Nicolas Nesi
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nicolasnesi.bsky.social
Nicolas Nesi
@nicolasnesi.bsky.social
Phylogenomics fruitbats 🦇 | Metatranscriptomics respiratory microbiome | Genomics bacteria 🦠
IR Inserm UMR 1311 DYNAMICURE Université Caen Normandie - CHU Caen
Reposted by Nicolas Nesi
New in #Systematic_Biology, syaf082 #OpenAccess
"PhyloCNN: Improving tree representation and neural network architecture for deep learning from trees in phylodynamics and..."
Perez, M.F., & Gascuel, O. @isyeb.mnhn.fr
#tree_models #diversification #HIV #primates
➡️ academic.oup.com/sysbio/artic...
November 25, 2025 at 8:04 AM
Reposted by Nicolas Nesi
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/

Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
PhyloWeaver – Interactive phylogenetic tree editor
Edit and visualize phylogenetic trees directly in your browser. PhyloWeaver lets you interactively rearrange tree topologies and export high-quality figures for publications and presentations.
yawak.jp
November 18, 2025 at 1:59 AM
Reposted by Nicolas Nesi
NEW pub in @science.org 🥳

Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?

For over 15 years, #phylogenomic studies have been divided.

We provide new evidence suggesting that...

🔗: www.science.org/doi/10.1126/...
November 13, 2025 at 8:34 PM
Reposted by Nicolas Nesi
If you're interested in understanding discordance in phylogenomic analyses, the @evojlinnsoc.bsky.social's special issue 'Phylogenomic Discordance: Patterns, Processes, and Solutions' is for you!

tinyurl.com/v2eces3s

I'll be sharing a few articles a week until we're through the issue! (1/n)🧪
Phylogenomic Discordance: Patterns, Processes, and Solutions
Phylogenomics, the study of evolutionary relationships using genomic data, has revolutionized our understanding of the Tree of Life. As a field, phylogenomics h
academic.oup.com
September 29, 2025 at 4:00 PM
Reposted by Nicolas Nesi
If you like genomics, speciation, and primates, this PhD position is for you! Unraveling the genomic architecture of speciation and gene flow in guenons, a diverse group of African monkeys. Funding through DTP. Do reach out with questions! #genomics #genome_assembly
evol.mcmaster.ca/brian/evoldi...
October 23, 2025 at 3:11 PM
Reposted by Nicolas Nesi
A new era in natural history publishing begins. 🐢✨

Introducing the Handbook of the Reptiles of the World!
October 28, 2025 at 10:10 AM
Reposted by Nicolas Nesi
My lab is hiring a 2-yr hummingbird evolution and genomics postdoc and a 1-yr salaried research and lab tech. Both with full U. Wyoming benefits. Please spread the word! Info below. Best consideration date Nov 1, start dates early Spring 2026.
October 14, 2025 at 8:08 PM
Reposted by Nicolas Nesi
As I argue in #PlatypusMatters, Australia has the world's best mammals, but is sadly the worst place on Earth to be a mammal, with the planet's worst #extinction rate.
The Christmas Island shrew is now the latest species to be officially declared extinct.
www.theguardian.com/environment/...
And then there were none: Australia’s only shrew declared extinct
The tally of Australian mammals extinct since 1788 is now 39 species – far more than for any other country
www.theguardian.com
October 11, 2025 at 3:05 PM
Reposted by Nicolas Nesi
A paper in Nature Ecology & Evolution presents a time-calibrated phylogeny of Fungi. This timescale suggests an older age of crown Fungi, as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems. #phylo 🧪
A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution
Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).
go.nature.com
October 11, 2025 at 1:01 AM
Reposted by Nicolas Nesi
Super excited to finally share this! #CollectionsAreEssential
September 22, 2025 at 7:50 PM
Reposted by Nicolas Nesi
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
September 25, 2025 at 9:29 PM
Reposted by Nicolas Nesi
🖥️ Explore the latest from Bioinformatics Advances: "Termal: A fast and interactive terminal-based viewer for multiple sequence alignments"

Full article available: https://doi.org/10.1093/bioadv/vbaf208
September 24, 2025 at 9:03 AM
Reposted by Nicolas Nesi
Check out our new preprint! We compare sequence versus synteny approaches for resolving a challenging #phylogenetic problem. In this case, synteny is far more informative! Also includes the first chromosome-level #genome for the enigmatic #fish family Gyrinocheilidae. doi.org/10.1101/2025...
September 22, 2025 at 1:22 PM
Reposted by Nicolas Nesi
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM
Reposted by Nicolas Nesi
Scientists often use models to study how species evolved, but these models are not always perfect. Here, Ziheng Yang (Darwin Wallace Medal winner) looks at how small changes in data or assumptions can affect the results of these studies. Check it out below 👇🌍🧪
On measures of influence and discordance in phylogenomic analyses
Abstract. As models are approximate descriptions of real biological processes, and data are collected often with errors and contaminations, sensitivity or
doi.org
September 12, 2025 at 9:30 AM
Reposted by Nicolas Nesi
C. Zhang, R. Nielsen and S. Mirarab integrate all ASTRAL-like methods into a single package called ASTER, comprising several tools that collectively enhance the scalability, accuracy, and versatility of species tree inference.

🔗 doi.org/10.1093/molbev/msaf172

#evobio #molbio #compbio
ASTER: A Package for Large-Scale Phylogenomic Reconstructions
Abstract. Many algorithms are available for inferring species trees from various input types while accounting for gene tree discordance. Several quartet-ba
doi.org
August 18, 2025 at 7:13 AM
Reposted by Nicolas Nesi
A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package. #Microbiome #OmicsData #DataAnalysis #R @natprot.nature.com 🧬 🖥️
www.nature.com/articles/s41...
August 13, 2025 at 8:31 AM
Reposted by Nicolas Nesi
Cette loi affaiblit la protection de l’environnement sous la pression de l’agro-industrie.

✍️ La pétition envoie un message fort : les citoyens ne veulent pas sacrifier le vivant. Pour espérer un referendum il faut qu’on soit 4,8 millions.

✒️ Alors on signe.
👥 On partage.
🗣️ Et on interpelle !
July 21, 2025 at 3:59 PM
Reposted by Nicolas Nesi
Here is a very cool piebald Ethiopian epauletted fruit bat (Epomophorus labiatus) that we caught last month in Lilongwe, Malawi! 🦇

Piebaldism is a rare genetic condition caused by the absence of melonocytes in certain patches of skin and fur.

#bats #research #fieldwork #malawi #wildlife
July 17, 2025 at 11:58 AM
Reposted by Nicolas Nesi
**JOBS ALERT**

The Virology Unit at @PasteurCambodia
hiring 1 Scientist and 2 Postdocs to join our fast-moving, field-connected, research-driven team on emerging viruses and zoonoses.

🧪🧬🥼🦠🔬🐓💉🦇😷

Limited time to apply — and we need people to start ASAP.**👇
July 11, 2025 at 12:28 AM
Reposted by Nicolas Nesi
Ever wanted to infer a morphological or total-evidence phylogeny in BEAST2?
It’s long overdue, but we now have a tutorial on Taming the BEAST to talk you through the process 💻🌳⚙️
Thanks to Joëlle Barido-Sottani for helping me pull this together!
taming-the-beast.org/tutorials/To...
Total Evidence Tutorial
taming-the-beast.org
July 8, 2025 at 6:12 AM
Reposted by Nicolas Nesi
Fun fact: The greater sage grouse attracts females of its species by inflating two yellow air sacs on its chest and bouncing them around to produce a unique sound.💄🐦🍸 #naturalhabitatshorts #naturalhabitok #naturalhabitat
July 3, 2025 at 3:46 PM