Welcome!

I am a Ph.D. student in the Biostatistics department of Univerity of Michigan - Ann Arbor. Under the advisory of Goncalo Abecasis, my research focuses on statistical genetics. I have speicalties in next generation sequencing studies (NGS).

Collaborating with excellent colleagues, I have research experiences in sequencing reads alignment, variant callings, quality checks, and genetics association studies. Applying statistical genetics knowledge, I have been studying age-related macular degeneration disease using ~3,300 sequencing samples.

Education

Ph.D. Biostatistics
University of Michigan, Ann Arbor, MI
Advisor: Gonçalo R. Abecasis
Thesis: Statistical methods and analysis in next generation sequencing.
 2013 (Expected)
M.S. Mathematics and Statistics
University of Minnesota Duluth, Duluth, MN
Advisor: Kang L. James
 2007
B.E. Automation
Tsinghua University, Beijing, China
Advisor: Chongrong Li
 2005

Research

Publication

Published

  1. Li B, Chen W, Zhan X, Busonero F, Sanna S, et al. (2012) A likelihood-based framework for variant calling and de novo mutation detection in families. PLoS Genet 8(10): e1002944.
  2. The 1000 Genomes Project Consortium. A map of human genome variation from population scale sequencing. Nature. 2010 Oct 28; 467(7319): 1061-73.

In revision

  1. Zhan X*, Larson D*, Wang C*, Koboldt D, Sergeev Y, Fulton R, Fulton L, Fronick C, Branham K, Bragg-Gresham J, Jun G, Hu Y, Kang HM, Liu DJ, Othman M, Brooks Matthew, Ratnapryia, Boleda A, Wilson R, Heckenlively J, Chew E, Stambolian D, Mardis E, Swaroop A, Abecasis GR, Targeted Sequencing, Augmented with Public Resources, Identifies a Rare Complement 3 Allele Associated with AMD
  2. Wang C*, Zhan X*, Abecasis GR, Estimating individual ancestry from extremely low-coverage sequencing data
  3. Liu DJ*, Peloso GM*, Zhan X*, Zawistowski M, Kathiresan S, Abecasis GR, Meta-analysis of gene-level rare variant test
  4. Zhang P, Zhan X, Rosenberg NA, Zollner S. Genotype imputation reference panel selection using maximal phylogenetic diversity
  5. He Z, Zhang M, Zhan X, Lu Q, Genetic Random Field: a statistical framework for modeling joint association
  6. Hu Y, Willer C, Zhan X, Kang HM, Abecasis GR, Accurate local ancestry inference in exome sequenced admixed individuals with off targeted sequence reads
  7. Zhan X*, Liu DJ*: TASER (TabAnno and SEqmineR): an integrated toolset for next-generation sequence data analysis

Submitted

  1. Li B*, Zhan X*, Trost M, Anderson P, Kang H and Abecasis GR, QPLOT: quality assessment plots for next generation sequence runs

In preparation

  1. Ratnapriya R, Zhan X, Fariss R, Chakarova C, English M, Branham K, Campos M, Morrison M, Waseem N, Friedman J, Brooks M, Rajasimha H, Jacobson S, Sood R, Liu P, Klein M, Chew E, Stambolian D, DeAngelis M, Bhattacharya S, Heckenlively J, Abecasis GR, Swaroop A, Rare and common variant in extracellular matrix gene, FBN2 in macular degeneration
  2. Li J, Zhan X, Wang H, Environmental impacts on the performance of silicon photovoltaic panels, (plan to submit to Renewable Energy)

* Equal contribution first author

Teaching

1. Interuniversity Consortium for Political and Social Research (ICPSR)
Summer Program in Quantitative Methods of Social Research
Teaching Assistant - Longitudinal Analysis (taught by Dr. Michael Berbaum)		 Jul 2012
2. Department of Mathematics and Statistics,
University of Minnesota-Duluth, Duluth, MN
Teaching Assistant - Differential Equations (taught by Dr. Marshall Hampton)
 Sep 2005 - Dec 2005
3. Department of Mathematics and Statistics,
University of Minnesota-Duluth, Duluth, MN
Teaching Assistant - Calculus III (taught by Chad Pierson)
 Sep 2005 - Dec 2005

Software

I can efficiently process large data sets in C++, Python, R and bash.

Selected software list
rvtestsFast, handy association test software for family/unrelated studies and quantitaive/binary trait. Single variant test (score test, Wald test), burden tests (CMC, SKAT, VT) are implemented.
checkVCF.pyValidation software for VCF file (used in lipid consortium)
TabAnnoFast annotation software; also integrated in EPACTS
seqMinerEfficiently load and process VCF files (preferrably use with TabAnno)
KARMAIllumina and ABI SOLiD sequence reads aligner
QPLOTQuality check and visualize sequence alignment files
PolymuttFamily-based genotype caller
ThunderVCFLow-coverage genotype calling using Hidden Markov-chain Model (HMM)
LASERAncestry inference using off-target reads (suitable for target/exome sequencing)

Skill

  • Proficient in: C/C++, Python, R, Bash
  • Comfortable with: Java, Perl, SAS, MATLAB/Simulink, Scheme, LaTeX, Javascript, PHP5, CSS, HTML
  • System administration: Linux, MOSIX cluster, Amazon Cloud
  • Capable of analyzing "big data", such as sequencing data

Contact

Xiaowei Zhan
CT 4624, 1415 Washington Heights
Department of Biostatistics
University of Michigan
Ann Arbor, MI 48109
O: (734) 763 - 5315
M: (218) 260 - 2988
F: (734) 615 - 8322
: zhanxw@umich.edu