Kai Tan, PhD

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Associate Professor of Pediatrics
Department: Pediatrics

Contact information
The Children's Hospital of Philadelphia
Division of Oncology
Department of Pediatrics
3501 Civic Center Blvd.
4004 Colket Translational Research Bldg.
Philadelphia, PA 19104
Office: 267-425-0050
Lab: 267-425-0058
Education:
B.S. (Biochemistry)
Beloit College, 1997.
Ph.D. (Computational Biology)
Washington University in St. Louis, 2004.
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Description of Research Expertise

Gene expression variation plays a major role in driving phenotypic variation. Our lab is interested in Systems Biology of gene regulation. The advent of various bulk and single-cell omics technologies increasingly allows us to interrogate the status of a cell’s components and to determine how, when, and where these molecules interact with each other. By combining omics experiments and computational modeling, we are studying gene regulatory networks in several model systems.

I. Model gene regulatory networks in development and disease

We are studying gene regulatory networks controlling development and differentiation of hematopoietic stem cells, T cells, and oncogenesis. Specific projects include:

1) Identify and characterize keys transcription factors and enhancers that control cell/tissue-specific gene expression.

2) Understand how 3-dimensional genome organization controls cell/tissue-specific gene expression.

3) Understand how mutations in regulatory DNA sequences contribute to pathogenesis.

II. Discover molecular networks as biomarkers for human diseases

Molecular networks are increasingly serving as tools to unravel the basis of human diseases. We are developing network-based approaches to identifying disease-related sub-networks that can serve as biomarkers for the diagnosis and prognosis of diseases and as candidates for novel therapeutics.

Selected Publications

Gao L, Uzun Y, Gao P, He B, Ma X, Wang J, Han S, Tan K.: Identifying noncoding risk variants using disease-relevant gene regulatory networks Nature Communications Feb 2018.

Tober J, Maijenburg MW, Y, Gao L, Hadland BK, Gao P, Clarke R, Bernstein I, Keller G, Tan K*, Speck NA*.: Maturation of hematopoietic stem cells from prehematopoietic stem cells is accompanied by up-regulation of PD-L1. Journal of Experimental Medicine Dec 2017.

Yu W, He B, Tan K: Identifying topologically associating domains and subdomains by Gaussian mixture model and proportion test. Nature Communications 8(1): 535, Sept 2017.

Li Y, Gao L, Hadland B, Tan K*, Speck NA*: CD27 marks murine embryonic hematopoietic stem cells and type II pre-hematopoietic stem cells. Blood 130(3): 372-376, July 2017.

He B, Xing S, Chen C, Gao P, Teng L, Shan Q, Gullicksrud JA, Martin MD, Yu S, Harty JT, Badovinac VP, Tan K*, Xue HH*: CD8+ T cells utilize highly dynamic enhancer repertoires and regulatory circuitry in response to infections. Immunity 45(6): 1341-1354, Dec 2016.

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

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(10): 959-962, Oct 2015.

Cai X, Gao L, Teng L, Ge J, Oo Z, Kumar A, Gilliland GD, Mason PJ, Tan K and Speck NA.: 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 X, Gao Long, Lee CF, Gao P, Karamanlidis G, Garcia-Menendez L, Tian R and Tan K: Revealing pathway dynamics in heart diseases by analyzing multiple differential networks. PLoS Computational Biology 11(6): e1004332, Jun 2015.

He B, Chen C, Teng L, and Tan K.: Global view of enhancer-promoter interactome in human cells. Proc Natl Acad Sci 111(21): E2191-9, May 2014.

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Last updated: 09/15/2018
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