Antibody Profiling of Patients With Prostate Cancer Reveals Differences in Antibody Signatures Among Disease Stages
Potluri HK, Ng TL, Newton MA, Zhang J, Maher CA, Nelson PS, McNeel DG
J Immunother Cancer 2020 Dec;8(2)
Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy
Krug K, Jaehnig EJ, Satpathy S, Blumenberg L, Karpova A, Anurag M, Miles G, Mertins P, Geffen Y, Tang LC, Heiman DI, Cao S, Maruvka YE, Lei JT, Huang C, Kothadia RB, Colaprico A, Birger C, Wang J, Dou Y, Wen B, Shi Z, Liao Y, Wiznerowicz M, Wyczalkowski MA, Chen XS, Kennedy JJ, Paulovich AG, Thiagarajan M, Kinsinger CR, Hiltke T, Boja ES, Mesri M, Robles AI, Rodriguez H, Westbrook TF, Ding L, Getz G, Clauser KR, Fenyo D, Ruggles KV, Zhang B, Mani DR, Carr SA, Ellis MJ, Gillette MA Clinical Proteomic Tumor Analysis Consortium (Contributors include: Maher C)
Cell 2020 Nov 25;183(5):1436-1456
SV-HotSpot: Detection and Visualization of Hotspots Targeted by Structural Variants Associated With Gene Expression
Eteleeb AM, Quigley DA, Zhao SG, Pham D, Yang R, Dehm SM, Luo J, Feng FY, Dang HX, Maher CA
Sci Rep 2020 Sep 28;10(1):15890
Cell-Free DNA Alterations in the AR Enhancer and Locus Predict Resistance to AR-Directed Therapy in Patients With Metastatic Prostate Cancer
Dang HX, Chauhan PS, Ellis H, Feng W, Harris PK, Smith G, Qiao M, Dienstbach K, Beck R, Atkocius A, Qaium F, Luo J, Michalski JM, Picus J, Pachynski RK, Maher CA, Chaudhuri AA
JCO Precis Oncol 2020;4:680-713
Pan-Cancer Proteogenomic Analysis Reveals Long and Circular Noncoding RNAs Encoding Peptides
Othoum G, Coonrod E, Zhao S, Dang HX, Maher CA
NAR Cancer 2020 Sep;2(3):zcaa015
The DNA Methylation Landscape of Advanced Prostate Cancer
Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjostrom M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM*, Maher CA*, Small EJ*, Quigley DA*, Feng FY* (*Co-senior author)
Nat Genet 2020 Aug;52(8):778-789
The Clonal Evolution of Metastatic Colorectal Cancer
Dang HX, Krasnick BA, White BS, Grossman JG, Strand MS, Zhang J, Cabanski CR, Miller CA, Fulton RS, Goedegebuure SP, Fronick CC, Griffith M, Larson DE, Goetz BD, Walker JR, Hawkins WG, Strasberg SM, Linehan DC, Lim KH, Lockhart AC, Mardis ER, Wilson RK, Ley TJ, Maher CA*, Fields RC* (*Co-senior author)
Sci Adv 2020 Jun 10;6(24):eaay9691
Long Non-Coding RNA RAMS11 Promotes Metastatic Colorectal Cancer Progression
Silva-Fisher JM, Dang HX, White NM, Strand MS, Krasnick BA, Rozycki EB, Jeffers GGL, Grossman JG, Highkin MK, Tang C, Cabanski CR, Eteleeb A, Mudd J, Goedegebuure SP, Luo J, Mardis ER, Wilson RK, Ley TJ, Lockhart AC, Fields RC*, Maher CA* (*Co-senior author)
Nat Commun 2020 May 1;11(1):2156
The Human Tumor Atlas Network: Charting Tumor Transitions Across Space and Time at Single-Cell Resolution
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jane-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH Human Tumor Atlas Network (Contributors include: Maher CA)
Cell 2020 Apr 16;181(2):236-249
Long Non-Coding RNA LCAL62 / LINC00261 Is Associated With Lung Adenocarcinoma Prognosis
Dang HX, White NM, Rozycki EB, Felsheim BM, Watson MA, Govindan R, Luo J, Maher CA
Heliyon 2020 Mar 5;6(3):e03521
Heparin-Based Hydrogel Scaffolding Alters the Transcriptomic Profile and Increases the Chemoresistance of MDA-MB-231 Triple-Negative Breast Cancer Cells
Menon N, Dang HX, Datla US, Moarefian M, Lawrence CB, Maher CA, Jones CN
Biomater Sci 2020 May 21;8(10):2786-2796
Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer
Li Y, Yang R, Henzler CM, Ho Y, Passow C, Auch B, Carreira S, Nava Rodrigues D, Bertan C, Hwang TH, Quigley DA, Dang HX, Morrissey C, Fraser M, Plymate SR, Maher CA, Feng FY, de Bono JS, Dehm SM
Clin Cancer Res 2020 Apr 15;26(8):1965-1976
Sclerosing Epithelioid Mesenchymal Neoplasm of the Pancreas - A Proposed New Entity
Basturk O, Weigelt B, Adsay V, Benhamida JK, Askan G, Wang L, Arcila ME, Zamboni G, Fukushima N, Gularte-Merida R, Da Cruz Paula A, Selenica P, Kumar R, Pareja F, Maher CA, Scholes J, Oda Y, Santini D, Doyle LA, Petersen I, Flucke U, Koelsche C, Reynolds SJ, Yavas A, Deimling AV, Reis-Filho JS, Klimstra DS
Mod Pathol 2020 Mar;33(3):456-467
Novel RB1-Loss Transcriptomic Signature Is Associated With Poor Clinical Outcomes Across Cancer Types
Chen WS, Alshalalfa M, Zhao SG, Liu Y, Mahal BA, Quigley DA, Wei T, Davicioni E, Rebbeck TR, Kantoff PW, Maher CA, Knudsen KE, Small EJ, Nguyen PL, Feng FY
Clin Cancer Res 2019 Jul 15;25(14):4290-4299
Genomic Drivers of Poor Prognosis and Enzalutamide Resistance in Metastatic Castration-Resistant Prostate Cancer
Chen WS, Aggarwal R, Zhang L, Zhao SG, Thomas GV, Beer TM, Quigley DA, Foye A, Playdle D, Huang J, Lloyd P, Lu E, Sun D, Guan X, Rettig M, Gleave M, Evans CP, Youngren J, True L, Lara P, Kothari V, Xia Z, Chi KN, Reiter RE, Maher CA, Feng FY, Small EJ, Alumkal JJ West Coast Prostate Cancer Dream Team
Eur Urol 2019 Nov;76(5):562-571
Clinical and Genomic Implications of Luminal and Basal Subtypes Across Carcinomas
Zhao SG, Chen WS, Das R, Chang SL, Tomlins SA, Chou J, Quigley DA, Dang HX, Barnard TJ, Mahal BA, Gibb EA, Liu Y, Davicioni E, Duska LR, Posadas EM, Jolly S, Spratt DE, Nguyen PL, Maher CA, Small EJ, Feng FY
Clin Cancer Res 2019 Apr 15;25(8):2450-2457
CD4+ T Cells Induce Rejection of Urothelial Tumors After Immune Checkpoint Blockade
Sato Y, Bolzenius JK, Eteleeb AM, Su X, Maher CA, Sehn JK, Arora VK
JCI Insight 2018 Dec 6;3(23)
Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer
Lei JT, Shao J, Zhang J, Iglesia M, Chan DW, Cao J, Anurag M, Singh P, He X, Kosaka Y, Matsunuma R, Crowder R, Hoog J, Phommaly C, Goncalves R, Ramalho S, Peres RMR, Punturi N, Schmidt C, Bartram A, Jou E, Devarakonda V, Holloway KR, Lai WV, Hampton O, Rogers A, Tobias E, Parikh PA, Davies SR, Li S, Ma CX, Suman VJ, Hunt KK, Watson MA, Hoadley KA, Thompson EA, Chen X, Kavuri SM, Creighton CJ, Maher CA, Perou CM, Haricharan S, Ellis MJ
Cell Rep 2018 Aug 7;24(6):1434-1444e7
Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer
Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Ryan CJ, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H, Gilbert LA, Lara PN Jr, Evans CP, Goldstein TC, Stuart JM, Tomlins SA, Spratt DE, Cheetham RK, Cheng DT, Farh K, Gehring JS, Hakenberg J, Liao A, Febbo PG, Shon J, Sickler B, Batzoglou S, Knudsen KE, He HH, Huang J, Wyatt AW, Dehm SM, Ashworth A, Chinnaiyan AM, Maher CA, Small EJ, Feng FY
Cell 2018 Jul 26;174(3):758-769e9
Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma
Sharpnack MF, Ranbaduge N, Srivastava A, Cerciello F, Codreanu SG, Liebler DC, Mascaux C, Miles WO, Morris R, McDermott JE, Sharpnack JL, Amann J, Maher CA, Machiraju R, Wysocki VH, Govindan R, Mallick P, Coombes KR, Huang K, Carbone DP
J Thorac Oncol 2018 Oct;13(10):1519-1529
Genomic and Transcriptomic Heterogeneity in Metaplastic Carcinomas of the Breast
Piscuoglio S, Ng CKY, Geyer FC, Burke KA, Cowell CF, Martelotto LG, Natrajan R, Popova T, Maher CA, Lim RS, Bruijn I, Mariani O, Norton L, Vincent-Salomon A, Weigelt B, Reis-Filho JS
NPJ Breast Cancer 2017 Dec 1;3:48
ClonEvol: Clonal Ordering and Visualization in Cancer Sequencing
Dang HX, White BS, Foltz SM, Miller CA, Luo J, Fields RC, Maher CA
Ann Oncol 2017 Dec 1;28(12):3076-3082
Comprehensive Discovery of Noncoding RNAs in Acute Myeloid Leukemia Cell Transcriptomes
Zhang J, Griffith M, Miller CA, Griffith OL, Spencer DH, Walker JR, Magrini V, McGrath SD, Ly A, Helton NM, Trissal M, Link DC, Dang HX, Larson DE, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Klco JM, Mardis ER, Ley TJ, Wilson RK, Maher CA
Exp Hematol 2017 Nov;55:19-33
Increased Breast Tissue Receptor Activator of Nuclear Factor-KappaB Ligand (RANKL) Gene Expression Is Associated With Higher Mammographic Density in Premenopausal Women
Toriola AT, Dang HX, Hagemann IS, Appleton CM, Colditz GA, Luo J, Maher CA
Oncotarget 2017 May 17;8(43):73787-73792
Multi-Institutional Analysis Shows That Low PCAT-14 Expression Associates With Poor Outcomes in Prostate Cancer
White NM, Zhao SG, Zhang J, Rozycki EB, Dang HX, McFadden SD, Eteleeb AM, Alshalalfa M, Vergara IA, Erho N, Arbeit JM, Karnes RJ, Den RB, Davicioni E, Maher CA
Eur Urol 2017 Feb;71(2):257-266
Visualizing Tumor Evolution With the Fishplot Package for R
Miller CA, McMichael J, Dang HX, Maher CA, Ding L, Ley TJ, Mardis ER, Wilson RK
BMC Genomics 2016 Nov 7;17(1):880
Comprehensive Genomic Analysis Reveals FLT3 Activation and a Therapeutic Strategy for a Patient With Relapsed Adult B-Lymphoblastic Leukemia
Griffith M, Griffith OL, Krysiak K, Skidmore ZL, Christopher MJ, Klco JM, Ramu A, Lamprecht TL, Wagner AH, Campbell KM, Lesurf R, Hundal J, Zhang J, Spies NC, Ainscough BJ, Larson DE, Heath SE, Fronick C, O'Laughlin S, Fulton RS, Magrini V, McGrath S, Smith SM, Miller CA, Maher CA, Payton JE, Walker JR, Eldred JM, Walter MJ, Link DC, Graubert TA, Westervelt P, Kulkarni S, DiPersio JF, Mardis ER, Wilson RK, Ley TJ
Exp Hematol 2016 Jul;44(7):603-13
A Genomic Case Study of Mixed Fibrolamellar Hepatocellular Carcinoma
Griffith OL, Griffith M, Krysiak K, Magrini V, Ramu A, Skidmore ZL, Kunisaki J, Austin R, McGrath S, Zhang J, Demeter R, Graves T, Eldred JM, Walker J, Larson DE, Maher CA, Lin Y, Chapman W, Mahadevan A, Miksad R, Nasser I, Hanto DW, Mardis ER
Ann Oncol 2016 Jun;27(6):1148-54
An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer
Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyo D
Mol Cell Proteomics 2016 Mar;15(3):1060-71
INTEGRATE: Gene Fusion Discovery Using Whole Genome and Transcriptome Data
Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA
Genome Res 2016 Jan;26(1):108-18
Mycoplasma Infection Alters Cancer Stem Cell Properties in Vitro
Gedye C, Cardwell T, Dimopoulos N, Tan BS, Jackson H, Svobodova S, Anaka M, Behren A, Maher C, Hofmann O, Hide W, Caballero O, Davis ID, Cebon J
Stem Cell Rev 2016 Feb;12(1):156-61
NFATc1 Promotes Prostate Tumorigenesis and Overcomes PTEN Loss-Induced Senescence
Manda KR, Tripathi P, Hsi AC, Ning J, Ruzinova MB, Liapis H, Bailey M, Zhang H, Maher CA, Humphrey PA, Andriole GL, Ding L, You Z, Chen F
Oncogene 2016 Jun 23;35(25):3282-92
Optimizing Cancer Genome Sequencing and Analysis
Griffith M, Miller CA, Griffith OL, Krysiak K, Skidmore ZL, Ramu A, Walker JR, Dang HX, Trani L, Larson DE, Demeter RT, Wendl MC, McMichael JF, Austin RE, Magrini V, McGrath SD, Ly A, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Maher CA, Ding L, Klco JM, Mardis ER, Ley TJ, Wilson RK
Cell Syst 2015 Sep 23;1(3):210-223
Genome Modeling System: A Knowledge Management Platform for Genomics
Griffith M, Griffith OL, Smith SM, Ramu A, Callaway MB, Brummett AM, Kiwala MJ, Coffman AC, Regier AA, Oberkfell BJ, Sanderson GE, Mooney TP, Nutter NG, Belter EA, Du F, Long RL, Abbott TE, Ferguson IT, Morton DL, Burnett MM, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundal J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim KH, Lu C, Harris CC, Maher N, Maher CA, Magrini VJ, Abbott BS, Chen K, Clark E, Das I, Fan X, Hawkins AE, Hepler TG, Wylie TN, Leonard SM, Schroeder WE, Shi X, Carmichael LK, Weil MR, Wohlstadter RW, Stiehr G, McLellan MD, Pohl CS, Miller CA, Koboldt DC, Walker JR, Eldred JM, Larson DE, Dooling DJ, Ding L, Mardis ER, Wilson RK
PLoS Comput Biol 2015 Jul 9;11(7):e1004274
Pan-Cancer Transcriptome Analysis Reveals Long Noncoding RNAs With Conserved Function
Cabanski CR, White NM, Dang HX, Silva-Fisher JM, Rauck CE, Cicka D, Maher CA
RNA Biol 2015 Jun 3;12(6):628-42
Loss of Trop2 Causes ErbB3 Activation Through a Neuregulin-1-Dependent Mechanism in the Mesenchymal Subtype of HNSCC
Zhang K, Jones L, Lim S, Maher CA, Adkins D, Lewis J, Kimple RJ, Fertig EJ, Chung CH, Van Tine BA, Ellis MJ, Herrlich A, Michel LS
Oncotarget 2014 Oct 15;5(19):9281-94
Transcriptome Sequencing Reveals Altered Long Intergenic Non-Coding RNAs in Lung Cancer
White NM, Cabanski CR, Silva-Fisher JM, Dang HX, Govindan R, Maher CA
Genome Biol 2014 Aug 13;15(8):429
Comprehensive Molecular Profiling of Lung Adenocarcinoma The Cancer Genome Atlas Research Network (Contributors include: Maher CA)
Nature 2014 Jul 31;511(7511):543-550
SigFuge: Single Gene Clustering of RNA-Seq Reveals Differential Isoform Usage Among Cancer Samples
Kimes PK, Cabanski CR, Wilkerson MD, Zhao N, Johnson AR, Perou CM, Makowski L, Maher CA, Liu Y, Marron JS, Hayes DN
Nucleic Acids Res 2014 Oct 1;42(14):e113
cDNA Hybrid Capture Improves Transcriptome Analysis on Low-Input and Archived Samples
Cabanski CR, Magrini V, Griffith M, Griffith OL, McGrath S, Zhang J, Walker J, Ly A, Demeter R, Fulton RS, Pong WW, Gutmann DH, Govindan R, Mardis ER, Maher CA
J Mol Diagn 2014 Jul;16(4):440-51
Characterization of the Genomic Features and Expressed Fusion Genes in Micropapillary Carcinomas of the Breast
Natrajan R, Wilkerson PM, Marchio C, Piscuoglio S, Ng CK, Wai P, Lambros MB, Samartzis EP, Dedes KJ, Frankum J, Bajrami I, Kopec A, Mackay A, A'hern R, Fenwick K, Kozarewa I, Hakas J, Mitsopoulos C, Hardisson D, Lord CJ, Kumar-Sinha C, Ashworth A, Weigelt B, Sapino A, Chinnaiyan AM, Maher CA, Reis-Filho JS
J Pathol 2014 Apr;232(5):553-65
A Comprehensive Promoter Landscape Identifies a Novel Promoter for CD133 in Restricted Tissues, Cancers, and Stem Cells
Sompallae R, Hofmann O, Maher CA, Gedye C, Behren A, Vitezic M, Daub CO, Devalle S, Caballero OL, Carninci P, Hayashizaki Y, Lawlor ER, Cebon J, Hide W
Front Genet 2013 Oct 29;4:209
Transcription Factors OVOL1 and OVOL2 Induce the Mesenchymal to Epithelial Transition in Human Cancer
Roca H, Hernandez J, Weidner S, McEachin RC, Fuller D, Sud S, Schumann T, Wilkinson JE, Zaslavsky A, Li H, Maher CA, Daignault-Newton S, Healy PN, Pienta KJ
PLoS One 2013 Oct 4;8(10):e76773
Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts
Li S, Shen D, Shao J, Crowder R, Liu W, Prat A, He X, Liu S, Hoog J, Lu C, Ding L, Griffith OL, Miller C, Larson D, Fulton RS, Harrison M, Mooney T, McMichael JF, Luo J, Tao Y, Goncalves R, Schlosberg C, Hiken JF, Saied L, Sanchez C, Giuntoli T, Bumb C, Cooper C, Kitchens RT, Lin A, Phommaly C, Davies SR, Zhang J, Kavuri MS, McEachern D, Dong YY, Ma C, Pluard T, Naughton M, Bose R, Suresh R, McDowell R, Michel L, Aft R, Gillanders W, DeSchryver K, Wilson RK, Wang S, Mills GB, Gonzalez-Angulo A, Edwards JR, Maher C, Perou CM, Mardis ER, Ellis MJ
Cell Rep 2013 Sep 26;4(6):1116-30
Recurrent Reciprocal RNA Chimera Involving YPEL5 and PPP1CB in Chronic Lymphocytic Leukemia
Velusamy T, Palanisamy N, Kalyana-Sundaram S, Sahasrabuddhe AA, Maher CA, Robinson DR, Bahler DW, Cornell TT, Wilson TE, Lim MS, Chinnaiyan AM, Elenitoba-Johnson KS
Proc Natl Acad Sci U S A 2013 Feb 19;110(8):3035-40
Characterization of the EZH2-MMSET Histone Methyltransferase Regulatory Axis in Cancer
Asangani IA, Ateeq B, Cao Q, Dodson L, Pandhi M, Kunju LP, Mehra R, Lonigro RJ, Siddiqui J, Palanisamy N, Wu YM, Cao X, Kim JH, Zhao M, Qin ZS, Iyer MK, Maher CA, Kumar-Sinha C, Varambally S, Chinnaiyan AM
Mol Cell 2013 Jan 10;49(1):80-93
Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers
Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher CA, Fulton R, Fulton L, Wallis J, Chen K, Walker J, McDonald S, Bose R, Ornitz D, Xiong D, You M, Dooling DJ, Watson M, Mardis ER, Wilson RK
Cell 2012 Sep 14;150(6):1121-34
Comprehensive Genomic Characterization of Squamous Cell Lung Cancers
Hammerman PS, Hayes DN, Wilkerson MD, Schultz N, Bose R, Chu A, Collisson EA, Cope L, Creighton CJ, Getz G, Herman JG, Johnson BE, Kucherlapati R, Ladanyi M, Maher CA, Robertson G, Sander C, Shen R, Sinha R, Sivachenko A, Thomas RK, Travis WD, Tsao MS, Weinstein JN, Wigle DA, Baylin SB, Govindan R, Meyerson M
Nature 2012 Sep 27;489(7417):519-25
Genetic and Epigenetic Loss of MicroRNA-31 Leads to Feed-Forward Expression of EZH2 in Melanoma
Asangani IA, Harms PW, Dodson L, Pandhi M, Kunju LP, Maher CA, Fullen DR, Johnson TM, Giordano TJ, Palanisamy N, Chinnaiyan AM
Oncotarget 2012 Sep;3(9):1011-25
Whole-Genome Analysis Informs Breast Cancer Response to Aromatase Inhibition
Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LL, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang LW, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, Mardis ER
Nature 2012 Jun 10;486(7403):353-60
From Sequence to Molecular Pathology, and a Mechanism Driving the Neuroendocrine Phenotype in Prostate Cancer
Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, Jones EC, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Zhao Y, Marra MA, Fanjul A, Maher CA, Chinnaiyan AM, Rubin MA, Beltran H, Sahinalp SC, Gleave ME, Volik SV, Collins CC
J Pathol 2012 Jul;227(3):286-97
Integrated Genome and Transcriptome Sequencing Identifies a Novel Form of Hybrid and Aggressive Prostate Cancer
Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, Mo F, Li E, Fazli L, Hurtado-Coll A, Jones EC, Butterfield YS, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Jones SJ, Hirst M, Marra MA, Maher CA, Chinnaiyan AM, Sahinalp SC, Gleave ME, Volik SV, Collins CC
J Pathol 2012 May;227(1):53-61
Next Generation Sequencing of Prostate Cancer From a Patient Identifies a Deficiency of Methylthioadenosine Phosphorylase, an Exploitable Tumor Target
Collins CC, Volik SV, Lapuk AV, Wang Y, Gout PW, Wu C, Xue H, Cheng H, Haegert A, Bell RH, Brahmbhatt S, Anderson S, Fazli L, Hurtado-Coll A, Rubin MA, Demichelis F, Beltran H, Hirst M, Marra M, Maher CA, Chinnaiyan AM, Gleave M, Bertino JR, Lubin M, Wang Y
Mol Cancer Ther 2012 Mar;11(3):775-83
Functionally Recurrent Rearrangements of the MAST Kinase and Notch Gene Families in Breast Cancer
Robinson DR, Kalyana-Sundaram S, Wu YM, Shankar S, Cao X, Ateeq B, Asangani IA, Iyer M, Maher CA, Grasso CS, Lonigro RJ, Quist M, Siddiqui J, Mehra R, Jing X, Giordano TJ, Sabel MS, Kleer CG, Palanisamy N, Natrajan R, Lambros MB, Reis-Filho JS, Kumar-Sinha C, Chinnaiyan AM
Nat Med 2011 Nov 20;17(12):1646-51
A p53/miRNA-34 Axis Regulates Snail1-Dependent Cancer Cell Epithelial-Mesenchymal Transition
Kim NH, Kim HS, Li XY, Lee I, Choi HS, Kang SE, Cha SY, Ryu JK, Yoon D, Fearon ER, Rowe RG, Lee S, Maher CA, Weiss SJ, Yook JI
J Cell Biol 2011 Oct 31;195(3):417-33
Coordinated Regulation of Polycomb Group Complexes Through MicroRNAs in Cancer
Cao Q, Mani RS, Ateeq B, Dhanasekaran SM, Asangani IA, Prensner JR, Kim JH, Brenner JC, Jing X, Cao X, Wang R, Li Y, Dahiya A, Wang L, Pandhi M, Lonigro RJ, Wu YM, Tomlins SA, Palanisamy N, Qin Z, Yu J, Maher CA, Varambally S, Chinnaiyan AM
Cancer Cell 2011 Aug 16;20(2):187-99
Transcriptome Sequencing Across a Prostate Cancer Cohort Identifies PCAT-1, an Unannotated LincRNA Implicated in Disease Progression
Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, Laxman B, Asangani IA, Grasso CS, Kominsky HD, Cao X, Jing X, Wang X, Siddiqui J, Wei JT, Robinson D, Iyer HK, Palanisamy N, Maher CA, Chinnaiyan AM
Nat Biotechnol 2011 Jul 31;29(8):742-9
Deep Sequencing Reveals Distinct Patterns of DNA Methylation in Prostate Cancer
Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, Kalyana-Sundaram S, Huang C, Shankar S, Jing X, Iyer M, Hu M, Sam L, Grasso C, Maher CA, Palanisamy N, Mehra R, Kominsky HD, Siddiqui J, Yu J, Qin ZS, Chinnaiyan AM
Genome Res 2011 Jul;21(7):1028-41
Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis
Javelle M, Klein-Cosson C, Vernoud V, Boltz V, Maher C, Timmermans M, Depege-Fargeix N, Rogowsky PM
Plant Physiol 2011 Oct;157(2):790-803
Mechanistic Rationale for Inhibition of Poly(ADP-Ribose) Polymerase in ETS Gene Fusion-Positive Prostate Cancer
Brenner JC, Ateeq B, Li Y, Yocum AK, Cao Q, Asangani IA, Patel S, Wang X, Liang H, Yu J, Palanisamy N, Siddiqui J, Yan W, Cao X, Mehra R, Sabolch A, Basrur V, Lonigro RJ, Yang J, Tomlins SA, Maher CA, Elenitoba-Johnson KS, Hussain M, Navone NM, Pienta KJ, Varambally S, Feng FY, Chinnaiyan AM
Cancer Cell 2011 May 17;19(5):664-78
Targeting of MicroRNA-142-3p in Dendritic Cells Regulates Endotoxin-Induced Mortality
Sun Y, Varambally S, Maher CA, Cao Q, Chockley P, Toubai T, Malter C, Nieves E, Tawara I, Wang Y, Ward PA, Chinnaiyan A, Reddy P
Blood 2011 Jun 9;117(23):6172-83
A Comparison of Single Molecule and Amplification Based Sequencing of Cancer Transcriptomes
Sam LT, Lipson D, Raz T, Cao X, Thompson J, Milos PM, Robinson D, Chinnaiyan AM, Kumar-Sinha C, Maher CA
PLoS One 2011 Mar 1;6(3):e17305
NGSQC: Cross-Platform Quality Analysis Pipeline for Deep Sequencing Data
Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F
BMC Genomics 2010 Dec 2;11 Suppl 4:S7
HPeak: An HMM-Based Algorithm for Defining Read-Enriched Regions in ChIP-Seq Data
Qin ZS, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM
BMC Bioinformatics 2010 Jul 2;11:369
Rearrangements of the RAF Kinase Pathway in Prostate Cancer, Gastric Cancer and Melanoma
Palanisamy N, Ateeq B, Kalyana-Sundaram S, Pflueger D, Ramnarayanan K, Shankar S, Han B, Cao Q, Cao X, Suleman K, Kumar-Sinha C, Dhanasekaran SM, Chen YB, Esgueva R, Banerjee S, LaFargue CJ, Siddiqui J, Demichelis F, Moeller P, Bismar TA, Kuefer R, Fullen DR, Johnson TM, Greenson JK, Giordano TJ, Tan P, Tomlins SA, Varambally S, Rubin MA, Maher CA, Chinnaiyan AM
Nat Med 2010 Jul;16(7):793-8
A Genome-Wide Characterization of MicroRNA Genes in Maize
Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D
PLoS Genet 2009 Nov;5(11):e1000716
miR-24 Inhibits Cell Proliferation by Targeting E2F2, MYC, and Other Cell-Cycle Genes Via Binding to "Seedless" 3'UTR MicroRNA Recognition Elements
Lal A, Navarro F, Maher CA, Maliszewski LE, Yan N, O'Day E, Chowdhury D, Dykxhoorn DM, Tsai P, Hofmann O, Becker KG, Gorospe M, Hide W, Lieberman J
Mol Cell 2009 Sep 11;35(5):610-25
Chimeric Transcript Discovery by Paired-End Transcriptome Sequencing Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, Khrebtukova I, Barrette TR, Grasso C, Yu J, Lonigro RJ, Schroth G, Kumar-Sinha C, Chinnaiyan AM
Proc Natl Acad Sci U S A 2009 Jul 28;106(30):12353-8
The Transcriptional Network That Controls Growth Arrest and Differentiation in a Human Myeloid Leukemia Cell Line
FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y
Nat Genet 2009 May;41(5):553-62
ProbeMatch: Rapid Alignment of Oligonucleotides to Genome Allowing Both Gaps and Mismatches
Kim YJ, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM
Bioinformatics 2009 Jun 1;25(11):1424-5
Transcriptome Sequencing to Detect Gene Fusions in Cancer Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM
Nature 2009 Mar 5;458(7234):97-101
The Sorghum Bicolor Genome and the Diversification of Grasses
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS
Nature 2009 Jan 29;457(7229):551-6
Genome-Wide Analysis of Cancer/Testis Gene Expression
Hofmann O, Caballero OL, Stevenson BJ, Chen YT, Cohen T, Chua R, Maher CA, Panji S, Schaefer U, Kruger A, Lehvaslaiho M, Carninci P, Hayashizaki Y, Jongeneel CV, Simpson AJ, Old LJ, Hide W
Proc Natl Acad Sci U S A 2008 Dec 23;105(51):20422-7
Genomic Loss of MicroRNA-101 Leads to Overexpression of Histone Methyltransferase EZH2 in Cancer
Varambally S, Cao Q, Mani RS, Shankar S, Wang X, Ateeq B, Laxman B, Cao X, Jing X, Ramnarayanan K, Brenner JC, Yu J, Kim JH, Han B, Tan P, Kumar-Sinha C, Lonigro RJ, Palanisamy N, Maher CA, Chinnaiyan AM
Science 2008 Dec 12;322(5908):1695-9
Genome-Wide Analysis for Discovery of Rice MicroRNAs Reveals Natural Antisense MicroRNAs (Nat-miRNAs)
Lu C, Jeong DH, Kulkarni K, Pillay M, Nobuta K, German R, Thatcher SR, Maher C, Zhang L, Ware D, Liu B, Cao X, Meyers BC, Green PJ
Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4951-6
Construction, Alignment and Analysis of Twelve Framework Physical Maps That Represent the Ten Genome Types of the Genus Oryza
Kim H, Hurwitz B, Yu Y, Collura K, Gill N, SanMiguel P, Mullikin JC, Maher C, Nelson W, Wissotski M, Braidotti M, Kudrna D, Goicoechea JL, Stein L, Ware D, Jackson SA, Soderlund C, Wing RA
Genome Biol 2008;9(2):R45
Identifying MicroRNAs in Plant Genomes Maher C, Timmermans M, Stein L, Ware D
Proceedings of IEEE Computer Society Bioinformatics Conference 2004:718-723
Creating Genetic Applications for Informal Science Learning in Multi-User Virtual Environments Maher C, Corbit M
Journal of Network and Computer Applications 2002;25;295-308
Creating Genetic Applications for Informal Science Learning in Multi-User Virtual Worlds Maher C, Corbit M
Proceedings of the IEEE 8th International Workshop on Enabling Technologies: Infrastructure for Collaborative Enterprises 2001