赵黎｜清华大学｜学者主页

2026

A predicted structural interactome reveals binding interference from intrinsically disordered regions

Jun-Hui Peng, Li Zhao

PLoS Comput. Biol.

DOI

2026

Molecular evolution of CO2-sensing ab1C neurons underlies divergent sensory responses in the Drosophila suzukii species group

Alice Gadau, S. Mills, Xin-Yu-Zhu Jiang, Cong Li, N. Svetec, Ziyu Xu, Wan-He Li, Katherine I. Nagel, Li Zhao

PLoS Genetics

DOI

2026

HP6/Umbrea, a rapidly evolving Drosophila HP1-family paralog, is a candidate HP1a-recruited plasticizer of heterochromatin

UnJin Lee, Li Zhao

bioRxiv

DOI

2026

Evolution of MOSN, a novel sex-specifically spliced neuronal gene in the Aedes aegypti mosquito

Yael N. Tsitohay, N. Basrur, U. Palatini, Alexandra E. DeFoe, Thomas A. Jones, Jun-Hui Peng, Margaret Herre, Li Zhao, Sean R. Eddy, Nadav Shai, L. Vosshall

bioRxiv

DOI

2026

Regulatory divergence and effector turnover shape species-specific bacterial clearance in Drosophilidae

Cong Li, Bing-Jun Wang, Jun-Hui Peng, N. Svetec, Li Zhao

bioRxiv

DOI

2026

Machine learning for evolutionary genetics and molecular evolution

N. Svetec, UnJin Lee, Li Zhao

Trends in Genetics

DOI

2025

Comparative single-cell analysis of transcriptional bursting reveals the role of genome organization in de novo transcript origination

UnJin Lee, Cong Li, Christopher B. Langer, N. Svetec, Li Zhao

Proceedings of the National Academy of Sciences of the United States of America

DOI

2025

Gene regulatory networks and essential transcription factors for de novo-originated genes

Junhui Peng, Bing-Jun Wang, Nicolas Svetec, Li Zhao

Nature Ecology & Evolution

DOI

2025

De Novo Genes: Current Status and Future Goals

Claudio Casola, Victor Luria, Nikolaos Vakirlis, Li Zhao

Genome Biology and Evolution

DOI

2024

The origin and structural evolution of de novo genes in Drosophila

Jun-Hui Peng, Li Zhao

Nature Communications

DOI

2024

CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in eukaryotes

Isabel E. Wassing, Atsuya Nishiyama, Reia Shikimachi, Qingyuan Jia, Amika Kikuchi, Moeri Hiruta, Keita Sugimura, Xin Hong, Yoshie Chiba, Jun-Hui Peng, Christopher Jenness, M. Nakanishi, Li Zhao, K. Arita, H. Funabiki

Science Advances

DOI

2024

De Novo Genes

Li Zhao, N. Svetec, D. Begun

Annual Review of Genetics

DOI

2024

The three-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence

UnJin Lee, Deanna Arsala, Sheng-Qian Xia, Cong Li, Mujahid Ali, N. Svetec, Christopher B. Langer, Débora R. Sobreira, Ittai E Eres, Dylan Sosa, Jian-Hai Chen, Li Zhang, Patrick Reilly, Alexander Guzzetta, J. J. Emerson, Peter Andolfatto, Qi Zhou, Li Zhao, Man-Yuan Long

Science Advances

DOI

2024

A Synergistic, Cultivator Model of De Novo Gene Origination

UnJin Lee, Shawn Mozeika, Li Zhao

Genome Biology and Evolution

DOI

2024

The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions

Jun-Hui Peng, N. Svetec, H. Molina, Li Zhao

Molecular biology and evolution

DOI

2024

Identification of a specialized lipid barrier for Drosophila metamorphosis

Lena Lampe, Clare L. Newell, Bing-Jun Wang, Rami Makki, Cyrille Alexandre, Ian S. Gilmore, Li Zhao, Alex P. Gould

bioRxiv

DOI

2024

Quantifying Transcriptome Turnover on Phylogenies by Modeling Gene Expression as a Binary Trait

Ammon Thompson, Michael R. May, Ben R. Hopkins, Nerisa E Riedl, O. Barmina, Benjamin J. Liebeskind, Li Zhao, D. Begun, A. Kopp

bioRxiv

DOI

2023

Autoregulatory control of mitochondrial glutathione homeostasis

Yu-Yang Liu, Shanshan Liu, Anju Tomar, Frederick S. Yen, G. Unlu, Nathalie Ropek, Ross A. Weber, Ying Wang, Artem Khan, Mark Gad, Jun-Hui Peng, E. Terzi, Hanan Alwaseem, Alexandra E. Pagano, Søren Heissel, H. Molina, Benjamin Allwein, Timothy C. Kenny, R. Possemato, Li Zhao, R. Hite, Ekaterina V. Vinogradova, S. Mansy, Kıvanç Birsoy

Science

DOI

2023

Two novel, tightly linked, and rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought

Krithika Venkataraman, Nadav Shai, Priyanka Lakhiani, Sarah Zylka, Jieqing Zhao, Margaret Herre, Joshua Zeng, Lauren A. Neal, Henrik Molina, Li Zhao, L. Vosshall

eLife

DOI

2023

De novo genes: from non-genic to genic.

Li Zhao

Nature reviews genetics

DOI

2023

The evolution and mutational robustness of chromatin accessibility in Drosophila

Samuel Khodursky, Eric B. Zheng, N. Svetec, Sylvia M. Durkin, Sigi Benjamin, Alice Gadau, Xia Wu, Li Zhao

bioRxiv

DOI

2023

CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS

Isabel E. Wassing, Atsuya Nishiyama, Moeri Hiruta, Qingyuan Jia, Reia Shikimachi, Amika Kikuchi, Keita Sugimura, Xin Hong, Yoshie Chiba, Jun-Hui Peng, Christopher Jenness, M. Nakanishi, Li Zhao, K. Arita, H. Funabiki

bioRxiv

DOI

2022

Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins

Eric B. Zheng, Li Zhao

eLife

DOI

2022

Systematic identification of unannotated ORFs in Drosophila reveals evolutionary heterogeneity

Eric B. Zheng, Li Zhao

2021

Population biology of accessory gland-expressed de novo genes in Drosophila melanogaster.

J. Cridland, Alex C. Majane, Li Zhao, D. Begun

Genetics

DOI

2021

Intermolecular Interactions Drive Protein Adaptive and Coadaptive Evolution at Both Species and Population Levels

Jun-Hui Peng, N. Svetec, Li Zhao

Molecular biology and evolution

DOI

2021

Transcriptional and mutational signatures of the aging germline

Evan Witt, Christopher B. Langer, N. Svetec, Li Zhao

bioRxiv

DOI

2021

Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis

Evan Witt, Zhan Shao, Chun Hu, H. Krause, Li Zhao

bioRxiv

DOI

2020

The evolution of sex-biased gene expression in the Drosophila brain

Samuel Khodursky, N. Svetec, Sylvia M. Durkin, Li Zhao

bioRxiv

DOI

2020

Behavioral and Genomic Sensory Adaptations Underlying the Pest Activity of Drosophila suzukii

Sylvia M. Durkin, M. Chakraborty, A. Abrieux, K. Lewald, Alice Gadau, N. Svetec, Jun-Hui Peng, Miriam Kopyto, Christopher B. Langer, J. Chiu, J. J. Emerson, Li Zhao

bioRxiv

DOI

2020

Transcription Factors Drive Opposite Relationships between Gene Age and Tissue Specificity in Male and Female Drosophila Gonads

Evan Witt, N. Svetec, Sigi Benjamin, Li Zhao

bioRxiv

DOI

2019

Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila

Evan Witt, Sigi Benjamin, N. Svetec, Li Zhao

bioRxiv

DOI

2018

Improved reference genome of Aedes aegypti informs arbovirus vector control

B. Matthews, Olga Dudchenko, Sarah B. Kingan, S. Koren, I. Antoshechkin, Jacob E. Crawford, William J. Glassford, Margaret Herre, S. Redmond, Noah H. Rose, Gareth D. Weedall, Yang Wu, S. Batra, Carlos A. Brito-Sierra, S. Buckingham, C. Campbell, Saki Chan, E. Cox, Benjamin R. Evans, T. Fansiri, I. Filipović, Albin Fontaine, A. Gloria-Soria, R. Hall, V. Joardar, Andrew K. Jones, Raissa G. G. Kay, V. Kodali, Joyce V. Lee, G. Lycett, Sara N. Mitchell, Jill Muehling, Michael R. Murphy, A. Omer, F. Partridge, P. Peluso, A. P. Aiden, V. Ramasamy, Gordana Rašić, Sourav Roy, K. Saavedra-Rodriguez, S. Sharan, Atashi Sharma, M. Smith, Joe Turner, Allison M. Weakley, Zhilei Zhao, Omar S. Akbari, W. C. Iv Black, Han Cao, A. Darby, C. Hill, J. Johnston, Terence D. Murphy, A. Raikhel, D. B. Sattelle, Igor V. Sharakhov, Bradley J. White, Li Zhao, Erez Lieberman Aiden, R. Mann, L. Lambrechts, Jeffrey R. Powell, Maria V. Sharakhova, Z. Tu, H. M. Robertson, C. McBride, A. Hastie, J. Korlach, D. Neafsey, A. Phillippy, L. Vosshall

Nature

DOI

2017

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

B. Matthews, Olga Dudchenko, S. Kingan, S. Koren, I. Antoshechkin, Jacob E. Crawford, William J. Glassford, Margaret Herre, S. Redmond, Noah H. Rose, Gareth D. Weedall, Yang Wu, S. Batra, Carlos A. Brito-Sierra, S. Buckingham, C. Campbell, Saki Chan, E. Cox, Benjamin R. Evans, T. Fansiri, I. Filipović, Albin Fontaine, A. Gloria-Soria, R. Hall, V. Joardar, Andrew K. Jones, Raissa G. G. Kay, V. Kodali, Joyce V. Lee, G. Lycett, Sara N. Mitchell, Jill Muehling, Michael R. Murphy, A. Omer, F. Partridge, P. Peluso, A. P. Aiden, V. Ramasamy, Gordana Rašić, Sourav Roy, K. Saavedra-Rodriguez, S. Sharan, Atashi Sharma, M. Smith, Joe Turner, Allison M. Weakley, Zhilei Zhao, O. Akbari, W. Black, Han Cao, A. Darby, C. Hill, J. Johnston, Terence D. Murphy, A. Raikhel, D. Sattelle, I. Sharakhov, B. White, Li Zhao, Erez Lieberman Aiden, R. Mann, L. Lambrechts, J. Powell, M. Sharakhova, Z. Tu, H. M. Robertson, C. McBride, A. Hastie, J. Korlach, D. Neafsey, Adam M. Phllippy, L. Vosshall

bioRxiv

DOI

2017

Genomics of parallel adaptation at two timescales in Drosophila

Li Zhao, D. Begun

PLoS Genetics

DOI

2016

The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster

N. Svetec, J. Cridland, Li Zhao, D. Begun

PLoS Genetics

DOI

2015

Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster

N. Svetec, Li Zhao, P. Saelao, Joanna C. Chiu, D. Begun

BMC Evolutionary Biology

DOI

2015

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans

Li Zhao, J. Wit, N. Svetec, D. Begun

PLoS Genetics

DOI

2015

Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies

Xueyan Li, D. Fan, Wei Zhang, Gui-Chun Liu, Lu Zhang, Li Zhao, Xiao-Dong Fang, Lei Chen, Yang Dong, Yuan Chen, Yun Ding, Ruo-Ping Zhao, Mingji Feng, Ya-Bing Zhu, Yue Feng, Xuan-Ting Jiang, De-Ying Zhu, Hui Xiang, Xikang Feng, Shuai-Cheng Li, Jun Wang, Guo-Jie Zhang, Marcus R. Kronforst, Wen Wang

Nature Communications

DOI

2014

Genome-wide sequencing of small RNAs reveals a tissue-specific loss of conserved microRNA families in Echinococcus granulosus

Yun Bai, Zhuangzhi Zhang, Lei Jin, Hui Kang, Yongqiang Zhu, Lu Zhang, Xia Li, Feng-qin Ma, Li Zhao, Bao-Xin Shi, Jun Li, D. McManus, Wen-Bao Zhang, Sheng-Yue Wang

BMC Genomics

DOI

2014

Training Set Selection for the Prediction of Essential Genes

Jian Cheng, Zhao Xu, Wenwu Wu, Li Zhao, Xiangchen Li, Yan-Lin Liu, Shi-Heng Tao

PLoS ONE

DOI

2014

Origin and spread of de novo genes in Drosophila melanogaster populations

Li Zhao, P. Saelao, Corbin D. Jones, D. Begun

Science

DOI

2013

Genome of Drosophila suzukii, the Spotted Wing Drosophila

J. Chiu, Xuan-Ting Jiang, Li Zhao, C. Hamm, J. Cridland, P. Saelao, K. Hamby, Ernest K. Lee, Rosanna S. Kwok, Guo-Jie Zhang, F. Zalom, V. Walton, D. Begun

G3: Genes, Genomes, Genetics

DOI

2012

Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans

Qi Zhou, Hongmei Zhu, Quanfei Huang, Li Zhao, Guo-Jie Zhang, S. Roy, Beatriz Vicoso, Zhao-Ling Xuan, J. Ruan, Yue Zhang, Ruo-Ping Zhao, C. Ye, Xiu-Qing Zhang, Jun Wang, Wen Wang, D. Bachtrog

BMC Genomics

DOI

2011

Transcriptome profiling and digital gene expression by deep-sequencing in normal/regenerative tissues of planarian Dugesia japonica.

Yun-Fei Qin, Hui-Min Fang, Qing-Nan Tian, Zhen-Xia Bao, P. Lu, Jin-Mei Zhao, Jia Mai, Zhao-Yu Zhu, Lin-Lin Shu, Li Zhao, San-Jun Chen, Feng Liang, Yi-Zhe Zhang, Shou-Tao Zhang

Genomics

DOI

2010

Single base–resolution methylome of the silkworm reveals a sparse epigenomic map

Hui Xiang, Jing-De Zhu, Quan Chen, F. Dai, Xin Li, Mu-Wang Li, Hong-Yu Zhang, Guo-Jie Zhang, Dong Li, Yang Dong, Li Zhao, Ying Lin, Dao-Jun Cheng, Jian Yu, Jin-Feng Sun, Xiao-Yu Zhou, Ke-Long Ma, Ying-Hua He, Yang-Xing Zhao, Shicheng Guo, M. Ye, Guang-Wu Guo, Ying-Rui Li, Rui-Qiang Li, Xiu-Qing Zhang, Li-Jia Ma, K. Kristiansen, Qiu-Hong Guo, Jian-Hao Jiang, S. Beck, Q. Xia, Wen Wang, Jun Wang

Nature Biotechnology

DOI

2010

A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y-Linked Male Fertility Genes

Yun Ding, Li Zhao, Shuang Yang, Yu Jiang, Yuan Chen, Ruo-Ping Zhao, Yue Zhang, Guo-Jie Zhang, Yang Dong, Hai-Jing Yu, Qi Zhou, Wen Wang

PLoS Genetics

DOI

2010

Up for grabs

Nature Biotechnology

DOI

2008

Short Homologous Sequences Are Strongly Associated with the Generation of Chimeric RNAs in Eukaryotes

Xin Li, Li Zhao, Hui-Feng Jiang, Wen Wang

Journal of Molecular Evolution

DOI

2006

我国转型期城镇非正规就业与非正规经济（1990-2004）

胡鞍钢，赵黎

《清华大学学报(哲学社会科学版)》，Vol. 21, No. 3

下载原文 DOI

精选作品

期刊论文

A predicted structural interactome reveals binding interference from intrinsically disordered regions

Molecular evolution of CO2-sensing ab1C neurons underlies divergent sensory responses in the Drosophila suzukii species group

HP6/Umbrea, a rapidly evolving Drosophila HP1-family paralog, is a candidate HP1a-recruited plasticizer of heterochromatin

Evolution of MOSN, a novel sex-specifically spliced neuronal gene in the Aedes aegypti mosquito

Regulatory divergence and effector turnover shape species-specific bacterial clearance in Drosophilidae

Machine learning for evolutionary genetics and molecular evolution

Comparative single-cell analysis of transcriptional bursting reveals the role of genome organization in de novo transcript origination

Gene regulatory networks and essential transcription factors for de novo-originated genes

De Novo Genes: Current Status and Future Goals

The origin and structural evolution of de novo genes in Drosophila

CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in eukaryotes

De Novo Genes

The three-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence

A Synergistic, Cultivator Model of De Novo Gene Origination

The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions

Identification of a specialized lipid barrier for Drosophila metamorphosis

Quantifying Transcriptome Turnover on Phylogenies by Modeling Gene Expression as a Binary Trait

Autoregulatory control of mitochondrial glutathione homeostasis

Two novel, tightly linked, and rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought

De novo genes: from non-genic to genic.

The evolution and mutational robustness of chromatin accessibility in Drosophila

CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS

Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins

Systematic identification of unannotated ORFs in Drosophila reveals evolutionary heterogeneity

Population biology of accessory gland-expressed de novo genes in Drosophila melanogaster.

Intermolecular Interactions Drive Protein Adaptive and Coadaptive Evolution at Both Species and Population Levels

Transcriptional and mutational signatures of the aging germline

Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis

The evolution of sex-biased gene expression in the Drosophila brain

Behavioral and Genomic Sensory Adaptations Underlying the Pest Activity of Drosophila suzukii

Transcription Factors Drive Opposite Relationships between Gene Age and Tissue Specificity in Male and Female Drosophila Gonads

Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila

Improved reference genome of Aedes aegypti informs arbovirus vector control

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

Genomics of parallel adaptation at two timescales in Drosophila

The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster

Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans

Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies

Genome-wide sequencing of small RNAs reveals a tissue-specific loss of conserved microRNA families in Echinococcus granulosus

Training Set Selection for the Prediction of Essential Genes

Origin and spread of de novo genes in Drosophila melanogaster populations

Genome of Drosophila suzukii, the Spotted Wing Drosophila

Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans

Transcriptome profiling and digital gene expression by deep-sequencing in normal/regenerative tissues of planarian Dugesia japonica.

Single base–resolution methylome of the silkworm reveals a sparse epigenomic map

A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y-Linked Male Fertility Genes

Up for grabs

Short Homologous Sequences Are Strongly Associated with the Generation of Chimeric RNAs in Eukaryotes

我国转型期城镇非正规就业与非正规经济（1990-2004）