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ORCIDBioinformatics, 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, Zhongsong Man, Lu Gao, Lei Cai, Qian Lu, Jiahong Dong:
The role of CpG island methylator phenotype in the clinical course of hepatocellular carcinoma. 9-15 - Michael B. Sohn, Jiarui Lu, Hongzhe Li:
A compositional mediation model for a binary outcome: Application to microbiome studies. 16-21 - Kevin A. Murgas, Yanlin Ma, Lidea K. Shahidi, Sayan Mukherjee, Andrew S. Allen, Darryl Shibata, Marc D. Ryser:
A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors. 22-29 - Jun-Liang Lin, Tsung-Ting Hsieh, Yi-An Tung, Xuan-Jun Chen, Yu-Chun Hsiao, Chia-Lin Yang, Tyng-Luh Liu, Chien-Yu Chen:
ezGeno: an automatic model selection package for genomic data analysis. 30-37 - Jian Song, Changbin Yu:
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, Nick Leiby, Francis C. Motta, Steven B. Haase, Jed Singer:
Improved datasets and evaluation methods for the automatic prediction of DNA-binding proteins. 44-51 - Chao Wang, Ying Ju, Quan Zou, Chen Lin:
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, Guy Georges, Sebastian Kelm, Jiye Shi, Anna Vangone, Charlotte M. Deane:
Co-evolutionary distance predictions contain flexibility information. 65-72 - Roy González-Alemán, Daniel Platero-Rochart, David Hernández-Castillo, Erix Wiliam Hernández-Rodríguez, Julio Caballero, Fabrice Leclerc, Luis Alberto Montero-Cabrera:
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, Jian Zhan, Yaoqi Zhou:
De novo protein design by an energy function based on series expansion in distance and orientation dependence. 86-93 - Jianzhao Gao, Shuangjia Zheng, Mengting Yao, Peikun Wu:
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, Gui-Jun Zhang:
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, Jianwen Chen, Huiying Zhao, Yaoqi Zhou, Yuedong Yang:
Structure-aware protein-protein interaction site prediction using deep graph convolutional network. 125-132 - Oleksii Nikolaienko, Per Eystein Lønning, Stian Knappskog:
ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions. 133-140 - Tristan Mary-Huard, Sarmistha Das, Indranil Mukhopadhyay, Stéphane Robin:
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, Thomas P. Quinn, John P. Cunningham:
Learning sparse log-ratios for high-throughput sequencing data. 157-163 - Matteo Borella, Graziano Martello, Davide Risso, Chiara Romualdi:
PsiNorm: a scalable normalization for single-cell RNA-seq data. 164-172 - Alberto Zenere, Olof Rundquist, Mika Gustafsson, Claudio Altafini:
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, Hyukpyo Hong, Boseung Choi, Jae Kyoung Kim, Kresimir Josic:
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, Lei Xie:
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, Lan Huang, Yan Wang, Kai He, Xueteng Cui, Yao Wang, Qin Ma, Juan Cui:
DeepSec: a deep learning framework for secreted protein discovery in human body fluids. 228-235 - Margaret Woodhouse, Shatabdi Sen, David A. Schott, John L. Portwood II, Michael Freeling, Justin W. Walley, Carson M. Andorf, James C. Schnable:
qTeller: a tool for comparative multi-genomic gene expression analysis. 236-242 - Mirae Kim, Soonwoo Hong, Thomas E. Yankeelov, Hsin-Chih Yeh, Yen-Liang Liu:
Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics. 243-249 - Hualin Liu, Jinshui Zheng, Dexin Bo, Yun Yu, Weixing Ye, Donghai Peng, Ming Sun:
BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis. 250-251 - Fulong Yu, Vijay G. Sankaran, Guo-Cheng Yuan:
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, Eva Maria Novoa:
ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. 257-260 - Andrew Olson, Doreen Ware:
Ranked choice voting for representative transcripts with TRaCE. 261-264 - François Ancien, Fabrizio Pucci, Wim F. Vranken, Marianne Rooman:
MutaFrame - an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome. 265-266 - Frédéric Mahé, Lucas Czech, Alexandros Stamatakis, Christopher Quince, Colomban de Vargas, Micah Dunthorn, Torbjørn Rognes:
Swarm v3: towards tera-scale amplicon clustering. 267-269 - Guillem Salazar, Hans-Joachim Ruscheweyh, Falk Hildebrand, Silvia G. Acinas, Shinichi Sunagawa:
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, Sun Kim:
BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud. 275-277 - Junyi Xin, Yanling Wu, Shuai Ben, Shuwei Li, Haiyan Chu, Meilin Wang, Molin Wang, Mingyang Song, Mulong Du, Zhengdong Zhang:
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, Julia M. Sattler, Friedrich Frischknecht:
SPOT: a web-tool enabling swift profiling of transcriptomes. 284-285 - Jun Chen, Xianyang Zhang:
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, Steven S. Andrews:
Python interfaces for the Smoldyn simulator. 291-293 - Ramiro Magno, Isabel Duarte, Ana-Teresa Maia:
quincunx: an R package to query, download and wrangle PGS Catalog data. 294-296 - Pedro B. P. S. Reis, Djork-Arné Clevert, Miguel Machuqueiro:
pKPDB: a protein data bank extension database of pKa and pI theoretical values. 297-298 - Andrew D. Yates, Jeremy Adams, Somesh Chaturvedi, Robert Davies, Matthew R. Laird, Rasko Leinonen, Rishi Nag, Nathan C. Sheffield, Oliver Hofmann, Thomas M. Keane:
Refget: standardized access to reference sequences. 299-300 - Anthony Xu, Aravind Venkateswaran, Lianguizi Zhou, Andreas Zankl:
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, Jin Liu:
MR-Corr2: a two-sample Mendelian randomization method that accounts for correlated horizontal pleiotropy using correlated instrumental variants. 303-310 - Shengji Jia, Lei Shi:
Efficient change-points detection for genomic sequences via cumulative segmented regression. 311-317 - Nisha Singh, Hukam C. Rawal, Ulavappa B. Angadi, Tilak Raj Sharma, Nagendra Kumar Singh, Tapan Kumar Mondal:
A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz). 318-324 - Yunxiao Ren, Trinad Chakraborty, Swapnil Doijad, Linda Falgenhauer, Jane Falgenhauer, Alexander Goesmann, Anne-Christin Hauschild, Oliver Schwengers, Dominik Heider:
Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. 325-334 - Hongwei Huo, Pengfei Liu, Chenhui Wang, Hongbo Jiang, Jeffrey Scott Vitter:
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, Yulia Yakovleva, Olga Bochkareva, Nikita Alexeev:
PaReBrick: PArallel REarrangements and BReaks identification toolkit. 357-363 - Jae Yong Ryu, Jeong Hyun Lee, Byung Ho Lee, Jin Sook Song, Sunjoo Ahn, Kwang-Seok Oh:
PredMS: a random forest model for predicting metabolic stability of drug candidates in human liver microsomes. 364-368 - Rahul Kaushik, Kam Y. J. Zhang:
ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures. 369-376 - Constantin Schneider, Andrew Buchanan, Bruck Taddese, Charlotte M. Deane:
DLAB: deep learning methods for structure-based virtual screening of antibodies. 377-383 - Benedek Dankó, Péter Szikora, Tamás Pór, Alexa Szeifert, Endre Sebestyén:
SplicingFactory - splicing diversity analysis for transcriptome data. 384-390 - Lyla Atta, Arpan Sahoo, Jean Fan:
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories. 391-396 - Yi-Pei Chen, Laura B. Ferguson, Nihal A. Salem, George Zheng, R. Dayne Mayfield, Mohammed Eslami:
RNA Solutions: Synthesizing Information to Support Transcriptomics (RNASSIST). 397-403 - Mohammed Eslami, Amin Espah Borujeni, Hamed Eramian, Mark Weston, George Zheng, Joshua Urrutia, Carolyn Corbet, Diveena Becker, Paul Maschhoff, Katie Clowers, Alexander Cristofaro, Hamid Doost Hosseini, D. Benjamin Gordon, Yuval Dorfan, Jedediah Singer, Matthew Vaughn, Niall Gaffney, John Fonner, Joe Stubbs, Christopher A. Voigt, Enoch Yeung:
Prediction of whole-cell transcriptional response with machine learning. 404-409 - Baoshan Ma, Ge Yan, Bingjie Chai, Xiaoyu Hou:
XGBLC: an improved survival prediction model based on XGBoost. 410-418 - Tianying Wang, Wodan Ling, Anna M. Plantinga, Michael C. Wu, Xiang Zhan:
Testing microbiome association using integrated quantile regression models. 419-425 - Haitao Fu, Feng Huang, Xuan Liu, Yang Qiu, Wen Zhang:
MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks. 426-434 - Yingjun Ma, Yuanyuan Ma:
Hypergraph-based logistic matrix factorization for metabolite-disease interaction prediction. 435-443 - Seungyoon Nam, Sungyoung Lee, Sungjin Park, Jinhyuk Lee, Aron Park, Yon Hui Kim, Taesung Park:
PATHOME-Drug: a subpathway-based polypharmacology drug-repositioning method. 444-452 - Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, Roman Bauer:
BioDynaMo: a modular platform for high-performance agent-based simulation. 453-460 - Yiheng Zhu, Zhenqiu Ouyang, Wenbo Chen, Ruiwei Feng, Danny Z. Chen, Ji Cao, Jian Wu:
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, Afshin Fassihi, Fahimeh Ghasemi:
Accelerating Big Data Analysis through LASSO-Random Forest Algorithm in QSAR Studies. 469-475 - Yang Xu, Priyojit Das, Rachel Patton McCord:
SMILE: mutual information learning for integration of single-cell omics data. 476-486 - Gianvito Pio, Paolo Mignone, Giuseppe Magazzù, Guido Zampieri, Michelangelo Ceci, Claudio Angione:
Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction. 487-493 - Kishlay Jha, Aidong Zhang:
Continual knowledge infusion into pre-trained biomedical language models. 494-502 - Shuxia Guo, Xuan Zhao, Shengdian Jiang, Liya Ding, Hanchuan Peng:
Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons. 503-512 - Mohamed Amgad, Lamees A. Atteya, Hagar Hussein, Kareem Hosny Mohammed, Ehab Hafiz, Maha A. T. Elsebaie, Pooya Mobadersany, David Manthey, David A. Gutman, Habiba Elfandy, Lee A. D. Cooper:
Explainable nucleus classification using Decision Tree Approximation of Learned Embeddings. 513-519 - John F. Graf, Sanghee Cho, Elizabeth McDonough, Alex Corwin, Anup Sood, Andreas Lindner, Manuela Salvucci, Xanthi Stachtea, Sandra Van Schaeybroeck, Philip D. Dunne, Pierre Laurent-Puig, Daniel B. Longley, Jochen H. M. Prehn, Fiona Ginty:
FLINO: a new method for immunofluorescence bioimage normalization. 520-526 - Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao, Jianfeng Li, Mingjie Wang, Haitao Wang, Ziyu Tao, Tao Wu, Yichao Zheng, Xuejun Li, Xue-Song Liu:
UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data. 527-529 - Cecilia Sensalari, Steven Maere, Rolf Lohaus:
ksrates: positioning whole-genome duplications relative to speciation events in KS distributions. 530-532 - Kenneth I Brewer, Glenn J. Gaffield, Malavika Puri, Ronald R. Breaker:
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria. 533-535 - Brian M. Schilder, Jack Humphrey, Towfique Raj:
echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline. 536-539 - Itsuki Sugita, Shohei Matsuyama, Hiroki Dobashi, Daisuke Komura, Shumpei Ishikawa:
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, Nicholas Vlachos, Alison Laufer Halpin:
GAMMA: a tool for the rapid identification, classification and annotation of translated gene matches from sequencing data. 546-548 - Kohei Hagiwara, Michael N. Edmonson, David A. Wheeler, Jinghui Zhang:
indelPost: harmonizing ambiguities in simple and complex indel alignments. 549-551 - Amélie Barozet, Kevin Molloy, Marc Vaisset, Christophe Zanon, Pierre Fauret, Thierry Siméon, Juan Cortés:
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, Dong-Jun Yu, Gui-Jun Zhang:
ATPdock: a template-based method for ATP-specific protein-ligand docking. 556-558 - Alan Kwong, Andrew P. Boughton, Mukai Wang, Peter Vandehaar, Michael Boehnke, Gonçalo R. Abecasis, Hyun Min Kang:
FIVEx: an interactive eQTL browser across public datasets. 559-561 - Pieter Verschaffelt, James H. Collier, Alexander Botzki, Lennart Martens, Peter Dawyndt, Bart Mesuere:
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, Katharina Nöh, Jörg Stelling:
PolyRound: polytope rounding for random sampling in metabolic networks. 566-567 - Xiaotao Shen, Si Wu, Liang Liang, Songjie Chen, Kévin Contrepois, Zheng-Jiang Zhu, Michael P. Snyder:
metID: an R package for automatable compound annotation for LC-MS-based data. 568-569 - Peter Zhang, Alida Palmisano, Ravindra Kumar, Ming-Chung Li, James H. Doroshow, Yingdong Zhao:
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, James J. Cai:
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. 580-582 - Maria Llambrich, Eudald Correig, Josep Gumà, Jesús Brezmes, Raquel Cumeras:
Amanida: an R package for meta-analysis of metabolomics non-integral data. 583-585 - Paola Paci, Giulia Fiscon:
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, Chiara Pastrello, Mark Abovsky, Sara Rahmati, Igor Jurisica:
miRAnno - network-based functional microRNA annotation. 592-593 - Rodrigo Fernandez-Gonzalez, Negar Balaghi, Kelly Wang, Ray Hawkins, Katheryn Rothenberg, Christopher McFaul, Clara Schimmer, Michelle Ly, Ana Maria do Carmo, Gordana Scepanovic, Gonca Erdemci-Tandogan, Veronica Castle:
PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images. 594-596
Volume 38, Number 3, January 2022
- Gaetan De Waele, Jim Clauwaert, Gerben Menschaert, Willem Waegeman:
CpG Transformer for imputation of single-cell methylomes. 597-603 - Thomas Krannich, W. Timothy J. White, Sebastian Niehus, Guillaume Holley, Bjarni V. Halldórsson, Birte Kehr:
Population-scale detection of non-reference sequence variants using colored de Bruijn graphs. 604-611 - Alexander G. McFarland, Nolan W. Kennedy, Carolyn E. Mills, Danielle Tullman-Ercek, Curtis Huttenhower, Erica M. Hartmann:
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, Rob Phillips:
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, Haipeng Gong:
BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models. 648-654 - Qichang Zhao, Haochen Zhao, Kai Zheng, Jianxin Wang:
HyperAttentionDTI: improving drug-protein interaction prediction by sequence-based deep learning with attention mechanism. 655-662 - Lenore Pipes, Rasmus Nielsen:
AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees. 663-670 - Seonwoo Min, Byunghan Lee, Sungroh Yoon:
TargetNet: functional microRNA target prediction with deep neural networks. 671-677 - Yawei Wang, Yuning Yang, Zhiqiang Ma, Ka-Chun Wong, Xiangtao Li:
EDCNN: identification of genome-wide RNA-binding proteins using evolutionary deep convolutional neural network. 678-686 - Elan Shatoff, Ralf Bundschuh:
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, Claire Lesieur:
A computational methodology to diagnose sequence-variant dynamic perturbations by comparing atomic protein structures. 703-709 - Masaki Tagashira, Kiyoshi Asai:
ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures. 710-719 - Shi-Hao Feng, Chun-Qiu Xia, Hong-Bin Shen:
CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks. 720-729 - Ramón Viñas, Helena Andrés-Terré, Pietro Liò, Kevin Bryson:
Adversarial generation of gene expression data. 730-737 - Musu Yuan, Liang Chen, Minghua Deng:
scMRA: a robust deep learning method to annotate scRNA-seq data with multiple reference datasets. 738-745 - Lujing Zheng, Zhenhuan Liu, Yang Yang, Hong-Bin Shen:
Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning. 746-753 - Fabrizio Angaroni, Kevin Chen, Chiara Damiani, Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti:
PMCE: efficient inference of expressive models of cancer evolution with high prognostic power. 754-762 - Kuei-Yueh Ko, Cho-Yi Chen, Hsueh-Fen Juan, Hsuan-Cheng Huang:
Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis. 763-769 - Jiacheng Leng, Ling-Yun Wu:
Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs. 770-777 - Rebecca L. Rubinstein, Mikayla A. Borton, Haiyan Zhou, Michael Shaffer, David W. Hoyt, James Stegen, Christopher S. Henry, Kelly C. Wrighton, Roelof Versteeg:
ORT: a workflow linking genome-scale metabolic models with reactive transport codes. 778-784 - Ya-Ru Miao, Meng-Xuan Xia, Mei Luo, Tao Luo, Mei Yang, An-Yuan Guo:
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, Xiaomeng Liu, Ziming Huang, Xiaohong Liu, Kaixian Chen, Hualiang Jiang, Mingyue Zheng:
Multi-instance learning of graph neural networks for aqueous pKa prediction. 792-798 - Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu:
HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations. 799-808 - Qiufu Li, Linlin Shen:
Neuron segmentation using 3D wavelet integrated encoder-decoder network. 809-817 - Rui Zhu, Xiongfei Li, Sa Huang, Xiaoli Zhang:
Multimodal medical image fusion using adaptive co-occurrence filter-based decomposition optimization model. 818-826 - Min-Qi Xue, Xi-Liang Zhu, Ge Wang, Ying-Ying Xu:
DULoc: quantitatively unmixing protein subcellular location patterns in immunofluorescence images based on deep learning features. 827-833 - Ankush Sharma, Akshay Akshay, Marie Rogne, Ragnhild Eskeland:
ShinyArchR.UiO: user-friendly, integrative and open-source tool for visualization of single-cell ATAC-seq data using ArchR. 834-836 - Tyll Stöcker, Lena Altrogge, Caroline Marcon, Yan Naing Win, Frank Hochholdinger, Heiko Schoof:
MuWU: Mutant-seq library analysis and annotation. 837-838 - Frank Vogt, Gautam Shirsekar, Detlef Weigel:
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, Laura Jareno, Angel Rubio:
Rediscover: an R package to identify mutually exclusive mutations. 844-845 - Nicolò Rossi, Andrea Colautti, L. Iacumin, Carla Piazza:
WGA-LP: a pipeline for whole genome assembly of contaminated reads. 846-848 - Eugenia Voytik, Isabell Bludau, Sander Willems, Fynn M. Hansen, Andreas-David Brunner, Maximilian T. Strauss, Matthias Mann:
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, Carla Mavian, Alberto Riva, Mattia Prosperi, Marco Salemi, Brittany Rife Magalis:
Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. 856-860 - Xiaoheng Cheng, Michael Degiorgio:
BalLeRMix +: mixture model approaches for robust joint identification of both positive selection and long-term balancing selection. 861-863 - Hemil Panchiwala, Shalin Shah, Hannes Planatscher, Mykola Zakharchuk, Matthias König, Andreas Dräger:
The systems biology simulation core library. 864-865 - Genaro Camele, Sebastian Menazzi, Hernán Chanfreau, Agustin Marraco, Waldo Hasperué, Matias D. Butti, Martin C. Abba:
Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation. 866-868 - Mukta G. Palshikar, Shannon P. Hilchey, Martin S. Zand, Juilee Thakar:
WikiNetworks: translating manually created biological pathways for topological analysis. 869-871 - Hai-Long Trieu, Makoto Miwa, Sophia Ananiadou:
BioVAE: a pre-trained latent variable language model for biomedical text mining. 872-874 - Tobias Greisager Rehfeldt, Konrad Krawczyk, Mathias Bøgebjerg, Veit Schwämmle, Richard Röttger:
MS2AI: automated repurposing of public peptide LC-MS data for machine learning applications. 875-877 - Joseph D. Romano, Trang T. Le, William G. La Cava, John T. Gregg, Daniel J. Goldberg, Praneel Chakraborty, Natasha L. Ray, Daniel S. Himmelstein, Weixuan Fu, Jason H. Moore:
PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods. 878-880 - Michael Nodzenski, Min Shi, Juno M. Krahn, Alison S. Wise, Yuanyuan Li, Leping Li, David M. Umbach, Clarice R. Weinberg:
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, Benny Chain:
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, Ingelin Steinsland, Miina Ollikainen, Emma Cazaly, Jaakko Kaprio, Yuval Benjamini, Kristina Gervin, Robert Lyle:
Modeling dependency structures in 450k DNA methylation data. 885-891 - Luca Barbon, Victoria Offord, Elizabeth J. Radford, Adam P. Butler, Sebastian S. Gerety, David J. Adams, Hong Kee Tan, Andrew J. Waters:
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, Florence Mauger, Jean-Francois Deleuze, Edith Le Floch:
PIntMF: Penalized Integrative Matrix Factorization method for multi-omics data. 900-907 - Serhan Yilmaz, Mohamad Fakhouri, Mehmet Koyutürk, A. Ercüment Çiçek, Öznur Tastan:
Uncovering complementary sets of variants for predicting quantitative phenotypes. 908-917 - Chengze Shen, Paul Zaharias, Tandy J. Warnow:
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. 918-924 - Giuseppe Cattaneo, Umberto Ferraro Petrillo, Raffaele Giancarlo, Francesco Palini, Chiara Romualdi:
The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis. 925-932 - Deyou Tang, Yucheng Li, Daqiang Tan, Juan Fu, Yelei Tang, Jiabin Lin, Rong Zhao, Hongli Du, Zhongming Zhao:
KCOSS: an ultra-fast k-mer counter for assembled genome analysis. 933-940 - Vineet Thumuluri, Hannah-Marie Martiny, José Juan Almagro Armenteros, Jesper Salomon, Henrik Nielsen, Alexander Rosenberg Johansen:
NetSolP: predicting protein solubility in Escherichia coli using language models. 941-946 - Ziwei Xie, Jinbo Xu:
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, Jianyi Yang:
Toward the assessment of predicted inter-residue distance. 962-969 - Carlos G. Oliver, Vincent Mallet, Pericles Philippopoulos, William L. Hamilton, Jérôme Waldispühl:
Vernal: a tool for mining fuzzy network motifs in RNA. 970-976 - Hmrishav Bandyopadhyay, Zihao Deng, Leiting Ding, Sinuo Liu, Mostofa Rafid Uddin, Xiangrui Zeng, Sima Behpour, Min Xu:
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, Nina N. Popova:
Guide tree optimization with genetic algorithm to improve multiple protein 3D-structure alignment. 985-989 - Fusong Ju, Jianwei Zhu, Qi Zhang, Guozheng Wei, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction. 990-996 - Haotian Teng, Ye Yuan, Ziv Bar-Joseph:
Clustering spatial transcriptomics data. 997-1004 - Jin Jin, Yue Wang:
T2-DAG: a powerful test for differentially expressed gene pathways via graph-informed structural equation modeling. 1005-1014 - Galina Boldina, Paul Fogel, Corinne Rocher, Charles Bettembourg, George Luta, Franck Augé:
A2Sign: Agnostic Algorithms for Signatures - a universal method for identifying molecular signatures from transcriptomic datasets prior to cell-type deconvolution. 1015-1021 - Pontus Eriksson, Nour-al-dain Marzouka, Gottfrid Sjödahl, Carina Bernardo, Fredrik Liedberg, Mattias Höglund:
A comparison of rule-based and centroid single-sample multiclass predictors for transcriptomic classification. 1022-1029 - Jonathan R. Bowles, Caroline Hoppe, Hilary L. Ashe, Magnus Rattray:
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, Jonathan Bac, Alexander Chervov, Vassili Soumelis, Andrei Yu. Zinovyev:
Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data. 1045-1051 - Michael Nodzenski, Min Shi, Juno M. Krahn, Alison S. Wise, Yuanyuan Li, Leping Li, David M. Umbach, Clarice R. Weinberg:
GADGETS: a genetic algorithm for detecting epistasis using nuclear families. 1052-1058 - Robert Warmerdam, Pauline Lanting, Patrick Deelen, Lude Franke:
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores. 1059-1066 - Aastha Khatiwada, Bethany J. Wolf, Ayse Selen Yilmaz, Paula S. Ramos, Maciej Pietrzak, Andrew Lawson, Kelly J. Hunt, Hang J. Kim, Dongjun Chung:
GPA-Tree: statistical approach for functional-annotation-tree-guided prioritization of GWAS results. 1067-1074 - Omar Maddouri, Xiaoning Qian, Byung-Jun Yoon:
Deep graph representations embed network information for robust disease marker identification. 1075-1086 - Ofir Yaish, Yaron Orenstein:
Computational modeling of mRNA degradation dynamics using deep neural networks. 1087-1101 - Guy Shtar, Lior Rokach, Bracha Shapira, Elkana Kohn, Matitiahu Berkovitch, Maya Berlin:
Explainable multimodal machine learning model for classifying pregnancy drug safety. 1102-1109 - Jianan Li, Keisuke Yanagisawa, Yasushi Yoshikawa, Masahito Ohue, Yutaka Akiyama:
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, Lisanna Paladin, Silvio C. E. Tosatto, Damiano Piovesan:
ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications. 1129-1130 - Dietmar Rieder, Georgios Fotakis, Markus Ausserhofer, Rene Geyeregger, Wolfgang Paster, Zlatko Trajanoski, Francesca Finotello:
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction. 1131-1132 - Rory Munro, Roberto Santos, Alexander Payne, Teri Forey, Solomon Osei, Nadine Holmes, Matthew Loose:
minoTour, real-time monitoring and analysis for nanopore sequencers. 1133-1135 - Jonathan Dhenin, Diogo B. Lima, Mathieu Dupré, Julia Chamot-Rooke:
TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics. 1136-1138 - Michael Uhl, Dominik Rabsch, Florian Eggenhofer, Rolf Backofen:
Peakhood: individual site context extraction for CLIP-seq peak regions. 1139-1140 - Yoochan Myung, Douglas E. V. Pires, David B. Ascher:
CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function. 1141-1143 - Kirsten Van Huffel, Michiel Stock, Bernard De Baets:
BioCCP.jl: collecting coupons in combinatorial biotechnology. 1144-1145 - Jean Charle Yaacoub, James Gleave, Francesco Gentile, Abraham C. Stern, Artem Cherkasov:
DD-GUI: a graphical user interface for deep learning-accelerated virtual screening of large chemical libraries (Deep Docking). 1146-1148 - Lucas S. P. Rudden, Samuel C. Musson, Justin L. P. Benesch, Matteo T. Degiacomi:
Biobox: a toolbox for biomolecular modelling. 1149-1151 - Myungjin Lee, Mateo Reveiz, Reda Rawi, Peter D. Kwong, Gwo-Yu Chuang:
GLYCO: a tool to quantify glycan shielding of glycosylated proteins. 1152-1154 - Luis García-Jimeno, Coral Fustero Torre, María José Jiménez-Santos, Gonzalo Gómez-López, Tomás Di Domenico, Fátima Al-Shahrour:
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses. 1155-1156 - Thomas Sheffield, Jason Brown, Sarah Davidson, Katie Paul Friedman, Richard S. Judson:
tcplfit2: an R-language general purpose concentration-response modeling package. 1157-1158 - Alissa L. Severson, Thorfinn Sand Korneliussen, Ida Moltke:
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, Paul I. Costea, Lucas Paoli, Renato Alves, Roman Thielemann, Shinichi Sunagawa, Peer Bork:
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, Jonas Zierer, Karsten Suhre, Jan Krumsiek:
maplet: an extensible R toolbox for modular and reproducible metabolomics pipelines. 1168-1170 - Miroslav Kratochvíl, Laurent Heirendt, St Elmo Wilken, Taneli Pusa, Sylvain Arreckx, Alberto Noronha, Marvin van Aalst, Venkata P. Satagopam, Oliver Ebenhöh, Reinhard Schneider, Christophe Trefois, Wei Gu:
COBREXA.jl: constraint-based reconstruction and exascale analysis. 1171-1172 - Florence Jornod, Thomas Jaylet, Ludek Bláha, Denis Sarigiannis, Luc Tamisier, Karine Audouze:
AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development. 1173-1175 - Boyang Tom Jin, Feng Xu, Raymond T. Ng, James C. Hogg:
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, Wolfgang Huber:
MatrixQCvis: shiny-based interactive data quality exploration for omics data. 1181-1182
Volume 38, Number 5, February 2022
- Michele Leone, Eugenia Galeota, Marco Masseroli, Mattia Pelizzola:
Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions. 1183-1190 - Jonathan Raad, Leandro A Bugnon, Diego H. Milone, Georgina Stegmayer:
miRe2e: a full end-to-end deep model based on transformers for prediction of pre-miRNAs. 1191-1197 - Nicholas J. Dimonaco, Wayne Aubrey, Kim Kenobi, Amanda Clare, Christopher J. Creevey:
No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study. 1198-1207 - Matthew Hayes, Angela Nguyen, Rahib Islam, Caryn Butler, Ethan Tran, Derrick Mullins, Chindo Hicks:
HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery. 1208-1215 - Yan Miao, Fu Liu, Tao Hou, Yun Liu:
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, Aaron R. Quinlan:
trfermikit: a tool to discover VNTR-associated deletions. 1231-1234 - José Bonet, Mandi Chen, Marc Dabad, Simon Heath, Abel Gonzalez-Perez, Núria López-Bigas, Jens Lagergren:
DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data. 1235-1243 - Yang Fan, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, Tao Qin:
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, Luis Checa Ruano, Alexandra Moine-Franel, Michael Nilges, Karen Druart, Guillaume Bouvier, Olivier Sperandio:
InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions. 1261-1268 - Yusuke Matsui, Yuichi Abe, Kohei Uno, Satoru Miyano:
RoDiCE: robust differential protein co-expression analysis for cancer complexome. 1269-1276 - David Buterez, Ioana Bica, Ifrah Tariq, Helena Andrés-Terré, Pietro Liò:
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, Shenwei Huang, Yanbin Yin:
HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data. 1295-1303 - Fei Qin, Xizhi Luo, Feifei Xiao, Guoshuai Cai:
SCRIP: an accurate simulator for single-cell RNA sequencing data. 1304-1311 - Maneesha Aluru, Harsh Shrivastava, Sriram P. Chockalingam, Shruti Shivakumar, Srinivas Aluru:
EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks. 1312-1319 - Paul Scherer, Maja Trebacz, Nikola Simidjievski, Ramón Viñas, Zohreh Shams, Helena Andrés-Terré, Mateja Jamnik, Pietro Liò:
Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases. 1320-1327 - Johannes Smolander, Sini Junttila, Mikko S. Venäläinen, Laura L. Elo:
scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data. 1328-1335 - Daniel Schwabe, Martin Falcke:
On the relation between input and output distributions of scRNA-seq experiments. 1336-1343 - Tianci Song, Kathleen K. Markham, Zhuliu Li, Kristen E. Muller, Kathleen Greenham, Rui Kuang:
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network. 1344-1352 - Weiwen Wang, Xiwen Zhang, Dao-Qing Dai:
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, Jianguo Lu, Alioune Ngom:
A network-based drug repurposing method via non-negative matrix factorization. 1369-1377 - Tao Sun, Mengci Li, Xiangtian Yu, Dandan Liang, Guoxiang Xie, Chao Sang, Wei Jia, Tianlu Chen:
3MCor: an integrative web server for metabolome-microbiome-metadata correlation analysis. 1378-1384 - Vigneshwaran Namasivayam, Katja Stefan, Katja Silbermann, Jens Pahnke, Michael Wiese, Sven Marcel Stefan:
Structural feature-driven pattern analysis for multitarget modulator landscapes. 1385-1392 - Shunfu Mao, Yue Zhang, Georg Seelig, Sreeram Kannan:
CellMeSH: probabilistic cell-type identification using indexed literature. 1393-1402 - Lulu Chen, Chiung-Ting Wu, Chia-Hsiang Lin, Rujia Dai, Chunyu Liu, Robert Clarke, Guoqiang Yu, Jennifer E. Van Eyk, David M. Herrington, Yue Wang:
swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution. 1403-1410 - Pasquale Cascarano, Maria Colomba Comes, Andrea Sebastiani, Arianna Mencattini, Elena Loli Piccolomini, Eugenio Martinelli:
DeepCEL0 for 2D single-molecule localization in fluorescence microscopy. 1411-1419 - Andrew Cox, Chanhee Park, Prasad Koduru, Kathleen Wilson, Olga Weinberg, Weina Chen, Rolando García, Daehwan Kim:
Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms. 1420-1426 - Herbert Teun Kruitbosch, Yasmin Mzayek, Sara Omlor, Paolo Guerra, Andreas Milias-Argeitis:
A convolutional neural network for segmentation of yeast cells without manual training annotations. 1427-1433 - Zuguang Gu, Daniel Hübschmann:
spiralize: an R package for visualizing data on spirals. 1434-1436 - Wesley S. van de Geer, Job van Riet, Harmen J. G. van de Werken:
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, Martin Steinegger, Steven L. Salzberg:
PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools. 1440-1442 - James M. Ferguson, Hasindu Gamaarachchi, Thanh Nguyen, Alyne Gollon, Stephanie Tong, Chiara Aquilina-Reid, Rachel Bowen-James, Ira W. Deveson:
InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses. 1443-1446 - Andrzej Zielezinski, Sebastian Deorowicz, Adam Gudys:
PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences. 1447-1449 - Chrispin Chaguza, Gerry Tonkin-Hill, Stephanie W. Lo, James Hadfield, Nicholas J. Croucher, Simon R. Harris, Stephen D. Bentley:
RCandy: an R package for visualizing homologous recombinations in bacterial genomes. 1450-1451 - Sebastian Bittrich, Yana Rose, Joan Segura, Robert Lowe, John D. Westbrook, Jose M. Duarte, Stephen K. Burley:
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB. 1452-1454 - Damla Ovek, Ameer Taweel, Zeynep Abali, Ece Tezsezen, Yunus Emre Koroglu, Chung-Jung Tsai, Ruth Nussinov, Ozlem Keskin, Attila Gürsoy:
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, Carlos G. Oliver, Jonathan Broadbent, William L. Hamilton, Jérôme Waldispühl:
RNAglib: a python package for RNA 2.5 D graphs. 1458-1459 - Zuguang Gu, Daniel Hübschmann:
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, Rodrigo J. S. Dalmolin, Bruce A. J. Ponder, Kerstin B. Meyer, Mauro A. A. Castro:
TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves. 1463-1464 - Jordan C. Rozum, Dávid Deritei, Kyu Hyong Park, Jorge Gómez Tejeda Zañudo, Réka Albert:
pystablemotifs: Python library for attractor identification and control in Boolean networks. 1465-1466 - Sven Thiele, Axel von Kamp, Pavlos Stephanos Bekiaris, Philipp Schneider, Steffen Klamt:
CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks. 1467-1469 - Husen M. Umer, Enrique Audain, Yafeng Zhu, Julianus Pfeuffer, Timo Sachsenberg, Janne Lehtiö, Rui Mamede Branca, Yasset Pérez-Riverol:
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, Qin Zhong, Jing Yang, Yongjie Duan, Wenjun Wang, Chengkun Wu, Kunlun He:
DeepKG: an end-to-end deep learning-based workflow for biomedical knowledge graph extraction, optimization and applications. 1477-1479 - Christopher D. Sanchez, J. Benjamin Brown, Omree Gal-Oz, Esther Singer:
EcoPLOT: dynamic analysis of biogeochemical data. 1480-1482
Volume 38, Number 6, March 2022
- Zuhal Ozcan, Francis A. San Lucas, Justin W. Wong, Kyle Chang, Konrad H. Stopsack, Jerry Fowler, Yasminka A. Jakubek, Paul Scheet:
Chromosomal imbalances detected via RNA-sequencing in 28 cancers. 1483-1490 - Juan A. Ferrer-Bonsoms, Xabier Morales, Pegah T. Afshar, Wing Hung Wong, Angel Rubio:
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, Zandora Hastenreiter, Thiago Augusto Silva Monteiro, Thieres Tayroni Martins da Silva, Francisco Pereira Lobo:
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, Changbin Yu:
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, Siavash Mirarab:
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, Martin Pirkl, Domagoj Cevid, Peter Bühlmann, Niko Beerenwinkel:
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, Bin Ma:
SPEQ: quality assessment of peptide tandem mass spectra with deep learning. 1568-1574 - Hui Wan, Liang Chen, Minghua Deng:
scNAME: neighborhood contrastive clustering with ancillary mask estimation for scRNA-seq data. 1575-1583 - Moran Sharon, Ekaterina Vinogradov, Chanan M. Argov, Or Lazarescu, Yazeed Zoabi, Idan Hekselman, Esti Yeger Lotem:
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, Anuradha Surendra, Thao T. Nguyen, Graeme Taylor, Hongbin Xu, Irina Alecu, Roberto Ortega, Julianna J. Tomlinson, Angela M. Crawley, Michaeline McGuinty, Michael G. Schlossmacher, Rachel Saunders-Pullman, Miroslava Cuperlovic-Culf, Steffany A. L. Bennett, Theodore J. Perkins:
BATL: Bayesian annotations for targeted lipidomics. 1593-1599 - Judith Bernett, Dominik Krupke, Sepideh Sadegh, Jan Baumbach, Sándor P. Fekete, Tim Kacprowski, Markus List, David B. Blumenthal:
Robust disease module mining via enumeration of diverse prize-collecting Steiner trees. 1600-1606 - Ruiyi Zhang, Yunan Luo, Jianzhu Ma, Ming Zhang, Sheng Wang:
scPretrain: multi-task self-supervised learning for cell-type classification. 1607-1614 - Cecilia Noecker, Alexander Eng, Efrat Muller, Elhanan Borenstein:
MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data. 1615-1623 - Tim Adams, Marcin Namysl, Alpha Tom Kodamullil, Sven Behnke, Marc Jacobs:
Benchmarking table recognition performance on biomedical literature on neurological disorders. 1624-1630 - Kaiqiao Li, Sijie Yao, Zhenyu Zhang, Biwei Cao, Christopher M. Wilson, Denise Kalos, Pei Fen Kuan, Ruoqing Zhu, Xuefeng Wang:
Efficient gradient boosting for prognostic biomarker discovery. 1631-1638 - Yuanwei Xu, Katrina Nash, Animesh Acharjee, Georgios V. Gkoutos:
CACONET: a novel classification framework for microbial correlation networks. 1639-1647 - Helena Balabin, Charles Tapley Hoyt, Colin Birkenbihl, Benjamin M. Gyori, John A. Bachman, Alpha Tom Kodamullil, Paul G. Plöger, Martin Hofmann-Apitius, Daniel Domingo-Fernández:
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. 1648-1656 - Sebastian Stammler, Tobias Kussel, Phillipp Schoppmann, Florian Stampe, Galina Tremper, Stefan Katzenbeisser, Kay Hamacher, Martin Lablans:
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, Lamia Alsubaie, Nagarajan Kathiresan, Katsuhiko Mineta, Taghrid Aloraini, Fuad Al Mutairi, Majid Alfadhel, Takashi Gojobori, Ahmad Alfares, Robert Hoehndorf:
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning. 1677-1684 - Marc Melkonian, Camille Juigné, Olivier Dameron, Gwenaël Rabut, Emmanuelle Becker:
Towards a reproducible interactome: semantic-based detection of redundancies to unify protein-protein interaction databases. 1685-1691 - Loan Vulliard, Joel Hancock, Anton Kamnev, Christopher W. Fell, Joana Ferreira da Silva, Joanna I Loizou, Vanja Nagy, Loïc Dupré, Jörg Menche:
BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations. 1692-1699 - Coleman R. Harris, Eliot T. McKinley, Joseph T. Roland, Qi Liu, Martha J. Shrubsole, Ken S. Lau, Robert J. Coffey, Julia Wrobel, Simon N. Vandekar:
Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images. 1700-1707 - Diogo A. C. Narciso, Ana Pereira, Nuno O. Dias, Luis F. Melo, Fernando Gomes Martins:
Characterization of biofilm structure and properties via processing of 2D optical coherence tomography images in BISCAP. 1708-1715 - Xuejian Li, Shiqiang Ma, Jin Liu, Jijun Tang, Fei Guo:
Inferring gene regulatory network via fusing gene expression image and RNA-seq data. 1716-1723 - Laura Fancello, Alessandro Guida, Gianmaria Frige, Arnaud Céol, Gabriele Babini, Giovanni Luca Scaglione, Mario Zanfardino, Tommaso Mazza, Lorenzo Ferrando, Pier Giuseppe Pelicci, Luca Mazzarella:
TMBleR: a bioinformatic tool to optimize TMB estimation and predictive power. 1724-1726 - Stefan Ebmeyer, Roelof Dirk Coertze, Fanny Berglund, Erik Kristiansson, D. G. Joakim Larsson:
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids. 1727-1728 - Soohyun Lee, Clara R. Bakker, Carl Vitzthum, Burak Han Alver, Peter J. Park:
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs. 1729-1731 - Zhenhua Yu, Fang Du:
AMC: accurate mutation clustering from single-cell DNA sequencing data. 1732-1734 - Chaoran Chen, Sarah Nadeau, Michael Yared, Philippe Voinov, Ning Xie, Cornelius Roemer, Tanja Stadler:
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants. 1735-1737 - Fei-Liao Lai, Feng Gao:
GC-Profile 2.0: an extended web server for the prediction and visualization of CpG islands. 1738-1740 - Dimitri Höhler, Wayne Pfeiffer, Vassilios Ioannidis, Heinz Stockinger, Alexandros Stamatakis:
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, Ronaldo Romario Tunque Cahui, Emilio Garcia-Rios, Layla Hirsh, Gustavo D. Parisi, María Silvina Fornasari, Nicolas Palopoli:
CoDNaS-RNA: a database of conformational diversity in the native state of RNA. 1745-1748 - Philipp Junk, Christina Kiel:
HOMELETTE: a unified interface to homology modelling software. 1749-1751 - Jan Brezovsky, Aravind Selvaram Thirunavukarasu, Bartlomiej Surpeta, Carlos Eduardo Sequeiros-Borja, Nishita Mandal, Dheeraj Kumar Sarkar, Cedrix Jurgal Dongmo Foumthuim, Nikhil Agrawal:
TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them. 1752-1753 - Elijah A. MacCarthy, Chengxin Zhang, Yang Zhang, Dukka B. KC:
GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool. 1754-1755 - Yang Xu, Simon J. Baumgart, Christian M. Stegmann, Sikander Hayat:
MACA: marker-based automatic cell-type annotation for single-cell expression data. 1756-1760 - Abbas Alameer, Davide Chicco:
geoCancerPrognosticDatasetsRetriever: a bioinformatics tool to easily identify cancer prognostic datasets on Gene Expression Omnibus (GEO). 1761-1763 - Ilaria De Marinis, Prisca Lo Surdo, Gianni Cesareni, Livia Perfetto:
SIGNORApp: a Cytoscape 3 application to access SIGNOR data. 1764-1766 - Roberto Maria Pellegrino, Matteo Giulietti, Husam B. R. Alabed, Sandra Buratta, Lorena Urbanelli, Francesco Piva, Carla Emiliani:
LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario. 1767-1769 - Jacob Neumann, Yen Ting Lin, Abhishek Mallela, Ely F. Miller, Joshua Colvin, Abell T. Duprat, Ye Chen, William S. Hlavacek, Richard G. Posner:
Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit. 1770-1772 - Aleksandra Gruca, Joanna Henzel, Iwona Kostorz, Tomasz Steclik, Lukasz Wróbel, Marek Sikora:
MAINE: a web tool for multi-omics feature selection and rule-based data exploration. 1773-1775 - Huan He, Sunyang Fu, Liwei Wang, Sijia Liu, Andrew Wen, Hongfang Liu:
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, Roger Vargas, Michael Harris, Brendan Jeffrey, L. Elaine Epperson, David Durbin, Michael Strong, Max Salfinger, Zamin Iqbal, Irada Akhundova, Sergo Vashakidze, Valeriu Crudu, Alex Rosenthal, Maha R. Farhat:
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, Rasmus Nielsen:
SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing. 1801-1808 - Renan Valieris, Rodrigo D. Drummond, Alexandre Defelicibus, Emmanuel Dias-Neto, Rafael Rosales, Israel T. da Silva:
A mixture model for determining SARS-Cov-2 variant composition in pooled samples. 1809-1815 - Jyun-Hong Lin, Liang-Chi Chen, Shu-Chi Yu, Yao-Ting Huang:
LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants. 1816-1822 - Qian Feng, Kathryn E. Tiedje, Shazia Ruybal-Pesántez, Gerry Tonkin-Hill, Michael F. Duffy, Karen P. Day, Heejung Shim, Yao-Ban Chan:
An accurate method for identifying recent recombinants from unaligned sequences. 1823-1829 - Christopher Bennett, Micah Thornton, Chanhee Park, Gervaise Henry, Yun Zhang, Venkat S. Malladi, Daehwan Kim:
SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers. 1830-1837 - Fabio Cunial, Olgert Denas, Djamal Belazzougui:
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, Roy González-Alemán, Erix Wiliam Hernández-Rodríguez, Fabrice Leclerc, Julio Caballero, Luis Alberto Montero-Cabrera:
RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics. 1863-1869 - Kirill E. Medvedev, Jimin Pei, Nick V. Grishin:
DisEnrich: database of enriched regions in human dark proteome. 1870-1876 - Brennan Abanades, Guy Georges, Alexander Bujotzek, Charlotte M. Deane:
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation. 1877-1880 - Carlos Outeiral, Daniel A. Nissley, Charlotte M. Deane:
Current structure predictors are not learning the physics of protein folding. 1881-1887 - Jaspreet Singh, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou:
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, Gui-Jun Zhang:
DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning. 1895-1903 - Raj S. Roy, Farhan Quadir, Elham Soltanikazemi, Jianlin Cheng:
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, Giulia Cesaro, Barbara Di Camillo:
Identify, quantify and characterize cellular communication from single-cell RNA sequencing data with scSeqComm. 1920-1929 - Camille Roquencourt, Stanislas Grassin-Delyle, Etienne A. Thévenot:
ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath. 1930-1937 - Shuang Song, Lin Hou, Jun S. Liu:
A data-adaptive Bayesian regression approach for polygenic risk prediction. 1938-1946 - Jiashun Xiao, Mingxuan Cai, Xianghong Hu, Xiang Wan, Gang Chen, Can Yang:
XPXP: improving polygenic prediction by cross-population and cross-phenotype analysis. 1947-1955 - Di Xiao, Hani Jieun Kim, Ignatius Pang, Pengyi Yang:
Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities. 1956-1963 - Xiaoqing Ru, Xiucai Ye, Tetsuya Sakurai, Quan Zou:
NerLTR-DTA: drug-target binding affinity prediction based on neighbor relationship and learning to rank. 1964-1971 - Eran Agmon, Ryan K. Spangler, Christopher J. Skalnik, William Poole, Shayn M. Peirce, Jerry H. Morrison, Markus W. Covert:
Vivarium: an interface and engine for integrative multiscale modeling in computational biology. 1972-1979 - David A. Hughes, Kurt Taylor, Nancy McBride, Matthew A. Lee, Dan Mason, Deborah A. Lawlor, Nicholas J. Timpson, Laura J. Corbin:
metaboprep: an R package for preanalysis data description and processing. 1980-1987 - Luca Cilibrasi, Pietro Pinoli, Anna Bernasconi, Arif Canakoglu, Matteo Chiara, Stefano Ceri:
ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time. 1988-1994 - Min Li, Zhangli Lu, Yifan Wu, Yaohang Li:
BACPI: a bi-directional attention neural network for compound-protein interaction and binding affinity prediction. 1995-2002 - Hehuan Ma, Yatao Bian, Yu Rong, Wenbing Huang, Tingyang Xu, Weiyang Xie, Geyan Ye, Junzhou Huang:
Cross-dependent graph neural networks for molecular property prediction. 2003-2009 - Xi Wang, Xiang Zhou, Qinglin Yan, Shaofeng Liao, Wenqin Tang, Peiyu Xu, Yangzhenyu Gao, Qian Li, Zhihui Dou, Weishan Yang, Beifang Huang, Jinhong Li, Zhuqing Zhang:
LLPSDB v2.0: an updated database of proteins undergoing liquid-liquid phase separation in vitro. 2010-2014 - Walid M. Abdelmoula, Sylwia Stopka, Elizabeth C. Randall, Michael Regan, Jeffrey N. Agar, Jann N. Sarkaria, William M. Wells III, Tina Kapur, Nathalie Y. R. Agar:
massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation. 2015-2021 - Hongjia Li, Hui Zhang, Xiaohua Wan, Zhidong Yang, Chengmin Li, Jintao Li, Renmin Han, Ping Zhu, Fa Zhang:
Noise-Transfer2Clean: denoising cryo-EM images based on noise modeling and transfer. 2022-2029 - Cui-Xiang Lin, Hong-Dong Li, Chao Deng, Shannon Erhardt, Jun Wang, Xiaoqing Peng, Jianxin Wang:
AlzCode: a platform for multiview analysis of genes related to Alzheimer's disease. 2030-2032 - Emira Cherif, Fatou Seck Thiam, Mohammad Salma, Georgina Rivera-Ingraham, Fabienne Justy, Theo Deremarque, Damien Breugnot, Jean-Claude Doudou, Rodolphe E. Gozlan, Marine Combe:
ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking pathogen variants. 2033-2035 - Chen Hong, Robin Thiele, Lars Feuerbach:
GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis. 2036-2038 - Chao Zhou, Huimin Wang, Hongyu Zhao, Tao Wang:
fastANCOM: a fast method for analysis of compositions of microbiomes. 2039-2041 - Nicole E. Kramer, Eric S. Davis, Craig Wenger, Erika Deoudes, Sarah M. Parker, Michael I. Love, Douglas H. Phanstiel:
Plotgardener: cultivating precise multi-panel figures in R. 2042-2045 - Daniel Cameron, Ruining Dong, Anthony T. Papenfuss:
StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem. 2046-2048 - Mitchell R. Vollger, Peter Kerpedjiev, Adam M. Phillippy, Evan E. Eichler:
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps. 2049-2051 - Benjamin Crysup, Bruce Budowle, August E. Woerner:
ProSynAR: a reference aware read merger. 2052-2053 - Xiaoqiong Bao, Kaiyu Zhu, Xuefei Liu, Zhihang Chen, Ziwei Luo, Qi Zhao, Jian Ren, Zhixiang Zuo:
MeRIPseqPipe: an integrated analysis pipeline for MeRIP-seq data based on Nextflow. 2054-2056 - Natalia García-García, Javier Tamames, Fernando Puente-Sánchez:
M&Ms: a versatile software for building microbial mock communities. 2057-2059 - Mattia Miotto, Alexandros Armaos, Lorenzo Di Rienzo, Giancarlo Ruocco, Edoardo Milanetti, Gian Gaetano Tartaglia:
Thermometer: a webserver to predict protein thermal stability. 2060-2061 - Stephen Price, Stéphane Tombeur, Alexander Hudson, Nanda Kumar Sathiyamoorthy, Paul Smyth, Anjana Singh, Mara Peccianti, Elisa Baroncelli, Ahmed Essaghir, Ilaria Ferlenghi, Sanjay Kumar Phogat, Gurpreet Singh:
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, Vittorio Fortino:
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds. 2066-2069 - Pablo Librado, Ludovic Orlando:
Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics. 2070-2071 - Yonghui Dong, Yana Kazachkova, Meng Gou, Liat Morgan, Tal Wachsman, Ehud Gazit, Rune Isak Dupont Birkler:
RawHummus: an R Shiny app for automated raw data quality control in metabolomics. 2072-2074 - Rosa D. Hernansaiz-Ballesteros, Christian H. Holland, Aurélien Dugourd, Julio Saez-Rodriguez:
FUNKI: interactive functional footprint-based analysis of omics data. 2075-2076 - Sebastien Lelong, Xinghua Zhou, Cyrus Afrasiabi, Zhongchao Qian, Marco Alvarado Cano, Ginger Tsueng, Jiwen Xin, Julia Mullen, Yao Yao, Ricardo Avila, Greg Taylor, Andrew I. Su, Chunlei Wu:
BioThings SDK: a toolkit for building high-performance data APIs in biomedical research. 2077-2079 - Shuang Song, Lin Hou, Jun S. Liu:
Erratum to: A data-adaptive Bayesian regression approach for polygenic risk prediction. 2080
Volume 38, Number 8, April 2022
- Richard Wilton, Alexander S. Szalay:
Performance optimization in DNA short-read alignment. 2081-2087 - Jessie J. F. Medeiros, Jose-Mario Capo-Chichi, Liran I Shlush, John E. Dick, Andrea Arruda, Mark D. Minden, Sagi Abelson:
SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes-derived data. 2088-2095 - David J. H. Shih, Ruoxing Li, Peter Müller, W. Jim Zheng, Kim-Anh Do, Shiaw-Yih Lin, Scott L. Carter:
CNGPLD: case-control copy-number analysis using Gaussian process latent difference. 2096-2101 - Nadav Brandes, Dan Ofer, Yam Peleg, Nadav Rappoport, Michal Linial:
ProteinBERT: a universal deep-learning model of protein sequence and function. 2102-2110 - Bas Stringer, Hans de Ferrante, Sanne Abeln, Jaap Heringa, K. Anton Feenstra, Reza Haydarlou:
PIPENN: protein interface prediction from sequence with an ensemble of neural nets. 2111-2118 - Kathryn E. Kirchoff, Shawn M. Gomez:
EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning. 2119-2126 - Dehan Cai, Yanni Sun:
Reconstructing viral haplotypes using long reads. 2127-2134 - Jun Zhang, Ke Yan, Qingcai Chen, Bin Liu:
PreRBP-TL: prediction of species-specific RNA-binding proteins based on transfer learning. 2135-2143 - Alexey Markin, Sanket Wagle, Tavis K. Anderson, Oliver Eulenstein:
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, Gabriel Peyré, Laura Cantini:
Optimal transport improves cell-cell similarity inference in single-cell omics data. 2169-2177 - Xiaohan Xing, Fan Yang, Hang Li, Jun Zhang, Yu Zhao, Mingxuan Gao, Junzhou Huang, Jianhua Yao:
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, Oscar A. Davalos, Lihong Zhao, Katrina K. Hoyer, Suzanne S. Sindi:
ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders. 2194-2201 - Mete Akgün, Nico Pfeifer, Oliver Kohlbacher:
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, Ryan M. Wyllie, Ramdane Harouaka, Paul A. Jensen:
A reinforcement learning framework for pooled oligonucleotide design. 2219-2225 - Cheng Yan, Guihua Duan, Na Li, Lishen Zhang, Fang-Xiang Wu, Jianxin Wang:
PDMDA: predicting deep-level miRNA-disease associations with graph neural networks and sequence features. 2226-2234 - Chaoyu Zhu, Zhihao Yang, Xiaoqiong Xia, Nan Li, Fan Zhong, Lei Liu:
Multimodal reasoning based on knowledge graph embedding for specific diseases. 2235-2245 - Mengting Niu, Quan Zou, Chunyu Wang:
GMNN2CD: identification of circRNA-disease associations based on variational inference and graph Markov neural networks. 2246-2253 - Yahui Long, Min Wu, Yong Liu, Yuan Fang, Chee Keong Kwoh, Jinmiao Chen, Jiawei Luo, Xiaoli Li:
Pre-training graph neural networks for link prediction in biomedical networks. 2254-2262 - Thomas Hillerton, Deniz Seçilmis, Sven Nelander, Erik L. L. Sonnhammer:
Fast and accurate gene regulatory network inference by normalized least squares regression. 2263-2268 - Ioan Ieremie, Rob M. Ewing, Mahesan Niranjan:
TransformerGO: predicting protein-protein interactions by modelling the attention between sets of gene ontology terms. 2269-2277 - Anne-Christin Hauschild, Marta Lemanczyk, Julian O. Matschinske, Tobias Frisch, Olga I. Zolotareva, Andreas Holzinger, Jan Baumbach, Dominik Heider:
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, Jacob J. Hughey, Lisa Bastarache, Joshua C. Denny, Qingxia Chen:
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, Olga A. Tarasova, Gilles Marcou, Dragos Horvath, Vladimir Poroikov, Alexandre Varnek:
HIV-1 drug resistance profiling using amino acid sequence space cartography. 2307-2314 - Junfeng Yao, Wen Sun, ZhongQuan Jian, Qingqiang Wu, Xiaoli Wang:
Effective knowledge graph embeddings based on multidirectional semantics relations for polypharmacy side effects prediction. 2315-2322 - Meiling Wang, Wei Shao, Xiaoke Hao, Shuo Huang, Daoqiang Zhang:
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, Daming Zhu:
mzMD: visualization-oriented MS data storage and retrieval. 2333-2340 - Naama Wagner, Oren Avram, Dafna Gold-Binshtok, Ben Zerah, Doron Teper, Tal Pupko:
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, Ann E. Loraine:
Integrated Genome Browser App Store. 2348-2349 - Simon Penel, Hugo Menet, Théo Tricou, Vincent Daubin, Eric Tannier:
Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation. 2350-2352 - Leandro G. Radusky, Luis Serrano:
pyFoldX: enabling biomolecular analysis and engineering along structural ensembles. 2353-2355 - Alexander Lachmann, Zhuorui Xie, Avi Ma'ayan:
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. 2356-2357 - Alexander Cope, Felicity Anderson, John Favate, Michael Jackson, Amanda Mok, Anna Kurowska, Junchen Liu, Emma Mackenzie, Vikram Shivakumar, Peter Tilton, Sophie M. Winterbourne, Siyin Xue, Kostas Kavoussanakis, Liana F. Lareau, Premal Shah, Edward W. J. Wallace:
riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow. 2358-2360 - Daoyu Duan, Sijia He, Emina Huang, Ziyi Li, Hao Feng:
NeuCA web server: a neural network-based cell annotation tool with web-app and GUI. 2361-2363 - Hagai Levi, Nima Rahmanian, Ran Elkon, Ron Shamir:
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, Luis Sordo Vieira, Reinhard C. Laubenbacher, Julia Chifman:
SteadyCellPhenotype: a web-based tool for the modeling of biological networks with ternary logic. 2369-2370 - Simon Ott, Adriano Barbosa-Silva, Matthias Samwald:
LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs. 2371-2373 - Anna Pedrola, Sebastià Franch-Expósito, Sara Lahoz, Roger Esteban-Fabró, Rodrigo Dienstmann, Laia Bassaganyas, Jordi Camps:
PCIG: a web-based application to explore immune-genomics interactions across cancer types. 2374-2376 - M. Michael Gromiha, Christine A. Orengo, Ramanathan Sowdhamini, Janet M. Thornton:
Srinivasan (1962-2021) in Bioinformatics and beyond. 2377-2379
Volume 38, Number 9, April 2022
- Youngmok Jung, Dongsu Han:
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, Jie Rong, Yang Liu, Weikang Gong, Chunhua Li:
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, Meng Jiang, Pietro Hiram Guzzi, Tijana Milenkovic:
Modeling multi-scale data via a network of networks. 2544-2553 - Eduardo Vieira de Souza, Pedro Ferrari Dalberto, Vinicius Pellisoli Machado, Adriana Canedo, Alan Saghatelian, Pablo Machado, Luiz Augusto Basso, Cristiano Valim Bizarro:
µProteInS - a proteogenomics pipeline for finding novel bacterial microproteins encoded by small ORFs. 2612-2614 - Giovanni Birolo, Andrea Telatin:
BamToCov: an efficient toolkit for sequence coverage calculations. 2617-2618 - Manuel Ugidos, María José Nueda, José Manuel Prats-Montalbán, Alberto Ferrer, Ana Conesa, Sonia Tarazona:
MultiBaC: an R package to remove batch effects in multi-omic experiments. 2657-2658 - Fengyuan Hu, Jia Lu, Louise S. Matheson, Manuel D. Díaz-Muñoz, Alexander Saveliev, Martin Turner:
Correction to: ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes. 2673 - Thimothée Virgoulay, François Rousset, Raphaël Leblois:
Correction to: GSpace: an exact coalescence simulator of recombining genomes under isolation by distance. 2674
Volume 38, Number 10, May 2022
- Mengtian Li, Lei M. Li:
RegScaf: a regression approach to scaffolding. 2675-2682 - Yu Li, Siyuan Chen, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Kevin Y. Yip, Xin Gao:
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, Migun Shakya, Ryan Connor, Karen Davenport, Mark Flynn, Adán Myers y Gutiérrez, Bin Hu, Po-E Li, Elais Player Jackson, Yan Xu, Patrick S. G. Chain:
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts. 2700-2704 - Liangpeng Nie, Lijun Quan, Tingfang Wu, Ruji He, Qiang Lyu:
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, Hao Wu, Bin Liu:
TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view tensor learning model. 2712-2718 - Marcos A. Caraballo-Ortiz, Sayaka Miura, Maxwell D. Sanderford, Tenzin Dolker, Qiqing Tao, Steven Weaver, Sergei L. Kosakovsky Pond, Sudhir Kumar:
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, Robert L. Jernigan:
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier. 2727-2733 - Bahareh Behkamal, Mahmoud Naghibzadeh, Andrea Pagnani, Mohammad Reza Saberi, Kamal Al Nasr:
LPTD: a novel linear programming-based topology determination method for cryo-EM maps. 2734-2741 - Tadeo E. Saldaño, Nahuel Escobedo, Julia Marchetti, Diego Javier Zea, Juan Mac Donagh, Ana Julia Velez Rueda, Eduardo Gonik, Agustina García Melani, Julieta Novomisky Nechcoff, Martín N. Salas, Tomás Peters, Nicolás Demitroff, Sebastian Fernandez Alberti, Nicolas Palopoli, María Silvina Fornasari, Gustavo D. Parisi:
Impact of protein conformational diversity on AlphaFold predictions. 2742-2748 - Weiguang Mao, Maziyar Baran Pouyan, Dennis Kostka, Maria Chikina:
Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data. 2749-2756 - Vasileios Tsiamis, Veit Schwämmle:
VIQoR: a web service for visually supervised protein inference and protein quantification. 2757-2764 - Mengqi Zhang, F. Richard Guo:
BSDE: barycenter single-cell differential expression for case-control studies. 2765-2772 - Wancen Mu, Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael I. Love:
Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets. 2773-2780 - Zhong Chen, You Lu, Bo Cao, Wensheng Zhang, Andrea Edwards, Kun Zhang:
Driver gene detection through Bayesian network integration of mutation and expression profiles. 2781-2790 - Gregory J. Boggy, G. W. McElfresh, Eisa Mahyari, Abigail B. Ventura, Scott G. Hansen, Louis J. Picker, Benjamin N. Bimber:
BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data. 2791-2801 - Antoine Passemiers, Yves Moreau, Daniele Raimondi:
Fast and accurate inference of gene regulatory networks through robust precision matrix estimation. 2802-2809 - Aron Park, Minjae Joo, Kyungdoc Kim, Won-Joon Son, Gyutae Lim, Jinhyuk Lee, Jung Ho Kim, Dae Ho Lee, Seungyoon Nam:
A comprehensive evaluation of regression-based drug responsiveness prediction models, using cell viability inhibitory concentrations (IC50 values). 2810-2817 - Sajal Kumar, Mingzhou Song:
Overcoming biases in causal inference of molecular interactions. 2818-2825 - Yan Ding, Xiaoqian Jiang, Yejin Kim:
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, Momoko Hamano, Michio Iwata, Toru Nakamura, Shinya Oki, Yoshihiro Yamanishi:
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach. 2839-2846 - Yang Li, Guanyu Qiao, Xin Gao, Guohua Wang:
Supervised graph co-contrastive learning for drug-target interaction prediction. 2847-2854 - Yang Li, Shaodong Xu, Shuangge Ma, Mengyun Wu:
Network-based cancer heterogeneity analysis incorporating multi-view of prior information. 2855-2862 - Yu Wei, Shanshan Li, Zhonglin Li, Ziwei Wan, Jianping Lin:
Interpretable-ADMET: a web service for ADMET prediction and optimization based on deep neural representation. 2863-2871 - Bailey S. Rose, Jody C. May, Jaqueline A. Picache, Simona G. Codreanu, Stacy D. Sherrod, John A. McLean:
Improving confidence in lipidomic annotations by incorporating empirical ion mobility regression analysis and chemical class prediction. 2872-2879 - Michael Mayers, Roger Tu, Dylan Steinecke, Tong Shu Li, Núria Queralt-Rosinach, Andrew I. Su:
Design and application of a knowledge network for automatic prioritization of drug mechanisms. 2880-2891 - Tian Bai, Jiayu Xu, Zhenting Zhang, Shuyu Guo, Xiao Luo:
Context-aware learning for cancer cell nucleus recognition in pathology images. 2892-2898 - Yurun Lu, Zhan-Ying Feng, Songmao Zhang, Yong Wang:
Annotating regulatory elements by heterogeneous network embedding. 2899-2911 - Xian F. Mallory, Luay Nakhleh:
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, Erik L. L. Sonnhammer:
InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm. 2918-2919 - Cédric Lood, Alejandro Correa Rojo, Deniz Sinar, Emma Verkinderen, Rob Lavigne, Vera van Noort:
SASpector: analysis of missing genomic regions in draft genomes of prokaryotes. 2920-2921 - Manish Goel, Korbinian Schneeberger:
plotsr: visualizing structural similarities and rearrangements between multiple genomes. 2922-2926 - Chiann-Ling C. Yeh, Clara J. Amorosi, Soyeon Showman, Maitreya J. Dunham:
PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment. 2927-2929 - Chun-Chieh Liao, Po-Ying Fu, Chih-Wei Huang, Chia-Hsien Chuang, Yun Yen, Chung-Yen Lin, Shu-Hwa Chen:
MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification. 2930-2931 - Hao Zhang, Qixin Chang, Zekun Yin, Xiaoming Xu, Yanjie Wei, Bertil Schmidt, Weiguo Liu:
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, Lluís Ribas de Pouplana, Adrian Gabriel Torres:
tRNAstudio: facilitating the study of human mature tRNAs from deep sequencing datasets. 2934-2936 - Morgan Shine, Chengxin Zhang, Anna Marie Pyle:
AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. 2937-2939 - Andrea Carenzo, Federico Pistore, Mara S. Serafini, Deborah Lenoci, Armando G. Licata, Loris De Cecco:
hacksig: a unified and tidy R framework to easily compute gene expression signature scores. 2940-2942 - Givanna H. Putri, Simon Anders, Paul Theodor Pyl, John E. Pimanda, Fabio Zanini:
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, Huimin Wang, Zhicheng Ji:
findPC: An R package to automatically select the number of principal components in single-cell analysis. 2949-2951 - Moosa Rezwani, Ali Akbar Pourfathollah, Farshid Noorbakhsh:
rbioapi: user-friendly R interface to biologic web services' API. 2952-2953 - Marek Slenker, Petr Koutecký, Karol Marhold:
MorphoTools2: an R package for multivariate morphometric analysis. 2954-2955 - Agustin Gonzalez-Reymundez, Alexander Grueneberg, Guanqi Lu, Filipe Couto Alves, Gonzalo Rincon, Ana I Vazquez:
MOSS: multi-omic integration with sparse value decomposition. 2956-2958 - Noriaki Sato, Yoshinori Tamada, Guangchuang Yu, Yasushi Okuno:
CBNplot: Bayesian network plots for enrichment analysis. 2959-2960 - Brad Reisfeld, Aline de Conti, Fatiha El Ghissassi, Lamia Benbrahim-Tallaa, William Gwinn, Yann Grosse, Mary Schubauer-Berigan:
kc-hits: a tool to aid in the evaluation and classification of chemical carcinogens. 2961-2962 - Nicolas Captier, Jane Merlevede, Askhat Molkenov, Ainur Seisenova, Altynbek Zhubanchaliyev, Petr V. Nazarov, Emmanuel Barillot, Ulykbek Kairov, Andrei Yu. Zinovyev:
BIODICA: a computational environment for Independent Component Analysis of omics data. 2963-2964 - Alina Nicheperovich, Adrian M. Altenhoff, Christophe Dessimoz, Sina Majidian:
OMAMO: orthology-based alternative model organism selection. 2965-2966 - Nicole J. Lake, Lily Zhou, Jenny Xu, Monkol Lek:
MitoVisualize: a resource for analysis of variants in human mitochondrial RNAs and DNA. 2967-2969 - Christoph Harmel, Samy Sid Ahmed, Robin Koch, Jana Tünnermann, Tania Distler, Andrea Imle, Luca Giorgetti, Emanuel Bahn, Oliver T. Fackler, Frederik Graw:
VisuStatR: visualizing motility and morphology statistics on images in R. 2970-2972
Volume 38, Number 11, May 2022
- Yuxuan Du, Fengzhu Sun:
HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs. 2973-2979 - Seungjin Na, Hyunjin Choi, Eunok Paek:
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, Qiao Liu, Zhuoran Fu, Wanwen Zeng, Boheng Zhang, Xuegong Zhang, Rui Jiang, Hairong Lv:
scGraph: a graph neural network-based approach to automatically identify cell types. 2996-3003 - Manqi Cai, Molin Yue, Tianmeng Chen, Jinling Liu, Erick Forno, Xinghua Lu, Timothy Billiar, Juan C. Celedón, Chris McKennan, Wei Chen, Jiebiao Wang:
Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution. 3004-3010 - Abdullah Karaaslanli, Satabdi Saha, Selin Aviyente, Tapabrata Maiti:
scSGL: kernelized signed graph learning for single-cell gene regulatory network inference. 3011-3019 - Yifu Lu, Zhuohan Yu, Yunhe Wang, Zhiqiang Ma, Ka-Chun Wong, Xiangtao Li:
GMHCC: high-throughput analysis of biomolecular data using graph-based multiple hierarchical consensus clustering. 3020-3028 - Habib Daneshpajouh, Bowen Chen, Neda Shokraneh, Shohre Masoumi, Kay C. Wiese, Maxwell W. Libbrecht:
Continuous chromatin state feature annotation of the human epigenome. 3029-3036 - Hongfei Liu, Zhanerke Akhatayeva, Chuanying Pan, Mingzhi Liao, Xianyong Lan:
Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq. 3037-3043 - Yen-Wen Wang, Cécile Ané:
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, Marina Sokolova, Jean-Christophe Grenier, Robert G. Beiko, Julie Hussin:
deepSimDEF: deep neural embeddings of gene products and gene ontology terms for functional analysis of genes. 3051-3061 - Feng Jiao, Moxun Tang:
Quantification of transcription noise's impact on cell fate commitment with digital resolutions. 3062-3069 - Szabolcs Cselgo Kovács, Balázs Szappanos, Roland Tengölics, Richard A. Notebaart, Balázs Papp:
Underground metabolism as a rich reservoir for pathway engineering. 3070-3077 - Suhyun Hwangbo, Sungyoung Lee, Seungyeoun Lee, Heungsun Hwang, Inyoung Kim, Taesung Park:
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, Sourish S. Iyengar, John T. Ormerod, Heeva Baharlou, Andrew N. Harman, Ellis Patrick:
spicyR: spatial analysis of in situ cytometry data in R. 3099-3105 - Shaojing Wang, Guoqiang Li, Zitong Liao, Yunke Cao, Yuan Yun, Zhaoying Su, Xuefeng Tian, Ziyu Gui, Ting Ma:
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, Adam D. Ewing:
Methylartist: tools for visualizing modified bases from nanopore sequence data. 3109-3112 - Jonathan S. Abebe, Alexander M. Price, Katharina E. Hayer, Ian Mohr, Matthew D. Weitzman, Angus C. Wilson, Daniel P. Depledge:
DRUMMER - rapid detection of RNA modifications through comparative nanopore sequencing. 3113-3115 - Sheila M. Gaynor, Kenneth E. Westerman, Lea L. Ackovic, Xihao Li, Zilin Li, Alisa Manning, Anthony A. Philippakis, Xihong Lin:
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, Javier Garcia-Pardo, Aleksander Kuriata, Jordi Pujols, Salvador Ventura, Sebastian Kmiecik:
A3D database: structure-based predictions of protein aggregation for the human proteome. 3121-3123 - Alejandro Cáceres, Juan R. González:
teff: estimation of Treatment EFFects on transcriptomic data using causal random forest. 3124-3125 - Dongyuan Song, Nan Miles Xi, Jingyi Jessica Li, Lin Wang:
scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. 3126-3127 - Dario Righelli, Lukas M. Weber, Helena L. Crowell, Brenda Pardo, Leonardo Collado-Torres, Shila Ghazanfar, Aaron T. L. Lun, Stephanie C. Hicks, Davide Risso:
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. 3128-3131 - Ali Amiryousefi, Bernardo Williams, Mohieddin Jafari, Jing Tang:
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, Daphné Chopard, Irena Spasic:
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, Bert Droesbeke, Karoly Erdos, Rolando Fernandez, Alasdair J. G. Gray, Muhammad Haseeb, Simon Jupp, Flavia Penim, Cyril Pommier, Philippe Rocca-Serra, Mélanie Courtot, Frederik Coppens:
ELIXIR biovalidator for semantic validation of life science metadata. 3141-3142 - Danyi Zou, Ye Yuan, Luming Xu, Shijun Lei, Xingbo Li, Xiaohuan Lu, Xingyue Wang, Xiaoqiong Li, Lin Wang, Zheng Wang:
PltDB: a blood platelets-based gene expression database for disease investigation. 3143-3145 - Virginie Uhlmann, Zsuzsanna Püspöki, Adrien Depeursinge, Michael Unser, Daniel Sage, Julien Fageot:
Steer'n'Detect: fast 2D template detection with accurate orientation estimation. 3146-3148 - François Laurent, Hippolyte Verdier, Maxime Duval, Alexander Serov, Christian L. Vestergaard, Jean-Baptiste Masson:
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, Jamshed Khan, Sergey Madaminov, Michael Ferdman, Rob Johnson, Prashant Pandey, Rob Patro:
An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation. 3155-3163 - Li Chen, Ye Wang, Fengdi Zhao:
Exploiting deep transfer learning for the prediction of functional non-coding variants using genomic sequence. 3164-3172 - Ye Yue, Yi-Juan Hu:
A new approach to testing mediation of the microbiome at both the community and individual taxon levels. 3173-3180 - Carlos A. Garcia-Prieto, Francisco Martínez-Jiménez, Alfonso Valencia, Eduard Porta-Pardo:
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, Liang Zhao:
Small molecule generation via disentangled representation learning. 3200-3208 - Isak Johansson-Åkhe, Björn Wallner:
InterPepScore: a deep learning score for improving the FlexPepDock refinement protocol. 3209-3215 - Qi Liu, Chih-Yuan Hsu, Jia Li, Yu Shyr:
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, Yuanghua Huang:
Genomic sequences and RNA-binding proteins predict RNA splicing efficiency in various single-cell contexts. 3231-3237 - Doruk Cakmakci, Gun Kaynar, Caroline Bund, Martial Piotto, Francois Proust, Izzie-Jacques Namer, A. Ercüment Çiçek:
Targeted metabolomics analyses for brain tumor margin assessment during surgery. 3238-3244 - Dries Van Daele, Bram Weytjens, Luc De Raedt, Kathleen Marchal:
OMEN: network-based driver gene identification using mutual exclusivity. 3245-3251 - Alexander M. Waldrop, John B. Cheadle, Kira Bradford, Alexander Preiss, Robert F. Chew, Jonathan R. Holt, Yaphet Kebede, Nathan Braswell, Matthew Watson, Virginia Hench, Andrew Crerar, Chris M. Ball, Carl Schreep, P. J. Linebaugh, Hannah Hiles, Rebecca R. Boyles, Chris Bizon, Ashok Kumar Krishnamurthy, Steven Cox:
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, Heike Adel, Jannik Strötgen, Dietrich Klakow:
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, Jie Zheng, Guizhao Liang:
DFBP: a comprehensive database of food-derived bioactive peptides for peptidomics research. 3275-3280 - Wenxiu Wang, Hamidreza Heydarian, Teun A. P. M. Huijben, Sjoerd Stallinga, Bernd Rieger:
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, Inbar Gahali-Sass, Sharon Kredo-Russo, Naomi B. Zak, Merav Bassan:
Exodus: sequencing-based pipeline for quantification of pooled variants. 3288-3290 - Martin Hunt, Jeremy Swann, Bede Constantinides, Philip Fowler, Zamin Iqbal:
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads. 3291-3293 - Shaohui Xie, Xiaotian He, Shan He, Zexuan Zhu:
CURC: a CUDA-based reference-free read compressor. 3294-3296 - Russell B. Davidson, Jess Woods, T. Chad Effler, Mathialakan Thavappiragasam, Julie C. Mitchell, Jerry M. Parks, Ada Sedova:
OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances. 3297-3298 - Dibyajyoti Maity, Debnath Pal:
MD DaVis: interactive data visualization of protein molecular dynamics. 3299-3301 - Genis Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluis Gelpí:
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools. 3302-3303 - Joan Segura, Yana Rose, Sebastian Bittrich, Stephen K. Burley, Jose M. Duarte:
RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies. 3304-3305 - Akio Onogi, Aisaku Arakawa:
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, Nasir M. Rajpoot, Fayyaz A. Minhas:
REET: robustness evaluation and enhancement toolbox for computational pathology. 3312-3314 - Jonathan U. Harrison, Onur Sen, Andrew D. McAinsh, Nigel J. Burroughs:
Kinetochore tracking in 3D from lattice light-sheet imaging data with KiT. 3315-3317
Volume 38, Number 13, June 2022
- Andrea Guarracino, Simon Heumos, Sven Nahnsen, Pjotr Prins, Erik Garrison:
ODGI: understanding pangenome graphs. 3319-3326 - Yi Nian Niu, Eric G. Roberts, Danielle Denisko, Michael M. Hoffman:
Assessing and assuring interoperability of a genomics file format. 3327-3336 - Bo Yang, Yan Yang, Xueping Su:
Deep structure integrative representation of multi-omics data for cancer subtyping. 3337-3342 - Diego Santoro, Leonardo Pellegrina, Matteo Comin, Fabio Vandin:
SPRISS: approximating frequent k-mers by sampling reads, and applications. 3343-3350 - Ruheng Wang, Junru Jin, Quan Zou, Kenta Nakai, Leyi Wei:
Predicting protein-peptide binding residues via interpretable deep learning. 3351-3360 - Martin M. Femenias, Juan C. Santos, Jack W. Sites, Luciano J. Avila, Mariana Morando:
ExplorATE: a new pipeline to explore active transposable elements from RNA-seq data. 3361-3366 - Nadia Tahiri, Bernard Fichet, Vladimir Makarenkov:
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, Gary Peltz:
An automated multi-modal graph-based pipeline for mouse genetic discovery. 3385-3394 - Kapil Devkota, Henri Schmidt, Matthew Werenski, James M. Murphy, Mert Erden, Victor Arsenescu, Lenore J. Cowen:
GLIDER: function prediction from GLIDE-based neighborhoods. 3395-3406 - Cesim Erten, Aissa Houdjedj, Hilal Kazan, Ahmed Amine Taleb Bahmed:
PersonaDrive: a method for the identification and prioritization of personalized cancer drivers. 3407-3414 - Yang Bai, Yang Li, Yu Shen, Mingyu Yang, Wentao Zhang, Bin Cui:
AutoDC: an automatic machine learning framework for disease classification. 3415-3421 - Christoph Bueschl, Maria Doppler, Elisabeth Varga, Bernhard Seidl, Mira Flasch, Benedikt Warth, Jürgen Zanghellini:
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, Yueyang Huang, Lihang Liu, Donglong He, Wei Wang, Xiaomin Fang, Xiaonan Zhang, Fan Wang, Hua Wu, Haifeng Wang:
HelixADMET: a robust and endpoint extensible ADMET system incorporating self-supervised knowledge transfer. 3444-3453 - Tim Kucera, Matteo Togninalli, Laetitia Meng-Papaxanthos:
Conditional generative modeling for de novo protein design with hierarchical functions. 3454-3461 - Philippe Weitz, Yinxi Wang, Kimmo Kartasalo, Lars Egevad, Johan Lindberg, Henrik Grönberg, Martin Eklund, Mattias Rantalainen:
Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression-based convolutional neural networks. 3462-3469 - Erik N. Bergstrom, Mousumy Kundu, Noura Tbeileh, Ludmil B. Alexandrov:
Examining clustered somatic mutations with SigProfilerClusters. 3470-3473 - Alexander N. Stein, Anoushka Joglekar, Chi-Lam Poon, Hagen U. Tilgner:
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, Kevin M. Shebek, Linda J. Broadbelt, Keith E. J. Tyo:
MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics. 3484-3487 - Zilong Zhang, Feifei Cui, Wei Su, Lijun Dou, Anqi Xu, Chen Cao, Quan Zou:
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, Taesu Chung, Dongsup Kim:
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, Lixin Cheng:
meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data. 3513-3522 - Itunu G. Osuntoki, Andrew Harrison, Hongsheng Dai, Yanchun Bao, Nicolae Radu Zabet:
ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data. 3523-3531 - Ariel A. Aptekmann, J. Buongiorno, D. Giovannelli, M. Glamoclija, Diego U. Ferreiro, Yana Bromberg:
mebipred: identifying metal-binding potential in protein sequence. 3532-3540 - Yansu Wang, Ximei Luo, Quan Zou:
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, Surag Nair, Akshay Balsubramani, Anshul Kundaje:
Accelerating in silico saturation mutagenesis using compressed sensing. 3557-3564 - Gleb Zhelezov, James H. Degnan:
Trying out a million genes to find the perfect pair with RTIST. 3565-3573 - Qin Wang, Jun Wei, Yuzhe Zhou, Mingzhi Lin, Ruobing Ren, Sheng Wang, Shuguang Cui, Zhen Li:
Prior knowledge facilitates low homologous protein secondary structure prediction with DSM distillation. 3574-3581 - Fei Li, Ziqiao Zhang, Jihong Guan, Shuigeng Zhou:
Effective drug-target interaction prediction with mutual interaction neural network. 3582-3589 - Turkan Haliloglu, Aysima Hacisuleyman, Burak Erman:
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, Yihui Li, Amin Emad:
Looking at the BiG picture: incorporating bipartite graphs in drug response prediction. 3609-3620 - Matthias Kirchler, Stefan Konigorski, Matthias Norden, Christian Meltendorf, Marius Kloft, Claudia Schurmann, Christoph Lippert:
transferGWAS: GWAS of images using deep transfer learning. 3621-3628 - Huidong Liu, Tahsin Kurc:
Deep learning for survival analysis in breast cancer with whole slide image data. 3629-3637 - Blas Chaves-Urbano, Barbara Hernando, Maria J. Garcia, Geoff MacIntyre:
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, Ivana Hutarová Vareková, Jan Hutar, Aliaksei Chareshneu, Karel Berka, Radka Svobodová Vareková:
OverProt: secondary structure consensus for protein families. 3648-3650 - Baptiste Kerouanton, Sebastian Schäfer, Lena Ho, Sonia Chothani, Owen J. L. Rackham:
CLIPreg: constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq. 3651-3653 - Wenpin Hou, Zhicheng Ji:
Palo: spatially aware color palette optimization for single-cell and spatial data. 3654-3656 - Laurence Legon, Christophe Corre, Declan G. Bates, Ahmad A. Mannan:
gcFront: a tool for determining a Pareto front of growth-coupled cell factory designs. 3657-3659 - Léo P. M. Diaz, Michael P. H. Stumpf:
HyperGraphs.jl: representing higher-order relationships in Julia. 3660-3661 - Leqi Tian, Zhenjiang Li, Guoxuan Ma, Xiaoyue Zhang, Ziyin Tang, Siheng Wang, Jian Kang, Donghai Liang, Tianwei Yu:
Metapone: a Bioconductor package for joint pathway testing for untargeted metabolomics data. 3662-3664 - Pablo Monfort-Lanzas, Raphael Gronauer, Leonie Madersbacher, Christoph Schatz, Dietmar Rieder, Hubert Hackl:
MIO: microRNA target analysis system for immuno-oncology. 3665-3667 - Bartosz Adamczyk, Maciej Antczak, Marta Szachniuk:
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures. 3668-3670 - Sylvain Prigent, Cesar Augusto Valades-Cruz, Ludovic Leconte, Jean Salamero, Charles Kervrann:
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, Julian D. Schwab, Silke D. Werle, Nensi Ikonomi, Ludwig Lausser, Hans A. Kestler:
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, Robert B. Scharpf:
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. 3677-3683 - Wei-Zhi Song, Shan Zhang, Torsten Thomas:
MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads. 3684-3688 - Yi-Juan Hu, Glen A. Satten:
A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome. 3689-3697 - Peter J. Bradbury, Terry M. Casstevens, Sarah E. Jensen, L. C. Johnson, Z. R. Miller, Brandon Monier, M. C. Romay, B. Song, Edward S. Buckler:
The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. 3698-3702 - Hai-Yun Wang, Jian-Ping Zhao, Chun-Hou Zheng, Yan-Sen Su:
scCNC: a method based on capsule network for clustering scRNA-seq data. 3703-3709 - Nik Tavakolian, João Guilherme Frazão, Devin Bendixsen, Rike Stelkens, Chun-Biu Li:
Shepherd: accurate clustering for correcting DNA barcode errors. 3710-3716 - Sumit Tarafder, Mazharul Islam, Swakkhar Shatabda, Atif Rahman:
Figbird: a probabilistic method for filling gaps in genome assemblies. 3717-3724 - Sarah Lutteropp, Céline Scornavacca, Alexey M. Kozlov, Benoit Morel, Alexandros Stamatakis:
NetRAX: accurate and fast maximum likelihood phylogenetic network inference. 3725-3733 - Cheng Ye, Bryan Thornlow, Angie S. Hinrichs, Alexander Kramer, Cade Mirchandani, Devika Torvi, Robert Lanfear, Russell Corbett-Detig, Yatish Turakhia:
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2. 3734-3740 - Yupei You, Michael B. Clark, Heejung Shim:
NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing. 3741-3748 - Niels Johan Christensen, Samuel Demharter, Meera Vieira Machado, Lykke Pedersen, Marco Salvatore, Valdemar Stentoft-Hansen, Miquel Triana Iglesias:
Identifying interactions in omics data for clinical biomarker discovery using symbolic regression. 3749-3758 - Frantisek Malinka, Ashkan Zareie, Jan Procházka, Radislav Sedlacek, Vendula Novosadova:
Batch alignment via retention orders for preprocessing large-scale multi-batch LC-MS experiments. 3759-3767 - Yilei Huang, Harald Ringbauer:
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes. 3768-3777 - Rick Wertenbroek, Simone Rubinacci, Ioannis Xenarios, Yann Thoma, Olivier Delaneau:
XSI - a genotype compression tool for compressive genomics in large biobanks. 3778-3784 - Marzieh Ayati, Serhan Yilmaz, Mark R. Chance, Mehmet Koyutürk:
Functional characterization of co-phosphorylation networks. 3785-3793 - Wonjin Yoon, Richard Jackson, Aron Lagerberg, Jaewoo Kang:
Sequence tagging for biomedical extractive question answering. 3794-3801 - Ahmed A. Metwally, Tom Zhang, Si Wu, Ryan Kellogg, Wenyu Zhou, Kévin Contrepois, Hua Tang, Michael Snyder:
Robust identification of temporal biomarkers in longitudinal omics studies. 3802-3811 - Pavel Vazquez, Kayoko Shoji, Steffen Novik, Stefan Krauss, Simon Rayner:
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences. 3812-3817 - Souvik Seal, Debashis Ghosh:
MIAMI: mutual information-based analysis of multiplex imaging data. 3818-3826 - Matthew Crown, Natália Teruel, Rafael Najmanovich, Matthew Bashton:
SPEAR: Systematic ProtEin AnnotatoR. 3827-3829 - Piyush Ranjan, Christopher A. Brown, John R. Erb-Downward, Robert P. Dickson:
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data. 3830-3832 - Parthajit Roy, Dhananjay Bhattacharyya:
MetBP: a software tool for detection of interaction between metal ion-RNA base pairs. 3833-3834 - Michal Zurkowski, Tomasz Zok, Marta Szachniuk:
DrawTetrado to create layer diagrams of G4 structures. 3835-3836 - Varun Ullanat, Nikhil Kasukurthi, Shruthi Viswanath:
PrISM: precision for integrative structural models. 3837-3839 - Pu Huang, Erin Davis, Xia Cao, Hunter J. Cameron:
riboCleaner: a pipeline to identify and quantify rRNA read contamination from RNA-seq data in plants. 3840-3843 - Emil K. Gustavsson, David Zhang, Regina H. Reynolds, Sonia García-Ruíz, Mina Ryten:
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2. 3844-3846 - Daniele Bizzarri, Marcel J. T. Reinders, Marian Beekman, P. Eline Slagboom, Erik van den Akker:
MiMIR: R-shiny application to infer risk factors and endpoints from Nightingale Health's 1H-NMR metabolomics data. 3847-3849 - Philipp Wegner, Sebastian Schaaf, Mischa Uebachs, Daniel Domingo-Fernández, Yasamin Salimi, Stephan Gebel, Astghik Sargsyan, Colin Birkenbihl, Stephan Springstubbe, Thomas Klockgether, Juliane Fluck, Martin Hofmann-Apitius, Alpha Tom Kodamullil:
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, Philip J. Lupo, Benjamin Tycko, John S. Witte, Charlotte A. Hobbs, Ming Li:
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci. 3853-3862 - Maria Osmala, Gökcen Eraslan, Harri Lähdesmäki:
ChromDMM: a Dirichlet-multinomial mixture model for clustering heterogeneous epigenetic data. 3863-3870 - Vinzenz May, Leonard Koch, Björn Fischer-Zirnsak, Denise Horn, Petra Gehle, Uwe Kornak, Dieter Beule, Manuel Holtgrewe:
ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise. 3871-3876 - Yang-Ming Yeh, Yi-Chang Lu:
MSRCall: a multi-scale deep neural network to basecall Oxford Nanopore sequences. 3877-3884 - Mobeen Ur Rehman, Hilal Tayara, Quan Zou, Kil To Chong:
i6mA-Caps: a CapsuleNet-based framework for identifying DNA N6-methyladenine sites. 3885-3891 - Marcell Szikszai, Michael J. Wise, Amitava Datta, Max Ward, David H. Mathews:
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families. 3892-3899 - Jaswinder Singh, Kuldip K. Paliwal, Thomas Litfin, Jaspreet Singh, Yaoqi Zhou:
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling. 3900-3910 - Antoine Moniot, Yann Guermeur, Sjoerd Jacob de Vries, Isaure Chauvot de Beauchêne:
ProtNAff: protein-bound Nucleic Acid filters and fragment libraries. 3911-3917 - Michael Komodromos, Eric O. Aboagye, Marina Evangelou, Sarah Filippi, Kolyan Ray:
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, Banu Tiryaki, A. Ercüment Çiçek:
A unifying network modeling approach for codon optimization. 3935-3941 - Yuge Wang, Tianyu Liu, Hongyu Zhao:
ResPAN: a powerful batch correction model for scRNA-seq data through residual adversarial networks. 3942-3949 - Yucheng Wang, Tyler J. Gorrie-Stone, Olivia A. Grant, Alexandria D. Andrayas, Xiaojun Zhai, Klaus D. McDonald-Maier, Leonard C. Schalkwyk:
InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias. 3950-3957 - Joseph Szymborski, Amin Emad:
RAPPPID: towards generalizable protein interaction prediction with AWD-LSTM twin networks. 3958-3967 - Alicja W. Nowakowska, Malgorzata Kotulska:
Topological analysis as a tool for detection of abnormalities in protein-protein interaction data. 3968-3975 - Yiqi Tong, Fuzhen Zhuang, Huajie Zhang, Chuyu Fang, Yu Zhao, Deqing Wang, Hengshu Zhu, Bin Ni:
Improving biomedical named entity recognition by dynamic caching inter-sentence information. 3976-3983 - Hayda Almeida, Adrian Tsang, Abdoulaye Baniré Diallo:
Improving candidate Biosynthetic Gene Clusters in fungi through reinforcement learning. 3984-3991 - Xuexue Liu, Ludovic Orlando:
mapDATAge: a ShinyR package to chart ancient DNA data through space and time. 3992-3994 - Cheng Zhong, Kangenbei Liao, Wei Chen, Qianlong Liu, Baolin Peng, Xuanjing Huang, Jiajie Peng, Zhongyu Wei:
Hierarchical reinforcement learning for automatic disease diagnosis. 3995-4001 - Qibing Jiang, Praneeth Sudalagunta, Maria C. Silva, Rafael R. Canevarolo, Xiaohong Zhao, Khandakar Tanvir Ahmed, Raghunandan Reddy Alugubelli, Gabriel Deavila, Alexandre Tungesvik, Lia Perez, Robert A. Gatenby, Robert J. Gillies, Rachid Baz, Mark B. Meads, Kenneth H. Shain, Ariosto Siqueira Silva, Wei Zhang:
CancerCellTracker: a brightfield time-lapse microscopy framework for cancer drug sensitivity estimation. 4002-4010 - Pritam Dey, Zhengwu Zhang, David B. Dunson:
Outlier detection for multi-network data. 4011-4018 - Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu:
PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data. 4019-4026 - Yang Cao, Qingyang Dong, Dan Wang, Pengcheng Zhang, Ying Liu, Chao Niu:
microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization. 4027-4029 - Matej Lexa, Monika Cechova, Son Hoang Nguyen, Pavel Jedlicka, Viktor Tokan, Zdenek Kubat, Roman Hobza, Eduard Kejnovský:
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, Rohan Misra, Steven C. Almo, Ulrich G. Steidl, Hannes E. Bülow, Deyou Zheng:
HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elements. 4036-4038 - Tsukasa Fukunaga, Wataru Iwasaki:
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, Shi-Jie Chen:
Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences. 4042-4043 - Liesa Salzer, Michael Witting, Philippe Schmitt-Kopplin:
MobilityTransformR: an R package for effective mobility transformation of CE-MS data. 4044-4045 - Gordon T. Luu, Michael A. Freitas, Itzel Lizama-Chamu, Catherine S. McCaughey, Laura M. Sanchez, Mingxun Wang:
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, Divya Sharma, R. Prabakaran, Fathima Ridha, Mugdha Mohkhedkar, Vani Janakiraman, M. Michael Gromiha:
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, Honglin Fang, Xiao Wang, Miao Wang, Shuqin Li, Lachlan J. M. Coin, Fuyi Li, Jiangning Song:
DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions. 4053-4061 - Yang Chen, Shue Chen, Elissa P. Lei:
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, Kailong Li, Tingfang Wu, Qiang Lyu:
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, Zhenyao Ye, Tianzhou Ma:
High-dimension to high-dimension screening for detecting genome-wide epigenetic and noncoding RNA regulators of gene expression. 4078-4087 - Bader F. Al-Anzi, Mohammad Khajah, Saja A. Fakhraldeen:
Predicting and explaining the impact of genetic disruptions and interactions on organismal viability. 4088-4099 - Mitra Darvish, Enrico Seiler, Svenja Mehringer, René Rahn, Knut Reinert:
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, Fengquan Zhou, Jie Wang, Seth Blackshaw, Jiang Qian:
LRLoop: a method to predict feedback loops in cell-cell communication. 4117-4126 - Lise Pomiès, Céline Brouard, Harold Duruflé, Élise Maigné, Clément Carré, Louise Gody, Fulya Trösser, George Katsirelos, Brigitte Mangin, Nicolas B. Langlade, Simon de Givry:
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, Luca Becchetti:
Biological Random Walks: multi-omics integration for disease gene prioritization. 4145-4152 - Zhongjian Cheng, Qichang Zhao, Yaohang Li, Jianxin Wang:
IIFDTI: predicting drug-target interactions through interactive and independent features based on attention mechanism. 4153-4161 - Tim Breitenbach, Matthias Jürgen Schmitt, Thomas Dandekar:
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, Andreas Bender, Sebastian J. Vollmer:
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures. 4178-4184 - Francesco P. Panei, Rachel Torchet, Hervé Ménager, Paraskevi Gkeka, Massimiliano Bonomi:
HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design. 4185-4193 - Shuya Ikeda, Hiromasa Ono, Tazro Ohta, Hirokazu Chiba, Yuki Naito, Yuki Moriya, Shuichi Kawashima, Yasunori Yamamoto, Shinobu Okamoto, Susumu Goto, Toshiaki Katayama:
TogoID: an exploratory ID converter to bridge biological datasets. 4194-4199 - Jakub Wiedemann, Jacek Kaczor, Maciej Milostan, Tomasz Zok, Jacek Blazewicz, Marta Szachniuk, Maciej Antczak:
RNAloops: a database of RNA multiloops. 4200-4205 - Yanan Wang, Changyuan Hu, Terry Kwok, Christopher A. Bain, Xiangyang Xue, Robin B. Gasser, Geoffrey I. Webb, Alex Boussioutas, Xian Shen, Roger J. Daly, Jiangning Song:
DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images. 4206-4213 - Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristóbal Gallardo-Alba, Alice Giani, Olivier Fedrigo, Erich D. Jarvis:
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. 4214-4216 - Fawaz Dabbaghie, Jana Ebler, Tobias Marschall:
BubbleGun: enumerating bubbles and superbubbles in genome graphs. 4217-4219 - Aaron Chuah, Sean Li, Andrea Do, Matthew A. Field, Dan Andrews:
StabilitySort: assessment of protein stability changes on a genome-wide scale to prioritize potentially pathogenic genetic variation. 4220-4222 - Alice Wittig, Fábio Miranda, Martin Hölzer, Tom Altenburg, Jakub M. Bartoszewicz, Sebastian Beyvers, Marius A. Dieckmann, Ulrich Genske, Sven H. Giese, Melania Nowicka, Hugues Richard, Henning Schiebenhoefer, Anna-Juliane Schmachtenberg, Paul Sieben, Ming Tang, Julius Tembrockhaus, Bernhard Y. Renard, Stephan Fuchs:
CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance. 4223-4225 - Gökhan Özsari, Ahmet Süreyya Rifaioglu, Ahmet Atakan, Tunca Dogan, Maria Jesus Martin, Rengül Çetin-Atalay, Volkan Atalay:
SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins. 4226-4229 - Torbjørn Rognes, Lonneke Scheffer, Victor Greiff, Geir Kjetil Sandve:
CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. 4230-4232 - Serena Rosignoli, Alessandro Paiardini:
DockingPie: a consensus docking plugin for PyMOL. 4233-4234 - Pietro Hiram Guzzi, Luisa Di Paola, Alessandro Giuliani, Pierangelo Veltri:
PCN-Miner: an open-source extensible tool for the analysis of Protein Contact Networks. 4235-4237 - Feng Zhou, Adam S. Butterworth, Jennifer L. Asimit:
Flashfm-ivis: interactive visualization for fine-mapping of multiple quantitative traits. 4238-4242 - Xiaoming Fu, Xinyi Zhou, Dongyang Gu, Zhixing Cao, Ramon Grima:
DelaySSAToolkit.jl: stochastic simulation of reaction systems with time delays in Julia. 4243-4245 - Ángel Rodríguez-Cerro, Sergio Sancho, Miriam Rodríguez, Miguel A. Gamón, Léna Guitou, Rafael J. Martínez, Javier Buceta:
ANISE: an application to design mechanobiology simulations of planar epithelia. 4246-4247 - Zuguang Gu, Daniel Hübschmann:
Pkgndep: a tool for analyzing dependency heaviness of R packages. 4248-4251 - Yizhuo Wang, Christopher R. Flowers, Ziyi Li, Xuelin Huang:
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis. 4252-4254
Volume 38, Number 18, September 2022
- Lance D. Hentges, Martin J. Sergeant, Christopher B. Cole, Damien J. Downes, Jim R. Hughes, Stephen Taylor:
LanceOtron: a deep learning peak caller for genome sequencing experiments. 4255-4263 - Zeheng Bai, Yao-zhong Zhang, Satoru Miyano, Rui Yamaguchi, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto:
Identification of bacteriophage genome sequences with representation learning. 4264-4270 - Xinjie Li, Shengli Zhang, Hongyan Shi:
An improved residual network using deep fusion for identifying RNA 5-methylcytosine sites. 4271-4277 - Vlad-Rares Danaila, Catalin Buiu:
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, Gunnar Rätsch, André Kahles, Kjong-Van Lehmann:
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing. 4293-4300 - Jimin Pei, Jing Zhang, Qian Cong:
Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling. 4301-4311 - Marina A. Pak, Dmitry N. Ivankov:
Best templates outperform homology models in predicting the impact of mutations on protein stability. 4312-4320 - Yeganeh Madadi, Jian Sun, Hao Chen, Robert W. Williams, Siamak Yousefi:
Detecting retinal neural and stromal cell classes and ganglion cell subtypes based on transcriptome data with deep transfer learning. 4321-4329 - Keita Iida, Jumpei Kondo, Johannes Nicolaus Wibisana, Masahiro Inoue, Mariko Okada:
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes. 4330-4336 - Yongwen Zhuang, Brooke N. Wolford, Kisung Nam, Wenjian Bi, Wei Zhou, Cristen J. Willer, Bhramar Mukherjee, Seunggeun Lee:
Incorporating family disease history and controlling case-control imbalance for population-based genetic association studies. 4337-4343 - Sam F. L. Windels, Noël Malod-Dognin, Natasa Przulj:
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, Yasin Tepeli, Joana P. Gonçalves:
Overcoming selection bias in synthetic lethality prediction. 4360-4368 - Maria Mahbub, Sudarshan Srinivasan, Edmon Begoli, Gregory D. Peterson:
BioADAPT-MRC: adversarial learning-based domain adaptation improves biomedical machine reading comprehension task. 4369-4379 - Yuhao Chen, Yanshi Hu, Xiaotian Hu, Cong Feng, Ming Chen:
CoGO: a contrastive learning framework to predict disease similarity based on gene network and ontology structure. 4380-4386 - Shujie Ren, Liang Yu, Lin Gao:
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, Gabriel Pik Liang Marini, Sock Hoai Chan, Siao Ting Chong, Ee Ling Chew, Haoda Lu, Laurent Gole, Weimiao Yu, Joanne Ngeow:
Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level. 4395-4402 - Eef M. Jonkheer, Dirk-Jan M. van Workum, Siavash Sheikhizadeh Anari, Balázs Brankovics, Jorn R. de Haan, Lidija Berke, Theo A. J. van der Lee, Dick de Ridder, Sandra Smit:
PanTools v3: functional annotation, classification and phylogenomics. 4403-4405 - Zhixia Xiao, Hon-Ming Lam:
ShinySyn: a Shiny/R application for the interactive visualization and integration of macro- and micro-synteny data. 4406-4408 - Brian Y. Chen, William Bone, Kim Lorenz, Michael Levin, Marylyn D. Ritchie, Benjamin F. Voight:
ColocQuiaL: a QTL-GWAS colocalization pipeline. 4409-4411 - Alexis Dereeper, Marilyne Summo, Damien F. Meyer:
PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes. 4412-4414 - Vonn Walter, Hyo Young Choi, Xiaobei Zhao, Yan Gao, Jeremiah Holt, D. Neil Hayes:
DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference. 4415-4417 - Gabriel Cia, Jean Marc Kwasigroch, Marianne Rooman, Fabrizio Pucci:
SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants. 4418-4419 - Jason Yeung, Andrew L. Routh:
ViReMaShiny: an interactive application for analysis of viral recombination data. 4420-4422 - Yoann Dufresne, Téo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi:
The K-mer File Format: a standardized and compact disk representation of sets of k-mers. 4423-4425 - Hyun Kil Shin, Hang-Suk Chun, Sangwoo Lee, Se-Myo Park, Daeui Park, Myung-Gyun Kang, Sungbo Hwang, Jung-Hwa Oh, Hyoung-Yun Han, Woo-Keun Kim, Seokjoo Yoon:
ToxSTAR: drug-induced liver injury prediction tool for the web environment. 4426-4427 - Chih-Hao Lu, Chih-Chieh Chen, Chin-Sheng Yu, Yen-Yi Liu, Jia-Jun Liu, Sung-Tai Wei, Yu-Feng Lin:
MIB2: metal ion-binding site prediction and modeling server. 4428-4429 - Federico Ansaloni, Nicolò Gualandi, Mauro Esposito, Stefano Gustincich, Remo Sanges:
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments. 4430-4433 - Eric Ruan, Erika Nemeth, Richard A. Moffitt, Lorena Sandoval, Mitchell J. Machiela, Neal D. Freedman, Wen-Yi Huang, Wendy Wong, Kai-Ling Chen, Brian Park, Kevin Jiang, Belynda Hicks, Jia Liu, Daniel E. Russ, Lori M. Minasian, Paul F. Pinsky, Stephen J. Chanock, Montserrat Garcia-Closas, Jonas S. Almeida:
PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project. 4434-4436 - Panteleimon G. Takis, Ivan Vuckovic, Tricia Tan, Aleksandar Denic, John C. Lieske, Matthew R. Lewis, Slobodan Macura:
NMRpQuant: an automated software for large scale urinary total protein quantification by one-dimensional 1H NMR profiles. 4437-4439 - Franco Pradelli, Giovanni Minervini, Silvio C. E. Tosatto:
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models. 4440-4441 - Mengyuan Kan, Avantika R. Diwadkar, Supriya Saxena, Haoyue Shuai, Jaehyun Joo, Blanca E. Himes:
REALGAR: a web app of integrated respiratory omics data. 4442-4445 - Zaiqiao Meng, Anya Okhmatovskaia, Maxime Polleri, Yannan Shen, Guido Powell, Zihao Fu, Iris Ganser, Meiru Zhang, Nicholas B. King, David L. Buckeridge, Nigel Collier:
BioCaster in 2021: automatic disease outbreaks detection from global news media. 4446-4448 - Chih-Hsuan Wei, Alexis Allot, Kevin Riehle, Aleksandar Milosavljevic, Zhiyong Lu:
tmVar 3.0: an improved variant concept recognition and normalization tool. 4449-4451 - Ammar Qaseem, Stefan Günther:
CPRiL: compound-protein relationships in literature. 4452-4453 - Yi-An Chen, Rodolfo S. Allendes Osorio, Kenji Mizuguchi:
TargetMine 2022: a new vision into drug target analysis. 4454-4456
Volume 38, Number 19, September 2022
- Ke Zhang, Chenxi Wang, Liping Sun, Jie Zheng:
Prediction of gene co-expression from chromatin contacts with graph attention network. 4457-4465 - Maciej Piernik, Dariusz Brzezinski, Pawel Sztromwasser, Klaudia Pacewicz, Weronika Majer-Burman, Michal Gniot, Dawid Sielski, Oleksii Bryzghalov, Alicja Wozna, Pawel Zawadzki:
DBFE: distribution-based feature extraction from structural variants in whole-genome data. 4466-4473 - Jinfa Ma, Jane Y. Wu, Li Zhu:
Detection of orthologous exons and isoforms using EGIO. 4474-4480 - Andre Lamurias, Mantas Sereika, Mads Albertsen, Katja Hose, Thomas Dyhre Nielsen:
Metagenomic binning with assembly graph embeddings. 4481-4487 - Gabriela Alejandra Merino, Rabie Saidi, Diego H. Milone, Georgina Stegmayer, Maria Jesus Martin:
Hierarchical deep learning for predicting GO annotations by integrating protein knowledge. 4488-4496 - Pengyu Zhang, Yingfu Wu, Haoru Zhou, Bing Zhou, Hongming Zhang, Hao Wu:
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, Simon Crouzet, Elodie Laine, Alessandra Carbone:
Deep Local Analysis evaluates protein docking conformations with locally oriented cubes. 4505-4512 - Chunxiang Peng, Xiao-Gen Zhou, Yuhao Xia, Jun Liu, Minghua Hou, Gui-Jun Zhang:
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, Yuk Yee Leung, Matei Ionita, Li-San Wang, Mingyao Li:
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, Shixiong Zhang, Yanchun Liang, Ka-Chun Wong, Xiangtao Li:
scWMC: weighted matrix completion-based imputation of scRNA-seq data via prior subspace information. 4537-4545 - Wei Peng, Hancheng Liu, Wei Dai, Ning Yu, Jianxin Wang:
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, Chengkun Wu, Xiao-Chen Zhang, Xinyi Xiao, Yanlong Qiu, Wentao Zhao, Tingjun Hou, Dong-Sheng Cao:
MICER: a pre-trained encoder-decoder architecture for molecular image captioning. 4562-4572 - Jing Jiang, Ruisheng Zhang, Zhili Zhao, Jun Ma, Yunwu Liu, Yongna Yuan, Bojuan Niu:
MultiGran-SMILES: multi-granularity SMILES learning for molecular property prediction. 4573-4580 - Sichao Qiu, Guoxian Yu, Xudong Lu, Carlotta Domeniconi, Maozu Guo:
Isoform function prediction by Gene Ontology embedding. 4581-4588 - Melissa Kimble, S. Allers, K. Campbell, Chaofan Chen, Laura M. Jackson, Benjamin L. King, Samantha Silverbrand, G. York, Kate Beard:
medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata. 4589-4597 - Jie Wang, Nazia Tabassum, Tanjin Taher Toma, Yibo Wang, Andreas Gahlmann, Scott T. Acton:
3D GAN image synthesis and dataset quality assessment for bacterial biofilm. 4598-4604 - Hongyi Duanmu, Shristi Bhattarai, Hongxiao Li, Zhan Shi, Fusheng Wang, George Teodoro, Keerthi Gogineni, Preeti Subhedar, Umay Kiraz, Emiel A. M. Janssen, Ritu Aneja, Jun Kong:
A spatial attention guided deep learning system for prediction of pathological complete response using breast cancer histopathology images. 4605-4612 - Jeremy Muhlich, Yu-An Chen, Clarence Han-Wei Yapp, Douglas Russell, Sandro Santagata, Peter K. Sorger:
Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. 4613-4621 - Adrian Friebel, Tim Johann, Dirk Drasdo, Stefan Hoehme:
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, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu:
FastRemap: a tool for quickly remapping reads between genome assemblies. 4633-4635 - Shuangquan Zhang, Lili Yang, Xiaotian Wu, Nan Sheng, Yuan Fu, Anjun Ma, Yan Wang:
MMGraph: a multiple motif predictor based on graph neural network and coexisting probability for ATAC-seq data. 4636-4638 - Quan Shi, Shiping Liu, Karsten Kristiansen, Longqi Liu:
The FASTQ+ format and PISA. 4639-4642 - Shiyu Jiang, Hemn Barzan Abdalla, Chuyun Bi, Yi Zhu, Xuechen Tian, Yixin Yang, Aloysius Wong:
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, Francesco Marrafino, Stefano Piotto:
YAMACS: a graphical interface for GROMACS. 4645-4646 - Athena Chen, Kai Kammers, H. Benjamin Larman, Robert B. Scharpf, Ingo Ruczinski:
Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER. 4647-4649 - Xiaotao Shen, Chuchu Wang, Michael P. Snyder:
massDatabase: utilities for the operation of the public compound and pathway database. 4650-4651 - Bartlomiej Szawulak, Marcin Radom, Piotr Formanowicz:
Comparing Petri net-based models of biological systems using Holmes. 4652-4653 - Yuanyuan Li, Jun Wu, Donghuan Lu, Chao Xu, Yefeng Zheng, Hanchuan Peng, Lei Qu:
mBrainAligner-Web: a web server for cross-modal coherent registration of whole mouse brains. 4654-4655 - Manuel Rueda, Roberto Ariosa, Mauricio Moldes, Jordi Rambla:
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, Yun William Yu:
Theory of local k-mer selection with applications to long-read alignment. 4659-4669 - Wenhuan Zeng, Anupam Gautam, Daniel H. Huson:
DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome. 4670-4676 - Galen F. Gao, Coyin Oh, Gordon Saksena, Davy Deng, Lindsay C. Westlake, Barbara A. Hill, Michael Reich, Steven E. Schumacher, Ashton C. Berger, Scott L. Carter, Andrew D. Cherniack, Matthew Meyerson, Barbara Tabak, Rameen Beroukhim, Gad Getz:
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, Rui Chen, Quan Wang, Qiang Wei, Ying Ji, Xue Zhong, Bingshan Li:
TVAR: assessing tissue-specific functional effects of non-coding variants with deep learning. 4697-4704 - Zhenxing Guo, Andrew M. Shafik, Peng Jin, Hao Wu:
Differential RNA methylation analysis for MeRIP-seq data under general experimental design. 4705-4712 - Jack Kuipers, Jochen Singer, Niko Beerenwinkel:
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence. 4713-4719 - Belinda Phipson, Choon Boon Sim, Enzo R. Porrello, Alex W. Hewitt, Joseph E. Powell, Alicia Oshlack:
propeller: testing for differences in cell type proportions in single cell data. 4720-4726 - Marie Oestreich, Lisa Holsten, Shobhit Agrawal, Kilian Dahm, Philipp Koch, Han Jin, Matthias Becker, Thomas Ulas:
hCoCena: horizontal integration and analysis of transcriptomics datasets. 4727-4734 - Yun Zhang, Hao Sun, Aishwarya Mandava, Brian D. Aevermann, Tobias R. Kollmann, Richard H. Scheuermann, Xing Qiu, Yu Qian:
FastMix: a versatile data integration pipeline for cell type-specific biomarker inference. 4735-4744 - Yue Cao, Yingxin Lin, Ellis Patrick, Pengyi Yang, Jean Yee Hwa Yang:
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, Kyunghyun Cho, Richard Bonneau:
NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction. 4762-4770 - Aditya Jadhav, Tarun Kumar, Mohit Raghavendra, Tamizhini Loganathan, Manikandan Narayanan:
Predicting cross-tissue hormone-gene relations using balanced word embeddings. 4771-4781 - Xuan Liu, Congzhi Song, Shichao Liu, Menglu Li, Xionghui Zhou, Wen Zhang:
Multi-way relation-enhanced hypergraph representation learning for anti-cancer drug synergy prediction. 4782-4789 - Priya Tiwary, Akshayraj Madhubalan, Amit Gautam:
No means 'No': a non-improper modeling approach, with embedded speculative context. 4790-4796 - Bintao He, Yan Zhang, Fa Zhang, Renmin Han:
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network. 4797-4805 - Hong-Dong Li, Cui-Xiang Lin, Jiantao Zheng:
GTFtools: a software package for analyzing various features of gene models. 4806-4808 - Lucas Czech, Moises Exposito-Alonso:
grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads. 4809-4811 - Parham Kazemi, Johnathan Wong, Vladimir Nikolic, Hamid Mohamadi, René L. Warren, Inanç Birol:
ntHash2: recursive spaced seed hashing for nucleotide sequences. 4812-4813 - Sean M. Solari, Remy B. Young, Vanessa R. Marcelino, Samuel C. Forster:
expam - high-resolution analysis of metagenomes using distance trees. 4814-4816 - Dominik Buchner, Till-Hendrik Macher, Florian Leese:
APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data. 4817-4819 - Oladele A. Oluwayiose, Haotian Wu, Feng Gao, Andrea A. Baccarelli, Tamar Sofer, J. Richard Pilsner:
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses. 4820-4822 - Alexander L. R. Lubbock, Carlos F. Lopez:
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, Agustín Lahoz:
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, German A. Preciat Gonzalez, Ronan M. T. Fleming:
MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions. 4831-4832 - Kavishwar B. Wagholikar, Layne Ainsworth, David Zelle, Kira Chaney, Michael Mendis, Jeffrey G. Klann, Alexander J. Blood, Angela Miller, Rupendra Chulyadyo, Michael Oates, William J. Gordon, Samuel J. Aronson, Benjamin M. Scirica, Shawn N. Murphy:
I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform. 4833-4836 - Mujeen Sung, Minbyul Jeong, Yonghwa Choi, Donghyeon Kim, Jinhyuk Lee, Jaewoo Kang:
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, Tim Bleimehl, Ron Henkel, Jamie Munro, Sebastian Müller, Axel Morgner, Jakob Laenge, Anke Pachauer, Alexander Erdl, Jens Weimar, Kirsten Walther Langendorf, Vincent Vialard, Thorsten Liebig, Martin Preusse, Dagmar Waltemath, Alexander Jarasch:
CovidGraph: a graph to fight COVID-19. 4843-4845 - Yifan Gui, Shuangshuang Xie, Yanan Wang, Ping Wang, Renzhi Yao, Xukai Gao, Yutian Dong, Gaoang Wang, Kuan Yoow Chan:
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, Carlos A. Elena-Real, Juan Cortés, Pau Bernadó, Miguel A. Andrade-Navarro:
The sequence context in poly-alanine regions: structure, function and conservation. 4851-4858 - Junjie Wang, Jie Hu, Huiting Sun, Mengdie Xu, Yun Yu, Yun Liu, Liang Cheng:
MGPLI: exploring multigranular representations for protein-ligand interaction prediction. 4859-4867 - Takaho Tsuchiya, Hiroki Hori, Haruka Ozaki:
CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells. 4868-4877 - Haoyang Li, Hanmin Li, Juexiao Zhou, Xin Gao:
SD2: spatially resolved transcriptomics deconvolution through integration of dropout and spatial information. 4878-4884 - Ziyi Li, Yizhuo Wang, Irene Ganan-Gomez, Simona Colla, Kim-Anh Do:
A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data. 4885-4892 - Christoph Müssel, Nensi Ikonomi, Silke D. Werle, Felix M. Weidner, Markus Maucher, Julian D. Schwab, Hans A. Kestler:
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, Andreas Aufschnaiter, Martin Ott, Jesse G. Meyer:
Multi-omic integration by machine learning (MIMaL). 4908-4918 - Han Cao, Youcheng Zhang, Jan Baumbach, Paul R. Burton, Dominic B. Dwyer, Nikolaos Koutsouleris, Julian O. Matschinske, Yannick Marcon, Sivanesan Rajan, Thilo Rieg, Patricia Ryser-Welch, Julian Späth, Carl Herrmann, Emanuel Schwarz:
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning. 4919-4926 - Bo Wang, Andy Law, Tim Regan, Nicholas Parkinson, Joby Cole, Clark D. Russell, David H. Dockrell, Michael U. Gutmann, J. Kenneth Baillie:
Systematic comparison of ranking aggregation methods for gene lists in experimental results. 4927-4933 - Gregory J. Hunt, Mark A. Dane, James E. Korkola, Laura M. Heiser, Johann Gagnon-Bartsch:
Systematic replication enables normalization of high-throughput imaging assays. 4934-4940 - Jin-Xian Hu, Yang Yang, Ying-Ying Xu, Hong-Bin Shen:
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images. 4941-4948 - Chao Zhang, Siavash Mirarab:
ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees. 4949-4950 - J. Harry Moore, Matthias R. Bauer, Jeff Guo, Atanas Patronov, Ola Engkvist, Christian Margreitter:
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, Anuli C. Uzozie, Siyuan Chen, Ye Su, Philipp F. Lange:
SQuAPP - simple quantitative analysis of proteins and PTMs. 4956-4958 - Nahuel Escobedo, Ronaldo Romario Tunque Cahui, Gastón Caruso, Emilio Garcia-Rios, Layla Hirsh, Alexander Miguel Monzon, Gustavo D. Parisi, Nicolas Palopoli:
CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure. 4959-4961 - Hansaim Lim, Chung-Jung Tsai, Ozlem Keskin, Ruth Nussinov, Attila Gürsoy:
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, Xianyang Zhang:
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, Xiangmei Li, Qian Wang, Junwei Han:
DRviaSPCN: a software package for drug repurposing in cancer via a subpathway crosstalk network. 4975-4977 - Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek, Eva Smijáková:
AEON.py: Python library for attractor analysis in asynchronous Boolean networks. 4978-4980 - Philipp Schneider, Pavlos Stephanos Bekiaris, Axel von Kamp, Steffen Klamt:
StrainDesign: a comprehensive Python package for computational design of metabolic networks. 4981-4983 - Soya Shinkai, Hiroya Itoga, Koji Kyoda, Shuichi Onami:
PHi-C2: interpreting Hi-C data as the dynamic 3D genome state. 4984-4986 - Lijuan Liu, Penghao Qian:
Manifold classification of neuron types from microscopic images. 4987-4989 - Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomás Helikar, Marc R. Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger:
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. 4990-4993 - Geir Kjetil Sandve, Victor Greiff:
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, David Ellinghaus:
EagleImp: fast and accurate genome-wide phasing and imputation in a single tool. 4999-5006 - Athanasios Baltzis, Leila Mansouri, Suzanne Jin, Björn E. Langer, Ionas Erb, Cédric Notredame:
Highly significant improvement of protein sequence alignments with AlphaFold2. 5007-5011 - Jouni Sirén, Benedict Paten:
GBZ file format for pangenome graphs. 5012-5018 - Yanming Wei, Quan Zou, Furong Tang, Liang Yu:
WMSA: a novel method for multiple sequence alignment of DNA sequences. 5019-5025 - Gourab Ghosh Roy, Nicholas Geard, Karin Verspoor, Shan He:
MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk. 5026-5032 - Satwik Acharyya, Xiang Zhou, Veerabhadran Baladandayuthapani:
SpaceX: gene co-expression network estimation for spatial transcriptomics. 5033-5041 - Zhongyuan Xu, Jiawei Luo, Zehao Xiong:
scSemiGAN: a single-cell semi-supervised annotation and dimensionality reduction framework based on generative adversarial network. 5042-5048 - Victor Bernal, Venustiano Soancatl-Aguilar, Jonas Bulthuis, Victor Guryev, Peter Horvatovich, Marco Grzegorczyk:
GeneNetTools: tests for Gaussian graphical models with shrinkage. 5049-5054 - Gavin M. Douglas, Molly G. Hayes, Morgan G. I. Langille, Elhanan Borenstein:
Integrating phylogenetic and functional data in microbiome studies. 5055-5063 - Michael A Kochen, H. Steven Wiley, Song Feng, Herbert M. Sauro:
SBbadger: biochemical reaction networks with definable degree distributions. 5064-5072 - Yanfei Li, Chang Sun, Jin-Mao Wei, Jian Liu:
Drug-Protein interaction prediction by correcting the effect of incomplete information in heterogeneous information. 5073-5080 - Michal Ziemski, Anja Adamov, Lina Kim, Lena Flörl, Nicholas A. Bokulich:
Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue. 5081-5091 - Xingze Wang, Guoxian Yu, Jun Wang, Azlan Mohd Zain, Wei Guo:
Lung cancer subtype diagnosis using weakly-paired multi-omics data. 5092-5099 - Yutai Hou, Yingce Xia, Lijun Wu, Shufang Xie, Yang Fan, Jinhua Zhu, Tao Qin, Tie-Yan Liu:
Discovering drug-target interaction knowledge from biomedical literature. 5100-5107 - Kaimei Huang, Binghu Lin, Jinyang Liu, Yankun Liu, Jingwu Li, Geng Tian, Jialiang Yang:
Predicting colorectal cancer tumor mutational burden from histopathological images and clinical information using multi-modal deep learning. 5108-5115 - Ji-Hye Choi, Hui-Seon Choi, Seong-Ho Cho, Ji-Hye Lee, Hyun Goo Woo:
CGV: Cancer Genome Viewer, a web service for integrative cancer genome and pharmacogenomic data analysis. 5116-5118 - Milan A. Clasen, Louise U. Kurt, Marlon D. M. Santos, Diogo B. Lima, Fan Liu, Fábio C. Gozzo, Valmir C. Barbosa, Paulo C. Carvalho:
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, Simon Mutch, Robert Turnbull, Sebastián Duchêne:
Phytest: quality control for phylogenetic analyses. 5124-5125 - Jonathan Moody, Tsukasa Kouno, Jen-Chien Chang, Yoshinari Ando, Piero Carninci, Jay W. Shin, Chung-Chau Hon:
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, Shwetha V. Kumar, James M. Melott, Mary A. Rohrdanz, Chris Wakefield, Zhenlin Ju, Doris R. Siwak, Yiling Lu, Bradley M. Broom, John N. Weinstein, Gordon B. Mills, Rehan Akbani:
RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data. 5131-5133 - Wenhao Li, Martin P. Boer, Bart-Jan van Rossum, Chaozhi Zheng, Ronny V. L. Joosen, Fred A. van Eeuwijk:
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, Shaozhen Ding, Pengli Cai, Dachuan Zhang, Mengying Han, Qian-Nan Hu:
BioBulkFoundary: a customized webserver for exploring biosynthetic potentials of bulk chemicals. 5137-5138 - Kevin Mildau, Justin J. J. van der Hooft, Mira Flasch, Benedikt Warth, Yasin El Abiead, Gunda Koellensperger, Jürgen Zanghellini, Christoph Bueschl:
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, Lin Hou:
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, Erhu Liu, Zhifang Wu, Yao Li, Yuan Liu, Xiaoran Yin:
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data. 5151-5159 - Chunting Liu, Jiangning Song, Hiroyuki Ogata, Tatsuya Akutsu:
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites. 5160-5167 - Matteo Manfredi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio:
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, David L. Swofford, Laura Salter Kubatko:
Estimation of speciation times under the multispecies coalescent. 5182-5190 - Roy González-Alemán, Daniel Platero-Rochart, Alejandro Rodríguez-Serradet, Erix Wiliam Hernández-Rodríguez, Julio Caballero, Fabrice Leclerc, Luis Alberto Montero-Cabrera:
MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics. 5191-5198 - Josef Paul Kynast, Felix Schwägerl, Birte Höcker:
ATLIGATOR: editing protein interactions with an atlas-based approach. 5199-5205 - Courtney Schiebout, H. Robert Frost:
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, Travis S. Johnson, Yue Wang, Yunlong Liu, Kun Huang, Yijie Wang:
AIscEA: unsupervised integration of single-cell gene expression and chromatin accessibility via their biological consistency. 5236-5244 - Yue Zhao, Lianbo Yu, Xue Wu, Haoran Li, Kevin R. Coombes, Kin Fai Au, Lijun Cheng, Lang Li:
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, Hailiang Zhang, Zhimin Zhang, Hongmei Lu:
Prediction of drug-likeness using graph convolutional attention network. 5262-5269 - Sendong Zhao, Aobo Wang, Bing Qin, Fei Wang:
Biomedical evidence engineering for data-driven discovery. 5270-5278 - Yiqing Zhao, Matthew Brush, Chen Wang, Alex H. Wagner, Hongfang Liu, Robert R. Freimuth:
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, Xuecong Fu, Serena Abraham, Shen Jin, Robert F. Murphy:
Improving and evaluating deep learning models of cellular organization. 5299-5306 - Haoda Lu, Min Zang, Gabriel Pik Liang Marini, Xiangxue Wang, Yiping Jiao, Nianfei Ao, Kok Haur Ong, Xinmi Huo, Longjie Li, Eugene Yujun Xu, Wilson Wen Bin Goh, Weimiao Yu, Jun Xu:
A novel pipeline for computerized mouse spermatogenesis staging. 5307-5314 - Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks:
GTDB-Tk v2: memory friendly classification with the genome taxonomy database. 5315-5316 - Duoyuan Chen, Taikui Zhang, Yamao Chen, Hong Ma, Ji Qi:
Tree2GD: a phylogenomic method to detect large-scale gene duplication events. 5317-5321 - Haocheng Gu, Hao Cheng, Anjun Ma, Yang Li, Juexin Wang, Dong Xu, Qin Ma:
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, Steffany A. L. Bennett, Miroslava Cuperlovic-Culf:
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, Gaoyu Wang, Giorgio A. Ascoli, Jiangning Zhou, Lijuan 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, Aysun Urhan, Alvaro Assis de Souza, Akash Singh, Thomas Abeel:
HAT: haplotype assembly tool using short and error-prone long reads. 5352-5359 - Dehan Cai, Jiayu Shang, Yanni Sun:
HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization. 5360-5367 - Yuxuan Pang, Lantian Yao, Jingyi Xu, Zhuo Wang, Tzong-Yi Lee:
Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities. 5368-5374 - Gang Wu, Marc D. Ruben, Lauren J. Francey, Yin Yeng Lee, Ron C. Anafi, John B. Hogenesch:
An in silico genome-wide screen for circadian clock strength in human samples. 5375-5382 - Surabhi Jagtap, Abdulkadir Çelikkanat, Aurélie Pirayre, Frédérique Bidard, Laurent Duval, Fragkiskos D. Malliaros:
BraneMF: integration of biological networks for functional analysis of proteins. 5383-5389 - Stephan Fischer, Jesse A. Gillis:
Defining the extent of gene function using ROC curvature. 5390-5397 - Jiayuan Zhong, Chongyin Han, Yangkai Wang, Pei Chen, Rui Liu:
Identifying the critical state of complex biological systems by the directed-network rank score method. 5398-5405 - Yue Hong, Pengyu Luo, Shuting Jin, Xiangrong Liu:
LaGAT: link-aware graph attention network for drug-drug interaction prediction. 5406-5412 - Theodore Groth, Alexander D. Diehl, Rudiyanto Gunawan, Sriram Neelamegham:
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, Andre Franke:
MAGScoT: a fast, lightweight and accurate bin-refinement tool. 5430-5433 - Nicolas Serge Matthieu Robert, Fatih Sarigol, Elisabeth Zieger, Oleg Simakov:
SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes. 5434-5436 - Christian Anthon, Giulia Ilaria Corsi, Jan Gorodkin:
CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design. 5437-5439 - Mateusz Chilinski, Dariusz Plewczynski:
ConsensuSV - from the whole-genome sequencing data to the complete variant list. 5440-5442 - Téo Lemane, Rayan Chikhi, Pierre Peterlongo:
k mdiff, large-scale and user-friendly differential k-mer analyses. 5443-5445 - Sean M. Cascarina, Eric D. Ross:
The LCD-Composer webserver: high-specificity identification and functional analysis of low-complexity domains in proteins. 5446-5448 - Alexios Chatzigoulas, Zoe Cournia:
DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design. 5449-5451 - Christos P. Feidakis, Radoslav Krivák, David Hoksza, Marian Novotny:
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands. 5452-5453 - Todor Gitchev, Gabriel Zala, Peter Meister, Daniel Jost:
3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion. 5454-5456 - Ramón Díaz-Uriarte, Pablo Herrera-Nieto:
EvAM-Tools: tools for evolutionary accumulation and cancer progression models. 5457-5459 - Eugenio Del Prete, Ana Margarida Campos, Fabio Della Rocca, Carmela Gallo, Angelo Fontana, Genoveffa Nuzzo, Claudia Angelini:
ADViSELipidomics: a workflow for analyzing lipidomics data. 5460-5462 - Bo Wen, Eric J. Jaehnig, Bing Zhang:
OmicsEV: a tool for comprehensive quality evaluation of omics data tables. 5463-5465 - Philipp Wegner, Geena Mariya Jose, Vanessa Lage-Rupprecht, Sepehr Golriz Khatami, Bide Zhang, Stephan Springstubbe, Marc Jacobs, Thomas Linden, Cindy Ku, Bruce Schultz, Martin Hofmann-Apitius, Alpha Tom Kodamullil:
Common data model for COVID-19 datasets. 5466-5468 - Guillaume Wacquet, Alain Lefebvre:
EcoTransLearn: an R-package to easily use transfer learning for ecological studies - a plankton case study. 5469-5471
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