fast hierarchical clustering for large-scale single-cell data. 3964-3965 - Xiayuan Huang
E-Pedigrees: a large-scale automatic family pedigree prediction application. 3966-3968 - Pol Castellano-Escuder
The fobitools framework: the first steps towards food enrichment analysis. 3969-3971 - Nicolas Ruffini
IntelliPy: a GUI for analyzing IntelliCage data. 3972-3973 - Almut Heinken
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations. 3974-3975 - Victor-Bogdan Popescu
NetControl4BioMed: a web-based platform for controllability analysis of protein-protein interaction networks. 3976-3978 - Juan Carlos Aledo
ptm: an R package for the study of methionine sulfoxidation and other posttranslational modifications. 3979-3980 - Piyush More
LipiDisease: associate lipids to diseases using literature mining. 3981-3982 - Miguel Roncoroni
A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. 3983-3985 - Yanan Wang, Litao Yang, Geoffrey I. Webb
OCTID: a one-class learning-based Python package for tumor image detection. 3986-3988 - Alexis Coullomb
Tysserand - fast and accurate reconstruction of spatial networks from bioimages. 3989-3991 - David R. Stirling
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis. 3992-3994 - Nita Mulliqi
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology. 3995-3997 - John S. H. Danial
DeepSinse: deep learning-based detection of single molecules. 3998-4000
Volume 37, Number 22, November 2021
- Claire Marks
Humanization of antibodies using a machine learning approach on large-scale repertoire data. 4041-4047 - Amnon Koren
TIGER: inferring DNA replication timing from whole-genome sequence data. 4001-4005 - Joachim Wolff
Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs. 4006-4013 - Yusha Liu, Keith A. Baggerly, Elias Orouji
Methylation-eQTL analysis in cancer research. 4014-4022 - Christoffer Flensburg, Alicia Oshlack, Ian J. Majewski
Detecting copy number alterations in RNA-Seq using SuperFreq. 4023-4032 - Chen Wang
Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family. 4033-4040 - Fatemeh Almodaresi
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index. 4048-4055 - Lukas Hübner
Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG. 4056-4063 - Alexey Markin
Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model. 4064-4074 - Wenze Ding
SAMF: a self-adaptive protein modeling framework. 4075-4082 - Cyril Malbranke
Improving sequence-based modeling of protein families using secondary-structure quality assessment. 4083-4090 - Chunman Zuo
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data. 4091-4099 - Stefano Mangiola
Interfacing Seurat with the R tidy universe. 4100-4107 - Yuantong Li
Peel learning for pathway-related outcome prediction. 4108-4114 - Yifei Shen
scDetect: a rank-based ensemble learning algorithm for cell type identification of single-cell RNA sequencing in cancer. 4115-4122 - Jared Brown
Normalization by distributional resampling of high throughput single-cell RNA-sequencing data. 4123-4128 - Qiwei Li
Bayesian modeling of spatial molecular profiling data via Gaussian process. 4129-4136 - Liangying Yin
A framework to decipher the genetic architecture of combinations of complex diseases: applications in cardiovascular medicine. 4137-4147 - Ruilin Li
Fast numerical optimization for genome sequencing data in population biobanks. 4148-4155 - Suvankar Halder
Bistability in cell signalling and its significance in identifying potential drug-targets. 4156-4163 - Abhinav Kaushik
CyAnno: a semi-automated approach for cell type annotation of mass cytometry datasets. 4164-4171 - Jun Cheng
BERTMHC: improved MHC-peptide class II interaction prediction with transformer and multiple instance learning. 4172-4179 - Kunal Kundu, Lindley Darden, John Moult
MecCog: a knowledge representation framework for genetic disease mechanism. 4180-4186 - Brian D. Williamson
Super LeArner Prediction of NAb Panels (SLAPNAP): a containerized tool for predicting combination monoclonal broadly neutralizing antibody sensitivity. 4187-4192 - Joon-Yong Lee
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry-mass spectrometry. 4193-4201 - Ahmed A. Zayed
efam: an expanded, metaproteome-supported HMM profile database of viral protein families. 4202-4208 - Tess Homan, Hélène Delanoë-Ayari, Albano C. Meli
MorphoScript: a dedicated analysis to assess the morphology and contractile structures of cardiomyocytes derived from stem cells. 4209-4215 - Aidan C. Daly
A convolutional neural network for common coordinate registration of high-resolution histology images. 4216-4226 - José Marcos Moreno-Cabrera
CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools. 4227-4229 - Luigi Grassi
DetectIS: a pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data. 4230-4232 - U. Stenzel, Susanne Horn
Bathometer: lightning fast depth-of-reads query. 4233-4234 - Oleg Shpynov
Semi-supervised peak calling with SPAN and JBR genome browser. 4235-4237 - Cerag Oguztuzun, Pelin Yasar, Kerim Yavuz, Mesut Muyan
MotifGenie: a Python application for searching transcription factor binding sequences using ChIP-Seq datasets. 4238-4239 - Mireia Ramos-Rodríguez
UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C. 4240-4242 - Taher Mun
LevioSAM: fast lift-over of variant-aware reference alignments. 4243-4245 - Franziska Lang
NeoFox: annotating neoantigen candidates with neoantigen features. 4246-4247 - Jonathon Lefaive
Sparse allele vectors and the savvy software suite. 4248-4250 - Wei Zhang
cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data. 4251-4252 - Marco Antonio Tangaro
ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy. 4253-4254 - Jike Wang, Huiyong Sun
DeepChargePredictor: a web server for predicting QM-based atomic charges via state-of-the-art machine-learning algorithms. 4255-4257 - José Ramón Macías
3DBionotes COVID-19 edition. 4258-4260 - Virginie Lollier
Oligator: a flexible interface to draw oligosaccharide structures and generate their theoretical tandem mass spectra. 4261-4262 - James Shiniti Nagai
CrossTalkeR: analysis and visualization of ligand-receptorne tworks. 4263-4265 - Jialei Duan
FBA: feature barcoding analysis for single cell RNA-Seq. 4266-4268 - Xianjun Dong
powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis. 4269-4271 - Guangyu Yang, Leslie Cope, Zitong He, Liliana Florea
Jutils: a visualization toolkit for differential alternative splicing events. 4272-4274 - Mengying Han
ChemHub: a knowledgebase of functional chemicals for synthetic biology studies. 4275-4276 - Song-Yao Zhang, Shaowu Zhang
Funm6AViewer: a web server and R package for functional analysis of context-specific m6A RNA methylation. 4277-4279 - Javier J. Castillo-Arnemann
PaIntDB: network-based omics integration and visualization using protein-protein interactions in Pseudomonas aeruginosa. 4280-4281 - Xin Yu
EnMCB: an R/bioconductor package for predicting disease progression based on methylation correlated blocks using ensemble models. 4282-4284 - Marie Macnee
SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities. 4285-4287 - Qingqing Huang, Zhengtang Tan, Yanjing Li, Wenzhu Wang, Mei Lang, Changying Li, Zhiyun Guo
Tfcancer: a manually curated database of transcription factors associated with human cancers. 4288-4290 - Yanan Wang, Nicolas Coudray, Yun Zhao
HEAL: an automated deep learning framework for cancer histopathology image analysis. 4291-4295 - Alona Levy-Jurgenson
Erratum to: Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging. 4296 - Ben Galili
On the stability of log-rank test under labeling errors. 4297 - Mark F. Rogers
CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome. 4298
Volume 37, Number 23, December 2021
- Erfaneh Gharavi, Aaron Gu, Guangtao Zheng, Jason P. Smith, Hyun Jae Cho, Aidong Zhang, Donald E. Brown, Nathan C. Sheffield
Embeddings of genomic region sets capture rich biological associations in lower dimensions. 4299-4306 - Thomas Gatter
Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more. 4307-4313 - Xiang Wu, Liang Yu
EPSOL: sequence-based protein solubility prediction using multidimensional embedding. 4314-4320 - Xiaopeng Jin, Qing Liao
S2L-PSIBLAST: a supervised two-layer search framework based on PSI-BLAST for protein remote homology detection. 4321-4327 - László Dobson
PolarProtPred: predicting apical and basolateral localization of transmembrane proteins using putative short linear motifs and deep learning. 4328-4335 - Mohammad Hallal
TempoMAGE: a deep learning framework that exploits the causal dependency between time-series data to predict histone marks in open chromatin regions at time-points with missing ChIP-seq datasets. 4336-4342 - Valentine U. Nlebedim
Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries. 4343-4349 - Kai-Long Zhao, Jun Liu, Xiao-Gen Zhou
MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction. 4350-4356 - Yuhao Xia, Chunxiang Peng, Xiao-Gen Zhou
A sequential niche multimodal conformational sampling algorithm for protein structure prediction. 4357-4365 - Sina Ghadermarzi, Bartosz Krawczyk, Jiangning Song
XRRpred: accurate predictor of crystal structure quality from protein sequence. 4366-4374 - Mohamed Machat, Florent Langenfeld
Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics. 4375-4382 - Faezeh Bayat, Maxwell W. Libbrecht
VSS: variance-stabilized signals for sequencing-based genomic signals. 4383-4391 - Minsheng Hao
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map. 4392-4398 - Rui Fan
Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores. 4399-4404 - Elan Ness-Cohn
TimeCycle: topology inspired method for the detection of cycling transcripts in circadian time-series data. 4405-4413 - Jia-Juan Tu
Differential network analysis by simultaneously considering changes in gene interactions and gene expression. 4414-4423 - Paul D. Donovan
tsRNAsearch: a pipeline for the identification of tRNA and ncRNA fragments from small RNA-sequencing data. 4424-4430 - Yasin Kaymaz
HieRFIT: a hierarchical cell type classification tool for projections from complex single-cell atlas datasets. 4431-4436 - Ruilin Li
Survival analysis on rare events using group-regularized multi-response Cox regression. 4437-4443 - Guillermo Reales
RápidoPGS: a rapid polygenic score calculator for summary GWAS data without a test dataset. 4444-4450 - Ben Galili
On the stability of log-rank test under labeling errors. 4451-4459 - Michael Aichem
Visual exploration of large metabolic models. 4460-4468 - Meng Wang
AdaTiSS: a novel data-Adaptive robust method for identifying Tissue Specificity Scores. 4469-4476 - Tong Zhang, Shao-Wu Zhang, Yan Li:
Identifying driver genes for individual patients through inductive matrix completion. 4477-4484 - Deshan Zhou
MultiDTI: drug-target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network. 4485-4492 - Leonard Schmiester
Efficient gradient-based parameter estimation for dynamic models using qualitative data. 4493-4500 - Mustafa Coskun
Node similarity-based graph convolution for link prediction in biological networks. 4501-4508 - Fatemeh Yassaee Meybodi, Changiz Eslahchi
Predicting anti-cancer drug response by finding optimal subset of drugs. 4509-4516 - Akash Bahai
EpitopeVec: linear epitope prediction using deep protein sequence embeddings. 4517-4525 - Marco Notaro
HEMDAG: a family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction. 4526-4533 - Hongxin He
HFBD: a biomarker knowledge database for heart failure heterogeneity and personalized applications. 4534-4539 - Ling Cai
Assessing consistency across functional screening datasets in cancer cells. 4540-4547 - Rens Janssens
Fully unsupervised deep mode of action learning for phenotyping high-content cellular images. 4548-4555 - Éloi Durant
Panache: a web browser-based viewer for linearized pangenomes. 4556-4558 - Patrick Adelberger
Coral: a web-based visual analysis tool for creating and characterizing cohorts. 4559-4561 - Mehrdad Oveisi
iNucs: inter-nucleosome interactions. 4562-4563 - Miguel D. Fernández-de-Bobadilla
PATO: Pangenome Analysis Toolkit. 4564-4566 - Valentin Junet
CNN-PepPred: an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets - application to peptide-MHC class II binding prediction. 4567-4568 - Xianjie Huang
Cellsnp-lite: an efficient tool for genotyping single cells. 4569-4571 - Heng Li
New strategies to improve minimap2 alignment accuracy. 4572-4574 - Prasun Kumar
Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures. 4575-4577 - Matthew L. Speir
UCSC Cell Browser: visualize your single-cell data. 4578-4580 - Gang Wu
Normalized coefficient of variation (nCV): a method to evaluate circadian clock robustness in population scale data. 4581-4583 - Jordan H. Creed, Christopher M. Wilson, Alex C. Soupir
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data. 4584-4586 - Alisa Pavel
VOLTA: adVanced mOLecular neTwork Analysis. 4587-4588 - Zachary B. Abrams
RCytoGPS: an R package for reading and visualizing cytogenetics data. 4589-4590 - Denise Wolrab
LipidQuant 1.0: automated data processing in lipid class separation-mass spectrometry quantitative workflows. 4591-4592 - Alan E. Murphy
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics. 4593-4596 - Chuming Chen
COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases. 4597-4598 - Ivana Hutarová Vareková, Jan Hutar, Adam Midlik
2DProts: database of family-wide protein secondary structure diagrams. 4599-4601
Volume 37, Number 24, December 2021
- Yingying Yu
iDNA-ABT: advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization. 4603-4610 - Tuukka Norri
Founder reconstruction enables scalable and seamless pangenomic analysis. 4611-4619 - Niko Popitsch
Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data. 4620-4625 - Dhong-Gun Won, Dong-Wook Kim
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints. 4626-4634 - Weibing Wang, Lin Gao
CCIP: predicting CTCF-mediated chromatin loops with transitivity. 4635-4642 - Kristoffer Sahlin
Accurate spliced alignment of long RNA sequencing reads. 4643-4651 - Chao Zhou, Hongyu Zhao
Transformation and differential abundance analysis of microbiome data incorporating phylogeny. 4652-4660 - Peter Peresíni
Nanopore base calling on the edge. 4661-4667 - Hangyuan Yang
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein-protein interaction information. 4668-4676 - Maya Gupta, Paul Zaharias
Accurate large-scale phylogeny-aware alignment using BAli-Phy. 4677-4683 - Wenjia He
Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides. 4684-4693 - Adrian C. D. Fuchs
An astonishing wealth of new proteasome homologs. 4694-4703 - Haoyun Lei, E. Michael Gertz, Alejandro A. Schäffer, Xuecong Fu, Yifeng Tao, Kerstin Heselmeyer-Haddad, Irianna Torres, Guibo Li
Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data. 4704-4711 - Zheng-Chang Lu
Phosphate binding sites prediction in phosphorylation-dependent protein-protein interactions. 4712-4718 - Akila J. Seneviratne, Sean Peters, David Clarke, Michael Dausmann, Michael Hecker, Brett Tully
Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE). 4719-4726 - Yixin Zhao
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. 4727-4736 - Shuang Song
Openness weighted association studies: leveraging personal genome information to prioritize non-coding variants. 4737-4743 - Lily Agranat-Tamir, Shamam Waldman, Naomi Rosen, Benjamin Yakir, Shai Carmi, Liran Carmel
LINADMIX: evaluating the effect of ancient admixture events on modern populations. 4744-4755 - Benjamin B. Chu
A fast data-driven method for genotype imputation, phasing and local ancestry inference: MendelImpute.jl. 4756-4763 - Qi Yan
CHIT: an allele-specific method for testing the association between molecular quantitative traits and phenotype-genotype interaction. 4764-4770 - Xiaodi Yang
Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction. 4771-4778 - Cheng Liang
Cancer subtype identification by consensus guided graph autoencoders. 4779-4786 - Junwei Liu
GdClean: removal of Gadolinium contamination in mass cytometry data. 4787-4792 - Xiaoqi Wang
BioERP: biomedical heterogeneous network-based self-supervised representation learning approach for entity relationship predictions. 4793-4800 - Diego Azael Salazar
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets. 4801-4809 - Mehrad Mahmoudian
Stable Iterative Variable Selection. 4810-4817 - Guoxian Yu
DMIL-IsoFun: predicting isoform function using deep multi-instance learning. 4818-4825 - Jodie Ashford, João Reis-Cunha, Igor Lobo, Francisco Pereira Lobo, Felipe Campelo
Organism-specific training improves performance of linear B-cell epitope prediction. 4826-4834 - Tilman Hinnerichs, Robert Hoehndorf
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions. 4835-4843 - Yanming Zhu
Automatic improvement of deep learning-based cell segmentation in time-lapse microscopy by neural architecture search. 4844-4850 - Wim Thiels
spheresDT/Mpacts-PiCS: cell tracking and shape retrieval in membrane-labeled embryos. 4851-4856 - Parker Knight, Marie-Pierre L. Gauthier, Carolina E. Pardo, Russell P. Darst, Kevin Kapadia, Hadley Browder, Eliza Morton, Alberto Riva
Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data. 4857-4859 - Jonathan R. Belyeu
Unfazed: parent-of-origin detection for large and small de novo variants. 4860-4861 - Guillermo Dufort y Álvarez
RENANO: a REference-based compressor for NANOpore FASTQ files. 4862-4864 - Sebastiaan Valkiers
ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity. 4865-4867 - Andreas Rempel
SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction. 4868-4870 - Hamed Khakzad
Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data. 4871-4872 - Kliment Olechnovic, Ceslovas Venclovas
VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures. 4873-4875 - Daniel Quetschlich
NaViA: a program for the visual analysis of complex mass spectra. 4876-4878 - Guoxia Wen
AQUARIUM: accurate quantification of circular isoforms using model-based strategy. 4879-4881 - Laurent Excoffier
fastsimcoal2: demographic inference under complex evolutionary scenarios. 4882-4885 - Arnaud M. Wolfer
peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC-MS profiling datasets. 4886-4888 - François Moreews
PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX. 4889-4891 - Zhiqiang Zhang, Yuhao Dan, Yaochen Xu, Jiarui Zhang, Xiaoqi Zheng, Jiantao Shi
The DNA methylation haplotype (mHap) format and mHapTools. 4892-4894 - Zachary Prince, Deeptanshu Jha, Rahul Singh
DUI: the drug use insights web server. 4895-4897 - Ciaran M. Welsh, David P. Nickerson, Anand K. Rampadarath
libOmexMeta: enabling semantic annotation of models to support FAIR principles. 4898-4900 - Benjamin Schmid
3Dscript.server: true server-side 3D animation of microscopy images using a natural language-based syntax. 4901-4902 - Denise Wolrab, Eva Cífková, Pavel Cán, Miroslav Lísa
Corrigendum to: LipidQuant 1.0: automated data processing in lipid class separation-mass spectrometry quantitative workflows. 4903 - Benjamin D. Redelings
Erratum to: BAli-Phy version 3: model-based co-estimation of alignment and phylogeny. 4904
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