Li Lei @lilei0051.bsky.social · 21/06/2026 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... 001
Li Lei @lilei0051.bsky.social · 29/01/2026Excited 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 #Geneticsonlinelibrary.wiley.comPhenotypically Wild Barley Shows Evidence of Introgression From Domesticated BarleyMultiple 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... 042
Li Lei @lilei0051.bsky.social · 08/01/2026Hi all, please join our session in Plant and Animal Genome Conference next Tuesday afternoon. #PAG2026 000
Li Lei @lilei0051.bsky.social · 09/12/2025Plant 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! 043
Reposted by Li LeiLi Lei @lilei0051.bsky.social · 21/10/2025It’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! 001
Li Lei @lilei0051.bsky.social · 21/10/2025It’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! 001
Reposted by Li LeiPeter Morrell @peterlmorrell.bsky.social · 14/07/2025Decoding 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 PlantCaduceuspnas.orgPNASProceedings 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... 021
Li Lei @lilei0051.bsky.social · 07/08/2025Fascinating 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.research.arcadiascience.comPhylogenies and biological foundation modelsBiological 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... 000
Li Lei @lilei0051.bsky.social · 06/06/2025Our 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...frontiersin.orgFrontiers | Editorial: Crop Domestication and Selection – An Evolutionary View Affecting the Development of Agronomic TraitsCrop domestication – the evolution of wild plants for human use – is central to agriculture. Through artificial selection, humans have shaped traits like lar... 010
Reposted by Li LeiPeter Morrell @peterlmorrell.bsky.social · 05/06/2025New 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...journals.plos.orgSodium azide mutagenesis induces a unique pattern of mutationsAuthor 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 ... 053
Li Lei @lilei0051.bsky.social · 13/03/2025I’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 021
Li Lei @lilei0051.bsky.social · 12/03/2025Thrilled 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 120
Li Lei @lilei0051.bsky.social · 01/03/2025I’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...openai.com1,000 Scientist AI Jam Session: Advancing science with the U.S. national labsOpenAI and nine national labs bring together leading scientists for first-of-its kind event. 010
Li Lei @lilei0051.bsky.social · 09/01/2025Heading to #PAG 32 in San Diego. Welcome to join our workshop of Plant Cistrome on Tuseday 4pm! 110
Li Lei @lilei0051.bsky.social · 12/12/2024Thrilled to be invited to review a grant for the European Research Council! Honored to contribute to advancing groundbreaking research on a global scale. 020
Li Lei @lilei0051.bsky.social · 02/12/2024After 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! 000
Li Lei @lilei0051.bsky.social · 02/11/2024I’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! 021
Li Lei @lilei0051.bsky.social · 21/10/2024Hi 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! 030
Li Lei @lilei0051.bsky.social · 16/10/2024Our review manuscript is out! Welcome to check: doi.org/10.1093/pcp/...doi.orgEnhancers in Plant Development, Adaptation, and EvolutionAbstract. Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene 011
Reposted by Li LeiPeter Morrell @peterlmorrell.bsky.social · 08/08/2024This 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...nature.comAdaptive gene loss in the common bean pan-genome during range expansion and domestication - Nature CommunicationsCommon 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... 002
Reposted by Li LeiPeter Morrell @peterlmorrell.bsky.social · 08/07/2024Chaochih 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. 001
Li Lei @lilei0051.bsky.social · 04/07/2024Our manuscript about barley introgression is online now, welcome to read it! 010
Li Lei @lilei0051.bsky.social · 09/06/2024I 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. 050
Reposted by Li LeiPeter Morrell @peterlmorrell.bsky.social · 08/05/2024We'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...doi.orgSodium azide mutagenesis induces a unique pattern of mutationsbioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution 043