Volume 37, Issue 14, July 2021

ORIGINAL PAPERS

GENOME ANALYSIS

A gene-level methylome-wide association analysis identifies novel Alzheimer’s disease genes

Chong Wu and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 1933–1940, https://doi.org/10.1093/bioinformatics/btab045

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De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance

Corentin Molitor and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 1941–1945, https://doi.org/10.1093/bioinformatics/btab048

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SEQUENCE ANALYSIS

Succinct dynamic de Bruijn graphs

Bahar Alipanahi and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 1946–1952, https://doi.org/10.1093/bioinformatics/btaa546

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A semisupervised model to predict regulatory effects of genetic variants at single nucleotide resolution using massively parallel reporter assays

Zikun Yang and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 1953–1962, https://doi.org/10.1093/bioinformatics/btab040

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STRUCTURAL BIOINFORMATICS

SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs

Qingzhen Hou and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 1963–1971, https://doi.org/10.1093/bioinformatics/btab034

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GENE EXPRESSION

Using single-cell cytometry to illustrate integrated multi-perspective evaluation of clustering algorithms using Pareto fronts

Givanna H Putri and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 1972–1981, https://doi.org/10.1093/bioinformatics/btab038

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Robust gene coexpression networks using signed distance correlation

Javier Pardo-Diaz and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 1982–1989, https://doi.org/10.1093/bioinformatics/btab041

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Comparison of observation-based and model-based identification of alert concentrations from concentration–expression data

Franziska Kappenberg and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 1990–1996, https://doi.org/10.1093/bioinformatics/btab043

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ICN: extracting interconnected communities in gene co-expression networks

Qiong Wu and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 1997–2003, https://doi.org/10.1093/bioinformatics/btab047

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McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data

Israa Alqassem and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2004–2011, https://doi.org/10.1093/bioinformatics/btab050

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SYSTEMS BIOLOGY

Predictive and interpretable models via the stacked elastic net

Armin Rauschenberger and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2012–2016, https://doi.org/10.1093/bioinformatics/btaa535

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Enzyme promiscuity prediction using hierarchy-informed multi-label classification

Gian Marco Visani and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2017–2024, https://doi.org/10.1093/bioinformatics/btab054

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DATABASES AND ONTOLOGIES

Cellinker: a platform of ligand–receptor interactions for intercellular communication analysis

Yang Zhang and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2025–2032, https://doi.org/10.1093/bioinformatics/btab036

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BIOIMAGE INFORMATICS

Narrative scientific data visualization in an immersive environment

Richen Liu and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2033–2041, https://doi.org/10.1093/bioinformatics/btab052

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Biophysical informatics approach for quantifying phenotypic heterogeneity in cancer cell migration in confined microenvironments

Xingjian Zhang and Michael Mak

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2042–2052, https://doi.org/10.1093/bioinformatics/btab053

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APPLICATIONS NOTES

GENOME ANALYSIS

Scool: a new data storage format for single-cell Hi-C data

Joachim Wolff and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2053–2054, https://doi.org/10.1093/bioinformatics/btaa924

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muCNV: genotyping structural variants for population-level sequencing

Goo Jun and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2055–2057, https://doi.org/10.1093/bioinformatics/btab199

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SEQUENCE ANALYSIS

amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool

Travis J Lawrence and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2058–2060, https://doi.org/10.1093/bioinformatics/btaa917

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HRIBO: high-throughput analysis of bacterial ribosome profiling data

Rick Gelhausen and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2061–2063, https://doi.org/10.1093/bioinformatics/btaa959

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STRUCTURAL BIOINFORMATICS

quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories

Vincent Mallet and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2064–2065, https://doi.org/10.1093/bioinformatics/btaa925

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SYSTEMS BIOLOGY

obaDIA: one-step biological analysis pipeline for data-independent acquisition and other quantitative proteomics data

Jun Yan and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2066–2067, https://doi.org/10.1093/bioinformatics/btaa893

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GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Chen Chen and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2068–2069, https://doi.org/10.1093/bioinformatics/btaa902

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COSIFER: a Python package for the consensus inference of molecular interaction networks

Matteo Manica and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2070–2072, https://doi.org/10.1093/bioinformatics/btaa942

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DATA AND TEXT MINING

Mortality Tracker: the COVID-19 case for real time web APIs as epidemiology commons

Jonas S Almeida and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2073–2074, https://doi.org/10.1093/bioinformatics/btaa933

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EWASex: an efficient R-package to predict sex in epigenome-wide association studies

Jesper Beltoft Lund and others

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2075–2076, https://doi.org/10.1093/bioinformatics/btaa949

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ERRATUM

Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees

Martin R Smith

Bioinformatics, Volume 37, Issue 14, July 2021, Pages 2077–2078, https://doi.org/10.1093/bioinformatics/btab200

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CORRIGENDUM

Corrigendum to: HRIBO: high-throughput analysis of bacterial ribosome profiling data

Bioinformatics, Volume 37, Issue 14, July 2021, Page 2079, https://doi.org/10.1093/bioinformatics/btab256

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