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Section: Databases and ontologies
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Journal Article

uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization

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Haiyang Bian and others
Bioinformatics, Volume 41, Issue 4, April 2025, btaf149, https://doi.org/10.1093/bioinformatics/btaf149
Published: 02 April 2025
Journal Article

BioArchLinux: community-driven fresh reproducible software repository for life sciences

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Guoyi Zhang and others
Bioinformatics, Volume 41, Issue 3, March 2025, btaf106, https://doi.org/10.1093/bioinformatics/btaf106
Published: 11 March 2025
Journal Article

ESCARGOT: an AI agent leveraging large language models, dynamic graph of thoughts, and biomedical knowledge graphs for enhanced reasoning

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Nicholas Matsumoto and others
Bioinformatics, Volume 41, Issue 2, February 2025, btaf031, https://doi.org/10.1093/bioinformatics/btaf031
Published: 22 January 2025
Journal Article

FungiFun3: systemic gene set enrichment analysis for fungal species

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Albert Garcia Lopez and others
Bioinformatics, Volume 40, Issue 11, November 2024, btae620, https://doi.org/10.1093/bioinformatics/btae620
Published: 22 November 2024
Journal Article

ViralPrimer: a web server to monitor viral nucleic acid amplification tests’ primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox

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Norbert Deutsch and others
Bioinformatics, Volume 40, Issue 11, November 2024, btae657, https://doi.org/10.1093/bioinformatics/btae657
Published: 05 November 2024
Journal Article

scToppR: a coding-friendly R interface to ToppGene

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Bryan Granger and Stefano Berto
Bioinformatics, Volume 40, Issue 11, November 2024, btae582, https://doi.org/10.1093/bioinformatics/btae582
Published: 28 September 2024
Journal Article

RCPedia: a global resource for studying and exploring retrocopies in diverse species

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Helena B Conceição and others
Bioinformatics, Volume 40, Issue 9, September 2024, btae530, https://doi.org/10.1093/bioinformatics/btae530
Published: 06 September 2024
Journal Article

KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models

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Nicholas Matsumoto and others
Bioinformatics, Volume 40, Issue 6, June 2024, btae353, https://doi.org/10.1093/bioinformatics/btae353
Published: 03 June 2024
Journal Article

A machine-readable specification for genomics assays

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Ali Sina Booeshaghi and others
Bioinformatics, Volume 40, Issue 4, April 2024, btae168, https://doi.org/10.1093/bioinformatics/btae168
Published: 05 April 2024
Journal Article

The IDSM mass spectrometry extension: searching mass spectra using SPARQL

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Jakub Galgonek and Jiří Vondrášek
Bioinformatics, Volume 40, Issue 4, April 2024, btae174, https://doi.org/10.1093/bioinformatics/btae174
Published: 01 April 2024
Journal Article

PyCoM: a python library for large-scale analysis of residue–residue coevolution data

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Philipp Bibik and others
Bioinformatics, Volume 40, Issue 4, April 2024, btae166, https://doi.org/10.1093/bioinformatics/btae166
Published: 26 March 2024
Journal Article

PERSEUS: an interactive and intuitive web-based tool for pedigree visualization

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Nicole Pradas and others
Bioinformatics, Volume 40, Issue 2, February 2024, btae060, https://doi.org/10.1093/bioinformatics/btae060
Published: 03 February 2024
Journal Article

Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics

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Megan M Shuey and others
Bioinformatics, Volume 39, Issue 11, November 2023, btad655, https://doi.org/10.1093/bioinformatics/btad655
Published: 01 November 2023
Journal Article

BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs

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Jackson Callaghan and others
Bioinformatics, Volume 39, Issue 9, September 2023, btad570, https://doi.org/10.1093/bioinformatics/btad570
Published: 14 September 2023
Journal Article

FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms

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Federico Bianca and others
Bioinformatics, Volume 39, Issue 9, September 2023, btad549, https://doi.org/10.1093/bioinformatics/btad549
Published: 06 September 2023
Journal Article

CCIBP: a comprehensive cosmetic ingredients bioinformatics platform

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Linlin Gong and others
Bioinformatics, Volume 39, Issue 7, July 2023, btad416, https://doi.org/10.1093/bioinformatics/btad416
Published: 03 July 2023
Journal Article

The NanoFlow Repository

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Jessie E Arce and others
Bioinformatics, Volume 39, Issue 6, June 2023, btad368, https://doi.org/10.1093/bioinformatics/btad368
Published: 07 June 2023
Journal Article

excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

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Jonathan D Ogata and others
Bioinformatics, Volume 39, Issue 4, April 2023, btad198, https://doi.org/10.1093/bioinformatics/btad198
Published: 17 April 2023
Journal Article

sInterBase: a comprehensive database of Escherichia coli sRNA–mRNA interactions

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Shani Cohen and others
Bioinformatics, Volume 39, Issue 4, April 2023, btad172, https://doi.org/10.1093/bioinformatics/btad172
Published: 12 April 2023
Journal Article

eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species

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Min Yang and others
Bioinformatics, Volume 39, Issue 4, April 2023, btad173, https://doi.org/10.1093/bioinformatics/btad173
Published: 05 April 2023