Yves Clément
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yvesclement.bsky.social
Yves Clément
@yvesclement.bsky.social
1.8K followers 1.1K following 730 posts
Assistant Prof @ U-Paris-Cité | Institut Jacques Monod
Molecular evolution and bioinformatics (and some other things, too)
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yvesclement.bsky.social
I…
phdemetri.bsky.social Demetri @phdemetri.bsky.social · 7h
I believe eigen fly. I believe eigen touch the sky.
November 26, 2025 at 7:40 PM
yvesclement.bsky.social
Ô joie, ô bonheur, ô félicité.
Il est revenu le temps, pour l'enfant, de lui faire des lavages de nez
a man with a mustache is laughing with his mouth open in a blue shirt .
ALT: a man with a mustache is laughing with his mouth open in a blue shirt .
media.tenor.com
November 25, 2025 at 1:51 PM
Reposted by Yves Clément
sinamajidian.bsky.social
Our trilogy of orthology publications is online!
Review on Hierarchical Orthologous Groups doi.org/10.1007/s00239-025-10277-1

OrthoXML-Tools doi.org/10.1007/s00239-025-10271-7

A great community effort on Quest for Orthologs in the era of Data Deluge and AI doi.org/10.1007/s00239-025-10272-6
https://link.springer.com/article/10.1007/s00239-025-10277-1 Conceptual overview of hierarchical orthologous groups. An example of one HOG, or gene family. A Species tree with four taxa: plant (green), fish (blue), human (orange), and mouse (yellow), each with one or more genes. B The implied gene tree, dubbed “HOG tree,” and inferred nested HOG composition. Duplication nodes (red) can be deduced based on the species tree topology and clusters of homologous genes at each level. Ancestral genes from which the HOGs descended are shown in gray. C HOGs returned at different taxonomic levels. Consider a gene family that was present in the last eukaryotic common ancestor (LECA). At this level, a single HOG encompasses all genes descending from that ancestral gene. At the Vertebrata level, this gene underwent duplication, leading to two distinct copies, i.e., HOGs. At the Mammalia level, a second duplication further subdivides one of these HOGs, showing how deeper HOGs split into nested subHOGs at more recent levels. The HOG composition implies that a loss event occurred after the mammalian speciation https://link.springer.com/article/10.1007/s00239-025-10272-6 Summary of the QfO8 meeting. a Hot topics and future directions in method development and applications within the QfO community, namely artificial intelligence, protein domains, protein structure, RNA and splicing isoforms. b Definition of orthology and paralogy, including various paralogous subtypes (e.g. in-paralogs and out-paralogs). c Duplications and functional divergence. d Applications of orthology https://link.springer.com/article/10.1007/s00239-025-10271-7 Overview of the OrthoXML File Format (simplified). A schematic representation of an OrthoXML file, a standardized XML-based format for representing orthology data. OrthoXML follows a hierarchical structure where elements are enclosed within opening < tag > and closing </tag > tags. < orthoXML > is the root element enclosing other elements. The < species > element contains information about genes. An OrthoXML file can include a < taxonomy > element, which specifies the species tree used to generate the file. Additionally, the < groups > element encapsulates the orthology and paralogy relationships among genes
November 21, 2025 at 4:26 PM
Reposted by Yves Clément
bffo.bsky.social
From @csoneson.bsky.social , @markrobinsonca.bsky.social & colleagues in @plos.org #Computational #Biology | Building a continuous #benchmarking ecosystem in #bioinformatics | #Education 🧬 🖥️ 🧪 🔓  
⬇️
journals.plos.org/ploscompbiol...
Building a continuous benchmarking ecosystem in bioinformatics
Benchmarking, which involves collecting reference datasets and demonstrating method performance, is a requirement for the development of new computational tools, but also becomes a domain of its own t...
journals.plos.org
November 15, 2025 at 5:11 PM
yvesclement.bsky.social
xkcd.com/3172/
Fifteen Years
xkcd.com
November 25, 2025 at 9:27 AM
Reposted by Yves Clément
francoissabot.bsky.social
With many colleagues, we tried to gather the future prospects and challenges for #Pangenomics and #Pangenome research in agronomy, that can however be adopted more largely

hal.science/hal-05357866/

@ird-fr.bsky.social @inrae-france.bsky.social #FAIR #OpenScience #vizu
A possible pipeline for the uses of a pangenome graph. This pipeline can be roughly divided into three main sections (on the right): build a graph, using it, and adding reads. A first pangenome graph is created, usually with almost complete haplotype as- semblies. Since graph creating methods vary, and may be fraught with errors (unaligned regions, broken paths), assessing the quality of a graph is useful (this can be applied after each subsequent step). Similarly, it is also crucial to be able to visualize the graph, espe- cially on particular loci of interest (can also be done throughout the pipe-line). The graph can be augmented with additional data increasing allele counts, including known con- tig alignment or read mapping. Several augmentation iterations, with different types of data, can be considered. Since most analyses focus on genes and transposable elements, it is usually useful to add an annotation (available on one or several reference genomes), which projected to the graph. This graph, possibly extended with new variants and an- notation, should be then shared with the community, following FAIR practices. Most analyses then focus on graphs with only one species, and the graph can be analyzed in order to find regions of interest. However, dual pangenomics, which studies the joint diversities of two species, can be envisioned. More generally, many species can also be modeled, for instance in the case of meta-genomics. Low coverage sequencing data of individuals can be compared or aligned to the graph in order to produce large genotyp- ing sets enabling population genetics studies (i.e. coalescence, association). Other omics (e.g. RNA-Seq, ChIP-Seq, Hi-C, LC-MS, BS-Seq etc.) data can be added to the graph, and potentially aggregated to multi-omic layers.
November 25, 2025 at 9:19 AM
yvesclement.bsky.social
I’ve got one: the phone call from the daycare center at 2 in the afternoon
faineg.bsky.social Faine Greenwood @faineg.bsky.social · 3d
few sounds on earth are more terror inducing than the highly infectious-sounding cough of a small child with a respiratory illness
faineg.bsky.social Faine Greenwood @faineg.bsky.social · 3d
Finally boarded my plane to Oslo and I am sitting in front of a child who appears to be suffering from an acute case of plague

I guess I am being punished for something

(Thank God I had a N-95 mask)
November 23, 2025 at 3:43 PM
Reposted by Yves Clément
luismsilva.bsky.social
Time to publish responsibly: DAFNEE, a database of academia-friendly journals in ecology and evolutionary biology url:

academic.oup.com/jeb/article/...
November 22, 2025 at 3:55 PM
Reposted by Yves Clément
monniauxd.bsky.social
Les universités françaises sont sommées d’à la fois concurrencer Oxford et le MIT et fournir les services
d’un community college auprès de publics en difficulté, le tout à bon marché et avec une bureaucratie
paralysante. Ensuite, on reproche aux universitaires de ne pas y parvenir.
November 21, 2025 at 11:57 AM
Reposted by Yves Clément
alexdemendoza.bsky.social
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics
Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.
www.nature.com
November 18, 2025 at 12:00 PM
Reposted by Yves Clément
filipedevadder.bsky.social
New Neuron paper by Mitchell, Dahly, Bishop tears apart the “autism is caused by the microbiome” story. Tiny n, noisy 16S, contradictory taxa, vague “dysbiosis”. It reads like an autopsy of a hype bubble.
www.cell.com/neuron/fullt...
Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism
Claims that the gut microbiome causally contributes to autism regularly appear in the scientific literature and popular press. Mitchell et al. critically examine influential studies underpinning these...
www.cell.com
November 19, 2025 at 3:03 PM
Reposted by Yves Clément
lemonde.fr
Amine Kessaci, militant écologiste : « Non, je ne me tairai pas. Je dirai et répéterai que mon frère Mehdi est mort pour rien. Je dirai la violence du narcotrafic »
Amine Kessaci, militant écologiste : « Non, je ne me tairai pas. Je dirai et répéterai que mon frère Mehdi est mort pour rien. Je dirai la violence du narcotrafic »
Connu pour son combat contre les ravages du trafic de drogue dans les quartiers populaires de Marseille, le frère de Mehdi, 20 ans, assassiné le 13 novembre, dénonce, dans une tribune au « Monde », « la lâcheté des commanditaires » et exhorte l’Etat à « comprendre qu’une lutte à mort est engagée ».
www.lemonde.fr
November 19, 2025 at 5:00 AM
Reposted by Yves Clément
monniauxd.bsky.social
On m'a un certain nombre de fois sorti que telle ou telle chose (ou tel ou tel auteur) est bien sûr connue de toute personne ayant fait des études supérieures.

Beaucoup de monde devrait regarder cette image et la comprendre.
Two stick characters, Cueball and Ponytail (wearing a ponytail) are talking. [Ponytail and Cueball are talking. Ponytail has her hand raised, palm up, towards Cueball.] Ponytail: Silicate chemistry is second nature to us geochemists, so it's easy to forget that the average person probably only knows the formulas for olivine and one or two feldspars. Cueball: And quartz, of course. Ponytail: Of course. [Caption below the panel] Even when they're trying to compensate for it, experts in anything wildly overestimate the average person's familiarity with their field.
November 15, 2025 at 7:28 PM
Reposted by Yves Clément
evomg-dn.bsky.social
🚨 15 days left to apply!
Be part of EvoMG-DN and advance your PhD career in evolutionary genomics.
👉 www.evomg-dn.eu

#PhD #DoctoralTraining #ResearchCareers #LifeSciences #BiomedicalResearch #Genomics #EvolutionaryBiology #MSCA #HorizonEurope #EUResearch #ResearchOpportunities #PhDPositions
November 14, 2025 at 10:19 AM
Reposted by Yves Clément
camilleberthelot.bsky.social
Still looking for our perfect doctoral candidate as part of @evomg-dn.bsky.social - come and join us to work on the evolutionary pressures that shape gene expression and disease in the uterus!

Please RT (or is it RB? not sure how our lingo has changed!)
November 14, 2025 at 10:22 AM
yvesclement.bsky.social
So I guess there’s no more excuses for not getting your RNA-seq right
marmole6.bsky.social Emilio Mármol Sánchez @marmole6.bsky.social · 12d
🦣🧬🦣🤯💥We are pleased to share our new paper about ancient RNA expression profiles from the Woolly Mammoth, now published in Cell @cellpress.bsky.social

www.cell.com/cell/fulltex...

If you want to know more, read the 🧵 below:
November 14, 2025 at 4:52 PM
Reposted by Yves Clément
jrotwitguez.bsky.social
🔊New perspective piece out @genomebiolevol.bsky.social.

"The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity" 💡🌀🌈
doi.org/10.1093/gbe/...

Co-led with @mbrasovives.bsky.social and @diegoharta.bsky.social

Check out our thread! 🧵👇 (1/n)
Validate User
doi.org
November 14, 2025 at 9:11 AM
Reposted by Yves Clément
jamieheather.bsky.social
My generation had to deal with datasets where Excel had autocorrected gene names to dates. Future generations are going to have to deal with the hallucinations of slopbots.
August 14, 2025 at 2:03 PM
Reposted by Yves Clément
claireplacial.bsky.social
Passe moi la pelle j’ai des idées d’usage
November 14, 2025 at 7:39 AM
Reposted by Yves Clément
jlsteenwyk.bsky.social
Just gonna put this here for now
www.science.org/doi/10.1126/...
bsky.app/profile/jlst...
November 13, 2025 at 7:23 PM
yvesclement.bsky.social
So I guess we can *finally* put that debate to rest and move on to another one
November 13, 2025 at 7:42 PM
yvesclement.bsky.social
10 ans.
Tellement loin et tellement proche. La sidération est partie, mais l’incompréhension et la tristesse sont restées.
Pensées aux victimes et à leurs proches
#13Novembre
November 13, 2025 at 5:29 PM
yvesclement.bsky.social
This should be interesting
clauswilke.com Claus Wilke @clauswilke.com · 13d
I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python?
blog.genesmindsmachines.com/p/python-is-...
Python is not a great language for data science. Part 1: The experience
It may be a good language for data science, but it’s not a great one.
blog.genesmindsmachines.com
November 13, 2025 at 5:00 PM
Reposted by Yves Clément
clauswilke.com
I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python?
blog.genesmindsmachines.com/p/python-is-...
Python is not a great language for data science. Part 1: The experience
It may be a good language for data science, but it’s not a great one.
blog.genesmindsmachines.com
November 13, 2025 at 4:16 PM