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David Enard

@denard.bsky.social
1.4K followers 301 following 194 posts

Evolutionary Biologist. Ancient epidemics. Genomic adaptation.

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Reposted by David Enard
Max Reuter @maxreuter.bsky.social · 07/10/2026
Our paper on detecting (or not) balancing selection is now out, in all its typeset beauty, in the October issue of @molbioevol.bsky.social: academic.oup.com/mbe/article/...
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Jean Léon Maître @maitrejl.bsky.social · 06/10/2026
📣Our department is hiring a new group leader!📣 Want to start your team in a vibrant scientific environment in the center of Paris? I was very lucky to do that 10 years ago, reach out if you have any question. Apply by December 18th: jpi-recruitment-curie-umr3215-u934.curie.fr
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Philippe Batut @philippebatut.bsky.social · 10/09/2026
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
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Bat1K Genome Project @bat1kgenomes.bsky.social · 23/09/2026
Where did bats come from?🦇🌍 After decades of debate, the biggest bat genome + fossil study ever done has an answer - and it’s not where anyone expected! 🤩OUR PHASE 1 FLAGSHIP is out today in nature! doi.org/10.1038/s415... A thread 🧵
doi.org
Reference genomes and fossils revise bat family phylogeny and biogeography - Nature
An updated phylogeny of bats is presented, based on new genome assemblies and many ancient fossils and including all known bat families.
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Pleuni Pennings @pleunipennings.bsky.social · 29/09/2026
I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...
abetterscientist.wordpress.com
Postdoc position on drug resistance evolution in Montpellier, France
I have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…
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Jeremy Van Cleve @vancleve.theoretical.bio · 29/09/2026
My group is recruiting a Ph.D student for Fall 2027! We're a friendly group of mathematically-minded and computationally-inspired biologists studying topics including social evolution, host-pathogen interactions, genetics, and demography. See vancleve.theoretical.bio for more info!
vancleve.theoretical.bio
van cleve research group
Van Cleve Research Group – theoretical evolution & ecology at the University of Kentucky
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David Enard @denard.bsky.social · 18/09/2026
2/2) Bat immune response is very often discussed in terms of bats' immune system being the most derived, I am not sure. that we can make this assumption based on current evidence.
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David Enard @denard.bsky.social · 18/09/2026
1/2) The question now is how bats and primates could possibly develop such different susceptibilities (and thus adaptation to) RNA vs. DNA viruses. Answering will likely first require uncovering who is more like ancestral mammals. www.nature.com/articles/s41...
nature.com
Insights into longevity and virus-driven adaptation from Myotis bat genomes - Nature
Comparative and functional analyses of Myotis bats uncover unique patterns of adaptation in virus-interacting proteins and longevity-associated pathways, linking two hallmarks of bat biology.
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Dmitri Petrov @petrovadmitri.bsky.social · 17/09/2026
We are searching for an Assistant Professor in Evolutionary Biology! Looking for colleagues asking fundamental questions relating to evolutionary processes and drivers of evolutionary patterns. If you think it is you, please do apply! And please repost. facultypositions.stanford.edu/jobs/assista...
facultypositions.stanford.edu
Assistant Professor in Evolutionary Biology - Stanford University, California, United States
The Department of Biology at Stanford University seeks applicants for a tenure-track Assistant Professor in Evolutionary Biology. A successful candidate will conduct research that asks fundamental que...
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David Enard @denard.bsky.social · 05/07/2026
Does someone know what game Paraguay was playing yesterday? Asking because it was not soccer. Clearly the referee was also confused. Sad to see teams who forgot that it is also about entertaining the public with beautiful technical fits.
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Jonathan Pritchard @jkpritch.bsky.social · 23/05/2026
Some deep work by my former student Matthew Aguirre on what the properties of cis- and trans eQTLs can teach us about the structure of gene regulatory networks!
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David Enard @denard.bsky.social · 20/05/2026
Ils ont entouré le cadre prévu?
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David Enard @denard.bsky.social · 20/05/2026
Your work is very inspiring, a lot to do around compensatory evolution. For us it indirectly reveals virus-driven adaptation, with the big advantage of being hopefully able to do it just with divergence. Viruses seem very good at forcing changes where they usually do not happen due to constraint.
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David Enard @denard.bsky.social · 20/05/2026
Deeply interesting comment on a paper on compensatory evolution following "host" adaptation to a selfish genetic element. Reminescent of our finding of compensatory protein stability evolution after ancient viral epidemics. #evolution www.nature.com/articles/s41...
nature.com
The long reach of the Red Queen - Nature Reviews Genetics
Red Queen dynamics describe a mode of evolution in which interacting biological entities continually adapt and counteradapt. This Comment discusses the pervasiveness of these dynamics within genomes, ...
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David Enard @denard.bsky.social · 16/05/2026
It is unfortunate that this has to be reminded so much to reviewers at all steps: doing this things right or at least as well as possible IS in itself a strong innovation.
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David Enard @denard.bsky.social · 15/05/2026
You know you have great collaborators when they bring your own enthusiasm back at times when it has been vacillating. You know who you are :).
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David Enard @denard.bsky.social · 27/04/2026
A bad case of using a non official gene/protein name that makes it even worse by introducing ambiguity with another gene name. This makes curation efforts far more difficult: pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov
Naf1 Regulates HIV-1 Latency by Suppressing Viral Promoter-Driven Gene Expression in Primary CD4+ T Cells
HIV-1 latency is characterized by reversible silencing of viral transcription driven by the long terminal repeat (LTR) promoter of HIV-1. Cellular and viral factors regulating LTR activity contribute ...
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David Enard @denard.bsky.social · 09/04/2026
2/2) lastz requires to pre-softmask the genomes extensively which is itself very computationally costly, and since it is often a handful of problematic jobs, it seems more efficient to have lastz mask problematic repeats itself? @hillermich.bsky.social have you though about improving lastz?
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David Enard @denard.bsky.social · 09/04/2026
1/2) #bioinformatics people interested in #genome alignment, has anyone tried to do "adaptive seeding throttling" where after a long run time a lastz job would go into an adaptive mode where it detects that a specific repeat is initiating too many seeds, which would trigger lastz to mask it?
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David Enard @denard.bsky.social · 29/03/2026
I have been told that in reference to the big confs in my field, the smaller ones are always very inclusive. Having observed social dynamics at those big confs I see where they come from.
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David Enard @denard.bsky.social · 29/03/2026
I have now heard repeatedly from non-US PIs they stopped to go to American confs because the PIs there being socially exclusive and not including much anyone else in social interactions. I have also seen it, I find it disconcerting to this day.
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David Enard @denard.bsky.social · 21/03/2026
Wow, incredible shot indeed!
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Russ Corbett-Detig @russcd.bsky.social · 24/02/2026
@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs). If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 03/03/2026
Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!
github.com
GitHub - RILAB/argprep: Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files.
Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files. - RILAB/argprep
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Amy Goldberg @amygoldberg.bsky.social · 05/03/2026
The Goldberg lab at UCLA is hiring one or more postdocs. Flexible start date. We develop methods to study population genetics of humans, our primate relatives, and our pathogens. www.goldberglab.org/join
goldberglab.org
Amy Goldberg, PhD - Join
The Goldberg lab is moving to UCLA summer 2025, and recruiting postdocs and graduate students. We are a computational lab with occasional wet lab or field collaborators. We will be located in the Depa...
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Yulin Zhang @yulinzhang.bsky.social · 05/03/2026
Have you ever wondered how many archaic populations contributed DNA to modern humans? We know about Neanderthals and Denisovans, but the fossil and genetic evidence suggests a much more complex history! www.biorxiv.org/content/10.6...
biorxiv.org
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Chris Fiscus @fiscuscj.bsky.social · 02/03/2026
Excited to share our new preprint! 🍇🧬 We analyzed 639 genomes across 48 grape species to understand how hybridization drives adaptation. • ~14% of average Vitis genome is introgressed • Most parallel adaptations are shared via gene flow • Two "hybrid species" are actually hybrid swarms
biorxiv.org
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Mathieu Gautier @mgda76.bsky.social · 25/02/2026
For those interested, a new version (v3.1.0) of poolfstat is now on CRAN, including new functions and updates, new stats (Fh, Fd, FdM) implemented in sliding.windows.fstat; and a revised vignette. [cran.r-project.org/web/packages/poo…...)
cran.r-project.org
poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data
Functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, Patterson's F2, F3, F3*, F4 and D parameters) in population genomics studies from allele count or Pool-S...
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David Enard @denard.bsky.social · 21/02/2026
Thinking more about it, maybe the complex mutations at high enough frequencies to see them, and thus having any chance to fix later are those that change less amino acids? The complex mutations that change many aas are more deleterious?
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David Enard @denard.bsky.social · 20/02/2026
Interesting! It would be a great positive control to test BUSTED-MH. My first thought is that the overall dN/dS could go down while the w2 category of positively selected codons in the model could still go up. Since there are more nonsyn than syn sites, surprising to see dN/dS go down?
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David Enard @denard.bsky.social · 20/02/2026
And the ref, sorry, shameless self-advertizing: academic.oup.com/mbe/article/...
academic.oup.com
Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses
Abstract. Inference and interpretation of evolutionary processes, in particular of the types and targets of natural selection affecting coding sequences, a
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David Enard @denard.bsky.social · 20/02/2026
Indeed the higher number of parameters decreases statistical power, but the positives ones are far more likely to be true positives.
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David Enard @denard.bsky.social · 20/02/2026
To add one thing: if you have the data to run both classic dN/dS tests and MK tests, choose the latter. dN/dS tests are blind to positive selection in the important, constrained proteome, while MK test will work regardless of constraint, if DFE well estimated. #evolution #adaptation #popgen
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David Enard @denard.bsky.social · 20/02/2026
Synonymous substitution rate variation.
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David Enard @denard.bsky.social · 20/02/2026
5/5) The claims that lack of congruence between dN/dS and MK tests questions their validity are very weak: there are well known, well identified and well studied reasons why that would be the case. Maybe the field should pay better attention to latest sel tests developments, all above is discussed.
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David Enard @denard.bsky.social · 20/02/2026
4/5) This is the true hidden killer: classic dN/dS tests are very sensitive to positive selection in weakly constrained, fast evolving immune genes. At the same time, the inflation of PN due to likely ongoing balancing selection in the same genes kills the power of MK test to detect excess of DN.
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David Enard @denard.bsky.social · 20/02/2026
3/5) The classic dN/dS tests only have statistical power when the selective constraint surrounding the positively selected sites is weak. Beyond needing dN/dS>1, also a matter of statistical power depending on the total number of substitutions. MK approaches really shine in the constrained genome,
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David Enard @denard.bsky.social · 20/02/2026
2/5) First, the dN/dS tests used in the past comparisons output many false positive results because they do not account for synonymous substitutions or complex multinucleotide substitutions. Look at the -MH tests in HYPHY to account for this.
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David Enard @denard.bsky.social · 20/02/2026
1/5) Re-reading this excellent paper on using mutation-selection balance models to quantify positive selection. The discussed lack of congruence between MK approaches and classic dN/dS test is entirely unsurprising, see thread below. www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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David Enard @denard.bsky.social · 19/02/2026
Ah, les rapports d'activité tellement lourds qu'ils retardent les dites activités, avec des formats ubuesques et la plupart du temps redondants avec les années passées. Aussi devoir rendre ces foutus rapports quand il suffit d'aller voir Google Scholar. La plaie...
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David Enard @denard.bsky.social · 18/02/2026
Always a great feeling when the new labs in the EEB Department @uofa-eeb.bsky.social each attract multiple fantastic new grad students. Very happy to see younger colleagues succeed.
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David Enard @denard.bsky.social · 17/02/2026
Great news for anyone using ARGs in non-model species: www.biorxiv.org/content/10.1...
biorxiv.org
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Lluis Quintana-Murci @lquintanamurci.bsky.social · 16/02/2026
Happy to share our last study on how age, biological sex and genetics affect not only the extent of antibody responses against viruses but also the specific viral epitopes recognised. Thanks to Axel Olin @EtiennePatin @LabExMI @institutpasteur @cdf1530 @CNRS www.nature.com/articles/s41...
nature.com
Demographic and genetic factors shape the epitope specificity of the human antibody repertoire against viruses - Nature Immunology
Patin and colleagues present a mineable Resource database for identifying demographic and genetic factors that impact antiviral antibody repertoires in humans.
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Nandita Garud @nanditagarud.bsky.social · 12/02/2026
I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.
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Benjamin Vernot @benvernot.bsky.social · 13/02/2026
Are you interested in human DNA from ancient sediments? Do you want to do a PhD in Vienna? We have two open positions in our group! You can learn more and apply here (scroll down to the very bottom, ours are the last two listings): careers.univie.ac.at/en/praedoc/s...
careers.univie.ac.at
Vienna Doctoral School of Ecology and Evolution
The Vienna Doctoral School of Ecology and Evolution is dedicated to educating students to advance our understanding of the ecology and evolution of extant and ancestral organisms, populations, and communities. In Ecology, the focus is on uncovering the mechanistic and evolutionary drivers of patterns and processes across biological scales, from gene regulation to ecosystem structure and function, including the role of communities in biogeochemical cycles and their adaptive responses to environmental change. In Evolution, we investigate the processes shaping changes in organization and dynamics of organisms, populations, and species at molecular, developmental, morphological, and physiological levels.
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David Enard @denard.bsky.social · 09/02/2026
Counting publications is such a poor proxy for scientific productivity. Counting discoveries, with a bonus for discoveries that were not anticipated, and important insights is a much better proxy. I am wondering if there are standardized, systematic ways of quantifying this.
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David Enard @denard.bsky.social · 30/01/2026
That looks great! To avoid errors due to starting with spotty gene annotations (gene loss vs. not annotated), I would suggest re-annotating every genome used with TOGA2 from the Hiller lab: github.com/hillerlab/TO... Many annotations out there are not optimal and TOGA2 has great power and accuracy.
github.com
GitHub - hillerlab/TOGA2: TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments
TOGA2: A faster, more versatile successor of Tool to infer Orthologs from Genome Alignments - hillerlab/TOGA2
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Laurie Belcher @lauriebelch.bsky.social · 29/01/2026
Calling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)
biorxiv.org
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Lucie Etienne @lucievirevolte.bsky.social · 26/01/2026
📣 *Abstract submission by January 31st* "Host adaptations to viral infections” International Meeting May 10th-13th 2026 @cnrs.fr Station Biologique Roscoff, Brittany, France Register & Join us +amazing international speakers! #CNRS @cnrsbiologie.bsky.social #IRP www.insb.cnrs.fr/fr/evenement...
insb.cnrs.fr
Rapid host adaptations in response to viral infections
Viruses threaten all living organisms leading to molecular conflicts which have shaped hosts over evolutionary timescales. This meeting seeks to gather scientists from diverse disciplines including genomics, population genetics, innate immunology, virology, and beyond, to explore the evolution, diversity, molecular basis, and dynamics of these conflicts.
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 23/01/2026
PEQG! My favorite conference ever*. Single session, fantastic talks, great discussions. Only once every 2 years. And in the best conference location too! Abstract deadline coming up Feb 5! *Disclosure: I am required to say it's the best conference because it is and I told my mom I wouldn't lie.
genetics-gsa.org
Homepage - 2026 Population, Evolutionary, and Quantitative Genetics Conference
Visit our website to learn more.
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