Keyword Connections

•  Annette Kim
•  Kasey Vickers

•  Taewan Kim
•  Thomas Andl

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Publications

• Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.
  Cancer Genome Atlas Research Network, Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AA, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho TH, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni HV, Drummond JA, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R
  (2016) N Engl J Med 374: 135-45
• Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
  Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Harvard FlyBase curators, Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M
  (2007) Nature 450: 219-32
• Comprehensive molecular portraits of human breast tumours.
  Cancer Genome Atlas Network
  (2012) Nature 490: 61-70
• Evolutionary flux of canonical microRNAs and mirtrons in Drosophila.
  Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
  (2010) Nat Genet 42: 6-9; author reply 9-10
• Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.
  Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM, Cancer Genome Atlas Network, Stuart JM, Benz CC, Laird PW
  (2018) Cell 173: 291-304.e6
• Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.
  Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ, TCGA Research Network, Weinstein JN, Kwiatkowski DJ, Lerner SP
  (2017) Cell 171: 540-556.e25
• Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.
  Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ, Cancer Genome Atlas Research Network, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M
  (2018) Cell 173: 338-354.e15
• Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma.
  Cancer Genome Atlas Research Network. Electronic address: wheeler@bcm.edu, Cancer Genome Atlas Research Network
  (2017) Cell 169: 1327-1341.e23
• Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide.
  Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y
  (2008) Cell 133: 116-27
• Consensus on biomarkers for neuroendocrine tumour disease.
  Oberg K, Modlin IM, De Herder W, Pavel M, Klimstra D, Frilling A, Metz DC, Heaney A, Kwekkeboom D, Strosberg J, Meyer T, Moss SF, Washington K, Wolin E, Liu E, Goldenring J
  (2015) Lancet Oncol 16: e435-e446
• lncRNA MIR100HG-derived miR-100 and miR-125b mediate cetuximab resistance via Wnt/β-catenin signaling.
  Lu Y, Zhao X, Liu Q, Li C, Graves-Deal R, Cao Z, Singh B, Franklin JL, Wang J, Hu H, Wei T, Yang M, Yeatman TJ, Lee E, Saito-Diaz K, Hinger S, Patton JG, Chung CH, Emmrich S, Klusmann JH, Fan D, Coffey RJ
  (2017) Nat Med 23: 1331-1341
• Biomarkers to the rescue in a lung nodule epidemic.
  Massion PP
  (2014) J Clin Oncol 32: 725-6
• Estrogen Metabolite 16α-Hydroxyestrone Exacerbates Bone Morphogenetic Protein Receptor Type II-Associated Pulmonary Arterial Hypertension Through MicroRNA-29-Mediated Modulation of Cellular Metabolism.
  Chen X, Talati M, Fessel JP, Hemnes AR, Gladson S, French J, Shay S, Trammell A, Phillips JA, Hamid R, Cogan JD, Dawson EP, Womble KE, Hedges LK, Martinez EG, Wheeler LA, Loyd JE, Majka SJ, West J, Austin ED
  (2016) Circulation 133: 82-97
• Repolarization reserve: a moving target.
  Roden DM
  (2008) Circulation 118: 981-2
• SZGR: a comprehensive schizophrenia gene resource.
  Jia P, Sun J, Guo AY, Zhao Z
  (2010) Mol Psychiatry 15: 453-62
• Novel animal models for studying complex brain disorders: BAC-driven miRNA-mediated in vivo silencing of gene expression.
  Garbett KA, Horváth S, Ebert PJ, Schmidt MJ, Lwin K, Mitchell A, Levitt P, Mirnics K
  (2010) Mol Psychiatry 15: 987-95
• Porous Silicon and Polymer Nanocomposites for Delivery of Peptide Nucleic Acids as Anti-MicroRNA Therapies.
  Beavers KR, Werfel TA, Shen T, Kavanaugh TE, Kilchrist KV, Mares JW, Fain JS, Wiese CB, Vickers KC, Weiss SM, Duvall CL
  (2016) Adv Mater 28: 7984-7992
• Conservation of small RNA pathways in platypus.
  Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z, Kellis M, Grützner F, Stark A, Hannon GJ
  (2008) Genome Res 18: 995-1004
• Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes.
  Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
  (2007) Genome Res 17: 1865-79
• Initial sequence and comparative analysis of the cat genome.
  Pontius JU, Mullikin JC, Smith DR, Agencourt Sequencing Team, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G, NISC Comparative Sequencing Program, O'Brien SJ
  (2007) Genome Res 17: 1675-89
• p53 regulates epithelial-mesenchymal transition through microRNAs targeting ZEB1 and ZEB2.
  Kim T, Veronese A, Pichiorri F, Lee TJ, Jeon YJ, Volinia S, Pineau P, Marchio A, Palatini J, Suh SS, Alder H, Liu CG, Dejean A, Croce CM
  (2011) J Exp Med 208: 875-83
• microRNA-mediated regulation of mTOR complex components facilitates discrimination between activation and anergy in CD4 T cells.
  Marcais A, Blevins R, Graumann J, Feytout A, Dharmalingam G, Carroll T, Amado IF, Bruno L, Lee K, Walzer T, Mann M, Freitas AA, Boothby M, Fisher AG, Merkenschlager M
  (2014) J Exp Med 211: 2281-95
• Mining diverse small RNA species in the deep transcriptome.
  Vickers KC, Roteta LA, Hucheson-Dilks H, Han L, Guo Y
  (2015) Trends Biochem Sci 40: 4-7
• MiRNA inhibition in tissue engineering and regenerative medicine.
  Beavers KR, Nelson CE, Duvall CL
  (2015) Adv Drug Deliv Rev 88: 123-37
• MicroRNA-31 initiates lung tumorigenesis and promotes mutant KRAS-driven lung cancer.
  Edmonds MD, Boyd KL, Moyo T, Mitra R, Duszynski R, Arrate MP, Chen X, Zhao Z, Blackwell TS, Andl T, Eischen CM
  (2016) J Clin Invest 126: 349-64
• Atrial natriuretic peptide is negatively regulated by microRNA-425.
  Arora P, Wu C, Khan AM, Bloch DB, Davis-Dusenbery BN, Ghorbani A, Spagnolli E, Martinez A, Ryan A, Tainsh LT, Kim S, Rong J, Huan T, Freedman JE, Levy D, Miller KK, Hata A, Del Monte F, Vandenwijngaert S, Swinnen M, Janssens S, Holmes TM, Buys ES, Bloch KD, Newton-Cheh C, Wang TJ
  (2013) J Clin Invest 123: 3378-82
• Epithelial stem cell mutations that promote squamous cell carcinoma metastasis.
  White RA, Neiman JM, Reddi A, Han G, Birlea S, Mitra D, Dionne L, Fernandez P, Murao K, Bian L, Keysar SB, Goldstein NB, Song N, Bornstein S, Han Z, Lu X, Wisell J, Li F, Song J, Lu SL, Jimeno A, Roop DR, Wang XJ
  (2013) J Clin Invest 123: 4390-404
• Anti-microRNA-21 oligonucleotides prevent Alport nephropathy progression by stimulating metabolic pathways.
  Gomez IG, MacKenna DA, Johnson BG, Kaimal V, Roach AM, Ren S, Nakagawa N, Xin C, Newitt R, Pandya S, Xia TH, Liu X, Borza DB, Grafals M, Shankland SJ, Himmelfarb J, Portilla D, Liu S, Chau BN, Duffield JS
  (2015) J Clin Invest 125: 141-56
• MiR-15 family regulates postnatal mitotic arrest of cardiomyocytes.
  Porrello ER, Johnson BA, Aurora AB, Simpson E, Nam YJ, Matkovich SJ, Dorn GW, van Rooij E, Olson EN
  (2011) Circ Res 109: 670-9
• Control of very low-density lipoprotein secretion by N-ethylmaleimide-sensitive factor and miR-33.
  Allen RM, Marquart TJ, Jesse JJ, Baldán A
  (2014) Circ Res 115: 10-22
• The Vasculature in Prediabetes.
  Wasserman DH, Wang TJ, Brown NJ
  (2018) Circ Res 122: 1135-1150
• MicroRNA-26a regulates pathological and physiological angiogenesis by targeting BMP/SMAD1 signaling.
  Icli B, Wara AK, Moslehi J, Sun X, Plovie E, Cahill M, Marchini JF, Schissler A, Padera RF, Shi J, Cheng HW, Raghuram S, Arany Z, Liao R, Croce K, MacRae C, Feinberg MW
  (2013) Circ Res 113: 1231-41
• Systemic delivery of microRNA-181b inhibits nuclear factor-κB activation, vascular inflammation, and atherosclerosis in apolipoprotein E-deficient mice.
  Sun X, He S, Wara AKM, Icli B, Shvartz E, Tesmenitsky Y, Belkin N, Li D, Blackwell TS, Sukhova GK, Croce K, Feinberg MW
  (2014) Circ Res 114: 32-40
• Genomic Characterization of Esophageal Squamous Cell Carcinoma Reveals Critical Genes Underlying Tumorigenesis and Poor Prognosis.
  Qin HD, Liao XY, Chen YB, Huang SY, Xue WQ, Li FF, Ge XS, Liu DQ, Cai Q, Long J, Li XZ, Hu YZ, Zhang SD, Zhang LJ, Lehrman B, Scott AF, Lin D, Zeng YX, Shugart YY, Jia WH
  (2016) Am J Hum Genet 98: 709-27
• Genetic architecture of microRNA expression: implications for the transcriptome and complex traits.
  Gamazon ER, Ziliak D, Im HK, LaCroix B, Park DS, Cox NJ, Huang RS
  (2012) Am J Hum Genet 90: 1046-63
• Let It Be: microRNAs impact interstitial lung disease.
  Lawson WE, Blackwell TS, Gauldie J
  (2011) Am J Respir Crit Care Med 183: 1-2
• Loss of miRNA biogenesis induces p19Arf-p53 signaling and senescence in primary cells.
  Mudhasani R, Zhu Z, Hutvagner G, Eischen CM, Lyle S, Hall LL, Lawrence JB, Imbalzano AN, Jones SN
  (2008) J Cell Biol 181: 1055-63
• miR-8 microRNAs regulate the response to osmotic stress in zebrafish embryos.
  Flynt AS, Thatcher EJ, Burkewitz K, Li N, Liu Y, Patton JG
  (2009) J Cell Biol 185: 115-27
• miR-30-HNF4γ and miR-194-NR2F2 regulatory networks contribute to the upregulation of metaplasia markers in the stomach.
  Sousa JF, Nam KT, Petersen CP, Lee HJ, Yang HK, Kim WH, Goldenring JR
  (2016) Gut 65: 914-24
• Müller glial microRNAs are required for the maintenance of glial homeostasis and retinal architecture.
  Wohl SG, Jorstad NL, Levine EM, Reh TA
  (2017) Nat Commun 8: 1603