Publications:
* indicates co-first author, equal contribution.
Bold text highlights the Zhao lab members.
Preprints:
Gene regulatory networks and essential transcription factors for de novo originated genes.
Peng J, Wang B, Svetec N, Zhao L.
[preprint] Available from:
https://www.biorxiv.org/content/10.1101/2024.10.11.617838v1.abstract
Identification of a specialized lipid barrier for Drosophila metamorphosis.
Lampe L, Newell CL, Wang B, Makki R, Alexandre C, Gilmore IS, Zhao L, Gould AP.
[preprint] Available from:
https://www.biorxiv.org/content/10.1101/2024.10.11.617838v1.abstract
Quantifying transcriptome turnover on phylogenies by modeling gene expression as a binary trait.
Thompson A, May MR, Hopkins B, Riedl N, Barmina O, Liebeskind BJ, Zhao L, Begun DJ, Kopp A.
[preprint] Available from:
https://www.biorxiv.org/content/10.1101/2024.10.03.616564v1.abstract
Published:
• The three-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence.
Lee U*, Arsala D*, Xia S*, Li C, Ali M, Svetec N, Langer CB, Sobreira DR, Eres I, Sosa D, Chen J, Zhang L, Reilly P, Guzzetta A, Emerson JJ, Andolfatto P, Zhao L, Long M (2024).
Science Advances. 10(51). DOI:10.1126/sciadv.adn6625.
Preprint || Journal || PDF
• CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in eukaryotes.
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 (2024).
Science Advances. 10(34). DOI:10.1126/sciadv.adp5753.
Preprint || Journal || PDF
• De novo genes.
Zhao L, Svetec N, Begun DJ (2024).
Annual Review of Genetics. (58). DOI: 10.1146/annurev-genet-111523-102413.
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• A Synergistic, Cultivator Model of De Novo Gene Origination.
Lee U, Mozeika S, Zhao L (2024).
Genome Biology and Evolution. evae103. DOI: 10.1093/gbe/evae103.
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• The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions.
Peng J, Svetec N, Molina H, Zhao L (2024).
Molecular Biology and Evolution. 41(4). DOI:10.1093/molbev/msae065.
Preprint || Journal || PDF
• The origin and structural evolution of de novo genes in Drosophila.
Peng J, Zhao L (2024).
Nature Communications. 15(1):810. DOI:10.1038/s41467-024-45028-1.
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• De novo genes: from non-genic to genic.
Zhao L (2024).
Nature Reviews Genetics. 25(2):81. DOI:10.1038/s41576-023-00672-z.
Journal || PDF
• Autoregulatory control of mitochondrial glutathione homeostasis.
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 (2023).
Science. :eadf4154. DOI:10.1126/science.adf4154.
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• The evolution and mutational robustness of chromatin accessibility in Drosophila.
Khodursky S*, Zheng EB*, Svetec N, Durkin SM, Benjamin S, Gadau A, Wu X, Zhao L (2023).
Genome Biology. 24(1):232. DOI: 10.1186/s13059-023-03079-5.
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• Transcriptional and mutational signatures of the ageing germline.
Witt E, Langer CB, Svetec N, Zhao L (2023).
Nature Ecology & Evolution. 7(3):440-449. DOI:10.1038/s41559-022-01958-x.
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• Rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought.
Venkataraman K, Shai N, Lakhiani P, Zylka S, Zhao J, Herre M, Zeng J, Neal LA, Molina H, Zhao L, Vosshall LV (2023).
eLife. 12:e80489. DOI: 10.1101/2022.03.01.482582.
Preprint || Journal
• Sex differences in inter-individual gene expression variability across human tissues.
Khodursky S, Jiang CS, Zheng EB, Vaughan R, Schrider DR, Zhao L (2022).
PNAS Nexus. DOI:10.1093/pnasnexus/pgac243.
Preprint || Journal
• Protein evidence of unannotated ORFs in Drosophila reveals unappreciated diversity in the evolution of young proteins.
Zheng EB, Zhao L (2022).
eLife. 11:e78772. DOI:10.7554/eLife.78772.
Preprint || Journal
• Population biology of accessory gland-expressed de novo genes in Drosophila melanogaster.
Cridland JM, Majane AC, Zhao L, Begun DJ (2022).
Genetics. 2022;220:iyab207. DOI:10.1093/genetics/iyab207
Journal
• Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels.
Peng J, Svetec N, Zhao L (2022).
Molecular Biology and Evolution. msab350. DOI:10.1093/molbev/msab350.
Preprint || Journal
• Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis.
Witt E, Shao Z, Hu C, Krause HM, Zhao L (2021).
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/
• Behavioral and genomic sensory adaptations underlying the pest activity of Drosophila suzukii.
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).
Molecular Biology and Evolution. msab048. DOI:10.1093/molbev/msab048.
Preprint || Journal || PDF.
• Transcription factors drive opposite relationships between gene age and tissue specificity in male and female Drosophila gonads.
Witt E, Svetec N, Benjamin S, Zhao L (2021).
Molecular Biology and Evolution. msab011. DOI:10.1093/molbev/msab011.
Preprint || Journal || PDF.
• The evolution of sex-biased gene expression in the Drosophila brain.
Khodursky S*, Svetec N*, Durkin S, Zhao L (2020).
Genome Research. 30:874-884. DOI:10.1101/gr.259069.119.
Preprint || Journal || PDF.
• A hominid-specific shift in cerebellar expression, upstream retrotransposons, and a potential cis-regulatory mechanism: bioinformatics analyses of the mu-opioid receptor gene.
Levran O, Even-Tov E, Zhao L (2020).
Heredity. 124:325–335. DOI:10.1038/s41437-019-0282-3.
Journal || PDF.
• Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila.
Witt E, Benjamin S, Svetec N, Zhao L (2019).
eLife. 8:e47138. DOI:10.7554/eLife.47138.
Preprint || Journal || PDF.
eLife Insight link. RU Press news story link.
• Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors.
Li S, Zheng EB, Zhao L, Liu S (2019).
Cell Reports. 28:2689-2703.e4. DOI:10.1016/j.celrep.2019.07.103.
Preprint || Journal || PDF.
• Functional analysis of a putative target of spatially varying selection in the Menin1 gene of Drosophila melanogaster.
Svetec N, Saelao P, Cridland JM, Hoffmann AA, Begun DJ (2019).
G3: Genes, Genomes, Genetics. 9: 73–80. DOI:10.1534/g3.118.200818.
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• Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control.
Matthews BJ, Dudchenko O, Kingan S, et al…, Zhao L, et al…, Vosshall LB (2018).
Nature 563, 501–507. DOI:10.1038/s41586-018-0692-z
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• Genomics of parallel adaptation at two timescales in the Drosophila model.
Zhao L, Begun DJ (2017).
PLOS Genetics. 13 (10), e1007016. DOI:10.1371/journal.pgen.1007016.
Journal
• The adaptive significance of natural genetic variation in the DNA damage response of Drosophila melanogaster.
Svetec N, Cridland JM, Zhao L, Begun DJ (2016).
PLOS Genetics. 12(3): e1005869. DOI:10.1371/journal.pgen.1005869.
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• Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies.
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).
Nature communications. 6:8212. DOI:10.1038/ncomms9212.
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• Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans.
Zhao L, Wit J, Svetec N, Begun DJ.(2015).
PLOS Genetics. 11(5): e1005184. DOI:10.1371/journal.pgen.1005184.
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• Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster.
Svetec N, Zhao L, Saelao P, Chiu JC, Begun DJ (2015).
BMC Evolutionary Biology. 15:41. DOI:10.1186/s12862-015-0316-2.
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• Origin and spread of de novo genes in Drosophila melanogaster populations.
Zhao L, Saelao P, Jones CD, and Begun DJ (2014).
Science 343:769–772. DOI:10.1126/science.1248286.
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• Genome of Drosophila suzukii, the spotted wing Drosophila.
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).
G3: Genes, Genomes, Genetics 3:2257–2271. DOI:10.1534/g3.113.008185.
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• Deciphering neo-sex and B chromosome evolution by complete genome of Drosophila albomicans.
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).
BMC genomics 13:109. DOI:10.1186/1471-2164-13-109.
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• Molecular cloning and characterization of Izumo1 gene from sheep and cashmere goat reveal alternative splicing.
Xing WJ, Han BD, Wu Q, Zhao L, Bao XH, Bou S (2011).
Molecular Biology Reports, 38(3): 1995-2006. DOI:10.1007/s11033-010-0322-9.
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• A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes.
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).
PLOS Genetics 6:p. e1001255. DOI:10.1371/journal.pgen.1001255.
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• Single base-resolution methylome of the silkworm reveals a sparse epigenomic map.
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).
Nature Biotechnology. 28:516-20. DOI:10.1038/nbt.1626.
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• Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes.
Li X*, Zhao L*, Jiang H, Wang W (2009).
Journal of Molecular Evolution. 68:56-65. DOI:10.1007/s00239-008-9187-0.
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