Quantitative Biomedical Research Center

Publications

2021

  • BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52. Hatchi E, Goehring L, Landini S, Skourti-Stathaki K, DeConti DK, Abderazzaq FO, Banerjee P, Demers TM, Wang YE, Quackenbush J, Livingston DM.  Nature. 2021 Mar;591(7851):665-670. doi: 10.1038/s41586-020-03150-2. Epub 2021 Feb 3. PMID: 33536619.

2019

  • Inhibition of de novo lipogenesis targets androgen receptor signaling in castration-resistant prostate cancer.  Zadra G, Ribeiro CF, Chetta P, Ho Y, Cacciatore S, Gao X, Syamala S, Bango C, Photopoulos C, Huang Y, Tyekucheva S, Bastos DC, Tchaicha J, Lawney B, Uo T,D’Anello L, Csibi A, Kalekar R, Larimer B, Ellis L, Butler LM, Morrissey C, McGovern K, Palombella VJ, Kutok JL, Mahmood U, Bosari S, Adams J, Peluso S, Dehm SM, Plymate SR, Loda M.  PNAS. 2019. 116(2):631-640. [PubMed]

2018

  • Loss of Tight Junction Protein Claudin 18 Promotes Progressive Neoplasia Development in Mouse Stomach.  Hagen SJ, Ang LH, Zheng Y, Karahan SN, Wu J, Wang YE, Caron TJ, Gad AP, Muthupalani S, Fox JG. Gastroenterology. 2018, 155(6):1852-1867. [PubMed]
  • Plasma circulating extracellular RNAs in left ventricular remodeling post-myocardial infarction.  Danielson KM, Shah R, Yeri A, Liu X, Garcia FC, Silverman M, Tanriverdi K, Das A, Xiao C, Jerosch-Herold M, Heydari B, Abbasi S, Keuren-Jensen, KV, Freedman JE, Wang YE, Rosenzweig A, Kwong RY, Das S. EBioMedicine. 2018. 32:172-181 [PubMed]
  • Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling. Giraldez MD, Spengler RM, Etheridge A, Godoy PM, Barczak AJ, Srinivasan S, De Hoff PL,Tanriverdi K, Courtright A, Lu S, Khoory J, Rubio R, Baxter D, Driedonks TAP, Buermans HPJ, Nolte-‘t Hoen ENM, Jiang H, Wang K, Ghiran I, Wang YE, Van Keuren-Jensen K, Freedman JE, Woodruff PG, Laurent LC, Erle DJ, Galas DJ, Tewari M.  Nat. Biotech. 2018. 36(8):746-757 [PubMed]
  • Kinase-independent function of E-type cyclins in liver cancer. Geng Y, Michowski W, Chick JM, Wang YE, Jecrois ME, Sweeney KE, Liu L, Han RC, Ke N, Zagozdzon A, Sicinska E, Bronson RT, Gygi SP, Sicinski P.  PNAS. 2018, 115(5):1015-1020 [PubMed]

2017

  • Constitutive Ras signaling and Ink4a/Arf inactivation cooperate during the development of B-ALL in mice. Sewastianik T, Jiang M, Sukhdeo K, Patel SS, Roberts K, Kang Y, Alduaij A, Dennis PS, Lawney B, Liu R, Song Z, Xiong J, Zhang Y, Lemieux ME, Pinkus GS, Rich JN, Weinstock DM, Mullighan CG, Sharpless NE, Carrasco RD.  Blood Adv. 2017, 1(25):2361-2374. [PubMed]
  • WebMeV: a Cloud Platform for Analyzing and Visualizing Cancer Genomic Data. Wang YE, Kutnetsov L, Partensky A, Farid J, Quackenbush J. , Cancer Res. 2017, 77(21):e11-e14 [PubMed]
  • HIF Activation Causes Synthetic Lethality between the VHL Tumor Suppressor and the EZH1 Histone Methyltransferase. Chakraborty AA, Nakamura E, Qi J, Creech A, Jaffe JD, Paulk J, Novak JS, Nagulapalli K, McBrayer SK, Cowley GS, Pineda J, Song J, Wang YE, Carr SA, Root DE, Signoretti S, Bradner JE, Kaelin WG. Trans Med.2017, 9(398):eeal5272 [PubMed]
  • High Throughput Sequencing of Extracellular RNA from Human Plasma. Danielson KM, Rubio R,  Abderazzaq F, Das S, Wang YE. PLoS One. 2017, 12(1):e0164644 [PubMed]

2016

  • Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors. Elias KM, Emori MM, Westerling T, Long H, Budina-Kolomets A, Li F, MacDuffie E, Davis MR, Holman A, Lawney B, Freedman ML, Quackenbush J, Brown M, Drapkin R.  JCI Insight. 2016 Aug 18;1(13) [PubMed]
  • Proteomic Landscape of Tissue-Specific Cyclin E Functions In Vivo.  Odajima J, Jung P, Ndassa-Colday Y, Ficaro S, Geng Y, Marco E, Michowski W, Wang YE, Litovchick L, DeCaprio JA, Marto J, Sicinski P. PLoS Genetics. 2016, 12(11): e1006429[PubMed]
  • RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes.  Bunch H, Lawney BP, Burkholder A, Ma D, Zheng X, Motola S, Fargo DC, Levine SS, Wang YE, Hu G. Genomics. 2016 Jul 16; S0888-7543(16)30072-6 [PubMed]
  • Diverse human extracellular RNAs are widely detected in human plasma.  Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, Das S, Shah R, Danielson K, Beaulieu L, Navarro FC, Wang Y, Galeev TR, Holman A, Kwong RY, Murthy V, Tanriverdi SE, Koupenova-Zamor M, Mikhalev E, Tanriverdi K. Nat Commun. 2016 Apr 26;7:11106. [PubMed]
  • ABCB5-Targeted Chemoresistance Reversal Inhibits Merkel Cell Carcinoma Growth. Kleffel S, Lee N, Lezcano C, Wilson BJ, Sobolewski K, Saab KR, Mueller H, Zhan Q, Posch C, Elco CP, DoRosario A, Garcia SS, Thakuria M, Wang YE, Wang LC, Murphy GF, Frank MH, Schatton T.  J Invest Dermatol. 2016 Apr;136(4):838-46.
  • Gender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma. De Rienzo A, Archer MA, Yeap BY, Dao N, Sciaranghella D, Sideris AC, Zheng Y, Holman AG, Wang YE, Dal Cin PS, Fletcher JA, Rubio R, Croft L, Quackenbush J, Sugarbaker PE, Munir KJ, Battilana JR, Gustafson CE, Chirieac LR, Ching SM, Wong J, Tay LC, Rudd S, Hercus R, Sugarbaker DJ, Richards WG, Bueno R.  Cancer 2016 Jan 15;76(2):319-28.[PubMed]

2015

  • Transcriptional elongation requires DNA break-induced signalling.  Bunch H, Lawney BP, Lin YF, Asaithamby A, Murshid A, Wang YE, Chen BP, Calderwood SK. Nat Commun. 2015 Dec 16;6:10191. doi: 10.1038/ncomms10191.[PubMed]
  • Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium. Laurent LC, Abdel-Mageed AB, Adelson PD, Arango J, Balaj L, Breakefield X, Carlson E, Carter BS, Majem B, Chen CC, Cocucci E, Danielson K, Courtright A, Das S, Abd Elmageed ZY, Enderle D, Ezrin A, Ferrer M, Freedman J, Galas D, Gandhi R, Huentelman MJ, Van Keuren-Jensen K, Kalani Y, Kim Y, Krichevsky AM, Lai C, Lal-Nag M, Laurent CD, Leonardo T, Li F, Malenica I, Mondal D, Nejad P, Patel T,  Raffai RL, Rubio R, Skog J, Spetzler R, Sun J, Tanriverdi K, Vickers K, Wang L, Wang Y, Wei Z, Weiner HL, Wong D, Yan IK, Yeri A, Gould S.  J Extracell Vesicles. 2015 Aug 28;4:26533[PubMed]
  • Circulating MicroRNA-30d Is Associated With Response to Cardiac Resynchronization Therapy in Heart Failure and Regulates Cardiomyocyte Apoptosis: A Translational Pilot Study. Melman YF, Shah R, Danielson K, Xiao J, Simonson B, Barth A, Chakir K, Lewis GD, Lavender Z, Truong QA, Kleber A, Das R, Rosenzweig A, Wang Y, Kass DA, Singh JP, Das S.  Circulation. 2015 Jun 23;131(25):2202-16.[PubMed]

2014

  • The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis. Jirawatnotai S, Sharma S, Michowski W, Suktitipat B, Geng Y, Quackenbush J, Elias JE, Gygi SP, Wang YE, Sicinski P.  Cell Cycle. 2014 Sep 15;13(18):2889-900 [PubMed]
  • Global epigenetic regulation of microRNAs in multiple myeloma.  Zhang W, Wang YE, Zhang Y, Leleu X, Reagan M, Zhang Y, Mishima Y, Glavey S, Manier S, Sacco A, Jiang B, Roccaro AM, Ghobrial IM. PLoS One. 2014;9(10):e110973.[PubMed]
  • Analyses of clinicopathological, molecular, and prognostic associations of KRAS codon 61 and codon 146 mutations in colorectal cancer: cohort study and literature review.Imamura Y, Lochhead P, Yamauchi M, Kuchiba A, Qian ZR, Liao X, Nishihara R, Jung S, Wu K, Nosho K, Wang YE, Peng S, Bass AJ, Haigis KM, Meyerhardt JA, Chan AT, Fuchs CS, Ogino S.(2014).  Mol Cancer, 2014, 13(1):135
  • CXCR4 pathway associated with family history of melanoma. Li WQ,Han J, Widlund HR, Correll M, Wang YE, Quackenbush J, Mihm MC, Canales AL, Wu S, Golub T, Hoshida Y, Hunter DJ, Murphy G, Kupper TS, Qureshi AA. (2014)  Cancer Causes Control, 25:125-32
  • Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: Preliminary assessment of cross-platform concordance.  Kelly AD, Hill KE, Correll M, Hu L, Wang YE, Rubio R, Duan S, Quackenbush J, Spentzos D. (2013)  Genomics, 2013, 102:8-14.

Before 2013

  • A Sequential Gene-Ratio Algorithm Defines a Novel Molecular Diagnostic Test for Malignant Pleural Mesothelioma. De Rienzo A, Richards WG, Yeap BY, Coleman MH, Sugarbaker P, Chirieac LR, Wang YE, Quackenbush J, Jensen RV, Bueno R. (2013)  Clinical Cancer Research, 19, 2493-502
  • Preoperative Diet Impacts the Adipose Tissue Response to Surgical Trauma. Nguyen B, Yu P, Tao M, Mauro C, Ilonzo G, Seidman MA, Wang YE, Ozaki CK. (2013)  Surgery, 153(4):584-93
  • Alterations in Diversity of the Oral Microbiome in Pediatric Inflammatory Bowel Disease.Docktor MJ, Paster BJ, Abramowicz S, Ingram J, Wang YE, Correll M, Jiang H, Cotton SL, Kokaras AS, Bousvaros A. (2011)  Inflammatory Bowel Disease, 18, 935-42
  • Analyses of Cyclin D1 ‘Interactome’ in Human Cancers Reveal a Function in DNA Repair. Jirawatnotai S, Hu Y, Elias JE, Becks, L, Bienvenu F, Zagozdzon A, Goswami T, Wang YE, Correll M, Quackenbush J, Livingston DM, Gygi SP, Sicinski P. (2011)  Nature, 474, 230-4