Publications

Preprints

[7] Sussman JH, Aldridge DA, Yu W, Chen C, Zellmer AM, Rong J, Parvaresh-Rizi A, Thadi A, Xu J, Bandyopadhyay S, Sun Y, Wu D, Hunter CM, Brosius S, Ahn K, Baxter AE, Koptyra MP, Vanguard RS, McGrory S, Resnick AC, Storm PB, Amankulor NM, Santi M, Viaene AN, Zhang N, De Reedt T, Cole K, Tan K. A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.  

[6] Xu J, Chen C, Vincent T, Polonen P, Hu J, Yoshimura S, Yu W, Sussman J, Chen C, Li EY, Diorio C, Shraim R, Newman H, Uppuluri L, Li A, Chen GM, Bandyopadhyay S, Ding Y, Xu JA, Lim T, Hus M, Thadi A, Ahn KJ, Wu C, Peng J, Sun Y, Wang A, Mehta R, Frank D, Meyer L, Loh ML, Raetz EA, Chen Z, Wood BL, Devidas M, Dunsmore KP, Winter SS, Chang T, Wu G, Pounds SB, Zhang NR, Carroll W, Hunger SP, Bernt K, Yang JJ, Mullighan CG, Tan K, Teachey DT. Identification and targeting of treatment resistant progenitor populations in T-cell acute lymphoblastic leukemia.

[5] Polonen P, Giacomo DD, Seffernick AE, Abdelrahman E, Kimura S, Benini F, Montefiori LE, Wood BL, Xu J, Cheng Z, Newman H, Myers J, Iacobucci I, Hedges D, Hui Y, Diori C, Uppuluri L, Frank D, Fan Y, Chang Y, Meshinchi S, Ries R, Shraim R, Bernt K, Devidas M, Winter S, Dunsmore KP, Carroll WL, Yang JJ, Vincent TL, Chen C, Loh M, Rampersaud E, Raetz E, Hunger SP, Tan K, Chang T, Wu G, Pounds SB, Mulligan CG, Teachey DT. The genomic basis of childhood T-lineage acute lymphoblastic leukemia.

[4] Wang Q, Boccalatte F, Gambi G, Nadorp B, Xu J, Akter F, Mullin C, Melnick A, Choe E, McCarter A, Dean N, Chen S, Lin K, Kodgule R, Rodriguez-Hernaez, Narang S, Avrampou K, King B, Kloetgen A, Tsirigos A, Ryan R, Teachey D, Tan K, Aifantis I, Chiang M. Native stem cell transcriptional circuits define cardinal features of high-risk early T-cell precursor acute lymphoblastic leukemia.

[3] Bandyopadhyay S, Duffy M, Ahn K, Pang M, Smith D, Duncan G, Sussman J, Zhang I, Huang J, Lin Y, Xiong B, Imtiaz T, Chen C, Thadi A, Chen C, Xu J, Reichart M, Pillai V, Snaith O, Oldridge D, Bhattacharyya S, Maillard I, Carroll M, Nelson C, Qin L, and Tan K. Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging.

[2] Cao Z, Peng J, Barrett DR, Liu Y, Chen C, Tan K, Bernt KM, Shi J. CRISPR-based functional genomics for dissecting tumor heterogeneity and therapeutic dependency in primary acute myeloid leukemia samples.

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

Papers in press and published

[86] Pavani G, Klein JG, Nations CC, Sussman JH, Tan K, An H, Abdulmalik O, Thom CS, Gearhart PA, Willen CM, Maguire JA, Chou ST, French DL, Gadus P. Modeling primitive and definitive erythropoiesis with induced pluripotent stem cells. 2024. Blood Advances. [pubmed]

[85] Hu Y, Rong J, Xie R, Xu Y, Peng J, Gao L, Tan K. Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes. 2024. Nature Methods. [pubmed]

[84] Li N, Zhu Q, Tian Y, Ahn KJ, Wang X, Cramer Z, Folkert IW, Yu P, Jou J, Adams-Tzivelekidis S, Sehgal P, Mahmoud NN, Aarons CB, Roses RE, Thomas-Tikhonenko A, Furth EE, Stanger BZ, Rustgi A, Haldar M, Katona BW, Tan K, Lengner CJ. Mapping and modeling human colorectal carcinoma interactions with the tumor microenvironment. 2023. Nature Communications. [pubmed]

[83] Sussman J, Xu J, Amankulor N, Tan K. Dissecting the tumor microenvironment of epigenetically-driven gliomas: opportunities for single-cell and spatial multiomics. 2023. Neuro-Oncology Advances. [pubmed]

[82] HuBMAP Consortium. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). 2023. Nature Cell Biology. [pubmed]

[81] Zezulin AU, Ye D, Howell E, Yen D, Bresciani E, Diemer J, Ren JG, Ahmad MH, Castilla LH, Touw IP, Minn AJ, Tong W, Liu PP, Tan K, Yu W, Speck NA. RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils. 2023. Genes & Development. [pubmed]

[80] Zhong L, Lu J, Fang J, Yao L, Yu W, Gui T, Duffy M, Holdreith N, Bautista C, Huang X, Bandyopadhyay S, Tan K, Chen C, Choi Y, Jiang JX, Yang S, Tong W, Dyment N, Qin L. Csf1 from marrow adipogenic precursors is required for osteoclast formation and hematopoiesis in bone. 2023. Elife. [pubmed link].

[79] Uzun Y, Wu H, Tan K. Integrating single-cell methylome and transcriptome data with MAPLE. 2023. Methods in Molecular Biology. [pubmed link].

[78] Antony C, George SS, Blum J, Somers P, Thorsheim CL, Wu-Corts DJ, Ai Y, Gao L, Lv K, Tremblay MG, Moss T, Tan K, Wilusz JE, Ganley AR, Pimkin M, Paralkar VR. Control of ribosomal RNA synthesis by hematopoietic transcription factors. 2022. Molecular Cell. [pubmed link].

[77] Chen GM, Chen C, Perazzelli J, Grupp SA, Barrett DM, Tan K. Characterization of leukemic resistance to CD19 targeted CAR T-cell therapy through deep genomic sequencing. 2022. Cancer Immunology Research. [pubmed link].

[76] Chen GM, Melenhorst JJ, Tan K. B-Cell targeting in CAR T-cell therapy: side effect or biological driver of CAR T-cell function? 2022. Science Translational Medicine. [pubmed link].

[75] Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen Y, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin J, Burlingame EA, Human Tumor Atlas Network; Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe’er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. MITI minimum information guidelines for highly multiplexed tissue images. 2022. Nature Methods. [pubmed link].

[74] Li EY, Xu J, Nelson ND, Teachey DT, Tan K, Romberg N, Behrens E, Pillai V.  Kikuchi-Fujimoto disease is mediated by an aberrant type I interferon response. 2022. Modern Pathology. [pubmed link].

[73] Yang Y, Mumau M, Tober J, Zhu Q, Bennett L, Hong C, Sung DC, Keller TCS, Uzun Y, Gao P, Shewale S, Chen M, Yang J, Chen X, Thomas SA, Tan K, Speck NA, Kahn ML. Endothelial MEKK3-KLF2/4 signaling integrates inflammatory and hemodynamic signals during definitive hematopoiesis. 2022. Blood. [pubmed link].

[72] Wolpaw AJ, Grossmann LD, Dessau JL, Dong MM, Aaron BJ, Brafford PA, Volgina D, Pascual-Pasto G, Rodriguez-Garcia A, Uzun Y, Arsenian-Henriksson M, Powell DJ Jr, Bosse KR, Kossenkov A, Tan K, Hogarty MD, Maris JM, Dang CV. Epigenetic state determines inflammatory sensing in neuroblastoma. 2022. Proc. Natl. Acad. Sci. [pubmed link].

[71] Melenhorst JJ, Chen GM, Wang M, Porter DL, Chen C, McKensie AC, Gao P, Bandyopadhyay S Sun H, Zhao Z, Lundh 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. 2022. Nature. [pubmed link] [Download Data and Code].

[70] Chen C, Yu W, Alikarami F, Qiu Q, Chen C, Flournoy J, Gao P, Uzun Y, Fang L, Davenport JW, Hu Y, Zhu Q, Wang K, Libbrecht C, Felmeister A, Rozich I, Ding Y, Hunger SP, Felix CA, Wu H, Brown PA, Guest EM, Barrett DM, Bernt KM, Tan K. Single-cell multiomics reveals increased plasticity, resistance populations and stem-cell-like blasts in KMT2A-rearranged leukemia. 2021. Blood. [pubmed link].

[69] Strub MD, Gao L, Tan K, McCray Jr. PB. Analysis of multiple gene co-expression networks to discover interactions favoring CFTR biogenesis and ΔF508-CFTR rescue. 2021. BMC Medical Genomics. [pubmed link].

[68] Wing A, Xu J, Meng W, Rosenfeld A, Li EY, Wertheim G, Paessler M, Bagg A, Frank D, Tan K, Teachey DT, Lim MS, Prak EL, Fajgenbaum DC, Pillai V. Transcriptome and unique cytokine microenvironment of Castleman disease. 2021. Modern Pathology. [pubmed link].

[67] 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. 2021. Genes & Development. [pubmed link].

[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] [Explore Data].

[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]

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.