Nikos Vakirlis
@vakirlis.bsky.social
G4 Group Leader at the Hellenic Pasteur Institute, Evolutionary Genomics Group. We study the evolution of novel genes and antimicrobial peptides. https://vakirlislab.com/
Really proud of this piece, led by @timothyfuqua.bsky.social , finally published in GBE! Tim's post perfectly explains what it hopes to achieve.
Timothy Fuqua@timothyfuqua.bsky.social · 2w ago@vakirlis.bsky.social and I are proposing a new term in the de-novo genes / molecular evolution cinematic universe. The term is: "Emergence Bias" and our perspective piece describing it was published in @genomebiolevol.bsky.social today! So, what is an emergence bias? (1/7)
🧬 Want to stay updated on protein science? Check out the @bpdmc.org monthly presentation series! Recent topics: • Computational antibody design • Energy-based models & structure • De novo small-molecule induced changes Learn more, watch past presentations, and join the community at bpdmc.org.
New work on using transformers (using gene order) for tasks in genomic epidemiology: www.biorxiv.org/content/10.6... We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection
Sam Horsfield@samuelhorsfield.bsky.social · 4mo agoOur new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
Drivers of cold adaptation and genome evolution in Antarctic fish, and a haplotype resolved assembly for an important model notothenioid species 🐟 🧬 Our new paper available on BioRxiv #BiodiversityGenomics #ColdAdaptation www.biorxiv.org/content/10.6...
Are there biases in how novel functions emerge in evolution at the promoter, enhancer and protein-coding DNA level? In this perspective piece we argue that yes! Led by @timothyfuqua.bsky.social
Timothy Fuqua@timothyfuqua.bsky.social · 4mo agoI’m excited to share the draft for our perspective piece on »Emergence Biases« that I wrote with @vakirlis.bsky.social on arxiv: arxiv.org/abs/2604.20477
Two (or more) PhD student positions are open with me in protein structure evolution (using AI). Please apply/spread the word. su.varbi.com/en/what:job/...
PhD student in Bioinformatics
The Department of Biochemistry and Biophysics SciLifeLab ( SciLifeLab ) is a national center for molecular biosciences with a focus on health and environmental research. The center combines frontl
su.varbi.com
This is what the US has descended to, openly bombing universities. www.nytimes.com/2026/03/30/w...
Iran Condemns Attacks on Its Universities, Warns of Retaliation
nytimes.com
This.
Mark A. Hanson@hansonmark.bsky.social · 6mo agoI appreciate someone took the time to write this. I profoundly disagree with their view, but if I take the spirit of what they're saying as a good faith attempt to raise a mental issue, there's at least a conversation to be had. Let's have it 1/🧵 www.science.org/content/arti... #AcademicChatter
1. I’m quite happy with this popular piece that Lee Dugatkin and I wrote recently. For the next two weeks it’s free to read on the American Scientist website.
Humbled by Evolution
Understanding the history and diversity of life inspires awe and wonder.
americanscientist.org
Dear friends and fans of evolutionary biology & medicine (#EvMed), deadlines for the 2026 meeting in Kiel Germany are coming up. Looks to be excellent! March 1, 2026: Abstract submission deadline and travel award decisions April 1, 2026: Abstract decisions open.substack.com/pub/evmedrev...
Abstracts due for the July Evolution and Medicine Conference in Kiel, Germany!
Early discounted registration is also open
open.substack.com
This is crazy www.science.org/doi/10.1126/...
RETRACTED: Integrative phylogenomics positions sponges at the root of the animal tree
Determining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constru...
science.org
CALL FOR PAPERS 📣 Special Issue: #GenomeArchitecture and #Evolution, organised by @eseb.bsky.social STN "STRiVE": Find out more here: tinyurl.com/2uza525c @ruifaria.bsky.social @kaybiodiversity.bsky.social @clairemerot.bsky.social @petrnguyen.bsky.social @aruizherrera.bsky.social
@ccasola.bsky.social, A. Owoyemi and @vakirlis.bsky.social test the hypothesis that many noncanonical proteins possess low stability in the cellular environment, finding that noncanonical proteins were enriched for degradation-related features. 🔗 doi.org/10.1093/gbe/evag009 #genome #evolution
Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms
Abstract. The comprehensive characterization of human proteins, a key objective in contemporary biology, has been revolutionized by the identification of t
doi.org
🧬 What does the starting material from which genes could emerge #denovo look like? 🌱 We used #RiboSeq to investigate the landscape of translated de novo ORFs in 3 #Arabidopsis species, and how they might be linked to gene birth! 📝 Check out our preprint here: doi.org/10.1101/2025...
Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis
Ancestrally non-genic sequences are now widely recognized as potential reservoirs for the de novo emergence of new genes. Across clades, some de novo genes were proven to have substantial phenotypic effects, and to contribute to the emergence of novel biological functions. Yet, still very little is known about the starting material from which de novo genes emerge, especially in plants. To fill this gap, we generated Ribosome Profiling data from the closely related species Arabidopsis halleri, A. lyrata and A. thaliana and characterized genome-wide patterns of translation across them. Synteny analysis revealed 211 Open Reading Frames (ORFs) that have emerged de novo within the Arabidopsis genus and already exhibit signs of active translation. Most of these de novo translated ORFs were species- and even accession-specific, indicating their transient nature, with patterns of polymorphism consistent with neutral evolution in natural populations. They were also significantly shorter and less expressed than conserved Coding DNA Sequences (CDS), and their GC content increased with phylogenetic conservation. While most of them were located in intergenic regions and are thus newly discovered, 34 were previously annotated as CDS in at least one genome, and are promising putative genes. Our results demonstrate the abundance of translation events outside of conserved CDS, and their role as starting material for the emergence of novel genes in plants. ### Competing Interest Statement The authors have declared no competing interest. Université de Lille, https://ror.org/0546v5182
doi.org
Can't recommend enough "Tree of Life" by @maxjtelford.bsky.social . I'd make it a must-read for everyone interested in evolution. Beautifully narrated and produced audiobook as well.
Two new chapters from my free online book in human genetics out this weekend! These complete Part 3 of the book, on human population structure and history: 3.3: Human prehistory [separate thread] 3.4: Ancient DNA: a genetic time capsule [this thread] web.stanford.edu/group/pritch...
An Owner's Guide to the Human Genome
An Owner's Guide to the Human Genome
web.stanford.edu
Jonathan Pritchard@jkpritch.bsky.social · 3y agoI'm delighted to release the first half of my new textbook in human genetics: web.stanford.edu/group/pritch... "An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"
In what's now become an annual tradition, I've written another piece for The Gist about how and why I hate A.I. On a bubble about to burst, a future rotted to its core, and the limits of the Mrs Doyle Theory of artificial intelligence. www.thegist.ie/guest-gist-2...
Guest Gist: 2026, Our Already Rotting Future
Seamus O'Reilly warns of AI maximum bubbledrive this year.
thegist.ie
@ccasola.bsky.social, V. Luria, @vakirlis.bsky.social & @lizhao.bsky.social discuss advances and open questions in de novo gene emergence and evolution presented at the SMBE Satellite Meeting on De Novo Gene Birth (@official-smbe.bsky.social). 🔗 doi.org/10.1093/gbe/evaf230 #genome #evolution
De Novo Genes: Current Status and Future Goals
Abstract. The recent Society for Molecular Biology and Evolution Satellite Meeting on De Novo Gene Birth, hosted at Texas A&M University on November 6
doi.org
New preprint from our lab, spearheaded by @maelledaunesse.bsky.social and in collaboration with Diego Villar! In which we ask, can we detect joint signatures suggestive of positive selection on transcriptomes and epigenomes?
Maëlle Daunesse@maelledaunesse.bsky.social · 9mo agoWe've just released our new preprint! 🐀✨ doi.org/10.1101/2025... How do gene expression and regulation evolve during adaptation? And how can we tell adaptive shifts apart from simple drift? @camilleberthelot.bsky.social 👇 A short thread on what we found in African mole-rats.
Check out our cover article by @timjanicke.bsky.social and colleagues about the role of sexual selection in animal speciation. academic.oup.com/evlett/artic.... The beautiful illustration is by Katharina Bóth.
There's just an awful lot of bad shit out there, people...
PowerAthleteHQ@powerathletehq.bsky.social · last yr.Anxiety might not be just in your head, it could be in your gut. Dr. Sabine Hazan explains how gut bugs from an anxious donor can transfer that anxiety through fecal transplant. 🎧 TUNE IN to Power Athlete Radio Ep 802: The Gut War w/ Dr. Sabine Hazan 🔗 pahq.co/EP802
We are excited to welcome our three new SMBE Fellows! Ioanna Kotari, Shady Kuster, and Haoran Cai will join @molbioevol.bsky.social and @genomebiolevol.bsky.social as writing fellows. Keep an eye on our next Highlight articles in MBE and GBE! #society #scicomm #evobio #molbio #genome #evolution
When I see someone trying to sell this shit I feel the urge to remind people of the "metaverse". Remember how it was the future of the internet 5 years ago? Meta alone has already lost $70B on this nonsense. Imagine how much good they could have done with that money. www.techbuzz.ai/articles/met...
Meta's Reality Labs burns $4.4B as VR bet hits $70B loss
Meta's metaverse division posts massive Q3 loss despite beating expectations
techbuzz.ai
derek guy@dieworkwear.bsky.social · 10mo agoWhy would someone pay $20k for a robot controlled by a human in a remote location to do things more slowly and clumsily when the median wage for a maid or housekeeper is $33k per year, which is typically spread across 10-20 households?
🧬 Now published in Bioinformatics Advances: “Advances and challenges in understanding evolution through genome comparison.” Read the full paper here: https://doi.org/10.1093/bioadv/vbaf223
Absolutely embarassing. www.techbuzz.ai/articles/ope...
our next evol-mut-circle seminar (21 Oct, 15:00 UTC) features Timothy Fuqua on "De novo promoters emerge more readily from random DNA than genomic DNA" www.biorxiv.org/content/10.1... DM me to join the email list. Full schedule: www.molevol.org/evol-mut-cir... #popgen, #mutation, #evobio
De-novo promoters emerge more readily from random DNA than from genomic DNA
Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...
biorxiv.org
The 2026 Workshop on Phylogenomics will take place between the 25th of January and 7th of February, in Cesky Krumlov, Czechia. 🧬🌳 Applications are now open! Deadline: 15th of November, 2025. Do not miss the chance to attend! Spread the word among colleagues! 🤗 evomics.org/apply-worksh...
📢 EvoMG-DN PhD applications are now open! Join our EU-funded MSCA network and explore evolution, ageing, and disease. 👉 www.evomg-dn.eu 📅 Apply by 30 November 2025 #PhD #DoctoralTraining #MSCA #HorizonEurope #Genomics #EvolutionaryBiology #BiomedicalResearch#EarlyCareerResearchers
A role model for everyone, scientist or not, a true hero. The world needs more Jane Goodalls, less Elon Musks. Rest In Peace.
NPR@npr.org · 11mo agoJUST IN: Jane Goodall, primatologist who transformed our understanding of the lives of apes, has died, according to an announcement from the Jane Goodall Institute.
SEPTEMBER's EDITOR's CHOICE: Intergenic, repetitive motifs that act as nucleosome repleted regions in the budding yeast genome, have evolved de novo into novel protein-coding genes: doi.org/10.1093/jeb/... @vakirlis.bsky.social @timothyfuqua.bsky.social
