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.
David Enard
@denard.bsky.social
Evolutionary Biologist. Ancient epidemics. Genomic adaptation.
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!
Matthew Aguirre@aguirre404.bsky.social · 2mo agoHappy to share that this is now out in Cell Genomics and a featured paper for Multi-Journal Submission from @cellpress.bsky.social — many thanks to the editorial team + our reviewers! Short recap + some further thoughts on the paper ⬇️ [1/7] www.cell.com/cell-genomic...
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...
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, ...
nature.com
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.
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 :).
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...
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 ...
pmc.ncbi.nlm.nih.gov
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?
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.
@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.
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 - 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
github.com
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
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...
goldberglab.org
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
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
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. [https://cran.r-project.org/web/packages/poolfstat/index.html](cran.r-project.org/web/packages...)
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...
cran.r-project.org
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
David Enard@denard.bsky.social · 6mo ago1/5) 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/...
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
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...
pnas.org
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.
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...
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.
nature.com
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.
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...
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.
careers.univie.ac.at
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.
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 - 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
github.com
Laurie Belcher@lauriebelch.bsky.social · 6mo agoCalling 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)
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
📣 *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...
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.
insb.cnrs.fr
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.
Homepage - 2026 Population, Evolutionary, and Quantitative Genetics Conference
Visit our website to learn more.
genetics-gsa.org
This is shaping up to be a great workshop. There is still time to register before the deadline! Please RT! #evolution #viruses #pathogens
Peter Sudmant@psudmant.bsky.social · 7mo agoRegistration deadline is fast approaching for the "Host adaptations to viral infections” Meeting May 10th-13th, 2026, at the CNRS Station Biologique de Roscoff, Brittany, France! JOIN US and the many amazing speakers! JOIN US! sites.google.com/berkeley.edu...
I forgot using tags again: #evolution #genomics #machinelearning #CNNs
David Enard@denard.bsky.social · 7mo ago1/5) After months scratching our heads (Is this why I am bald?) when analyzing the performance of CNNs to find sweeps in real genomes, postdoc Jesus Murga Moreno figured out that training with simulations with recombination that closely reflects the distribution of recombination in the real genome
1/5) After months scratching our heads (Is this why I am bald?) when analyzing the performance of CNNs to find sweeps in real genomes, postdoc Jesus Murga Moreno figured out that training with simulations with recombination that closely reflects the distribution of recombination in the real genome
