Frederic Lemoine (@fredebibs) header
Frederic Lemoine (@fredebibs) profile picture

Frederic Lemoine

@fredebibs

Bioinformatics @institutpasteur ; data science, ngs, transcriptomics, biotech, evolution, phylogeny,... golang

 Paris, France
Joined March 2009
  • Tweets529
  • Following834
  • Followers723
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Photo by Frederic Lemoine (@fredebibs)Photo by Frederic Lemoine (@fredebibs)Photo by Frederic Lemoine (@fredebibs)Photo by Frederic Lemoine (@fredebibs)Photo by Frederic Lemoine (@fredebibs)Photo by Frederic Lemoine (@fredebibs)Photo by Frederic Lemoine (@fredebibs)Photo by Frederic Lemoine (@fredebibs)Photo by Frederic Lemoine (@fredebibs)
Frederic Lemoine retweeted
Vince Buffalo (@vsbuffalo) profile picture
Vince Buffalo@vsbuffaloOct 13
My time at the Gates Foundation/IDM recently wrapped up! I'm looking for senior/staff roles in AI for science, probabilistic inference, or scientific software — in Seattle or the SF Bay Area. Also open to consulting. Here's what I've been working on:
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Frederic Lemoine retweeted
Heng Li (@lh3lh3) profile picture
Heng Li@lh3lh3Jan 6
Now published in Algorithms for Molecular Biology: link.springer.com/article/10…. Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.
Improving spliced alignment by modeling splice sites with deep learning

Improving spliced alignment by modeling splice sites with deep learning

Algorithms for Molecular Biology - Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the...

link.springer.com
Heng Li (@lh3lh3) profile pictureHeng Li@lh3lh317 Jun 2025
Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986
Image from Heng Li (@lh3lh3)
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Frederic Lemoine retweeted
Sergei Pond (@sergeilkp) profile picture
Sergei Pond
@sergeilkpSep 11
I've spent ~30 years writing @hyphy_software to study selection & evolution. That era is coming to a close. HyPhy is passing the torch to HyphAeon (high-FAY-on): a ~2M parameter geometric transformer running in the browser that does things we never built it to do. 🧵👇
Image from Sergei Pond (@sergeilkp)
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Our recently published study in PLoS Computational Biology introduces DIPScan, a method to identify deletion-containing viral genomes in sequencing data and correct consensus genomes that might otherwise include erroneous mutations doi.org/10.1371/journal.pcbi…
Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to...

Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to...

Author summary Over the past few years, viral genome sequencing has become a cornerstone of epidemic surveillance, and generating accurate consensus viral genomes is essential for this effort....

journals.plos.org
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Frederic Lemoine retweeted
SciencesNetwork (@SciencesNetwork) profile picture
SciencesNetwork@SciencesNetworkMar 13
Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to influenza virus biorxiv.org/content/10.64898…
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Frederic Lemoine retweeted
bioRxiv Bioinfo (@biorxiv_bioinfo) profile picture
bioRxiv Bioinfo@biorxiv_bioinfoMar 13
Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to influenza virus biorxiv.org/content/10.64898… #biorxiv_bioinfo
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PhyML now implements the Bayesian phylogenetic bootstrap! To test it: option "--bayesian_bootstrap" with the latest commits of PhyML: github.com/stephaneguindon/p… Example: `phyml -d nt -i align.phy -m GTR -b 100 --bayesian_bootstrap`
GitHub - stephaneguindon/phyml: PhyML -- Phylogenetic estimation using (Maximum) Likelihood

GitHub - stephaneguindon/phyml: PhyML -- Phylogenetic estimation using (Maximum) Likelihood

PhyML -- Phylogenetic estimation using (Maximum) Likelihood - stephaneguindon/phyml

github.com
Frederic Lemoine (@fredebibs) profile pictureFrederic Lemoine@fredebibs9 Nov 2024
Replying to @fredebibs
This is now published in @MolBioEvol , Thanks to the reviewers who helped improve the manuscript! doi.org/10.1093/molbev/msae2…
The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches

The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches

Abstract. Felsenstein's bootstrap is the most commonly used method to measure branch support in phylogenetics. Current sequencing technologies can result i

academic.oup.com
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#TalentsCNRS 🥈 Sarah Cohen-Boulakia, professeure des universités Université Paris-Saclay au @LisnLab (CNRS/@UnivParisSaclay /@centralesupelec /@Inria), s’est vue remettre la médaille d’argent du @CNRS pour ses recherches en sciences des données et en bioinformatique.
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🌟 Join the Institut Pasteur as Scientific Director! 🌍 We're seeking a visionary scientist to shape global health through innovation and excellence. Help us drive cutting-edge research. Feel free to share with qualified candidates in your network! 👉 research.pasteur.fr/en/job/i…
The Institut Pasteur is looking for a Scientific Director - Research

The Institut Pasteur is looking for a Scientific Director - Research

The Institut Pasteur is a global leader in scientific excellence, and drives its mission to tackle humanity’s most pressing health challenges. Founded in 1887 by Louis Pasteur, and led since January...

research.pasteur.fr
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Our new preprint: « The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches » biorxiv.org/content/10.1101/… In this approach, bootstrap MSA sites are given continuous weights rather than being sampled with replacement.
The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches

The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches

Felsenstein’s bootstrap is the most commonly used method to measure branch support in phylogenetics. Current sequencing technologies can result in massive sampling of taxa (e.g. SARS-CoV-2). In this...

biorxiv.org
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This is now published in @MolBioEvol , Thanks to the reviewers who helped improve the manuscript! doi.org/10.1093/molbev/msae2…
The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches

The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches

Abstract. Felsenstein's bootstrap is the most commonly used method to measure branch support in phylogenetics. Current sequencing technologies can result i

academic.oup.com
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Mission accomplie 👏 Nos coureurs ont brillamment terminé les #20kmdeParis 🏃‍♀️ Merci à eux et à tous les donateurs qui soutiennent le #Pasteurdon. Votre générosité fait la différence pour la recherche 🌟
Image from Institut Pasteur, since 1887 (@institutpasteur)
Image from Institut Pasteur, since 1887 (@institutpasteur)
Image from Institut Pasteur, since 1887 (@institutpasteur)
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Go #TeamPasteur 🏃‍♀️🏃‍♂️ 60 coureurs passionnés sont sur la ligne de départ des #20kmdeParis pour soutenir la recherche et le #Pasteurdon. 🎗️ Merci à nos athlètes et à tous ceux qui encouragent la générosité au profit de la science !
Image from Institut Pasteur, since 1887 (@institutpasteur)
Image from Institut Pasteur, since 1887 (@institutpasteur)
Image from Institut Pasteur, since 1887 (@institutpasteur)
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EPFL has several faculty positions open this year, including in life sciences (aka including neuroscience!) 🧠🧬🦠 Great starting conditions, base yearly funding, top students, and … I mean, it’s gorgeous- quality of life is A+… epfl.ch/about/working/page-2…
Image from Mackenzie Weygandt Mathis, PhD (@TrackingActions)
Image from Mackenzie Weygandt Mathis, PhD (@TrackingActions)
Image from Mackenzie Weygandt Mathis, PhD (@TrackingActions)
Image from Mackenzie Weygandt Mathis, PhD (@TrackingActions)
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Accounting for partner notification in epidemiological birth-death models medrxiv.org/content/10.1101/…
Accounting for partner notification in epidemiological birth-death models

Accounting for partner notification in epidemiological birth-death models

Phylodynamics bridges the gap between classical epidemiology and pathogen genome sequence data by estimating epidemiological parameters from time-scaled pathogen phylogenetic trees. The models used...

medrxiv.org
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Looking for a PhD position in 2025? 🧑‍🎓 Interested in endometriosis research? 🩸 We are looking for a computational candidate for the Pasteur-Paris University PhD program to join a fantastic international collab between my lab, @afilimon and L. Doridot! Please RT!
Image from Camille Berthelot @camilleberthelot.bsky.social (@CamLBerthelot)
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Frederic Lemoine retweeted
VanRijLab (@VanRijLab) profile picture
VanRijLab@VanRijLab19 Aug 2024
We are recruiting! For an @ERC_Research-funded project, we are PhD student(s) and postdoc to work on small RNAs in vector mosquitoes. Please RT or forward to interested candidates. @radboudumc_weet radboudumc.nl/vacatures/1458… radboudumc.nl/en/vacancies/1…
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Frederic Lemoine retweeted
Rayan Chikhi (@RayanChikhi) profile picture
Rayan Chikhi@RayanChikhi31 Jul 2024
Today we’re excited to freely share an early-version of, perhaps, the world’s most expansive genetics dataset: Logan. #bioinformatics #petabase #genetics #genomics #openscience biorxiv.org/content/10.1101/…
Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity

Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity

The NCBI Sequence Read Archive (SRA) is the largest public repository of DNA sequencing data, containing the most comprehensive snapshot of Earth’s genetic diversity to date. As its size exceeds 50.0...

biorxiv.org
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Frederic Lemoine retweeted
Nico Rascovan (@NRascovan) profile picture
Nico Rascovan@NRascovan26 Jul 2024
Our lab at @institutpasteur initiated the #Olympiome2024, a @metasub initiative to study changes in the urban microbiome during the #joParis2024! If you want to know more, here a thread about it. (1/X)
Image from Nico Rascovan (@NRascovan)
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Frederic Lemoine retweeted
Cedric Notredame (@cnotred) profile picture
Cedric Notredame@cnotred15 Jul 2024
🚀 NAR Genomics & Bioinformatics now ranks #8 among bioinformatics journals with a 2023 impact factor of 4.0! We're opening 3 Deputy Editor positions. Join our team: academic.oup.com/nargab/page… #Bioinformatics #AcademicJobs #nargab
Now Recruiting: Deputy Editor

Now Recruiting: Deputy Editor

Oxford University Press invites applications for the position of Deputy Editor for NAR Genomics and Bioinformatics. There are three Deputy Editor positions ava

academic.oup.com
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"Much Ado About Nothing: Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to evade (Over-)optimization". Faster tree inference in RAxML-NG biorxiv.org/content/10.1101/…
Much Ado About Nothing: Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping...

Much Ado About Nothing: Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping...

Maximum Likelihood (ML) based phylogenetic inference constitutes a challenging optimization problem. Given a set of aligned input sequences, phylogenetic inference tools strive to determine the tree...

biorxiv.org
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