Volume 37, Issue 12, June 2021

ORIGINAL PAPERS

GENOME ANALYSIS

Liftoff: accurate mapping of gene annotations

Alaina Shumate and Steven L Salzberg

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1639–1643, https://doi.org/10.1093/bioinformatics/btaa1016

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Genome-scale de novo assembly using ALGA

Sylwester Swat and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1644–1651, https://doi.org/10.1093/bioinformatics/btab005

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A rarefaction-based extension of the LDM for testing presence–absence associations in the microbiome

Yi-Juan Hu and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1652–1657, https://doi.org/10.1093/bioinformatics/btab012

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Alignment-free Genomic Analysis via a Big Data Spark Platform

Umberto Ferraro Petrillo and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1658–1665, https://doi.org/10.1093/bioinformatics/btab014

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SEQUENCE ANALYSIS

MAGUS: Multiple sequence Alignment using Graph clUStering

Vladimir Smirnov and Tandy Warnow

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1666–1672, https://doi.org/10.1093/bioinformatics/btaa992

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V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data

Susana Posada-Céspedes and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1673–1680, https://doi.org/10.1093/bioinformatics/btab015

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STRUCTURAL BIOINFORMATICS

DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins

Stelios K Mylonas and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1681–1690, https://doi.org/10.1093/bioinformatics/btab009

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GENE EXPRESSION

Identification of differentially expressed gene modules in heterogeneous diseases

Olga Zolotareva and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1691–1698, https://doi.org/10.1093/bioinformatics/btaa1038

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Compression of quantification uncertainty for scRNA-seq counts

Scott Van Buren and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1699–1707, https://doi.org/10.1093/bioinformatics/btab001

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GENETICS AND POPULATION ANALYSIS

A framework for modeling epistatic interaction

David B Blumenthal and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1708–1716, https://doi.org/10.1093/bioinformatics/btaa990

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SYSTEMS BIOLOGY

GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level

Zahra Razaghi-Moghadam and Zoran Nikoloski

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1717–1723, https://doi.org/10.1093/bioinformatics/btaa996

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Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification

Eric Bach and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1724–1731, https://doi.org/10.1093/bioinformatics/btaa998

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CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations

Alexey Ovchinnikov and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1732–1738, https://doi.org/10.1093/bioinformatics/btab010

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DATA AND TEXT MINING

Using drug descriptions and molecular structures for drug–drug interaction extraction from literature

Masaki Asada and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1739–1746, https://doi.org/10.1093/bioinformatics/btaa907

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REVIEW

SYSTEMS BIOLOGY

Single-cell systems analysis: decision geometry in outliers

Lianne Abrahams

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1747–1755, https://doi.org/10.1093/bioinformatics/btaa1078

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APPLICATIONS NOTES

GENOME ANALYSIS

SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments

Zhanlin Chen and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1756–1758, https://doi.org/10.1093/bioinformatics/btaa1039

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methylclock: a Bioconductor package to estimate DNA methylation age

Dolors Pelegí-Sisó and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1759–1760, https://doi.org/10.1093/bioinformatics/btaa825

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COVID-Align: accurate online alignment of hCoV-19 genomes using a profile HMM

Frédéric Lemoine and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1761–1762, https://doi.org/10.1093/bioinformatics/btaa871

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SEQUENCE ANALYSIS

GalaxyCloudRunner: enhancing scalable computing for Galaxy

Nuwan Goonasekera and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1763–1765, https://doi.org/10.1093/bioinformatics/btaa860

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PHYLOGENETICS

MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R

John A Rhodes and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1766–1768, https://doi.org/10.1093/bioinformatics/btaa868

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STRUCTURAL BIOINFORMATICS

Machine-OlF-Action: a unified framework for developing and interpreting machine-learning models for chemosensory research

Anku Gupta and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1769–1771, https://doi.org/10.1093/bioinformatics/btaa1104

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GENE EXPRESSION

Varmole: a biologically drop-connect deep neural network model for prioritizing disease risk variants and genes

Nam D Nguyen and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1772–1775, https://doi.org/10.1093/bioinformatics/btaa866

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SYSTEMS BIOLOGY

HOPS: high-performance library for (non-)uniform sampling of convex-constrained models

Johann F Jadebeck and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1776–1777, https://doi.org/10.1093/bioinformatics/btaa872

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DATA AND TEXT MINING

PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS

Nick Strayer and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1778–1780, https://doi.org/10.1093/bioinformatics/btaa870

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DATABASES AND ONTOLOGIES

Identifiers.org: Compact Identifier services in the cloud

Manuel Bernal-Llinares and others

Bioinformatics, Volume 37, Issue 12, June 2021, Pages 1781–1782, https://doi.org/10.1093/bioinformatics/btaa864

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CORRIGENDA

Corrigendum to: ASpli: Integrative analysis of splicing landscapes through RNA-Seq assays

Estefania Mancini and others

Bioinformatics, Volume 37, Issue 12, June 2021, Page 1783, https://doi.org/10.1093/bioinformatics/btab345

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EpiDope: a deep neural network for linear B-cell epitope prediction

Maximilian Collatz and others

Bioinformatics, Volume 37, Issue 12, June 2021, Page 1784, https://doi.org/10.1093/bioinformatics/btab390

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