Yun S. Song @yun_s_song
Professor of EECS and Statistics at UC Berkeley. Mathematical and computational biologist. Joined March 2016-
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Highlighting some work I've enjoyed reading recently: "DNA language models are powerful predictors of genome-wide variant effects" by @gsbenegas, Sanjit Batra, and @yun_s_song: pnas.org/doi/10.1073/pn… It's simply incredible unsupervised DNA language models can learn so much!
momi3 is here! This is an impressive extension that achieves a 1000x speedup over momi2. Very pleased to see my former PhD student, Jonathan Terhorst, thriving in his career as a PI. doi.org/10.1101/2024.0…
For those in the NY area, SAVE THE DATE (& register) for a Symposium on Human Genetics at Columbia University: Oct 10-11 2024. Talks will also be streamed.
Probabilistic Modeling in Genomics (aka ProbGen) is an exceptional conference in computational biology. This year it will be held in Vienna, Austria, April 10-12 2024. Please consider submitting an abstract (due on Feb 15) to present your work! oeaw.ac.at/gmi/news-event…
Congratulations to @youngtableaux for having his really nice work (with me and @yun_s_song) on testing for exchangeability or feature independence officially come out! dx.doi.org/10.1214/23-AOA…
I've gotten several requests recently for permission to use the notes from my computational biology class: github.com/pachterlab/BI-… A reminder that they're licensed under CC BY 4.0: you're free to share and adapt, just give appropriate credit and indicate if changes were made.
Lior Pachter @lpachter
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960 Followers 324 Following Scientist working on the Quantitative Understanding of Human Metabolism and the Molecular Basis of Aging.Highlighting some work I've enjoyed reading recently: "DNA language models are powerful predictors of genome-wide variant effects" by @gsbenegas, Sanjit Batra, and @yun_s_song: pnas.org/doi/10.1073/pn… It's simply incredible unsupervised DNA language models can learn so much!
This is exciting work. Faster and better sampling of ancestral recombination graphs (the fundamental structure of genetic ancestry) is a game changer for many questions in population genetics.
We are delighted to share our work on a robust, accurate method for sampling genome-wide genealogies (aka ARGs) from the full posterior distribution. This is a product of years of hard work by @YunDeng5, who is jointly advised by @ras_nielsen and me. doi.org/10.1101/2024.0… 1/n
Online now @Nature the final version of Sandra Nakandakari’s universal LIPSTIC paper! Thanks to @MempelThorsten and the other reviewers for their very useful input. *Special* thanks to @KamphorstAlice for stepping in to help us out! nature.com/articles/s4158…
Why does the @arcinstitute post preprints on its website and not on @biorxivpreprint? The two are not equivalent. @biorxivpreprint provides a DOI (big deal because preprints can't just be changed on a whim). E.g. this "paper" doesn't even have a date. arcinstitute.org/manuscripts/Evo
Motivated by weekend morning tweets, I'd like to talk about normalization of soft corruption in academia. First, a story about my advisor, Lev Ginzburg, who fled Russia in the 70's and arrived in US with $50 in his pocket, a wife, and a new born child... 1/x (sorry long)
I am late to my own party, but I wanted to write a short 🧵 to put this talk in context. First of all, the @TEDTalks team was amazing; there is so much that goes into these seemingly short talks. It was an amazing experience and I made some new friends. ted.com/talks/hani_goo…
Want to annotate HLA/KIR genes and genotype them in a phased assembly? Try Immuannot, a new method from our group. It can identify novel alleles and reveal complex haplotype structures that short-read based methods may have troubles with. Available at github.com/YingZhou001/Im…
My first method work in a new field, we developed an assembly based annotation tool for HLA/KIR genes. Enjoyed working with Heng @lh3lh3 and Li @mourisl ! biorxiv.org/content/10.110…
Today is my last day as a Professor. Tomorrow I become Professor Emeritus. The 50+ years I've been in the field has seen revolutionary advances in both biology and computer science and it has been a joy to in the midst of that.
Thrilled that my new book Most Delicious Poison selected by @ScienceNews as one of 12 top science books of 2023! sciencenews.org/article/scienc…
Roy Rocklin, 1953-2023 rocklinlab.org/news/roy-david…
I’ll be presenting GPN-MSA at #ASHG, Reviewers’ Choice Poster PB4125 Fri 3-5PM. Come chat about DNA language models! x.com/yun_s_song/sta…
We recently posted a preprint describing GPN-MSA, a DNA language model that leverages whole-genome alignments across multiple species while taking only a few hours to train. This thread summarizes its performance on the human genome. doi.org/10.1101/2023.1… 1/12
Our work on computing likelihoods under the Discrete-Time Wright-Fisher model is out now in @GeneticsGSA . We used our machinery to look at recurrent mutation in large samples and see how demography and sample size interact when estimating selection academic.oup.com/genetics/artic…
#ASHG2023 I will be presenting a poster about my project in Ancestral Recombination Graph inference advised by professor @yun_s_song and @ras_nielsen, Friday 3pm-5pm, entitled “Efficient Bayesian inference of genome-wide genealogies for large samples”, at PB4128. Trailers:
@yun_s_song 3&4 applied for our @NatureRevGenet RNA-Seq: the teenage years review - the Editorial team was not a fan of the title but they wanted something dry and descriptive. I'm so glad I pushed back with a good argument. nature.com/articles/s4157…
@yun_s_song Congratulations Yun and team! Look forward to reading it.
@yun_s_song Congrats @yun_s_song for your perseverance. Your are doing your research off the beaten track. That is rare and demonstrates your independence of thought.
.@NatureRevGenet asked me to write about an inspiring article, and one immediately came to my mind. Whether you've read the original article or not, I hope you'll take 5-10 minutes to read my professional and personal perspective rdcu.be/dpwTH. @RockefellerUniv
amazing work by @gsbenegas!!! well fought and well deserved 👏✨
After 2 rejections & 4 rounds of review (all by the same journal), our first GPN paper is finally published: pnas.org/doi/10.1073/pn… We feel jaded, but it was worth the effort and we are grateful to the reviewers for their time & helpful feedback. Some lessons learned: (1/2)