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Bioinformatics  
Volume 37 Issue 21
 
1 November 2021
 
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MESSAGE FROM THE ISCB
 
 
 
2020 ISCB Innovatory Award: Xiaole Shirley Liu 
 
Christiana N Fogg; Diane E Kovats; Ron Shamir
 
 
2020 ISCB accomplishments by a Senior Scientist Award: Steven Salzberg 
 
Christiana N Fogg; Diane E Kovats; Ron Shamir
 
 
2020 Outstanding contributions to ISCB award: Judith Blake 
 
Christiana N Fogg; Diane E Kovats; Ron Shamir
 
 
 
ISMB 2021
 
 
 
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems border= 
 
Andreas Dräger; TomáÅ¡ Helikar; Matteo Barberis ; Marc Birtwistle; Laurence Calzone ...
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
phyLoSTM: a novel deep learning model on disease prediction from longitudinal microbiome data 
 
Divya Sharma; Wei Xu
 
 
 
Deep Subspace Mutual Learning for cancer subtypes prediction 
 
Bo Yang; Ting-Ting Xin; Shan-Min Pang; Meng Wang ; Yi-Jie Wang
 
 
 
SEQUENCE ANALYSIS
 
 
 
pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification 
 
Benjamin R Weeder; Mary A Wood; Ellysia Li; Abhinav Nellore ; Reid F Thompson
 
 
 
PHYLOGENETICS
 
 
 
wQFM: highly accurate genome-scale species tree estimation from weighted quartets 
 
Mahim Mahbub; Zahin Wahab; Rezwana Reaz; M Saifur Rahman ; Md Shamsuzzoha Bayzid
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework border= 
 
Lewis Moffat; David T Jones
 
 
Improved estimation of model quality using predicted inter-residue distance 
 
Lisha Ye; Peikun Wu; Zhenling Peng; Jianzhao Gao ; Jian Liu ...
 
 
 
SAMPDI-3D: predicting the effects of protein and DNA mutations on protein'DNA interactions 
 
Gen Li; Shailesh Kumar Panday; Yunhui Peng; Emil Alexov
 
 
Structural discrimination analysis for constraint selection in protein modeling 
 
Guilherme F Bottino; Allan J R Ferrari; Fabio C Gozzo; Leandro Martínez
 
 
 
GENE EXPRESSION
 
 
 
CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data 
 
Chengchen Zhao; Wenchao Xiu; Yuwei Hua ; Naiqian Zhang; Yong Zhang
 
 
Differential transcript usage analysis of bulk and single-cell RNA-seq data with DTUrtle border= 
 
Tobias Tekath; Martin Dugas
 
 
Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments border= 
 
Nuha BinTayyash; Sokratia Georgaka; S T John ; Sumon Ahmed; Alexis Boukouvalas ...
 
 
Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging border= 
 
Alona Levy-Jurgenson; Xavier Tekpli; Zohar Yakhini
 
 
Sparse least trimmed squares regression with compositional covariates for high-dimensional data 
 
Gianna Serafina Monti; Peter Filzmoser
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Mediation analysis for survival data with high-dimensional mediators 
 
Haixiang Zhang; Yinan Zheng; Lifang Hou; Cheng Zheng ; Lei Liu
 
 
Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR border= 
 
Peter M Bourke; Roeland E Voorrips; Christine A Hackett ; Geert van Geest; Johan H Willemsen ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
MHCVision: estimation of global and local false discovery rate for MHC class I peptide binding prediction border= 
 
Phorutai Pearngam; Sira Sriswasdi; Trairak Pisitkun ; Andrew R Jones
 
 
Linear functional organization of the omic embedding space border= 
 
A Xenos; N Malod-Dognin; S Milinković; N Pržulj
 
 
Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli border= 
 
Rudan Xu; Zahra Razaghi-Moghadam; Zoran Nikoloski
 
 
 
DATA AND TEXT MINING
 
 
 
Medical concept normalization in clinical trials with drug and disease representation learning border= 
 
Zulfat Miftahutdinov; Artur Kadurin; Roman Kudrin ; Elena Tutubalina
 
 
TIGA: target illumination GWAS analytics 
 
Jeremy J Yang; Dhouha Grissa; Christophe G Lambert; Cristian G Bologa; Stephen L Mathias ...
 
 
scAMACE: model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation 
 
Jiaxuan Wangwu; Zexuan Sun; Zhixiang Lin
 
 
MERIDA: a novel Boolean logic-based integer linear program for personalized cancer therapy border= 
 
Kerstin Lenhof; Nico Gerstner; Tim Kehl ; Lea Eckhart; Lara Schneider ...
 
 
Predicting correlated outcomes from molecular data border= 
 
Armin Rauschenberger; Enrico Glaab
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases border= 
 
Maxime Delmas; Olivier Filangi; Nils Paulhe ; Florence Vinson; Christophe Duperier ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Foveal blur-boosted segmentation of nuclei in histopathology images with shape prior knowledge and probability map constraints 
 
Hongyi Duanmu; Fusheng Wang; George Teodoro; Jun Kong
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
JBrowseR: an R interface to the JBrowse 2 genome browser border= 
 
Elliot A Hershberg; Garrett Stevens; Colin Diesh; Peter Xie ; Teresa De Jesus Martinez ...
 
 
Custom workflows to improve joint variant calling from multiple related tumour samples: FreeBayesSomatic and Strelka2Pass 
 
S Hollizeck; S Q Wong; B Solomon; D Chandrananda ; S-J Dawson
 
 
ACES: Analysis of Conservation with an Extensive list of Species border= 
 
Evin M Padhi; Jeffrey K Ng; Elvisa Mehinovic; Eleanor I Sams ; Tychele N Turner
 
 
mspack: efficient lossless and lossy mass spectrometry data compression 
 
Felix Hanau; Hannes Röst; Idoia Ochoa
 
 
utr.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation 
 
Yating Liu; Joseph D Dougherty
 
 
BleTIES: annotation of natural genome editing in ciliates using long read sequencing border= 
 
Brandon K B Seah; Estienne C Swart
 
 
 
SEQUENCE ANALYSIS
 
 
 
FlexTaxD: flexible modification of taxonomy databases for improved sequence classification 
 
David Sundell; Caroline Öhrman; Daniel Svensson; Edvin Karlsson ; Björn Brindefalk ...
 
 
RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data border= 
 
Sara Hetzel; Pay Giesselmann; Knut Reinert ; Alexander Meissner; Helene Kretzmer
 
 
Prowler: a novel trimming algorithm for Oxford Nanopore sequence data 
 
Simon Lee; Loan T Nguyen; Ben J Hayes; Elizabeth M Ross
 
 
TCRpair: prediction of functional pairing between HLA-A*02:01-restricted T-cell receptor alpha and beta chains 
 
Anja Mösch; Dmitrij Frishman
 
 
CONSTAX2: improved taxonomic classification of environmental DNA markers 
 
Julian A Liber; Gregory Bonito; Gian Maria Niccolò Benucci
 
 
PZLAST: an ultra-fast amino acid sequence similarity search server against public metagenomes border= 
 
Hiroshi Mori; Hitoshi Ishikawa; Koichi Higashi ; Yoshiaki Kato; Toshikazu Ebisuzaki ...
 
 
MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences 
 
Thomas Haschka; Loic Ponger; Christophe Escudé; Julien Mozziconacci
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data border= 
 
Sreenath Nair; Mihály Váradi; Nurul Nadzirin ; LukáÅ¡ Pravda; Stephen Anyango ...
 
 
FRETraj: integrating single-molecule spectroscopy with molecular dynamics border= 
 
Fabio D Steffen; Roland K O Sigel; Richard Börner
 
 
ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution border= 
 
Burak T Kaynak; She Zhang; Ivet Bahar ; Pemra Doruker
 
 
pyconsFold: a fast and easy tool for modeling and docking using distance predictions border= 
 
J Lamb; A Elofsson
 
 
 
GENE EXPRESSION
 
 
 
Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment 
 
Dylan Kotliar; Andrés Colubri
 
 
HGC: fast hierarchical clustering for large-scale single-cell data 
 
Ziheng Zou; Kui Hua; Xuegong Zhang
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
E-Pedigrees: a large-scale automatic family pedigree prediction application 
 
Xiayuan Huang; Nicholas Tatonetti; Katie LaRow; Brooke Delgoffee ; John Mayer ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
The fobitools framework: the first steps towards food enrichment analysis 
 
Pol Castellano-Escuder; Cristina Andrés-Lacueva; Alex Sánchez-Pla
 
 
IntelliPy: a GUI for analyzing IntelliCage data border= 
 
Nicolas Ruffini; Marianne B Müller; Ulrich Schmitt; Susanne Gerber
 
 
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations border= 
 
Almut Heinken; Stefanía Magnúsdóttir; Ronan M T Fleming ; Ines Thiele
 
 
NetControl4BioMed: a web-based platform for controllability analysis of protein'protein interaction networks border= 
 
Victor-Bogdan Popescu; José Ángel Sánchez-Martín; Daniela Schacherer ; Sadra Safadoust; Negin Majidi ...
 
 
ptm: an R package for the study of methionine sulfoxidation and other posttranslational modifications 
 
Juan Carlos Aledo
 
 
 
DATA AND TEXT MINING
 
 
 
LipiDisease: associate lipids to diseases using literature mining border= 
 
Piyush More; Laura Bindila; Philipp Wild; Miguel Andrade-Navarro ; Jean-Fred Fontaine
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive border= 
 
Miguel Roncoroni; Bert Droesbeke; Ignacio Eguinoa; Kim De Ruyck ; Flora D'Anna ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
OCTID: a one-class learning-based Python package for tumor image detection 
 
Yanan Wang; Litao Yang; Geoffrey I Webb; Zongyuan Ge ; Jiangning Song
 
 
Tysserand'fast and accurate reconstruction of spatial networks from bioimages 
 
Alexis Coullomb; Vera Pancaldi
 
 
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis border= 
 
David R Stirling; Anne E Carpenter; Beth A Cimini
 
 
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology border= 
 
Nita Mulliqi; Kimmo Kartasalo; Henrik Olsson ; Xiaoyi Ji; Lars Egevad ...
 
 
DeepSinse: deep learning-based detection of single molecules 
 
John S H Danial; Raed Shalaby; Katia Cosentino; Marwa M Mahmoud ; Fady Medhat ...
 
 
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