Chris Maher.jpg

Christopher A. Maher, PhD

Assistant Professor
Department of Medicine
Oncology Division
Stem Cell Biology
Department of Biomedical Engineering
McDonnell Genome Institute

Research Interests

  • Computational biology
  • Bioinformatics
  • Genomics
  • Cancer


Peer-reviewed Manuscripts

  • 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
  • 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
  • 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 Sep 11; [Epub ahead of print]
  • 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; [Epub ahead of print]
  • INTEGRATE-Neo: A Pipeline for Personalized Gene Fusion Neoantigen Discovery
    Zhang J, Mardis ER, Maher CA
    Bioinformatics 2017 Feb 15;33(4):555-557
  • 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
  • Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer
    Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyo D, Ellis MJ, Carr SA
    NCI CPTAC (Contributors include: Maher C)

    Nature 2016 May 25;534(7605):55-62
  • 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
  • ChimeraScan: A Tool for Identifying Chimeric Transcription in Sequencing Data
    Iyer MK, Chinnaiyan AM, Maher CA
    Bioinformatics 2011 Oct 15;27(20):2903-4
  • 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)
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    Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4951-6
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    Genome Biol 2008;9(2):R45
  • Evolution of Arabidopsis MicroRNA Families Through Duplication Events
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    Genome Res 2006 Apr;16(4):510-9
  • Identifying MicroRNAs in Plant Genomes
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    Proceedings of IEEE Computer Society Bioinformatics Conference 2004:718-723
  • Creating Genetic Applications for Informal Science Learning in Multi-User Virtual Environments
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    Journal of Network and Computer Applications 2002;25;295-308
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    Proceedings of the IEEE 8th International Workshop on Enabling Technologies: Infrastructure for Collaborative Enterprises 2001