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Bioinformatics  
Volume 38 Issue 2
 
15 January 2022
 
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ORIGINAL PAPER
 
 
 
 
GENOME ANALYSIS
 
 
 
MR-Corr2: a two-sample Mendelian randomization method that accounts for correlated horizontal pleiotropy using correlated instrumental variants 
 
Qing Cheng; Tingting Qiu; Xiaoran Chai; Baoluo Sun ; Yingcun Xia ...
 
 
Efficient change-points detection for genomic sequences via cumulative segmented regression 
 
Shengji Jia; Lei Shi
 
 
A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz) 
 
Nisha Singh; Hukam C Rawal; Ulavappa B Angadi; Tilak Raj Sharma ; Nagendra Kumar Singh ...
 
 
Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning border= 
 
Yunxiao Ren; Trinad Chakraborty; Swapnil Doijad ; Linda Falgenhauer; Jane Falgenhauer ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
CIndex: compressed indexes for fast retrieval of FASTQ files 
 
Hongwei Huo; Pengfei Liu; Chenhui Wang; Hongbo Jiang ; Jeffrey Scott Vitter
 
 
 
Tiara: deep learning-based classification system for eukaryotic sequences border= 
 
Michał Karlicki; Stanisław Antonowicz; Anna Karnkowska
 
 
FastqCLS: a FASTQ compressor for long-read sequencing via read reordering using a novel scoring model 
 
Dohyeon Lee; Giltae Song
 
 
 
PHYLOGENETICS
 
 
 
PaReBrick: PArallel REarrangements and BReaks identification toolkit border= 
 
Alexey Zabelkin; Yulia Yakovleva; Olga Bochkareva; Nikita Alexeev
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
PredMS: a random forest model for predicting metabolic stability of drug candidates in human liver microsomes 
 
Jae Yong Ryu; Jeong Hyun Lee; Byung Ho Lee; Jin Sook Song ; Sunjoo Ahn ...
 
 
ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures 
 
Rahul Kaushik; Kam Y J Zhang
 
 
 
DLAB: deep learning methods for structure-based virtual screening of antibodies border= 
 
Constantin Schneider; Andrew Buchanan; Bruck Taddese; Charlotte M Deane
 
 
 
GENE EXPRESSION
 
 
 
SplicingFactory'splicing diversity analysis for transcriptome data border= 
 
Benedek Dankó; Péter Szikora; Tamás Pór; Alexa Szeifert ; Endre Sebestyén
 
 
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories 
 
Lyla Atta; Arpan Sahoo; Jean Fan
 
 
RNA Solutions: Synthesizing Information to Support Transcriptomics (RNASSIST) border= 
 
Yi-Pei Chen; Laura B Ferguson; Nihal A Salem; George Zheng ; R Dayne Mayfield ...
 
 
Prediction of whole-cell transcriptional response with machine learning 
 
Mohammed Eslami; Amin Espah Borujeni; Hamed Eramian; Mark Weston ; George Zheng ...
 
 
XGBLC: an improved survival prediction model based on XGBoost 
 
Baoshan Ma; Ge Yan; Bingjie Chai; Xiaoyu Hou
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Testing microbiome association using integrated quantile regression models 
 
Tianying Wang; Wodan Ling; Anna M Plantinga; Michael C Wu ; Xiang Zhan
 
 
 
SYSTEMS BIOLOGY
 
 
 
MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks 
 
Haitao Fu; Feng Huang; Xuan Liu; Yang Qiu ; Wen Zhang
 
 
Hypergraph-based logistic matrix factorization for metabolite'disease interaction prediction 
 
Yingjun Ma; Yuanyuan Ma
 
 
PATHOME-Drug: a subpathway-based polypharmacology drug-repositioning method 
 
Seungyoon Nam; Sungyoung Lee; Sungjin Park; Jinhyuk Lee ; Aron Park ...
 
 
BioDynaMo: a modular platform for high-performance agent-based simulation border= 
 
Lukas Breitwieser; Ahmad Hesam; Jean de Montigny; Vasileios Vavourakis ; Alexandros Iosif ...
 
 
TGSA: protein'protein association-based twin graph neural networks for drug response prediction with similarity augmentation 
 
Yiheng Zhu; Zhenqiu Ouyang; Wenbo Chen; Ruiwei Feng ; Danny Z Chen ...
 
 
Accelerating Big Data Analysis through LASSO-Random Forest Algorithm in QSAR Studies 
 
Fahimeh Motamedi; Horacio Pérez-Sánchez; Alireza Mehridehnavi; Afshin Fassihi ; Fahimeh Ghasemi
 
 
SMILE: mutual information learning for integration of single-cell omics data 
 
Yang Xu; Priyojit Das; Rachel Patton McCord
 
 
 
DATA AND TEXT MINING
 
 
 
Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction 
 
Gianvito Pio; Paolo Mignone; Giuseppe Magazzù; Guido Zampieri ; Michelangelo Ceci ...
 
 
Continual knowledge infusion into pre-trained biomedical language models 
 
Kishlay Jha; Aidong Zhang
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons 
 
Shuxia Guo; Xuan Zhao; Shengdian Jiang; Liya Ding ; Hanchuan Peng
 
 
Explainable nucleus classification using Decision Tree Approximation of Learned Embeddings 
 
Mohamed Amgad; Lamees A Atteya; Hagar Hussein; Kareem Hosny Mohammed ; Ehab Hafiz ...
 
 
FLINO: a new method for immunofluorescence bioimage normalization border= 
 
John Graf; Sanghee Cho; Elizabeth McDonough; Alex Corwin ; Anup Sood ...
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data border= 
 
Shixiang Wang; Yi Xiong; Longfei Zhao; Kai Gu ; Yin Li ...
 
 
ksrates: positioning whole-genome duplications relative to speciation events in KS distributions 
 
Cecilia Sensalari; Steven Maere; Rolf Lohaus
 
 
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria border= 
 
Kenneth I Brewer; Glenn J Gaffield; Malavika Puri ; Ronald R Breaker
 
 
echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline 
 
Brian M Schilder; Jack Humphrey; Towfique Raj
 
 
Viola: a structural variant signature extractor with user-defined classifications border= 
 
Itsuki Sugita; Shohei Matsuyama; Hiroki Dobashi ; Daisuke Komura; Shumpei Ishikawa
 
 
 
SEQUENCE ANALYSIS
 
 
 
HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes border= 
 
Jie Tan; Zhencheng Fang; Shufang Wu ; Qian Guo; Xiaoqing Jiang ...
 
 
GAMMA: a tool for the rapid identification, classification and annotation of translated gene matches from sequencing data 
 
Richard A Stanton; Nicholas Vlachos; Alison Laufer Halpin
 
 
indelPost: harmonizing ambiguities in simple and complex indel alignments 
 
Kohei Hagiwara; Michael N Edmonson; David A Wheeler; Jinghui Zhang
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations 
 
Amélie Barozet; Kevin Molloy; Marc Vaisset; Christophe Zanon ; Pierre Fauret ...
 
 
INTERCAAT: identifying interface residues between macromolecules 
 
Steven Grudman; J Eduardo Fajardo; Andras Fiser
 
 
ATPdock: a template-based method for ATP-specific protein'ligand docking 
 
Liang Rao; Ning-Xin Jia; Jun Hu; Dong-Jun Yu ; Gui-Jun Zhang
 
 
 
GENE EXPRESSION
 
 
 
FIVEx: an interactive eQTL browser across public datasets 
 
Alan Kwong; Andrew P Boughton; Mukai Wang; Peter VandeHaar ; Michael Boehnke ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Unipept Visualizations: an interactive visualization library for biological data 
 
Pieter Verschaffelt; James Collier; Alexander Botzki; Lennart Martens ; Peter Dawyndt ...
 
 
purgeR: inbreeding and purging in pedigreed populations border= 
 
Eugenio López-Cortegano
 
 
 
SYSTEMS BIOLOGY
 
 
 
PolyRound: polytope rounding for random sampling in metabolic networks border= 
 
Axel Theorell; Johann F Jadebeck; Katharina Nöh; Jörg Stelling
 
 
metID: an R package for automatable compound annotation for LCâˆ'MS-based data border= 
 
Xiaotao Shen; Si Wu; Liang Liang; Songjie Chen ; Kévin Contrepois ...
 
 
TPWshiny: an interactive R/Shiny app to explore cell line transcriptional responses to anti-cancer drugs 
 
Peter Zhang; Alida Palmisano; Ravindra Kumar; Ming-Chung Li ; James H Doroshow ...
 
 
SGI: automatic clinical subgroup identification in omics datasets border= 
 
Mustafa Buyukozkan; Karsten Suhre; Jan Krumsiek
 
 
timeOmics: an R package for longitudinal multi-omics data integration 
 
Antoine Bodein; Marie-Pier Scott-Boyer; Olivier Perin; Kim-Anh Lê Cao ; Arnaud Droit
 
 
 
DATA AND TEXT MINING
 
 
 
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database border= 
 
Daniel Osorio; Marieke L Kuijjer; James J Cai
 
 
Amanida: an R package for meta-analysis of metabolomics non-integral data border= 
 
Maria Llambrich; Eudald Correig; Josep Gumà; Jesús Brezmes ; Raquel Cumeras
 
 
SWIMmeR: an R-based software to unveiling crucial nodes in complex biological networks 
 
Paola Paci; Giulia Fiscon
 
 
AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data 
 
Christina Wong; Bo Li
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
miRAnno'network-based functional microRNA annotation 
 
Tomas Tokar; Chiara Pastrello; Mark Abovsky; Sara Rahmati ; Igor Jurisica
 
 
 
BIOIMAGE INFORMATICS
 
 
 
PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images 
 
Rodrigo Fernandez-Gonzalez; Negar Balaghi; Kelly Wang; Ray Hawkins ; Katheryn Rothenberg ...
 
 
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