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PAVEL SUMAZIN

TitleAssistant Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Pediatrics
DivisionPediatrics-Oncology
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    In the Regulatory Circuits Lab (https://www.bcm.edu/research/labs/regulatory-circuits) 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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    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. Bright SJ, Flint DB, Chakraborty S, McFadden CH, Yoon DS, Bronk L, Titt U, Mohan R, Grosshans DR, Sumazin P, Shaitelman SF, Asaithamby A, Sawakuchi GO. Non-homologous end joining is more important than proton linear energy transfer in dictating cell death. Int J Radiat Oncol Biol Phys. 2019 Aug 16. PMID: 31425731.
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    2. Rombaut D, Chiu HS, Decaesteker B, Everaert C, Yigit N, Peltier A, Janoueix-Lerosey I, Bartenhagen C, Fischer M, Roberts S, D'Haene N, De Preter K, Speleman F, Denecker G, Sumazin P, Vandesompele J, Lefever S, Mestdagh P. Author Correction: Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes. Sci Rep. 2019 Jul 17; 9(1):10536. PMID: 31311990.
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    3. Rombaut D, Chiu HS, Decaesteker B, Everaert C, Yigit N, Peltier A, Janoueix-Lerosey I, Bartenhagen C, Fischer M, Roberts S, D'Haene N, De Preter K, Speleman F, Denecker G, Sumazin P, Vandesompele J, Lefever S, Mestdagh P. Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes. Sci Rep. 2019 Apr 05; 9(1):5685. PMID: 30952905.
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    4. Zhang J, Liu P, Tao J, Wang P, Zhang Y, Song X, Che L, Sumazin P, Ribback S, Kiss A, Schaff Z, Cigliano A, Dombrowski F, Cossu C, Pascale RM, Calvisi DF, Monga SP, Chen X. TEA Domain Transcription Factor 4 Is the Major Mediator of Yes-Associated Protein Oncogenic Activity in Mouse and Human Hepatoblastoma. Am J Pathol. 2019 May; 189(5):1077-1090. PMID: 30794805.
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    5. Fu Y, Zorman B, Sumazin P, Sanna PP, Repunte-Canonigo V. Epitranscriptomics: Correlation of N6-methyladenosine RNA methylation and pathway dysregulation in the hippocampus of HIV transgenic rats. PLoS One. 2019; 14(1):e0203566. PMID: 30653517.
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    6. Ustianenko D, Chiu HS, Treiber T, Weyn-Vanhentenryck SM, Treiber N, Meister G, Sumazin P, Zhang C. LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs. Mol Cell. 2018 07 19; 71(2):271-283.e5. PMID: 30029005.
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    7. Zhang Y, Paikari A, Sumazin P, Ginter Summarell CC, Crosby JR, Boerwinkle E, Weiss MJ, Sheehan VA. Metformin induces FOXO3-dependent fetal hemoglobin production in human primary erythroid cells. Blood. 2018 07 19; 132(3):321-333. PMID: 29884740.
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    8. Chiu HS, Martínez MR, Komissarova EV, Llobet-Navas D, Bansal M, Paull EO, Silva J, Yang X, Sumazin P, Califano A. The number of titrated microRNA species dictates ceRNA regulation. Nucleic Acids Res. 2018 05 18; 46(9):4354-4369. PMID: 29684207.
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    9. Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS, Sood AK, Gunaratne PH, Sumazin P. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Rep. 2018 04 03; 23(1):297-312.e12. PMID: 29617668.
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    10. Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 04 03; 23(1):194-212.e6. PMID: 29617660.
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    11. Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 04 09; 33(4):690-705.e9. PMID: 29622464.
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    12. Bielamowicz K, Fousek K, Byrd TT, Samaha H, Mukherjee M, Aware N, Wu MF, Orange JS, Sumazin P, Man TK, Joseph SK, Hegde M, Ahmed N. Trivalent CAR T cells overcome interpatient antigenic variability in glioblastoma. Neuro Oncol. 2018 03 27; 20(4):506-518. PMID: 29016929.
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    13. Woodfield SE, Shi Y, Patel RH, Jin J, Major A, Sarabia SF, Starosolski Z, Zorman B, Gupta SS, Chen Z, Ibarra AM, Bissig KD, Ghaghada KB, Sumazin P, López-Terrada D, Vasudevan SA. A Novel Cell Line Based Orthotopic Xenograft Mouse Model That Recapitulates Human Hepatoblastoma. Sci Rep. 2017 12 19; 7(1):17751. PMID: 29259231.
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    14. Barzi M, Pankowicz FP, Zorman B, Liu X, Legras X, Yang D, Borowiak M, Bissig-Choisat B, Sumazin P, Li F, Bissig KD. Erratum: A novel humanized mouse lacking murine p450 oxidoreductase for studying human drug metabolism. Nat Commun. 2017 10 17; 8(1):984. PMID: 29042563.
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    15. Barzi M, Pankowicz FP, Zorman B, Liu X, Legras X, Yang D, Borowiak M, Bissig-Choisat B, Sumazin P, Li F, Bissig KD. A novel humanized mouse lacking murine P450 oxidoreductase for studying human drug metabolism. Nat Commun. 2017 06 28; 8(1):39. PMID: 28659616.
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    16. 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 05 30; 18(1):418. PMID: 28558729.
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    17. 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. 2017 01; 65(1):104-121. PMID: 27775819.
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    18. 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 08 30; 7:12642. PMID: 27572891.
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    19. 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 HV, Hu J, Shi Y, Gaber MW, Hicks MJ, Thompson PA, Lu Y, Mills GB, Finegold M, Goss JA, Parsons DW, Vasudevan SA, Sumazin P, López-Terrada D, Bissig KD. Novel patient-derived xenograft and cell line models for therapeutic testing of pediatric liver cancer. J Hepatol. 2016 08; 65(2):325-33. PMID: 27117591.
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    20. 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 Nov 17; 6:8891. PMID: 26573325.
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    21. 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.
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    22. 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.
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    23. 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.
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    24. 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.
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    25. 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.
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    26. 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.
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    27. 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 01; 28(7):765-82. PMID: 24636986.
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    28. 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 (ERa)-positive mammary adenocarcinomas. Oncogene. 2014 Nov 27; 33(48):5511-5522. PMID: 24276237.
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    29. 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.
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    30. 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.
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    31. 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.
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    32. 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.
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    33. 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 08; 6:377. PMID: 20531406.
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    34. Zhou X, Sumazin P, Rajbhandari P, Califano A. A systems biology approach to transcription factor binding site prediction. PLoS One. 2010 Mar 26; 5(3):e9878. PMID: 20360861.
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    35. 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.
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    36. 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 04; 115(5):975-84. PMID: 19965633.
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    37. 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 07; 106(27):11294-9. PMID: 19549844.
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    38. 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.
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    39. 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 06; 106(1):244-9. PMID: 19118200.
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    40. Smith AD, Sumazin P, Zhang MQ. Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol. 2007; 3:73. PMID: 17224917.
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    41. 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.
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    42. 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.
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    43. 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 01; 102(5):1560-5. PMID: 15668401.
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    44. Sumazin P, Chen G, Hata N, Smith AD, Zhang T, Zhang MQ. DWE: discriminating word enumerator. Bioinformatics. 2005 Jan 01; 21(1):31-8. PMID: 15333453.
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    45. Schones DE, Sumazin P, Zhang MQ. Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics. 2005 Feb 01; 21(3):307-13. PMID: 15319260.
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    46. 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.
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    47. Wildenberg A, Skiena S, Sumazin P. Deconvolving sequence variation in mixed DNA populations. J Comput Biol. 2003; 10(3-4):635-52. PMID: 12935349.
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