Kai Tan, PhD

Kai Tan, PhD

Kai Tan, PhD, is a associate professor in the Department of Pediatrics and an investigator in the Center for Childhood Cancer Research at The Children's Hospital of Philadelphia.

Locations: Main Campus
Appointments and Referrals: 1-800-TRY-CHOP (1-800-879-2467)

Background

Education and Training

Medical School

Internship

Residency

Fellowship

Postdoctoral Fellowship - University of California San Diego, San Diego, CA

Additional Training

Undergraduate Degree

BS in Biochemistry - Beloit College, Beloit, WI

Graduate Degree

PHD in Computational Biology - Washington University in St. Louis, St. Louis, MO

Titles and Academic Titles

Associate Professor

Associate Professor of Pediatrics, Perelman School of Medicine at the University of Pennsylvania

Departments and Services

Research Interests

Publications

Papers

2016

Holmfeldt P, Ganuza M, Marathe H, He B, Hall T, Kang G, Moen J, Parieck J, Saulsberry A, Cico A, Gaut L, McGoldrick D, Finkelstein D, Tan K and McKinney-Freeman S. Functional screen identifies regulators of murine hematopoietic stem cell repopulation. J Exp Med. 2016 Feb 15. pii: jem.20150806. [Epub ahead of print].

Huang J, Wang K, Wei P, Liu X, Liu X, Tan K, Boerwinkle E, Potash JB, Han S. FLAGS: A Flexible and Adaptive Association Test for Gene Sets Using Summary Statistics. Genetics 202: 919-29, Mar 2016.

He, B and Tan K. Understanding transcriptional regulatory networks using computational models. Current Opinion in Genes & Development  37: 101-108, Mar 2016.

2015

Cao Z, Chen C, He B, Tan K* and Lu C*. : A microfluidic device for profiling genome-wide histone modifications using 100 cells.  Nature Methods 12: 959-962, 2015.

Teng Li, He Bing, Wang Jiahui, Tan Kai: 4DGenome: a comprehensive database of chromatin interactions. Bioinformatics 31(15): 2560-4, Aug 2015.

Cai Xiongwei, Gao Long, Teng Li, Ge Jingping, Oo Zaw Min, Kumar Ashish R, Gilliland D Gary, Mason Philip J, Tan Kai, Speck Nancy A: Runx1 Deficiency Decreases Ribosome Biogenesis and Confers Stress Resistance to Hematopoietic Stem and Progenitor Cells. Cell stem cell 17(2): 165-77, Aug 2015.

Ma Xiaoke, Gao Long, Karamanlidis Georgios, Gao Peng, Lee Chi Fung, Garcia-Menendez Lorena, Tian Rong, Tan Kai: Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks. PLoS computational biology 11(6): e1004332, Jun 2015.

2014

Li Y, Esain V, Teng L, Xu J, Kwan W, Frost I, Yzaguirre A, Maijenburg MW, Tober J, Dzierzak E, Orkin SH, Tan K, North TE, and Speck NA. Inflammatory signaling regulates embryonic hematopoietic stem and progenitor cell production. Genes & Development 28(23): 2597-612, Dec 2014.

Dogan Meeshanthini V, Shields Bridget, Cutrona Carolyn, Gao Long, Gibbons Frederick X, Simons Ronald, Monick Martha, Brody Gene H, Tan Kai, Beach Steven R H, Philibert Robert A: The effect of smoking on DNA methylation of peripheral blood mononuclear cells from African American women. BMC genomics 15: 151, 2014.

Ma Xiaoke, Gao Long, Tan Kai: Modeling disease progression using dynamics of pathway connectivity. Bioinformatics 30(16): 2343-50, Aug 2014.

Steinke Farrah C, Yu Shuyang, Zhou Xinyuan, He Bing, Yang Wenjing, Zhou Bo, Kawamoto Hiroshi, Zhu Jun, Tan Kai, Xue Hai-Hui: TCF-1 and LEF-1 act upstream of Th-POK to promote the CD4(+) T cell fate and interact with Runx3 to silence Cd4 in CD8(+) T cells. Nature immunology 15(7): 646-56, Jul 2014.

He Bing, Chen Changya, Teng Li, Tan Kai: Global view of enhancer-promoter interactome in human cells. Proceedings of the National Academy of Sciences of the United States of America 111(21): E2191-9, May 2014.

Teng Li, He Bing, Gao Peng, Gao Long, Tan Kai: Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets. Nucleic acids research 42(4): e24, Feb 2014.

Abstracts

2015

Tang W, Gao P, Wingert B, Gu Z, Chen C, He B, Ma X, Gao L, and Tan K.: Epigenomic profiling during the development of diabetic nephropathy reveals new genetic and epigenetic effectors of the disease. American Diabetes Association 75th scientific sessions. Boston 2015.

Gao P, Uzun Y, Salamati S, He B, Coffey J, Tsalikian E, and Tan K.: Epigenomic profiling of primary human T cells reveals enhancers associated with type 1 diabetes susceptibility. American Diabetes Association 75th scientific sessions, Boston, MA. 2015.

2014

Ma X, He B, Teng L, and Tan K.: Identifying causal noncoding variants using tissue specific gene regulatory networks. American Society of Human Genetics annual meeting,San Diego, CA. 2014.

He B, Chen C, Teng L, and Tan K. : Global view of enhancer-promoter interactome in human cells. Cold Spring Harbor meeting on global regulation of gene expression. Cold Spring Harbor, NY. Cold Spring Harbor meeting on global regulation of gene expression. Cold Spring Harbor, NY. 2014.

Cao Z, Chen C, He B, Tan K, and Lu C.: Ultrasensitive microfluidic ChIP-Seq with small number of cells. American Institute of Chemical Engineers annual meeting, Atlanta, 2014.

Books

Chapters
2007

Cao Z, Chen C, He B, Tan K, and Lu C.: Ultrasensitive microfluidic ChIP-Seq with small number of cells. American Institute of Chemical Engineers annual meeting, Atlanta, 2014.

2005

Ideker T, Tan K, and Uetz P.: Visualization and integration of protein interaction networks. Protein-Protein Interactions: A molecular cloning manual 2005.

Posters and Presentations

Lectures by Invitation
2016

Tan K. Highly Dynamic Repertoire of Enhancers During CD8+ T cell Responses to Infections. Department of Biochemistry, Penn State College of Medicine, Hersey, PA; March 2016.

2015

Tan K.  Epigenomic landscape of embryonic hematopoiesis. NIH Progenitor Cell Biology Consortium Hematopoietic meeting, Children's' Hospital of Boston, Boston, MA; July 2015.

Tan K. Systematic analysis of enhancer and promoter interactions", Bioinformatics Seminar, University of California, Los Angeles, CA; May 2015.

Tan K. Transcriptional regulatory networks in normal development and oncogenesis. Dept. of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA; May 2015.

Tan K. Systematic analysis of enhancer and promoter interactions. Center for Computational Biology and Bioinformatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN; April 2015.

2014

Tan K. Network dynamics during healthy and disease development. School of Computer Science and Technology, Xi’Dian University, Xi'an, China; November 2014.

Awards and Honors

2011-2013, March of Dimes Basil O'Connor Starter Scholar Research Award
2009-2011, NSF Computing Innovation Fellows Award
2009-2010, PhRMA Foundation Junior Faculty Research Starter Award
2004-2006, IBM postdoctoral fellowship

Editorial and Academic Positions

Editorial Positions
Associate Editor

2014-present, Associate Editor, PLos Computational Biology
2013-present, Associate Editor, BMC Genomics

Ad hoc Reviewer

Genome Research
Genome Biology
Nature Biotechnology
Developmental Cell
Cell Systems
Nucleic Acids Research
Bioinformatics
Journal of Clinical Investigation
BMC Bioinformatics
BMC Genomics
BMC Systems Biology
Genomics
Molecular Systems Biology
Nature Genetics
Nature Methods
PLos Computational Biology
Proceedings of the National Academy of Sciences USA
Science

Academic and Institutional Committees

2016-present, Center for Childhood Cancer Research, Children’s Hospital of Philadelphia

2016-present, Institute of Biomedical Informatics, University of Pennsylvania Perelman School of Medicine

2016-present, Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine

2016-present, Penn Institute for Immunology, University of Pennsylvania Perelman School of Medicine

2016-present, Genomics & Computational Biology (GCB) Graduate Group, University of Pennsylvania Perelman Medical School

2016-present, Cell & Molecular Biology (CAMB) Graduate Group, University of Pennsylvania Perelman School of Medicine

2016-present, Seminar Committee, Department of Biomedical & Health Informatics, Children’s Hospital of Philadelphia

2016-present, Quantitative analysis and Cancer subcommittees, Understand the causes and Develop Therapies for rare & complex diseases work group, CHOP RI thematic work group

2016-present, Biostatistics Graduate Group, University of Pennsylvania Perelman School of Medicine

July 2016, Program committee member, Intelligent Systems for Molecular Biology, Orlando, USA 

October 2016, Program committee member, MidAtlantic Bioinformatics Conference, Philadelphia, USA

2015, ZRG1BST-U(50) (4DNucleome U54 panel, NIH), Leukemia & Lymphoma Society

July 2015, Program committee member, Intelligent Systems for Molecular Biology, Dublin, Ireland

2014-2019, Career Development Panel, Leukemia & Lymphoma Society, USA

April 2014, Program committee member, International Conference on Research in Computational Molecular Biology, Pittsburg, USA

2013, ZAI-PA-I-J1/ZAI1-ALW-I-J1 panel (Autoimmunity centers of excellence), National Institutes of Health, USA

July 2013, Program committee member, Intelligent Systems for Molecular Biology, Berlin, Germany

2013, Progenitor Cell Biology Consortium review panel, National Institutes of Health, USA

2013, Biodata Management and Analysis (BDMA) study section, National Institutes of Health, USA

April 2013, Program committee member, International Conference on Research in  Computational Molecular Biology, Beijing, China

2012-2021, Genomics, Computational Biology, and Technology (GCAT) study section, National Institutes of Health, USA

April 2012, Program committee member, SIAM International Conference on Data Mining, Anaheim, USA

2012, Leukemia & Lymphoma Research, UK, external reviewer

2012, Austrian Science Foundation, Austria, external reviewer

2010, Biotechnology and Biological Sciences Research Council, UK , external reviewer

December 2010, Program committee member, IEEE International Conference on Bioinformatics & Biomedicine, Hong Kong, China

November 2009, Program committee member, IEEE International Conference on Bioinformatics & Biomedicine, Washington DC, USA

June 2009, Program committee member, Intelligent Systems for Molecular Biology, Stockholm, Sweden

June 2009, Program committee member, European Conference on Computational Biology, Stockholm, Sweden

November 2008, Program committee member, IEEE International Conference on Bioinformatics & Biomedicine, Philadelphia, USA

Leadership and Memberships

International

2000-present, International Society for Computational Biology
2003-present, Sigma Xi
2005-present, International Society for Systems Biology
2008-present, International Society for Stem Cell Research
2014, Program committee member, International Conference on Research in Computational Molecular Biology, Pittsburgh, USA
2015, Program committee member, Intelligent Systems for Molecular Biology, Dublin, Ireland
2016, Program committee member, Intelligent Systems for Molecular Biology, Orlando, USA

National

2014, Program committee member, International Conference on Research in Computational Molecular Biology, Pittsburgh, USA 
2015, Program committee member, Intelligent Systems for Molecular Biology, Dublin, Ireland
2016, Program committee member, Intelligent Systems for Molecular Biology, Orlando, USA