Lightnews — Scholar-powered news

Reposted by BF Francis Ouellette

Scott C Edmunds @scedmunds.bsky.social · 7d

Thank you OBF (and especially Taz) for this lovely post about the GigaScience team. I've been going to your #BOSC meetings since 2011 and will miss catching up with you all each summer, but hopefully it's not goodbye!

Open Bioinformatics Foundation @openbio.bsky.social · 8d

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

2 7

BF Francis Ouellette @bffo.bsky.social · 7d

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

2 4

BF Francis Ouellette @bffo.bsky.social · 7d

Thank you @openbio.bsky.social for summarizing a great (but too short) #OpenScience #OpenAccess story … All of us lost a great team of friends and colleagues in this sad story.

4

Reposted by BF Francis Ouellette

Open Bioinformatics Foundation @openbio.bsky.social · 8d

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

1 12 8

Reposted by BF Francis Ouellette

maniagnosis @maniagnosis.bsky.social · 9d

These are all valuable suggestions for handling the (sudden) end of a project.

Keep in mind that code which is not actively being used and maintained is dead and will quickly become useless.

Also few projects will be adopted by an active open source community.

BF Francis Ouellette @bffo.bsky.social · 9d

From @richlitt.bsky.social and colleagues in @arxiv-cs-cl.bsky.social | 10 quick tips for making your software outlive your job | 🧪 🔓 #ProfessionalDevelopment #Education #OpenSource #OpenScience
⬇️
arxiv.org/abs/2505.06484

10 quick tips for making your software outlive your job

Loss of key personnel has always been a risk for research software projects. Key members of the team may have to step away due to illness or burnout, to care for a family member, from a loss of financ...

arxiv.org

1 3

BF Francis Ouellette @bffo.bsky.social · 9d

If this had been in PLOS CB, it would have been a Ten Simple Rules (TSR) paper, not a Quick Tips (QT) paper. As we write in our TSR about writing a QT paper (in Rule 1): "Ten Simple Rules are more to develop soft skills, career promotion/advancement ..." 🧪🔓
⬇️
journals.plos.org/ploscompbiol...

Ten simple rules for writing a PLOS Computational Biology quick tips article

journals.plos.org

1

BF Francis Ouellette @bffo.bsky.social · 9d

From @richlitt.bsky.social and colleagues in @arxiv-cs-cl.bsky.social | 10 quick tips for making your software outlive your job | 🧪 🔓 #ProfessionalDevelopment #Education #OpenSource #OpenScience
⬇️
arxiv.org/abs/2505.06484

10 quick tips for making your software outlive your job

Loss of key personnel has always been a risk for research software projects. Key members of the team may have to step away due to illness or burnout, to care for a family member, from a loss of financ...

arxiv.org

1 1 6

Reposted by BF Francis Ouellette

Genetics Society of America @genetics-gsa.bsky.social · 12d

📢 NEW GENOME ALERT

In #G3journal, Frandsen et al. present a chromosome-scale assembly of the tetraploid epazote, a perennial plant growing in tropical climates in the Americas with regional culinary and medicinal importance. buff.ly/Vbp0rde

4 4

Reposted by BF Francis Ouellette

Bioinformatics Advances @bioinfoadv.bsky.social · 12d

🧰 Now published in Bioinformatics Advances: "Atlantool: A command line tool to retrieve DNA and RNA sequencing reads from BAM files by the read identifier"

Read the full paper here: https://doi.org/10.1093/bioadv/vbaf226

Authors include: @nibor.org, @egiannoulatou.bsky.social

1 2 4

BF Francis Ouellette @bffo.bsky.social · 12d

From @borja-pitarch.bsky.social and colleagues in #OUP 's #DATABASE journal | A review on #GeneOntology evaluations | #Bioinformatics #Genomics #Review #OpenScience #GO 🧬 🖥️ 🧪 🔓🇪🇸
⬇️
academic.oup.com/database/art...

A review on Gene Ontology evaluations

Abstract. The analysis of the large and heterogeneous datasets that characterize modern biology demands systems capable of representing biological knowledg

academic.oup.com

1 9

BF Francis Ouellette @bffo.bsky.social · 12d

From @cellpress.bsky.social #Genomics | Galaxy #single-cell & spatial omics community update: Navigating new frontiers in 2025 | #Bioinformatics #Genomics #OpenScience #OpenSource #Perspective #UseGalaxy 🧬 🖥️ 🧪 🔓
⬇️
www.cell.com/cell-genomic...

Galaxy single-cell & spatial omics community update: Navigating new frontiers in 2025

The Galaxy single-cell and spatial omics community (SPOC) brings together over 175 tools, 120+ training resources, and a global user community in a unified FAIR platform. By integrating leading suites...

www.cell.com

2 8

Reposted by BF Francis Ouellette

Scott C Edmunds @scedmunds.bsky.social · 14d

Only just noticed @crossref.bsky.social posted their interview with me talking about winning one of the inaugural Crossref Metadata awards was finally published on my last day of work. It's always good to end on a high!

www.crossref.org/blog/raising...

Raising the standard: GigaScience Press on metadata and discoverability - Crossref

To mark Crossref’s 25th anniversary, we launched our first Metadata Awards to highlight members with the best metadata practices. GigaScience Press, based in Hong Kong, was the leader among small publ...

www.crossref.org

2 6

Reposted by BF Francis Ouellette

John M. Drake @jdrakephd.bsky.social · 14d

Newly expanded version of my guide to scientific writing -- known as the “15 steps” -- published in PLOS Computational Biology. Special thanks to Éric Marty for creating a fantastic visualization.

Check it out: journals.plos.org/ploscompbiol...

#ScientificWriting #PLOSComputationalBiology

1 21 36

BF Francis Ouellette @bffo.bsky.social · 13d

From @jdrakephd.bsky.social & @bahanbug.bsky.social in @plos.org #Computational #Biology | How to write a scientific paper in fifteen steps | #Education #Science 🧪 🔓 #GoodReadingForAll CC/ @ppalagi.bsky.social
⬇️
journals.plos.org/ploscompbiol...

How to write a scientific paper in fifteen steps

journals.plos.org

6 9

Reposted by BF Francis Ouellette

Hilda Bastian @hildabast.bsky.social · 17d

Want to be able to start micro-editing on Wikipedia in a few minutes – and know why you could be very glad you did? Then my new post @plos.org is just what you need!

absolutelymaybe.plos.org/2025/09/21/w...

#Wikipedia

Wikipedia Is Vital: Channeling Energy Into Micro-Edits Is a Win-Win-Win - Absolutely Maybe

Wikipedia is, “without exaggeration, the digital world’s factual foundation,” wrote Josh Dzieza recently. It’s a target because of that, squarely in the…

absolutelymaybe.plos.org

1 35 61

Reposted by BF Francis Ouellette

Yeshes.Online 📎🌻🖖♾️ @yeshes.online · 14d

Important for #autistic people and other marginalized groups who are being targeted using health systems databases (particularly those on medicaid and medicare in the U.S.).

There is an ethical responsibility to stop targeting and de-identifying data is one of the best ways to help all of us.

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

From @plos.org #Computational #Biology | Ten quick tips for protecting health data using de-identification and perturbation of structured datasets | #Bioinformatics #Education #PLOSCBQT #OpenScience #DataScience 🧬 🖥️ 🧪 🔓 🇿🇦 CC/ @ppalagi.bsky.social
⬇️
journals.plos.org/ploscompbiol...

Ten quick tips for protecting health data using de-identification and perturbation of structured datasets

Author summary Healthcare systems and health research programmes collect large amounts of patient data that are often shared both within organisations and across institutional boundaries. Health data ...

journals.plos.org

1 4

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

From @plos.org #Computational #Biology | Ten quick tips for protecting health data using de-identification and perturbation of structured datasets | #Bioinformatics #Education #PLOSCBQT #OpenScience #DataScience 🧬 🖥️ 🧪 🔓 🇿🇦 CC/ @ppalagi.bsky.social
⬇️
journals.plos.org/ploscompbiol...

Ten quick tips for protecting health data using de-identification and perturbation of structured datasets

Author summary Healthcare systems and health research programmes collect large amounts of patient data that are often shared both within organisations and across institutional boundaries. Health data ...

journals.plos.org

2 7

BF Francis Ouellette @bffo.bsky.social · 15d

From @plos.org #Computational #Biology | Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings | #Africa #HPC #PLOSCBTSR 🖥️ 🧪 🔓
⬇️
journals.plos.org/ploscompbiol...

Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings

journals.plos.org

4 4

BF Francis Ouellette @bffo.bsky.social · 17d

9 more days … #Africa #Bioinformatics #Health #Informatics #Education

African Bioinformatics Institute @abinstitute.bsky.social · 28d

Opportunity alert 🚨 for an MSc in Computational health Informatics at the University of Cape Town . A limited number of fully funded scholarships are available! All nationalities are eligible to apply! 📆Deadline: 30 September 2025

ℹ️More information below ⬇️

3 2

Reposted by BF Francis Ouellette

African Bioinformatics Institute @abinstitute.bsky.social · 27d

“From Data to Discovery: Opportunities with the African Bioinformatics Institute” delivered at the recent Data for Health in Africa Meeting & 5th DS-I Africa Consortium Meeting in Accra, Ghana. Explore ABI’s vision as well current and future activities: www.linkedin.com/pulse/showca...

1 2

Reposted by BF Francis Ouellette

Anna Panchenko @panchenko-lab.bsky.social · 20d

How do histone mutations contribute to cancer development?
Our new study reveals that these mutations impact critical sites where histones interact with DNA or proteins, in some cases disrupting genome maintenance.
academic.oup.com/nar/article/...

Cancer histone mutations impact protein binding and DNA repair with possible links to genomic instability

Abstract. Histones are key epigenetic factors that regulate the accessibility and compaction of eukaryotic genomes, affecting DNA replication and repair, a

academic.oup.com

1 2

BF Francis Ouellette @bffo.bsky.social · 19d

From #NAR journal | #Cancer #histone mutations impact protein binding and DNA repair with possible links to genomic instability | From my friend @davidlandsman.bsky.social & former colleague @panchenko-lab.bsky.social | #Bioinformatics #Genomics 🧬 🖥️ 🧪 🔓 🇨🇦
⬇️
academic.oup.com/nar/article/...

Validate User

academic.oup.com

1 2

BF Francis Ouellette @bffo.bsky.social · 27d

Not sure if this (these?) positions are filled yet, but as an ex-MSL tenured PI, and a fan of Micro, I can only highly recommend this position and department… Great city, great University, great campus, greatest students and great colleagues! Go for it!

Reposted by BF Francis Ouellette

UBC Microbiology and Immunology @ubcmicroimmuno.bsky.social · Jul 22

Microbiology and Immunology and the Michael Smith Labs are seeking candidates for an Assistant Professor of Teaching in STEM Public Engagement position.

Learn more and apply at: www.msl.ubc.ca/careers/

#IndigenousinSTEM #BlackInNature #WomenInSTEM #MinoritiesInSTEM #DiversityInSTEM #STEMEducation

2 24 17

Reposted by BF Francis Ouellette

Dimitri Drekonja, MD, MS @dimitridrekonja.bsky.social · 27d

Ezra Klein thinks that “black people are stupid” and “gay people should be stoned to death” is practicing politics the “right way”

Can we stop pretending he is some political sage?

1 31 560