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Bioinformatics  
Volume 38 Issue 1
 
1 January 2022
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies 
 
Dmitry Meleshko; Iman Hajirasouliha; Anton Korobeynikov
 
 
The role of CpG island methylator phenotype in the clinical course of hepatocellular carcinoma 
 
Jun Yan; Zhongsong Man; Lu Gao; Lei Cai ; Qian Lu ...
 
 
A compositional mediation model for a binary outcome: Application to microbiome studies 
 
Michael B Sohn; Jiarui Lu; Hongzhe Li
 
 
A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors 
 
Kevin A Murgas; Yanlin Ma; Lidea K Shahidi; Sayan Mukherjee ; Andrew S Allen ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
ezGeno: an automatic model selection package for genomic data analysis 
 
Jun-Liang Lin; Tsung-Ting Hsieh; Yi-An Tung; Xuan-Jun Chen ; Yu-Chun Hsiao ...
 
 
 
Alpha-XIC: a deep neural network for scoring the coelution of peak groups improves peptide identification by data-independent acquisition mass spectrometry 
 
Jian Song; Changbin Yu
 
 
Improved datasets and evaluation methods for the automatic prediction of DNA-binding proteins 
 
Alexander Zaitzeff; Nicholas Leiby; Francis C Motta; Steven B Haase ; Jedediah M Singer
 
 
DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA 
 
Chao Wang; Ying Ju; Quan Zou; Chen Lin
 
 
 
PHYLOGENETICS
 
 
 
ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation border= 
 
Miguel Arenas
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Co-evolutionary distance predictions contain flexibility information 
 
Dominik Schwarz; Guy Georges; Sebastian Kelm; Jiye Shi ; Anna Vangone ...
 
 
 
BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics 
 
Roy González-Alemán; Daniel Platero-Rochart; David Hernández-Castillo; Erix W Hernández-Rodríguez ; Julio Caballero ...
 
 
DAMA: a method for computing multiple alignments of protein structures using local structure descriptors border= 
 
Paweł Daniluk; Tymoteusz Oleniecki; Bogdan Lesyng
 
 
De novo protein design by an energy function based on series expansion in distance and orientation dependence 
 
Shide Liang; Zhixiu Li; Jian Zhan; Yaoqi Zhou
 
 
Precise estimation of residue relative solvent accessible area from Calpha atom distance matrix using a deep learning method 
 
Jianzhao Gao; Shuangjia Zheng; Mengting Yao; Peikun Wu
 
 
A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization 
 
Jun Liu; Kai-Long Zhao; Guang-Xing He; Liu-Jing Wang ; Xiao-Gen Zhou ...
 
 
OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding border= 
 
Gang Xu; Qinghua Wang; Jianpeng Ma
 
 
DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning 
 
Akila Katuwawala; Bi Zhao; Lukasz Kurgan
 
 
Structure-aware protein'protein interaction site prediction using deep graph convolutional network 
 
Qianmu Yuan; Jianwen Chen; Huiying Zhao; Yaoqi Zhou ; Yuedong Yang
 
 
 
GENE EXPRESSION
 
 
 
ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions border= 
 
Oleksii Nikolaienko; Per Eystein Lønning; Stian Knappskog
 
 
Querying multiple sets of P-values through composed hypothesis testing 
 
Tristan Mary-Huard; Sarmistha Das; Indranil Mukhopadhyay; Stéphane Robin
 
 
Joint eQTL mapping and inference of gene regulatory network improves power of detecting both cis- and trans-eQTLs 
 
Xin Zhou; Xiaodong Cai
 
 
Learning sparse log-ratios for high-throughput sequencing data border= 
 
Elliott Gordon-Rodriguez; Thomas P Quinn; John P Cunningham
 
 
PsiNorm: a scalable normalization for single-cell RNA-seq data border= 
 
Matteo Borella; Graziano Martello; Davide Risso; Chiara Romualdi
 
 
 
SYSTEMS BIOLOGY
 
 
 
Using high-throughput multi-omics data to investigate structural balance in elementary gene regulatory network motifs border= 
 
Alberto Zenere; Olof Rundquist; Mika Gustafsson ; Claudio Altafini
 
 
Multi-omics data integration by generative adversarial network 
 
Khandakar Tanvir Ahmed; Jiao Sun; Sze Cheng; Jeongsik Yong ; Wei Zhang
 
 
Hierarchical Bayesian models of transcriptional and translational regulation processes with delays 
 
Mark Jayson Cortez; Hyukpyo Hong; Boseung Choi; Jae Kyoung Kim ; Krešimir Josić
 
 
Inferring causality in biological oscillators border= 
 
Jonathan Tyler; Daniel Forger; Jae Kyoung Kim
 
 
 
DATA AND TEXT MINING
 
 
 
A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype border= 
 
Di He; Lei Xie
 
 
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona border= 
 
Kai Cao; Yiguang Hong; Lin Wan
 
 
A span-based joint model for extracting entities and relations of bacteria biotopes 
 
Mei Zuo; Yang Zhang
 
 
DeepSec: a deep learning framework for secreted protein discovery in human body fluids border= 
 
Dan Shao; Lan Huang; Yan Wang ; Kai He; Xueteng Cui ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
qTeller: a tool for comparative multi-genomic gene expression analysis 
 
Margaret R Woodhouse; Shatabdi Sen; David Schott; John L Portwood, II ; Michael Freeling ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics border= 
 
Mirae Kim; Soonwoo Hong; Thomas E Yankeelov ; Hsin-Chih Yeh; Yen-Liang Liu
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis 
 
Hualin Liu; Jinshui Zheng; Dexin Bo; Yun Yu ; Weixing Ye ...
 
 
CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis border= 
 
Fulong Yu; Vijay G Sankaran; Guo-Cheng Yuan
 
 
Optimal linkage disequilibrium splitting border= 
 
Florian Privé
 
 
ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data 
 
Leszek P Pryszcz; Eva Maria Novoa
 
 
Ranked choice voting for representative transcripts with TRaCE border= 
 
Andrew J Olson; Doreen Ware
 
 
 
SEQUENCE ANALYSIS
 
 
 
MutaFrame'an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome border= 
 
François Ancien; Fabrizio Pucci; Wim Vranken ; Marianne Rooman
 
 
Swarm v3: towards tera-scale amplicon clustering border= 
 
Frédéric Mahé; Lucas Czech; Alexandros Stamatakis; Christopher Quince ; Colomban de Vargas ...
 
 
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes border= 
 
Guillem Salazar; Hans-Joachim Ruscheweyh; Falk Hildebrand ; Silvia G Acinas; Shinichi Sunagawa
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts border= 
 
Chie Motono; Shunsuke Yanagida; Miwa Sato ; Takatsugu Hirokawa
 
 
 
GENE EXPRESSION
 
 
 
BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud 
 
Sungjoon Park; Dohoon Lee; Youngkuk Kim; Sangsoo Lim ; Heejoon Chae ...
 
 
CoSMeD: a user-friendly web server to estimate 5-year survival probability of left-sided and right-sided colorectal cancer patients using molecular data 
 
Junyi Xin; Yanling Wu; Shuai Ben; Shuwei Li ; Haiyan Chu ...
 
 
FlowGrid enables fast clustering of very large single-cell RNA-seq data 
 
Xiunan Fang; Joshua W K Ho
 
 
SPOT: a web-tool enabling swift profiling of transcriptomes 
 
Elias B Farr; Julia M Sattler; Friedrich Frischknecht
 
 
 
GENETIC AND POPULATION ANALYSIS
 
 
 
D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies 
 
Jun Chen; Xianyang Zhang
 
 
 
SYSTEMS BIOLOGY
 
 
 
MomentClosure.jl: automated moment closure approximations in Julia border= 
 
Augustinas Sukys; Ramon Grima
 
 
Python interfaces for the Smoldyn simulator 
 
Dilawar Singh; Steven S Andrews
 
 
 
DATA AND TEXT MINING
 
 
 
quincunx: an R package to query, download and wrangle PGS Catalog data border= 
 
Ramiro Magno; Isabel Duarte; Ana-Teresa Maia
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
pKPDB: a protein data bank extension database of pKa and pI theoretical values 
 
Pedro B P S Reis; Djork-Arné Clevert; Miguel Machuqueiro
 
 
Refget: standardized access to reference sequences border= 
 
Andrew D Yates; Jeremy Adams; Somesh Chaturvedi; Robert M Davies ; Matthew Laird ...
 
 
Ontoclick: a web browser extension to facilitate biomedical knowledge curation 
 
Anthony Xu; Aravind Venkateswaran; Lianguizi Zhou; Andreas Zankl
 
 
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