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Frederic Lemoine @fredebibs

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

Joined March 2009
  • Tweets 525
  • Following 832
  • Followers 721
12 Photos and videos
Frederic Lemoine retweeted
SciencesNetwork@SciencesNetwork
Mar 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
Mar 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

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

github.com
Frederic Lemoine@fredebibs
9 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…
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Frederic Lemoine retweeted
CNRS à Paris-Saclay@CNRSIdFSud
18 Dec 2024
#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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Frederic Lemoine retweeted
Institut Pasteur, since 1887@institutpasteur
2 Dec 2024
🌟 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 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

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

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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Frederic Lemoine retweeted
Institut Pasteur, since 1887@institutpasteur
13 Oct 2024
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 🌟
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Frederic Lemoine retweeted
Institut Pasteur, since 1887@institutpasteur
13 Oct 2024
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 !
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Frederic Lemoine retweeted
Mackenzie Weygandt Mathis, PhD@TrackingActions
3 Oct 2024
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…
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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

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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Frederic Lemoine retweeted
Camille Berthelot @camilleberthelot.bsky.social@CamLBerthelot
10 Sep 2024
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!
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Frederic Lemoine retweeted
VanRijLab@VanRijLab
19 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
31 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

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
26 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)
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Frederic Lemoine retweeted
Cedric Notredame@cnotred
15 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

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...

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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If you want to give it a try, a Nextflow workflow is available here github.com/evolbioinfo/bayes… Input: MSA Output: Phylogenetic tree with bayesian supports a figure with distribution of branch lengths.

GitHub - evolbioinfo/bayesian_bootstrap

Contribute to evolbioinfo/bayesian_bootstrap development by creating an account on GitHub.

github.com
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It uses 1) goalign github.com/evolbioinfo/goali… to generate weights (goalign build weightboot) , 2) PhyML github.com/stephaneguindon/p… to infer trees (it supports continous site weights with option "--weights"), and 3) gotree github.com/evolbioinfo/gotre… to compute supports

GitHub - evolbioinfo/goalign: Goalign is a set of command line tools and an API to manipulate...

Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language. - evolbioinfo/goalign

github.com
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