University of California, Berkeley Doctor of Philosophy Dec 2008
Department of Integrative Biology, Berkeley, CA, USA
Ph.D in Population Genetics, with Monty Slatkin
Cornell University Master of Science Aug 2004
Department of Biological Statistics and Computational Biology, Ithaca, NY, USA
M.S in Biometry, with Rasmus Nielsen
University of Science and Technology of China Bachelor of Science June 2002
School of Life Sciences, Hefei, China
Postdoc Fellow, Department of Integrative Biology Jan 2009-June 2009
University of California, Berkeley, with Rasmus Nielsen
Associated Investigator, Beijing Institute of Genomics June 2009- current
With Chung-I Wu
Research Interests ______________________________________________________
My research focuses on using statistical and computational approaches in addressing questions in Population Genomics and Molecular Evolution. My major research interests are:
a) The genetic basis of adaptation. Darwinian positive selection, which reshapes species for the better fit of their offspring, is a very interesting topic that really attracts me. I will be exploring this direction both in terms of long term evolution (Comparative Genomics) and short term standing variations (Population Genetics);
b) Species evolutionary history. The demographic history of a species is not only very important for understanding the history of evolution, but also build a foundation for discerning species adaptation. My research in this direction focuses mainly on human evolutionary history and two domesticated species (i.e. Rice and Dogs).
c) Population Genetics of development and evo-devo. Organismal development is an amazing cellular orchestra starting from a single zygote. This group of cells with diverse functions are first built following large scale construction and deconstruction of many components (morphogenesis). Subsequently, they are actively maintained though homeostasis. There are many interesting population genetic and evolutionary questions in this regard. For example, what is the genealogical relationship of all cells within a multi-cellular organism? What are the roles of stem cells in the genealogy? How this genealogy might differ within and between species?
• Wang G*, Zhai W*, et al, Wu C-I#, Zhang,Y-P#. The genomics of selection in dogs and the parallel evolution between dogs and humans (Equal contribution, in press with Nature Communications)
• Hu Z, Fu Y-X, Greenberg AJ, Wu C-I#, Zhai W# (2013) 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)
• Zhai W, Nielsen R, Goldman N, Yang Z. Looking for darwin in genomic sequences--validity and success of statistical methods. Mol Biol Evol. 2012 Oct;29(10):2889-93.
• Sun M, Gao L, Liu Y, Zhao Y, Wang X, Pan Y, Ning T, Cai H, Yang H, Zhai W#, Ke Y#. Whole genome sequencing and evolutionary analysis of human papilloma-virus type 16 in central China. PLoS One. 2012;7(5):e36577. (# co-corresponding author)
• 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#. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science. 2011 Oct 7;334(6052):94-8.
• Tao Y*, Ruan J*, Yeh SH*, Lu X*, Wang Y*, Zhai W*, Cai J*, et al Chen DS#, Chen PJ#, Wu CI#. 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)
• He Z*, Zhai W*, Wen H*, Tang T, Wang Y, Lu X, Greenberg AJ, Hudson RR, Wu CI#, Shi S#. Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet. 2011 Jun;7(6):e1002100. (* Equal contribution)
• Green RE*, Krause J*, Briggs AW*, Maricic T*, Stenzel U*, Kircher M*, Patterson N*, Li H, Zhai W, et al, Reich D#, Pääbo S#. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22. (10 breakthroughs of the year, AAAS Newcomb-Cleveland Prize for the best paper of the year)
• Zhai W, Nielsen R, Slatkin M. 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, Slatkin M, Nielsen R.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, Todd MJ, Nielsen R. Is haplotype block identification useful for association mapping studies? Genet Epidemiol. 2004 Jul;27(1):80-3.
• Lecturer Workshop for Molecular Evolution
(class of 50 students and staff members across China) Dec. 2011
Center for Computational and Evolutionary Biology, Institute of Zoology, CAS
• Lecturer Fall 2010
• GSI MCB142/IB c163 Survey of Genetics
Senior undergraduate class on Genetics Fall 2006 UC Berkeley
• GSI Bio1B General Biology
Junior undergraduate class on Biology Fall 2005 UC Berkeley
• TA BTRY 602 Statistical Methods II
Graduate class on Introductory Statistics, Spring 2004 Cornell University
• TA BTRY 602 Statistical Methods II
Graduate class on Introductory Statistics, Spring 2003 Cornell University
• TA BTRY 601 Statistical Methods I
Graduate class on Introductory Statistics, Fall 2002 Cornell University
• “The evolution of somatic cells: a few cases of studying normal homeostasis and cancer” 1st Meeting of Genetic Diversity of Chinese Populations (GDCP), Shanghai, Sep 2012
• “Neutrality vs. natural selection in the evolution of cancer cells within multicellular organisms– A study of human hepatocellular carcinoma” 4Th International Conference on Biomedical and Environmental Sciences & Technology (icBEST-2012), April, Guangzhou, China, 2012. (Substitute for Prof Chung-I Wu).
• “Evidence for adaptive evolution of micro-indels in the whole genome of Drosophila melanogaster”, , Nov, ，2011.
• “Evolution of the population of cancer cells in one case of hepatocellular carcinoma (HCC)”, James Watson Symposium on Cancer, Cold Spring Harbor Asia meeting. April 2010
• “Exploring Variation in the dN/dS Ratio Among Sites and Lineages Using Mutational Mappings: Applications to the Influenza Virus”, Society for Molecular Biology and Evolution (SMBE) annual meeting, June, Barcelona, Spain. 2008