Internal Medicine

Kai Tan, PhD


Associate Professor of Internal Medicine  - Bioinformatics and Computational Biology

Contact Information

Web: Kai Tan Laboratory (Children's Hospital of Philadellphia)


BS, Beloit College
PhD, Washington University in Saint Louis

Post Doctorate, University of California San Diego

Education/Training Program Affiliations

Interdisciplinary Graduate Program in Genetics
Interdisciplinary Graduate Program in Informatics
Interdisciplinary Graduate Program in Neuroscience
Medical Scientist Training Program

Research Summary

Our lab is interested in gene regulatory networks in normal and disease development. In particular, we focus on understanding how genetic and epigenetic factors interact to control gene expression. Towards this goal, we are conducting interdisciplinary research, combining wet-lab and computation along the following two lines: Model gene regulatory networks in development We are studying gene networks controlling hematopoietic stem cell fate using functional genomic assays and computational modeling. In this biological context, we are pursuing the following projects: 1) Identify transcriptional enhancers that control developmental-stage-specific gene expression. We are developing computational tools to predict enhancers. We are also developing a high through-put assay to validate our computational predictions. 2) Understand the interaction between transcription factor binding and chromatin modifications and its effect on gene expression during hematopoietic stem cell fate specification. 3) Integrate genomic and interactome data to discover gene regulatory pathways during hematopoietic stem cell fate specification. Discover molecular networks as biomarkers for human diseases Molecular interaction 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.

Center, Program and Institute Affiliations

Center for Bioinformatics and Computational Biology
Center for Gene Therapy of Cystic Fibrosis and other Genetic Diseases
Environmental Health Sciences Research Center
Holden Comprehensive Cancer Center
Institute for Clinical and Translational Science
Iowa Initiative in Human Genetics

Selected Publications

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Fan R, Bonde S, Gao P, Sotomayor B, Chen C, Mouw T, Zavazava N, Tan K.  Dynamic HoxB4 Regulatory Network During Hematopoietic Stem Cell Development.  Blood.  2012. 119:e139-147.

Teng L, Tan K.  Finding combinatorial histone code by semi-supervised biclustering.  BMC Genomics.  2012. 13:301.

Kim J, Gao L, Tan K.  Multi-analyte Network Markers for Tumor Prognosis.  Plos One.  2012. 7(12):e52973.

Ucar D, Hu Q, Tan K.  Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering.  Nucleic Acids Res.  2011. 39:4063-75.

Teng L, Firpi H, Tan K.  Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers.  Nucleic Acids Res.  2011. 39:7371-1.

Kim J, Tan K.  Discover protein complexes in protein-protein interaction networks using parametric local modularity.  BMC Bioinformatics.  2010. 11(1):521.

Firpi H, Ucar D, Tan K.  Discover regulatory DNA elements using chromatin signatures and artificial neural network.  Bioinformatics.  2010. 26:1579-86.

Tan K, Ideker T.  Protein interaction networks.  World Scientific, New Jersey.  2007. 

Ideker T, Tan K, Uetz P.  Visualization and integration of protein interaction networks.  Cold Spring Harbor Laboratory Press.  2005. 

Date Last Modified: 09/06/2016 - 15:07:37