Lightnews — Scholar-powered news

International Society for Biocuration @biocurator.bsky.social · 17h

The results of the 2025-2026 Executive Committee elections are in. Congratulations to our new and returning members:
Susan Bello
Kalpana Panneerselvam
Ranjana Kishore
Thank you to all the candidates and all who voted.
www.biocuration.org/executive-co...

Executive Committee Election Results – International Society for Biocuration

www.biocuration.org

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Ensembl @ensembl.org · 22h

FungiDB/VEuPathDB + Ensembl are teaming up to enhance fungal & oomycete genome resources — and we need your input!

Complete the survey by Nov 1st, 2025:  zurl.co/gKjC1

Your feedback will help guide decisions on genome curation, annotation & data integration.

Qualtrics Survey | Qualtrics Experience Management

The most powerful, simple and trusted way to gather experience data. Start your journey to experience management and try a free account today.

zurl.co

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APPRIS database @appris.bsky.social · 22h

We have recalculated APPRIS principal isoforms for GENCODE v48 / Ensembl 114 human.

GENCODE added loss of function genes to this version and we discovered that this caused the TRIFID scores to change, affecting some of the PRINCIPAL:2 -> PRINCIPAL:5 isoforms.

Our fault, we asked for the change!

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PhytoKeys @phytokeys.pensoft.net · 2d

A comprehensive survey has documented 169 vascular plant taxa, including new northern records, in east-central Baffin Island, enhancing understanding of Arctic biodiversity and floristic patterns.

🔗 doi.org/10.3897/phyt...

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Galaxy Project @galaxyproject.bsky.social · 22h

Galaxy 25.0 steps up the game in data management. Now you can set up and manage InvenioRDM / Zenodo (or S3, Dropbox, etc.) integrations from a dedicated section in User Preferences — clean UI, prioritized sources, and true “Export datasets” support.

Read more: (1/2)

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International Society for Biocuration @biocurator.bsky.social · 21h

There is still time to sign up for ISB's annual general meeting on Oct 27th. We'll have a short update on the society followed by talks from our career award winners. All are welcome to join us www.biocuration.org/annual-gener...

Annual General Meeting – International Society for Biocuration

www.biocuration.org

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The Arabidopsis Information Resource (TAIR) @tairnews.bsky.social · 5d

"44th public release of TAIR@Phoenix data"

Read more here: https://arabidopsis.org/news/breaking-news#301

#News

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Bioinformatics Advances @bioinfoadv.bsky.social · 7d

🗂️ Now published in Bioinformatics Advances: “Metadata harmonization from biological datasets with language models”

Read the full paper here: https://doi.org/10.1093/bioadv/vbaf241

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ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 7d

🏙️ Last week, #ERGA joined the @vertebrategenomes.bsky.social #VGP Conference in NYC, a great chance to connect with @ebpgenome.bsky.social projects and share progress on #FAIR genome assemblies & reporting under @biogeneurope.bsky.social
www.erga-biodiversity.eu/post/erga-me... #genomes #conference

ERGA meets VGP in New York City

Last week, ERGA was present at the Vertebrate Genomes Project 2025 Conference, held at The Rockefeller University in New York City from September 30 and October 1. ERGA and VGP share a long-standing c...

www.erga-biodiversity.eu

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Michael Tress @michaeltress.bsky.social · 15d

So, our definitive paper on the human reference gene set is out this week in Database (Oxford).

We merged and compared @ensembl.org / @gencodegenes.bsky.social , RefSeq and UniProtKB coding genes and investigated the agreements and discrepancies.

Details of what we found in the thread ...

Counts of the merged Ensembl/GENCODE, RefSeq and UniProtKB coding genes with the most likely explanations for the outliers for each gene set. For example, most Ensembl/GENCODE singletons are readthrough genes.

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GlyGen @glygen.bsky.social · 6d

The 2025 Nobel Prize in Physiology or Medicine recognizes Brunkow, Ramsdell, and Sakaguchi for their discovery of Tregs and the regulatory role of FOXP3, an O-GlcNAcylated protein.

Explore FOXP3 on the GlyGen portal: glygen.org and learn more here: www.nature.com/articles/s41...

#glycotime

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ICPSR @icpsr.bsky.social · 8d

📈Data Alert!📈 ICPSR offers new and updated data to meet your research needs. Perfect for researchers, students, and data enthusiasts. Start exploring! Check it out ➡️ http://myumi.ch/ICPSR-new-releases

#NewReleases #DataUpdate #DataDriven

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BioGRID @biogrid.bsky.social · 8d

BioGRID #CRISPR Database v2.0.18 is released w/ 2,217 screens from 418 different publications including 94,000+ genes, 825 cell lines, 145 cell types & 29 phenotypes including 101 #glioblastoma related screens and 116 #fanconianemia related screens 🧪
@biogrid.bsky.social

BioGRID ORCS Version 2.0.18 Released

The BioGRID ORCS curated CRISPR database has been updated to include CRISPR screens from a total of 418 different publications. These additions bring the total number of curated CRISPR screens in our ...

orcs.thebiogrid.org

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JAX Genomic Education @jaxeducation.bsky.social · 8d

🖥️🧬 STEM educators: How can #bioinformatics introduce your students to real-world genomics?

@jacksonlab.bsky.social's module provides an overview of bioinformatics, helping students learn to manage and analyze large amounts of data to propel scientific discoveries.

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GlyGen @glygen.bsky.social · 8d

🌐Commun Fund Data Ecosystem ASHG 2025 Networking Event

Discover groundbreaking research via posters, lightning talks, demos and more!
📆Date: October 14 | 7-9PM ET at the Westin Boston Seaport District

Registration open (space limited to 100): docs.google.com/forms/d/e/1F...

#glycotime #CFDE

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The Transmitter @thetransmitter.bsky.social · 8d

To celebrate the first anniversary of the release of FlyWire, we asked nine neuroscientists to share how they are using connectome data in their research and what they hope is in store for the future of fly connectomics.

By @franciscorr25.bsky.social

#neuroskyence

bit.ly/3Wx5nt3

How FlyWire is redefining Drosophila research, one year in

Nine Drosophila researchers share how the connectome transformed the field and what additional new tools they would like to see.

bit.ly

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Skype a Scientist @skypeascientist.bsky.social · 16d

On October 7th, learn how to communicate genetics topics to classrooms and informal settings with with @robomalley.bsky.social from @pged.bsky.social!

This is for teachers and all other kinds of educators.

RSVP for free here: givebutter.com/8TVNiA

DNA floats in the background of a texty event flyer that says "Personal genetics engagement in classrooms and communities, Learn about genetic advances and about how to bring conversations about ethical, legal, and social dimensions of genetics into classrooms and informal science learning. Tuesday October 7, 2025, 12pm EDT. brought to you by Skype a scientist and the personal genetics education and dialogue program. RSVP at linktr.ee/skypeascientist

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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 12d

An important new item on the status of model organism databases: these resources, built and refined over decades, are at risk. www.nature.com/articles/d41...

Model organism databases face budget cuts and closures

Beyond the crucial data they contain, these digital archives have provided an important space for academic communities to exchange ideas and resources.

www.nature.com

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Alliance of Genome Resources @alliancegenome.bsky.social · 12d

Nature has published an article on the crisis facing MODs
Model organism databases face budget cuts and closures www.nature.com/articles/d41...
@zfinmod.bsky.social @xenbase.bsky.social @yeastgenome.bsky.social @mousegenome.bsky.social @ratgenome.bsky.social @geneontology.bsky.social @nature.com

Model organism databases face budget cuts and closures

Beyond the crucial data they contain, these digital archives have provided an important space for academic communities to exchange ideas and resources.

www.nature.com

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Nature Portfolio @natureportfolio.nature.com · 12d

A Perspective in Nature introduces the Biodiversity Cell Atlas initiative, which aims to create comprehensive single-cell molecular atlases across the eukaryotic tree of life. go.nature.com/46HnmDn 🔒

This is figure 1, which shows thattThe BCA aims at molecularly characterizing cell types across the eukaryotic tree of life.

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FlyBase @flybase.bsky.social · 13d

It's #TechnicalAdvances update time; the papers added in September are here wiki.flybase.org/wiki/FlyBase.... Want your paper with with a new technique, reagent, or resource featured next month? Flag it when you #FTYP!

FlyBase:Papers with technical advances - FlyBase Wiki

Authors of the papers listed below suggest that they include a technical advance, new type of reagent, or resource likely to be useful for other researchers. Author suggestions have been collected via the Fast-Track Your Paper tool since October 2020, with those most recently submitted at the top. Please note, there will be a lag time before listed papers can be found on FlyBase (FBrf links will become active when available) and the submission date does not necessarily match the publication date of the paper.

wiki.flybase.org

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DDI Alliance @ddialliance.bsky.social · 13d

Collaboration is key! 🔑 The DDI Alliance brings together international experts, orgs, and projects to develop open metadata standards for research data. Join the global community: ddialliance.org/mission

#MetadataStandard #FAIRdata #Collaboration

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BF Francis Ouellette @bffo.bsky.social · 14d

From #OUP 's #DATABASE journal | Navigating #OpenSource waters: the pharmaceutical #industry's role in #bioontology development | #Bioinformatics #Genomics #Ontology #OpenScience 🧬 🖥️ 🧪 🔓 🇩🇰
⬇️
academic.oup.com/database/art...

Navigating open-source waters: the pharmaceutical industry’s role in bioontology development

Abstract. Bioontologies are core to many data management strategies, artificial intelligence and machine learning initiatives, and search functionality wit

academic.oup.com

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Open Bioinformatics Foundation @openbio.bsky.social · 15d

An open letter about the recent cuts at GigaScience: www.open-bio.org/2025/09/30/2...
(open for signatures until the end of October)

#OpenScience #OpenData #GigaScience

Scott Edmunds cuts the cake at the 2025 GigaScience birthday party at ISMB/ECCB 2025

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Genetics Society of America @genetics-gsa.bsky.social · 14d

📢 NEW GENOME ALERT

In #G3journal, Lozier et al. generated the first chromosome-level genome assembly of the American Bumblebee. This study will power comparative conservation genomics analyses to identify possible genetic differences between pollinators. buff.ly/IYIKqFD

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