Publications:
* indicates co-first author, equal contribution.
Bold text highlights the Zhao lab members.
Preprints:
Lena Lampe, Clare L Newell, Bing-Jun Wang, Rami Makki, Cyrille Alexandre, Ian S Gilmore, Li Zhao, Alex P Gould. Identification of a specialized lipid barrier for Drosophila metamorphosis. [preprint] Available from:
https://www.biorxiv.org/content/10.1101/2024.10.11.617838v1.abstract
Ammon Thompson, Michael R May, Ben Hopkins, Nerisa Riedl, Olga Barmina, Benjamin J Liebeskind, Li Zhao, David Begun, Artyom Kopp. Quantifying transcriptome turnover on phylogenies by modeling gene expression as a binary trait. [preprint] Available from:
https://www.biorxiv.org/content/10.1101/2024.10.03.616564v1.abstract
Lee U, Arsala D, Xia S, Li C, Ali M, Svetec N, Langer CB, Sobreira D, Eres I, Sosa D, Chen J, Zhang L, Reilly P, Guzzetta A, Emerson J, Andolfatto P, Zhao L, Long M. The 3-Dimensional Genome Drives the Evolution of Asymmetric Gene Duplicates via Enhancer Capture-Divergence. [preprint]. 2024 January. Available from: http://biorxiv.org/content/early/2024/01/06/2022.11.30.518413.abstract. doi: https://doi.org/10.1101/2022.11.30.518413.
Published:
• Wassing IE, Nishiyama A, Shikimachi R, Jia Q, Kikuchi A, Hiruta M, Sugimura K, Hong X, Chiba Y, Peng J, Jenness C, Nakanishi M, Zhao L, Arita K, Funabiki H. CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in eukaryotes. Science Advances. 2024 Aug ; 10(34) . doi: 10.1126/sciadv.adp5753. Preprint || Journal || PDF
• Zhao L, Svetec N, Begun DJ. De novo genes. Annual Review of Genetics. 2024 July 24 ; (58). doi.org/10.1146/annurev-genet-111523-102413. PubMed PMID: 39088850; Journal || PDF
• Lee U, Mozeika S, Zhao L. A Synergistic, Cultivator Model of De Novo Gene Origination. Genome Biology and Evolution. 2024 May 15 ; evae103. doi.org/10.1093/gbe/evae103. PubMed PMID: 38748819; Journal || PDF
• Peng J, Svetec N, Molina H, Zhao L. The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions. Molecular Biology and Evolution. 2024 Apr 2;41(4). doi: 10.1093/molbev/msae065. PubMed PMID: 38518286; PubMed Central PMCID: PMC11017328..Preprint || Journal || PDF
• Peng J, Zhao L. The origin and structural evolution of de novo genes in Drosophila. Nature Communications. 2024 Jan 27;15(1):810. DOI: 10.1038/s41467-024-45028-1. Preprint || Journal || PDF
• Zhao L (2023). De novo genes: from non-genic to genic. Nature Reviews Genetics. 2024 Feb;25(2):81. https://doi.org/10.1038/s41576-023-00672-z. Journal || PDF
• Liu Y, Liu S, Tomar A, Yen FS, Unlu G, Ropek N, Weber RA, Wang Y, Khan A, Gad M, Peng J, Terzi E, Alwaseem H, Pagano AE, Heissel S, Molina H, Allwein B, Kenny TC, Possemato RL, Zhao L, Hite RK, Vinogradova EV, Mansy SS, Birsoy K. Autoregulatory control of mitochondrial glutathione homeostasis. Science. 2023 Nov 2;:eadf4154. doi: 10.1126/science.adf4154. Journal || PDF
• Khodursky S*, Zheng EB*, Svetec N, Durkin SM, Benjamin S, Gadau A, Wu X, Zhao L (2023). The evolution and mutational robustness of chromatin accessibility in Drosophila. Genome Biology. 24(1):232. doi: 10.1186/s13059-023-03079-5. Preprint || Journal || PDF
• Witt E, Langer CB, Svetec N, Zhao L (2023). Transcriptional and mutational signatures of the ageing germline. Nature Ecology & Evolution. 7(3):440-449. https://doi.org/10.1038/s41559-022-01958-x. Preprint || Journal || PDF
• Venkataraman K, Shai N, Lakhiani P, Zylka S, Zhao J, Herre M, Zeng J, Neal LA, Molina H, Zhao L, Vosshall LV. (2023). Rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought. eLife. 12:e80489. doi: https://doi.org/10.1101/2022.03.01.482582. Preprint || Journal
• Khodursky S, Jiang CS, Zheng EB, Vaughan R, Schrider DR, Zhao L (2022). Sex differences in inter-individual gene expression variability across human tissues. PNAS Nexus. DOI:10.1093/pnasnexus/pgac243. Preprint || Journal
• Zheng EB, Zhao L (2022). Protein evidence of unannotated ORFs in Drosophila reveals unappreciated diversity in the evolution of young proteins. eLife. 11:e78772. doi: 10.7554/eLife.78772. Preprint || Journal
• Cridland JM, Majane AC, Zhao L, Begun DJ (2022). Population biology of accessory gland-expressed de novo genes in Drosophila melanogaster. Genetics. 2022;220:iyab207. Journal
• Peng J, Svetec N, Zhao L (2022). Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels. Molecular Biology and Evolution. msab350. doi: 10.1093/molbev/msab350 Preprint || Journal
• Witt E, Shao Z, Hu C, Krause HM, Zhao L (2021). Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis. PLOS Genetics. 17(8):e1009728. doi: 10.1371/journal.pgen.1009728. Preprint || Journal
Webapp for testis single cell sequencing results: https://zhao.labapps.rockefeller.edu/gene-expr/
• Durkin SM, Chakraborty M, Abrieux A, Lewald KM, Gadau A, Svetec N, Peng J, Kopyto M, Langer CB, Chiu JC, Emerson JJ, Zhao L (2021). Behavioral and genomic sensory adaptations underlying the pest activity of Drosophila suzukii. Molecular Biology and Evolution. msab048. doi: 10.1093/molbev/msab048. Preprint || Journal || PDF.
• Witt E, Svetec N, Benjamin S, Zhao L (2021). Transcription factors drive opposite relationships between gene age and tissue specificity in male and female Drosophila gonads. Molecular Biology and Evolution. msab011. doi: 10.1093/molbev/msab011. Preprint || Journal || PDF.
• Khodursky S*, Svetec N*, Durkin S, Zhao L (2020). The evolution of sex-biased gene expression in the Drosophila brain. Genome Research. doi:10.1101/gr.259069.119. Preprint || Journal || PDF.
• Levran O, Even-Tov E, Zhao L (2020). A hominid-specific shift in cerebellar expression, upstream retrotransposons, and a potential cis-regulatory mechanism: bioinformatics analyses of the mu-opioid receptor gene. Heredity 124:325–335. doi:10.1038/s41437-019-0282-3. Journal || PDF.
• Witt E, Benjamin S, Svetec N, Zhao L (2019). Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila. eLife 8:e47138. Preprint || Journal || PDF.
eLife Insight link. RU Press news story link.
• Li S, Zheng EB, Zhao L, Liu S. (2019). Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors. Cell Reports 28:2689-2703.e4. Preprint || Journal || PDF.
• Svetec N, Saelao P, Cridland JM, Hoffmann AA, Begun DJ (2019). Functional analysis of a putative target of spatially varying selection in the Menin1 gene of Drosophila melanogaster. G3: Genes, Genomes, Genetics 9: 73–80. Journal || PDF
• Matthews BJ, Dudchenko O, Kingan S, et al…, Zhao L, et al…, Vosshall LB (2018). Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control. Nature 563, 501–507. Preprint || Journal || PDF
• Zhao L, Begun DJ (2017). Genomics of parallel adaptation at two timescales in the Drosophila model. PLOS Genetics. 13 (10), e1007016 . PDF
• Svetec N, Cridland JM, Zhao L, Begun DJ (2016). The adaptive significance of natural genetic variation in the DNA damage response of Drosophila melanogaster. PLOS Genetics. 12(3): e1005869. PDF
• Li X, Fan D, Zhang W, Liu G, Zhang L, Zhao L, Fang X, Chen L, Dong Y, Chen Y, Ding Y, Zhao R, Feng M, Zhu Y, Feng Y, Jiang X, Zhu D, Xiang H, Feng X, Li S, Wang J, Zhang G, Kronforst M R, Wang W, (2015). Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. Nature communications. 6:8212. PDF
• Zhao L, Wit J, Svetec N, Begun DJ. (2015). Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans. PLOS Genetics. 11(5): e1005184. PDF
• Svetec N, Zhao L, Saelao P, Chiu JC, Begun DJ. (2015). Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster. BMC Evolutionary Biology. 15:41 PDF
• Zhao L, Saelao P, Jones CD, and Begun DJ. (2014). Origin and spread of de novo genes in Drosophila melanogaster populations. Science 343:769–772. PDF
• Chiu JC, Jiang X, Zhao L, Hamm CA, Cridland JM, Saelao P, Hamby KA, Lee EK, Kwok RS, Zhang G, Zalom FG, Walton VM, Begun DJ. (2013). Genome of Drosophila suzukii, the spotted wing Drosophila. G3: Genes, Genomes, Genetics 3:2257–2271. PDF
• Zhou Q*, Zhu HM*, Huang QF*, Zhao L*, Zhang GJ*, Roy SW, Vicoso B, Xuan ZL, Ruan J, Zhang Y, Zhao RP, Ye C, Zhang XQ, Wang J, Wang W, Bachtrog D. (2012) Deciphering neo-sex and B chromosome evolution by complete genome of Drosophila albomicans. BMC genomics 13:109 PDF
• Xing WJ, Han BD, Wu Q, Zhao L, Bao XH, Bou S. Molecular cloning and characterization of Izumo1 gene from sheep and cashmere goat reveal alternative splicing. Molecular Biology Reports 2011, 38(3): 1995-2006 PDF
• Ding Y*, Zhao L*, Yang S, Jiang Y, Chen Y, Zhao R, Zhang Y, Zhang G, Dong Y, Yu H, Zhou Q, Wang W. (2010) A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes. PLOS Genetics 6:p. e1001255 PDF
• Xiang H, Zhu J, Chen Q, Dai F, Li X, Li M, Zhang H, Zhang G, Li D, Dong Y, Zhao L, Lin Y, Cheng D, Yu J, Sun J, Zhou X, Ma K, He Y, Zhao Y, Guo S, Ye M, Guo G, Li Y, Li R, Zhang X, Ma L, Kristiansen K, Guo Q, Jiang J, Beck S, Xia Q, Wang W, Wang J. (2010) Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nature Biotechnology 28:516-20 PDF
• Li X*, Zhao L*, Jiang H, Wang W. (2009) Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes. Journal of Molecular Evolution 68:56-65 PDF