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Items: 41

1.

LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs.

Ustianenko D, Chiu HS, Treiber T, Weyn-Vanhentenryck SM, Treiber N, Meister G, Sumazin P, Zhang C.

Mol Cell. 2018 Jul 19;71(2):271-283.e5. doi: 10.1016/j.molcel.2018.06.029.

PMID:
30029005
2.

Metformin induces FOXO3-dependent fetal hemoglobin production in human primary erythroid cells.

Zhang Y, Paikari A, Sumazin P, Ginter Summarell CC, Crosby JR, Boerwinkle E, Weiss MJ, Sheehan VA.

Blood. 2018 Jul 19;132(3):321-333. doi: 10.1182/blood-2017-11-814335. Epub 2018 Jun 8.

PMID:
29884740
3.

The number of titrated microRNA species dictates ceRNA regulation.

Chiu HS, Martínez MR, Komissarova EV, Llobet-Navas D, Bansal M, Paull EO, Silva J, Yang X, Sumazin P, Califano A.

Nucleic Acids Res. 2018 May 18;46(9):4354-4369. doi: 10.1093/nar/gky286.

4.

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.

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; Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R.

Cancer Cell. 2018 Apr 9;33(4):690-705.e9. doi: 10.1016/j.ccell.2018.03.014. Epub 2018 Apr 2.

5.

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context.

Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS; Cancer Genome Atlas Research Network, Sood AK, Gunaratne PH, Sumazin P.

Cell Rep. 2018 Apr 3;23(1):297-312.e12. doi: 10.1016/j.celrep.2018.03.064.

6.

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.

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; Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C.

Cell Rep. 2018 Apr 3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063.

7.

A Novel Cell Line Based Orthotopic Xenograft Mouse Model That Recapitulates Human Hepatoblastoma.

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.

Sci Rep. 2017 Dec 19;7(1):17751. doi: 10.1038/s41598-017-17665-8.

8.

Erratum: A novel humanized mouse lacking murine p450 oxidoreductase for studying human drug metabolism.

Barzi M, Pankowicz FP, Zorman B, Liu X, Legras X, Yang D, Borowiak M, Bissig-Choisat B, Sumazin P, Li F, Bissig KD.

Nat Commun. 2017 Oct 17;8(1):984. doi: 10.1038/s41467-017-01314-9.

9.

Trivalent CAR T cells overcome interpatient antigenic variability in glioblastoma.

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.

Neuro Oncol. 2018 Mar 27;20(4):506-518. doi: 10.1093/neuonc/nox182.

PMID:
29016929
10.

A novel humanized mouse lacking murine P450 oxidoreductase for studying human drug metabolism.

Barzi M, Pankowicz FP, Zorman B, Liu X, Legras X, Yang D, Borowiak M, Bissig-Choisat B, Sumazin P, Li F, Bissig KD.

Nat Commun. 2017 Jun 28;8(1):39. doi: 10.1038/s41467-017-00049-x. Erratum in: Nat Commun. 2017 Oct 17;8(1):984.

11.

High-throughput validation of ceRNA regulatory networks.

Chiu HS, Martínez MR, Bansal M, Subramanian A, Golub TR, Yang X, Sumazin P, Califano A.

BMC Genomics. 2017 May 30;18(1):418. doi: 10.1186/s12864-017-3790-7.

12.

Genomic analysis of hepatoblastoma identifies distinct molecular and prognostic subgroups.

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.

Hepatology. 2017 Jan;65(1):104-121. doi: 10.1002/hep.28888. Epub 2016 Nov 29.

PMID:
27775819
13.

Reprogramming metabolic pathways in vivo with CRISPR/Cas9 genome editing to treat hereditary tyrosinaemia.

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.

Nat Commun. 2016 Aug 30;7:12642. doi: 10.1038/ncomms12642.

14.

Novel patient-derived xenograft and cell line models for therapeutic testing of pediatric liver cancer.

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.

J Hepatol. 2016 Aug;65(2):325-33. doi: 10.1016/j.jhep.2016.04.009. Epub 2016 Apr 23.

15.

Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney.

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.

Nat Commun. 2015 Nov 17;6:8891. doi: 10.1038/ncomms9891.

16.

An updated h-index measures both the primary and total scientific output of a researcher.

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.

Discoveries (Craiova). 2015 Jul-Sep;3(3). pii: e50. Epub 2015 Sep 30.

17.

Direct ChIP-Seq significance analysis improves target prediction.

Bansal M, Mendiratta G, Anand S, Kushwaha R, Kim R, Kustagi M, Iyer A, Chaganti RS, Califano A, Sumazin P.

BMC Genomics. 2015;16 Suppl 5:S4. doi: 10.1186/1471-2164-16-S5-S4. Epub 2015 May 26.

18.

Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.

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.

Genome Res. 2015 Feb;25(2):257-67. doi: 10.1101/gr.178194.114. Epub 2014 Nov 5.

19.

Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency.

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.

Stem Cells. 2015 Feb;33(2):367-77. doi: 10.1002/stem.1870.

20.

Overexpression and constitutive nuclear localization of cohesin protease Separase protein correlates with high incidence of relapse and reduced overall survival in glioblastoma multiforme.

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.

J Neurooncol. 2014 Aug;119(1):27-35. doi: 10.1007/s11060-014-1458-6. Epub 2014 May 4. Erratum in: J Neurooncol. 2014 Aug;119(1):37. Ahmed, Nabil M [Corrected to Ahmed, Nabil].

21.

The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.

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.

Genes Dev. 2014 Apr 1;28(7):765-82. doi: 10.1101/gad.237404.114. Epub 2014 Mar 17.

22.

MMTV-Espl1 transgenic mice develop aneuploid, estrogen receptor alpha (ERα)-positive mammary adenocarcinomas.

Mukherjee M, Ge G, Zhang N, Edwards DG, Sumazin P, Sharan SK, Rao PH, Medina D, Pati D.

Oncogene. 2014 Nov 27;33(48):5511-5522. doi: 10.1038/onc.2013.493. Epub 2013 Nov 25.

23.

A molecular signature predictive of indolent prostate cancer.

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.

Sci Transl Med. 2013 Sep 11;5(202):202ra122. doi: 10.1126/scitranslmed.3006408. Erratum in: Sci Transl Med. 2013 Sep 18;5(203):203er9.

24.

tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma.

Maute RL, Schneider C, Sumazin P, Holmes A, Califano A, Basso K, Dalla-Favera R.

Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1404-9. doi: 10.1073/pnas.1206761110. Epub 2013 Jan 7.

25.

Whole exome sequencing to identify a novel gene (caveolin-1) associated with human pulmonary arterial hypertension.

Austin ED, Ma L, LeDuc C, Berman Rosenzweig E, Borczuk A, Phillips JA 3rd, Palomero T, Sumazin P, Kim HR, Talati MH, West J, Loyd JE, Chung WK.

Circ Cardiovasc Genet. 2012 Jun;5(3):336-43. doi: 10.1161/CIRCGENETICS.111.961888. Epub 2012 Apr 2.

26.

An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma.

Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A.

Cell. 2011 Oct 14;147(2):370-81. doi: 10.1016/j.cell.2011.09.041.

27.

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.

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.

Mol Syst Biol. 2010 Jun 8;6:377. doi: 10.1038/msb.2010.31.

28.

A systems biology approach to transcription factor binding site prediction.

Zhou X, Sumazin P, Rajbhandari P, Califano A.

PLoS One. 2010 Mar 26;5(3):e9878. doi: 10.1371/journal.pone.0009878.

29.

Correlating measurements across samples improves accuracy of large-scale expression profile experiments.

Alvarez MJ, Sumazin P, Rajbhandari P, Califano A.

Genome Biol. 2009;10(12):R143. doi: 10.1186/gb-2009-10-12-r143. Epub 2009 Dec 30.

30.

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells.

Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim WK, Kitagawa Y, Schneider C, Alvarez MJ, Califano A, Dalla-Favera R.

Blood. 2010 Feb 4;115(5):975-84. doi: 10.1182/blood-2009-06-227017. Epub 2009 Dec 3.

31.

BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma.

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.

Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11294-9. doi: 10.1073/pnas.0903854106. Epub 2009 Jun 23.

32.

Identification of the human mature B cell miRNome.

Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J Jr, Chen CZ, Califano A, Dalla-Favera R.

Immunity. 2009 May;30(5):744-52. doi: 10.1016/j.immuni.2009.03.017. Epub 2009 May 14.

33.

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes.

Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G.

Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):244-9. doi: 10.1073/pnas.0806445106. Epub 2008 Dec 31.

34.

Tissue-specific regulatory elements in mammalian promoters.

Smith AD, Sumazin P, Zhang MQ.

Mol Syst Biol. 2007;3:73. Epub 2007 Jan 16.

35.

DNA motifs in human and mouse proximal promoters predict tissue-specific expression.

Smith AD, Sumazin P, Xuan Z, Zhang MQ.

Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6275-80. Epub 2006 Apr 10.

36.

Mining ChIP-chip data for transcription factor and cofactor binding sites.

Smith AD, Sumazin P, Das D, Zhang MQ.

Bioinformatics. 2005 Jun;21 Suppl 1:i403-12.

PMID:
15961485
37.

Identifying tissue-selective transcription factor binding sites in vertebrate promoters.

Smith AD, Sumazin P, Zhang MQ.

Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1560-5. Epub 2005 Jan 24.

38.

Genome-wide prediction and analysis of function-specific transcription factor binding sites.

Long F, Liu H, Hahn C, Sumazin P, Zhang MQ, Zilberstein A.

In Silico Biol. 2004;4(4):395-410.

PMID:
15506990
39.

DWE: discriminating word enumerator.

Sumazin P, Chen G, Hata N, Smith AD, Zhang T, Zhang MQ.

Bioinformatics. 2005 Jan 1;21(1):31-8. Epub 2004 Aug 27.

PMID:
15333453
40.

Similarity of position frequency matrices for transcription factor binding sites.

Schones DE, Sumazin P, Zhang MQ.

Bioinformatics. 2005 Feb 1;21(3):307-13. Epub 2004 Aug 19.

PMID:
15319260
41.

Deconvolving sequence variation in mixed DNA populations.

Wildenberg A, Skiena S, Sumazin P.

J Comput Biol. 2003;10(3-4):635-52.

PMID:
12935349

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