BF Francis Ouellette @bffo.bsky.social · 3h#Dans5Jourss #Éducation #Bioinformatiques #Génomiques #ScienceOuverte #Réseautage #Montréal #VenezVoir >> @ircm.bsky.social @mon-bug.bsky.social 000
BF Francis Ouellette @bffo.bsky.social · 3h#In5days #Bioinformatics #Genomics #OpenScience #Networking #Montréal #ComeAndSee >> @ircm.bsky.social @mon-bug.bsky.social 000
BF Francis Ouellette @bffo.bsky.social · 08/10/2026From #OUP 's #DATABASE journal | GeneReL: a large language model-powered platform for gene regulatory relationship extraction with community curation | #OpenScience #BioCuration #Bioinformatics #LLM #CommunityDrivenCuration |🧬🖥️🧪🔓🌱 CC/ @tairnews.bsky.social ⬇️ academic.oup.com/database/art...academic.oup.comGeneReL: a large language model-powered platform for gene regulatory relationship extraction with community curationAbstract. Gene regulatory networks provide fundamental insights into plant biology, yet extracting structured interaction data from scientific literature r 000
Reposted by BF Francis OuelletteMikhail Khodorkovsky @khodorkovsky.com · 07/10/2026Today marks 20 years since Novaya Gazeta journalist Anna Politkovskaya was murdered in Moscow. She recognized Putin's true nature earlier than most—and the regime could never erase the truth she died to tell. 10338158
BF Francis Ouellette @bffo.bsky.social · 08/10/2026From Andy Göbel & Tilman D. Rachner in @plos.org #Computational #Biology | Ten simple rules for preparing and delivering effective funding pitches in competitive grant applications | #Education #PLOSCBTSR #OpenScience #OralPresentations | 🧪🔓 ⬇️ journals.plos.org/ploscompbiol...journals.plos.orgTen simple rules for preparing and delivering effective funding pitches in competitive grant applicationsIn grant applications, oral presentations can be an integral part of the evaluation process. Funding pitches are a specific form of pitch presentations delivered during competitive review procedures t... 001
BF Francis Ouellette @bffo.bsky.social · 03/10/2026Yes, I agree: 😞 #Bioinformatics #Workflow #Reproducibility #UseGalaxy | 🧬🖥️🧪 CC/ @galaxyproject.bsky.social 130
BF Francis Ouellette @bffo.bsky.social · 03/10/2026From the @nationalobserver.com | America still doesn't understand how deep the rift goes | #CanPoli 🇨🇦 CC/ @mark-carney.bsky.social ⬇️ www.nationalobserver.com/2026/09/29/o... 000
Reposted by BF Francis OuelletteMontréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 01/10/2026Montréal Bioinformatics User Group (MonBUG) #Education #Bioinformatics #Genomics #OpenScience #In2WeeksMinus1Day | 🧬🖥️🧪🔓 CC/ @ircm.bsky.social @umontreal-en.bsky.social @mcgill.ca ⬇️ monbug.ca 022
Reposted by BF Francis OuelletteMontréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 01/10/2026Groupe d’intérêt en bio-informatique de Montréal (MonBUG) #Éducation #Bioinformatiques #Génomiques #ScienceOuverte #Dans2SemainesMoins1Jour | 🧬🖥️🧪🔓 CC/ @ircm.bsky.social @umontreal-en.bsky.social @mcgill.ca ⬇️ monbug.ca 011
Reposted by BF Francis OuelletteTurgut Mesut Yılmaz @turgutmesut.bsky.social · 27/09/2026📢 Very happy to see ARTS-DB 2.0 out in Database! 🧬 A lot of work went into bringing bacterial and fungal target-directed genome mining together with updated BGC predictions and an improved interface. Great to finally share it with the community! 🚀 📄: doi.org/10.1093/data... #TDGM #NPs #SecMet 042
Reposted by BF Francis OuelletteRan Blekhman @blekhman.bsky.social · 23/09/2026We have to stop using "paper count" as a useful scientific metric. More writing output no longer means more knowledge gained www.washingtonpost.com/education/20...washingtonpost.comOne professor’s AI-assisted output: 200 papers and 14 books this yearAn online platform removed 257 papers written or co-written by the University of Chicago’s Nicholas Polson after other academics raised questions. 1011347
BF Francis Ouellette @bffo.bsky.social · 26/09/2026"I love that blogs are making a comeback." Yes, me too! 021
BF Francis Ouellette @bffo.bsky.social · 26/09/2026From @turgutmesut.bsky.social Semih Erdogmus @canerbagci.bsky.social @nadineziemert.bsky.social in #OUP 's #DATABASE journal | ARTS-DB 2.0: an expanded database for target-directed genome mining across #Bacteria and #Fungi | #Bioinformatics #OpenScience | 🧬🖥️🧪🔓🇩🇪 ⬇️ academic.oup.com/database/art...academic.oup.comARTS-DB 2.0: an expanded database for target-directed genome mining across bacteria and fungiAbstract. The increasing prevalence of antimicrobial resistance requires efficient strategies to prioritize biosynthetic gene clusters (BGCs) that may enco 042
BF Francis Ouellette @bffo.bsky.social · 26/09/2026From #OUP 's #DATABASE journal | I-NOWJ: adaptive context selection and knowledge-guided learning for substance use named entity recognition | #OpenScience #BioCreative #ToxHabits #NLP #Clinic #ClinicalNamedEntity | 🧪🔓🇻🇳 ⬇️ academic.oup.com/database/art...academic.oup.comI-NOWJ: adaptive context selection and knowledge-guided learning for substance use named entity recognitionAbstract. Substance use information in clinical narratives is clinically important but is typically documented in unstructured and informal text, making au 000
BF Francis Ouellette @bffo.bsky.social · 26/09/2026From the @agbiodata.bsky.social team in #OUP 's #DATABASE journal |The future is FAIR: a community framework for enhanced data management and data sharing | #Bioinformatics #Genomics #OpenScience #AgBioData #FAIR #BioCuration | 🧬🖥️🧪🔓 ⬇️ academic.oup.com/database/art...academic.oup.comThe future is FAIR: a community framework for enhanced data management and data sharingAbstract. The AgBioData consortium is a community-driven initiative supporting >40 genomic, genetic, and breeding (GGB) databases for agricultural resea 021
Reposted by BF Francis OuelletteLarry Hunter @proflhunter.bsky.social · 23/09/2026Someone in the administration (not at NIH) ordered NIH's eRA electronic research administration system shut down. That's a pretty heavy handed intervention, especially in the last week of the fiscal year. Does not bode well. 0105
BF Francis Ouellette @bffo.bsky.social · 24/09/2026From #NCBI Insight | A New Way to Explore Connections in Biomedical Literature | #OpenScience #Education #Research #PubMed #PubMedLink #CitationLink #CouldMakeAGoodDATABASEPaper | 🧪🔓 ⬇️ ncbiinsights.ncbi.nlm.nih.gov/2026/09/24/e...ncbiinsights.ncbi.nlm.nih.govA New Way to Explore Connections in Biomedical Literature - NCBI InsightsWe’re excited to announce the launch of Linked Discoveries™, a new experimental pilot resource developed by the National Library of Medicine (NLM) that helps researchers, clinicians, information speci... 053
BF Francis Ouellette @bffo.bsky.social · 22/09/2026From @stephenturner.us on #PairedEnds | AI + Biosecurity in 4 minutes | #OpenScience #Education #Bioinformatics #Genomics #Biosecurity #AI #StephenOnTV #ScienceInTheNews #Great4Minutes | 🧬🖥️🧪🔓 ⬇️ blog.stephenturner.us/p/ai-biosecu...blog.stephenturner.usAI + Biosecurity in 4 minutesI got four minutes on live TV news to take on an important but nuanced topic. 062
BF Francis Ouellette @bffo.bsky.social · 22/09/2026From #OUP 's #DATABASE journal | U-Plant and U-Plant DISCOVER: an open-source database for botanic garden collections management and public engagement | #OpenScience #Education #BotanicGardenCollection #Plant #OpenScience #OpenAccess #PublicAccess | 🧪🔓 ⬇️ academic.oup.com/database/art...academic.oup.comU-Plant and U-Plant DISCOVER: an open-source database for botanic garden collections management and public engagementAbstract. Botanic gardens manage diverse plant collections and associated data that support research, conservation, education, and public engagement. Effec 001
BF Francis Ouellette @bffo.bsky.social · 22/09/2026From #OUP 's #DATABASE journal | Enhancing the SIB Literature Services ( #SIBiLS ) with annotations to support biocuration | #Bioinformatics #SIBLiteratureServices #OpenScience #TextMining #Literature #Biocuration #Medline #PubMedCentral | CC/ @sib.swiss | 🧬🖥️🧪🔓 ⬇️ academic.oup.com/database/art...academic.oup.comEnhancing the SIB Literature Services (SIBiLS) with annotations to support biocurationAbstract. Text-mining techniques are essential tools to efficiently access information within an increasing number of publications. The SIB Literature Serv 042
Reposted by BF Francis OuelletteMontréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 21/09/2026Study or work in bioinformatics in Greater Montréal? MonBUG invites trainees to propose a 10-minute, in-person talk and share their work with a welcoming local community. Students, postdocs, and research professionals are welcome: monbug.ca/en/contact/monbug.caContact - MonBUG 013
Reposted by BF Francis OuelletteMontréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 21/09/2026Vous étudiez ou travaillez en bioinformatique dans la grande région de Montréal? MonBUG invite les personnes en formation à proposer une présentation de 10 minutes, en personne, devant une communauté accueillante. Étudiant·es, postdocs et pros de recherche : monbug.ca/fr/contact/monbug.caContact - MonBUG 012
BF Francis Ouellette @bffo.bsky.social · 20/09/2026From #OUP 's @bioinfoadv.bsky.social journal | annoreport: an interactive tool for #Metagenome #Annotation | #Bioinformatics #OpenScience #Genomics #OpenSource #BioCuration #WouldHaveBeenAGoodDATABASEPaper | 🧬🖥️🧪🔓 ⬇️ academic.oup.com/bioinformati...academic.oup.comannoreport: an interactive tool for metagenome annotationAbstractSummary. Gene annotation of metagenome-assembled genomes is a critical step in determining the functional potential of microbial communities from e 031
Reposted by BF Francis OuelletteHans-Rudolf Hotz @hrhotz.bsky.social · 09/09/2026in case you still believe that @galaxyproject.bsky.social cannot be used for image analysis: onlinelibrary.wiley.com/doi/10.1111/...onlinelibrary.wiley.comBioimage management and analysis in Galaxy: Tools, workflows, training, and community practicesImage analysis in the life sciences is constrained by fragmented software ecosystems, heterogeneous data formats, and limited reproducibility. These barriers hinder the reuse of image analysis method... 022
Reposted by BF Francis OuelletteScott C Edmunds @scedmunds.bsky.social · 16/09/2026Just realised its #PeerReviewWeek, so I thought I'd re-share my piece from last year on why we need a FAIR Principles for Peer Review doi.org/10.59350/dpr... 163
BF Francis Ouellette @bffo.bsky.social · 19/09/2026From Jamie J. Alnasir in @plos.org #Computational #Biology | Twelve quick tips for designing AI-driven HPC workflows | #Bioinformatics #Education #PLOSCBQT #AI #ML #HPC #Workflows | 🧬🖥️🧪🔓 ⬇️ journals.plos.org/ploscompbiol...journals.plos.orgTwelve quick tips for designing AI-driven HPC workflows 020
BF Francis Ouellette @bffo.bsky.social · 17/09/2026From Thomas Sharpton (at @oregonstate.edu ) in @plos.org #Computational #Biology | A practical risk framework for large language model use in life science research | #Bioinformatics #Education #LLM #PromptDesign #Framework #Research #LifeSciences | 🧬 🖥️ 🧪 🔓 ⬇️ journals.plos.org/ploscompbiol...journals.plos.orgA practical risk framework for large language model use in life science researchResponsible use of large language models (LLMs) in life science research demands a unified approach to risk, yet existing guidance treats prompting and verification as separate topics rather than as i... 151
BF Francis Ouellette @bffo.bsky.social · 17/09/2026From our paper that came out yesterday: journals.plos.org/ploscompbiol... 000
BF Francis Ouellette @bffo.bsky.social · 17/09/2026From @elescak.bsky.social @anamaq.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for elevating Indigenous partnerships in research | #Education #PLOSCBTSR #Research #OpenScience #IndigenousPeoples | 🧪🔓 ⬇️ journals.plos.org/ploscompbiol...journals.plos.orgTen simple rules for elevating Indigenous partnerships in research 021
BF Francis Ouellette @bffo.bsky.social · 17/09/2026From the @bioinfoadv.bsky.social journal | Phil Bourne (1953–2026): from small molecules to big data—the journey of a multifaceted visionary | #Bioinformatics #Pioneer @rcsbpdb.bsky.social @iscb.bsky.social #PLOSCBTSR #OpenScience #OpenAccess #DataScience |🧬🖥️🧪🔓❤️ ⬇️ academic.oup.com/bioinformati...academic.oup.comPhil Bourne (1953–2026): from small molecules to big data—the journey of a multifaceted visionaryAbstract. Born in London in 1953 and raised in Australia, Phil Bourne spent over four decades in science moving across scales: from crystal structures to t 2115
Reposted by BF Francis OuellettePLOS @plos.org · 28/05/2026Today PLOS publishes Redefining Publishing: Practical pathways to open science, the public report from our 18-month research and design project. The report asks how publishing can better support open science. Explore the report: plos.io/4o3bsun #OpenScienceexplore.plos.orgRedefining publishing for the Open Science eraExplore innovative publishing models that support open science, enhance research transparency, and foster global collaboration in the evolving landscape of scholarly communication. 12718
BF Francis Ouellette @bffo.bsky.social · 16/09/2026Happy to see this one out in @plos.org #Computational #Biology | Ten simple rules for suggesting reviewers during a paper submission | #Education #PLOSCBTSR #Writing #Reviewing #Rule10PayItForward | 🧪🔓 🇺🇸🇨🇭🇧🇷🇨🇦 CC/ @ppalagi.bsky.social @fmacg.bsky.social ⬇️ journals.plos.org/ploscompbiol...journals.plos.orgTen simple rules for suggesting reviewers during a paper submission 086
BF Francis Ouellette @bffo.bsky.social · 16/09/2026From #NCBI Insight | dbGaP Modernization Update | #OpenScience #Bioinformatics #Genomics #GWAS #Human #WebServer #DatabaseOfGenotypeAndPhenotype #dbGaPLEnfantTerribleDuNCBI #UI #Modern #FaceLift | 🧬🖥️🧪🔓 ⬇️ ncbiinsights.ncbi.nlm.nih.gov/2026/09/16/d...ncbiinsights.ncbi.nlm.nih.govdbGaP Modernization Update - NCBI InsightsNCBI is modernizing the database of Genotype and Phenotype (dbGaP), a repository that collects human research study data from NIH-funded investigators and facilitates controlled-access to individual-l... 030
BF Francis Ouellette @bffo.bsky.social · 16/09/2026From @robertleaman.bsky.social et al in #OUP 's #DATABASE journal | MedHopQA: a disease-centred multi-hop reasoning benchmark and evaluation framework for LLM-based biomedical question answering | #OpenScience #LLM #Wikipedia #Mondo #NCBIGene #NCBITaxonomy |🧬🖥️🧪🔓 ⬇️ academic.oup.com/database/art...academic.oup.comMedHopQA: a disease-centred multi-hop reasoning benchmark and evaluation framework for LLM-based biomedical question answeringAbstract. Evaluating large language models (LLMs) in the biomedical domain requires benchmarks that can distinguish genuine reasoning from pattern matching 022
Reposted by BF Francis OuelletteISCB News @iscb.bsky.social · 16/09/2026🧬💻 Join the free Brandeis Online virtual panel for a conversation on the evolution of bioinformatics and biotechnology: "State of the Industry: Innovation, Impact, and What Comes Next" 📅Tuesday, September 22 at 12:00 PM EDT 🔗Register to join: tinyurl.com/yc5z5e8r 121
BF Francis Ouellette @bffo.bsky.social · 16/09/2026From #OUP 's #DATABASE journal | An integrated culturomic and genomic database and analysis platform for methanogenic archaea | #Bioinformatics #Genomics #OpenScience #Archea #MethArDB #MethArCT | 🧬🖥️🧪🔓 ⬇️ academic.oup.com/database/art...academic.oup.comAn integrated culturomic and genomic database and analysis platform for methanogenic archaeaAbstract. Methanogenic archaea research is challenged by limited strain resources, fragmented genomic data, inconsistent genome quality, substantial uncult 021
BF Francis Ouellette @bffo.bsky.social · 16/09/2026From @plos.org #Computational #Biology | Ten quick tips for spatial transcriptomics analysis | #Bioinformatics #Education #PLOSCBQT #Histology #Genomics #Transcriptomics #OpenScience | 🧬🖥️🧪🔓 ⬇️ journals.plos.org/ploscompbiol...journals.plos.orgTen quick tips for spatial transcriptomics analysisAuthor summary Spatial transcriptomics (ST) lets researchers measure gene expression while preserving the tissue location of each measurement. Where a cell sits, and which cells surround it, shape how... 094
BF Francis Ouellette @bffo.bsky.social · 12/09/2026From @narjournal.bsky.social #NARDatabaseIssue | KinaseDB: an integrated multi-omics platform for the human kinome with disease-specific target prioritization | #Bioinformatics #Database #OpenScience | 🧬🖥️🧪🔓 ⬇️ doi.org/10.1093/nar/...doi.orgKinaseDB: an integrated multi-omics platform for the human kinome with disease-specific target prioritizationAbstract. Protein kinases govern cellular signalling and disease progression and represent major therapeutic targets, yet comprehensive characterization ac 031
Reposted by BF Francis OuelletteGalaxy Project @galaxyproject.bsky.social · 09/09/2026The latest Galaxy newsletter is here! 📰✨ Catch up on Galaxy 26.1, Galaxy Labs, UseGalaxy Canada, research and training highlights, community news, jobs, and upcoming events across the Galaxy ecosystem. galaxyproject.org/news/2026-09... #usegalaxy #GalaxyProjectgalaxyproject.orgGalaxy Newsletter September 2026Explore Galaxy 26.1 and Galaxy Labs, welcome UseGalaxy Canada, see how Galaxy Australia is simplifying data movement, discover Galaxy-powered wildlife ecology and public-health workflows, and find job... 043
BF Francis Ouellette @bffo.bsky.social · 11/09/2026From @plos.org #Computational #Biology | Eight quick tips for requesting materials from natural history collections | #Bioinformatics #Education #PLOSCBQT #OpenScience #NHCs #Biodiversity | 🧬🖥️🧪🔓 ⬇️ journals.plos.org/ploscompbiol...journals.plos.orgEight quick tips for requesting materials from natural history collections 040
Reposted by BF Francis OuelletteDr. Leonid Kostrykin @kostrykin.bsky.social · 09/09/2026Our article about Galaxy as a workbench for bioimage data management & analysis, training & community practices, has been published in the Journal of Microscopy (Wiley). Congratulations to all authors and contributors. Special thanks to @beatrizserrano.bsky.social. CC @denbi.bsky.social #UseGalaxy 053
BF Francis Ouellette @bffo.bsky.social · 09/09/2026From @kostrykin.bsky.social and colleagues in the Journal of #Microscopy | Bioimage management and analysis in Galaxy: Tools, workflows, training, and community practices | #OpenScience #Bioinformatics #UseGalaxy CC/ @galaxyproject.bsky.social | 🧬🖥️🧪🔬🔓 ⬇️ onlinelibrary.wiley.com/doi/10.1111/...onlinelibrary.wiley.comBioimage management and analysis in Galaxy: Tools, workflows, training, and community practicesImage analysis in the life sciences is constrained by fragmented software ecosystems, heterogeneous data formats, and limited reproducibility. These barriers hinder the reuse of image analysis method.... 020
Reposted by BF Francis OuelletteMontréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 09/09/2026Tonight at 5:30 p.m. ET: Jérôme Waldispühl ( @waldispuhl.bsky.social ), from McGill's School of Computer Science, continues the MonBUG evening with "Leveling up (meta)genomics research | #MonBUG #Bioinformatics #Education #MetaGenomics | 🧬🖥️🧪 ⬇️ monbug.ca/en/monbug.caMonBUG 011
Reposted by BF Francis OuelletteMontréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 09/09/2026Ce soir à 17h30: Jérôme Waldispühl ( @waldispuhl.bsky.social ), de l'École d'informatique de McGill, poursuit la soirée MonBUG avec « Levelling up (meta)genomics research » | #MonBUG #Bioinformatics #Education #MetaGenomics | 🧬🖥️🧪 ⬇️ monbug.ca/fr/monbug.caMonBUG 011
Reposted by BF Francis OuelletteMontréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 09/09/2026Tonight at 5:30 p.m. ET: Georgi Merhi ( @georgimerhi.bsky.social ) opens the MonBUG evening with "A genome in the lice-stack: metagenomic recovery of Bartonella quintana." | #MonBUG #Bioinformatics #Education #MetaGenomics | 🧬🖥️🧪 | CC/ @bjesseshapiro.bsky.social ⬇️ monbug.ca/en/monbug.caMonBUG 011
Reposted by BF Francis OuelletteMontréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 09/09/2026Ce soir à 17h30, Georgi Merhi ( @georgimerhi.bsky.social ) ouvre la soirée MonBUG avec « A genome in the lice-stack: metagenomic recovery of Bartonella quintana » | #MonBUG #Bioinformatics #Education #MetaGenomics | 🧬🖥️🧪 | CC/ @bjesseshapiro.bsky.social ⬇️ monbug.ca/fr/monbug.caMonBUG 011
BF Francis Ouellette @bffo.bsky.social · 09/09/2026#NCBI has released ver 237 of #RefSeq, which includes 495,290,394 proteins, 86,067,871 RNAs, and sequences from 184,752 organisms, and many others (see posting, hint in picture !) | #OpenScience #OpenData #Genomics #Proteomics #Bioinformatics | 🧬🖥️🧪🔓 ⬇️ ncbiinsights.ncbi.nlm.nih.gov/2026/09/08/r...ncbiinsights.ncbi.nlm.nih.govNow Available: RefSeq Release 237 - NCBI InsightsRefSeq release 237 is now available online and from the FTP site! You can access RefSeq data through NCBI Datasets. The release is provided in several directories as a complete dataset and also as div... 093
Reposted by BF Francis OuelletteMontréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 08/09/2026Tomorrow, Wednesday, Sept. 9: Jérôme Waldispühl ( @waldispuhl.bsky.social ), from McGill's School of Computer Science, will continue the MonBUG evening with "Leveling up (meta)genomics research." | #MonBUG #Bioinformatics #Education #MetaGenomics | 🧬🖥️🧪 ⬇️ monbug.ca/en/monbug.caMonBUG 021
Reposted by BF Francis OuelletteMontréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 08/09/2026Demain, mercredi 9 septembre: Jérôme Waldispühl ( @waldispuhl.bsky.social ), de l'École d'informatique de McGill, poursuivra la soirée MonBUG avec « Levelling up (meta)genomics research » | #MonBUG #Bioinformatics #Education #MetaGenomics | 🧬🖥️🧪 ⬇️ monbug.ca/fr/monbug.caMonBUG 011