BF Francis Ouellette
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bffo.bsky.social
BF Francis Ouellette
@bffo.bsky.social
3K followers 4.7K following 350 posts
Bioinformatics 🧬🖥️🧪
#PLOS Comp Biol Education Sect. Editor;
#DATABASE OUP Associate Editor;
#OpenScience #OpenAccess #OpenData;
friend of @jxtxfoundation.bsky.social,
@abinstitute.bsky.social
- I am 🇨🇦
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bffo.bsky.social
BF Francis Ouellette @bffo.bsky.social · Nov 29
Be Open so the world can see how great you are!

#OpenScience
#OpenAccess
#OpenData
#OpenSource
#OpenEducationalResources
Reposted by BF Francis Ouellette
daanspeth.bsky.social
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...

The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
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GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:21 PM
bffo.bsky.social
From the @narjournal.bsky.social #NARDatabaseIssue | #DDBJ update in 2025: system integration for global data-sharing including #pathogen surveillance | #Bioinformatics #Database #Genomics #OpenScience #OpenData 🧬 🖥️🧪🔓 🇯🇵
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academic.oup.com/nar/advance-...
DDBJ update in 2025: system integration for global data-sharing including pathogen surveillance
Abstract. The Bioinformation and DNA Data Bank of Japan Center (https://www.ddbj.nig.ac.jp/) continues to serve as a global core infrastructure for biologi
academic.oup.com
November 25, 2025 at 5:05 PM
Reposted by BF Francis Ouellette
martinsteinegger.bsky.social
I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI
recursecenter.bsky.social Recurse Center @recursecenter.bsky.social · 14d
What’s the lore behind choosing your career path ?
November 24, 2025 at 2:42 AM
Reposted by BF Francis Ouellette
seqera.io
By modernizing legacy pipelines, optimizing CEs, and automating large-scale data analysis, Champions Oncology were able to cut turnaround time from days to hours while significantly reducing compute costs ⏩
November 25, 2025 at 11:45 AM
bffo.bsky.social
From Sameer Velankar & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #AlphaFold #Protein #Structure #Database 2025: a redesigned interface and updated structural coverage | #Bioinformatics #Proteomics #OpenScience #AFDB 🧪🔓 CC/ @ebi.embl.org
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academic.oup.com/nar/advance-...
AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage
Abstract. The AlphaFold Protein Structure Database (AFDB; https://alphafold.ebi.ac.uk), developed by EMBL–EBI and Google DeepMind, provides open access to
academic.oup.com
November 24, 2025 at 12:56 AM
bffo.bsky.social
From @narjournal.bsky.social #NARDatabaseIssue | MiMeDB 2.0: the Human Microbial Metabolome Database for 2026 | #Bioinformatics #Metabolomics #Database #OpenScience #Human 🧪🔓🇨🇦 CC/ @wishartnode.bsky.social
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academic.oup.com/nar/advance-...
MiMeDB 2.0: the Human Microbial Metabolome Database for 2026
Abstract. The Microbial Metabolome Database (MiMeDB) (https://mimedb.org) is a comprehensive, freely accessible resource linking human-associated microbes
academic.oup.com
November 24, 2025 at 12:40 AM
bffo.bsky.social
From @wormsense.bsky.social in @plos.org #Computational #Biology | Ten simple rules for maximizing summer research experiences for students, mentors, & research groups | ❤️ Rule 1: A great short-term project is like a great short film | #Education #PLOSCBTSR 🧪🔓
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journals.plos.org/ploscompbiol...
Ten simple rules for maximizing summer research experiences for students, mentors, and research groups
Whether hosted by colleges, universities, stand-alone research institutions, federal research labs, or private companies, immersive summer (6–12 weeks) research experiences build students’ confidence ...
journals.plos.org
November 22, 2025 at 6:07 PM
bffo.bsky.social
From @natureportfolio.nature.com #Scientific #Data | The ICGC ARGO data dictionary for standardizing global cancer clinical data | #Cancer #ClinicalData #Bioinformatics #Genomics #OpenScience 🧬 🖥️ 🧪 🔓
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www.nature.com/articles/s41...
The ICGC ARGO data dictionary for standardizing global cancer clinical data - Scientific Data
Scientific Data - The ICGC ARGO data dictionary for standardizing global cancer clinical data
www.nature.com
November 22, 2025 at 5:57 PM
Reposted by BF Francis Ouellette
brian.teague.bio
I agree with EVERY SINGLE ONE of these rules. I came to most of them on my own because I never had any mentorship for my mentorship. And despite being published in PLOS Comp Bio, they apply to EVERY undergraduate and masters student project.
November 19, 2025 at 6:26 PM
bffo.bsky.social
From @plos.org #Computational #Biology | Ten simple rules for early-career researchers supervising short-term student projects | #Education #Bioinformatics #OpenScience #PLOSCBTSR #ECR 🧪 🔓 CC/ @knaegle.bsky.social
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journals.plos.org/ploscompbiol...
Ten simple rules for early-career researchers supervising short-term student projects
Author summary Supervising undergraduate or master’s research projects is a vital aspect of academic life, offering opportunities for both student development and supervisor growth. For many early-car...
journals.plos.org
November 19, 2025 at 6:18 PM
Reposted by BF Francis Ouellette
genomebc.bsky.social
In this clip Dr. Goodridge explains why he studies Salmonella, which causes 93 million cases of illness worldwide each year.

🎧 Listen to the full episode of Nice Genes! – Gut Check: link.cohostpodcasting.com/b87cc2cc-6ed...

#NiceGenesPodcast #Genomics #Microbiome #FoodSafety #GutBrainConnection
November 19, 2025 at 5:52 PM
bffo.bsky.social
From the @genomebrowser.bsky.social team in @narjournal.bsky.social #NARDatabaseIssue | The UCSC Genome Browser database: 2026 update | #Bioinformatics #Genomics #Database #OpenScience 🧬 🖥️🧪🔓
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academic.oup.com/nar/advance-...
The UCSC Genome Browser database: 2026 update
Abstract. Now in its 25th year of operation, the UCSC Genome Browser (https://genome.ucsc.edu) provides a central location for researchers around the world
academic.oup.com
November 19, 2025 at 6:04 PM
bffo.bsky.social
From @gillespm.bsky.social and colleagues in @narjournal.bsky.social #NARDatabaseIssue | The #Reactome Knowledgebase 2026 | #Bioinformatics #Proteomics #Human #OpenScience #OpenData #OpenSource #Database #GlobalCoreBiodata and @elixir-europe.org resource 🧬 🖥️🧪🔓
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academic.oup.com/nar/advance-...
The Reactome Knowledgebase 2026
Abstract. The Reactome Knowledgebase (https://reactome.org) is a freely accessible, expert-curated, open-source, and open-data resource that describes huma
academic.oup.com
November 19, 2025 at 5:52 PM
bffo.bsky.social
From @csoneson.bsky.social , @markrobinsonca.bsky.social & colleagues in @plos.org #Computational #Biology | Building a continuous #benchmarking ecosystem in #bioinformatics | #Education 🧬 🖥️ 🧪 🔓  
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journals.plos.org/ploscompbiol...
Building a continuous benchmarking ecosystem in bioinformatics
Benchmarking, which involves collecting reference datasets and demonstrating method performance, is a requirement for the development of new computational tools, but also becomes a domain of its own t...
journals.plos.org
November 15, 2025 at 5:11 PM
Reposted by BF Francis Ouellette
dstansby.bsky.social
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".

ome-zarr-book.readthedocs.io
An Introduction to OME-Zarr for Big Bioimaging Data
ome-zarr-book.readthedocs.io
November 4, 2025 at 3:33 PM
Reposted by BF Francis Ouellette
zoognosisjoy.bsky.social
Evidence of domestication syndrome associated with urbanization in racoons. 🧪
frontiersinzoology.biomedcentral.com/articles/10....
November 15, 2025 at 12:12 PM
Reposted by BF Francis Ouellette
jxtxfoundation.bsky.social
The James P. Taylor Foundation for Open Science is pleased to announce the recipients of the 2025 JXTX+CSHL Genome Informatics Scholarships. JXTX provides support for students to attend conferences in CompBio and data science, where they can present their work [1/8]
November 6, 2025 at 3:27 PM
bffo.bsky.social
From the @narjournal.bsky.social #NARDatabaseIssue | EMBL's European Bioinformatics Institute (EMBL-EBI) in 2025 | #Bioinformatics #OpenData #OpenScience #Proteomics #Genomics #Bioimaging 🧬 🖥️🧪🔓
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academic.oup.com/nar/advance-...
EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2025
Abstract. The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolec
academic.oup.com
November 15, 2025 at 2:38 PM
Reposted by BF Francis Ouellette
sneumann.bsky.social
This celebrates 20 years since #MassBank started in Japan. The new system developed at @ipbhalle.bsky.social went live in June at both massbank.eu and massbank.jp. We had >20 releases of reference spectra submitted by not only the #metabolomics, #exposomics and #EnvironmentalScience communities.
MassBank
massbank.eu
November 13, 2025 at 8:40 AM
Reposted by BF Francis Ouellette
galaxyproject.bsky.social
Galaxy showed up strong at Genome Informatics 2025 with new posters, new tools, and new ideas for making genomics more open and accessible.

Catch the highlights from Anton Nekrutenko, Mike Schatz, and Delphine Larivière 👉 galaxyproject.org/news/2025-11...
Galaxy at Genome Informatics 2025
Galaxy was in full force at Genome Informatics 2025, presenting cutting-edge work on scalable analysis, interactive workflows, and high-quality genome curation.
galaxyproject.org
November 11, 2025 at 7:18 PM
bffo.bsky.social
From @sneumann.bsky.social and colleagues in @narjournal.bsky.social #NARDatabaseIssue | MassBank: an open and FAIR mass spectral data resource | #Bioinformatics #Proteomics #OpenScience #FAIR #Database 🧪🔓
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academic.oup.com/nar/advance-...
MassBank: an open and FAIR mass spectral data resource
Abstract. The open spectral library MassBank (https://massbank.jp/) started in 2006 in Japan, as one of the first open source and open access cross-vendor
academic.oup.com
November 12, 2025 at 3:12 PM
bffo.bsky.social
From the @narjournal.bsky.social #NARDatabaseIssue | ProteomeXchange consortium in 2026: making proteomics data #FAIR | #Bioinformatics #Proteomics #OpenScience 🧪🔓
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academic.oup.com/nar/article/...
The ProteomeXchange consortium in 2026: making proteomics data FAIR
Abstract. The ProteomeXchange consortium of proteomics resources (http://www.proteomexchange.org) was established to standardize open data practices in the
academic.oup.com
November 10, 2025 at 4:21 PM
bffo.bsky.social
From @ngehlenborg.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for making biomedical data resources accessible | I like Rule 10:Focus on progress over perfection | #Education #Bioinformatics #PLOSCBTSR #OpenScience 🧬 🖥️ 🧪 🔓
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journals.plos.org/ploscompbiol...
Ten simple rules for making biomedical data resources accessible
journals.plos.org
November 7, 2025 at 6:06 PM
Reposted by BF Francis Ouellette
scedmunds.bsky.social
Thank you Francis for all you've done for the journal. We put in a lot of effort to build up an excellent and very experienced Ed Board, and seeing so many of them resigning in this manner is sad but shows they've taken their responsibilities seriously.
November 7, 2025 at 12:38 PM
bffo.bsky.social
I was one of the Editorial Board Members at @gigascience.bsky.social who resigned from the Editorial Board.
🧪 🔓
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retractionwatch.com/2025/11/03/d...
Dozens of board members resign from big-data journal after mass staff firings
More than three-fifths of the editorial board of a biomedical sciences journal resigned after the publication’s operations moved from Hong Kong to Shenzhen, China, and the editors and software team…
retractionwatch.com
November 4, 2025 at 3:46 PM