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ORCIDBioinformatics, Volume 38
Volume 38, Number 1, December 2021
- Dmitry Meleshko, Iman Hajirasouliha, Anton I. Korobeynikov
:
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies. 1-8
- Jun Yan, Zhongsong Man, Lu Gao, Lei Cai, Qian Lu, Jiahong Dong:
The role of CpG island methylator phenotype in the clinical course of hepatocellular carcinoma. 9-15 - Michael B. Sohn, Jiarui Lu, Hongzhe Li:
A compositional mediation model for a binary outcome: Application to microbiome studies. 16-21 - Kevin A. Murgas, Yanlin Ma, Lidea K. Shahidi, Sayan Mukherjee, Andrew S. Allen, Darryl Shibata, Marc D. Ryser:
A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors. 22-29 - Jun-Liang Lin, Tsung-Ting Hsieh, Yi-An Tung, Xuan-Jun Chen, Yu-Chun Hsiao, Chia-Lin Yang, Tyng-Luh Liu, Chien-Yu Chen:
ezGeno: an automatic model selection package for genomic data analysis. 30-37 - Jian Song, Changbin Yu:
Alpha-XIC: a deep neural network for scoring the coelution of peak groups improves peptide identification by data-independent acquisition mass spectrometry. 38-43 - Alexander Zaitzeff, Nick Leiby, Francis C. Motta, Steven B. Haase, Jed Singer:
Improved datasets and evaluation methods for the automatic prediction of DNA-binding proteins. 44-51 - Chao Wang, Ying Ju, Quan Zou, Chen Lin:
DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA. 52-57 - Miguel Arenas:
ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation. 58-64 - Dominik Schwarz, Guy Georges, Sebastian Kelm, Jiye Shi, Anna Vangone, Charlotte M. Deane:
Co-evolutionary distance predictions contain flexibility information. 65-72 - Roy González-Alemán, Daniel Platero-Rochart, David Hernández-Castillo, Erix Wiliam Hernández-Rodríguez, Julio Caballero, Fabrice Leclerc, Luis Alberto Montero-Cabrera:
BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics. 73-79 - Pawel Daniluk, Tymoteusz Oleniecki, Bogdan Lesyng:
DAMA: a method for computing multiple alignments of protein structures using local structure descriptors. 80-85 - Shide Liang, Zhixiu Li, Jian Zhan, Yaoqi Zhou:
De novo protein design by an energy function based on series expansion in distance and orientation dependence. 86-93 - Jianzhao Gao, Shuangjia Zheng, Mengting Yao, Peikun Wu:
Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method. 94-98 - Jun Liu, Kai-Long Zhao, Guang-Xing He, Liu-Jing Wang, Xiao-Gen Zhou, Gui-Jun Zhang:
A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization. 99-107 - Gang Xu, Qinghua Wang, Jianpeng Ma:
OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding. 108-114 - Akila Katuwawala, Bi Zhao, Lukasz A. Kurgan:
DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning. 115-124 - Qianmu Yuan, Jianwen Chen, Huiying Zhao, Yaoqi Zhou, Yuedong Yang:
Structure-aware protein-protein interaction site prediction using deep graph convolutional network. 125-132 - Oleksii Nikolaienko, Per Eystein Lønning, Stian Knappskog:
ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions. 133-140 - Tristan Mary-Huard, Sarmistha Das, Indranil Mukhopadhyay, Stéphane Robin:
Querying multiple sets of P-values through composed hypothesis testing. 141-148 - Xin Zhou, Xiaodong Cai:
Joint eQTL mapping and inference of gene regulatory network improves power of detecting both cis- and trans-eQTLs. 149-156 - Elliott Gordon-Rodríguez, Thomas P. Quinn, John P. Cunningham:
Learning sparse log-ratios for high-throughput sequencing data. 157-163 - Matteo Borella, Graziano Martello, Davide Risso, Chiara Romualdi:
PsiNorm: a scalable normalization for single-cell RNA-seq data. 164-172 - Alberto Zenere, Olof Rundquist, Mika Gustafsson, Claudio Altafini:
Using high-throughput multi-omics data to investigate structural balance in elementary gene regulatory network motifs. 173-178 - Khandakar Tanvir Ahmed, Jiao Sun, Sze Cheng, Jeongsik Yong, Wei Zhang:
Multi-omics data integration by generative adversarial network. 179-186 - Mark Jayson Cortez, Hyukpyo Hong, Boseung Choi, Jae Kyoung Kim, Kresimir Josic:
Hierarchical Bayesian models of transcriptional and translational regulation processes with delays. 187-195 - Jonathan Tyler, Daniel B. Forger, Jae Kyoung Kim:
Inferring causality in biological oscillators. 196-203 - Di He, Lei Xie:
A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype. 204-210 - Kai Cao, Yiguang Hong, Lin Wan:
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona. 211-219 - Mei Zuo, Yang Zhang:
A span-based joint model for extracting entities and relations of bacteria biotopes. 220-227 - Dan Shao, Lan Huang, Yan Wang, Kai He, Xueteng Cui, Yao Wang, Qin Ma, Juan Cui:
DeepSec: a deep learning framework for secreted protein discovery in human body fluids. 228-235 - Margaret Woodhouse, Shatabdi Sen, David A. Schott, John L. Portwood II, Michael Freeling, Justin W. Walley, Carson M. Andorf, James C. Schnable:
qTeller: a tool for comparative multi-genomic gene expression analysis. 236-242 - Mirae Kim, Soonwoo Hong, Thomas E. Yankeelov, Hsin-Chih Yeh, Yen-Liang Liu:
Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics. 243-249 - Hualin Liu, Jinshui Zheng, Dexin Bo, Yun Yu, Weixing Ye, Donghai Peng, Ming Sun:
BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis. 250-251 - Fulong Yu, Vijay G. Sankaran, Guo-Cheng Yuan:
CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis. 252-254 - Florian Privé:
Optimal linkage disequilibrium splitting. 255-256 - Leszek P. Pryszcz, Eva Maria Novoa:
ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. 257-260 - Andrew Olson, Doreen Ware:
Ranked choice voting for representative transcripts with TRaCE. 261-264 - François Ancien, Fabrizio Pucci, Wim F. Vranken, Marianne Rooman:
MutaFrame - an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome. 265-266 - Frédéric Mahé, Lucas Czech, Alexandros Stamatakis, Christopher Quince, Colomban de Vargas, Micah Dunthorn, Torbjørn Rognes:
Swarm v3: towards tera-scale amplicon clustering. 267-269 - Guillem Salazar, Hans-Joachim Ruscheweyh, Falk Hildebrand, Silvia G. Acinas, Shinichi Sunagawa:
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes. 270-272 - Chie Motono, Shunsuke Yanagida, Miwa Sato, Takatsugu Hirokawa:
MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts. 273-274 - Sungjoon Park, Dohoon Lee, Youngkuk Kim, Sangsoo Lim, Heejoon Chae, Sun Kim:
BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud. 275-277 - Junyi Xin, Yanling Wu, Shuai Ben, Shuwei Li, Haiyan Chu, Meilin Wang, Molin Wang, Mingyang Song, Mulong Du, Zhengdong Zhang:
CoSMeD: a user-friendly web server to estimate 5-year survival probability of left-sided and right-sided colorectal cancer patients using molecular data. 278-281 - Xiunan Fang, Joshua W. K. Ho:
FlowGrid enables fast clustering of very large single-cell RNA-seq data. 282-283 - Elias B. Farr, Julia M. Sattler, Friedrich Frischknecht:
SPOT: a web-tool enabling swift profiling of transcriptomes. 284-285 - Jun Chen, Xianyang Zhang:
D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies. 286-288 - Augustinas Sukys, Ramon Grima:
MomentClosure.jl: automated moment closure approximations in Julia. 289-290 - Dilawar Singh, Steven S. Andrews:
Python interfaces for the Smoldyn simulator. 291-293 - Ramiro Magno, Isabel Duarte, Ana-Teresa Maia:
quincunx: an R package to query, download and wrangle PGS Catalog data. 294-296 - Pedro B. P. S. Reis, Djork-Arné Clevert, Miguel Machuqueiro:
pKPDB: a protein data bank extension database of pKa and pI theoretical values. 297-298 - Andrew D. Yates, Jeremy Adams, Somesh Chaturvedi, Robert Davies, Matthew R. Laird, Rasko Leinonen, Rishi Nag, Nathan C. Sheffield, Oliver Hofmann, Thomas M. Keane:
Refget: standardized access to reference sequences. 299-300 - Anthony Xu, Aravind Venkateswaran, Lianguizi Zhou, Andreas Zankl:
Ontoclick: a web browser extension to facilitate biomedical knowledge curation. 301-302
Volume 38, Number 2, January 2022
- Qing Cheng, Tingting Qiu, Xiaoran Chai, Baoluo Sun, Yingcun Xia, Xingjie Shi, Jin Liu:
MR-Corr2: a two-sample Mendelian randomization method that accounts for correlated horizontal pleiotropy using correlated instrumental variants. 303-310 - Shengji Jia, Lei Shi:
Efficient change-points detection for genomic sequences via cumulative segmented regression. 311-317 - Nisha Singh, Hukam C. Rawal, Ulavappa B. Angadi, Tilak Raj Sharma, Nagendra Kumar Singh, Tapan Kumar Mondal:
A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz). 318-324 - Yunxiao Ren, Trinad Chakraborty, Swapnil Doijad, Linda Falgenhauer, Jane Falgenhauer, Alexander Goesmann, Anne-Christin Hauschild, Oliver Schwengers, Dominik Heider:
Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. 325-334 - Hongwei Huo, Pengfei Liu, Chenhui Wang, Hongbo Jiang, Jeffrey Scott Vitter:
CIndex: compressed indexes for fast retrieval of FASTQ files. 335-343 - Michal Karlicki, Stanislaw Antonowicz, Anna Karnkowska:
Tiara: deep learning-based classification system for eukaryotic sequences. 344-350 - Dohyeon Lee, Giltae Song:
FastqCLS: a FASTQ compressor for long-read sequencing via read reordering using a novel scoring model. 351-356 - Alexey Zabelkin, Yulia Yakovleva, Olga Bochkareva, Nikita Alexeev:
PaReBrick: PArallel REarrangements and BReaks identification toolkit. 357-363 - Jae Yong Ryu, Jeong Hyun Lee, Byung Ho Lee, Jin Sook Song, Sunjoo Ahn, Kwang-Seok Oh:
PredMS: a random forest model for predicting metabolic stability of drug candidates in human liver microsomes. 364-368 - Rahul Kaushik, Kam Y. J. Zhang:
ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures. 369-376 - Constantin Schneider, Andrew Buchanan, Bruck Taddese, Charlotte M. Deane:
DLAB: deep learning methods for structure-based virtual screening of antibodies. 377-383 - Benedek Dankó, Péter Szikora, Tamás Pór, Alexa Szeifert, Endre Sebestyén:
SplicingFactory - splicing diversity analysis for transcriptome data. 384-390 - Lyla Atta, Arpan Sahoo, Jean Fan:
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories. 391-396 - Yi-Pei Chen, Laura B. Ferguson, Nihal A. Salem, George Zheng, R. Dayne Mayfield, Mohammed Eslami:
RNA Solutions: Synthesizing Information to Support Transcriptomics (RNASSIST). 397-403 - Mohammed Eslami, Amin Espah Borujeni, Hamed Eramian, Mark Weston, George Zheng, Joshua Urrutia, Carolyn Corbet, Diveena Becker, Paul Maschhoff, Katie Clowers, Alexander Cristofaro, Hamid Doost Hosseini, D. Benjamin Gordon, Yuval Dorfan, Jedediah Singer, Matthew Vaughn, Niall Gaffney, John Fonner, Joe Stubbs, Christopher A. Voigt, Enoch Yeung:
Prediction of whole-cell transcriptional response with machine learning. 404-409 - Baoshan Ma, Ge Yan, Bingjie Chai, Xiaoyu Hou:
XGBLC: an improved survival prediction model based on XGBoost. 410-418 - Tianying Wang, Wodan Ling, Anna M. Plantinga, Michael C. Wu, Xiang Zhan:
Testing microbiome association using integrated quantile regression models. 419-425 - Haitao Fu, Feng Huang, Xuan Liu, Yang Qiu, Wen Zhang:
MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks. 426-434 - Yingjun Ma, Yuanyuan Ma:
Hypergraph-based logistic matrix factorization for metabolite-disease interaction prediction. 435-443 - Seungyoon Nam, Sungyoung Lee, Sungjin Park, Jinhyuk Lee, Aron Park, Yon Hui Kim, Taesung Park:
PATHOME-Drug: a subpathway-based polypharmacology drug-repositioning method. 444-452 - Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, Roman Bauer:
BioDynaMo: a modular platform for high-performance agent-based simulation. 453-460 - Yiheng Zhu, Zhenqiu Ouyang, Wenbo Chen, Ruiwei Feng, Danny Z. Chen, Ji Cao, Jian Wu:
TGSA: protein-protein association-based twin graph neural networks for drug response prediction with similarity augmentation. 461-468 - Fahimeh Motamedi, Horacio Pérez Sánchez, Alireza Mehridehnavi, Afshin Fassihi, Fahimeh Ghasemi:
Accelerating Big Data Analysis through LASSO-Random Forest Algorithm in QSAR Studies. 469-475 - Yang Xu, Priyojit Das, Rachel Patton McCord:
SMILE: mutual information learning for integration of single-cell omics data. 476-486 - Gianvito Pio, Paolo Mignone, Giuseppe Magazzù, Guido Zampieri, Michelangelo Ceci, Claudio Angione:
Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction. 487-493 - Kishlay Jha, Aidong Zhang:
Continual knowledge infusion into pre-trained biomedical language models. 494-502 - Shuxia Guo, Xuan Zhao, Shengdian Jiang, Liya Ding, Hanchuan Peng:
Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons. 503-512 - Mohamed Amgad, Lamees A. Atteya, Hagar Hussein, Kareem Hosny Mohammed, Ehab Hafiz, Maha A. T. Elsebaie, Pooya Mobadersany, David Manthey, David A. Gutman, Habiba Elfandy, Lee A. D. Cooper:
Explainable nucleus classification using Decision Tree Approximation of Learned Embeddings. 513-519 - John F. Graf, Sanghee Cho, Elizabeth McDonough, Alex Corwin, Anup Sood, Andreas Lindner, Manuela Salvucci, Xanthi Stachtea, Sandra Van Schaeybroeck, Philip D. Dunne, Pierre Laurent-Puig, Daniel B. Longley, Jochen H. M. Prehn, Fiona Ginty:
FLINO: a new method for immunofluorescence bioimage normalization. 520-526 - Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao, Jianfeng Li, Mingjie Wang, Haitao Wang, Ziyu Tao, Tao Wu, Yichao Zheng, Xuejun Li, Xue-Song Liu:
UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data. 527-529 - Cecilia Sensalari, Steven Maere, Rolf Lohaus:
ksrates: positioning whole-genome duplications relative to speciation events in KS distributions. 530-532 - Kenneth I Brewer, Glenn J. Gaffield, Malavika Puri, Ronald R. Breaker:
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria. 533-535 - Brian M. Schilder, Jack Humphrey, Towfique Raj:
echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline. 536-539 - Itsuki Sugita, Shohei Matsuyama, Hiroki Dobashi, Daisuke Komura, Shumpei Ishikawa:
Viola: a structural variant signature extractor with user-defined classifications. 540-542 - Jie Tan, Zhencheng Fang, Shufang Wu, Qian Guo, Xiaoqing Jiang, Huaiqiu Zhu:
HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes. 543-545 - Richard A. Stanton, Nicholas Vlachos, Alison Laufer Halpin:
GAMMA: a tool for the rapid identification, classification and annotation of translated gene matches from sequencing data. 546-548 - Kohei Hagiwara, Michael N. Edmonson, David A. Wheeler, Jinghui Zhang:
indelPost: harmonizing ambiguities in simple and complex indel alignments. 549-551 - Amélie Barozet, Kevin Molloy, Marc Vaisset, Christophe Zanon, Pierre Fauret, Thierry Siméon, Juan Cortés:
MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations. 552-553 - Steven Grudman, J. Eduardo Fajardo, András Fiser:
INTERCAAT: identifying interface residues between macromolecules. 554-555 - Liang Rao, Ning-Xin Jia, Jun Hu, Dong-Jun Yu, Gui-Jun Zhang:
ATPdock: a template-based method for ATP-specific protein-ligand docking. 556-558 - Alan Kwong, Andrew P. Boughton, Mukai Wang, Peter Vandehaar, Michael Boehnke, Gonçalo R. Abecasis, Hyun Min Kang:
FIVEx: an interactive eQTL browser across public datasets. 559-561 - Pieter Verschaffelt, James H. Collier, Alexander Botzki, Lennart Martens, Peter Dawyndt, Bart Mesuere:
Unipept Visualizations: an interactive visualization library for biological data. 562-563 - Eugenio López-Cortegano:
purgeR: inbreeding and purging in pedigreed populations. 564-565 - Axel Theorell, Johann F. Jadebeck, Katharina Nöh, Jörg Stelling:
PolyRound: polytope rounding for random sampling in metabolic networks. 566-567 - Xiaotao Shen, Si Wu, Liang Liang, Songjie Chen, Kévin Contrepois, Zheng-Jiang Zhu, Michael P. Snyder:
metID: an R package for automatable compound annotation for LC-MS-based data. 568-569 - Peter Zhang, Alida Palmisano, Ravindra Kumar, Ming-Chung Li, James H. Doroshow, Yingdong Zhao:
TPWshiny: an interactive R/Shiny app to explore cell line transcriptional responses to anti-cancer drugs. 570-572 - Mustafa Buyukozkan, Karsten Suhre, Jan Krumsiek:
SGI: automatic clinical subgroup identification in omics datasets. 573-576 - Antoine Bodein, Marie-Pier Scott-Boyer, Olivier Périn, Kim-Anh Lê Cao, Arnaud Droit:
timeOmics: an R package for longitudinal multi-omics data integration. 577-579 - Daniel Osório, Marieke L. Kuijjer, James J. Cai:
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. 580-582 - Maria Llambrich, Eudald Correig, Josep Gumà, Jesús Brezmes, Raquel Cumeras:
Amanida: an R package for meta-analysis of metabolomics non-integral data. 583-585 - Paola Paci, Giulia Fiscon:
SWIMmeR: an R-based software to unveiling crucial nodes in complex biological networks. 586-588 - Christina Wong, Bo Li:
AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data. 589-591 - Tomás Tokár, Chiara Pastrello, Mark Abovsky, Sara Rahmati, Igor Jurisica:
miRAnno - network-based functional microRNA annotation. 592-593 - Rodrigo Fernandez-Gonzalez, Negar Balaghi, Kelly Wang, Ray Hawkins, Katheryn Rothenberg, Christopher McFaul, Clara Schimmer, Michelle Ly, Ana Maria do Carmo, Gordana Scepanovic, Gonca Erdemci-Tandogan, Veronica Castle:
PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images. 594-596
Volume 38, Number 3, January 2022
- Gaetan De Waele, Jim Clauwaert, Gerben Menschaert, Willem Waegeman:
CpG Transformer for imputation of single-cell methylomes. 597-603 - Thomas Krannich, W. Timothy J. White, Sebastian Niehus, Guillaume Holley, Bjarni V. Halldórsson, Birte Kehr:
Population-scale detection of non-reference sequence variants using colored de Bruijn graphs. 604-611 - Alexander G. McFarland, Nolan W. Kennedy, Carolyn E. Mills, Danielle Tullman-Ercek, Curtis Huttenhower, Erica M. Hartmann:
Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper. 612-620 - Spiro C. Stilianoudakis, Maggie A. Marshall, Mikhail G. Dozmorov:
preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution. 621-630 - Arbel D. Tadmor, Rob Phillips:
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study. 631-647 - Yanhua Qiao, Xiaolei Zhu, Haipeng Gong:
BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models. 648-654 - Qichang Zhao, Haochen Zhao, Kai Zheng, Jianxin Wang:
HyperAttentionDTI: improving drug-protein interaction prediction by sequence-based deep learning with attention mechanism. 655-662