Volume 37, Issue 21, November 2021

MESSAGE FROM THE ISCB

2020 ISCB Innovatory Award: Xiaole Shirley Liu

Christiana N Fogg and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3697–3698, https://doi.org/10.1093/bioinformatics/btaa509

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2020 ISCB accomplishments by a Senior Scientist Award: Steven Salzberg

Christiana N Fogg and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3699–3700, https://doi.org/10.1093/bioinformatics/btaa508

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2020 Outstanding contributions to ISCB award: Judith Blake

Christiana N Fogg and others

Bioinformatics, Volume 37, Issue 21, November 2021, Page 3701, https://doi.org/10.1093/bioinformatics/btaa511

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ISMB 2021

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Andreas Dräger and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3702–3706, https://doi.org/10.1093/bioinformatics/btab229

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ORIGINAL PAPERS

GENOME ANALYSIS

phyLoSTM: a novel deep learning model on disease prediction from longitudinal microbiome data

Divya Sharma and Wei Xu

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3707–3714, https://doi.org/10.1093/bioinformatics/btab482

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Deep Subspace Mutual Learning for cancer subtypes prediction

Bo Yang and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3715–3722, https://doi.org/10.1093/bioinformatics/btab625

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SEQUENCE ANALYSIS

pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification

Benjamin R Weeder and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3723–3733, https://doi.org/10.1093/bioinformatics/btab628

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PHYLOGENETICS

wQFM: highly accurate genome-scale species tree estimation from weighted quartets

Mahim Mahbub and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3734–3743, https://doi.org/10.1093/bioinformatics/btab428

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STRUCTURAL BIOINFORMATICS

Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework

Lewis Moffat and David T Jones

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3744–3751, https://doi.org/10.1093/bioinformatics/btab491

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Improved estimation of model quality using predicted inter-residue distance

Lisha Ye and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3752–3759, https://doi.org/10.1093/bioinformatics/btab632

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SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions

Gen Li and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3760–3765, https://doi.org/10.1093/bioinformatics/btab567

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Structural discrimination analysis for constraint selection in protein modeling

Guilherme F Bottino and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3766–3773, https://doi.org/10.1093/bioinformatics/btab425

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GENE EXPRESSION

CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data

Chengchen Zhao and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3774–3780, https://doi.org/10.1093/bioinformatics/btab488

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Differential transcript usage analysis of bulk and single-cell RNA-seq data with DTUrtle

Tobias Tekath and Martin Dugas

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3781–3787, https://doi.org/10.1093/bioinformatics/btab629

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Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments

Nuha BinTayyash and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3788–3795, https://doi.org/10.1093/bioinformatics/btab486

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Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging

Alona Levy-Jurgenson and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3796–3804, https://doi.org/10.1093/bioinformatics/btab569

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Sparse least trimmed squares regression with compositional covariates for high-dimensional data

Gianna Serafina Monti and Peter Filzmoser

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3805–3814, https://doi.org/10.1093/bioinformatics/btab572

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GENETICS AND POPULATION ANALYSIS

Mediation analysis for survival data with high-dimensional mediators

Haixiang Zhang and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3815–3821, https://doi.org/10.1093/bioinformatics/btab564

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Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR

Peter M Bourke and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3822–3829, https://doi.org/10.1093/bioinformatics/btab574

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SYSTEMS BIOLOGY

MHCVision: estimation of global and local false discovery rate for MHC class I peptide binding prediction

Phorutai Pearngam and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3830–3838, https://doi.org/10.1093/bioinformatics/btab479

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Linear functional organization of the omic embedding space

A Xenos and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3839–3847, https://doi.org/10.1093/bioinformatics/btab487

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Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli

Rudan Xu and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3848–3855, https://doi.org/10.1093/bioinformatics/btab575

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DATA AND TEXT MINING

Medical concept normalization in clinical trials with drug and disease representation learning

Zulfat Miftahutdinov and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3856–3864, https://doi.org/10.1093/bioinformatics/btab474

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TIGA: target illumination GWAS analytics

Jeremy J Yang and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3865–3873, https://doi.org/10.1093/bioinformatics/btab427

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scAMACE: model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation

Jiaxuan Wangwu and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3874–3880, https://doi.org/10.1093/bioinformatics/btab426

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MERIDA: a novel Boolean logic-based integer linear program for personalized cancer therapy

Kerstin Lenhof and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3881–3888, https://doi.org/10.1093/bioinformatics/btab546

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Predicting correlated outcomes from molecular data

Armin Rauschenberger and Enrico Glaab

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3889–3895, https://doi.org/10.1093/bioinformatics/btab576

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DATABASES AND ONTOLOGIES

FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases

Maxime Delmas and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3896–3904, https://doi.org/10.1093/bioinformatics/btab627

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BIOIMAGE INFORMATICS

Foveal blur-boosted segmentation of nuclei in histopathology images with shape prior knowledge and probability map constraints

Hongyi Duanmu and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3905–3913, https://doi.org/10.1093/bioinformatics/btab418

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APPLICATIONS NOTES

GENOME ANALYSIS

JBrowseR: an R interface to the JBrowse 2 genome browser

Elliot A Hershberg and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3914–3915, https://doi.org/10.1093/bioinformatics/btab459

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Custom workflows to improve joint variant calling from multiple related tumour samples: FreeBayesSomatic and Strelka2Pass

S Hollizeck and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3916–3919, https://doi.org/10.1093/bioinformatics/btab606

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ACES: Analysis of Conservation with an Extensive list of Species

Evin M Padhi and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3920–3922, https://doi.org/10.1093/bioinformatics/btab684

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mspack: efficient lossless and lossy mass spectrometry data compression

Felix Hanau and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3923–3925, https://doi.org/10.1093/bioinformatics/btab636

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utr.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation

Yating Liu and Joseph D Dougherty

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3926–3928, https://doi.org/10.1093/bioinformatics/btab635

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BleTIES: annotation of natural genome editing in ciliates using long read sequencing

Brandon K B Seah and Estienne C Swart

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3929–3931, https://doi.org/10.1093/bioinformatics/btab613

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SEQUENCE ANALYSIS

FlexTaxD: flexible modification of taxonomy databases for improved sequence classification

David Sundell and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3932–3933, https://doi.org/10.1093/bioinformatics/btab621

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RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data

Sara Hetzel and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3934–3935, https://doi.org/10.1093/bioinformatics/btab663

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Prowler: a novel trimming algorithm for Oxford Nanopore sequence data

Simon Lee and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3936–3937, https://doi.org/10.1093/bioinformatics/btab630

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TCRpair: prediction of functional pairing between HLA-A*02:01-restricted T-cell receptor α and β chains

Anja Mösch and Dmitrij Frishman

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3938–3940, https://doi.org/10.1093/bioinformatics/btab573

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CONSTAX2: improved taxonomic classification of environmental DNA markers

Julian A Liber and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3941–3943, https://doi.org/10.1093/bioinformatics/btab347

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PZLAST: an ultra-fast amino acid sequence similarity search server against public metagenomes

Hiroshi Mori and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3944–3946, https://doi.org/10.1093/bioinformatics/btab492

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MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences

Thomas Haschka and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3947–3949, https://doi.org/10.1093/bioinformatics/btab430

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STRUCTURAL BIOINFORMATICS

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data

Sreenath Nair and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3950–3952, https://doi.org/10.1093/bioinformatics/btab424

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FRETraj: integrating single-molecule spectroscopy with molecular dynamics

Fabio D Steffen and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3953–3955, https://doi.org/10.1093/bioinformatics/btab615

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ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution

Burak T Kaynak and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3956–3958, https://doi.org/10.1093/bioinformatics/btab496

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pyconsFold: a fast and easy tool for modeling and docking using distance predictions

J Lamb and A Elofsson

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3959–3960, https://doi.org/10.1093/bioinformatics/btab353

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GENE EXPRESSION

Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment

Dylan Kotliar and Andrés Colubri

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3961–3963, https://doi.org/10.1093/bioinformatics/btab689

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HGC: fast hierarchical clustering for large-scale single-cell data

Ziheng Zou and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3964–3965, https://doi.org/10.1093/bioinformatics/btab420

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GENETICS AND POPULATION ANALYSIS

E-Pedigrees: a large-scale automatic family pedigree prediction application

Xiayuan Huang and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3966–3968, https://doi.org/10.1093/bioinformatics/btab419

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SYSTEMS BIOLOGY

The fobitools framework: the first steps towards food enrichment analysis

Pol Castellano-Escuder and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3969–3971, https://doi.org/10.1093/bioinformatics/btab626

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IntelliPy: a GUI for analyzing IntelliCage data

Nicolas Ruffini and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3972–3973, https://doi.org/10.1093/bioinformatics/btab682

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DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

Almut Heinken and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3974–3975, https://doi.org/10.1093/bioinformatics/btab622

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NetControl4BioMed: a web-based platform for controllability analysis of protein–protein interaction networks

Victor-Bogdan Popescu and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3976–3978, https://doi.org/10.1093/bioinformatics/btab570

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ptm: an R package for the study of methionine sulfoxidation and other posttranslational modifications

Juan Carlos Aledo

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3979–3980, https://doi.org/10.1093/bioinformatics/btab348

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DATA AND TEXT MINING

LipiDisease: associate lipids to diseases using literature mining

Piyush More and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3981–3982, https://doi.org/10.1093/bioinformatics/btab559

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DATABASES AND ONTOLOGIES

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Miguel Roncoroni and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3983–3985, https://doi.org/10.1093/bioinformatics/btab421

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BIOIMAGE INFORMATICS

OCTID: a one-class learning-based Python package for tumor image detection

Yanan Wang and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3986–3988, https://doi.org/10.1093/bioinformatics/btab416

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Tysserand—fast and accurate reconstruction of spatial networks from bioimages

Alexis Coullomb and Vera Pancaldi

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3989–3991, https://doi.org/10.1093/bioinformatics/btab490

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CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis

David R Stirling and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3992–3994, https://doi.org/10.1093/bioinformatics/btab634

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OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology

Nita Mulliqi and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3995–3997, https://doi.org/10.1093/bioinformatics/btab578

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DeepSinse: deep learning-based detection of single molecules

John S H Danial and others

Bioinformatics, Volume 37, Issue 21, November 2021, Pages 3998–4000, https://doi.org/10.1093/bioinformatics/btab352

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