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Bioinformatics, Volume 38
Volume 38, Number 1, December 2021
- Dmitry Meleshko, Iman Hajirasouliha, Anton I. Korobeynikov
:
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies. 1-8 - Jun Yan
The role of CpG island methylator phenotype in the clinical course of hepatocellular carcinoma. 9-15 - Michael B. Sohn
A compositional mediation model for a binary outcome: Application to microbiome studies. 16-21 - Kevin A. Murgas
A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors. 22-29 - Jun-Liang Lin
ezGeno: an automatic model selection package for genomic data analysis. 30-37 - Jian Song
Alpha-XIC: a deep neural network for scoring the coelution of peak groups improves peptide identification by data-independent acquisition mass spectrometry. 38-43 - Alexander Zaitzeff
Improved datasets and evaluation methods for the automatic prediction of DNA-binding proteins. 44-51 - Chao Wang
DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA. 52-57 - Miguel Arenas
ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation. 58-64 - Dominik Schwarz
Co-evolutionary distance predictions contain flexibility information. 65-72 - Roy González-Alemán
BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics. 73-79 - Pawel Daniluk, Tymoteusz Oleniecki, Bogdan Lesyng
DAMA: a method for computing multiple alignments of protein structures using local structure descriptors. 80-85 - Shide Liang, Zhixiu Li
De novo protein design by an energy function based on series expansion in distance and orientation dependence. 86-93 - Jianzhao Gao
Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method. 94-98 - Jun Liu, Kai-Long Zhao, Guang-Xing He, Liu-Jing Wang, Xiao-Gen Zhou
A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization. 99-107 - Gang Xu, Qinghua Wang, Jianpeng Ma
OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding. 108-114 - Akila Katuwawala, Bi Zhao, Lukasz A. Kurgan
DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning. 115-124 - Qianmu Yuan
Structure-aware protein-protein interaction site prediction using deep graph convolutional network. 125-132 - Oleksii Nikolaienko
ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions. 133-140 - Tristan Mary-Huard
Querying multiple sets of P-values through composed hypothesis testing. 141-148 - Xin Zhou, Xiaodong Cai
Joint eQTL mapping and inference of gene regulatory network improves power of detecting both cis- and trans-eQTLs. 149-156 - Elliott Gordon-Rodríguez
Learning sparse log-ratios for high-throughput sequencing data. 157-163 - Matteo Borella, Graziano Martello, Davide Risso
PsiNorm: a scalable normalization for single-cell RNA-seq data. 164-172 - Alberto Zenere
Using high-throughput multi-omics data to investigate structural balance in elementary gene regulatory network motifs. 173-178 - Khandakar Tanvir Ahmed, Jiao Sun, Sze Cheng, Jeongsik Yong, Wei Zhang
Multi-omics data integration by generative adversarial network. 179-186 - Mark Jayson Cortez
Hierarchical Bayesian models of transcriptional and translational regulation processes with delays. 187-195 - Jonathan Tyler, Daniel B. Forger, Jae Kyoung Kim
Inferring causality in biological oscillators. 196-203 - Di He
A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype. 204-210 - Kai Cao, Yiguang Hong, Lin Wan
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona. 211-219 - Mei Zuo, Yang Zhang
A span-based joint model for extracting entities and relations of bacteria biotopes. 220-227 - Dan Shao
DeepSec: a deep learning framework for secreted protein discovery in human body fluids. 228-235 - Margaret Woodhouse
qTeller: a tool for comparative multi-genomic gene expression analysis. 236-242 - Mirae Kim
Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics. 243-249 - Hualin Liu
BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis. 250-251 - Fulong Yu
CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis. 252-254 - Florian Privé:
Optimal linkage disequilibrium splitting. 255-256 - Leszek P. Pryszcz
ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. 257-260 - Andrew Olson
Ranked choice voting for representative transcripts with TRaCE. 261-264 - François Ancien
MutaFrame - an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome. 265-266 - Frédéric Mahé
Swarm v3: towards tera-scale amplicon clustering. 267-269 - Guillem Salazar
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes. 270-272 - Chie Motono, Shunsuke Yanagida, Miwa Sato, Takatsugu Hirokawa:
MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts. 273-274 - Sungjoon Park, Dohoon Lee, Youngkuk Kim, Sangsoo Lim, Heejoon Chae
BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud. 275-277 - Junyi Xin
CoSMeD: a user-friendly web server to estimate 5-year survival probability of left-sided and right-sided colorectal cancer patients using molecular data. 278-281 - Xiunan Fang, Joshua W. K. Ho
FlowGrid enables fast clustering of very large single-cell RNA-seq data. 282-283 - Elias B. Farr
SPOT: a web-tool enabling swift profiling of transcriptomes. 284-285 - Jun Chen
D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies. 286-288 - Augustinas Sukys, Ramon Grima
MomentClosure.jl: automated moment closure approximations in Julia. 289-290 - Dilawar Singh
Python interfaces for the Smoldyn simulator. 291-293 - Ramiro Magno
quincunx: an R package to query, download and wrangle PGS Catalog data. 294-296 - Pedro B. P. S. Reis
pKPDB: a protein data bank extension database of pKa and pI theoretical values. 297-298 - Andrew D. Yates
Refget: standardized access to reference sequences. 299-300 - Anthony Xu, Aravind Venkateswaran
Ontoclick: a web browser extension to facilitate biomedical knowledge curation. 301-302
Volume 38, Number 2, January 2022
- Qing Cheng, Tingting Qiu, Xiaoran Chai, Baoluo Sun, Yingcun Xia, Xingjie Shi
MR-Corr2: a two-sample Mendelian randomization method that accounts for correlated horizontal pleiotropy using correlated instrumental variants. 303-310 - Shengji Jia
Efficient change-points detection for genomic sequences via cumulative segmented regression. 311-317 - Nisha Singh
A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz). 318-324 - Yunxiao Ren
Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. 325-334 - Hongwei Huo
CIndex: compressed indexes for fast retrieval of FASTQ files. 335-343 - Michal Karlicki, Stanislaw Antonowicz, Anna Karnkowska
Tiara: deep learning-based classification system for eukaryotic sequences. 344-350 - Dohyeon Lee, Giltae Song
FastqCLS: a FASTQ compressor for long-read sequencing via read reordering using a novel scoring model. 351-356 - Alexey Zabelkin
PaReBrick: PArallel REarrangements and BReaks identification toolkit. 357-363 - Jae Yong Ryu
PredMS: a random forest model for predicting metabolic stability of drug candidates in human liver microsomes. 364-368 - Rahul Kaushik
ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures. 369-376 - Constantin Schneider
DLAB: deep learning methods for structure-based virtual screening of antibodies. 377-383 - Benedek Dankó
SplicingFactory - splicing diversity analysis for transcriptome data. 384-390 - Lyla Atta
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories. 391-396 - Yi-Pei Chen
RNA Solutions: Synthesizing Information to Support Transcriptomics (RNASSIST). 397-403 - Mohammed Eslami
Prediction of whole-cell transcriptional response with machine learning. 404-409 - Baoshan Ma
XGBLC: an improved survival prediction model based on XGBoost. 410-418 - Tianying Wang
Testing microbiome association using integrated quantile regression models. 419-425 - Haitao Fu
MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks. 426-434 - Yingjun Ma
Hypergraph-based logistic matrix factorization for metabolite-disease interaction prediction. 435-443 - Seungyoon Nam
PATHOME-Drug: a subpathway-based polypharmacology drug-repositioning method. 444-452 - Lukas Breitwieser
BioDynaMo: a modular platform for high-performance agent-based simulation. 453-460 - Yiheng Zhu
TGSA: protein-protein association-based twin graph neural networks for drug response prediction with similarity augmentation. 461-468 - Fahimeh Motamedi, Horacio Pérez Sánchez, Alireza Mehridehnavi
Accelerating Big Data Analysis through LASSO-Random Forest Algorithm in QSAR Studies. 469-475 - Yang Xu
SMILE: mutual information learning for integration of single-cell omics data. 476-486 - Gianvito Pio
Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction. 487-493 - Kishlay Jha
Continual knowledge infusion into pre-trained biomedical language models. 494-502 - Shuxia Guo
Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons. 503-512 - Mohamed Amgad
Explainable nucleus classification using Decision Tree Approximation of Learned Embeddings. 513-519 - John F. Graf
FLINO: a new method for immunofluorescence bioimage normalization. 520-526 - Shixiang Wang
UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data. 527-529 - Cecilia Sensalari
ksrates: positioning whole-genome duplications relative to speciation events in KS distributions. 530-532 - Kenneth I Brewer
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria. 533-535 - Brian M. Schilder
echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline. 536-539 - Itsuki Sugita, Shohei Matsuyama, Hiroki Dobashi, Daisuke Komura
Viola: a structural variant signature extractor with user-defined classifications. 540-542 - Jie Tan, Zhencheng Fang, Shufang Wu, Qian Guo, Xiaoqing Jiang, Huaiqiu Zhu
HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes. 543-545 - Richard A. Stanton
GAMMA: a tool for the rapid identification, classification and annotation of translated gene matches from sequencing data. 546-548 - Kohei Hagiwara
indelPost: harmonizing ambiguities in simple and complex indel alignments. 549-551 - Amélie Barozet
MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations. 552-553 - Steven Grudman, J. Eduardo Fajardo, András Fiser
INTERCAAT: identifying interface residues between macromolecules. 554-555 - Liang Rao, Ning-Xin Jia, Jun Hu
ATPdock: a template-based method for ATP-specific protein-ligand docking. 556-558 - Alan Kwong
FIVEx: an interactive eQTL browser across public datasets. 559-561 - Pieter Verschaffelt
Unipept Visualizations: an interactive visualization library for biological data. 562-563 - Eugenio López-Cortegano:
purgeR: inbreeding and purging in pedigreed populations. 564-565 - Axel Theorell, Johann F. Jadebeck
PolyRound: polytope rounding for random sampling in metabolic networks. 566-567 - Xiaotao Shen
metID: an R package for automatable compound annotation for LC-MS-based data. 568-569 - Peter Zhang
TPWshiny: an interactive R/Shiny app to explore cell line transcriptional responses to anti-cancer drugs. 570-572 - Mustafa Buyukozkan, Karsten Suhre, Jan Krumsiek
SGI: automatic clinical subgroup identification in omics datasets. 573-576 - Antoine Bodein, Marie-Pier Scott-Boyer, Olivier Périn, Kim-Anh Lê Cao, Arnaud Droit
timeOmics: an R package for longitudinal multi-omics data integration. 577-579 - Daniel Osório, Marieke L. Kuijjer
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. 580-582 - Maria Llambrich
Amanida: an R package for meta-analysis of metabolomics non-integral data. 583-585 - Paola Paci
SWIMmeR: an R-based software to unveiling crucial nodes in complex biological networks. 586-588 - Christina Wong, Bo Li
AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data. 589-591 - Tomás Tokár
miRAnno - network-based functional microRNA annotation. 592-593 - Rodrigo Fernandez-Gonzalez
PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images. 594-596
Volume 38, Number 3, January 2022
- Gaetan De Waele
CpG Transformer for imputation of single-cell methylomes. 597-603 - Thomas Krannich
Population-scale detection of non-reference sequence variants using colored de Bruijn graphs. 604-611 - Alexander G. McFarland
Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper. 612-620 - Spiro C. Stilianoudakis, Maggie A. Marshall, Mikhail G. Dozmorov
preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution. 621-630 - Arbel D. Tadmor
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study. 631-647 - Yanhua Qiao, Xiaolei Zhu
BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models. 648-654 - Qichang Zhao
HyperAttentionDTI: improving drug-protein interaction prediction by sequence-based deep learning with attention mechanism. 655-662 - Lenore Pipes
AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees. 663-670 - Seonwoo Min
TargetNet: functional microRNA target prediction with deep neural networks. 671-677 - Yawei Wang, Yuning Yang
EDCNN: identification of genome-wide RNA-binding proteins using evolutionary deep convolutional neural network. 678-686 - Elan Shatoff
dsRBPBind: modeling the effect of RNA secondary structure on double-stranded RNA-protein binding. 687-693 - Xiaotian Hu, Cong Feng, Yincong Zhou, Andrew P. Harrison, Ming Chen
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks. 694-702 - Lorenza Pacini
A computational methodology to diagnose sequence-variant dynamic perturbations by comparing atomic protein structures. 703-709 - Masaki Tagashira
ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures. 710-719 - Shi-Hao Feng
CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks. 720-729 - Ramón Viñas, Helena Andrés-Terré, Pietro Liò
Adversarial generation of gene expression data. 730-737 - Musu Yuan
scMRA: a robust deep learning method to annotate scRNA-seq data with multiple reference datasets. 738-745 - Lujing Zheng, Zhenhuan Liu, Yang Yang
Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning. 746-753 - Fabrizio Angaroni, Kevin Chen, Chiara Damiani, Giulio Caravagna
PMCE: efficient inference of expressive models of cancer evolution with high prognostic power. 754-762 - Kuei-Yueh Ko
Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis. 763-769 - Jiacheng Leng
Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs. 770-777 - Rebecca L. Rubinstein
ORT: a workflow linking genome-scale metabolic models with reactive transport codes. 778-784 - Ya-Ru Miao
ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction. 785-791 - Jiacheng Xiong, Zhaojun Li, Guangchao Wang, Zunyun Fu, Feisheng Zhong, Tingyang Xu
Multi-instance learning of graph neural networks for aqueous pKa prediction. 792-798 - Lizhi Liu
HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations. 799-808 - Qiufu Li
Neuron segmentation using 3D wavelet integrated encoder-decoder network. 809-817 - Rui Zhu
Multimodal medical image fusion using adaptive co-occurrence filter-based decomposition optimization model. 818-826 - Min-Qi Xue, Xi-Liang Zhu
DULoc: quantitatively unmixing protein subcellular location patterns in immunofluorescence images based on deep learning features. 827-833 - Ankush Sharma
ShinyArchR.UiO: user-friendly, integrative and open-source tool for visualization of single-cell ATAC-seq data using ArchR. 834-836 - Tyll Stöcker
MuWU: Mutant-seq library analysis and annotation. 837-838 - Frank Vogt
vcf2gwas: Python API for comprehensive GWAS analysis using GEMMA. 839-840 - Erik Scott Wright
FindNonCoding: rapid and simple detection of non-coding RNAs in genomes. 841-843 - Juan A. Ferrer-Bonsoms
Rediscover: an R package to identify mutually exclusive mutations. 844-845 - Nicolò Rossi
WGA-LP: a pipeline for whole genome assembly of contaminated reads. 846-848 - Eugenia Voytik, Isabell Bludau, Sander Willems
AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge. 849-852 - Amy Dong, Xiaomin Bao
GPSmatch: an R package for comparing Genomic-binding Profile Similarity among transcriptional regulators using customizable databases. 853-855 - Simone Marini
Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. 856-860 - Xiaoheng Cheng
BalLeRMix +: mixture model approaches for robust joint identification of both positive selection and long-term balancing selection. 861-863 - Hemil Panchiwala
The systems biology simulation core library. 864-865 - Genaro Camele
Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation. 866-868 - Mukta G. Palshikar
WikiNetworks: translating manually created biological pathways for topological analysis. 869-871 - Hai-Long Trieu
BioVAE: a pre-trained latent variable language model for biomedical text mining. 872-874 - Tobias Greisager Rehfeldt
MS2AI: automated repurposing of public peptide LC-MS data for machine learning applications. 875-877 - Joseph D. Romano
PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods. 878-880 - Michael Nodzenski
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families. 881 - Matthew Carlucci, Algimantas Krisciunas, Haohan Li, Povilas Gibas, Karolis Koncevicius, Art Petronis, Gabriel Oh:
DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity. 882 - Thomas Peacock, James M. Heather, Tahel Ronel
Corrigendum to: Decombinator V4: an improved AIRR-C compliant software package for T-cell receptor sequence annotation. 883
Volume 38, Number 4, January 2022
- Haakon E. Nustad
Modeling dependency structures in 450k DNA methylation data. 885-891 - Luca Barbon, Victoria Offord, Elizabeth J. Radford, Adam P. Butler, Sebastian S. Gerety
Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments. 892-899 - Morgane Pierre-Jean
PIntMF: Penalized Integrative Matrix Factorization method for multi-omics data. 900-907 - Serhan Yilmaz
Uncovering complementary sets of variants for predicting quantitative phenotypes. 908-917 - Chengze Shen
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. 918-924 - Giuseppe Cattaneo
The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis. 925-932 - Deyou Tang
KCOSS: an ultra-fast k-mer counter for assembled genome analysis. 933-940 - Vineet Thumuluri, Hannah-Marie Martiny
NetSolP: predicting protein solubility in Escherichia coli using language models. 941-946 - Ziwei Xie
Deep graph learning of inter-protein contacts. 947-953 - Gabriele Pozzati, Wensi Zhu, Claudio Bassot, John Lamb, Petras Kundrotas, Arne Elofsson
Limits and potential of combined folding and docking. 954-961 - Zongyang Du, Zhenling Peng
Toward the assessment of predicted inter-residue distance. 962-969 - Carlos G. Oliver
Vernal: a tool for mining fuzzy network motifs in RNA. 970-976 - Hmrishav Bandyopadhyay
Cryo-shift: reducing domain shift in cryo-electron subtomograms with unsupervised domain adaptation and randomization. 977-984 - Maksim V. Shegay, Vytas K. Svedas, Vladimir V. Voevodin, Dmitry A. Suplatov
Guide tree optimization with genetic algorithm to improve multiple protein 3D-structure alignment. 985-989 - Fusong Ju
Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction. 990-996 - Haotian Teng
Clustering spatial transcriptomics data. 997-1004 - Jin Jin
T2-DAG: a powerful test for differentially expressed gene pathways via graph-informed structural equation modeling. 1005-1014 - Galina Boldina
A2Sign: Agnostic Algorithms for Signatures - a universal method for identifying molecular signatures from transcriptomic datasets prior to cell-type deconvolution. 1015-1021 - Pontus Eriksson
A comparison of rule-based and centroid single-sample multiclass predictors for transcriptomic classification. 1022-1029 - Jonathan R. Bowles
Scalable inference of transcriptional kinetic parameters from MS2 time series data. 1030-1036 - Madalina Ciortan, Matthieu Defrance
GNN-based embedding for clustering scRNA-seq data. 1037-1044 - Elise Amblard
Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data. 1045-1051 - Michael Nodzenski
GADGETS: a genetic algorithm for detecting epistasis using nuclear families. 1052-1058 - Robert Warmerdam
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores. 1059-1066 - Aastha Khatiwada
GPA-Tree: statistical approach for functional-annotation-tree-guided prioritization of GWAS results. 1067-1074 - Omar Maddouri
Deep graph representations embed network information for robust disease marker identification. 1075-1086 - Ofir Yaish
Computational modeling of mRNA degradation dynamics using deep neural networks. 1087-1101 - Guy Shtar
Explainable multimodal machine learning model for classifying pregnancy drug safety. 1102-1109 - Jianan Li
Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning. 1110-1117 - Lei Deng, Yibiao Huang, Xuejun Liu, Hui Liu
Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations. 1118-1125 - Shohre Masoumi, Maxwell W. Libbrecht, Kay C. Wiese
SigTools: exploratory visualization for genomic signals. 1126-1128 - Martina Bevilacqua
ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications. 1129-1130 - Dietmar Rieder, Georgios Fotakis
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction. 1131-1132 - Rory Munro, Roberto Santos
minoTour, real-time monitoring and analysis for nanopore sequencers. 1133-1135 - Jonathan Dhenin
TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics. 1136-1138 - Michael Uhl
Peakhood: individual site context extraction for CLIP-seq peak regions. 1139-1140 - Yoochan Myung
CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function. 1141-1143 - Kirsten Van Huffel
BioCCP.jl: collecting coupons in combinatorial biotechnology. 1144-1145 - Jean Charle Yaacoub
DD-GUI: a graphical user interface for deep learning-accelerated virtual screening of large chemical libraries (Deep Docking). 1146-1148 - Lucas S. P. Rudden
Biobox: a toolbox for biomolecular modelling. 1149-1151 - Myungjin Lee
GLYCO: a tool to quantify glycan shielding of glycosylated proteins. 1152-1154 - Luis García-Jimeno, Coral Fustero Torre
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses. 1155-1156 - Thomas Sheffield
tcplfit2: an R-language general purpose concentration-response modeling package. 1157-1158 - Alissa L. Severson
LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data. 1159-1161 - Thea Van Rossum
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes. 1162-1164 - Jin Li, Feng Chen, Hong Liang, Jingwen Yan
MoNET: an R package for multi-omic network analysis. 1165-1167 - Kelsey Chetnik, Elisa Benedetti, Daniel P. Gomari, Annalise Schweickart, Richa Batra, Mustafa Buyukozkan, Zeyu Wang, Matthias Arnold
maplet: an extensible R toolbox for modular and reproducible metabolomics pipelines. 1168-1170 - Miroslav Kratochvíl
COBREXA.jl: constraint-based reconstruction and exascale analysis. 1171-1172 - Florence Jornod
AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development. 1173-1175 - Boyang Tom Jin
Mian: interactive web-based microbiome data table visualization and machine learning platform. 1176-1178 - Mohammad Taher Pilehvar, Adam Bernard, Damian Smedley, Nigel Collier
PheneBank: a literature-based database of phenotypes. 1179-1180 - Thomas Naake
MatrixQCvis: shiny-based interactive data quality exploration for omics data. 1181-1182
Volume 38, Number 5, February 2022
- Michele Leone
Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions. 1183-1190 - Jonathan Raad
miRe2e: a full end-to-end deep model based on transformers for prediction of pre-miRNAs. 1191-1197 - Nicholas J. Dimonaco
No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study. 1198-1207 - Matthew Hayes
HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery. 1208-1215 - Yan Miao
Virtifier: a deep learning-based identifier for viral sequences from metagenomes. 1216-1222 - Yushuang Liu, Shuping Jin, Hongli Gao, Xue Wang, Congjing Wang, Weifeng Zhou, Bin Yu
Predicting the multi-label protein subcellular localization through multi-information fusion and MLSI dimensionality reduction based on MLFE classifier. 1223-1230 - Peter McHale
trfermikit: a tool to discover VNTR-associated deletions. 1231-1234 - José Bonet, Mandi Chen
DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data. 1235-1243 - Yang Fan, Yingce Xia
Back translation for molecule generation. 1244-1251 - Yi-Jun Tang, Yihe Pang, Bin Liu
DeepIDP-2L: protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network. 1252-1260 - Vincent Mallet
InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions. 1261-1268 - Yusuke Matsui
RoDiCE: robust differential protein co-expression analysis for cancer complexome. 1269-1276 - David Buterez
CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention networks. 1277-1286 - Lu Pan, Huy Q. Dinh, Yudi Pawitan, Trung-Nghia Vu
Isoform-level quantification for single-cell RNA sequencing. 1287-1294 - Xiao Wang, Jia Wang, Han Zhang
HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data. 1295-1303 - Fei Qin
SCRIP: an accurate simulator for single-cell RNA sequencing data. 1304-1311 - Maneesha Aluru, Harsh Shrivastava, Sriram P. Chockalingam
EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks. 1312-1319 - Paul Scherer
Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases. 1320-1327 - Johannes Smolander
scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data. 1328-1335 - Daniel Schwabe
On the relation between input and output distributions of scRNA-seq experiments. 1336-1343 - Tianci Song, Kathleen K. Markham
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network. 1344-1352 - Weiwen Wang
springD2A: capturing uncertainty in disease-drug association prediction with model integration. 1353-1360 - Lulu Zhang, Xiao Liu, Xiaoxiang Chen, Antony R. Warden, Youyi Yu, Baozhen Huang, Xianting Ding
SCANCell reveals diverse inter-cluster interaction patterns in systemic lupus erythematosus across the disease spectrum. 1361-1368 - Seyedeh Shaghayegh Sadeghi
A network-based drug repurposing method via non-negative matrix factorization. 1369-1377 - Tao Sun
3MCor: an integrative web server for metabolome-microbiome-metadata correlation analysis. 1378-1384 - Vigneshwaran Namasivayam
Structural feature-driven pattern analysis for multitarget modulator landscapes. 1385-1392 - Shunfu Mao
CellMeSH: probabilistic cell-type identification using indexed literature. 1393-1402 - Lulu Chen, Chiung-Ting Wu, Chia-Hsiang Lin, Rujia Dai
swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution. 1403-1410 - Pasquale Cascarano, Maria Colomba Comes
DeepCEL0 for 2D single-molecule localization in fluorescence microscopy. 1411-1419 - Andrew Cox
Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms. 1420-1426 - Herbert Teun Kruitbosch
A convolutional neural network for segmentation of yeast cells without manual training annotations. 1427-1433 - Zuguang Gu
spiralize: an R package for visualizing data on spirals. 1434-1436 - Wesley S. van de Geer
ProteoDisco: a flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies. 1437-1439 - Christopher Pockrandt
PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools. 1440-1442 - James M. Ferguson
InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses. 1443-1446 - Andrzej Zielezinski
PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences. 1447-1449 - Chrispin Chaguza
RCandy: an R package for visualizing homologous recombinations in bacterial genomes. 1450-1451 - Sebastian Bittrich
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB. 1452-1454 - Damla Ovek
SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2-human mimicry and interactions. 1455-1457 - Vincent Mallet
RNAglib: a python package for RNA 2.5 D graphs. 1458-1459 - Zuguang Gu
Make Interactive Complex Heatmaps in R. 1460-1462 - Milena A. Cardoso, Luis E. A. Rizzardi, Leonardo W. Kume, Clarice S. Groeneveld, Sheyla Trefflich, Diego A. A. Morais
TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves. 1463-1464 - Jordan C. Rozum
pystablemotifs: Python library for attractor identification and control in Boolean networks. 1465-1466 - Sven Thiele
CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks. 1467-1469 - Husen M. Umer
Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides. 1470-1472 - Xiaoxi Dong, Kovidh Vegesna, Cory Brouwer, Weijun Luo
SBGNview: towards data analysis, integration and visualization on all pathways. 1473-1476 - Zongren Li
DeepKG: an end-to-end deep learning-based workflow for biomedical knowledge graph extraction, optimization and applications. 1477-1479 - Christopher D. Sanchez
EcoPLOT: dynamic analysis of biogeochemical data. 1480-1482
Volume 38, Number 6, March 2022
- Zuhal Ozcan
Chromosomal imbalances detected via RNA-sequencing in 28 cancers. 1483-1490 - Juan A. Ferrer-Bonsoms
On the identifiability of the isoform deconvolution problem: application to select the proper fragment length in an RNA-seq library. 1491-1496 - James K. Bonfield
CRAM 3.1: advances in the CRAM file format. 1497-1503 - Giovanni Marques de Castro
Cross-species prediction of essential genes in insects. 1504-1513 - Lesong Wei, Xiucai Ye, Tetsuya Sakurai, Zengchao Mu, Leyi Wei
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning. 1514-1524 - Jian Song
Alpha-Tri: a deep neural network for scoring the similarity between predicted and measured spectra improves peptide identification of DIA data. 1525-1531 - Uyen Mai
Completing gene trees without species trees in sub-quadratic time. 1532-1541 - (Withdrawn) Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking. 1542-1549
- Kim Philipp Jablonski
Identifying cancer pathway dysregulations using differential causal effects. 1550-1559 - Jialin Qu, Yuehua Cui
Gene set analysis with graph-embedded kernel association test. 1560-1567 - Soroosh Gholamizoj
SPEQ: quality assessment of peptide tandem mass spectra with deep learning. 1568-1574 - Hui Wan
scNAME: neighborhood contrastive clustering with ancillary mask estimation for scRNA-seq data. 1575-1583 - Moran Sharon
The differential activity of biological processes in tissues and cell subsets can illuminate disease-related processes and cell-type identities. 1584-1592 - Justin G. Chitpin
BATL: Bayesian annotations for targeted lipidomics. 1593-1599 - Judith Bernett
Robust disease module mining via enumeration of diverse prize-collecting Steiner trees. 1600-1606 - Ruiyi Zhang
scPretrain: multi-task self-supervised learning for cell-type classification. 1607-1614 - Cecilia Noecker
MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data. 1615-1623 - Tim Adams
Benchmarking table recognition performance on biomedical literature on neurological disorders. 1624-1630 - Kaiqiao Li
Efficient gradient boosting for prognostic biomarker discovery. 1631-1638 - Yuanwei Xu
CACONET: a novel classification framework for microbial correlation networks. 1639-1647 - Helena Balabin
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. 1648-1656 - Sebastian Stammler
Mainzelliste SecureEpiLinker (MainSEL): privacy-preserving record linkage using secure multi-party computation. 1657-1668 - Shumin Ren, Yanwen Jin, Yalan Chen, Bairong Shen
CRPMKB: a knowledge base of cancer risk prediction models for systematic comparison and personalized applications. 1669-1676 - Azza Althagafi
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning. 1677-1684 - Marc Melkonian
Towards a reproducible interactome: semantic-based detection of redundancies to unify protein-protein interaction databases. 1685-1691 - Loan Vulliard
BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations. 1692-1699 - Coleman R. Harris
Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images. 1700-1707 - Diogo A. C. Narciso
Characterization of biofilm structure and properties via processing of 2D optical coherence tomography images in BISCAP. 1708-1715 - Xuejian Li, Shiqiang Ma
Inferring gene regulatory network via fusing gene expression image and RNA-seq data. 1716-1723 - Laura Fancello, Alessandro Guida
TMBleR: a bioinformatic tool to optimize TMB estimation and predictive power. 1724-1726 - Stefan Ebmeyer, Roelof Dirk Coertze
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids. 1727-1728 - Soohyun Lee, Clara R. Bakker
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs. 1729-1731 - Zhenhua Yu
AMC: accurate mutation clustering from single-cell DNA sequencing data. 1732-1734 - Chaoran Chen
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants. 1735-1737 - Fei-Liao Lai
GC-Profile 2.0: an extended web server for the prediction and visualization of CpG islands. 1738-1740 - Dimitri Höhler
RAxML Grove: an empirical phylogenetic tree database. 1741-1742 - Célien Jacquemard, Guillaume Bret, Thomas Grutter, Esther Kellenberger
Comparing transmembrane protein structures with ATOLL. 1743-1744 - Martin Gonzalez Buitron
CoDNaS-RNA: a database of conformational diversity in the native state of RNA. 1745-1748 - Philipp Junk
HOMELETTE: a unified interface to homology modelling software. 1749-1751 - Jan Brezovsky
TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them. 1752-1753 - Elijah A. MacCarthy
GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool. 1754-1755 - Yang Xu
MACA: marker-based automatic cell-type annotation for single-cell expression data. 1756-1760 - Abbas Alameer
geoCancerPrognosticDatasetsRetriever: a bioinformatics tool to easily identify cancer prognostic datasets on Gene Expression Omnibus (GEO). 1761-1763 - Ilaria De Marinis, Prisca Lo Surdo
SIGNORApp: a Cytoscape 3 application to access SIGNOR data. 1764-1766 - Roberto Maria Pellegrino
LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario. 1767-1769 - Jacob Neumann, Yen Ting Lin
Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit. 1770-1772 - Aleksandra Gruca
MAINE: a web tool for multi-omics feature selection and rule-based data exploration. 1773-1775 - Huan He
MedTator: a serverless annotation tool for corpus development. 1776-1778 - Daniel Jiménez Sánchez, Mikel Ariz, José Mário Morgado, Iván Cortés-Domínguez, Carlos Ortiz-de-Solórzano:
Corrigendum to: NMF-RI: blind spectral unmixing of highly mixed multispectral flow and image cytometry data. 1779
Volume 38, Number 7, March 2022
- Maximillian G. Marin
Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome. 1781-1787 - Zachary Stephens, Alejandro Ferrer, Lisa Boardman, Ravishankar K. Iyer, Jean-Pierre A. Kocher
Telogator: a method for reporting chromosome-specific telomere lengths from long reads. 1788-1793 - Sandra Hui
SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing. 1801-1808 - Renan Valieris
A mixture model for determining SARS-Cov-2 variant composition in pooled samples. 1809-1815 - Jyun-Hong Lin, Liang-Chi Chen
LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants. 1816-1822 - Qian Feng
An accurate method for identifying recent recombinants from unaligned sequences. 1823-1829 - Christopher Bennett
SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers. 1830-1837 - Fabio Cunial
Fast and compact matching statistics analytics. 1838-1845 - Andrew J. Holbrook, Xiang Ji, Marc A. Suchard
From viral evolution to spatial contagion: a biologically modulated Hawkes model. 1846-1856 - Darvin Mertsch, Mario Stanke
End-to-end learning of evolutionary models to find coding regions in genome alignments. 1857-1862 - Daniel Platero-Rochart
RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics. 1863-1869 - Kirill E. Medvedev
DisEnrich: database of enriched regions in human dark proteome. 1870-1876 - Brennan Abanades
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation. 1877-1880 - Carlos Outeiral
Current structure predictors are not learning the physics of protein folding. 1881-1887 - Jaspreet Singh
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model. 1888-1894 - Sai-Sai Guo, Jun Liu, Xiao-Gen Zhou
DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning. 1895-1903 - Raj S. Roy
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers. 1904-1910 - Jiawei Mao, He Zhu, Luyao Liu, Zheng Fang, Mingming Dong, Hongqiang Qin, Mingliang Ye
MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides. 1911-1919 - Giacomo Baruzzo
Identify, quantify and characterize cellular communication from single-cell RNA sequencing data with scSeqComm. 1920-1929 - Camille Roquencourt
ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath. 1930-1937 - Shuang Song
A data-adaptive Bayesian regression approach for polygenic risk prediction. 1938-1946 - Jiashun Xiao, Mingxuan Cai
XPXP: improving polygenic prediction by cross-population and cross-phenotype analysis. 1947-1955 - Di Xiao, Hani Jieun Kim
Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities. 1956-1963 - Xiaoqing Ru
NerLTR-DTA: drug-target binding affinity prediction based on neighbor relationship and learning to rank. 1964-1971 - Eran Agmon
Vivarium: an interface and engine for integrative multiscale modeling in computational biology. 1972-1979 - David A. Hughes
metaboprep: an R package for preanalysis data description and processing. 1980-1987 - Luca Cilibrasi, Pietro Pinoli
ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time. 1988-1994 - Min Li
BACPI: a bi-directional attention neural network for compound-protein interaction and binding affinity prediction. 1995-2002 - Hehuan Ma
Cross-dependent graph neural networks for molecular property prediction. 2003-2009 - Xi Wang
LLPSDB v2.0: an updated database of proteins undergoing liquid-liquid phase separation in vitro. 2010-2014 - Walid M. Abdelmoula
massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation. 2015-2021 - Hongjia Li
Noise-Transfer2Clean: denoising cryo-EM images based on noise modeling and transfer. 2022-2029 - Cui-Xiang Lin
AlzCode: a platform for multiview analysis of genes related to Alzheimer's disease. 2030-2032 - Emira Cherif
ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking pathogen variants. 2033-2035 - Chen Hong
GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis. 2036-2038 - Chao Zhou, Huimin Wang, Hongyu Zhao
fastANCOM: a fast method for analysis of compositions of microbiomes. 2039-2041 - Nicole E. Kramer, Eric S. Davis
Plotgardener: cultivating precise multi-panel figures in R. 2042-2045 - Daniel Cameron
StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem. 2046-2048 - Mitchell R. Vollger
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps. 2049-2051 - Benjamin Crysup
ProSynAR: a reference aware read merger. 2052-2053 - Xiaoqiong Bao
MeRIPseqPipe: an integrated analysis pipeline for MeRIP-seq data based on Nextflow. 2054-2056 - Natalia García-García
M&Ms: a versatile software for building microbial mock communities. 2057-2059 - Mattia Miotto
Thermometer: a webserver to predict protein thermal stability. 2060-2061 - Stephen Price
TMQuery: a database of precomputed template modeling scores for assessment of protein structural similarity. 2062-2063 - Gregor Urban, Christophe N. Magnan, Pierre Baldi
SSpro/ACCpro 6: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, deep learning and structural similarity. 2064-2065 - Amirhossein Sakhteman, Arindam Ghosh
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds. 2066-2069 - Pablo Librado
Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics. 2070-2071 - Yonghui Dong
RawHummus: an R Shiny app for automated raw data quality control in metabolomics. 2072-2074 - Rosa D. Hernansaiz-Ballesteros
FUNKI: interactive functional footprint-based analysis of omics data. 2075-2076 - Sebastien Lelong, Xinghua Zhou, Cyrus Afrasiabi, Zhongchao Qian, Marco Alvarado Cano, Ginger Tsueng
BioThings SDK: a toolkit for building high-performance data APIs in biomedical research. 2077-2079 - Shuang Song, Lin Hou
Erratum to: A data-adaptive Bayesian regression approach for polygenic risk prediction. 2080
Volume 38, Number 8, April 2022
- Richard Wilton
Performance optimization in DNA short-read alignment. 2081-2087 - Jessie J. F. Medeiros, Jose-Mario Capo-Chichi, Liran I Shlush
SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes-derived data. 2088-2095 - David J. H. Shih
CNGPLD: case-control copy-number analysis using Gaussian process latent difference. 2096-2101 - Nadav Brandes
ProteinBERT: a universal deep-learning model of protein sequence and function. 2102-2110 - Bas Stringer, Hans de Ferrante, Sanne Abeln
PIPENN: protein interface prediction from sequence with an ensemble of neural nets. 2111-2118 - Kathryn E. Kirchoff
EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning. 2119-2126 - Dehan Cai
Reconstructing viral haplotypes using long reads. 2127-2134 - Jun Zhang, Ke Yan, Qingcai Chen
PreRBP-TL: prediction of species-specific RNA-binding proteins based on transfer learning. 2135-2143 - Alexey Markin
RF-Net 2: fast inference of virus reassortment and hybridization networks. 2144-2152 - Parth Garg, Sukriti Sacher, Mrinal, Atul, Prutyay Gautam, Arjun Ray
CICLOP: a robust and accurate computational framework for protein inner cavity detection. 2153-2161 - Pengpai Li, Zhi-Ping Liu
PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning. 2162-2168 - Geert-Jan Huizing
Optimal transport improves cell-cell similarity inference in single-cell omics data. 2169-2177 - Xiaohan Xing
Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis. 2178-2186 - Yi Cheng, Xiuli Ma
scGAC: a graph attentional architecture for clustering single-cell RNA-seq data. 2187-2193 - Abbas-Ali Heydari
ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders. 2194-2201 - Mete Akgün
Efficient privacy-preserving whole-genome variant queries. 2202-2210 - Yao Gong, Yue Chen
UbE3-APA: a bioinformatic strategy to elucidate ubiquitin E3 ligase activities in quantitative proteomics study. 2211-2218 - Benjamin M. David
A reinforcement learning framework for pooled oligonucleotide design. 2219-2225 - Cheng Yan, Guihua Duan, Na Li, Lishen Zhang, Fang-Xiang Wu
PDMDA: predicting deep-level miRNA-disease associations with graph neural networks and sequence features. 2226-2234 - Chaoyu Zhu
Multimodal reasoning based on knowledge graph embedding for specific diseases. 2235-2245 - Mengting Niu
GMNN2CD: identification of circRNA-disease associations based on variational inference and graph Markov neural networks. 2246-2253 - Yahui Long
Pre-training graph neural networks for link prediction in biomedical networks. 2254-2262 - Thomas Hillerton
Fast and accurate gene regulatory network inference by normalized least squares regression. 2263-2268 - Ioan Ieremie
TransformerGO: predicting protein-protein interactions by modelling the attention between sets of gene ontology terms. 2269-2277 - Anne-Christin Hauschild
Federated Random Forests can improve local performance of predictive models for various healthcare applications. 2278-2286 - Sehwan Moon, Hyunju Lee
MOMA: a multi-task attention learning algorithm for multi-omics data interpretation and classification. 2287-2296 - Rebecca Irlmeier
Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS. 2297-2306 - Karina Pikalyova, Alexey Orlov, Arkadii I. Lin
HIV-1 drug resistance profiling using amino acid sequence space cartography. 2307-2314 - Junfeng Yao, Wen Sun
Effective knowledge graph embeddings based on multidirectional semantics relations for polypharmacy side effects prediction. 2315-2322 - Meiling Wang
Identify connectome between genotypes and brain network phenotypes via deep self-reconstruction sparse canonical correlation analysis. 2323-2332 - Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang
mzMD: visualization-oriented MS data storage and retrieval. 2333-2340 - Naama Wagner, Oren Avram
Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors. 2341-2343 - Palash Pandey, Sanjeevani Arora, Gail L. Rosen
MetaMutationalSigs: comparison of mutational signature refitting results made easy. 2344-2347 - Sameer Shanbhag, Riddhi Patil, Noor Zahara, Chirag Shetty, Rachel Weidenhammer, Sneha Watharkar, Pranav Tambvekar, Philip P. Badzuh, Chester Dias, Narendra Vankayala, Prutha Kulkarni, Charan Vallapureddy, Shamika Kulkarni, Pooja Nikhare, Nowlan H. Freese
Integrated Genome Browser App Store. 2348-2349 - Simon Penel
Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation. 2350-2352 - Leandro G. Radusky
pyFoldX: enabling biomolecular analysis and engineering along structural ensembles. 2353-2355 - Alexander Lachmann
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. 2356-2357 - Alexander Cope
riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow. 2358-2360 - Daoyu Duan
NeuCA web server: a neural network-based cell annotation tool with web-app and GUI. 2361-2363 - Hagai Levi
The DOMINO web-server for active module identification analysis. 2364-2366 - Almut Heinken, Ines Thiele
Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities. 2367-2368 - Adam C. Knapp
SteadyCellPhenotype: a web-based tool for the modeling of biological networks with ternary logic. 2369-2370 - Simon Ott, Adriano Barbosa-Silva
LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs. 2371-2373 - Anna Pedrola, Sebastià Franch-Expósito
PCIG: a web-based application to explore immune-genomics interactions across cancer types. 2374-2376 - M. Michael Gromiha
Srinivasan (1962-2021) in Bioinformatics and beyond. 2377-2379
Volume 38, Number 9, April 2022
- Youngmok Jung
BWA-MEME: BWA-MEM emulated with a machine learning approach. 2404-2413 - Michael F. Sharpnack, Travis S. Johnson, Robert Chalkley, Zhi Han, David Carbone, Kun Huang, Kai He
TSAFinder: exhaustive tumor-specific antigen detection with RNAseq. 2422-2427 - Tong Zhou
An ensemble approach to predict binding hotspots in protein-RNA interactions based on SMOTE data balancing and Random Grouping feature selection strategies. 2452-2458 - Shawn Gu
Modeling multi-scale data via a network of networks. 2544-2553 - Eduardo Vieira de Souza
µProteInS - a proteogenomics pipeline for finding novel bacterial microproteins encoded by small ORFs. 2612-2614 - Giovanni Birolo
BamToCov: an efficient toolkit for sequence coverage calculations. 2617-2618 - Manuel Ugidos, María José Nueda
MultiBaC: an R package to remove batch effects in multi-omic experiments. 2657-2658 - Fengyuan Hu, Jia Lu, Louise S. Matheson
Correction to: ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes. 2673 - Thimothée Virgoulay
Correction to: GSpace: an exact coalescence simulator of recombining genomes under isolation by distance. 2674
Volume 38, Number 10, May 2022
- Mengtian Li
RegScaf: a regression approach to scaffolding. 2675-2682 - Yu Li
Deep learning identifies and quantifies recombination hotspot determinants. 2683-2691 - Xin Wei, Ziyi Li, Hongkai Ji, Hao Wu
EDClust: an EM-MM hybrid method for cell clustering in multiple-subject single-cell RNA sequencing. 2692-2699 - Chien-Chi Lo
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts. 2700-2704 - Liangpeng Nie
TransPPMP: predicting pathogenicity of frameshift and non-sense mutations by a Transformer based on protein features. 2705-2711 - Ke Yan, Hongwu Lv, Yichen Guo, Yongyong Chen
TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view tensor learning model. 2712-2718 - Marcos A. Caraballo-Ortiz
TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. 2719-2726 - Ambuj Kumar, Pranav M. Khade, Karin S. Dorman
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier. 2727-2733 - Bahareh Behkamal
LPTD: a novel linear programming-based topology determination method for cryo-EM maps. 2734-2741 - Tadeo E. Saldaño
Impact of protein conformational diversity on AlphaFold predictions. 2742-2748 - Weiguang Mao
Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data. 2749-2756 - Vasileios Tsiamis
VIQoR: a web service for visually supervised protein inference and protein quantification. 2757-2764 - Mengqi Zhang
BSDE: barycenter single-cell differential expression for case-control studies. 2765-2772 - Wancen Mu, Hirak Sarkar
Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets. 2773-2780 - Zhong Chen
Driver gene detection through Bayesian network integration of mutation and expression profiles. 2781-2790 - Gregory J. Boggy
BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data. 2791-2801 - Antoine Passemiers
Fast and accurate inference of gene regulatory networks through robust precision matrix estimation. 2802-2809 - Aron Park
A comprehensive evaluation of regression-based drug responsiveness prediction models, using cell viability inhibitory concentrations (IC50 values). 2810-2817 - Sajal Kumar
Overcoming biases in causal inference of molecular interactions. 2818-2825 - Yan Ding
Relational graph convolutional networks for predicting blood-brain barrier penetration of drug molecules. 2826-2831 - Xinmeng Li, Li-Ping Liu, Soha Hassoun
Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction. 2832-2838 - Ryohei Eguchi
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach. 2839-2846 - Yang Li
Supervised graph co-contrastive learning for drug-target interaction prediction. 2847-2854 - Yang Li
Network-based cancer heterogeneity analysis incorporating multi-view of prior information. 2855-2862 - Yu Wei, Shanshan Li
Interpretable-ADMET: a web service for ADMET prediction and optimization based on deep neural representation. 2863-2871 - Bailey S. Rose
Improving confidence in lipidomic annotations by incorporating empirical ion mobility regression analysis and chemical class prediction. 2872-2879 - Michael Mayers
Design and application of a knowledge network for automatic prioritization of drug mechanisms. 2880-2891 - Tian Bai
Context-aware learning for cancer cell nucleus recognition in pathology images. 2892-2898 - Yurun Lu
Annotating regulatory elements by heterogeneous network embedding. 2899-2911 - Xian F. Mallory
SimSCSnTree: a simulator of single-cell DNA sequencing data. 2912-2914 - Zhengyi Zhu, Glen A. Satten, Yi-Juan Hu
Integrative analysis of relative abundance data and presence-absence data of the microbiome using the LDM. 2915-2917 - Emma Persson
InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm. 2918-2919 - Cédric Lood
SASpector: analysis of missing genomic regions in draft genomes of prokaryotes. 2920-2921 - Manish Goel
plotsr: visualizing structural similarities and rearrangements between multiple genomes. 2922-2926 - Chiann-Ling C. Yeh
PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment. 2927-2929 - Chun-Chieh Liao, Po-Ying Fu
MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification. 2930-2931 - Hao Zhang
RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures. 2932-2933 - Marina Murillo-Recio, Ignacio Miguel Martínez de Lejarza Samper, Cristina Tuñí i Domínguez
tRNAstudio: facilitating the study of human mature tRNAs from deep sequencing datasets. 2934-2936 - Morgan Shine
AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. 2937-2939 - Andrea Carenzo
hacksig: a unified and tidy R framework to easily compute gene expression signature scores. 2940-2942 - Givanna H. Putri
Analysing high-throughput sequencing data in Python with HTSeq 2.0. 2943-2945 - Lu Lu, Joshua D. Welch
PyLiger: scalable single-cell multi-omic data integration in Python. 2946-2948 - Haotian Zhuang
findPC: An R package to automatically select the number of principal components in single-cell analysis. 2949-2951 - Moosa Rezwani
rbioapi: user-friendly R interface to biologic web services' API. 2952-2953 - Marek Slenker
MorphoTools2: an R package for multivariate morphometric analysis. 2954-2955 - Agustin Gonzalez-Reymundez
MOSS: multi-omic integration with sparse value decomposition. 2956-2958 - Noriaki Sato
CBNplot: Bayesian network plots for enrichment analysis. 2959-2960 - Brad Reisfeld
kc-hits: a tool to aid in the evaluation and classification of chemical carcinogens. 2961-2962 - Nicolas Captier
BIODICA: a computational environment for Independent Component Analysis of omics data. 2963-2964 - Alina Nicheperovich
OMAMO: orthology-based alternative model organism selection. 2965-2966 - Nicole J. Lake
MitoVisualize: a resource for analysis of variants in human mitochondrial RNAs and DNA. 2967-2969 - Christoph Harmel, Samy Sid Ahmed, Robin Koch
VisuStatR: visualizing motility and morphology statistics on images in R. 2970-2972
Volume 38, Number 11, May 2022
- Yuxuan Du
HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs. 2973-2979 - Seungjin Na
Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation. 2980-2987 - Bikash Shrestha, Badri Adhikari
Scoring protein sequence alignments using deep learning. 2988-2995 - Qijin Yin
scGraph: a graph neural network-based approach to automatically identify cell types. 2996-3003 - Manqi Cai
Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution. 3004-3010 - Abdullah Karaaslanli
scSGL: kernelized signed graph learning for single-cell gene regulatory network inference. 3011-3019 - Yifu Lu, Zhuohan Yu
GMHCC: high-throughput analysis of biomolecular data using graph-based multiple hierarchical consensus clustering. 3020-3028 - Habib Daneshpajouh
Continuous chromatin state feature annotation of the human epigenome. 3029-3036 - Hongfei Liu, Zhanerke Akhatayeva, Chuanying Pan, Mingzhi Liao
Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq. 3037-3043 - Yen-Wen Wang
KIMGENS: a novel method to estimate kinship in organisms with mixed haploid diploid genetic systems robust to population structure. 3044-3050 - Ahmad Pesaranghader, Stan Matwin
deepSimDEF: deep neural embeddings of gene products and gene ontology terms for functional analysis of genes. 3051-3061 - Feng Jiao
Quantification of transcription noise's impact on cell fate commitment with digital resolutions. 3062-3069 - Szabolcs Cselgo Kovács
Underground metabolism as a rich reservoir for pathway engineering. 3070-3077 - Suhyun Hwangbo
Kernel-based hierarchical structural component models for pathway analysis. 3078-3086 - Sifan Ye, Congyu Lu, Ye Qiu, Heping Zheng, Xingyi Ge, Aiping Wu, Zanxian Xia, Taijiao Jiang, Haizhen Zhu, Yousong Peng
An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses. 3087-3093 - Nicolas P. Canete
spicyR: spatial analysis of in situ cytometry data in R. 3099-3105 - Shaojing Wang
CnnPOGTP: a novel CNN-based predictor for identifying the optimal growth temperatures of prokaryotes using only genomic k-mers distribution. 3106-3108 - Seth W. Cheetham, Michaela Kindlova
Methylartist: tools for visualizing modified bases from nanopore sequence data. 3109-3112 - Jonathan S. Abebe, Alexander M. Price
DRUMMER - rapid detection of RNA modifications through comparative nanopore sequencing. 3113-3115 - Sheila M. Gaynor, Kenneth E. Westerman
STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis. 3116-3117 - Stéphane Samson, Etienne Lord, Vladimir Makarenkov
SimPlot++: a Python application for representing sequence similarity and detecting recombination. 3118-3120 - Aleksandra E. Badaczewska-Dawid
A3D database: structure-based predictions of protein aggregation for the human proteome. 3121-3123 - Alejandro Cáceres
teff: estimation of Treatment EFFects on transcriptomic data using causal random forest. 3124-3125 - Dongyuan Song, Nan Miles Xi
scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. 3126-3127 - Dario Righelli
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. 3128-3131 - Ali Amiryousefi
The ENDS of assumptions: an online tool for the epistemic non-parametric drug-response scoring. 3132-3133 - Kuangnan Fang, Rui Ren, Qingzhao Zhang, Shuangge Ma
iSFun: an R package for integrative dimension reduction analysis. 3134-3135 - Maxim Filimonov
Simulation and annotation of global acronyms. 3136-3138 - Xiaoyan Wang, Hongduo Liu, Shuangge Ma
GEInfo: an R package for gene-environment interaction analysis incorporating prior information. 3139-3140 - Isuru Udara Liyanage, Tony Burdett
ELIXIR biovalidator for semantic validation of life science metadata. 3141-3142 - Danyi Zou, Ye Yuan, Luming Xu, Shijun Lei, Xingbo Li, Xiaohuan Lu
PltDB: a blood platelets-based gene expression database for disease investigation. 3143-3145 - Virginie Uhlmann
Steer'n'Detect: fast 2D template detection with accurate orientation estimation. 3146-3148 - François Laurent
TRamWAy: mapping physical properties of individual biomolecule random motion in large-scale single-particle tracking experiments. 3149-3150 - Adriano Luca Martinelli, Maria Anna Rapsomaniki
ATHENA: analysis of tumor heterogeneity from spatial omics measurements. 3151-3153 - Correction to: MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification. 3154
Volume 38, Number 12, June 2022
- Fatemeh Almodaresi
An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation. 3155-3163 - Li Chen
Exploiting deep transfer learning for the prediction of functional non-coding variants using genomic sequence. 3164-3172 - Ye Yue
A new approach to testing mediation of the microbiome at both the community and individual taxon levels. 3173-3180 - Carlos A. Garcia-Prieto
Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools. 3181-3191 - Xiaoli Jiao, Hiromi Imamichi, Brad T. Sherman, Rishub Nahar, Robin L. Dewar, H. Clifford Lane, Tomozumi Imamichi, Weizhong Chang
QuasiSeq: profiling viral quasispecies via self-tuning spectral clustering with PacBio long sequencing reads. 3192-3199 - Yuanqi Du, Xiaojie Guo, Yinkai Wang, Amarda Shehu
Small molecule generation via disentangled representation learning. 3200-3208 - Isak Johansson-Åkhe
InterPepScore: a deep learning score for improving the FlexPepDock refinement protocol. 3209-3215 - Qi Liu
Dysregulated ligand-receptor interactions from single-cell transcriptomics. 3216-3221 - Ke Jin, Bo Li, Hong Yan, Xiao-Fei Zhang
Imputing dropouts for single-cell RNA sequencing based on multi-objective optimization. 3222-3230 - Ruiyan Hou
Genomic sequences and RNA-binding proteins predict RNA splicing efficiency in various single-cell contexts. 3231-3237 - Doruk Cakmakci, Gun Kaynar
Targeted metabolomics analyses for brain tumor margin assessment during surgery. 3238-3244 - Dries Van Daele
OMEN: network-based driver gene identification using mutual exclusivity. 3245-3251 - Alexander M. Waldrop
Dug: a semantic search engine leveraging peer-reviewed knowledge to query biomedical data repositories. 3252-3258 - Jasper Zhongyuan Zhang, Wei Xu, Pingzhao Hu
Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction. 3259-3266 - Lukas Lange
CLIN-X: pre-trained language models and a study on cross-task transfer for concept extraction in the clinical domain. 3267-3274 - Dongya Qin, Weichen Bo, Xin Zheng, Youjin Hao, Bo Li
DFBP: a comprehensive database of food-derived bioactive peptides for peptidomics research. 3275-3280 - Wenxiu Wang
Joint registration of multiple point clouds for fast particle fusion in localization microscopy. 3281-3287 - Ilya Vainberg-Slutskin, Noga Kowalsman, Yael Silberberg, Tal Cohen, Jenia Gold, Edith Kario, Iddo Weiner
Exodus: sequencing-based pipeline for quantification of pooled variants. 3288-3290 - Martin Hunt
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads. 3291-3293 - Shaohui Xie
CURC: a CUDA-based reference-free read compressor. 3294-3296 - Russell B. Davidson
OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances. 3297-3298 - Dibyajyoti Maity
MD DaVis: interactive data visualization of protein molecular dynamics. 3299-3301 - Genis Bayarri
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools. 3302-3303 - Joan Segura
RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies. 3304-3305 - Akio Onogi
An R package VIGoR for joint estimation of multiple linear learners with variational Bayesian inference. 3306-3309 - Daewon Lee
Nezzle: an interactive and programmable visualization of biological networks in Python. 3310-3311 - Alex Foote, Amina Asif
REET: robustness evaluation and enhancement toolbox for computational pathology. 3312-3314 - Jonathan U. Harrison
Kinetochore tracking in 3D from lattice light-sheet imaging data with KiT. 3315-3317
Volume 38, Number 13, June 2022
- Andrea Guarracino
ODGI: understanding pangenome graphs. 3319-3326 - Yi Nian Niu
Assessing and assuring interoperability of a genomics file format. 3327-3336 - Bo Yang
Deep structure integrative representation of multi-omics data for cancer subtyping. 3337-3342 - Diego Santoro, Leonardo Pellegrina
SPRISS: approximating frequent k-mers by sampling reads, and applications. 3343-3350 - Ruheng Wang
Predicting protein-peptide binding residues via interpretable deep learning. 3351-3360 - Martin M. Femenias
ExplorATE: a new pipeline to explore active transposable elements from RNA-seq data. 3361-3366 - Nadia Tahiri
Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance. 3367-3376 - Xiajie Wei, Jiayi Dong, Fei Wang
scPreGAN, a deep generative model for predicting the response of single-cell expression to perturbation. 3377-3384 - Zhuoqing Fang
An automated multi-modal graph-based pipeline for mouse genetic discovery. 3385-3394 - Kapil Devkota, Henri Schmidt
GLIDER: function prediction from GLIDE-based neighborhoods. 3395-3406 - Cesim Erten, Aissa Houdjedj, Hilal Kazan
PersonaDrive: a method for the identification and prioritization of personalized cancer drivers. 3407-3414 - Yang Bai
AutoDC: an automatic machine learning framework for disease classification. 3415-3421 - Christoph Bueschl
PeakBot: machine-learning-based chromatographic peak picking. 3422-3428 - Huaxu Yu, Tao Huan
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities. 3429-3437 - Hongyang Yu, Hongjiang C. Yu:
Powerful molecule generation with simple ConvNet. 3438-3443 - Shanzhuo Zhang, Zhiyuan Yan
HelixADMET: a robust and endpoint extensible ADMET system incorporating self-supervised knowledge transfer. 3444-3453 - Tim Kucera
Conditional generative modeling for de novo protein design with hierarchical functions. 3454-3461 - Philippe Weitz
Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression-based convolutional neural networks. 3462-3469 - Erik N. Bergstrom
Examining clustered somatic mutations with SigProfilerClusters. 3470-3473 - Alexander N. Stein
ScisorWiz: visualizing differential isoform expression in single-cell long-read data. 3474-3476 - Florian Privé
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics. 3477-3480 - Zhentao Liu, Zhengdong Zhang, Sheng Liang, Zhen Chen, Xiaoyao Xie, Tie Shen
CeCaFLUX: the first web server for standardized and visual instationary 13C metabolic flux analysis. 3481-3483 - Jonathan Strutz
MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics. 3484-3487 - Zilong Zhang
webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration. 3488-3489 - Melissa Grant-Peters, Charlotte Rich-Griffin, Jonathan E. Grant-Peters, Gianfelice Cinque, Calliope A. Dendrou
Photizo: an open-source library for cross-sample analysis of FTIR spectroscopy data. 3490-3492
Volume 38, Number 14, July 2022
- Wei Zhang, Aiyi Liu, Zhiwei Zhang, Guanjie Chen, Qizhai Li:
An adaptive direction-assisted test for microbiome compositional data. 3493-3500 - Dongchan Yang
DeepLUCIA: predicting tissue-specific chromatin loops using Deep Learning-based Universal Chromatin Interaction Annotator. 3501-3512 - Qiong Wu, Xubin Zheng, Kwong-Sak Leung, Man Hon Wong, Stephen Kwok-Wing Tsui
meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data. 3513-3522 - Itunu G. Osuntoki
ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data. 3523-3531 - Ariel A. Aptekmann
mebipred: identifying metal-binding potential in protein sequence. 3532-3540 - Yansu Wang
Effector-GAN: prediction of fungal effector proteins based on pretrained deep representation learning methods and generative adversarial networks. 3541-3548 - Hongyu Zhao, Kun Han, Chao Gao, Vithal Madhira, Umit Topaloglu, Yong Lu, Guangxu Jin
VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern. 3549-3556 - Jacob M. Schreiber
Accelerating in silico saturation mutagenesis using compressed sensing. 3557-3564 - Gleb Zhelezov
Trying out a million genes to find the perfect pair with RTIST. 3565-3573 - Qin Wang
Prior knowledge facilitates low homologous protein secondary structure prediction with DSM distillation. 3574-3581 - Fei Li
Effective drug-target interaction prediction with mutual interaction neural network. 3582-3589 - Turkan Haliloglu
Prediction of allosteric communication pathways in proteins. 3590-3599 - Shuyi Zhang, Jacob R. Leistico, Raymond J. Cho, Jeffrey B. Cheng, Jun S. Song
Spectral clustering of single-cell multi-omics data on multilayer graphs. 3600-3608 - David Earl Hostallero
Looking at the BiG picture: incorporating bipartite graphs in drug response prediction. 3609-3620 - Matthias Kirchler
transferGWAS: GWAS of images using deep transfer learning. 3621-3628 - Huidong Liu
Deep learning for survival analysis in breast cancer with whole slide image data. 3629-3637 - Blas Chaves-Urbano
CNpare: matching DNA copy number profiles. 3638-3641 - Siqi Shen, Ye Zheng, Sündüz Keles
scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data. 3642-3644 - Marina Ainciburu, Duncan M. Morgan, Erica A. K. Depasquale, J. Christopher Love, Felipe Prósper, Peter van Galen
WAT3R: recovery of T-cell receptor variable regions from 3′ single-cell RNA-sequencing. 3645-3647 - Adam Midlik
OverProt: secondary structure consensus for protein families. 3648-3650 - Baptiste Kerouanton
CLIPreg: constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq. 3651-3653 - Wenpin Hou
Palo: spatially aware color palette optimization for single-cell and spatial data. 3654-3656 - Laurence Legon
gcFront: a tool for determining a Pareto front of growth-coupled cell factory designs. 3657-3659 - Léo P. M. Diaz
HyperGraphs.jl: representing higher-order relationships in Julia. 3660-3661 - Leqi Tian
Metapone: a Bioconductor package for joint pathway testing for untargeted metabolomics data. 3662-3664 - Pablo Monfort-Lanzas
MIO: microRNA target analysis system for immuno-oncology. 3665-3667 - Bartosz Adamczyk, Maciej Antczak
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures. 3668-3670 - Sylvain Prigent, Cesar Augusto Valades-Cruz
STracking: a free and open-source Python library for particle tracking and analysis. 3671-3673 - Luis M. Rocha
On the feasibility of dynamical analysis of network models of biochemical regulation. 3674-3675 - Felix M. Weidner
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation. 3676
Volume 38, Number 15, August 2022
- Lily Zheng, Noushin Niknafs, Laura D. Wood, Rachel Karchin
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. 3677-3683 - Wei-Zhi Song
MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads. 3684-3688 - Yi-Juan Hu
A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome. 3689-3697 - Peter J. Bradbury
The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. 3698-3702 - Hai-Yun Wang, Jian-Ping Zhao
scCNC: a method based on capsule network for clustering scRNA-seq data. 3703-3709 - Nik Tavakolian
Shepherd: accurate clustering for correcting DNA barcode errors. 3710-3716 - Sumit Tarafder, Mazharul Islam, Swakkhar Shatabda
Figbird: a probabilistic method for filling gaps in genome assemblies. 3717-3724 - Sarah Lutteropp
NetRAX: accurate and fast maximum likelihood phylogenetic network inference. 3725-3733 - Cheng Ye, Bryan Thornlow, Angie S. Hinrichs
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2. 3734-3740 - Yupei You, Michael B. Clark
NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing. 3741-3748 - Niels Johan Christensen, Samuel Demharter
Identifying interactions in omics data for clinical biomarker discovery using symbolic regression. 3749-3758 - Frantisek Malinka
Batch alignment via retention orders for preprocessing large-scale multi-batch LC-MS experiments. 3759-3767 - Yilei Huang
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes. 3768-3777 - Rick Wertenbroek
XSI - a genotype compression tool for compressive genomics in large biobanks. 3778-3784 - Marzieh Ayati
Functional characterization of co-phosphorylation networks. 3785-3793 - Wonjin Yoon
Sequence tagging for biomedical extractive question answering. 3794-3801 - Ahmed A. Metwally
Robust identification of temporal biomarkers in longitudinal omics studies. 3802-3811 - Pavel Vazquez
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences. 3812-3817 - Souvik Seal
MIAMI: mutual information-based analysis of multiplex imaging data. 3818-3826 - Matthew Crown
SPEAR: Systematic ProtEin AnnotatoR. 3827-3829 - Piyush Ranjan, Christopher A. Brown, John R. Erb-Downward
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data. 3830-3832 - Parthajit Roy
MetBP: a software tool for detection of interaction between metal ion-RNA base pairs. 3833-3834 - Michal Zurkowski
DrawTetrado to create layer diagrams of G4 structures. 3835-3836 - Varun Ullanat, Nikhil Kasukurthi
PrISM: precision for integrative structural models. 3837-3839 - Pu Huang, Erin Davis
riboCleaner: a pipeline to identify and quantify rRNA read contamination from RNA-seq data in plants. 3840-3843 - Emil K. Gustavsson
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2. 3844-3846 - Daniele Bizzarri
MiMIR: R-shiny application to infer risk factors and endpoints from Nightingale Health's 1H-NMR metabolomics data. 3847-3849 - Philipp Wegner
Integrative data semantics through a model-enabled data stewardship. 3850-3852
Volume 38, Number 16, August 2022
- Chen Lyu, Manyan Huang, Nianjun Liu, Zhongxue Chen
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci. 3853-3862 - Maria Osmala
ChromDMM: a Dirichlet-multinomial mixture model for clustering heterogeneous epigenetic data. 3863-3870 - Vinzenz May, Leonard Koch
ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise. 3871-3876 - Yang-Ming Yeh
MSRCall: a multi-scale deep neural network to basecall Oxford Nanopore sequences. 3877-3884 - Mobeen Ur Rehman
i6mA-Caps: a CapsuleNet-based framework for identifying DNA N6-methyladenine sites. 3885-3891 - Marcell Szikszai
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families. 3892-3899 - Jaswinder Singh
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling. 3900-3910 - Antoine Moniot
ProtNAff: protein-bound Nucleic Acid filters and fragment libraries. 3911-3917 - Michael Komodromos
Variational Bayes for high-dimensional proportional hazards models with applications within gene expression. 3918-3926 - Elvis Han Cui, Dongyuan Song, Weng Kee Wong, Jingyi Jessica Li
Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime. 3927-3934 - Oya Ekin Karasan, Alper Sen
A unifying network modeling approach for codon optimization. 3935-3941 - Yuge Wang
ResPAN: a powerful batch correction model for scRNA-seq data through residual adversarial networks. 3942-3949 - Yucheng Wang
InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias. 3950-3957 - Joseph Szymborski
RAPPPID: towards generalizable protein interaction prediction with AWD-LSTM twin networks. 3958-3967 - Alicja W. Nowakowska
Topological analysis as a tool for detection of abnormalities in protein-protein interaction data. 3968-3975 - Yiqi Tong
Improving biomedical named entity recognition by dynamic caching inter-sentence information. 3976-3983 - Hayda Almeida
Improving candidate Biosynthetic Gene Clusters in fungi through reinforcement learning. 3984-3991 - Xuexue Liu
mapDATAge: a ShinyR package to chart ancient DNA data through space and time. 3992-3994 - Cheng Zhong
Hierarchical reinforcement learning for automatic disease diagnosis. 3995-4001 - Qibing Jiang, Praneeth Sudalagunta, Maria C. Silva, Rafael R. Canevarolo
CancerCellTracker: a brightfield time-lapse microscopy framework for cancer drug sensitivity estimation. 4002-4010 - Pritam Dey
Outlier detection for multi-network data. 4011-4018 - Matee Ullah, Fazal Hadi, Jiangning Song
PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data. 4019-4026 - Yang Cao
microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization. 4027-4029 - Matej Lexa
HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization. 4030-4032 - Benjamin C. Jackson:
gofasta: command-line utilities for genomic epidemiology research. 4033-4035 - Vinod Kumar Singh
HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elements. 4036-4038 - Tsukasa Fukunaga
Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families. 4039-4041 - Jun Li, Sicheng Zhang, Dong Zhang
Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences. 4042-4043 - Liesa Salzer
MobilityTransformR: an R package for effective mobility transformation of CE-MS data. 4044-4045 - Gordon T. Luu
TIMSCONVERT: a workflow to convert trapped ion mobility data to open data formats. 4046-4047 - Noé Fernández-Pozo, Aureliano Bombarely
EasyGDB: a low-maintenance and highly customizable system to develop genomics portals. 4048-4050 - Puneet Rawat
Ab-CoV: a curated database for binding affinity and neutralization profiles of coronavirus-related antibodies. 4051-4052
Volume 38, Number 17, September 2022
- Quanzhong Liu
DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions. 4053-4061 - Yang Chen
DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma. 4062-4069 - Yan Li, Lijun Quan, Yiting Zhou, Yelu Jiang
Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence. 4070-4077 - Hongjie Ke, Zhao Ren, Jianfei Qi, Shuo Chen, George C. Tseng
High-dimension to high-dimension screening for detecting genome-wide epigenetic and noncoding RNA regulators of gene expression. 4078-4087 - Bader F. Al-Anzi
Predicting and explaining the impact of genetic disruptions and interactions on organismal viability. 4088-4099 - Mitra Darvish
Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. 4100-4108 - Huanyu Tao, Xuejun Zhao, Keqiong Zhang, Peicong Lin, Sheng-You Huang
Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy. 4109-4116 - Ying Xin, Pin Lyu, Junyao Jiang
LRLoop: a method to predict feedback loops in cell-cell communication. 4117-4126 - Lise Pomiès
Gene regulatory network inference methodology for genomic and transcriptomic data acquired in genetically related heterozygote individuals. 4127-4134 - Jinge Yu, Xiangyu Luo
Identification of cell-type-specific spatially variable genes accounting for excess zeros. 4135-4144 - Michele Gentili, Leonardo Martini, Marialuisa Sponziello
Biological Random Walks: multi-omics integration for disease gene prioritization. 4145-4152 - Zhongjian Cheng, Qichang Zhao
IIFDTI: predicting drug-target interactions through interactive and independent features based on attention mechanism. 4153-4161 - Tim Breitenbach
Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing. 4162-4171 - Vivek Ramanan, Shanti Mechery, Indra Neil Sarkar
GenBank as a source to monitor and analyze Host-Microbiome data. 4172-4177 - Raphael Sonabend
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures. 4178-4184 - Francesco P. Panei
HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design. 4185-4193 - Shuya Ikeda
TogoID: an exploratory ID converter to bridge biological datasets. 4194-4199 - Jakub Wiedemann, Jacek Kaczor, Maciej Milostan, Tomasz Zok
RNAloops: a database of RNA multiloops. 4200-4205 - Yanan Wang, Changyuan Hu
DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images. 4206-4213 - Giulio Formenti
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. 4214-4216 - Fawaz Dabbaghie
BubbleGun: enumerating bubbles and superbubbles in genome graphs. 4217-4219 - Aaron Chuah
StabilitySort: assessment of protein stability changes on a genome-wide scale to prioritize potentially pathogenic genetic variation. 4220-4222 - Alice Wittig
CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance. 4223-4225 - Gökhan Özsari
SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins. 4226-4229 - Torbjørn Rognes
CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. 4230-4232 - Serena Rosignoli
DockingPie: a consensus docking plugin for PyMOL. 4233-4234 - Pietro Hiram Guzzi
PCN-Miner: an open-source extensible tool for the analysis of Protein Contact Networks. 4235-4237 - Feng Zhou
Flashfm-ivis: interactive visualization for fine-mapping of multiple quantitative traits. 4238-4242 - Xiaoming Fu
DelaySSAToolkit.jl: stochastic simulation of reaction systems with time delays in Julia. 4243-4245 - Ángel Rodríguez-Cerro, Sergio Sancho, Miriam Rodríguez
ANISE: an application to design mechanobiology simulations of planar epithelia. 4246-4247 - Zuguang Gu
Pkgndep: a tool for analyzing dependency heaviness of R packages. 4248-4251 - Yizhuo Wang
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis. 4252-4254
Volume 38, Number 18, September 2022
- Lance D. Hentges
LanceOtron: a deep learning peak caller for genome sequencing experiments. 4255-4263 - Zeheng Bai
Identification of bacteriophage genome sequences with representation learning. 4264-4270 - Xinjie Li, Shengli Zhang
An improved residual network using deep fusion for identifying RNA 5-methylcytosine sites. 4271-4277 - Vlad-Rares Danaila
Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning. 4278-4285 - Jun-Jie Zheng, Po-Wen Wang, Tzu-Wen Huang, Yao-Jong Yang, Hua-Sheng Chiu, Pavel Sumazin, Ting-Wen Chen
MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis. 4286-4292 - Hana Rozhonová, Daniel Danciu, Stefan Stark
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing. 4293-4300 - Jimin Pei
Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling. 4301-4311 - Marina A. Pak
Best templates outperform homology models in predicting the impact of mutations on protein stability. 4312-4320 - Yeganeh Madadi
Detecting retinal neural and stromal cell classes and ganglion cell subtypes based on transcriptome data with deep transfer learning. 4321-4329 - Keita Iida
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes. 4330-4336 - Yongwen Zhuang
Incorporating family disease history and controlling case-control imbalance for population-based genetic association studies. 4337-4343 - Sam F. L. Windels
Identifying cellular cancer mechanisms through pathway-driven data integration. 4344-4351 - Vincent Wagner, Benjamin Castellaz, Marco Oesting, Nicole Radde
Quasi-Entropy Closure: a fast and reliable approach to close the moment equations of the Chemical Master Equation. 4352-4359 - Colm Seale
Overcoming selection bias in synthetic lethality prediction. 4360-4368 - Maria Mahbub
BioADAPT-MRC: adversarial learning-based domain adaptation improves biomedical machine reading comprehension task. 4369-4379 - Yuhao Chen, Yanshi Hu
CoGO: a contrastive learning framework to predict disease similarity based on gene network and ontology structure. 4380-4386 - Shujie Ren, Liang Yu
Multidrug representation learning based on pretraining model and molecular graph for drug interaction and combination prediction. 4387-4394 - Longjie Li, Arun Mouli Kolinjivadi, Kok Haur Ong, David M. Young
Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level. 4395-4402 - Eef M. Jonkheer
PanTools v3: functional annotation, classification and phylogenomics. 4403-4405 - Zhixia Xiao
ShinySyn: a Shiny/R application for the interactive visualization and integration of macro- and micro-synteny data. 4406-4408 - Brian Y. Chen, William Bone
ColocQuiaL: a QTL-GWAS colocalization pipeline. 4409-4411 - Alexis Dereeper
PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes. 4412-4414 - Vonn Walter
DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference. 4415-4417 - Gabriel Cia
SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants. 4418-4419 - Jason Yeung
ViReMaShiny: an interactive application for analysis of viral recombination data. 4420-4422 - Yoann Dufresne
The K-mer File Format: a standardized and compact disk representation of sets of k-mers. 4423-4425 - Hyun Kil Shin
ToxSTAR: drug-induced liver injury prediction tool for the web environment. 4426-4427 - Chih-Hao Lu, Chih-Chieh Chen
MIB2: metal ion-binding site prediction and modeling server. 4428-4429 - Federico Ansaloni
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments. 4430-4433 - Eric Ruan, Erika Nemeth, Richard A. Moffitt
PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project. 4434-4436 - Panteleimon G. Takis
NMRpQuant: an automated software for large scale urinary total protein quantification by one-dimensional 1H NMR profiles. 4437-4439 - Franco Pradelli
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models. 4440-4441 - Mengyuan Kan
REALGAR: a web app of integrated respiratory omics data. 4442-4445 - Zaiqiao Meng
BioCaster in 2021: automatic disease outbreaks detection from global news media. 4446-4448 - Chih-Hsuan Wei
tmVar 3.0: an improved variant concept recognition and normalization tool. 4449-4451 - Ammar Qaseem
CPRiL: compound-protein relationships in literature. 4452-4453 - Yi-An Chen, Rodolfo S. Allendes Osorio
TargetMine 2022: a new vision into drug target analysis. 4454-4456
Volume 38, Number 19, September 2022
- Ke Zhang, Chenxi Wang
Prediction of gene co-expression from chromatin contacts with graph attention network. 4457-4465 - Maciej Piernik
DBFE: distribution-based feature extraction from structural variants in whole-genome data. 4466-4473 - Jinfa Ma
Detection of orthologous exons and isoforms using EGIO. 4474-4480 - Andre Lamurias
Metagenomic binning with assembly graph embeddings. 4481-4487 - Gabriela Alejandra Merino
Hierarchical deep learning for predicting GO annotations by integrating protein knowledge. 4488-4496 - Pengyu Zhang
CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types. 4497-4504 - Yasser Mohseni Behbahani
Deep Local Analysis evaluates protein docking conformations with locally oriented cubes. 4505-4512 - Chunxiang Peng, Xiao-Gen Zhou
Structural analogue-based protein structure domain assembly assisted by deep learning. 4513-4521 - Guangyi Chen, Zhi-Ping Liu
Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data. 4522-4529 - Chixiang Chen
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge. 4530-4536 - Yanchi Su, Fuzhou Wang
scWMC: weighted matrix completion-based imputation of scRNA-seq data via prior subspace information. 4537-4545 - Wei Peng
Predicting cancer drug response using parallel heterogeneous graph convolutional networks with neighborhood interactions. 4546-4553 - Ragunathan Mariappan, Aishwarya Jayagopal, Ho Zong Sien, Vaibhav Rajan
Neural Collective Matrix Factorization for integrated analysis of heterogeneous biomedical data. 4554-4561 - Jia-Cai Yi
MICER: a pre-trained encoder-decoder architecture for molecular image captioning. 4562-4572 - Jing Jiang
MultiGran-SMILES: multi-granularity SMILES learning for molecular property prediction. 4573-4580 - Sichao Qiu, Guoxian Yu
Isoform function prediction by Gene Ontology embedding. 4581-4588 - Melissa Kimble
medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata. 4589-4597 - Jie Wang
3D GAN image synthesis and dataset quality assessment for bacterial biofilm. 4598-4604 - Hongyi Duanmu
A spatial attention guided deep learning system for prediction of pathological complete response using breast cancer histopathology images. 4605-4612 - Jeremy Muhlich
Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. 4613-4621 - Adrian Friebel, Tim Johann
Guided interactive image segmentation using machine learning and color-based image set clustering. 4622-4628 - Jun Zhang, Fan Nie, Neng Huang, Peng Ni, Feng Luo, Jianxin Wang
Fec: a fast error correction method based on two-rounds overlapping and caching. 4629-4632 - Jeremie S. Kim
FastRemap: a tool for quickly remapping reads between genome assemblies. 4633-4635 - Shuangquan Zhang
MMGraph: a multiple motif predictor based on graph neural network and coexisting probability for ATAC-seq data. 4636-4638 - Quan Shi
The FASTQ+ format and PISA. 4639-4642 - Shiyu Jiang
HNOXPred: a web tool for the prediction of gas-sensing H-NOX proteins from amino acid sequence. 4643-4644 - Arkadeep Sarkar, Jacopo Santoro, Luigi Di Biasi
YAMACS: a graphical interface for GROMACS. 4645-4646 - Athena Chen
Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER. 4647-4649 - Xiaotao Shen
massDatabase: utilities for the operation of the public compound and pathway database. 4650-4651 - Bartlomiej Szawulak
Comparing Petri net-based models of biological systems using Holmes. 4652-4653 - Yuanyuan Li
mBrainAligner-Web: a web server for cross-modal coherent registration of whole mouse brains. 4654-4655 - Manuel Rueda
Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data. 4656-4657
Volume 38, Number 20, October 2022
- Jim Shaw
Theory of local k-mer selection with applications to long-read alignment. 4659-4669 - Wenhuan Zeng, Anupam Gautam
DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome. 4670-4676 - Galen F. Gao
Tangent normalization for somatic copy-number inference in cancer genome analysis. 4677-4686 - Xiaoguang Li, Xingdong Feng, Xu Liu
Heritability estimation for a linear combination of phenotypes via ridge regression. 4687-4696 - Hai Yang
TVAR: assessing tissue-specific functional effects of non-coding variants with deep learning. 4697-4704 - Zhenxing Guo, Andrew M. Shafik
Differential RNA methylation analysis for MeRIP-seq data under general experimental design. 4705-4712 - Jack Kuipers
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. 4713-4719 - Belinda Phipson
propeller: testing for differences in cell type proportions in single cell data. 4720-4726 - Marie Oestreich
hCoCena: horizontal integration and analysis of transcriptomics datasets. 4727-4734 - Yun Zhang
FastMix: a versatile data integration pipeline for cell type-specific biomarker inference. 4735-4744 - Yue Cao
scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction. 4745-4753 - Justine Labory, Gwendal Le Bideau, David Pratella, Jean-Elisée Yao, Samira Ait-El-Mkadem Saadi, Sylvie Bannwarth, Loubna El-Hami, Véronique Paquis-Flucklinger, Silvia Bottini
ABEILLE: a novel method for ABerrant Expression Identification empLoying machine LEarning from RNA-sequencing data. 4754-4761 - Ren Yi
NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction. 4762-4770 - Aditya Jadhav, Tarun Kumar
Predicting cross-tissue hormone-gene relations using balanced word embeddings. 4771-4781 - Xuan Liu
Multi-way relation-enhanced hypergraph representation learning for anti-cancer drug synergy prediction. 4782-4789 - Priya Tiwary
No means 'No': a non-improper modeling approach, with embedded speculative context. 4790-4796 - Bintao He
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network. 4797-4805 - Hong-Dong Li
GTFtools: a software package for analyzing various features of gene models. 4806-4808 - Lucas Czech
grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads. 4809-4811 - Parham Kazemi
ntHash2: recursive spaced seed hashing for nucleotide sequences. 4812-4813 - Sean M. Solari, Remy B. Young, Vanessa R. Marcelino
expam - high-resolution analysis of metagenomes using distance trees. 4814-4816 - Dominik Buchner, Till-Hendrik Macher
APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data. 4817-4819 - Oladele A. Oluwayiose
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses. 4820-4822 - Alexander L. R. Lubbock
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python. 4823-4825 - María Isabel Alcoriza-Balaguer, Juan Carlos García-Cañaveras, Francisco Javier Ripoll-Esteve, Marta Roca
LipidMS 3.0: an R-package and a web-based tool for LC-MS/MS data processing and lipid annotation. 4826-4828 - Mario Grassi, Fernando Palluzzi, Barbara Tarantino
SEMgraph: an R package for causal network inference of high-throughput data with structural equation models. 4829-4830 - Ines Thiele
MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions. 4831-4832 - Kavishwar B. Wagholikar
I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform. 4833-4836 - Mujeen Sung
BERN2: an advanced neural biomedical named entity recognition and normalization tool. 4837-4839 - Carsten Henneges, Joseph N. Paulson
GameRank: R package for feature selection and construction. 4840-4842 - Lea Gütebier
CovidGraph: a graph to fight COVID-19. 4843-4845 - Yifan Gui
pcnaDeep: a fast and robust single-cell tracking method using deep-learning mediated cell cycle profiling. 4846-4847 - John L. Spouge
A closed formula relevant to 'Theory of local k-mer selection with applications to long-read alignment' by Jim Shaw and Yun William Yu. 4848-4849
Volume 38, Number 21, October 2022
- Pablo Mier
The sequence context in poly-alanine regions: structure, function and conservation. 4851-4858 - Junjie Wang
MGPLI: exploring multigranular representations for protein-ligand interaction prediction. 4859-4867 - Takaho Tsuchiya
CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells. 4868-4877 - Haoyang Li
SD2: spatially resolved transcriptomics deconvolution through integration of dropout and spatial information. 4878-4884 - Ziyi Li
A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data. 4885-4892 - Christoph Müssel, Nensi Ikonomi
CANTATA - prediction of missing links in Boolean networks using genetic programming. 4893-4900 - Wenyi Zhao, Xun Gu, Shuqing Chen, Jian Wu, Zhan Zhou
MODIG: integrating multi-omics and multi-dimensional gene network for cancer driver gene identification based on graph attention network model. 4901-4907 - Quinn Dickinson
Multi-omic integration by machine learning (MIMaL). 4908-4918 - Han Cao
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning. 4919-4926 - Bo Wang
Systematic comparison of ranking aggregation methods for gene lists in experimental results. 4927-4933 - Gregory J. Hunt
Systematic replication enables normalization of high-throughput imaging assays. 4934-4940 - Jin-Xian Hu, Yang Yang
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images. 4941-4948 - Chao Zhang
ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees. 4949-4950 - J. Harry Moore
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules. 4951-4952 - Shun Liu, Jianchao Zhou, Ziyan Feng, Jiawen Zhang, Shuang Li, Zilong Jin, Chenfei Zhang, Shiliang Li, Gaoqi He, Honglin Li
VRPharmer: bringing virtual reality into pharmacophore-based virtual screening with interactive exploration and realistic visualization. 4953-4955 - Enes K. Ergin
SQuAPP - simple quantitative analysis of proteins and PTMs. 4956-4958 - Nahuel Escobedo
CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure. 4959-4961 - Hansaim Lim
HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry. 4962-4965 - Joshua Fry, Yangyang Li, Rendong Yang
ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data. 4966-4968 - Jun Chen
dICC: distance-based intraclass correlation coefficient for metagenomic reproducibility studies. 4969-4971 - Layla Aref, Lisa Bastarache, Jacob J. Hughey
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants. 4972-4974 - Jiashuo Wu
DRviaSPCN: a software package for drug repurposing in cancer via a subpathway crosstalk network. 4975-4977 - Nikola Benes
AEON.py: Python library for attractor analysis in asynchronous Boolean networks. 4978-4980 - Philipp Schneider
StrainDesign: a comprehensive Python package for computational design of metabolic networks. 4981-4983 - Soya Shinkai
PHi-C2: interpreting Hi-C data as the dynamic 3D genome state. 4984-4986 - Lijuan Liu
Manifold classification of neuron types from microscopic images. 4987-4989 - Anna Niarakis
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. 4990-4993 - Geir Kjetil Sandve
Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking. 4994-4996 - Correction to: Topological analysis as a tool for detection of abnormalities in protein-protein interaction data. 4997
- Correction to: Integrative data semantics through a model-enabled data stewardship. 4998
Volume 38, Number 22, November 2022
- Lars Wienbrandt
EagleImp: fast and accurate genome-wide phasing and imputation in a single tool. 4999-5006 - Athanasios Baltzis
Highly significant improvement of protein sequence alignments with AlphaFold2. 5007-5011 - Jouni Sirén
GBZ file format for pangenome graphs. 5012-5018 - Yanming Wei
WMSA: a novel method for multiple sequence alignment of DNA sequences. 5019-5025 - Gourab Ghosh Roy
MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk. 5026-5032 - Satwik Acharyya
SpaceX: gene co-expression network estimation for spatial transcriptomics. 5033-5041 - Zhongyuan Xu
scSemiGAN: a single-cell semi-supervised annotation and dimensionality reduction framework based on generative adversarial network. 5042-5048 - Victor Bernal
GeneNetTools: tests for Gaussian graphical models with shrinkage. 5049-5054 - Gavin M. Douglas
Integrating phylogenetic and functional data in microbiome studies. 5055-5063 - Michael A Kochen
SBbadger: biochemical reaction networks with definable degree distributions. 5064-5072 - Yanfei Li
Drug-Protein interaction prediction by correcting the effect of incomplete information in heterogeneous information. 5073-5080 - Michal Ziemski
Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue. 5081-5091 - Xingze Wang, Guoxian Yu
Lung cancer subtype diagnosis using weakly-paired multi-omics data. 5092-5099 - Yutai Hou
Discovering drug-target interaction knowledge from biomedical literature. 5100-5107 - Kaimei Huang
Predicting colorectal cancer tumor mutational burden from histopathological images and clinical information using multi-modal deep learning. 5108-5115 - Ji-Hye Choi
CGV: Cancer Genome Viewer, a web service for integrative cancer genome and pharmacogenomic data analysis. 5116-5118 - Milan A. Clasen
Increasing confidence in proteomic spectral deconvolution through mass defect. 5119-5120 - Brendon H. Cooper, Tsu-Pei Chiu, Remo Rohs
Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics. 5121-5123 - Wytamma Wirth
Phytest: quality control for phylogenetic analyses. 5124-5125 - Jonathan Moody
SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells. 5126-5128 - Ariel A. Hippen, Jake Crawford, Jacob R. Gardner, Casey S. Greene
wenda_gpu: fast domain adaptation for genomic data. 5129-5130 - Huma Shehwana
RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data. 5131-5133 - Wenhao Li
statgenMPP: an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations. 5134-5136 - Dandan Sun
BioBulkFoundary: a customized webserver for exploring biosynthetic potentials of bulk chemicals. 5137-5138 - Kevin Mildau
Homologue series detection and management in LC-MS data with homologueDiscoverer. 5139-5140 - Yi Ding, Kangwen Cai, Leiqin Liu, Zhiqiang Zhang, Xiaoqi Zheng, Jiantao Shi
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes. 5141-5143 - Nayang Shan, Yao Lu, Hao Guo, Dongyu Li, Jitong Jiang, Linlin Yan, Jiudong Gao, Yong Ren, Xing-Ming Zhao
CITEdb: a manually curated database of cell-cell interactions in human. 5144-5148 - Correction to: Efficient permutation-based genome-wide association studies for normal and skewed phenotypic distributions. 5149
Volume 38, Number 23, November 2022
- Hongqiang Lyu
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data. 5151-5159 - Chunting Liu, Jiangning Song
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites. 5160-5167 - Matteo Manfredi
E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants. 5168-5174 - Yuhao Chen, Xiaowei Wang
Evaluation of efficiency prediction algorithms and development of ensemble model for CRISPR/Cas9 gRNA selection. 5175-5181 - Jing Peng
Estimation of speciation times under the multispecies coalescent. 5182-5190 - Roy González-Alemán
MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics. 5191-5198 - Josef Paul Kynast
ATLIGATOR: editing protein interactions with an atlas-based approach. 5199-5205 - Courtney Schiebout
CAMML with the Integration of Marker Proteins (ChIMP). 5206-5213 - Nicolas Enjalbert-Courrech, Pierre Neuvial
Powerful and interpretable control of false discoveries in two-group differential expression studies. 5214-5221 - Xiaqiong Wang, Yalu Wen
A penalized linear mixed model with generalized method of moments estimators for complex phenotype prediction. 5222-5228 - Peixin Tian, Minhao Yao, Tao Huang, Zhonghua Liu
CoxMKF: a knockoff filter for high-dimensional mediation analysis with a survival outcome in epigenetic studies. 5229-5235 - Elham Jafari
AIscEA: unsupervised integration of single-cell gene expression and chromatin accessibility via their biological consistency. 5236-5244 - Yue Zhao
CEDA: integrating gene expression data with CRISPR-pooled screen data identifies essential genes with higher expression. 5245-5252 - Huiwei Zhou, Haibin Jiang, Weihong Yao, Xun Du:
Learning temporal difference embeddings for biomedical hypothesis generation. 5253-5261 - Jinyu Sun, Ming Wen, Huabei Wang, Yuezhe Ruan, Qiong Yang, Xiao Kang
Prediction of drug-likeness using graph convolutional attention network. 5262-5269 - Sendong Zhao
Biomedical evidence engineering for data-driven discovery. 5270-5278 - Yiqing Zhao
Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine. 5279-5287 - Ran Yang, Alexandra M. Stendahl, Katinka A Vigh-Conrad, Madison Held, Ana C. Lima, Donald F. Conrad
SATINN: an automated neural network-based classification of testicular sections allows for high-throughput histopathology of mouse mutants. 5288-5298 - Huangqingbo Sun
Improving and evaluating deep learning models of cellular organization. 5299-5306 - Haoda Lu
A novel pipeline for computerized mouse spermatogenesis staging. 5307-5314 - Pierre-Alain Chaumeil
GTDB-Tk v2: memory friendly classification with the genome taxonomy database. 5315-5316 - Duoyuan Chen
Tree2GD: a phylogenomic method to detect large-scale gene duplication events. 5317-5321 - Haocheng Gu, Hao Cheng
scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data. 5322-5325 - Emily Hashimoto-Roth, Anuradha Surendra, Mathieu Lavallée-Adam
METAbolomics data Balancing with Over-sampling Algorithms (META-BOA): an online resource for addressing class imbalance. 5326-5327 - Correction to: plotsr: visualizing structural similarities and rearrangements between multiple genomes. 5328
Volume 38, Number 24, December 2022
- Yufeng Liu
Neuron tracing from light microscopy images: automation, deep learning and bench testing. 5329-5339 - Ye Wang, Li Chen
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome. 5340-5351 - Ramin Shirali Hossein Zade
HAT: haplotype assembly tool using short and error-prone long reads. 5352-5359 - Dehan Cai
HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization. 5360-5367 - Yuxuan Pang
Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities. 5368-5374 - Gang Wu
An in silico genome-wide screen for circadian clock strength in human samples. 5375-5382 - Surabhi Jagtap
BraneMF: integration of biological networks for functional analysis of proteins. 5383-5389 - Stephan Fischer
Defining the extent of gene function using ROC curvature. 5390-5397 - Jiayuan Zhong
Identifying the critical state of complex biological systems by the directed-network rank score method. 5398-5405 - Yue Hong
LaGAT: link-aware graph attention network for drug-drug interaction prediction. 5406-5412 - Theodore Groth
GlycoEnzOnto: a GlycoEnzyme pathway and molecular function ontology. 5413-5420 - Vincent Ebert, Patrick Eiring, Dominic A. Helmerich, Rick Seifert, Markus Sauer, Sören Doose
Convex hull as diagnostic tool in single-molecule localization microscopy. 5421-5429 - Malte Rühlemann, Eike Matthias Wacker, David Ellinghaus
MAGScoT: a fast, lightweight and accurate bin-refinement tool. 5430-5433 - Nicolas Serge Matthieu Robert
SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes. 5434-5436 - Christian Anthon
CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design. 5437-5439 - Mateusz Chilinski
ConsensuSV - from the whole-genome sequencing data to the complete variant list. 5440-5442 - Téo Lemane
k mdiff, large-scale and user-friendly differential k-mer analyses. 5443-5445 - Sean M. Cascarina
The LCD-Composer webserver: high-specificity identification and functional analysis of low-complexity domains in proteins. 5446-5448 - Alexios Chatzigoulas
DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design. 5449-5451 - Christos P. Feidakis
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands. 5452-5453 - Todor Gitchev
3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion. 5454-5456 - Ramón Díaz-Uriarte
EvAM-Tools: tools for evolutionary accumulation and cancer progression models. 5457-5459 - Eugenio Del Prete
ADViSELipidomics: a workflow for analyzing lipidomics data. 5460-5462 - Bo Wen
OmicsEV: a tool for comprehensive quality evaluation of omics data tables. 5463-5465 - Philipp Wegner
Common data model for COVID-19 datasets. 5466-5468 - Guillaume Wacquet
EcoTransLearn: an R-package to easily use transfer learning for ecological studies - a plankton case study. 5469-5471
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