08/2024: Li, Nicolas, and David wrote a review article about de novo genes for Annual Review of Genetics. Please see the link here: https://www.annualreviews.org/content/journals/10.1146/annurev-genet-111523-102413. If you are not able to download the pdf, please send Li or Nicolas an email. Thank you, editors at the Annual Review of Genetics for the invitation.
08/2024: Congratulations on the recent work from Hiro Funabiki lab: https://www.science.org/doi/full/10.1126/sciadv.adp5753, in which Junhui helped with the Alphafold2 multimer structural modeling. Congratuions Junhui and all.
08/2024: We said goodbye to Xia Wu, Eli Woloshin, and Yufei Wang over the past two months. Xia moved to graduate school in Iowa, Eli to Spain, and Yufei to China. We wish they find excitement in their work and life, no matter where in the world they are.
06/2024: UnJin’s perspective about a cultivator model of de novo gene origin is published. The link is here: https://academic.oup.com/gbe/article/16/6/evae103/7674236. This cultivator-focused model posits the importance of selectively advantageous functions for the cultivator genes, rather than solely by the de novo genes, emphasizing the critical role of genome organization in the evolution of new genes. Congratulations, UnJin and Shawn!
1/2024: Congratulations, Junhui, on the paper regarding de novo protein structures: https://www.nature.com/articles/s41467-024-45028-1! We are very proud of this work and eagerly anticipate further insights into how structural novelty enables functional novelty.
11/2023: Junhui and Li contributed to a small part of the exceptional research led by Yuyang Liu and others at Birsoy Lab. Congratulations to Yuyang, Kivanc, and all the authors. The paper is recently published in Science https://www.science.org/doi/abs/10.1126/science.adf4154.
10/2023: Li wrote a synopsis for Nature Reviews Genetics. Please read her aspects about an important paper in the field https://www.nature.com/articles/s41576-023-00672-z. A pdf version without the need of subscription is here https://rdcu.be/dpwTH.
10/2023: Very proud that Sam and Eric’s paper is officially published in Genome Biology https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03079-5. Congratulations, Sam, Eric, and all authors!
08/2023 We welcomed Sasha Mills as our new research assistant in the lab. Sasha was an undergraduate researcher in Paul Schmidt’s lab at UPenn. We look forward to working on great science together with Sasha.
08/2023 We said goodbye to Vivian Yan, our research assistant who is heading to Mt Sinai for a PhD degree.
07/2027 Shawn passed his TRP. Congratulations to our new PhD candidate!
07/2023 We said goodbye to Sam Khodursky, the first-ever rotation student in the lab. Sam (or Dr. Khodursky) is heading to UPenn for an MD degree. We wish him all the best for a bright future and hope he will become an excellent physician-scientist “for the benefit of mankind” (RU’s motto).
07/2023 We had a lab retreat in upstate New York. The weather and the view were both gorgeous.
06/2023 We welcomed James Pham from Cornell University for summer research. James is part of the Tri-I Gateways to the Laboratory Summer Program https://mdphd.weill.cornell.edu/summer-program. James will conduct research until mid-August.
06/2023 We have a new preprint from the lab. Sam and Eric, as well as several other lab members (Nicolas, Sigi, Sylvia, Alice, Xia) studied the regulatory basis for open chromatin conformation https://www.biorxiv.org/content/10.1101/2023.06.26.546587v1. We are very proud of this work.
04/2023: Rockefeller University’s Seek magazine published an article about Li’s journey to studying new genes Seeking the origin story of de novo genes https://www.rockefeller.edu/news/33847-seeking-the-origin-story-of-de-novo-genes/. Thank you for writing this beautiful piece.
03/2023 Check Junhui’s new preprint here https://www.biorxiv.org/content/10.1101/2023.03.13.532420v2. Junhui used comparative genomics and structural modeling to study how brand new proteins originate and evolve. Check our surprising results in the preprint please.
01/2023 Evan’s paper entitled “Transcriptional and mutational signatures of the Drosophila ageing germline” is officially published in Nature Ecology & Evolution. The link is here. Congratulations, Evan, Chris, and Nico!
10/2022 Sam’s paper entitled “Sex differences in inter-individual gene expression variability across human tissues” has been officially accepted in PNAS Nexus. Congratulations, Sam! Thanks to all who contributed and helped with the project.
09/2022 UnJin and Bingjun join the lab as postdocs. Shawn joins the lab as a graduate student. Eli joins the lab as a research assistant. Welcome, all!
07/2022 We had a bittersweet moment to farewell Chris Langer, our research assistant and lab manager for the last three years. Chris will pursue his PhD degree at New York University Medical School. We are happy for him and glad that he will only be about 30 blocks away!
06/2022 We say goodbye to Xin Yu Zhu Jiang, our undergraduate student from Hunter College in the last two years. Xin Yu is going to graduate school at Weill Cornell Medical College. Congratulations, Xin Yu.
04/2022, 08/2022 Excited to share our new preprint by Eric Zheng and its updated version on 08/22. The link is here. In this work, Eric developed a novel method to use the mass-spectrometry method to identify unannotated ORFs and study the evolutionary principles of these small ORFs.
02/2022 After the rotation, Cong Li officially joined the lab for his PhD research. Welcome, Cong!
02/2022 Thanks to Vallee Foundation for writing the news to promote our science, Li Zhao named Allen Distinguished Investigator.
02/2022 Li is named Allen Distinguished Investigator! Thank you, Paul G. Allen Frontiers Group & Paul G. Allen Family Foundation for supporting our science. Together with the team of Mande Holford, we will study the evolution and functions of immune-related micropeptides.
01/2022 Dulce Moran from Bard Colleague starts her internship in the lab for this semester. Welcome, Dulce!
12/2021 Our preprint is officially accepted and published in MBE, Molecular Biology and Evolution. Congratulation to Junhui & Nico! Junhui spearheaded the project, and Nico helped extend the role of intermolecular interactions to a population level.
11/2021 We posted a new preprint “Transcriptional and mutational signatures of the aging germline” on bioRxiv. The link is here. We welcome and would appreciate your comments and suggestions.
11/2021 Evan defended his PhD on Nov. 19. Congratulations, Dr. Witt! https://twitter.com/lizzyzhao/status/1463156489728798734?s=20.
10/2021 Check the nice article from Seek Magazine for Sylvia & all’s work on egg-laying behavior of D. suzukii and closely related species https://seek.rockefeller.edu/this-fly-likes-its-fruit-fresh/ .
08/2021 Rotation student Cong Li arrived on campus and will work on exciting behavioral phenotypes of Drosophila.
07/2021 Our preprint of “Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis”, link here is accepted in PLOS Genetics! Congratulations, Evan, and our collaborators!
02/2021 Please check our published work on the egg-laying behavior evolution for D. suzukii. Thanks again for the wonderful colleagues from Joanna Chiu lab (), J.J. Emerson lab (), and our lab (), who made the collaborative work possible.
02/2021 Excited to share our new preprint entitled “Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis”, link here. In this manuscript we provided an answer for an important scientific problem that has been debated for many years, while opened the door for many other unknown questions. A wonderful collaboration with Henry Krause lab from University of Toronto.
01/2021 Our paper on the role of transcription factor in gene age and tissue specificity is out in MBE (Molecular Biology and Evolution), link here. Congratulation Evan, Nico, and Sigi!
01/2021 Congratulations to graduate student Alice Gadau on the Rosemary Grant Advanced award (link here)! So happy for her and all the awardees. Thank you the Society for the study of Evolution for your generous support to early career researchers.
12/2020 Please check our new preprint entitled “Transcription factors drive opposite relationships between gene age and tissue specificity in male and female Drosophila gonads” here. Congratulation to all the authors!
10/2020 We are very glad to host Xin Yu Zhu Jiang and Eamon Ho from Hunter College as undergraduate researchers. The Pandemic has made mentorship difficult, and we try our best to provide students a safe and rigorous research environment. Both Xin Yu and Eamon are Yalow scholars.
10/2020 We posted a preprint entitled “Behavioral and genomic sensory adaptations underlying the pest activity of Drosophila suzukii” on bioRxiv! Please find it here. A wonderful collaboration with the lab of J.J. Emerson at UC Irvine and Joanna Chiu at UC Davis. Congratulations, all!
08/2020 Li is named a 2020 Vallee Scholar. Thank you, The Vallee Foundation, for supporting our science! News please see here.
06/2020 Our paper The evolution of sex-biased gene expression in the Drosophila brain is officially accepted in Genome Research. FREE PDF link is here. Congratulations again, Sam, Nico, and Sylvia.
06/2020 Alice passed her TRP! Congratulations Alice. Look forward to the exciting research in the next several years.
04/2020 We have a preprint on The evolution of sex-biased gene expression in the Drosophila brain uploaded to bioRxiv. We are very excited about this work. Congratulations to Sam, Nico, and Sylvia.
03/2020: We received a large number of emails from Drosophila biologists who are interested in checking testis single-cell expression of their genes of interest. To help with it, we created a Shiny app, please check it here https://zhao.labapps.rockefeller.edu/gene-expr/ and let us know if you have questions or suggestions.
11/2019: The paper that Eran and Li contributed is out in Heredity. This work was led by Dr. Orna Levran. In this work, we studied the gene expression evolution of the mu-opioid receptors (MOR, OPRM1), and found a species-specific pattern for cerebellar expression. We then investigated the possible mechanism responsible for the novel patterns. Not only new genes evolve, functionally conserved genes evolve too.
09/2019: The paper that Eric and Li contributed is out in Cell Reports. This work was led by Dr. Sai Li (Liu lab) and Dr. Shixin Liu. This work studied the nonreciprocal cooperativity of pioneer transcriptionfactors Sox2 and Oct4 in vitro and in vivo. Congratulations, all!
08/2019: Our paper is published in eLife. In this paper, we studied the dynamics of de novo gene transcription and germline mutational load and bias. Congratulations, Evan, Sigi, and Nico!
07/2019: Li is named as a Rita Allen Foundation Scholar. Thank you, Rita Allen Foundation, for supporting our work.
06/2019: Alice Gadau joined our lab after a rotation. Welcome, Alice!
06/2019: We moved to the new campus on June 24, 2019. Check the amazing building that locates on top of FDR: https://snf-dr-rivercampus.rockefeller.edu.
04/2019: Sam passed his TRP! Great thanks to the committee members.
03/2019: Our lab is in the fly meeting this year! We have three talks and two posters, please check out our work and keep in touch.
Nicolas will give a talk in the Evolution platform at 4:45 pm , March 28.
Evan will give a talk in Reproduction and Gametogenesis at 4 pm, March 29.
Li will give a talk in the sex workshop in the evening of March 28.
Update: Sylvia won a poster award in the fly meeting!
12/2018: Nicolas’s paper on the role of an SNP of menin1 genes in spatially varying selection is out in G3.
11/2018: The Aedes aegypti mosquito paper that Li contributed is published in Nature.
10/2018: Sam Khodursky joined our lab after a rotation.
09/2018: Eric passed his TRP! Great thanks to the committee members.
08/2018: Evan passed his TRP! Great thanks to the committee members.
06/2018: Miriam Kopyto comes back to the lab as an SSRP researcher. Miriam is accepted in Yale University after SSRP research in our lab last year.
04/2018: Michelle Timlin joined our lab as a postgraduate research intern.
04/2018: Li is awarded the Irma T. Hirschl/Monique Weill-Caulier Trusts Research Award.
02/2018: Li is awarded an Alfred P. Sloan Research Fellowship.
01/2018: Eran Even-Tov joined the lab as a postdoctoral researcher.
10/2017: The population genomics of Drosophila hydei is published in PLOS Genetics.
09/2017: MD-PhD student Eric Zheng joined the lab after a rotation.
09/2017: Graduate student Evan Witt joined the lab after a rotation.
07/17/2017: Sylvia Durkin joined our lab as a research assistant.
07/17/2017: Sigi Benjamin-Hong joined our lab as a research associate.
06/26/2017: Miriam Kopyto joined the lab as an SSRP student. Miriam is a high school student in Long Island.
03/01/2017: Li & Nicolas started to set up the lab. “Hello, World!”