Last Name


TitleAssistant Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Pediatrics
AddressOne Baylor Plaza
Houston TX 77030
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    In the Regulatory Circuits Lab ( we infer pathophysiological consequences of genomic variants and aberrant gene expression through analyses of molecular profiles. Towards this goal we combine computational analyses and biochemical experiments, leveraging regulatory circuits to identify new driver genes and genomic variants that act in cis and in trans.

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    Computational biology

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Chiu HS, Martínez MR, Bansal M, Subramanian A, Golub TR, Yang X, Sumazin P, Califano A. High-throughput validation of ceRNA regulatory networks. BMC Genomics. 2017 May 30; 18(1):418. PMID: 28558729.
      View in: PubMed
    2. Sumazin P, Chen Y, Treviño LR, Sarabia SF, Hampton OA, Patel K, Mistretta TA, Zorman B, Thompson P, Heczey A, Comerford S, Wheeler DA, Chintagumpala M, Meyers R, Rakheja D, Finegold MJ, Tomlinson G, Parsons DW, López-Terrada D. Genomic Analysis of Hepatoblastoma Identifies Distinct Molecular and Prognostic Subgroups. Hepatology. 2016 Oct 24. PMID: 27775819.
      View in: PubMed
    3. Pankowicz FP, Barzi M, Legras X, Hubert L, Mi T, Tomolonis JA, Ravishankar M, Sun Q, Yang D, Borowiak M, Sumazin P, Elsea SH, Bissig-Choisat B, Bissig KD. Reprogramming metabolic pathways in vivo with CRISPR/Cas9 genome editing to treat hereditary tyrosinaemia. Nat Commun. 2016; 7:12642. PMID: 27572891.
      View in: PubMed
    4. Bissig-Choisat B, Kettlun-Leyton C, Legras XD, Zorman B, Barzi M, Chen LL, Amin MD, Huang YH, Pautler RG, Hampton OA, Prakash MM, Yang D, Borowiak M, Muzny D, Doddapaneni H, Hu J, Shi Y, Gaber WM, John Hicks M, Thompson PA, Lu Y, Mills GB, Finegold M, Goss JA, Williams Parsons D, Vasudevan SA, Sumazin P, Lopez-Terrada D, Bissig KD. Novel Patient-Derived Xenograft and Cell Line Models for Therapeutic Testing of Pediatric Liver Cancer. J Hepatol. 2016 Apr 23. PMID: 27117591.
      View in: PubMed
    5. Roy A, Kumar V, Zorman B, Fang E, Haines KM, Doddapaneni H, Hampton OA, White S, Bavle AA, Patel NR, Eldin KW, John Hicks M, Rakheja D, Leavey PJ, Skapek SX, Amatruda JF, Nuchtern JG, Chintagumpala MM, Wheeler DA, Plon SE, Sumazin P, Parsons DW. Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney. Nat Commun. 2015; 6:8891. PMID: 26573325.
      View in: PubMed
    6. Bucur O, Almasan A, Zubarev R, Friedman M, Nicolson GL, Sumazin P, Leabu M, Nikolajczyk BS, Avram D, Kunej T, Calin GA, Godwin AK, Adami HO, Zaphiropoulos PG, Richardson DR, Schmitt-Ulms G, Westerblad H, Keniry M, Grau GE, Carbonetto S, Stan RV, Popa-Wagner A, Takhar K, Baron BW, Galardy PJ, Yang F, Data D, Fadare O, Yeo KJ, Gabreanu GR, Andrei S, Soare GR, Nelson MA, Liehn EA. An updated h-index measures both the primary and total scientific output of a researcher. Discoveries (Craiova). 2015 Jul-Sep; 3(3). PMID: 26504901.
      View in: PubMed
    7. Bansal M, Mendiratta G, Anand S, Kushwaha R, Kim R, Kustagi M, Iyer A, Chaganti RS, Califano A, Sumazin P. Direct ChIP-Seq significance analysis improves target prediction. BMC Genomics. 2015; 16 Suppl 5:S4. PMID: 26040656.
      View in: PubMed
    8. Kushwaha R, Jagadish N, Kustagi M, Tomishima MJ, Mendiratta G, Bansal M, Kim HR, Sumazin P, Alvarez MJ, Lefebvre C, Villagrasa-Gonzalez P, Viale A, Korkola JE, Houldsworth J, Feldman DR, Bosl GJ, Califano A, Chaganti RS. Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency. Stem Cells. 2015 Feb; 33(2):367-77. PMID: 25336442; PMCID: PMC4305010.
    9. Chiu HS, Llobet-Navas D, Yang X, Chung WJ, Ambesi-Impiombato A, Iyer A, Kim HR, Seviour EG, Luo Z, Sehgal V, Moss T, Lu Y, Ram P, Silva J, Mills GB, Califano A, Sumazin P. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Res. 2015 Feb; 25(2):257-67. PMID: 25378249; PMCID: PMC4315299.
    10. Mukherjee M, Byrd T, Brawley VS, Bielamowicz K, Li XN, Merchant F, Maitra S, Sumazin P, Fuller G, Kew Y, Sun D, Powell SZ, Ahmed N, Zhang N, Pati D. Erratum to: Overexpression and constitutive nuclear localization of cohesin protease Separase protein correlates with high incidence of relapse and reduced overall survival in glioblastoma multiforme. J Neurooncol. 2014 Aug; 119(1):37. PMID: 24902668.
      View in: PubMed
    11. Mukherjee M, Byrd T, Brawley VS, Bielamowicz K, Li XN, Merchant F, Maitra S, Sumazin P, Fuller G, Kew Y, Sun D, Powell SZ, Ahmed N, Zhang N, Pati D. Overexpression and constitutive nuclear localization of cohesin protease Separase protein correlates with high incidence of relapse and reduced overall survival in glioblastoma multiforme. J Neurooncol. 2014 Aug; 119(1):27-35. PMID: 24792645; PMCID: PMC4160150.
    12. Llobet-Navas D, Rodríguez-Barrueco R, Castro V, Ugalde AP, Sumazin P, Jacob-Sendler D, Demircan B, Castillo-Martín M, Putcha P, Marshall N, Villagrasa P, Chan J, Sanchez-Garcia F, Pe'er D, Rabadán R, Iavarone A, Cordón-Cardó C, Califano A, López-Otín C, Ezhkova E, Silva JM. The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes Dev. 2014 Apr 1; 28(7):765-82. PMID: 24636986; PMCID: PMC4015488.
    13. Mukherjee M, Ge G, Zhang N, Edwards DG, Sumazin P, Sharan SK, Rao PH, Medina D, Pati D. MMTV-Espl1 transgenic mice develop aneuploid, estrogen receptor alpha (ER?)-positive mammary adenocarcinomas. Oncogene. 2014 Nov 27; 33(48):5511-22. PMID: 24276237; PMCID: PMC4032816.
    14. Irshad S, Bansal M, Castillo-Martin M, Zheng T, Aytes A, Wenske S, Le Magnen C, Guarnieri P, Sumazin P, Benson MC, Shen MM, Califano A, Abate-Shen C. A molecular signature predictive of indolent prostate cancer. Sci Transl Med. 2013 Sep 11; 5(202):202ra122. PMID: 24027026; PMCID: PMC3943244.
    15. Maute RL, Schneider C, Sumazin P, Holmes A, Califano A, Basso K, Dalla-Favera R. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proc Natl Acad Sci U S A. 2013 Jan 22; 110(4):1404-9. PMID: 23297232; PMCID: PMC3557069.
    16. Austin ED, Ma L, LeDuc C, Berman Rosenzweig E, Borczuk A, Phillips JA, Palomero T, Sumazin P, Kim HR, Talati MH, West J, Loyd JE, Chung WK. Whole exome sequencing to identify a novel gene (caveolin-1) associated with human pulmonary arterial hypertension. Circ Cardiovasc Genet. 2012 Jun; 5(3):336-43. PMID: 22474227; PMCID: PMC3380156.
    17. Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell. 2011 Oct 14; 147(2):370-81. PMID: 22000015; PMCID: PMC3214599.
    18. Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol. 2010 Jun 8; 6:377. PMID: 20531406; PMCID: PMC2913282.
    19. Zhou X, Sumazin P, Rajbhandari P, Califano A. A systems biology approach to transcription factor binding site prediction. PLoS One. 2010; 5(3):e9878. PMID: 20360861; PMCID: PMC2845628.
    20. Alvarez MJ, Sumazin P, Rajbhandari P, Califano A. Correlating measurements across samples improves accuracy of large-scale expression profile experiments. Genome Biol. 2009; 10(12):R143. PMID: 20042104; PMCID: PMC2812950.
    21. Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim WK, Kitagawa Y, Schneider C, Alvarez MJ, Califano A, Dalla-Favera R. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood. 2010 Feb 4; 115(5):975-84. PMID: 19965633; PMCID: PMC2817639.
    22. Saito M, Novak U, Piovan E, Basso K, Sumazin P, Schneider C, Crespo M, Shen Q, Bhagat G, Califano A, Chadburn A, Pasqualucci L, Dalla-Favera R. BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A. 2009 Jul 7; 106(27):11294-9. PMID: 19549844; PMCID: PMC2708681.
    23. Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J, Chen CZ, Califano A, Dalla-Favera R. Identification of the human mature B cell miRNome. Immunity. 2009 May; 30(5):744-52. PMID: 19446474; PMCID: PMC2764486.
    24. Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G. ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proc Natl Acad Sci U S A. 2009 Jan 6; 106(1):244-9. PMID: 19118200; PMCID: PMC2613038.
    25. Smith AD, Sumazin P, Zhang MQ. Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol. 2007; 3:73. PMID: 17224917; PMCID: PMC1800356.
    26. Smith AD, Sumazin P, Xuan Z, Zhang MQ. DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A. 2006 Apr 18; 103(16):6275-80. PMID: 16606849; PMCID: PMC1458868.
    27. Smith AD, Sumazin P, Das D, Zhang MQ. Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics. 2005 Jun; 21 Suppl 1:i403-12. PMID: 15961485.
      View in: PubMed
    28. Smith AD, Sumazin P, Zhang MQ. Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A. 2005 Feb 1; 102(5):1560-5. PMID: 15668401; PMCID: PMC547828.
    29. Sumazin P, Chen G, Hata N, Smith AD, Zhang T, Zhang MQ. DWE: discriminating word enumerator. Bioinformatics. 2005 Jan 1; 21(1):31-8. PMID: 15333453.
      View in: PubMed
    30. Schones DE, Sumazin P, Zhang MQ. Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics. 2005 Feb 1; 21(3):307-13. PMID: 15319260.
      View in: PubMed
    31. Long F, Liu H, Hahn C, Sumazin P, Zhang MQ, Zilberstein A. Genome-wide prediction and analysis of function-specific transcription factor binding sites. In Silico Biol. 2004; 4(4):395-410. PMID: 15506990.
      View in: PubMed
    32. Wildenberg A, Skiena S, Sumazin P. Deconvolving sequence variation in mixed DNA populations. J Comput Biol. 2003; 10(3-4):635-52. PMID: 12935349.
      View in: PubMed
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