default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
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 C. 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 G. 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
- Konstantin Krismer, Jennifer Hammelman, David K. Gifford:
seqgra: principled selection of neural network architectures for genomics prediction tasks. 2381-2388 - Johnny Hong, Ulas Karaoz, Perry de Valpine, William Fithian:
To rarefy or not to rarefy: robustness and efficiency trade-offs of rarefying microbiome data. 2389-2396 - Surag Nair, Avanti Shrikumar, Jacob M. Schreiber, Anshul Kundaje:
fastISM: performantin silicosaturation mutagenesis for convolutional neural networks. 2397-2403 - Youngmok Jung, Dongsu Han:
BWA-MEME: BWA-MEM emulated with a machine learning approach. 2404-2413 - Parker Hicks, Oluwatosin Oluwadare:
HiCARN: resolution enhancement of Hi-C data using cascading residual networks. 2414-2421 - 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 - Daniel Habermann, Hadi Kharimzadeh, Andreas Walker, Yang Li, Rongge Yang, Rolf Kaiser, Zabrina L. Brumme, Jörg Timm, Michael Roggendorf, Daniel Hoffmann:
HAMdetector: a Bayesian regression model that integrates information to detect HLA-associated mutations. 2428-2436 - Dingyao Zhang, Jingru Tian, Yadong Wang, Jun Lu:
Evitar: designing anti-viral RNA therapies against future RNA viruses. 2437-2443 - Linyuan Guo, Jiahua He, Peicong Lin, Sheng-You Huang, Jianxin Wang:
TRScore: a 3D RepVGG-based scoring method for ranking protein docking models. 2444-2451 - 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 - Junbo Jia, Luonan Chen:
Single-cell RNA sequencing data analysis based on non-uniformε-neighborhood network. 2459-2465 - Michael Soutschek, Fridolin Gross, Gerhard Schratt, Pierre-Luc Germain:
scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction. 2466-2473 - Susanna Holmström, Sampsa Hautaniemi, Antti Häkkinen:
POIBM: batch correction of heterogeneous RNA-seq datasets through latent sample matching. 2474-2480 - Chixiang Chen, Biyi Shen, Tianzhou Ma, Ming Wang, Rongling Wu:
A statistical framework for recovering pseudo-dynamic networks from static data. 2481-2487 - Mohit Goyal, Guillermo Serrano, Josepmaria Argemi, Ilan Shomorony, Mikel Hernaez, Idoia Ochoa:
JIND: joint integration and discrimination for automated single-cell annotation. 2488-2495 - Zhiqian Zhai, Yu L. Lei, Rongrong Wang, Yuying Xie:
Supervised capacity preserving mapping: a clustering guided visualization method for scRNA-seq data. 2496-2503 - Victoria Bourgeais, Farida Zehraoui, Blaise Hanczar:
GraphGONet: a self-explaining neural network encapsulating the Gene Ontology graph for phenotype prediction on gene expression. 2504-2511 - Salvatore Milite, Riccardo Bergamin, Lucrezia Patruno, Nicola Calonaci, Giulio Caravagna:
A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations. 2512-2518 - Claudia Skok Gibbs, Christopher A. Jackson, Giuseppe-Antonio Saldi, Andreas Tjärnberg, Aashna Shah, Aaron Watters, Nicholas De Veaux, Konstantine Tchourine, Ren Yi, Tymor Hamamsy, Dayanne M. Castro, Nicholas Carriero, Bram L. Gorissen, David Gresham, Emily R. Miraldi, Richard Bonneau:
High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0. 2519-2528 - Thomas Thorne, Paul D. W. Kirk, Heather A. Harrington:
Topological approximate Bayesian computation for parameter inference of an angiogenesis model. 2529-2535 - Xingyi Li, Min Li, Ju Xiang, Zhelin Zhao, Xuequn Shang:
SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data. 2536-2543 - Shawn Gu, Meng Jiang, Pietro Hiram Guzzi, Tijana Milenkovic:
Modeling multi-scale data via a network of networks. 2544-2553 - Yu-An Huang, Gui-Qing Pan, Jia Wang, Jian-Qiang Li, Jie Chen, Yang-Han Wu:
Heterogeneous graph embedding model for predicting interactions between TF and target gene. 2554-2560 - Tian Cai, Kyra Alyssa Abbu, Yang Liu, Lei Xie:
DeepREAL: a deep learning powered multi-scale modeling framework for predicting out-of-distribution ligand-induced GPCR activity. 2561-2570 - Yifan Wu, Min Gao, Min Zeng, Jie Zhang, Min Li:
BridgeDPI: a novel Graph Neural Network for predicting drug-protein interactions. 2571-2578 - Zhengyang Wang, Meng Liu, Youzhi Luo, Zhao Xu, Yaochen Xie, Limei Wang, Lei Cai, Qi Qi, Zhuoning Yuan, Tianbao Yang, Shuiwang Ji:
Advanced graph and sequence neural networks for molecular property prediction and drug discovery. 2579-2586 - Ruiqing Li, Xingqi Wu, Ao Li, Minghui Wang:
HFBSurv: hierarchical multimodal fusion with factorized bilinear models for cancer survival prediction. 2587-2594 - Emilie Pasche, Anaïs Mottaz, Déborah Caucheteur, Julien Gobeill, Pierre-André Michel, Patrick Ruch:
Variomes: a high recall search engine to support the curation of genomic variants. 2595-2601 - Fengsheng Wang, Leyi Wei:
Multi-scale deep learning for the imbalanced multi-label protein subcellular localization prediction based on immunohistochemistry images. 2602-2611 - 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 - Diego Javier Zea, Hugues Richard, Elodie Laine:
ASES: visualizing evolutionary conservation of alternative splicing in proteins. 2615-2616 - Giovanni Birolo, Andrea Telatin:
BamToCov: an efficient toolkit for sequence coverage calculations. 2617-2618 - David Chen, Gurjit S. Randhawa, Maximillian P. M. Soltysiak, Camila P. E. de Souza, Lila Kari, Shiva M. Singh, Kathleen A. Hill:
SomaticSiMu: a mutational signature simulator. 2619-2620 - Pawel F. Przytycki, Katherine S. Pollard:
CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements. 2621-2623 - Dania Machlab, Lukas Burger, Charlotte Soneson, Filippo M. Rijli, Dirk Schübeler, Michael B. Stadler:
monaLisa: an R/Bioconductor package for identifying regulatory motifs. 2624-2625 - Stefanie Mühlhausen, Laurence D. Hurst:
Transgene-design: a web application for the design of mammalian transgenes. 2626-2627 - Jakub Mlokosiewicz, Piotr Deszynski, Wiktoria Wilman, Igor Jaszczyszyn, Rajkumar Ganesan, Aleksandr Kovaltsuk, Jinwoo Leem, Jacob D. Galson, Konrad Krawczyk:
AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design. 2628-2630 - Vincenzo Bonnici, Rosalba Giugno:
PANPROVA: pangenomic prokaryotic evolution of full assemblies. 2631-2632 - Jan Ludwiczak, Aleksander Winski, Stanislaw Dunin-Horkawicz:
localpdb - a Python package to manage protein structures and their annotations. 2633-2635 - Nikolaos N. Louros, Rob van der Kant, Joost Schymkowitz, Frederic Rousseau:
StAmP-DB: a platform for structures of polymorphic amyloid fibril cores. 2636-2638 - Wei Vivian Li:
Phitest for analyzing the homogeneity of single-cell populations. 2639-2641 - Massimo Andreatta, Ariel J. Berenstein, Santiago J. Carmona:
scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets. 2642-2644 - Oscar E. Ospina, Christopher M. Wilson, Alex C. Soupir, Anders Berglund, Inna Smalley, Kenneth Y. Tsai, Brooke L. Fridley:
spatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics. 2645-2647 - Federico Agostinis, Chiara Romualdi, Gabriele Sales, Davide Risso:
NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data. 2648-2650 - Rana Aldisi, Emadeldin Hassanin, Sugirthan Sivalingam, Andreas Buness, Hannah Klinkhammer, Andreas Mayr, Holger Fröhlich, Peter M. Krawitz, Carlo Maj:
GenRisk: a tool for comprehensive genetic risk modeling. 2651-2653 - Stefano Camborda, Jan-Niklas Weder, Nadine Töpfer:
CobraMod: a pathway-centric curation tool for constraint-based metabolic models. 2654-2656 - 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 - Christoph Ogris, Miguel Castresana Aguirre, Erik L. L. Sonnhammer:
PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk. 2659-2660 - Andy Shi, Sheila M. Gaynor, Rounak Dey, Haoyu Zhang, Corbin Quick, Xihong Lin:
COVID-19 Spread Mapper: a multi-resolution, unified framework and open-source tool. 2661-2663 - Solenne Correard, Brittany Hewitson, Robin van der Lee, Wyeth W. Wasserman:
RevUP: an online scoring system for regulatory variants implicated in rare diseases. 2664-2666 - David Bunk, Julian Moriasy, Felix Thoma, Christopher Jakubke, Christof Osman, David Hörl:
YeastMate: neural network-assisted segmentation of mating and budding events inSaccharomyces cerevisiae. 2667-2669 - Sören Doose:
LOCAN: a python library for analyzing single-molecule localization microscopy data. 2670-2672 - 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, GW 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 - Genís 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