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Bioinformatics  
Volume 37 Issue 23
 
1 December 2021
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Embeddings of genomic region sets capture rich biological associations in lower dimensions 
 
Erfaneh Gharavi; Aaron Gu; Guangtao Zheng; Jason P Smith ; Hyun Jae Cho ...
 
 
Ry┼źt┼Ź: improved multi-sample transcript assembly for differential transcript expression analysis and more 
 
Thomas Gatter; Peter F Stadler
 
 
 
SEQUENCE ANALYSIS
 
 
 
EPSOL: sequence-based protein solubility prediction using multidimensional embedding 
 
Xiang Wu; Liang Yu
 
 
S2L-PSIBLAST: a supervised two-layer search framework based on PSI-BLAST for protein remote homology detection 
 
Xiaopeng Jin; Qing Liao; Bin Liu
 
 
PolarProtPred: predicting apical and basolateral localization of transmembrane proteins using putative short linear motifs and deep learning border= 
 
Laszlo Dobson; András Zeke; Gábor E Tusnády
 
 
 
TempoMAGE: a deep learning framework that exploits the causal dependency between time-series data to predict histone marks in open chromatin regions at time-points with missing ChIP-seq datasets 
 
Mohammad Hallal; Mariette Awad; Pierre Khoueiry
 
 
Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries border= 
 
Valentine U Nlebedim; Roy R Chaudhuri; Kevin Walters
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction 
 
Kai-Long Zhao; Jun Liu; Xiao-Gen Zhou; Jian-Zhong Su ; Yang Zhang ...
 
 
A sequential niche multimodal conformational sampling algorithm for protein structure prediction 
 
Yu-Hao Xia; Chun-Xiang Peng; Xiao-Gen Zhou; Gui-Jun Zhang
 
 
XRRpred: accurate predictor of crystal structure quality from protein sequence 
 
Sina Ghadermarzi; Bartosz Krawczyk; Jiangning Song; Lukasz Kurgan
 
 
 
Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics border= 
 
Mohamed Machat; Florent Langenfeld; Daniela Craciun ; Léa Sirugue; Taoufik Labib ...
 
 
 
GENE EXPRESSION
 
 
 
VSS: variance-stabilized signals for sequencing-based genomic signals border= 
 
Faezeh Bayat; Maxwell Libbrecht
 
 
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map 
 
Minsheng Hao; Kui Hua; Xuegong Zhang
 
 
Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores 
 
Rui Fan; Qinghua Cui
 
 
TimeCycle: topology inspired method for the detection of cycling transcripts in circadian time-series data border= 
 
Elan Ness-Cohn; Rosemary Braun
 
 
Differential network analysis by simultaneously considering changes in gene interactions and gene expression 
 
Jia-Juan Tu; Le Ou-Yang; Yuan Zhu; Hong Yan ; Hong Qin ...
 
 
tsRNAsearch: a pipeline for the identification of tRNA and ncRNA fragments from small RNA-sequencing data 
 
Paul D Donovan; Natalie M McHale; Morten T Venø; Jochen H M Prehn
 
 
HieRFIT: a hierarchical cell type classification tool for projections from complex single-cell atlas datasets 
 
Yasin Kaymaz; Florian Ganglberger; Ming Tang; Christian Haslinger ; Francesc Fernandez-Albert ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Survival analysis on rare events using group-regularized multi-response Cox regression 
 
Ruilin Li; Yosuke Tanigawa; Johanne M Justesen; Jonathan Taylor ; Trevor Hastie ...
 
 
RápidoPGS: a rapid polygenic score calculator for summary GWAS data without a test dataset border= 
 
Guillermo Reales; Elena Vigorito; Martin Kelemen ; Chris Wallace
 
 
On the stability of log-rank test under labeling errors border= 
 
Ben Galili; Anat Samohi; Zohar Yakhini
 
 
 
SYSTEMS BIOLOGY
 
 
 
Visual exploration of large metabolic models 
 
Michael Aichem; Tobias Czauderna; Yan Zhu; Jinxin Zhao; Matthias Klapperstück ...
 
 
AdaTiSS: a novel data-Adaptive robust method for identifying Tissue Specificity Scores 
 
Meng Wang; Lihua Jiang; Michael P Snyder
 
 
Identifying driver genes for individual patients through inductive matrix completion 
 
Tong Zhang; Shao-Wu Zhang; Yan Li
 
 
MultiDTI: drug'target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network 
 
Deshan Zhou; Zhijian Xu; WenTao Li; Xiaolan Xie ; Shaoliang Peng
 
 
Efficient gradient-based parameter estimation for dynamic models using qualitative data border= 
 
Leonard Schmiester; Daniel Weindl; Jan Hasenauer
 
 
 
DATA AND TEXT MINING
 
 
 
Node similarity-based graph convolution for link prediction in biological networks 
 
Mustafa Co┼čkun; Mehmet Koyutürk
 
 
Predicting anti-cancer drug response by finding optimal subset of drugs 
 
Fatemeh Yassaee Meybodi; Changiz Eslahchi
 
 
EpitopeVec: linear epitope prediction using deep protein sequence embeddings border= 
 
Akash Bahai; Ehsaneddin Asgari; Mohammad R K Mofrad; Andreas Kloetgen ; Alice C McHardy
 
 
HEMDAG: a family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction 
 
Marco Notaro; Marco Frasca; Alessandro Petrini; Jessica Gliozzo ; Elena Casiraghi ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
HFBD: a biomarker knowledge database for heart failure heterogeneity and personalized applications 
 
Hongxin He; Manhong Shi; Yuxin Lin; Chaoying Zhan ; Rongrong Wu ...
 
 
Assessing consistency across functional screening datasets in cancer cells border= 
 
Ling Cai; Hongyu Liu; John D Minna; Ralph J DeBerardinis ; Guanghua Xiao ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Fully unsupervised deep mode of action learning for phenotyping high-content cellular images 
 
Rens Janssens; Xian Zhang; Audrey Kauffmann; Antoine de Weck ; Eric Y Durand
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Panache: a web browser-based viewer for linearized pangenomes border= 
 
Éloi Durant; François Sabot; Matthieu Conte; Mathieu Rouard
 
 
Coral: a web-based visual analysis tool for creating and characterizing cohorts 
 
Patrick Adelberger; Klaus Eckelt; Markus J Bauer; Marc Streit ; Christian Haslinger ...
 
 
iNucs: inter-nucleosome interactions border= 
 
Mehrdad Oveisi; Manu Shukla; Nogayhan Seymen; Masae Ohno ; Yuichi Taniguchi ...
 
 
PATO: Pangenome Analysis Toolkit 
 
Miguel D Fernández-de-Bobadilla; Alba Talavera-Rodríguez; Lucía Chacón; Fernando Baquero; Teresa M Coque ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
CNN-PepPred: an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets'application to peptide'MHC class II binding prediction border= 
 
Valentin Junet; Xavier Daura
 
 
Cellsnp-lite: an efficient tool for genotyping single cells 
 
Xianjie Huang; Yuanhua Huang
 
 
New strategies to improve minimap2 alignment accuracy 
 
Heng Li
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures border= 
 
Prasun Kumar; Derek N Woolfson
 
 
 
GENE EXPRESSION
 
 
 
UCSC Cell Browser: visualize your single-cell data border= 
 
Matthew L Speir; Aparna Bhaduri; Nikolay S Markov; Pablo Moreno ; Tomasz J Nowakowski ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Normalized coefficient of variation (nCV): a method to evaluate circadian clock robustness in population scale data border= 
 
Gang Wu; Lauren J Francey; Marc D Ruben ; John B Hogenesch
 
 
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data border= 
 
Jordan H Creed; Christopher M Wilson; Alex C Soupir ; Christelle M Colin-Leitzinger; Gregory J Kimmel ...
 
 
VOLTA: adVanced mOLecular neTwork Analysis 
 
Alisa Pavel; Antonio Federico; Giusy del Giudice; Angela Serra; Dario Greco
 
 
 
DATA AND TEXT MINING
 
 
 
RCytoGPS: an R package for reading and visualizing cytogenetics data 
 
Zachary B Abrams; Dwayne G Tally; Lynne V Abruzzo; Kevin R Coombes
 
 
LipidQuant 1.0: automated data processing in lipid class separation'mass spectrometry quantitative workflows 
 
Denise Wolrab; Eva Cífková; Pavel ─'á┼ł; Miroslav Lísa ; Ond┼Öej Peterka ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics border= 
 
Alan E Murphy; Brian M Schilder; Nathan G Skene
 
 
COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases 
 
Chuming Chen; Karen E Ross; Sachin Gavali; Julie E Cowart ; Cathy H Wu
 
 
2DProts: database of family-wide protein secondary structure diagrams border= 
 
Ivana Huta┼Öová Va┼Öeková; Jan Huta┼Ö; Adam Midlik; Vladimír Horský ; Eva Hladká ...
 
 
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