Publications

2021

Intratumoural immune heterogeneity as a hallmark of tumour evolution and progression in hepatocellular carcinoma
Nature Communications, 12(1), 227. doi: 10.1038/s41467-020-20171-7
Nguyen PHD, Ma S, Phua CZJ, Kaya NA, Lai HLH, Lim CJ, Lim JQ, Wasser M, Lai L, Tam WL, Lim TKH, Wan WK, Loh T, Leow WQ, Pang YH, Chan CY, Lee SY, Cheow PC, Toh HC, Ginhoux F, Iyer S, Kow AWC, Young Dan Y, Chung A, Goh BKP, Albani S, Chow PKH#, Zhai W#, Chew V#.

2020

Structures of Echovirus 30 in complex with its receptors inform a rational prediction for enterovirus receptor usage
Nat Commun. 2020 Sep 4;11(1):4421. doi: 10.1038/s41467-020-18251-9
Wang, K., Zhu, L.,Sun, Y., Li, M., Zhao, X., Cui, L., Zhang, L., Gao, G. F., Zhai, W., Zhu, F.#, Rao, Z.#, Wang, X.#

Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows
National Science Review, 2020 7 (1), 113-127
Yanhua Qu*, Chunhai Chen, Ying Xiong, Huishang She, Yong E Zhang, Yalin Cheng, Shane DuBay, Dongming Li, Per GP Ericson, Yan Hao, Hongyuan Wang, Hongfeng Zhao, Gang Song, Hailin Zhang, Ting Yang, Chi Zhang, Liping Liang, Tianyu Wu, Jinyang Zhao, Qiang Gao, Weiwei Zhai, Fumin Lei*

2019

Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma
Nat Genet. 2019 Jul;51(7):1131-1136. (co-corresponding author)
Xu M*, Yao Y*, Chen H*, Zhang S*, et al Zhai W#, Zeng YX#, Liu J#

Passage adaptation correlates with the reduced efficacy of the influenza vaccine
Clinical Infectious Disease, OCT 1 2019 , Volume: 69 Issue: 7, Pages: 1198-1204
Chen H, Alvarez JJS, Ng SH, Nielsen R, Zhai W. ​

PSiTE: a Phylogeny guided Simulator for Tumor Evolution
Bioinformatics, 1 September 2019, Volume 35, Issue 17, Pages 3148–3150
Yang H, Lu B, Lai L, Lim A Alvarez J, Zhai W​

Clonal MET Amplification as a Determinant of Tyrosine Kinase Inhibitor Resistance in Epidermal Growth Factor Receptor-Mutant Non-Small-Cell Lung Cancer
J Clin Oncol. 2019 Jan 24:JCO1800177.
Lai GGY, Lim TH, Lim J, Liew PJR, Kwang XL, Nahar R, Aung ZW, Takano A, Lee YY, Lau DPX, Tan GS, Tan SH, Tan WL, Ang MK, Toh CK, Tan BS, Devanand A, Too CW, Gogna A, Ong BH, Koh TPT, Kanesvaran R, Ng QS, Jain A, Rajasekaran T, Yuan J, Lim TKH, Lim AST, Hillmer AM, Lim WT, Iyer NG, Tam WL, Zhai W, Tan EH, Tan DSW,

Proteomic profiling of HIV-1 infection of human CD4+ T cells identifies PSGL-1 as an HIV restriction factor
Nat Microbiol. 2019 Mar 4.
Liu Y, Fu Y, Wang Q, Li M, Zhou Z, Dabbagh D, Fu C, Zhang H, Li S, Zhang T, Gong J, Kong X, Zhai W, Su J, Sun J, Zhang Y, Yu XF, Shao Z, Zhou F, Wu Y, Tan X.

Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore.
Cell, 179(3), 736-749.e715. doi: https://doi.org/10.1016/j.cell.2019.09.019
Wu, D., Dou, J., Chai, X., Bellis, C., Wilm, A., Shih, C. C., . . . Wang, C. (2019).

Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health.
National Science Review, 6(4), 810-824. doi: 10.1093/nsr/nwz049
Ostrander, E. A., Wang, G.-D., Larson, G., vonHoldt, B. M., Davis, B. W., Jagannathan, V., . . . Consortium, D. K. (2019).

2018

Elucidating the genomic architecture of Asian EGFR-mutant lung adenocarcinoma through multi-region exome sequencing
Nat Commun. 2018 Jan 15;9(1):216 (Equal contribution)
Nahar R*, Zhai W*, Zhang T*, Takano A, Khng AJ, Lee YY, Liu X, Lim CH, Koh TPT, Aung ZW, Lim TKH, Veeravalli L, Yuan J, Teo ASM, Chan CX, Poh HM, Chua IML, Liew AA, Lau DPX, Kwang XL, Toh CK, Lim WT, Lim B, Tam WL, Tan EH, Hillmer AM#, Tan DSW#.   ​

Development of a new patient-derived xenograft humanised mouse model to study human-specific tumour microenvironment and immunotherapy
Gut 2018 Mar 30 Oct;67(10):1845-1854
Zhao Y, Shuen TWH, Toh TB, Chan XY, Liu M, Tan SY, Fan Y, Yang H, Lyer SG, Bonney GK, Loh E, Chang KTE, Tan TC, Zhai W, Chan JKY, Chow EK, Chee CE, Lee GH, Dan YY, Chow PK, Toh HC, Lim SG, Chen Q

Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates
Nature 2018 May;557(7706):575-579
Simoni Y, Becht E, Fehlings M, Loh CY, Koo SL, Teng KWW, Yeong JPS, Nahar R, Zhang T, Kared H, Duan K, Ang N, Poidinger M, Lee YY, Larbi A, Khng AJ, Tan E, Fu C, Mathew R, Teo M, Lim WT, Toh CK, Ong BH, Koh T, Hillmer AM, Takano A, Lim TKH, Tan EH, Zhai W, Tan DSW, Tan IB, Newell EW ​

2017

The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma
Nature Communications, 2017 Feb 27;8:4565 (IF 11.3, * Equal contribution)
Zhai W¶,*, Lim TK*, Zhang T*, Phang ST, Tiang Z, Guan P, Ng MH, Lim JQ, Yao F, Li Z, Ng PY, Yan J, Goh BK, Chung AY, Choo SP, Khor CC, Soon WW, Sung KW, Foo RS¶, Chow PK¶

Whole-genome sequencing of African dogs provides insights into adaptations against tropical parasites
Mol Biol Evol 2017 Oct 10
Liu YH, Wang L, Xu T, Guo X, Li Y, Yin TT, Yang HC, Yang H, Adeola AC, J Sanke O, O Otecko N, Wang M, Ma Y, S Charles O, S Sinding MH, Gopalakrishnan S, Samaniego JA, Hansen AJ, Fernandes C, Gaubert P, Budd J, M Dawuda P, Rueness EK, Jiang L, Zhai W, Gilbert MTP, Peng MS, Qi X, Wang GD, Zhang YP

The origin of chow chows in the light of the East Asian breeds
BMC Genomics, 2017 18:174 (# Co-corresponding, IF 3.9, featured article)
Yang H, Wang G, Wang M, Ma Y, Yin T, Fan R, Wu H, Zhong L, Irwin DM, Zhai W#, Zhang Y#.​

2016

Dynamic convergent evolution drives the passage adaptation across 48 years’ history of H3N2 influenza evolution
Mol Biol Evol. 2016 Dec;33(12):3133-3143 (IF 13.6)
Chen H, Deng Q, Ng SH, Lee RT, Maurer-Stroh S, Zhai W.

Point mutations in the major outer membrane protein drive hypervirulence of a rapidly expanding clone of Campylobacter jejuni
Proc Natl Acad Sci U S A, 2016 Sep 20;113(38):10690-5 (IF 9.4)
Wu Z, Periaswamy B, Sahin O, Yaeger M, Plummer P, Zhai W, Shen Z, Dai L, Chen SL#, Zhang Q#

Novel therapeutic targets on the horizon for lung cancer
Lancet Oncol. 2016 Aug;17(8):e347-62. Review (IF 24.7)
Tan WL, Jain A, Takano A, Newell EW, Iyer NG, Lim WT, Tan EH, Zhai W, Hillmer AM, Tam WL, Tan DS.

Out of southern East Asia: the natural history of domestic dogs across the world
Cell Res, 2016 Jan;26(1):21-33 (* joint first author，cover story, IF 14.8)
Wang,G-D*, Zhai, W*, Yang, H-C*, Wang, L*, Zhong, L , Liu Y-H, Fan, R-X, Yin,T-T, Zhu, C-L, Poyarkov, AD, Irwin,DM, Hytönen,MK, Lohi, H, Wu,C-I, Savolainen,P, Zhang, Y-P

​The Guardian: Dog DNA study reveals the incredible journey of man’s best friend by Tim Radford. (link)
Discovery: DNA Dates Dog Domestication Back 33,000 Years by JENNIFER VIEGAS. (link)
​The Washington Post: Where in the world dogs really came from by Yanan Wang. (link)
The Telegraph: Dog has been man’s best friend for 33,000 years, DNA study finds by Agency. (link)
Los Angeles Times: Man’s best friend for a long time: Dogs go back 33,000 years, study finds by Deborah Netburn. (link)
Xinhua News: Across China: Chinese scientists unravel origin, global migration of domestic dogs by Ranran Yue. (link)​

2014

Genetic convergence in the adaptation of dogs and humans to the high-altitude environment of the tibetan plateau
Genome Biol Evol. 2014 Aug;6(8):2122-8
Wang GD*, Fan RX*, Zhai W, Liu F, Wang L, Zhong L, Wu H, Yang HC, Wu SF, Zhu CL, Li Y, Gao Y, Ge RL, Wu CI, Zhang YP.​

2013

The Evolution of Small Insertions and Deletions in the Coding Genes of Drosophila melanogaster
Mol Biol Evol. 2013 Dec;30(12):2699-708 (* Equal contribution)
Chong Z*, Zhai W*, Li C, Gao M, Gong Q, Ruan J, Li J, Jiang L, Lv X, Hungate E, Wu CI#.

The genomics of selection in dogs and the parallel evolution between dogs and humans
Nat Commun. 2013;4:1860 (* Equal contribution)
Wang GD*, Zhai W*, Yang HC, Fan RX, Cao X, Zhong L, Wang L, Liu F, Wu H, Cheng LG, Poyarkov AD, Poyarkov NA Jr, Tang SS, Zhao WM, Gao Y, Lv XM, Irwin DM, Savolainen P, Wu CI#, Zhang YP#.

Nature: Dog genetics spur scientific spat by Ewen Callaway. 
The New York Times: From Fearsome Predator to Man’s Best Friend by Carl Zimmer. (link)
National Geographic: Dog and Human Genomes Evolved Together by Jane J. Lee. (link)
The Scientist: Dogs and Human Evolving Together by Dan Cossins. (link)
Live Science: Dogs and Humans Evolved Together, Study Suggests by Tia Ghose. (link)
Asian Scientist: Dogs And Humans Share An Evolutionary History, Study by Sim Shuzhen. (link)
Scientific American: Dog Genetics Spur Scientific Spat By Ewen Callaway and Nature magazine. (link)

Age-Dependent Transition from Cell-Level to Population-Level Control in Murine Intestinal Homeostasis Revealed by Coalescence Analysis
PLoS Genet 9(2): e1003326. (# co-corresponding author)
Hu Z, Fu Y-X, Greenberg AJ, Wu C-I#, Zhai W# (2013)

Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology
BMC Genomics. 2013 Oct 17;14:711
Ruan J*, Jiang L*, Chong Z*, Gong Q*, Li H, Li C, Tao Y, Zheng C, Zhai W, Turissini D, Cannon CH, Lu X#, Wu CI#.​

2012

Looking for darwin in genomic sequences–validity and success of statistical methods
Mol Biol Evol. 2012 Oct;29(10):2889-93
Zhai W, Nielsen R, Goldman N, Yang Z.

Whole genome sequencing and evolutionary analysis of human papilloma-virus type 16 in central China
PLoS One. 2012;7(5):e36577 (# co-corresponding author)
Sun M, Gao L, Liu Y, Zhao Y, Wang X, Pan Y, Ning T, Cai H, Yang H, Zhai W#, Ke Y#.​

2011

An Aboriginal Australian genome reveals separate human dispersals into Asia
Science. 2011 Oct 7;334(6052):94-8 (cover story)
Rasmussen M*, Guo X*, Wang Y*, Lohmueller KE*, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, et al, Nielsen R#, Wang J#, Willerslev E#.

Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data
Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):12042-7 (*Equal contribution)
Tao Y*, Ruan J*, Yeh SH*, Lu X*, Wang Y*, Zhai W*, Cai J*, et al Chen DS#, Chen PJ#, Wu CI#.

Two evolutionary histories in the genome of rice: the roles of domestication genes
PLoS Genet. 2011 Jun;7(6):e1002100 (* Equal contribution)
He Z*, Zhai W*, Wen H*, Tang T, Wang Y, Lu X, Greenberg AJ, Hudson RR, Wu CI#, Shi S#.​

2010

A draft sequence of the Neandertal genome
Science. 2010 May 7;328(5979):710-22 (10 breakthroughs of the year, AAAS Newcomb-Cleveland Prize,  best paper of the year for Science, cover story)
Green RE*, Krause J*, Briggs AW*, Maricic T*, Stenzel U*, Kircher M*, Patterson N*, Li H, Zhai W, et al, Reich D#, Pääbo S#.​

2009

An investigation of the statistical power of neutrality tests based on comparative and population genetic data
Mol Biol Evol. 2009 Feb;26(2):273-83
Zhai W, Nielsen R, Slatkin M.​

2007

Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virus
J Mol Evol. 2007 Sep;65(3):340-8
Zhai W, Slatkin M, Nielsen R.​

2004

Is haplotype block identification useful for association mapping studies?
Genet Epidemiol. 2004 Jul;27(1):80-3
Zhai W, Todd MJ, Nielsen R.​