Book chapters

[1] Tan K and Ideker T.  2007. Protein interaction networks. in Biological networks. World Scientific, New Jersey.

[2] Ideker T, Tan K, and Uetz P. 2005. Visualization and integration of protein interaction networks. in Protein-Protein Interactions: A molecular cloning manual. Cold Spring Harbor Laboratory Press.

Papers submitted for publication and in preparation

Tan K*, Kuo D*, Ravasi T, Luo, C, and Ideker T.  Divergence of binding sites of the Yap1 and Pdr1 transcription factors between two hemiascomyces yeasts.  * Equal contribution. In preparation.

Kuo D*, Tan K*, Zinman G*, Ravasi T, Bar-Joseph Z, and Ideker T. Evolution of the fungal response to anti-fungal therapy. * Equal contribution. Submitted.

Ravasi T*, Katayama S*, Bajic V*, Tan K*, and the FANTOM consortium. An atlas of combinatorial transcriptional regulation in mouse and man  * Equal contribution. Submitted.

Papers in press and published

[1] The FANTOM Consortium and RIKEN Omics Science Center.  2009. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics. 41(5):553-562. [pubmed link]

[2] Tan K*, Feizi H, Luo C, Fan S, Ravasi T, and Ideker T.  2008. A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in the DNA damage response. Proc. Natl. Acad. Sci. 105(8):2934-2939.(Corresponding author, Highlighted by Faculty of 1000). [pubmed link]

[3] Tan K, Tegner J, and Ravasi T.  2008.  Integrated approaches to uncover transcriptional regulatory networks in mammalian cells.  Genomics. 91(3): 219-231. [pubmed link]

[4] Tan K, Shlomi T, Feizi, H, Ideker T, and Sharan R. Transcriptional regulation of protein complexes within and across species. 2007. Proc. Natl. Acad. Sci. 104(4): 1283-1288. [pubmed link]

[5] Tan K, McCue LA, and Stormo GD.  2005. Making connections between novel transcription factors and their DNA motifs. Genome Research. 15(2): 312-320. [pubmed link]

[6] Liu, JJ, Tan K, and Stormo GD.  2003.  Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore forming bacteria.  Nucleic Acids Research. 31(23): 6891-6903. [pubmed link]

[7] Stormo GD and Tan K. 2002.  Mining Genome databases to identify and understand new gene regulatory systems. Current Opinion in Microbiology.  5:149-153. [pubmed link]

[8] Tan K, Moreno-Hagelsieb G, Collado-Vides J, Stormo, GD. 2001. A comparative genomics approach to prediction of new members of regulons. Genome Research. 11(4): 566-584. [pubmed link]

[9] Lu D, Futterer K, Korolev S, Zheng X, Tan K, Waksman G, Sadler JE. 1999. Crystal structure of enteropeptidase light chain complexed with an analog of the trypsinogen activation peptide. Journal of Molecular Biology. 292(2): 361-373. [pubmed link]

CONFERENCE PRESENTATIONS

Tan K, Feizi H, Luo C, Fan S, Ravasi T, and Ideker T.  2008. A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in the DNA damage response. Highlight Track. The 16th International Conference on on Intelligent Systems in Molecular Biology. Toronto, Canada.

Tan K, Feizi H, Luo C, Fan S, Ravasi T, and Ideker T.  2007. A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in the DNA damage response. The 8th International Conference on Systems Biology. Long Beach, USA .

Tan K, Shlomi T, Feizi H, Ideker T, Sharan R.  2006. Transcriptional regulation of protein complexes within and across Species.  The 46th Annual Meeting of the American Society for Cell Biology.  San Diego, USA .

Tan K and Stormo, GD. 2002.  Connecting  orphan  transcription factors with  orphan DNA binding sites. The 7th Annual Graduate Student Research Symposium.  Saint Louis, USA .

Tan K, Moreno-Hagelsieb G, Collado-Vides J, Stormo, GD. 2000. A comparative genomics approach to prediction of new members of regulons. The 8th conference on Intelligent Systems in Molecular Biology.  San Diego, USA .

INVITED TALKS

The 9th International Meeting on Microarray Gene Expression Databases 09/2006
Systems Biology: Global Regulation of Gene Expression. Cold Spring Harbor Laboratory 03/2008
The Logic of Gene Regulation, Janelia Farm Research Campus, HHMI 05/2008

Networks: Biological, Social and Internet, SIAM annual meeting

07/2008