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Program Director

Division of Genome Sciences

Program Director

Division of Genome Sciences

Education

B.Sc. (Hons.) University of Calcutta, 2001

M.Sc. University of Calcutta, 2003

Ph.D. Louisiana State University, 2008


View Biography

Biography

Dr. Sen joined the National Human Genome Research Institute's Extramural Research Program as a program director in 2019. He manages a portfolio of grants focused upon genomic data sciences, and is particularly interested in transitioning genomics from a centralized data repository model to cloud-based collaborative science. Apart from genomic data science, Dr. Sen’s grant portfolio also includes genomic technology development, including computational technologies. Dr. Sen also has an interest in training initiatives at NHGRI that aim to create an expanded and diverse bioinformatics workforce for managing the massive data volumes being produced in genomics.

Prior to his current position, Dr. Sen worked at NHGRI’s Intramural Research Program studying transcriptome changes in coronary artery disease, which was recognized through the C.W. Cotterman Award from the American Society of Human Genetics in 2014. Between 2016-2019, he served as the co-director of NCI’s Microbiome and Genetics Core Laboratory, where he developed and implemented an array of robotics-based microbiome sequencing methods and corresponding analysis software to help identify bacterial and fungal community changes associated with human disease.

He received his B.Sc. (Hons.) and M.Sc. degrees in zoology (in 2001 and 2003, respectively) from the University of Calcutta, his Ph.D. in biological sciences from Louisiana State University (in 2008) and completed postdoctoral training at NHGRI (2008-2013).

  • Biography

    Dr. Sen joined the National Human Genome Research Institute's Extramural Research Program as a program director in 2019. He manages a portfolio of grants focused upon genomic data sciences, and is particularly interested in transitioning genomics from a centralized data repository model to cloud-based collaborative science. Apart from genomic data science, Dr. Sen’s grant portfolio also includes genomic technology development, including computational technologies. Dr. Sen also has an interest in training initiatives at NHGRI that aim to create an expanded and diverse bioinformatics workforce for managing the massive data volumes being produced in genomics.

    Prior to his current position, Dr. Sen worked at NHGRI’s Intramural Research Program studying transcriptome changes in coronary artery disease, which was recognized through the C.W. Cotterman Award from the American Society of Human Genetics in 2014. Between 2016-2019, he served as the co-director of NCI’s Microbiome and Genetics Core Laboratory, where he developed and implemented an array of robotics-based microbiome sequencing methods and corresponding analysis software to help identify bacterial and fungal community changes associated with human disease.

    He received his B.Sc. (Hons.) and M.Sc. degrees in zoology (in 2001 and 2003, respectively) from the University of Calcutta, his Ph.D. in biological sciences from Louisiana State University (in 2008) and completed postdoctoral training at NHGRI (2008-2013).

Publications

Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, McCulloch JA, Anastasakis DG, Sarshad AA, Leonardi I, Collins N, Blatter JA, Han SJ, Tamoutounour S, Potapova S, Foster St Claire MB, Yuan W, Sen SK, Dreier MS, Hild B, Hafner M, Wang D, Iliev ID, Belkaid Y, Trinchieri G, Rehermann B. Laboratory mice born to wild mice have natural microbiota and model human immune responses . Science 2019 Aug 2;365(6452) [PubMed]

Johnston JJ, Williamson KA, Chou CM, Sapp JC, Ansari M, Chapman HM, Cooper DN, Dabir T, Dudley JN, Holt RJ, Ragge NK, Schäffer AA, Sen SK, Slavotinek AM, FitzPatrick DR, Glaser TM, Stewart F, Black GC, Biesecker LG. NAA10 polyadenylation signal variants cause syndromic microphthalmia. J Med Genet. 2019 Jul;56(7):444-452 [PubMed]

Harrison OJ, Linehan JL, Shih HY, Bouladoux N, Han SJ, Smelkinson M, Sen SK, Byrd AL, Enamorado M, Yao C, Tamoutounour S, Van Laethem F, Hurabielle C, Collins N, Paun A, Salcedo R, O'Shea JJ, Belkaid Y. Commensal-specific T cell plasticity promotes rapid tissue adaptation to injury. Science. 2019 Jan 4;363(6422) [PubMed]

Ma C, Han M, Heinrich B, Fu Q, Zhang Q, Sandhu M, Agdashian D, Terabe M, Berzofsky JA, Fako V, Ritz T, Longerich T, Theriot CM, McCulloch JA, Roy S, Yuan W, Thovarai V, Sen SK, Ruchirawat M, Korangy F, Wang XW, Trinchieri G, Greten TF. Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells. Science. 2018 May 25;360(6391) [PubMed]

Linehan JL, Harrison OJ, Han SJ, Byrd AL, Vujkovic-Cvijin I, Villarino AV, Sen SK, Shaik J, Smelkinson M, Tamoutounour S, Collins N, Bouladoux N, Dzutsev A, Rosshart SP, Arbuckle JH, Wang CR, Kristie TM, Rehermann B, Trinchieri G, Brenchley JM, O'Shea JJ, Belkaid Y. Non-classical immunity controls microbiota impact on skin immunity and tissue repair. Cell. 2018 Feb 8;172(4):784-796.e18 [PubMed]

Oguz C, Sen SK, Davis AR, Fu YP, O'Donnell CJ, Gibbons GH. Genotype-driven identification of a molecular network predictive of advanced coronary calcium in ClinSeq® and Framingham Heart Study cohorts. BMC Syst Biol. 2017 Oct 26;11(1):99 [PubMed]

Lazo-Fernandez Y, Aguilera G, Pham TD, Park AY, Beierwaltes WH, Sutliff RL, Verlander JW, Pacak K, Osunkoya AO, Ellis CL, Kim YH, Shipley GL, Wynne BM, Hoover RS, Sen SK, Plotsky PM, Wall SM. Pendrin localizes to the adrenal medulla and modulates catecholamine release. Am J Physiol Endocrinol Metab. 2015 Sep 15;309(6):E534-45 [PubMed]

Sen SK, Boelte KC, Barb JJ, Joehanes R, Zhao X, Cheng Q, Adams L, Teer JK, Accame DS, Chowdhury S, Singh LN; NISC Comparative Sequencing Program; CHARGE Consortium, Kavousi M, Peyser PA, Quigley L, Priel DL, Lau K, Kuhns DB, Yoshimura T, Johnson AD, Hwang SJ, Chen MY, Arai AE, Green ED, Mullikin JC, Kolodgie FD, O'Donnell CJ, Virmani R, Munson PJ, McVicar DW, Biesecker LG. Integrative DNA, RNA, and protein evidence connects TREML4 to coronary artery calcification. Am J Hum Genet. 2014 Jul 3;95(1):66-76 [PubMed]

Sen SK, Barb JJ, Cherukuri PF, Accame DS, Elkahloun AG, Singh LN, Lee-Lin SQ, NISC Comparative Sequencing Program, Kolodgie FD, Cheng Q, Zhao X, Chen MY, Arai AE, Green ED, Mullikin JC, Munson PJ, Biesecker LG. Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines. BMC Genomics. 2014 Mar 14;15:198 [PubMed]

Chandrasekharappa SC, Lach FP, Kimble DC, Kamat A, Teer JK, Donovan FX, Flynn  E, Sen SK, Thongthip S, Sanborn E, Smogorzewska A, Auerbach AD, Ostrander EA, NISC Comparative Sequencing Program. Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia. Blood. 2013 May 30;121(22):e138-48 [PubMed]

Joehanes R, Ying S, Huan T, Johnson AD, Raghavachari N, Wang R, Liu P, Woodhouse KA, Sen SK, Tanriverdi K, Courchesne P, Freedman JE, O'Donnell CJ, Levy D, Munson PJ. Gene expression signatures of coronary heart disease. Arterioscler Thromb Vasc Biol. 2013 Jun;33(6):1418-26 [PubMed]

Zook JM, Samarov D, McDaniel J, Sen SK, Salit M. Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing. PLoS One. 2012;7(7):e41356 [PubMed]

Cordaux R, Sen SK, Konkel MK, Batzer MA. Computational methods for the analysis of primate mobile elements. Methods Mol Biol. 2010; 628:137-51 [PubMed]

Srikanta D, Sen SK, Conlin EM, Batzer MA. Internal priming: an opportunistic pathway for L1 and Alu retrotransposition in hominins. Gene. 2009 Dec 15;448(2):233-41 [PubMed]

Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB. Mobile elements create structural variation: analysis of a complete human genome. Genome Res. 2009 Sep;19(9):1516-26 [PubMed]

Pace JK 2nd, Sen SK, Batzer MA, Feschotte C. Repair-mediated duplication by capture of proximal chromosomal DNA has shaped vertebrate genome evolution. PLoS Genet. 2009 May;5(5):e1000469 [PubMed]

Srikanta D, Sen SK, Huang CT, Conlin EM, Rhodes RM, Batzer MA. An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair. Genomics. 2009 Mar;93(3):205-12 [PubMed]

Han K, Lee J, Meyer TJ, Wang J, Sen SK, Srikanta D, Liang P, Batzer MA. Alu recombination-mediated structural deletions in the chimpanzee genome. PLoS Genet. 2007 Oct;3(10):1939-49 [PubMed]

Sen SK, Huang CT, Han K, Batzer MA. Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome. Nucleic Acids Res. 2007;35(11):3741-51 [PubMed]

Sen SK, Han K, Wang J, Lee J, Wang H, Callinan PA, Dyer M, Cordaux R, Liang P, Batzer MA. Human genomic deletions mediated by recombination between Alu elements. Am J Hum Genet. 2006 Jul;79(1):41-53 [PubMed]

Han K, Sen SK, Wang J, Callinan PA, Lee J, Cordaux R, Liang P, Batzer MA. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res. 2005 Jul 20;33(13):4040-52 [PubMed]

  • Publications

    Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, McCulloch JA, Anastasakis DG, Sarshad AA, Leonardi I, Collins N, Blatter JA, Han SJ, Tamoutounour S, Potapova S, Foster St Claire MB, Yuan W, Sen SK, Dreier MS, Hild B, Hafner M, Wang D, Iliev ID, Belkaid Y, Trinchieri G, Rehermann B. Laboratory mice born to wild mice have natural microbiota and model human immune responses . Science 2019 Aug 2;365(6452) [PubMed]

    Johnston JJ, Williamson KA, Chou CM, Sapp JC, Ansari M, Chapman HM, Cooper DN, Dabir T, Dudley JN, Holt RJ, Ragge NK, Schäffer AA, Sen SK, Slavotinek AM, FitzPatrick DR, Glaser TM, Stewart F, Black GC, Biesecker LG. NAA10 polyadenylation signal variants cause syndromic microphthalmia. J Med Genet. 2019 Jul;56(7):444-452 [PubMed]

    Harrison OJ, Linehan JL, Shih HY, Bouladoux N, Han SJ, Smelkinson M, Sen SK, Byrd AL, Enamorado M, Yao C, Tamoutounour S, Van Laethem F, Hurabielle C, Collins N, Paun A, Salcedo R, O'Shea JJ, Belkaid Y. Commensal-specific T cell plasticity promotes rapid tissue adaptation to injury. Science. 2019 Jan 4;363(6422) [PubMed]

    Ma C, Han M, Heinrich B, Fu Q, Zhang Q, Sandhu M, Agdashian D, Terabe M, Berzofsky JA, Fako V, Ritz T, Longerich T, Theriot CM, McCulloch JA, Roy S, Yuan W, Thovarai V, Sen SK, Ruchirawat M, Korangy F, Wang XW, Trinchieri G, Greten TF. Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells. Science. 2018 May 25;360(6391) [PubMed]

    Linehan JL, Harrison OJ, Han SJ, Byrd AL, Vujkovic-Cvijin I, Villarino AV, Sen SK, Shaik J, Smelkinson M, Tamoutounour S, Collins N, Bouladoux N, Dzutsev A, Rosshart SP, Arbuckle JH, Wang CR, Kristie TM, Rehermann B, Trinchieri G, Brenchley JM, O'Shea JJ, Belkaid Y. Non-classical immunity controls microbiota impact on skin immunity and tissue repair. Cell. 2018 Feb 8;172(4):784-796.e18 [PubMed]

    Oguz C, Sen SK, Davis AR, Fu YP, O'Donnell CJ, Gibbons GH. Genotype-driven identification of a molecular network predictive of advanced coronary calcium in ClinSeq® and Framingham Heart Study cohorts. BMC Syst Biol. 2017 Oct 26;11(1):99 [PubMed]

    Lazo-Fernandez Y, Aguilera G, Pham TD, Park AY, Beierwaltes WH, Sutliff RL, Verlander JW, Pacak K, Osunkoya AO, Ellis CL, Kim YH, Shipley GL, Wynne BM, Hoover RS, Sen SK, Plotsky PM, Wall SM. Pendrin localizes to the adrenal medulla and modulates catecholamine release. Am J Physiol Endocrinol Metab. 2015 Sep 15;309(6):E534-45 [PubMed]

    Sen SK, Boelte KC, Barb JJ, Joehanes R, Zhao X, Cheng Q, Adams L, Teer JK, Accame DS, Chowdhury S, Singh LN; NISC Comparative Sequencing Program; CHARGE Consortium, Kavousi M, Peyser PA, Quigley L, Priel DL, Lau K, Kuhns DB, Yoshimura T, Johnson AD, Hwang SJ, Chen MY, Arai AE, Green ED, Mullikin JC, Kolodgie FD, O'Donnell CJ, Virmani R, Munson PJ, McVicar DW, Biesecker LG. Integrative DNA, RNA, and protein evidence connects TREML4 to coronary artery calcification. Am J Hum Genet. 2014 Jul 3;95(1):66-76 [PubMed]

    Sen SK, Barb JJ, Cherukuri PF, Accame DS, Elkahloun AG, Singh LN, Lee-Lin SQ, NISC Comparative Sequencing Program, Kolodgie FD, Cheng Q, Zhao X, Chen MY, Arai AE, Green ED, Mullikin JC, Munson PJ, Biesecker LG. Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines. BMC Genomics. 2014 Mar 14;15:198 [PubMed]

    Chandrasekharappa SC, Lach FP, Kimble DC, Kamat A, Teer JK, Donovan FX, Flynn  E, Sen SK, Thongthip S, Sanborn E, Smogorzewska A, Auerbach AD, Ostrander EA, NISC Comparative Sequencing Program. Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia. Blood. 2013 May 30;121(22):e138-48 [PubMed]

    Joehanes R, Ying S, Huan T, Johnson AD, Raghavachari N, Wang R, Liu P, Woodhouse KA, Sen SK, Tanriverdi K, Courchesne P, Freedman JE, O'Donnell CJ, Levy D, Munson PJ. Gene expression signatures of coronary heart disease. Arterioscler Thromb Vasc Biol. 2013 Jun;33(6):1418-26 [PubMed]

    Zook JM, Samarov D, McDaniel J, Sen SK, Salit M. Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing. PLoS One. 2012;7(7):e41356 [PubMed]

    Cordaux R, Sen SK, Konkel MK, Batzer MA. Computational methods for the analysis of primate mobile elements. Methods Mol Biol. 2010; 628:137-51 [PubMed]

    Srikanta D, Sen SK, Conlin EM, Batzer MA. Internal priming: an opportunistic pathway for L1 and Alu retrotransposition in hominins. Gene. 2009 Dec 15;448(2):233-41 [PubMed]

    Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB. Mobile elements create structural variation: analysis of a complete human genome. Genome Res. 2009 Sep;19(9):1516-26 [PubMed]

    Pace JK 2nd, Sen SK, Batzer MA, Feschotte C. Repair-mediated duplication by capture of proximal chromosomal DNA has shaped vertebrate genome evolution. PLoS Genet. 2009 May;5(5):e1000469 [PubMed]

    Srikanta D, Sen SK, Huang CT, Conlin EM, Rhodes RM, Batzer MA. An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair. Genomics. 2009 Mar;93(3):205-12 [PubMed]

    Han K, Lee J, Meyer TJ, Wang J, Sen SK, Srikanta D, Liang P, Batzer MA. Alu recombination-mediated structural deletions in the chimpanzee genome. PLoS Genet. 2007 Oct;3(10):1939-49 [PubMed]

    Sen SK, Huang CT, Han K, Batzer MA. Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome. Nucleic Acids Res. 2007;35(11):3741-51 [PubMed]

    Sen SK, Han K, Wang J, Lee J, Wang H, Callinan PA, Dyer M, Cordaux R, Liang P, Batzer MA. Human genomic deletions mediated by recombination between Alu elements. Am J Hum Genet. 2006 Jul;79(1):41-53 [PubMed]

    Han K, Sen SK, Wang J, Callinan PA, Lee J, Cordaux R, Liang P, Batzer MA. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res. 2005 Jul 20;33(13):4040-52 [PubMed]

Last updated: October 23, 2019