AI Will Not Replace Biologists. But Biologists Who Understand AI Systems Will Replace Those Who Only Use AI Tools. Link: lilei4409.blogspot.com/2026/06/from...
Li Lei
@lilei0051.bsky.social
Biotech AI Scientist in industry, formal PI in DOE Joint Genome Institute. Interested in AI, population genetics, comparative genomics, bioinformatics. All opinions are mine and not @syngenta!
Excited to share our new Molecular Ecology paper with @peterlmorrell.bsky.social, @chaochihl.bsky.social, & collaborators: phenotypically wild barley shows evidence of introgression from domesticated barley in the WBDC collection. doi.org/10.1111/mec.... #Barley #Genetics
Phenotypically Wild Barley Shows Evidence of Introgression From Domesticated Barley
Multiple studies have reported genetic evidence of crop-to-wild introgression in phenotypically wild accessions of wild barley (Hordeum vulgare ssp. spontaneum). We examined 318 Wild Barley Diversity...
onlinelibrary.wiley.com
Hi all, please join our session in Plant and Animal Genome Conference next Tuesday afternoon. #PAG2026
Plant cistromics folks, let’s meet at #PAG2026 🌱 Join our Plant Cistromics session (Palm 8) to talk chromatin, regulatory elements & cis-reg networks in crops. 🗓 Tue, Jan 13 🕓 4:00 PM Come share data, ideas & future collabs!
It’s that time of year again — PAG abstract submissions are open! 🌿 I’m organizing a Plant Cistromics session this year, and we’d love to see your work. Submit an abstract and share your exciting research with the community!
It’s that time of year again — PAG abstract submissions are open! 🌿 I’m organizing a Plant Cistromics session this year, and we’d love to see your work. Submit an abstract and share your exciting research with the community!
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
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
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.
Phylogenies and biological foundation models
Biological foundation models are, at their core, evolutionary comparisons on massive scales. As with all comparative studies, evolutionary nonindependence determines their power. We chart how this aff...
research.arcadiascience.com
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...
Frontiers | Editorial: Crop Domestication and Selection – An Evolutionary View Affecting the Development of Agronomic Traits
Crop domestication – the evolution of wild plants for human use – is central to agriculture. Through artificial selection, humans have shaped traits like lar...
frontiersin.org
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...
Sodium azide mutagenesis induces a unique pattern of mutations
Author summary Sodium azide is frequently used as a mutagen for experimental studies in plants. It induces primarily C → T changes. We find that these most often occur when a cytosine (C) is followed ...
journals.plos.org
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...
1,000 Scientist AI Jam Session: Advancing science with the U.S. national labs
OpenAI and nine national labs bring together leading scientists for first-of-its kind event.
openai.com
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!
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...
Adaptive gene loss in the common bean pan-genome during range expansion and domestication - Nature Communications
Common bean is an evolutionary model for studying adaptive diversity in legumes. Here, the authors present the common bean pangenome based on five high-quality genomes and whole-genome reads of 339 wi...
nature.com
Peter Morrell@peterlmorrell.bsky.social · 2y agoAdaptive gene loss in the common bean pan-genome during range expansion and domestication - Roberto Papa & colleagues - www.biorxiv.org/content/10.1...
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.
bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 2y agoPhenotypically wild barley shows evidence of introgression from cultivated barley https://www.biorxiv.org/content/10.1101/2024.07.01.601622v1
Our manuscript about barley introgression is online now, welcome to read it!
bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 2y agoPhenotypically wild barley shows evidence of introgression from cultivated barley https://www.biorxiv.org/content/10.1101/2024.07.01.601622v1
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...
Sodium azide mutagenesis induces a unique pattern of mutations
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
doi.org