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!
Interested in AI, population genetics, comparative genomics, bioinformatics. All opinions are mine and not @syngenta!
Reposted by Li Lei
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!
October 21, 2025 at 3:10 AM
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!
October 21, 2025 at 3:10 AM
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!
Reposted by Li Lei
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...
www.pnas.org
July 14, 2025 at 10:36 PM
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.
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
August 7, 2025 at 10:55 PM
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...
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...
www.frontiersin.org
June 6, 2025 at 12:01 AM
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...
Reposted by Li Lei
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...
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
June 5, 2025 at 4:09 PM
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...
journals.plos.org/plosgenetics...
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
March 12, 2025 at 10:36 PM
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
March 1, 2025 at 12:05 AM
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...
Thrilled to be invited to review a grant for the European Research Council! Honored to contribute to advancing groundbreaking research on a global scale.
December 12, 2024 at 9:30 PM
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!
December 2, 2024 at 9:31 PM
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!
November 2, 2024 at 1:26 AM
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!
October 21, 2024 at 10:34 PM
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/...
Enhancers in Plant Development, Adaptation, and Evolution
Abstract. Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene
doi.org
October 16, 2024 at 5:21 PM
Our review manuscript is out! Welcome to check: doi.org/10.1093/pcp/...
Reposted by Li Lei
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...
August 8, 2024 at 9:58 PM
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...
Reposted by Li Lei
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.
Phenotypically wild barley shows evidence of introgression from cultivated barley https://www.biorxiv.org/content/10.1101/2024.07.01.601622v1
Phenotypically wild barley shows evidence of introgression from cultivated barley https://www.biorxiv.org/content/10.1101/2024.07.01.601622v1
Plant conservation hinges on preserving biodiversity, which is crucial for long-term adaptation. Mul
www.biorxiv.org
July 8, 2024 at 8:14 PM
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!
Phenotypically wild barley shows evidence of introgression from cultivated barley https://www.biorxiv.org/content/10.1101/2024.07.01.601622v1
Phenotypically wild barley shows evidence of introgression from cultivated barley https://www.biorxiv.org/content/10.1101/2024.07.01.601622v1
Plant conservation hinges on preserving biodiversity, which is crucial for long-term adaptation. Mul
www.biorxiv.org
July 4, 2024 at 10:24 PM
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.
June 9, 2024 at 8:11 PM
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.
Reposted by Li Lei
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...
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
May 8, 2024 at 6:13 PM
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...
We also find small indels are more abundant in treated lines.
doi.org/10.1101/2024...