Decoding nature’s grammar with DNA language models | PNAS www.pnas.org/doi/10.1073/... - Serguei Pakhomov was a great co-author for this commentary on PlantCaduceus

Fascinating read connecting Felsenstein’s 1985 insights to modern biological foundation models. Love the perplexity idea—curious how it could extend to multi-omics & even guide loss functions for phylogenetically balanced training.

Our editorial paper about evolution is out, welcome to check! Thanks for my co editors: Hong An, Tian Xiang, and my postdoc Bliss Beernink. www.frontiersin.org/journals/pla...

New paper w/ @plos.org! @chaochihl.bsky.social identifies a unique mutational pattern among sodium azide-induced mutants. SNPs in 'CC' context and indels. Thanks to @justinfay.bsky.social @lilei0051.bsky.social @giuliafrascarelli.bsky.social @nanoporetech.com et al journals.plos.org/plosgenetics...

I’m incredibly proud of my postdoc, @BlissBeernink, for delivering a fantastic talk at the @JGI Science Forum! Well done, and thank you for your great work! #Science #Research

Thrilled and honored to share my career development journey with the incredible high school students from Oakland High who visited Berkeley Lab today! Inspiring the next generation of scientists and innovators is truly a privilege. #STEM #CareerDevelopment #NextGenScientists

I’m thrilled to attend the 1,000 Scientist AI Jam Session: Advancing Science with the U.S. National Labs to test their new models—what an incredible opportunity! openai.com/global-affai...

Heading to #PAG 32 in San Diego. Welcome to join our workshop of Plant Cistrome on Tuseday 4pm!

Thrilled to be invited to review a grant for the European Research Council! Honored to contribute to advancing groundbreaking research on a global scale.

After weeks of hard work and dedication, even through the Thanksgiving break, my collaborators and I successfully submitted two proposals! I am deeply grateful to my amazing collaborators for their invaluable support and efforts throughout the proposal drafting process. Thank you all!

I’m thrilled to have been invited to give a job shadow session to Brentwood High School students! I shared my research and my journey to becoming a scientist with them, and they asked so many insightful questions. Thanks to those curious and enthusiastic high school students!

Hi all. Dr. Ronan O'Malley and I will organize a workshop of "Plant Cistromics" in #Plant and Animal Conference 2025 in Junary 14th at 4pm in San Diego. Welcome to join us at that time!

Our review manuscript is out! Welcome to check: doi.org/10.1093/pcp/...

This paper from Gaia Cortinovis, Roberto Papa, et al. is now out. Multiple domestications and introductions of common bean beyond the New World make this an interesting system for studying the genetic nature of adaptation. www.nature.com/articles/s41...

Chaochih Liu, @lilei0051.bsky.social, and many others contributed to our study of introgression from cultivated into wild barley. ~ 16% of wild barley accessions appear introgressed. Some individuals display domestication-relate traits, but typically, the portion of the genome affected is small.

Our manuscript about barley introgression is online now, welcome to read it!

I am really excited that my postdoc Bliss Beernink and I finished writing a review paper about plant enhancers in a month and half. That's so impressive! I am proud of our team! We submitted it today! I really appreciate her working so hard to write this manuscript with me.

We've found that the common chemical mutagen sodium azide produces a very specific pattern of mutations in a specific nucleotide context. The 2 nucleotide context limits the types of amino acid changes observed. We also find small indels are more abundant in treated lines. doi.org/10.1101/2024...