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.


[1] The Human Cell Atlas White Paper. The human cell atlas consortium. arXiv.

[2] Chen C, Yu W, Alikarami F, Qiu Q, Chen C, Flournoy J, Gao P, Uzun Y, Fang L, Hu Y, Zhu Q, Wang K, Libbrecht C, Felmeister A, Rozich I, Ding Y, Hunger SP, Wu H, Brown PA, Guest EM, Barrett DM, Bernt KM, Tan K. Single-cell multi-omics reveals elevated plasticity and stem-cell-like blasts relevant to the poor prognosis of KMT2A-rearranged leukemia. biorxiv.

[3] Peng T, Chen GM, Tan K. GLUER: integrative analysis of single-cell omics and imaging data. biorxiv.

[4] Melenhorst JJ, Chen GM, Wang M, Porter DL, Gao P, Bandyopadhyay S Pruteanu-Malinici I, Nobles CL, Maji S, Frey NV, Gill SI, Tian L, Kulikovskaya I, Gupta M, Davis MM, Fraietta JA, Brogdon JL, Young RM, Ambrose DE, Chew A, Levine BL, Siegel DL, Alanio C, Wherry JEBushman FD, Lacey SF, Tan K, June CH. Decade-long remissions of leukemia sustained by the persistence of activated CD4+ CAR T-cells. biorxiv.

[5] Howell ED, Yzaguirre AD, Gao P, Lis R, He B, Lakadamyali M, Rafii S, Tan K, Speck NA. The efficiency of hemogenic endothelial specification by RUNX1 is dependent on baseline chromatin accessibility of RUNX1-regulated TGFB target genes.


Papers in press and published

[66] Ding Y, Kim H, Madden K, Loftus JP, Chen GM, Allen DH, Zhang R, Xu J, Hu Y, Tasian SK, Tan K. Network analysis reveals synergistic genetic dependencies for rational combination therapy in Philadelphia chromosome-like acute lymphoblastic leukemia. 2021. Clinical Cancer Research. [pubmed link].

[65] Chen GM, Chen C, Das RK, Gao P, Chen C, Bandyopadhyay S, Ding Y, Uzun Y, Yu W, Zhu Q, Myers RM, Grupp SA, Barrett DM, Tan K. Integrative bulk and single-cell profiling of pre-manufacture T-cell populations reveals factors mediating long-term persistence of CAR T-cell therapy. 2021. Cancer Discovery. [pubmed link].

[64] Estevez B, Borst S, Jarocha DJ, Sudunagunta VS, Gonzalez M, Garifallou J, Hakonarson H, Gao P, Tan K, Liu PP, Bagga S, Holdreith N, Tong W, Speck NA, French DL, Gadue P, Poncz M. RUNX1 haploinsufficiency causes a marked deficiency of megakaryocyte-biased hematopoietic progenitor cells. 2021. Blood. [pubmed link].

[63] Hu Y, Peng T, Gao L, Tan K. CytoTalk: De novo construction of signal transduction networks using single-cell RNA-Seq data. 2021. Science Advances. [pubmed link].

[62] Merrell AJ, Peng T, Li J, Sun K, Li B, Katsuda T, Grompe M, Tan K, Stanger BZ. Dynamic transcriptional and epigenetic changes drive cellular plasticity in the liver. 2021. Hepatology. [pubmed link].

[61] Uzun Y, Wu H, Tan K. Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data. 2021. Genome Research. [pubmed link].

[60] Hsu J, Huang HT, Lee CT, Choudhuri A, Wilson NK, Abraham BJ, Moignard V, Kucinski I, Yu S, Hyde RK, Tober J, Cai X, Guo Y, Yang S, Superdock M, Trompouki E, Calero-Nieto FJ, Ghamari A, Jing J, Gao P, Gao L, Nguyen V, Robertson AL, Durand EM, Kathrein KL, Aifantis I, Gerber SA, Tong W, Tan K, Cantor AB, Zhou Y, Liu PP, Young RA, Gottgens B, Speck NA, Zon LI. CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation. 2020. Proc. Natl. Acad. Sci. [pubmed link].

[59] He B, Gao P, Ding Y, Chen C, Chen GM, Chen C, Kim H, Tasian SK, Hunger SP, Tan K. Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. 2020. Science Advances. [pubmed link].

[58] Gao P, Chen C, Howell ED, Li Y, Tober J, Uzun Y, He B, Gao L, Zhu Q, Siekmann A, Speck NA, Tan K. Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells. 2020. Genes & Development. [pubmed link].

[57] Zhu Q, Gao P, Tober J, Bennett L, Chen C, Uzun Y, Li Y, Mumau M, Yu W, He B, Speck NA, Tan K. Developmental trajectory of pre-hematopoietic stem cell formation from endothelium. 2020. Blood. [pubmed link].

[56] Yu W, Uzun Y, Zhu Q, Chen C, Tan K. scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data. 2020. Genome Biology. [pubmed link].

[55] The HTAN consortium. The Human Tumor Atlas Network: Charting tumor transitions across space and time at single-cell resolution. 2020. Cell. [pubmed link].

[54] Bellissimo DC, Chen C, Zhu Q, Bagga S, Lee C, He B, Wertheim GB, Jordan M, Tan K, Worthen GS, Gilliland DG, Speck NA. Runx1 negatively regulates inflammatory cytokine production by neutrophils in response to Toll-like receptor signaling. 2020. Blood Advances. [pubmed link].

[53] Chen GM, Azzam A, Ding Y, Barrett DM, Grupp SA, Tan K. Dissecting the tumor-immune landscape in chimeric antigen receptor T-cell therapy: key challenges and opportunities for a systems immunology approach. 2020. Clinical Cancer Research. [pubmed link].

[52] Chen C, Yu W, Tober J, Gao P, He B, Lee K, Trieu T, Blobel GA, Speck NA, Tan K. Spatial genome re-organization between fetal and adult hematopoietic stem cells. 2019. Cell Reports. [pubmed link].

[51] MacFarland SP, Naraparaju K, Iyer R, Guan P, Kolla V, Hu Y, Tan K, Brodeur GM. Mechanisms of entrectinib resistance in a neuroblastoma xenograft model. 2019. Molecular Cancer Therapeutics. [pubmed link].

[50] Packer JS, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murry JI. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. 2019. Science. [pubmed link].

[49] Hu Y, Chen C, Ding Y, Wen X, Wang B, Gao L, Tan K. Optimal control nodes in disease-perturbed networks as targets for combination therapy. 2019. Nature Communications. [pubmed link].

[48] Taylor DM, Aronow BJ, Tan K, Pediatric Cell Atlas consortium. The pediatric cell atlas: defining the growth phase of human development at single-cell resolution. 2019. Developmental Cell. [pubmed link].

[47] Peng T, Zhu Q, Yin P, Tan K. SCRABBLE: single-cell RNA-Seq imputation constrained by bulk RNA-Seq data. 2019. Genome Biology. [pubmed link].

[46] Gao P, Uzun Y, He B, Salamati SE, Coffey JKM, Tsalikian E, Tan K. Risk variants disrupting enhancers of TH1 and TREG cells in type 1 diabetes. 2019. Proc. Natl. Acad. Sci. [pubmed link].

[45] Nicetto D, Donahue G, Jain T, Peng T, Sidoli S, Sheng L, Montavon T, Becker JS, Grindheim JM, Blahnik K, Garcia BA, Tan K, Bonasio R, Jenuwein T, Zaret KS. H3K9me3-heterochromatin loss at protein coding genes enables developmental lineage specification. 2019. Science. [pubmed link].

[44] Gao L, Tober J, Gao P, Chen C, Tan K, Speck N. RUNX1 and the endothelial origin of blood. 2018. Experimental Hematology. [pubmed link].

[43] Behera V, Evans P, Face CJ, Hamagami N, Sankaranarayanan L, Keller CA, Giardine B, Tan K, Hardison RC, Shi J, Blobel GA. Exploring genetic variation to uncover rules of transcription factor binding and chromatin accessibility. 2018. Nature Communications. [pubmed link].

[42] Gao L, Uzun Y, Gao P, He B, Ma X, Wang J, Han S, Tan K. Identifying noncoding risk variants using disease-relevant regulatory networks. 2018. Nature Communications.  [pubmed link].

[41] Tober J, Maijenburg MW, Li Y, Gao L, Hadland BK, Gao P, Minoura K, Bernstein I, Tan K, and Speck N. Maturation of hematopoietic stem cell from prehematopoietic stem cells is accompanied by upregulation of PD-L1. 2017. Journal of Experimental Medicine. [pubmed link].

[40] Li F, He B, Ma X, Yu S, Bhave RR, Lentz SR, Tan K, Guzman ML, Zhao C, and Xue HH. Prostaglandin E1 and its analog misoprostol inhibit human CML stem cell self-renewal via ER4 receptor activation and repression of AP-1. 2017. Cell Stem Cell. [pubmed link].

[39] Yu W, He B, and Tan K. Identifying topologically associating domains and subdomains by Gaussian mixture model and proportion test. 2017. Nature Communications. [pubmed link].

[38] Li Y, Gao L, Hadland B, Tan K, and Speck NA. CD27 marks murine embryonic hematopoietic stem cells and type II pre-hematopoietic stem cells. 2017. Blood. [pubmed link].

[37] He B, Xing S, Chen C, Gao P, Teng L, Shan Q, Gullicksrud JA, Martin MD, Yu S, Harty JT, Badovinac VP, Tan K, and Xue HH. CD8+ T cells utilize highly dynamic enhancers repertoires and regulatory circuitry in response to infections. 2016. Immunity. [pubmed link].

[36] Gao T, He B, Liu S, Zhu H, Tan K, Qian J. EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types. 2016. Bioinformatics. [pubmed link].

[35] 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. 2016. Genetics. 202:919-929. [pubmed link].

[34] He B and Tan K. Understanding transcriptional regulatory networks using computational models. 2016. Current Opinion in Genes & Development. 37:101-108. [pubmed link].

[33] Holmfeldt P, Ganuza M, Marathe H, He B, Hall T, Kang G, Moen J, Pardieck J, Saulsberry AC, Cico A, Gaut L, McGoldrick D, Finkelstein D, Tan K, McKinney-Freeman S. Functional screen identifies regulators of murine hematopoietic stem cell repopulation. 2016. Journal of Experimental Medicine. 213: 433-449. [pubmed link].

[32] Chao Z, Chen C, He B, Tan K and Lu C. A microfluidic device for epigenomic profililng using 100 cells. 2015. Nature Methods. 12:959-962. [pubmed link].

[31] Cai X, Gao L, Teng L, Ge J, Oo Z, Kumar AR, Gilliland GD, Mason PJ, Tan K and Speck NA. Runx1 deficiency decreases ribosome biogenesis and confers stress resistance to hematopoietic stem and progenitor cells. 2015. Cell Stem Cell. 17:165-177.  [pubmed link].

[30] Ma X, Gao L, Karamanlidis G, Gao P, Lee C, Garcia-Menendez L, Tian R, and Tan K. Revealing pathway dynamics in heart diseases by analyzing multiple differential networks. 2015. Plos Computational Biology. 11:e1004332.  [pubmed link].

[29] Teng L, He B, Wang J, and Tan K. 4DGenome: a comprehensive database of chromatin interactions. 2015. Bioinformatics. 31:2560-2564. [pubmed link].

[28] Li Y, 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. 28:2597-2612. [pubmed link].

[27] Ma X, Gao L, and Tan K. Modeling disease progression using dynamics of pathway connectivity. 2014. Bioinformatics. 30(16)2343-50. 30:2343-2350. [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. 15:646-656. [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. 39:4063-75. [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. 20:1672-8. [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. 26:1579-1586.
[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. 140:744-752. [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. 41:553-562. [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. 105:2934-2939. (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: 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: 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: 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: 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: 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: 361-373. [pubmed link]