Sébastien Lemaire
@sbastienlemai16.bsky.social
In Almouzni Lab at Institut Curie, a bioinformatician among H3 histone variants afficionados, exploring their role in shaping chromatin in pediatric brain cancers.
Reposted by Sébastien Lemaire
Nature research paper: Estimation and mapping of the missing heritability of human phenotypes
go.nature.com/3LZQsph
go.nature.com/3LZQsph
Estimation and mapping of the missing heritability of human phenotypes - Nature
WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 complex traits and diseases.
go.nature.com
November 18, 2025 at 6:07 PM
Nature research paper: Estimation and mapping of the missing heritability of human phenotypes
go.nature.com/3LZQsph
go.nature.com/3LZQsph
Reposted by Sébastien Lemaire
Check out this map of megadiverse countries around the world! 🌍
EBP-affiliated groups are actively sequencing in several of these biodiversity hotspots as we move toward 5,000 high-quality reference genomes.
👉 Follow other EBP-affiliated projects — we’re in this together! go.bsky.app/CRvXDF4
EBP-affiliated groups are actively sequencing in several of these biodiversity hotspots as we move toward 5,000 high-quality reference genomes.
👉 Follow other EBP-affiliated projects — we’re in this together! go.bsky.app/CRvXDF4
November 18, 2025 at 10:29 PM
Check out this map of megadiverse countries around the world! 🌍
EBP-affiliated groups are actively sequencing in several of these biodiversity hotspots as we move toward 5,000 high-quality reference genomes.
👉 Follow other EBP-affiliated projects — we’re in this together! go.bsky.app/CRvXDF4
EBP-affiliated groups are actively sequencing in several of these biodiversity hotspots as we move toward 5,000 high-quality reference genomes.
👉 Follow other EBP-affiliated projects — we’re in this together! go.bsky.app/CRvXDF4
Reposted by Sébastien Lemaire
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 19, 2025 at 3:01 AM
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
Reposted by Sébastien Lemaire
Resolution limits attempts to deconvolute spatial transcriptomics & estimate cellular composition. This study presents Cell2Spatial, which maps #scRNAseq data to #SpatialTranscriptomics spots, facilitating precise reconstruction of tissue architecture @plosbiology.org 🧪 plos.io/47MhTvl
November 19, 2025 at 8:55 AM
Resolution limits attempts to deconvolute spatial transcriptomics & estimate cellular composition. This study presents Cell2Spatial, which maps #scRNAseq data to #SpatialTranscriptomics spots, facilitating precise reconstruction of tissue architecture @plosbiology.org 🧪 plos.io/47MhTvl
Reposted by Sébastien Lemaire
Epigenomic and transcriptomic germ-free ageing atlas reveals sterile inflammation as an intrinsic ageing feature https://www.biorxiv.org/content/10.1101/2025.11.19.689100v1
November 19, 2025 at 4:33 PM
Epigenomic and transcriptomic germ-free ageing atlas reveals sterile inflammation as an intrinsic ageing feature https://www.biorxiv.org/content/10.1101/2025.11.19.689100v1
Reposted by Sébastien Lemaire
A Consensus Statement in Nature Reviews Immunology clarifies the existing subset-based nomenclature for T cells. It also proposes an alternative modular nomenclature that is designed to be brief and flexible and to avoid ambiguity and unwanted implications. go.nature.com/3Xzfoqb #immunosky 🧪
November 19, 2025 at 2:17 PM
A Consensus Statement in Nature Reviews Immunology clarifies the existing subset-based nomenclature for T cells. It also proposes an alternative modular nomenclature that is designed to be brief and flexible and to avoid ambiguity and unwanted implications. go.nature.com/3Xzfoqb #immunosky 🧪
Reposted by Sébastien Lemaire
Evo2HiC: a multimodal foundation model for integrative analysis of genome sequence and architecture https://www.biorxiv.org/content/10.1101/2025.11.18.689171v1
November 19, 2025 at 10:47 AM
Evo2HiC: a multimodal foundation model for integrative analysis of genome sequence and architecture https://www.biorxiv.org/content/10.1101/2025.11.18.689171v1
Reposted by Sébastien Lemaire
every company in 2025
November 12, 2025 at 5:59 PM
every company in 2025
Reposted by Sébastien Lemaire
📄 BioContextAI is now slightly updated and published @natbiotech.nature.com
➡️ www.nature.com/articles/s41...
➡️ www.nature.com/articles/s41...
Glad to contribute to this collaborative community platform.
A case study shows MCP servers working together - combining BioContextAI Knowledgebase with our omnipath omnipathdb.org MCP (work in progress) to showcase interoperability. Looking forward to see how the ecosystem evolves!
A case study shows MCP servers working together - combining BioContextAI Knowledgebase with our omnipath omnipathdb.org MCP (work in progress) to showcase interoperability. Looking forward to see how the ecosystem evolves!
Preprint alert 🚨 Do you use chatbots in your work or even build MCP servers and agentic systems yourself?
Or would you like to find a way to use biomedical tools using natural language?
Then check out biocontext.ai, now out on bioRxiv: www.biorxiv.org/content/10.1...
Or would you like to find a way to use biomedical tools using natural language?
Then check out biocontext.ai, now out on bioRxiv: www.biorxiv.org/content/10.1...
November 7, 2025 at 1:57 PM
📄 BioContextAI is now slightly updated and published @natbiotech.nature.com
➡️ www.nature.com/articles/s41...
➡️ www.nature.com/articles/s41...
Reposted by Sébastien Lemaire
(1/N) Thrilled to share that our paper HiPoNet (High dimensional Point cloud Network) to be presented at NeurIPS 2025! HiPoNet treats an entire high-dimensional point cloud as a datapoint! It captures multi-scale geometry and topology of the cloud perform classification and regression tasks.
November 7, 2025 at 2:09 PM
(1/N) Thrilled to share that our paper HiPoNet (High dimensional Point cloud Network) to be presented at NeurIPS 2025! HiPoNet treats an entire high-dimensional point cloud as a datapoint! It captures multi-scale geometry and topology of the cloud perform classification and regression tasks.
Reposted by Sébastien Lemaire
A Perspective in Nature discusses how recent studies integrating multi-omics data with cell atlases across development for brains of humans and model organisms are revealing conserved and divergent patterns of brain development at the molecular and cellular levels. 🧪
The new frontier in understanding human and mammalian brain development - Nature
Recent studies integrating multi-omics data with cell atlases across development for brains of humans and model organisms are revealing conserved and divergent patterns of brain development at the molecular and cellular levels, and linking these to complex behavioural and neuropsychiatric phenotypes.
go.nature.com
November 7, 2025 at 2:38 PM
A Perspective in Nature discusses how recent studies integrating multi-omics data with cell atlases across development for brains of humans and model organisms are revealing conserved and divergent patterns of brain development at the molecular and cellular levels. 🧪
Reposted by Sébastien Lemaire
Congratulations to everyone involved in this fabulous #BICAN collection of papers in Nature creating a cell census of the developing human brain. These give new insights into #brain development, to help advance health and disease research.
More powerful tools for understanding the brain. 🧠🔍
Today, comprehensive, cross-species developing brain cell atlases were released to help advance health and disease research. 🧵
#studyBRAIN #BICAN
Today, comprehensive, cross-species developing brain cell atlases were released to help advance health and disease research. 🧵
#studyBRAIN #BICAN
November 7, 2025 at 5:05 PM
Reposted by Sébastien Lemaire
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Repair of DNA double-strand breaks leaves heritable impairment to genome function
Upon DNA breakage, a genomic locus undergoes alterations in three-dimensional chromatin architecture to facilitate signaling and repair. Although cells possess mechanisms to repair damaged DNA, it is ...
tinyurl.com
November 6, 2025 at 11:05 PM
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Reposted by Sébastien Lemaire
From carbon dioxide to starch—no plants required.
In Science, researchers developed a cell-free method of synthesizing starch from CO2 and hydrogen using a combination of chemical catalysts and a carefully selected set of enzymes.
Learn more: https://scim.ag/4hMvDtA #ScienceMagArchives
In Science, researchers developed a cell-free method of synthesizing starch from CO2 and hydrogen using a combination of chemical catalysts and a carefully selected set of enzymes.
Learn more: https://scim.ag/4hMvDtA #ScienceMagArchives
Cell-free chemoenzymatic starch synthesis from carbon dioxide
A designed chemoenzymatic cascade reaction enables cell-free synthesis of starch from carbon dioxide.
scim.ag
November 7, 2025 at 8:54 PM
From carbon dioxide to starch—no plants required.
In Science, researchers developed a cell-free method of synthesizing starch from CO2 and hydrogen using a combination of chemical catalysts and a carefully selected set of enzymes.
Learn more: https://scim.ag/4hMvDtA #ScienceMagArchives
In Science, researchers developed a cell-free method of synthesizing starch from CO2 and hydrogen using a combination of chemical catalysts and a carefully selected set of enzymes.
Learn more: https://scim.ag/4hMvDtA #ScienceMagArchives
Reposted by Sébastien Lemaire
I’ve spent many years explaining/defending biorxiv’s “no reviews” policy.
The logic was always that opening Word and opining is a far lower barrier than doing actual research, so noise’d be >> signal and we didn’t want to make subjective quality judgements.
LLMs mean it makes even more sense 1/2
The logic was always that opening Word and opining is a far lower barrier than doing actual research, so noise’d be >> signal and we didn’t want to make subjective quality judgements.
LLMs mean it makes even more sense 1/2
arXiv will no longer accept review articles and position papers unless they have been accepted at a journal or a conference and complete successful peer review.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
Attention Authors: Updated Practice for Review Articles and Position Papers in arXiv CS Category – arXiv blog
blog.arxiv.org
November 2, 2025 at 5:33 PM
I’ve spent many years explaining/defending biorxiv’s “no reviews” policy.
The logic was always that opening Word and opining is a far lower barrier than doing actual research, so noise’d be >> signal and we didn’t want to make subjective quality judgements.
LLMs mean it makes even more sense 1/2
The logic was always that opening Word and opining is a far lower barrier than doing actual research, so noise’d be >> signal and we didn’t want to make subjective quality judgements.
LLMs mean it makes even more sense 1/2
Reposted by Sébastien Lemaire
Hybridisation breaks species barriers in long-term coevolution of a cyanobacterial population.
buff.ly/EaJskBA
buff.ly/EaJskBA
November 2, 2025 at 11:28 PM
Hybridisation breaks species barriers in long-term coevolution of a cyanobacterial population.
buff.ly/EaJskBA
buff.ly/EaJskBA
Reposted by Sébastien Lemaire
Oyster: a neural network for modelling genomic sequences that enables exact position-specific k-mer contributions [new]
Models seq func. w/ position-specific k-mer contrib. via toggleable CNN, balancing interp. & accur.
Models seq func. w/ position-specific k-mer contrib. via toggleable CNN, balancing interp. & accur.
November 3, 2025 at 3:31 AM
Oyster: a neural network for modelling genomic sequences that enables exact position-specific k-mer contributions [new]
Models seq func. w/ position-specific k-mer contrib. via toggleable CNN, balancing interp. & accur.
Models seq func. w/ position-specific k-mer contrib. via toggleable CNN, balancing interp. & accur.
Reposted by Sébastien Lemaire
November 3, 2025 at 2:43 AM
Reposted by Sébastien Lemaire
NEW PAPER
Out in Science Advances: We have dissected the physiological role of all macroH2A histone variants. In mice, loss of macroH2A1.1 specifically results in profound metabolic reprogramming and kidney pathology.
DOI: 10.1126/sciadv.adz1242
Thread 1/7
Out in Science Advances: We have dissected the physiological role of all macroH2A histone variants. In mice, loss of macroH2A1.1 specifically results in profound metabolic reprogramming and kidney pathology.
DOI: 10.1126/sciadv.adz1242
Thread 1/7
October 30, 2025 at 9:56 AM
NEW PAPER
Out in Science Advances: We have dissected the physiological role of all macroH2A histone variants. In mice, loss of macroH2A1.1 specifically results in profound metabolic reprogramming and kidney pathology.
DOI: 10.1126/sciadv.adz1242
Thread 1/7
Out in Science Advances: We have dissected the physiological role of all macroH2A histone variants. In mice, loss of macroH2A1.1 specifically results in profound metabolic reprogramming and kidney pathology.
DOI: 10.1126/sciadv.adz1242
Thread 1/7
Reposted by Sébastien Lemaire
The remarkably long lifespan of bowhead whales could be due to an increased ability to repair DNA mutations, according to research in Nature. go.nature.com/4hzvDN7 🌏 🧪
October 29, 2025 at 10:08 PM
The remarkably long lifespan of bowhead whales could be due to an increased ability to repair DNA mutations, according to research in Nature. go.nature.com/4hzvDN7 🌏 🧪
Reposted by Sébastien Lemaire
Nature research paper: From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes
go.nature.com/4nVsl9z
go.nature.com/4nVsl9z
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes - Nature
A newly compiled atlas of species-wide structural variants and gene-based and graph pangenomes derived from highly complete assemblies of genomes from 1,086 natural isolates enable integrative genome-scale studies of Saccharomyces cerevisiae.
go.nature.com
October 20, 2025 at 6:19 PM
Nature research paper: From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes
go.nature.com/4nVsl9z
go.nature.com/4nVsl9z
Reposted by Sébastien Lemaire
GWAS vs GWIS vs GWiS
October 18, 2025 at 9:06 AM
GWAS vs GWIS vs GWiS
Reposted by Sébastien Lemaire
Amazing!!
Congrats to the team for uncovering this link
We are all phages …
Regular reminder to the “The frustrated gene” article from @hitenmadhani.bsky.social
Congrats to the team for uncovering this link
We are all phages …
Regular reminder to the “The frustrated gene” article from @hitenmadhani.bsky.social
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
www.biorxiv.org
October 17, 2025 at 6:41 PM
Amazing!!
Congrats to the team for uncovering this link
We are all phages …
Regular reminder to the “The frustrated gene” article from @hitenmadhani.bsky.social
Congrats to the team for uncovering this link
We are all phages …
Regular reminder to the “The frustrated gene” article from @hitenmadhani.bsky.social
Reposted by Sébastien Lemaire
A new computer model shows how genetic patterns in tumours can reveal the strength of past battles between cancer and the immune system, offering clues for predicting tumour behaviour and improving immunotherapy.
Immune system vs cancer
A computer model suggests that genetic information in cancer cells can reveal the strength of interactions between cancer and immune cells.
buff.ly
October 19, 2025 at 8:21 AM
A new computer model shows how genetic patterns in tumours can reveal the strength of past battles between cancer and the immune system, offering clues for predicting tumour behaviour and improving immunotherapy.
Reposted by Sébastien Lemaire
Surprisingly, mouse sperm can locate and swim through the tiny opening in #zebrafish eggs known as the micropyle, suggesting that some mechanisms guiding sperm toward eggs may be shared across distant species.
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buff.ly
October 19, 2025 at 10:01 AM
Surprisingly, mouse sperm can locate and swim through the tiny opening in #zebrafish eggs known as the micropyle, suggesting that some mechanisms guiding sperm toward eggs may be shared across distant species.