[PDF] Dan Xie - Sheng Zhong

31067_3DanXieresume.pdf 1 Dan Xie

Dan Xie

Cell phone: (217) 369-4349 gEmail: danxie2@uiuc.edu Website: http://biocomp.bioen.uiuc.edu/people/danxie/

EDUCATION

Ph.D in Bioengineering, University of Illinois at Urbana-Champaign, anticipated graduation date: May 2011

M. S. in Bioengineering, University of Science and Technology of China, 2006 B. S. in Electronic Science and Technology, University of Science and Technology of China, 2003

RESEARCH EXPERIENCE

Graduate Research Assistant, (advisor: Dr. Sheng Zhong) Department of Bioengineering, University of Illinois at Urbana-Champaign, 08/2006 Ȃ present

Keywords: computation biology, systems biology, gene regulatory networks, genomics, gene expression, cis-

regulatory elements, evolution, epigenetics, next generation sequencing

Highlights:

Developed a De Novo transcription factor binding site motif prediction algorithm called Dz

‹""•‘†—Ž‡Ǥdz Dz

‹""•‘†—Ž‡dz used information from the evolution of cis-regulatory modules to

boost its power in predicting sequence motifs on eukaryotic genomes. Developed a cross-species gene expression clustering algorithm that enabled us to study the evolution of gene coexpression networks. Studied the rewiring of gene regulatory networks in embryo preimplantation processes of human, mouse, and cow. This study revealed various mechanisms for the evolution of gene regulation, and discussed the important role of transposons in shaping the structure of gene regulatory networks.

Developed a statistical evolutionary model for gene regulation that considered the evolution of both

genome sequence and gene expression. Developed an evolutionary model based alignment algorithm that aligns DNA sequences considering their epigenetic states.

PUBLICATIONS

[1]. Chieh-Chun Chen, Dan Xie, Sheng Zhong. A biophysical model for epigenetic contribution to protein-DNA binding. In preparation [2]. Dan Xie, Chieh-Chun Chen, Xin He, Sheng Zhong. Towards an evolutionary model of transcription networks. Submitted [3]. Dan Xie, Xiaoyi Cao, Sheng Zhong. EpiAlignment: boosting sequence alignment with epigenetic information. Submitted 2 Dan Xie

[4]. Dan Xie, Chieh-Chun Chen, Leon Ptaszek, Shu Xiao, Xiaoyi Cao, Yanen Li, Douglas A. Melton, Harris A

Lewin, Chad Cowan, Sheng Zhong, (2010) Rewirable gene regulatory networks in the preimplantation development of three mammalian species. Genome Research. 20:804-815(This paper is a cover story and has been highlighted on Nature) [5]. Jun Cai, Dan Xie, Zhewen Fan, John Marden, Wing H. Wong, Sheng Zhong. (2010) Modeling Co- expression Across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells. PLoS Computation Biology.6(3):e1000707 [6]. Feng Hong, Fang Fang, Xuming He, Xiaoyi Cao, Hiram Chipperfield, Dan Xie, NG Huck Hui, Wing H. Wong, Sheng Zhong. (2009) Detecting early differentially expressed genes in a mixture of differentiating embryonic stem cells. PLoS Computational Biology. 5(12):e1000607 [7]. Dan Xie, Jun Cai, Na-Yu Chia, Huck H. Ng and Sheng Zhong. (2008) Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells. Genome Research. 18:1325-1335

[8]. Sheng Zhong and Dan Xie. (2007) Gene Ontology analysis in multiple gene clusters under multiple

hypothesis testing framework. Artificial Intelligence in Medicine. 41:105-115 (This paper is reviewed

by Editorial on Artificial Intelligence in Medicine 41:83-86) [9]. Chulyun Kim, Sangkyum Kim, Russell Dorer, Dan Xie, Jiawei Han, Sheng Zhong. (2007) TagSmart: Software for Analysis and Visualization of Yeast Mutant Fitness Data Measured by TAG Microarrays.

BMC Bioinformatics. 8:128

[10]. Dan Xie, Ao Li, Minghui Wang, Zhewen Fan and Huanqing Feng. (2005) LOCSVMPSI: a web server

for subcellular localization for eukayotic proteins using SVM and profile of PSI-BLAST. Nucleic Acids

Research. 33: W105-W110

PRESENTATIONS

Apr. 2010. Institute of Genome Biology(IGB) Fellows Symposium, Urbana, IL (Runner up in the poster competition)

Title: Rewirable gene regulatory networks in the preimplantation development of three mammalian species.

Poster presentation

Feb. 2008. Department of Bioengineering Seminar, Urbana, IL

Title: Gibbsmodule: Combining Gibbs sampler and local alignment for de novo discovery of cis-regulatory

modules.

TEACHING EXPERIENCE

Guest Lecturer for Statistical Analysis of Genomic Data (BIOE 398), 2010, Department of Bioengineering, University of Illinois at Urbana-Champaign Title: Statistics in Genome Annotation Teaching Assistant for Biomedical Instrumentation Lab (BIOE 415), 2007-2008, Department of Bioengineering, University of Illinois at Urbana-Champaign Duties: instructing experiment procedures, helping students in the lab, organizing student presentations and discussion, grading lab reports, answering questions during office hours Teaching Assistant for Data Structure, Linear Circuit Analysis, 2003-2006, 3 Dan Xie Department of Electronic Science and Technology, University of Science and Technology of China Duties: grading, answering questions during office hours

AWARDS

Mavis Future Faculty Awards, UIUC, 2010-2011

Conference Travel Awards for Graduate Students in UIUC, 03/ 2007, 03/2008, and 03/2010

Hua Wei Scholarship, USTC, 2005

Outstanding undergraduate student scholarship, USTC, 2003

REFERENCES

Sheng Zhong, Assistant Professor

Department of Bioengineering,

Universtiy of Illinois at Urbana-Champaign

(217) 419-0577, szhong@uiuc.edu

Harris Lewin, Professor of Immunogenetics

Gutgsell Endowed Chair, Department of Animal Science;

Direct, Institute of Genomic Biology,

University of Illinois at Urbana-Champaign

(217) 333-5998, h-lewin@illinois.edu Lisa Stubbs, Professor of Cell and Developmental Biology

School of Molecular and Cellular Biology

University of Illinois at Urbana-Champaign

(217) 244-4000, ljstubbs@illinois.edu

Eric Jakobsson, Professor

Department of Molecular and Integrative Physiology,

University of Illinois at Urbana-Champaign

(217) 244-2896, jake@ncsa.illinois.edu