@chromozz.bsky.social
Spread the word !
LLMs "mistakes" are features, NOT bugs.
LLMs "mistakes" are features, NOT bugs.
It seems this can't be emphasized enough. Chatbots and LLMs do not make mistakes (excepting any bugs in the code). They do not lie. They do not blackmail or cheat. They follow statistics. When the people who build these systems don't tell you this, they are either deluded or trying to mislead.
When a chatbot gets something wrong, it’s not because it made an error. It’s because on that roll of the dice, it happened to string together a group of words that, when read by a human, represents something false. But it was working entirely as designed. It was supposed to make a sentence & it did.
November 6, 2025 at 12:11 PM
Spread the word !
LLMs "mistakes" are features, NOT bugs.
LLMs "mistakes" are features, NOT bugs.
Reposted
A thoughtful and beautifully written @quantamagazine.bsky.social article about genome regulatory innovation at the origin of animals. Featuring some of our work and highlighting key open questions. Thanks to @philipcball.bsky.social for this fantastic piece.
I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...
www.quantamagazine.org/loops-of-dna...
Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine
New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.
www.quantamagazine.org
October 8, 2025 at 7:04 PM
A thoughtful and beautifully written @quantamagazine.bsky.social article about genome regulatory innovation at the origin of animals. Featuring some of our work and highlighting key open questions. Thanks to @philipcball.bsky.social for this fantastic piece.
Reposted
New paper!
We generated and/or (re)analyzed ~100 #metagenomics Hi-C datasets to provide a comprehensive analysis of bacterial and viral metagenomes across VERY different environments.
Congratulations to all authors especially Amaury Bignaud and @mmarbout.bsky.social for the huge work!
#metaHiC
We generated and/or (re)analyzed ~100 #metagenomics Hi-C datasets to provide a comprehensive analysis of bacterial and viral metagenomes across VERY different environments.
Congratulations to all authors especially Amaury Bignaud and @mmarbout.bsky.social for the huge work!
#metaHiC
You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
Phages with a broad host range are common across ecosystems - Nature Microbiology
Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.
www.nature.com
September 19, 2025 at 12:49 PM
New paper!
We generated and/or (re)analyzed ~100 #metagenomics Hi-C datasets to provide a comprehensive analysis of bacterial and viral metagenomes across VERY different environments.
Congratulations to all authors especially Amaury Bignaud and @mmarbout.bsky.social for the huge work!
#metaHiC
We generated and/or (re)analyzed ~100 #metagenomics Hi-C datasets to provide a comprehensive analysis of bacterial and viral metagenomes across VERY different environments.
Congratulations to all authors especially Amaury Bignaud and @mmarbout.bsky.social for the huge work!
#metaHiC
Reposted
www.cell.com/cell/abstrac...
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
A host organelle integrates stolen chloroplasts for animal photosynthesis
Sea slugs steal foreign chloroplasts and store them in specialized organelles that
facilitate photosynthesis and eventual digestion to mediate starvation resistance.
www.cell.com
September 17, 2025 at 5:04 PM
www.cell.com/cell/abstrac...
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
Reposted
"Transposable elements are vectors of recurrent transgenerational epigenetic inheritance"
Congrats Vincent Colot and team!
www.science.org/doi/10.1126/...
Congrats Vincent Colot and team!
www.science.org/doi/10.1126/...
Transposable elements are vectors of recurrent transgenerational epigenetic inheritance
DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...
www.science.org
September 18, 2025 at 8:27 PM
"Transposable elements are vectors of recurrent transgenerational epigenetic inheritance"
Congrats Vincent Colot and team!
www.science.org/doi/10.1126/...
Congrats Vincent Colot and team!
www.science.org/doi/10.1126/...
Reposted
In the early days of quantum chemistry, before we had computers to calculate the shapes of electron orbitals, one man invented a mechanical machine that simulated their shapes. My latest column for @chemistryworld.com
www.chemistryworld.com/opinion/the-...
www.chemistryworld.com/opinion/the-...
The simple machine that visualised atomic orbitals
In 1931, Harvey Elliott White developed a device that traced out the shapes of electron clouds by approximating solutions to the Schrödinger equation
www.chemistryworld.com
September 18, 2025 at 9:37 AM
In the early days of quantum chemistry, before we had computers to calculate the shapes of electron orbitals, one man invented a mechanical machine that simulated their shapes. My latest column for @chemistryworld.com
www.chemistryworld.com/opinion/the-...
www.chemistryworld.com/opinion/the-...
Reposted
Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9
September 11, 2025 at 7:55 PM
Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9
Reposted
Our paper is now out in Molecular Cell!
Check the thread in this former post:
www.cell.com/molecular-ce...
Check the thread in this former post:
www.cell.com/molecular-ce...
July 17, 2025 at 5:41 PM
Our paper is now out in Molecular Cell!
Check the thread in this former post:
www.cell.com/molecular-ce...
Check the thread in this former post:
www.cell.com/molecular-ce...
In @elife.bsky.social: Criticality-driven enhancer-promoter dynamics in Drosophila chromosomes doi.org/10.7554/eLif...
Criticality-driven enhancer-promoter dynamics in Drosophila chromosomes
doi.org
September 9, 2025 at 9:47 AM
In @elife.bsky.social: Criticality-driven enhancer-promoter dynamics in Drosophila chromosomes doi.org/10.7554/eLif...
Reposted
No new genes needed to fly - just rewire what you have! 🦇🧬
Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social
doi.org/10.1038/s415...
#EvoDevo #SingleCell #BatWings
Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social
doi.org/10.1038/s415...
#EvoDevo #SingleCell #BatWings
July 16, 2025 at 1:49 PM
No new genes needed to fly - just rewire what you have! 🦇🧬
Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social
doi.org/10.1038/s415...
#EvoDevo #SingleCell #BatWings
Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social
doi.org/10.1038/s415...
#EvoDevo #SingleCell #BatWings
Highly needed !
SOOOO MANY GENOMICS MODELSSSS! 😱 Often unclear which is best since they benchmark differently! In this preprint, we introduce GAME, a new framework that utilizes APIs to enable sustainable, uniform model evaluation so we can see which is actually best for each task. doi.org/10.1101/2025...
July 16, 2025 at 1:17 PM
Highly needed !
Reposted
Today marks the end of en-JUNE-eering, the month where I focused mostly on the nitty gritty of improving genomics ML infrastructure.
Here are some of the highlights:
Here are some of the highlights:
June 30, 2025 at 6:34 PM
Today marks the end of en-JUNE-eering, the month where I focused mostly on the nitty gritty of improving genomics ML infrastructure.
Here are some of the highlights:
Here are some of the highlights:
Reposted
📢 New paper out in Mol Syst Biol!
During the development of WT yeast colonies, small cell subpopulations experience transient, high-intensity mutational bursts. Such hypermutation episodes are modulated by the DNA damage tolerance pathway 🧬
🔗 www.embopress.org/doi/full/10....
During the development of WT yeast colonies, small cell subpopulations experience transient, high-intensity mutational bursts. Such hypermutation episodes are modulated by the DNA damage tolerance pathway 🧬
🔗 www.embopress.org/doi/full/10....
June 9, 2025 at 1:02 PM
📢 New paper out in Mol Syst Biol!
During the development of WT yeast colonies, small cell subpopulations experience transient, high-intensity mutational bursts. Such hypermutation episodes are modulated by the DNA damage tolerance pathway 🧬
🔗 www.embopress.org/doi/full/10....
During the development of WT yeast colonies, small cell subpopulations experience transient, high-intensity mutational bursts. Such hypermutation episodes are modulated by the DNA damage tolerance pathway 🧬
🔗 www.embopress.org/doi/full/10....
Reposted
tree of life core lab has put together such a manuscript, detailing a lot of information on the lab work needed for reference genomes for biodiversity which you can find here: www.biorxiv.org/content/10.1...
On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species
Since its inception in 2019, the Tree of Life programme at the Wellcome Sanger Institute has released high-quality, chromosomally-resolved reference genome assemblies for over 2000 species. Tree of Li...
www.biorxiv.org
June 4, 2025 at 3:15 PM
tree of life core lab has put together such a manuscript, detailing a lot of information on the lab work needed for reference genomes for biodiversity which you can find here: www.biorxiv.org/content/10.1...
Reposted
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Conservation of regulatory elements with highly diverged sequences across large evolutionary distances
Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...
rdcu.be
May 27, 2025 at 12:19 PM
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Reposted
Hi everyone!
The latest method from the Whitehouse lab: PCP
PCP uses a novel proximity barcoding strategy to simultaneously map 3D genome organization at various resolutions at the single molecule level:
Out soon, check the updated BioRxiv – little thread:
1/11
www.biorxiv.org/content/10.1...
The latest method from the Whitehouse lab: PCP
PCP uses a novel proximity barcoding strategy to simultaneously map 3D genome organization at various resolutions at the single molecule level:
Out soon, check the updated BioRxiv – little thread:
1/11
www.biorxiv.org/content/10.1...
May 30, 2025 at 7:55 PM
Hi everyone!
The latest method from the Whitehouse lab: PCP
PCP uses a novel proximity barcoding strategy to simultaneously map 3D genome organization at various resolutions at the single molecule level:
Out soon, check the updated BioRxiv – little thread:
1/11
www.biorxiv.org/content/10.1...
The latest method from the Whitehouse lab: PCP
PCP uses a novel proximity barcoding strategy to simultaneously map 3D genome organization at various resolutions at the single molecule level:
Out soon, check the updated BioRxiv – little thread:
1/11
www.biorxiv.org/content/10.1...
Reposted
🚨 We're hiring! 🚨
A 2-year postdoc position is now open in our lab to explore the fascinating world of yeast polyploid genomes, their structure, stability, and adaptive potential.
🔗 More info here:
docs.google.com/document/d/1...
Please repost!
#Postdoc #Genomics #Yeast #Polyploidy #Evolution
A 2-year postdoc position is now open in our lab to explore the fascinating world of yeast polyploid genomes, their structure, stability, and adaptive potential.
🔗 More info here:
docs.google.com/document/d/1...
Please repost!
#Postdoc #Genomics #Yeast #Polyploidy #Evolution
Postdoc_Evol_Genomics_Sorbonne.docx
Postdoctoral position in Yeast Evolutionary Genomics Hosting unit Laboratory of Computational, Quantitative, and Synthetic Biology (CQSB). The CQSB is an interdisciplinary research unit within the ...
docs.google.com
May 19, 2025 at 3:41 PM
🚨 We're hiring! 🚨
A 2-year postdoc position is now open in our lab to explore the fascinating world of yeast polyploid genomes, their structure, stability, and adaptive potential.
🔗 More info here:
docs.google.com/document/d/1...
Please repost!
#Postdoc #Genomics #Yeast #Polyploidy #Evolution
A 2-year postdoc position is now open in our lab to explore the fascinating world of yeast polyploid genomes, their structure, stability, and adaptive potential.
🔗 More info here:
docs.google.com/document/d/1...
Please repost!
#Postdoc #Genomics #Yeast #Polyploidy #Evolution
Reposted
Interested in chromatin architecture?
Checkout our new method - PCP - that can map genome organization as multi-way interactions as well as nucleosome footprint and nucleosome spacing at very high resolution.
www.biorxiv.org/content/10.1...
Checkout our new method - PCP - that can map genome organization as multi-way interactions as well as nucleosome footprint and nucleosome spacing at very high resolution.
www.biorxiv.org/content/10.1...
Chromatin architecture mapping by multiplex proximity tagging
Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a novel proximity-tagging method which assigns unique DNA b...
www.biorxiv.org
November 13, 2024 at 1:09 PM
Interested in chromatin architecture?
Checkout our new method - PCP - that can map genome organization as multi-way interactions as well as nucleosome footprint and nucleosome spacing at very high resolution.
www.biorxiv.org/content/10.1...
Checkout our new method - PCP - that can map genome organization as multi-way interactions as well as nucleosome footprint and nucleosome spacing at very high resolution.
www.biorxiv.org/content/10.1...
Great opportunity to work at the frontier between genomics and deep learning.
research.pasteur.fr/en/job/perma...
research.pasteur.fr/en/job/perma...
Group Head in AI and Mathematical Modeling Applied to Genomics - Research
The Bioinformatics and Biostatistics Hub at Institut Pasteur provides computational biology support to research units and platforms at the Institut Pasteur. Our mission is to: As the head of the Algor...
research.pasteur.fr
May 2, 2025 at 11:21 AM
Great opportunity to work at the frontier between genomics and deep learning.
research.pasteur.fr/en/job/perma...
research.pasteur.fr/en/job/perma...
Reposted
Last call: Tomorrow friday April 11th 🤘
April 10, 2025 at 11:14 AM
Last call: Tomorrow friday April 11th 🤘
Reposted
@sorbonne-universite.fr et @mnhn.fr organise cet échange entres spécialistes sur les applications actuelles, les perspectives d’avenir et les verrous méthodologiques liés à l’adoption de l’IA dans l’étude et la conservation de la biodiversité. Gratuit, sur inscription
L'IA pour comprendre et préserver la biodiversité
Dans le cadre du Sommet pour l'action sur l’IA 2025, du lancement de PostGenAI@Paris, et de l’initiative « IA responsable », SCAI propose un cycle de conférences sur les enjeux et les risques liés à l...
www.sorbonne-universite.fr
April 10, 2025 at 7:11 AM
@sorbonne-universite.fr et @mnhn.fr organise cet échange entres spécialistes sur les applications actuelles, les perspectives d’avenir et les verrous méthodologiques liés à l’adoption de l’IA dans l’étude et la conservation de la biodiversité. Gratuit, sur inscription
Reposted
The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...
April 2, 2025 at 8:47 AM
The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...
Reposted
The latest live-cell imaging work from the Boettiger lab measures chromosomal kinetics across genomic scales — it’s moving faster than you think! —, and puts a number on the ‘in vivo’ speed of cohesin loop extrusion itself.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
April 3, 2025 at 2:03 AM
The latest live-cell imaging work from the Boettiger lab measures chromosomal kinetics across genomic scales — it’s moving faster than you think! —, and puts a number on the ‘in vivo’ speed of cohesin loop extrusion itself.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Miloshev et al., 2025, Linker Histones Maintain Genome Stability and Drive the Process of Cellular Ageing [review] www.imrpress.com/journal/FBL/...
Interesting figure: we did observe NRL increase with ageing (onlinelibrary.wiley.com/doi/10.1111/...). Not sure about about loop sizes, to be checked
Interesting figure: we did observe NRL increase with ageing (onlinelibrary.wiley.com/doi/10.1111/...). Not sure about about loop sizes, to be checked
April 1, 2025 at 10:08 AM
Miloshev et al., 2025, Linker Histones Maintain Genome Stability and Drive the Process of Cellular Ageing [review] www.imrpress.com/journal/FBL/...
Interesting figure: we did observe NRL increase with ageing (onlinelibrary.wiley.com/doi/10.1111/...). Not sure about about loop sizes, to be checked
Interesting figure: we did observe NRL increase with ageing (onlinelibrary.wiley.com/doi/10.1111/...). Not sure about about loop sizes, to be checked
Reposted
Come start your lab in beautiful Strasbourg 🇫🇷 www.nature.com/naturecareer...
Call For Two Group Leader Positions - Strasbourg-Ville, Bas-Rhin (FR) job with IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) | 12837602
The Institute of Genetics, Molecular and Cellular Biology (IGBMC) is seeking two outstanding group leaders to establish independent research teams.
www.nature.com
March 22, 2025 at 1:50 PM
Come start your lab in beautiful Strasbourg 🇫🇷 www.nature.com/naturecareer...