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 in press and published

[28] Yan L, Esain V, Teng L, Xu J, Kwan W, Frost IM, Yzaguirre AD, Cai X, Cortest M, 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. 2014. Genes & Development. [link].

[27] Ma X, Gao L, and Tan K. Modeling disease progression using dynamics of pathway connectivity. 2014. Bioinformatics. 30(16)2343-50. [pubmed link].

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

[25] Steinke FC, Yu S, Zhou X, He B, Yang W, Zhou B, Kawamoto H, Zhu J, Tan K and Xue HH. Tcf1 and Lef1 act upstream of Th-POK to promoter CD4+ T cell lineage choice and cooperate with Runx3 to silence the Cd4 gene in CD8+ T cells. 2014. Nature Immunology. [pubmed link].

[24] Dogan MV, Shields B, Cutrona C, Gao L, Gibbons FX, Simons R, Monick M, Brody GH, Tan K, Beach CR, and Philibert RA. The effect of smoking on DNA methylation of peripheral blood mononuclear cells from African American women. 2014. BMC Genomics. 15:151. [pubmed link].

[23] Teng L, He B, Gao P, and Tan K. Discover context-specific combinatorial transcription factor interactions by integrating diverse Chip-Seq data sets. 2014. Nucleic Acids Research. 42(4):e24. [pubmed link].

[22] Soshnev AA, Baxley RM, Manak JR, Tan K, and Geyer PK. The insulator protein Suppressor of Hairy wing is an essential transcriptional repressor in the Drosophila ovary. 2013. Development. 140(17):3613-23. [pubmed link].

[21] Kim J, Gao L, and Tan K. Multi-analyte network markers for tumor prognosis. 2012. Plos One. 7:e52973. [pubmed link].

[20] Teng L and Tan K. Discovering distal regulatory elements by integrating multiple types of chromatin state maps. 2012. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine. [PDF]

[19] Teng L and Tan K. Finding combinatorial histone code by semi-supervised clustering. 2012. BMC Genomics. 13:301. [pubmed link]

[18] Fan R, Bonde S, Gao P, Sotomayor B, Chen C, Mouw T, Zavazava N, and Tan K. Dynamic HoxB4 regulatory network during embryonic stem cell differentiation to hematopoietic cells. 2012. Blood. 119:e139-47. [pubmed link]

[17] Soshnev AA, He B, Baxley RM, Jiang N, Hart CM, Tan K, and Geyer PK. Genome-wide studies of the multi-zinc finger Drosophila Suppressor of Hairy-wing protein in the ovary. 2012. Nucleic Acids Research. 40:5415-31. [pubmed link]

[16] Teng L, Firpi HA, and Tan K. Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers. 2011. Nucleic Acids Research. 39:7371-9. [pubmed link]

[15] Ucard D, Hu Q, and Tan K. Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering. 2011. Nucleic Acids Research. 39(10):4063-75. [pubmed link][Epigenie news][Epigenomics].

[14] Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, and Ideker T.  Co-evolution within a transcriptional network by compensatory trans and cis mutations. 2010. Genome Research. 20(12):1672-8. [pubmed link]

[13] Kim J and Tan K. Discover protein complexes in protein-protein interaction networks using parametric local modularity. 2010. BMC Bioinformatics. 11:521. [pubmed link]

[12] Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, and Ideker T. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. 2010. Genome Biology. 11:R77. [pubmed link]

[11] Firpi HA, Ucar D, and Tan K. Discover regulatory DNA elements using chromatin signature and artificial neural network. 2010. Bioinformatics. 26(13):1579-1586.
[pubmed link]

[10] Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic V, Tan K et al. An atlas of combinatorial transcriptional regulation in mouse and man. 2010. Cell. 140(5):744-752. [pubmed link]

[9] 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]

[8] 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. (Highlighted by Faculty of 1000). [pubmed link]

[7] 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]

[6] 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]

[4] 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]

[3] 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]

[2] 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]

[1] 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]