Baptiste Roelens (He/him)

The recombination frequency (cM/Mb) along chromosome 4 of A. thaliana (female meiosis). In full hybrids (grey), where polymorphism is distributed all along chromosomes, most crossovers occur in the regions surrounding the Centromere (Cen), and very few at chromosome ends (Tel: telomeres). In lines where polymorphism is restricted to chromosome ends (purple), the local recombination rate increases drastically, at the expense of the non-polymorphic regions (yellow).

🚨 First pre-print from my team !!

TL;DR: presence of polymorphism (sequence differences between the homologous chromosomes) can *increase* the local rate of recombination in Arabidopsis thaliana, turning cold regions of the genome hot (purple v. grey) !

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!

github.com/martinpacesa...

An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility Abstract. Retrotransposons, multi-copy sequences that propagate via copy-and-paste mechanisms, occupy large portions of eukaryotic genomes. A great majorit

Happy that our preprint from early this year, uncovering the regulation a somatically "hot" endogenous retroelement locus, has now found its home in @narjournal.bsky.social.
"TEsky"
doi.org/10.1093/nar/...

Bactéries miroir : la nouvelle menace mondiale ? Un collectif de 38 scientifiques s’est inquiété dans la revue Science de la possibilité de voir apparaître des bactéries miroir, qui pourraient perturber les écosystèmes et la santé publique si elles ...

J'étais hier sur France Inter, avec Hervé Chneiweiss pour discuter vie Miroir dans la Terre au carré. Replay ici: www.radiofrance.fr/franceinter/...

I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!

The current administration’s narrative that Harvard (and all universities) feel “entitled” to federal dollars misleads the public. Nor are these funds a “privilege” 1/n

🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸‍♀️. Try it now on 🤗 huggingface.co/spaces/mouse...

paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n

BiaPy: accessible deep learning on bioimages - Nature Methods Nature Methods - BiaPy: accessible deep learning on bioimages

🚀 Excited to share that our work on BiaPy has been published today in Nature Methods!
BiaPy makes deep learning accessible for bioimage analysis, from small datasets to terabyte-scale 3D images. 👇 (1/7)
🔗 www.nature.com/articles/s41...
#DeepLearning #BioimageAnalysis #OpenSource #BiaPy

Fellow ladies in science, as part of the disappearing species of international female scientists in France and perhaps every/elsewhere, I want to bring your special attention to our institute's open call for group leaders 👩‍🔬🦠🧪🔬🤓!!! Come join me in doing some coolicious science here 🙏!

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...

Une partie importante des sommes bloquées correspond à du financement fédéral de la recherche, vu la quantité de chercheurs travaillant à Harvard et ses structures associées comme l’hôpital universitaire, ça n’est pas énorme.

The Coming Out of a Transgender Scientist "I know that I am making the right decision because whenever I think about changing my gender role, I am flooded with feelings of relief."

We're disappointed to see Ben Barres's powerful book "The Autobiography of a Transgender Scientist" among the ~400 titles removed from the Naval Academy Library. Needless to say, we're proud to have published his book and will keep it — and his memory — alive.

Bioimaging and bioimage analysis friends, some help if you have 2-3 mins; for a paper, we're trying to estimate the number of biologists trained in open source software or tools in the last ~5 years. (1/2) #bioimaging #microscopy #bioimageanalysis

Messages anonymes! Messages anonymes!

Vous ne voulez pas d’OGM dans votre assiette

Pouvez vous svp m’expliquer pourquoi ?

Pour répondre c’est anonyme donc pas de censure

Reposts appréciés

ngl.link/yannduroc1

!! Postdoc position available to study homologous recombination in live cells through advanced microscopy analyses in a collaboration between our lab and Angela Taddei's lab, both at @institutcurie.bsky.social in Paris.
Apply to : job-ref-ib8q3lnnxn@emploi.beetween.com

If, hypothetically, a person were trying to set up a career panel series for bioimage analysis, what kinds of roles (or specific people) would you want to hear more about? Hypothetical nominations of all stripes welcome :) #bioimageanalysis

New German, Swiss, And Austrian Guidelines Recommend Trans Youth Care, Slam Cass Review The recommendations, released by the Association of the Scientific Medical Societies in Germany, come at a time when US politicians erroneously claim that Europe is "pulling back" on transgender care.

1. Major news in transgender care.

Germany, Switzerland, and Austria have just released their trans youth care guidelines.

They strongly recommend trans youth care and slam the
Cass Review in England.

Europe is not "pulling back" on trans care.

Subscribe to support our journalism.

Nipah virus G protein with 16813 ligands (mostly waters) mapped from similar structures.

ChimeraX can run Foldseek to find similar structures, such as distantly related homologs, and analyze the results, for example, mapping all ligands onto your query structure. Here are ligands mapped onto Nipah virus G protein. www.rbvi.ucsf.edu/chimerax/dat...

There have been people less than helpful in my journey here. I wanted to acknowledge those too, bc I know I am not unique in this experience. No thank you to the physics study assoc that made me sing songs about how women couldn't study physics without sleeping with the professor, the day I stepped into university life. No thank you to the 5th year physics student that decided to assign me a stripper name within the first minute of meeting me in the physics coffee corner in my first year. No thank you to the technician that was responsible for onboarding me on the use of the cluster in my third year who raised his eyebrows and asked me if that meant I was some sort of computer girl. No thank you to the senior researcher that sent me utterly inappropriate texts after a conference, then proceeded to apologise months later by telling me they had not been meant for me anyway so no hard feelings remain hopefully And no thank you to him for attending every conference I've been to since. No thank you to the people who told me that it was surprising that I was doing a PhD since I was a girl. No thank you to the man who mistook me for a coffee lady at a conference, and after having to correct him two times that I did not work there, responded with you should consider it. No thank you to the researcher that asked me what I was wearing underneath my outfit during a conference. No thank you to the physicist who declared to a room full of other physicists that biologists don't know how to design an experiment. No thank you to the people who have called me scary instead of strong and intimidating instead of intelligent. And finally, no thank you to the exec board of the TU Delft, whose knee-jerk reaction to being held up a mirror about the social safety at the university, was to sue the party holding up the mirror instead of looking at the problems they highlighted. ... You have made me feel like I do not belong in science & I cannot forgive you for that.

A friend included this anti-acknowledgement section on her PhD thesis. She also added the proposition: “Systematic bullying and undermining of girls and women in STEM starts early on and is the reason why they do not stay in science and related fields.”
Absurd we still need to go through this
🧪👩‍🔬

Ce qui se passe actuellement aux États-Unis est une preuve de plus que tous les projets de case X ou "troisième catégorie" à l'état civil les personnes non-binaires sont une impasse en terme de droits pour toutes les personnes trans, dont les personnes non-binaires elles-même.

Just wanted to give a shoutout to @marimo.io (cc @akshaykagrawal.bsky.social ). If u have been using Jupyter Notebooks, u should REALLY try Marimo. It is such an upgrade. We have been actively developing on it in the lab (integration with NLP LLMs) as well & are huge fans. Strongly recommend.

If you're interested in studying #ageing using an interesting model as a postdoc and want to relocate in France, think of the following finding scheme and contact me to discuss projects!

rea.ec.europa.eu/funding-and-....

There has been a lot of chatter today about Zelenskyy's meeting with Trump, some regarding this moment when White House correspondent Brian Glenn asked if the Ukrainian president plans to wear a suit. I want to address idea in this thread. 🧵

A screenshot of the code bia-bob generated after being tasked to use Astronomy specific libraries.

A screenshot of the code bia-bob generated after being tasked to write Python code always encapsulating code in functions.

A screenshot of the code bia-bob generated after being tasked to write Python code with Finnish variable names.

A screenshot of the code bia-bob generated after being tasked to write unnecessarily complicated Python code.

#biabob, the AI-based code generator for Jupyter Notebooks, can now be configured to generate code for other scientific domains🔭, coding-styles 🎭 and languages🗣️. Handle with care, as you can also use this to do stupid things. 😉 Feedback welcome🚀
pip install bia-bob==0.26.0
github.com/haesleinhuep...

📣 Un poste permanent d’IE en bioinformatique est ouvert sur la plateforme Migale.
👉 Description du profil sur jobs.inrae.fr/concours/con...
📝 Candidature jusqu’au 20 mars
Contactez-nous !

The Institute for Integrative Biology of the Cell (I2BC) is recruiting new group leaders interested in viruses of prokaryotic or eukaryotic cells. Located in France, near Paris.
Application deadline : March 15th, 2025
www.i2bc.paris-saclay.fr/wp-content/uploads/2025/01/I2BC-Virology-call_2025.pdf

How do cells prioritize molecular machines working on DNA? With which functional consequences? Here bs-less Yasmina Djeghmoum discovered and characterized transcription-recombination priority rules, and their role in promoting genome maintenance. 🧵
www.biorxiv.org/content/10.1...

Elimination of separase inhibition reveals absence of cohesin protection in oocyte metaphase II The meiotic segregation pattern to generate haploid gametes is mediated by step-wise cohesion removal by separase, first from chromosome arms in meiosis I, and then from the centromere region in meios...

Ever wanted to know what happens when separase is out of control during oocyte meiosis? Have a look at Safia's preprint!
www.biorxiv.org/content/10.1...

Cette année, mon cours @collegedefrance.bsky.social traitera de la régulation des gènes par les séquences enhancers. Une des clés de notre développement. Premier cours le vendredi 21 février à 10h. Entrée libre, salle chauffée. Amis et Collègues parisiens, merci de diffuser!

Really sad news, his writings were truly inspiring to me in grad school and I was fascinated by his use of genetics to probe the mechanisms of meiosis.