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Publications

2019

  • Basturk O, Weigelt B, Adsay V, Benhamida JK, Askan G, Wang L, Arcila ME, Zamboni G, Fukushima N, Gularte-Mérida 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. Sclerosing epithelioid mesenchymal neoplasm of the pancreas - a proposed new entity. Mod Pathol. 2019 Aug 5. doi: 10.1038/s41379-019-0334-5. [Epub ahead of print] PubMed PMID: 31383964.

  • 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. Novel RB1-Loss Transcriptomic Signature Is Associated with Poor Clinical Outcomes across Cancer Types. Clin Cancer Res. 2019 Jul 15;25(14):4290-4299. doi: 10.1158/1078-0432.CCR-19-0404. Epub 2019 Apr 22. PubMed PMID: 31010837.

  • 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. Genomic Drivers of Poor Prognosis and Enzalutamide Resistance in Metastatic Castration-resistant Prostate Cancer. Eur Urol. 2019 Mar 27. pii: S0302-2838(19)30206-4. doi: 10.1016/j.eururo.2019.03.020. [Epub ahead of print] PubMed PMID: 30928160.

  • 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. Clinical and Genomic Implications of Luminal and Basal Subtypes Across Carcinomas. Clin Cancer Res. 2019 Apr 15;25(8):2450-2457. doi: 10.1158/1078-0432.CCR-18-3121. Epub 2018 Dec 20. PubMed PMID: 30573691.

2018

  • Sato Y, Bolzenius JK, Eteleeb AM, Su X, Maher CA, Sehn JK, Arora VK. CD4+ T cells induce rejection of urothelial tumors after immune checkpoint blockade. JCI Insight. 2018 Dec 6;3(23). pii: 121062. doi: 10.1172/jci.insight.121062. [Epub ahead of print] PubMed PMID: 30518683.

  • 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. Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer. Cell Rep. 2018 Aug 7;24(6):1434-1444.e7. doi: 10.1016/j.celrep.2018.07.009. PubMed PMID: 30089255; PubMed Central PMCID: PMC6171747.

  • 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*. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. 2018 Jul 26;174(3):758-769.e9. doi: 10.1016/j.cell.2018.06.039. Epub 2018 Jul 19. PubMed PMID: 30033370. (* co-senior authors). 

  • 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.  Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma. J Thorac Oncol. 2018 Jul 11. pii: S1556-0864(18)30784-6. doi: 10.1016/j.jtho.2018.06.025. PubMed PMID: 30017829.

2017

  • Zhang J, Gao T, Maher CA. INTEGRATE-Vis: a tool for comprehensive gene fusion  visualization. Sci Rep. 2017 Dec 19;7(1):17808. doi: 10.1038/s41598-017-18257-2.  PubMed PMID: 29259323; PubMed Central PMCID: PMC5736641.

  • 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. Genomic and transcriptomic heterogeneity in metaplastic carcinomas of the breast. NPJ Breast Cancer. 2017 Dec 1;3:48. doi: 10.1038/s41523-017-0048-0. eCollection 2017. PubMed PMID: 29214215; PubMed Central PMCID: PMC5711926.

  • Dang HX, White BS, Foltz SM, Miller CA, Luo J, Fields RC, Maher CA. ClonEvol: clonal ordering and visualization in cancer sequencing. Ann Oncol. 2017 Sep 11. doi: 10.1093/annonc/mdx517. [Epub ahead of print] PubMed PMID: 28950321.

  • White NM, Maher CA. The potential use of lncRNAs found in the 8q24 region as biomarkers for colon cancer. Ann Oncol. 2017 Aug 1;28(8):1688-1689. doi: 10.1093/annonc/mdx337. PubMed PMID: 28838213.

  • 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. Comprehensive discovery of non-coding RNAs in acute myeloid leukemia cell transcriptomes. Exp Hematol. 2017 Jul 28. pii: S0301-472X(17)30701-4. doi:10.1016/j.exphem.2017.07.008. [Epub ahead of print] PubMed PMID: 28760689.

  • Zhang J, Mardis ER, Maher CA. INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery. Bioinformatics. 2017 Feb 15;33(4):555-557. doi: 10.1093/bioinformatics/btw674. PubMed PMID: 27797777; PubMed Central PMCID: PMC5408800.

  • 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. Multi-institutional Analysis Shows that Low PCAT-14 Expression Associates with Poor Outcomes in Prostate Cancer. Eur Urol. 2017 Feb;71(2):257-266. doi: 10.1016/j.eururo.2016.07.012. Epub 2016 Jul 22. PubMed PMID: 27460352.

  • Toriola AT, Dang HX, Hagemann IS, Appleton CM, Colditz GA, Luo J, Maher CA. Increased breast tissue receptor activator of nuclear factor- κB ligand (RANKL) gene expression is associated with higher mammographic density in premenopausal women. Oncotarget. 2017 May 17. doi: 10.18632/oncotarget.17909. [Epub ahead of print] PubMed PMID: 28575868.

2016

  • Miller CA, McMichael J, Dang HX, Maher CA, Ding L, Ley TJ, Mardis ER, Wilson RK. Visualizing tumor evolution with the fishplot package for R. BMC Genomics. 2016 Nov 7;17(1):880. PubMed PMID: 27821060; PubMed Central PMCID: PMC5100182.

  • 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. Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia. Exp Hematol. 2016 Jul;44(7):603-13. doi: 10.1016/j.exphem.2016.04.011. Epub 2016 May 13. PubMed PMID: 27181063; PubMed Central PMCID: PMC4914477.

  • Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA. INTEGRATE: gene fusion discovery using whole genome and transcriptome data. Genome Res. 2016 Jan;26(1):108-18. doi: 10.1101/gr.186114.114. Epub 2015 Nov 10. PubMed PMID: 26556708; PubMed Central PMCID: PMC4691743.

  • 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. A genomic case study of mixed fibrolamellar hepatocellular carcinoma. Ann Oncol. 2016 Mar 30. pii: mdw135. [Epub ahead of print] PubMed PMID: 27029710.

2015

  • 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. An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer. Mol Cell Proteomics. 2015 Dec 2. pii: mcp.M115.056226. [Epub ahead of print] PubMed PMID: 26631509.

  • Gedye C, Cardwell T, Dimopoulos N, Tan BS, Jackson H, Svobodová S, Anaka M, Behren A, Maher CA, Hofmann O, Hide W, Caballero O, Davis ID, Cebon J. Mycoplasma Infection Alters Cancer Stem Cell Properties in Vitro. Stem Cell Rev. 2015 Oct 30. [Epub ahead of print] PubMed PMID: 26514153.

  • Dang HX, Maher CA. Clonotyping for precision oncology. Drug Discov Today. 2015 Oct 19. pii: S1359-6446(15)00387-6. doi: 10.1016/j.drudis.2015.10.010. [Epub ahead of print] Review. PubMed PMID: 26494143.

  • 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. NFATc1 promotes prostate tumorigenesis and overcomes PTEN loss-induced senescence. Oncogene. 2015 Oct 19. doi: 10.1038/onc.2015.389. [Epub ahead of print] PubMed PMID: 26477312.

  • 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. Optimizing cancer genome sequencing and analysis. Cell Syst. 2015 Sep 23;1(3):210-223. PubMed PMID: 26645048; PubMed Central PMCID: PMC4669575.

  • 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. Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 2015 Jul 9;11(7):e1004274. doi: 10.1371/journal.pcbi.1004274. eCollection 2015 Jul. PubMed PMID: 26158448.

  • Cabanski CR, White NM, Dang HX, Silva-Fisher JM, Rauck CE, Cicka D, Maher CA. Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function. RNA Biol. 2015 Jun 3;12(6):628-42. doi: 10.1080/15476286.2015.1038012. PubMed PMID: 25864709.

2014

  • Zhang K, Jones L, Lim S, Maher CA, Adkins D, Lewis J, Kimple RJ, Fertig EJ, Chung CH, Herrlich A, Ellis MJ, Van Tine BA, Michel LS. Loss of Trop2 causes ErbB3 activation through a neuregulin-1-dependent mechanism in the mesenchymal subtype of HNSCC. Oncotarget. 2014 Oct 15;5(19):9281-94. PubMed PMID: 25238142; PubMed Central PMCID: PMC4253434.

  • White NM, Cabanski CR, Silva-Fisher JM, Dang HX, Govindan R, Maher CA. Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer. Genome Biol. 2014 Aug 13;15(8):429. doi: 10.1186/s13059-014-0429-8. PubMed PMID: 25116943; PubMed Central PMCID: PMC4156652.

  • Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31;511(7511):543-50. doi: 10.1038/nature13385. Epub 2014 Jul 9. PubMed PMID: 25079552; PubMed Central PMCID: PMC4231481.

  • Kimes PK, Cabanski CR, Wilkerson MD, Zhao N, Johnson AR, Perou CM, Makowski L, Maher CA, Liu Y, Marron JS, Hayes DN. SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples. Nucleic Acids Res. 2014;42(14):e113. doi: 10.1093/nar/gku521. Epub 2014 Jul 16. PubMed PMID: 25030904; PubMed Central PMCID: PMC4132703.

  • 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. cDNA hybrid capture improves transcriptome analysis on low-input and archived samples. J Mol Diagn. 2014 Jul;16(4):440-51. doi: 10.1016/j.jmoldx.2014.03.004. Epub 2014 May 9. PubMed PMID: 24814956; PubMed Central PMCID: PMC4078367.

  • Natrajan R, Wilkerson PM, Marchiò 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. Characterization of the genomic features and expressed fusion genes in micropapillary carcinomas of the breast. J Pathol. 2014 Apr;232(5):553-65. doi: 10.1002/path.4325. Epub 2014 Feb 5. PubMed PMID: 24395524; PubMed Central PMCID: PMC4013428.

2013

  • 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. A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells. Front Genet. 2013 Oct 29;4:209. doi: 10.3389/fgene.2013.00209. PubMed PMID: 24194746; PubMed Central PMCID: PMC3810939.

  • 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. Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts. Cell Rep. 2013 Sep 26;4(6):1116-30. doi: 10.1016/j.celrep.2013.08.022. Epub 2013 Sep 19. PubMed PMID: 24055055; PubMed Central PMCID: PMC3881975.

  • White NM, Feng FY, Maher CA. Recurrent Rearrangements in Prostate Cancer: Causes and Therapeutic Potential. Curr Drug Targets. 2013 Feb 11. PubMed PMID: 23410129; PubMed Central PMCID: PMC3733264.

  • 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. Recurrent reciprocal RNA chimera involving YPEL5 and PPP1CB in chronic lymphocytic leukemia. Proc Natl Acad Sci (2013) Feb 4. PubMed PMID: 23382248.

  • 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. Characterization of the EZH2-MMSET Histone Methyltransferase Regulatory Axis in Cancer. Mol Cell. 2013 Jan 10;49(1):80-93. PubMed PMID: 23159737; PubMed Central PMCID: PMC3547524.

2012

  • 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. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell. 2012 Sep 14;150(6):1121-34. PubMed PMID: 22980976.

  • The Cancer Genome Atlas Research Network; Maher CA, as a member of the Disease working group and Writing committee. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 9. doi: 10.1038/nature11404. [Epub ahead of print] PubMed PMID: 22960745.

  • Asangani IA, Harms PW, Dodson L, Pandhi M, Kunju LP, Maher CA, Fullen DR, Johnson TM, Giordano TJ, Palanisamy N, Chinnaiyan AM. Genetic and epigenetic loss of microRNA-31 leads to feed-forward expression of EZH2 in melanoma. Oncotarget. 2012 Aug 31. [Epub ahead of print] PubMed PMID: 22948084.

  • 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. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012 Jun 10;486(7403):353-60. doi: 10.1038/nature11143. PubMed PMID: 22722193; PubMed Central PMCID: PMC3383766.

  • 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, Hajiresouliha 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. From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. Journal of Pathology. 2012 May 3. doi: 10.1002/path.4047. [Epub ahead of print] PubMed PMID: 22553170.

  • 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. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. Journal of Pathology. 2012 Jan 4. doi: 10.1002/path.3987. [Epub ahead of print] PubMed PMID: 22294438.

  • Maher CA, Wilson RK. Chromothripsis and human disease: piecing together the shattering process. Cell. 2012 Jan 20;148(1-2):29-32. PubMed PMID: 22265399.

  • Collins CC, Volik SV, Lapuk A, 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 MA, Maher CA, Chinnaiyan AM, Gleave ME, Bertino JR, Lubin M, Wang Y. Next Generation Sequencing of Prostate Cancer from a Patient Identifies a Deficiency of Methylthioadenine Phosphorylase (MTAP), an Exploitable Tumor Target. Molecular Cancer Ther. 2012 Jan 17. [Epub ahead of print] PubMed PMID: 22252602.

  • 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. Discovery of MAST Kinase Fusions in Breast Cancer by Transcriptome Sequencing. Nature Medicine. 2011 Nov 20;17(12):1646-51. doi: 10.1038/nm.2580. PubMed PMID: 22101766; PubMed Central PMCID: PMC3233654.

  • 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. A p53/miRNA-34 axis regulates Snail1-dependent cancer cell epithelial-mesenchymal transition. J Cell Biol. 2011 Oct 31;195(3):417-33. doi: 10.1083/jcb.201103097. Epub 2011 Oct 24. PubMed PMID: 22024162; PubMed Central PMCID: PMC3206336.

  • Rubin MA, Maher CA, Chinnaiyan AM. Common gene rearrangements in prostate cancer. Journal of Clinical Oncology. 2011 Sep 20;29(27):3659-68. Epub 2011 Aug 22. Review. PubMed PMID: 21859993.

  • Iyer MK, Chinnaiyan AM, Maher CA. ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011 Oct 15;27(20):2903-4. doi: 10.1093/bioinformatics/btr467. Epub 2011 Aug 11. PubMed PMID: 21840877; PubMed Central PMCID: PMC3187648.

  • 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. Coordinated regulation of polycomb group complexes through microRNAs in cancer. Cancer Cell. 2011 Aug 16;20(2):187-99. doi: 10.1016/j.ccr.2011.06.016. PubMed PMID: 21840484; PubMed Central PMCID: PMC3157014.

  • 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. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nature Biotechnology. 2011 Jul 31;29(8):742-9. doi: 10.1038/nbt.1914. PubMed PMID: 21804560; PubMed Central PMCID: PMC3152676.

  • 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. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res. 2011 Jul;21(7):1028-41. doi: 10.1101/gr.119347.110. PubMed PMID: 21724842; PubMed Central PMCID: PMC3129246.

  • Javelle M, Klein-Cosson C, Vernoud V, Boltz V, Maher C, Timmermans M, Depège-Fargeix N, Rogowsky PM. Genome-wide characterization of the HD-ZIP IV transcription factor family in maize: preferential expression in the epidermis. Plant Physiol. 2011 Oct;157(2):790-803. doi: 10.1104/pp.111.182147. Epub 2011 Aug 8. PubMed PMID: 21825105; PubMed Central PMCID: PMC3192571.

  • 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. Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer. Cancer Cell. 2011 May 17;19(5):664-78. doi: 10.1016/j.ccr.2011.04.010. Erratum in: Cancer Cell. 2013 Apr 15;23(4):557. PubMed PMID: 21575865; PubMed Central PMCID: PMC3113473.

  • 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. Targeting of microRNA-142-3p in dendritic cells regulates endotoxin-induced mortality. Blood. 2011 Jun 9;117(23):6172-83. doi: 10.1182/blood-2010-12-325647. Epub 2011 Apr 7. PubMed PMID: 21474672; PubMed Central PMCID: PMC3122940.

  • Sam LT, Lipson D, Raz T, Cao X, Thompson J, Milos PM, Robinson D, Chinnaiyan AM, Kumar-Sinha C, Maher CA. A comparison of single molecule and amplification based sequencing of cancer transcriptomes. PLoS One. 2011 Mar 1;6(3):e17305. doi: 10.1371/journal.pone.0017305. PubMed PMID: 21390249; PubMed Central PMCID: PMC3046973.

  • Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F. NGSQC: cross-platform quality analysis pipeline for deep sequencing data. BMC Genomics. 2010 Dec 2;11 Suppl 4:S7. doi: 10.1186/1471-2164-11-S4-S7. PubMed PMID: 21143816; PubMed Central PMCID: PMC3005923.

  • Qin ZS, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics. 2010 Jul 2;11:369. doi: 10.1186/1471-2105-11-369. PubMed PMID: 20598134; PubMed Central PMCID: PMC2912305.

  • 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. Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med. 2010 Jul;16(7):793-8. doi: 10.1038/nm.2166. Epub 2010 Jun 6. PubMed PMID: 20526349; PubMed Central PMCID: PMC2903732.

  • Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D. A genome-wide characterization of microRNA genes in maize. PLoS Genet. 2009 Nov;5(11):e1000716. doi: 10.1371/journal.pgen.1000716. Epub 2009 Nov 20. PubMed PMID: 19936050; PubMed Central PMCID: PMC2773440.

  • 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. miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements. Mol Cell. 2009 Sep 11;35(5):610-25. doi: 10.1016/j.molcel.2009.08.020. PubMed PMID: 19748357; PubMed Central PMCID: PMC2757794.

  • 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. Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12353-8. doi: 10.1073/pnas.0904720106. Epub 2009 Jul 10. PubMed PMID: 19592507; PubMed Central PMCID: PMC2708976.

  • FANTOM Consortium (Maher, CA., member) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet. 2009 May;41(5):553-62. doi: 10.1038/ng.375. Epub 2009 Apr 19. PubMed PMID: 19377474.

  • Kim YJ, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM. ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. Bioinformatics. 2009 Jun 1;25(11):1424-5. doi: 10.1093/bioinformatics/btp178. Epub 2009 Apr 7. PubMed PMID: 19351619; PubMed Central PMCID: PMC2682521.

  • Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM. Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009 Mar 5;458(7234):97-101. doi: 10.1038/nature07638. Epub 2009 Jan 11. PubMed PMID: 19136943; PubMed Central PMCID: PMC2725402.

  • 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. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009 Jan 29;457(7229):551-6. doi: 10.1038/nature07723. PubMed PMID: 19189423.

  • 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. Genome-wide analysis of cancer/testis gene expression. Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20422-7. doi: 10.1073/pnas.0810777105. Epub 2008 Dec 16. PubMed PMID: 19088187; PubMed Central PMCID: PMC2603434.

  • 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. Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science. 2008 Dec 12;322(5908):1695-9. doi: 10.1126/science.1165395. Epub 2008 Nov 13. PubMed PMID: 19008416; PubMed Central PMCID: PMC2684823.

  • Lu, C., Jeong, D., Kulkarni, K., Pillay, M., Nobuta, K., German, R., Thatcher, S., Maher, C., Zhang, L., Ware, D., Liu, B., Cao, X., Meyers, B., Green, P. (2008) Genome-wide analysis for discovery of new rice miRNAs reveals natural antisense miRNAs (nat-miRNAs). Proceedings of the National Academy of Sciences 105(12): 4951-6.

  • 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. Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol. 2008;9(2):R45. doi: 10.1186/gb-2008-9-2-r45. Epub 2008 Feb 28. PubMed PMID: 18304353; PubMed Central PMCID: PMC2374706.

  • Maher C, Stein L, Ware D. Evolution of Arabidopsis microRNA families through duplication events. Genome Res. 2006 Apr;16(4):510-9. Epub 2006 Mar 6. PubMed PMID: 16520461; PubMed Central PMCID: PMC1457037.

  • Maher C, Timmermans M, Stein L, Ware D. Identifying microRNAs in plant genomes. Proceedings of IEEE Computer Society Bioinformatics Conference (CBS). 2004 August 16 – 19; Palo Alto, CA. IEEE. 2004. 718-723 p. 

  • Maher C, Corbit M. Creating genetic applications for informal science learning in multi-user virtual environments. Journal of Network and Computer Applications. 2002 25(4):295-308. doi:10.1006/jnca.2002.0136.

  • Maher C, Corbit M. Creating genetic applications for informal science learning in multi-user virtual worlds. Proceedings of the IEEE 8th International Workshop on Enabling Technologies: Infrastructure for collaborative enterprises (WETICE). 2001 June 20-22; Cambridge, MA. IEEE. 2001. 291 p.

Before 2012