Publications - Marco Marra
2011
Kuchenbauer F, Mah SM, Heuser M, McPherson A, Ruschmann J, Rouhi A, Berg T, Bullinger L, Argiropoulos B, Morin RD, Lai D, Starczynowski DT, Karsan A, Eaves CJ, Watahiki A, Wang Y, Aparicio SA, Ganser A, Krauter J, Döhner H, Döhner K, Marra MA, Camargo FD, Palmqvist L, Buske C, Humphries RK. Comprehensive analysis of mammalian miRNA* species and their role in myeloid cells. Blood. 2011 May 31.
McPherson AW, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MGF, Griffith M, Heravi-Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SdeFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLOS Comput Biol. 2011 May;7(5):e1001138.
Tucker T, Montpetit A, Chai D, Chan S, Chénier S, Coe BP, Delaney A, Eydoux P, Lam WL Langlois S, Lemyre E, Marra M, Qian H, Rouleau GA, Vincent D, Michaud JL, Friedman JM. Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation. BMC Med Genomics. 2011 Mar 25;4(1):25.
Slobodan J, Corbett R, Wye N, Schein JE, Marra MA, Coope RJN. High performance gel imaging with a commercial single lens reflex camera. Rev Sci Instrum. 2011 Mar;82(3):034301.
Steidl C, Shah SP, Woolcock BW, Rui L, Kawahara M, Farinha P, Johnson NA, Zhao Y, Telenius A, Ben-Neriah S, McPherson A, Meissner B, Okoye UC, Diepstra A, van den Berg A, Sun M, Leung G, Jones SJ, Connors JM, Huntsman DG, Savage KJ, Rimsza LM, Horsman DE, Staudt LM, Steidl U, Marra MA, Gascoyne RD. MHC Class II Transactivator CIITA is a Recurrent Gene Fusion Partner in Lymphoid Cancers. Nature. 2011 Mar 2.
Yap DB, Chu J, Berg T, Schapira M, Cheng SW, Moradian A, Morin RD, Mungall AJ, Meissner B, Boyle M, Marquez VE, Marra MA, Gascoyne RD, Humphries RK, Arrowsmith CH, Morin GB, Aparicio SA. Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation. Blood. 2011 Feb 24;117(8):2451-2459.
Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao YJ, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res. 2011 Feb;21(2):203-215.
Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao YJ, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One. 2011 Feb 15;6(2):e17121.
D'Souza C, Kronstad J, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd S, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich J, Fraser J, Meyer W, Carter D, Schein J, Krzywinski M, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BFF, Siddiqui A, Marra M, Jones S, Holt R, Birren B, Galagan J, Cuomo C. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. MBio. 2011 Feb 8;2(1). pii: e00342-10. doi: 10.1128/mBio.00342-10.
DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U, Alamouti SM, Tsui CK, Docking R, Levasseur A, Haridas S, Robertson G, Birol I, Holt R, Marra M, Hamelin RC, Hirst M, Jones SJM, Bohlmann J, Breuil C. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc Natl Acad Sci U SA. 2011 Feb 8;108(6):2504-2509.
Starczynowski D, Morin RD, McPherson A, Kuchenbauer F, Tohyama K, Hirst M, Humphries K, Marra M, Lam W, Karsan A. Genome-wide identification of human microRNAs located in leukemia-associated genomic alterations. Blood. 2011 Jan 13;117(2):595-607.
2010
Hirst M, Marra MA. Next Generation Sequencing Based Approaches to Epigenomics. Brief Funct Genomics. 2010 Dec;9(5-6):455-465.
The modENCODE Consortium. Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. Science. 2010 Dec 24;330(6012):1787-1797.
McLarren KW, Severson T, du Souich C, Stockton DW, Kratz LE, Cunningham D, Hendson G, Morin RD, Wu D, Paul JE, An J, Nelson TN, Chou A, DeBarber AE, Merkens LS, Michaud JL, Waters PJ, Yin J, McGillivray B, Demos M, Rouleau GA, Grzeschik K-H, Smith R, Tarpey PS, Kini U, Schwartz CE, Gecz J, Stratton MR, Arbour L, Hurlburt J, Van Allen MI, Herman GE, Zhao YJ, Moore R, Kelley RI, Jones SJ, Steiner RD, Raymond L, Marra MA, Boerkoel CF. Hypomorphic temperature-sensitive alleles of NSDHL cause CK syndrome. Am J Hum Genet. 2010 Dec 10;87(6):905-914.
Cheung KJ, Johnson NA, Affleck JG, Severson T, Steidl C, Ben-Neriah S, Schein J, Morin RD, Moore R, Shah SP, Qian H, Paul JE, Telenius A, Relander T, Lam W, Savage K, Connors JM, Brown C, Marra MA, Gascoyne RD, Horsman DE. Acquired TNFRSF14 Mutations in Follicular Lymphoma Are Associated with Worse Prognosis. Cancer Res. 2010 Nov 15;70(22):9166-9174.
Cerchietti LC, Hatzi K, Caldas-Lopes E, Yang SN, Figueroa ME, Morin RD, Hirst M, Mendez L, Shaknovich R, Cole P, Bhalla K, Gascoyne RD, Marra M, Chiosis G, Melnick A. BCL6 repression of EP300 provides a basis for rational combinatorial therapy in diffuse large B cell lymphomas. J Clin Invest. 2010 Nov 1. pii: 42869. doi: 10.1172/JCI42869.
Robertson G, Schein J, Chiu R, Field M, Jackman SD, Mungall K, Lee S, Okada SM, Corbett R, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield Y, Newsome R, Chan SK, Varhol R, Kamoh B, Prabhu A-L, Tam A, Zhao YJ, Moore R, Hirst M, Marra MA, Jones SJM, Hoodless PA, Birol I. De Novo Assembly and Analysis of Short-read Transcriptome Sequence Data. Nat Methods. 2010 Nov;7(11):909-912.
Jinno H, Morozova O, Jones KL, Biernaskie JA, Paris M, Hosokawa R, Rudnicki M, Chai Y, Rossi F, Marra MA, Miller FD. Convergent genesis of an adult neural crest-like dermal stem cell from distinct developmental origins. Stem Cells. 2010 Nov;28(11):2027-2040.
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct;28(10):1045-1048.
Law MJ, Lower KM, Voon HP, Hughes JR, Garrick D, Viprakasit V, Mitson M, De Gobbi M, Marra M, Morris A, Abbott A, Wilder SP, Taylor S, Santos GM, Cross J, Ayyub H, Jones S, Ragoussis J, Rhodes D, Dunham I, Higgs DR, Gibbons RJ. Cell. 2010 Oct 29;143(3):367-378.
Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, Senz J, McConechy MK, Anglesio MS, Kalloger SE, Yang W, Heravi-Moussavi A, Giuliany R, Chow C, Fee J, Zayed A, Prentice L, Melnyk N, Turashvili G, Delaney AD, Madore J, Yip S, McPherson AW, Ha G, Bell L, Fereday S, Tam A, Galletta L, Tonin PN, Provencher D, Miller D, Jones SJ, Moore RA, Morin GB, Oloumi A, Boyd N, Aparicio SA, Shih IeM, Mes-Masson AM, Bowtell DD, Hirst M, Gilks B, Marra MA, Huntsman DG. ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010 Oct 14;363(16):1532-1543.
Harris RA, Wang T, Coarfa C, Zhou X, Xi Y, Nagarajan RP, Hong C, Downey S, Johnson BE, Delaney A, Zhao YJ, Olshen A, Ballinger T, Schillebeeckx M, Echipare L, O’Geen H, Lister R, Pelizzola M, Chung W-Y, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker J, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Sequence-based profiling of DNA methylation: comparisons of methods and catalogue of allelic epigenetic modifications. Nat Biotechnol. 2010 Oct;28(10):1097-1105.
Griffith M, Griffith OL, Mwenifumbo J, Morin RD, Goya R, Tang MJ, Hou Y-C, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li HI, McDonald H, Teague K, Zhao YJ, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJM, Tai IT, Marra MA. Alternative expression analysis by RNA sequencing. Nat Methods. 2010 Oct;7(10):843-847.
Smith KM, Datti A, Fujitani M, Grinshtein N, Zhang L, Morozova O, Blakely KM, Rotenberg SA, Hansford LM, Miller FD, Yeger H, Irwin MS, Moffat J, Marra MA, Baruchel S, Wrana JL, Kaplan DR. Selective targeting of neuroblastoma tumour-initiating cells by compounds identified in stem cell-based small molecule screens. EMBO Mol Med. 2010 Sep;2(9):371-384.
Romanuik TL, Wang G, Morozova O, Delaney A, Marra MA, Sadar MD. LNCaP Atlas: Gene expression associated with in vivo progression to castration-recurrent prostate cancer. BMC Med Genomics. 2010 Sep 24;3(1):43.
Morozova O, Vojvodic M, Grinshtein N, Hansford L, Blakely K, Maslova A, Hirst M, Cezard T, Morin R, Moore R, Smith K, Miller F, Taylor P, Thiessen N, Varhol R, Zhao YJ, Jones S, Moffat J, Kislinger T, Moran M, Kaplan D, Marra M. Systems-level analysis of neuroblastoma tumor-initiating cells implicates AURKB as a novel drug target for neuroblastoma. Clin Cancer Res. 2010 Sep 15;16(18):4572-4582.
Petriv OI, Kuchenbauer F, Delaney AD, Lecault V, White A, Kent D, Marmolejo L, Heuser M, Berg T, Copley M, Ruschmann J, Sekulovic S, Antignano F, Kuroda E, Ho V, Benz C, Halim T, Giambra V, Krystal G, Takei CJF, Weng AP, Eaves C, Piret J, Marra MA, Humphries RK, Hansen CL. Comprehensive microRNA Expression Profiling of the Hematopoietic Hierarchy. Proc Natl Acad Sci USA. 2010 Aug 31;107(35):15443-15448.
Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes A, Griffith M, Yee J, Montgomery M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao YJ, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010 Aug 9;11(8):R82.
Morin RD, Zhao Y, Prabhu AL, Dhalla N, McDonald H, Pandoh P, Tam A, Zeng T, Hirst M, Marra M. Preparation and Analysis of MicroRNA Libraries Using the Illumina Massively Parallel Sequencing Technology. Methods Mol Biol. 2010;650:173-199.
Cheung KJ, Delaney A, Ben-Neriah S, Schein J, Lee T, Shah SP, Cheung D, Johnson NA, Mungall AJ, Telenius A, Lai B, Boyle M, Connors JM, Gascoyne RD, Marra MA, Horsman DE. High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy-neutral loss of heterozygosity and copy number alterations that target single genes. Genes Chromosomes Cancer. 2010 Aug;49(8):669-681.
Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao YJ, Hirst M, Verchere B, Helgason CD, Marra MA, Jones SJM, Hoodless PA. H3K4me1 Profiles Distinguish Functional Classes of Transcription Factor Binding Sites. Genome Res. 2010 Aug;20(8):1037-1051.
Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse1 SD, Johnson BE, Hong C, Nielsen C, Zhao YJ, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Conserved Role of Intragenic DNA Methylation in Regulating Alternative Promoters. Nature. 2010 Jul 8;466(7303):253-257.
Wong RTF, Flibotte S, Corbett R, Saeedi P, Jones SJM, Marra MA, Schein JE, Birol I. LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images. IEEE Transactions on Automation Science and Engineering. 2010 Jul; 7(3): 706-708.
Flibotte S ,Edgley ML, Chaudhry I,Taylor J, Neil SE, Rogula A, Zapf R, Hirst M, Butterfield Y, Jones SJ, Marra MA, Barstead RJ, Moerman DG. Whole-Genome profiling of mutagenesis in Caenorhabditis elegans. Genetics. 2010 Jun;185(2):431-441.
International Cancer Genome Consortium. International network of cancer genome projects. Nature. 2010 Apr 15;464(7291): 993-998.
Goya R, Sun MGF, Morin RD, Leung G, Ha G, Wiegand K, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP. SNVMix: predicting single nucleotide variants from next generation sequencing of tumors. Bioinformatics. 2010 Mar 15;26(6):730-736.
Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A. MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. Mol Hum Reprod. 2010 Jul;16(7):463-471. Rose AM, O'Neil NJ, Bilenky M, Butterfield YS, Malhis N, Flibotte S, Jones MR, Marra M, Baillie DL, Jones SJ. Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern. BMC Genomics. 2010 Feb 23;11(1):131. Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, Yap D, Humphries RK, Griffith OL, Shah S, Zhu H, Kimbara M, Shashkin P, Charlot JF, Tcherpakov M, Corbett R, Tam A, Varhol R, Smailus D, Moksa M, Zhao YJ, Delaney A, Qian H, Birol I, Schein J, Moore R, Holt R, Horsman DE, Connors JM, Jones S, Aparicio S, Hirst M, Gascoyne RD, Marra MA. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet. 2010 Feb ;42(2):181-185. (Featured in News and Views, Nat Genet. 2010 Feb;42(2):100-101.) Vrljicak P, Chang A, Morozova O, Wederell E, Niessen K, Marra M, Karsan A, Hoodless P. Genomic Analysis Distinguishes Phases of Early Development of the Mouse Atrio-Ventricular Canal. Physiol Genomics. 2010 Feb 4;40(3):150-157. Starczynowski DT, Kuchenbauer F, Argiropoulos B, Sung S, Morin R, Muranyi A, Hirst M, Hogge D, Marra M, Wells RA, Buckstein R, Lam W, Humphries RK, Karsan A. Identification of miR-145 and miR-146a as mediators of the 5q- syndrome phenotype. Nat Med. 2010 Jan;16(1):49-58. Costello JF, Krzywinski M, Marra MA. A first look at the entire human methylomes. Nat Biotechnol. 2009 Dec;27(12):1130-1132 The MGC Project Teams. The Completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 Dec;19(12):2324-2333. Biernaskie J, Paris M, Morozova O, Fagan BM, Marra M, Pevny L, Miller FD. SKPs derive from hair follicle precursors and exhibit properties of adult dermal stem cells. Cell Stem Cell. 2009 Dec 4;5(6):610-623.
Lehman AM, Friedman JM, Zahir FH, Eydoux P, Marra MA, Prisman L, Tsang E, Armstrong L. A characteristic syndrome associated with microduplication of 8q12, inclusive of CHD7. Eur J Med Genet. 2009 Nov-Dec;52(6):436-439. Birol I, Jackman S, Nielsen C, Qian J, Varhol R, Stazyk G, Zhao YJ, Hirst M, Schein J, Horsman D, Connors J, Gascoyne R, Marra M, Jones S. De novo Transcriptome Assembly with AbySS. Bioinformatics. 2009 Nov 1;25(21):2872-2877. Friedman JM, Adam S, Arbour L, Armstrong L, Baross A, Birch P, Boerkoel C, Chan S, Chai D, Delaney AD, Flibotte S, Gibson WT, Langlois S, Lemyre E, Li HI, MacLeod P, Mathers J, Michaud JL, McGillivray BC, Patel MS, Qian H, Rouleau GA, Van Allen MI, Yong S-L, Zahir FR, Eydoux P, Marra MA. Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500K SNP array genomic hybridization. BMC Genomics. 2009 Nov 16;10:526. Romanuik TL, Wang G, Holt RA, Jones SJM, Marra MA, Sadar MD. Identification of novel androgen-responsive genes by deep sequencing of LongSAGE libraries. BMC Genomics. 2009 Oct 15;10(1):476. Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Zhao YJ, Hirst M, Jones S, Marra MA. Next generation tag sequencing for cancer gene expression profiling. Genome Res. 2009 Oct;19(10):1825-1835. Shah SP, Morin R, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, Steidl C, Holt RA, Jones S, Sun M, Leung G, Moore R, Severson T, Taylor G, Teschendorff AE, Tse K, Turashvili G, Varhol R, Warren RL, Watson P, Zhao YJ, Caldas C, Huntsman D, Hirst M, Marra MA, Aparicio S. Mutational evolution and RNA editing in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009 Oct 8;461(7265):809-813. DiGuistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJM. De novo assembly of a genome sequence for the filamentous fungus, Grosmannia clavigera, assembled using Sanger, 454 and Illumina sequence data. Genome Biol. 2009 Sep 11;10(9):R94. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra M. Circos: an Information Aesthetic for Comparative Genomics. Genome Res. 2009 Sep;19(9):1639-1645. Halaschek-Wiener J, Amirabbasi-Beik M, Monfared N, Pieczyk M, Sailer C, Kollar A, Turnbull R, Agalaridis G, Yamada S, Oliveira L, Collins J, Meneilly G, Marra MA, Madden KM, Le ND, Connors JM, Brooks-Wilson AR. Genetic variation in healthy oldest-old. PloS One. 2009 Aug 14;4(8):e6641. Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet. 2009;10:135-151. Pugh T, Keyes M, Barclay L, Delaney A, Krzywinski M, Thomas D, Yang C, Agranovich A, McKenzie M, Morris WJ, Moore M, Marra MA. Sequence variant discovery in DNA repair genes from radiosensitive and radiotolerant prostate brachytherapy patients. Clin Cancer Res. 2009 Aug 1;15(15):5008-5016. Tucker T, Marra M, Friedman JM. Massively Parallel Sequencing: The Next Big Thing in Genetic Medicine. Am J Hum Genet. 14 Aug 2009;85(2):142-154. Friedländer MR, Adamidi C, Han T, Lebedeva S, Isenbarger TA, Hirst M, Marra M, Nusbaum C, Lee WL, Jenkin JC, Alvarado AS, Kim JK, Rajewsky N. High-resolution profiling and discovery of planarian small RNAs. Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11546-11551. Meissner B, Warner A, Wong K, Dube N, Lorch A, McKay SJ, Khattra J, Rogalski T, Somasiri A, Chaudhry I, Fox RM, Miller DM, Baillie DL, Holt RA, Jones SJM, Marra MA, Moerman DG. An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genet. 2009 Jun;5(6):e1000537. Shah S, Köbel M, Senz J, Morin RD, Clarke BA, Wiegand K, Leung G, Zayed A, Mehl E, Kalloger S, Sun M, Guiliany R, Yorida E, Jones S, Varhol R, Swenerton KD, Miller D, Clement PB, Crane C, Madore J, Provencher D, Leung P, DeFazio A, Khattra J, Turashvili G, Zhao YJ, Zeng T, Glover JNM, Vanderhyden B, Zhao C, Parkinson CA, Jimenez-Linan M, Mes-Masson AM, Brenton JD, Aparicio SA, Boyd N, Hirst M, Gilks CB, Marra MA, Huntsman DG. Mutation of the FOXL2 gene in granulosa cell tumors of the ovary. N Engl J Med. 2009 Jun 25;360(26):2719-2729. Wang X, Zhao JY, Wong K, Ehlers P, Kohara Y, Jones SJ, Marra MA, Holt RA, Moerman DG, Hansen D. Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE. BMC Genomics. 2009 May 9;10:213. Zahir FR, Langlois S, Gall K, Eydoux P, Marra MA, Friedman JM. A novel de novo 1.1 Mb duplication of 17q21.33 associated with cognitive impairment and other anomalies. Am J Med Genet A. 2009 Jun;149A(6):1257-62. Bovine Genome Sequencing and Analysis Consortium (incl Holt RA, Jones SJ, Marra MA, Moore R). The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution. Science. 2009 Apr 24;324(5926):522-528. Kent DG, Copley MR, Benz C, Wöhrer S, Dykstra BJ, Ma E, Cheyne J, Zhao YJ, Bowie M, Zhao Y, Gasparetto M, Delaney A, Smith C, Marra M, Eaves CJ. New Candidate Regulators of Hematopoietic Stem Cells with High Self-renewal Activity. Blood. 2009 Apr 17. Hillier LH, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Massively parallel sequencing of the poly-adenylated transcriptome of C. elegans. Genome Res. 2009 Apr;19(4):657-666. Hirst M and Marra MA. Epigenetics and human disease. Int J Biochem Cell Biol. 2009 Jan;41(1):136-146. Morozova O and Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics. 2008 Nov;92(5):255-264. (#1 most downloaded article from Genomics for 2008). Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu A-L, Zhao Y, McDonald H, Zeng T, Hirst M, Hansen CL, Marra MA, Humphries RK. In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res. 2008 Nov;18(11):1787-1797. Salvagiotto G, Zhao Y, Vodyanik M, Ruotti V, Stewart R, Marra M, Thomson J, Eaves C, and Slukvin I. Molecular profiling reveals similarities and differences between primitive subsets of hematopoietic cells generated in vitro from human embryonic stem cells and in vivo during embryogenesis. Exp Hematol. 2008 Oct;36(10):1377-1389. Morozova O, Morozov V, Hoffman B, Helgason CD, Marra MA. A seriation approach for visualization-driven discovery of co-expression pattern in Serial Analysis of Gene Expression (SAGE) data. PLOS ONE. 2008 Sep 12;3(9):e3205. Pugh TJ, Delaney AD, Farnoud N, Flibotte S, Griffith M, Li I, Qian H, Farinha P, Gascoyne RD, Marra MA. Impact of whole genome amplification on analysis of copy number variants. Nucleic Acids Res. 2008 Aug;36(13):e80. Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao Y, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones S, Hoodless PA. Global Analysis of In Vivo FoxA2 Binding Sites in Mouse Adult Liver Using Massively Parallel Sequencing. Nucleic Acids Res. 2008 Aug;36(14):4549-64. Epub 2008 Jul 8. D'Souza CA, Chopra V, Varhol R, Xie Y, Bohacec S, Zhao Y, Lee LLC, Bilenky M, Portales-Casamar E, He A, Wasseman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJM. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neurosci. 2008 Jul 14;9(1):66. Shin H, Hirst M, Bainbridge M, Magrini V, Mardis E, Moerman DG, Marra MA. Baillie DL, Jones SJM. Transcriptome analysis of C. elegans on novel expressed sequence tags (ESTs). BMC Biology. 2008 Jul 8;6(1):30. Morin RD, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh TJ, McDonald H, Varhol R, Jones SJM, Marra MA. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques. 2008 Jul;45(1)81-94. Raouf A, Zhao Y, To K, Stingl HJ, Delaney A, Barbara M, Iscove N, Jones S, McKinney S, Emerman J, Aparicio S, Marra M, Eaves C. Transcriptome analysis of the normal human mammary cell commitment and differentiation process. Cell Stem Cell. 2008 Jul 3;3(1):109-118. Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Hoodless PA, Jones S, Marra MA, Helgason CD. Identification of transcripts with enriched expression in the developing and adult pancreas. Genome Biol. 2008 Jun 14;9(6):R99. Morozova O and Marra MA. From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangemetns in tumors. Biochem. Cell Biol. 2008 Apr;86(2):81-91. Zahir F, Baross A, Delaney AD, Eydoux P, Ferdinandez ND, Marra M. Friedman JM. A patient with vertebral, cognitive and behavioural abnormalities and a de novo deletion of NRXN1a. J Med Genet. 2008 Apr;45(4):239-243. Epub 2007 Dec 5. Morin RD, O’Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu A-L, Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008;18(4):610-621. Griffith M. Tang MJ, Griffith OL, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Morin RD, Hirst M, Jones SJM, Morin GB, Tai IT. Marra M. ALEXA – A microarray design platform for alternative expression analysis. Nat Methods. 2008;5(2):118. Ralph SG, Chun HJE, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJM, Marra MA, Bohlmann J. Analysis of 6,464 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics. 2008;9(1):57. Zahir F, Baross A, Delaney AD, Eydoux P, Ferdinandez ND, Marra M, Friedman JM. A patient with vertebral, cognitive and behavioural abnormalities and a de novo deletion of NRXN1a. J Med Genet. 2007. Peng FY, Reid KE, Liao N, Schlosser J, Lijavetzky D, Holt R, Martínez Zapater JM, Jones S, Marra M, Bohlmann J, Lund ST. Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table Grape (Muscat Hamburg) and discovery of new candidate genes with possible roles in berry development. Gene. 2007;402(1-2):40-50. Krzywinski M, Bosdet I, Mathewson C, Wye N, Brebner J, Chiu R, Corbett R, Field M, Lee D, Pugh T, Volik S, Siddiqui A, Jones S, Schein J, Collins C, Marra A. A BAC clone fingerprinting approach to the detection of human genome rearrangements. Genome Biol. 2007;8(10):R224. Baross A, Delaney AD, Li HI, Nayar T, Flibotte S, Qian H, Chan SY, Asano J, Ally A, Cao M, Birch P, Brown-John M, Fernandes N, Go A, Kennedy G, Langlois S, Eydoux P, Friedman JM, Marra MA. Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data. BMC Bioinformatics. 2007;8(1):368. Huang P, Pleasance ED, Maydan JS, Hunt-Newbury R, O’Neil NJ, Mah A, Baillie DL, Marra MA, Moerman DG, Jones SJ. Identification and analysis of internal promoters in Caenorhabditis elegans operons. Genome Res. 2007;17(10):1478-1485. Stratford AL, Habibi G, Astanehe A, Jiang H, Hu K, Park E, Shadeo A, Buys TP, Lam W, Pugh T, Marra M, Nielsen TO, Klinge U, Mertens PR, Aparicio S, Dunn SE. Epidermal growth factor receptor (EGFR) is transcriptionally induced by the Y-box binding protein-1 (YB-1) and can be inhibited with Iressa in basal-like breast cancer providing a potential target for therapy. Breast Cancer Res. 2007;99(5):R61. Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastis D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, Mckay S, Okada HM, Pan J, Shultz AK, Tu D, Wong K, Zhao Z, Alexeyenko A, Burglin T, Sonnhammer E, Schnabel R, Jones SJ, Marra MA, Baillie DL, Moerman DG. High Throughput In Vivo Analysis of Gene Expression in C. Elegans. PloS Biology. 2007;5(9):e237. Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, McWilliam S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas F, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel R, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor J, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biol. 2007;8(8):R165. Hou J, Charters AM, Lee SC, Zhao Y, Wu MK, Jones SJM, Marra MA , Hoodless PA. A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE). BMC Dev Biol. 2007;7(1):92. Ruzanov P, Riddle DL, Marra MA, McKay SJ, Jones SM. Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults. Exp Gerontol. 2007;42(8):825-39. Pugh TJ, Bebb G, Barclay L, Sutcliffe M, Fee J, Salski C, O’Connor R, Ho C, Murray N, Melosky B, English J, Vielkind J, Horsman D, Laskin JJ, Marra MA. Correlations of EGFR mutations and increases in EGFR and copy number to gefitinib response in a retrospective analysis of lung cancer patients. BMC Cancer. 2007;7(1):128. Etchberger JF, Lorch A, Sleumer M, Zapf R, Jones SJ, Marra MA, Holt RA, Moerman DG, Hobert O. The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron. Genes Dev. 2007;21(31):1653-1674. Hu G, Linning R, Joseph C, McCallum B, Banks T, Cloutier S, Butterfield Y, Liu J, Kirkpatrick R, Stott J, Yang G, Smailus D, Jones S, Marra M, Schein J, Bakkeren G. Generation of a wheat leaf rust, Puccinia triticina, EST database from stage-specific cDNA libraries. Mol Plant Pathol. 2007;8(4):451-467. Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O'Connor MD, Zeng T, Mokda M, Fichter K, Mah D, Go A, Morin RD, Baross A, Zhao Y, Khattra J, Prabhu A-L, Pandoh P, McDonald H, Asano J, Dhalla N,Ma K, Lee S, Ally A, Chalal N, Menzies S, Siddiqui A, Holt R, Jones S, Gerhard DS, Thomson JA, Eaves CJ, Marra MA. LongSAGE profiling of 9 human embryonic stem cell lines. Genome Biol. 2007;8(6):R113. Margulies EH, Coope GM, Asimenos G, Thomas DJ, Dewey CN, Siepe A, Birney E, Keepe D, Schwart AS, Hou M, Taylot J, Nikolaev S, Montoya-Burgos JI, Loytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Schuler G, Church D, Rosenbloom KR, Kent J, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center,Washington University Genome Sequencing Center, Broad Institute. UCSC Genome Browser Team, British Columbia Cancer Agency Genome Sciences Centre (Field MA, Moore RA, Mathewson CA, Schein JE,and Marra MA), et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007;17(6):760-774. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007;4(8):651-657. Zahir F, Firth HV, Baross A, Delaney AD, Eydoux P, Gibson WT, Langlois S, Martin H, Willat L, Marra M, Friedman JM. A Novel Deletion14q11.2 Syndrome Identified By Array Genomic Hybridization. J Med Genet. 2007. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SMJ, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD,Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Broad Institute Genome Sequencing Platform and Broad Institute Whole Genome Assembly Team and , Marshall Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, and Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007;447(7141):167-177. Kelleher CT, Chiu R. Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin TM, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O’Connor K, Pradhu A-L, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJM, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ, Schein JE. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant J. 2007. Rhesus Macaque Genome Sequencing and Analysis Consortium (incl Jones SM, Marra MA, and Schein JE). Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316(5822):222-234. Zhao Y, Raouf A, Kent D, Khattra J, Delaney A, Schnerch A, Asano J, MacDonald H, Chan C, Jones S, Marra MA, Eaves CJ. A modified PCR-LongSAGE protocol identifies novel transcripts in human CD34+ bone marrow cells. Stem Cells. 2007. McGhee JD. Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJM, Moerman DG, Robertson AG. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol. 2007;302(2):627-645. Quayle SN, Heidi H, Delaney AD, Hirst M, Hwang D, Schein JE, Jones SJM, Marra MA, Sadar MD. Novel expressed sequences identified in a model of androgen independent prostate cancer. BMC Genomics. 2007;8:32. McLeod MP, Warren RL, Hsiao WWL, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD,Yang G, Stott JM, Schein JE. Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJM, Holt R, Brinkman FSL, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis D. The complete genome of Rhodococcus sp. RHA1: insights into a catabolic powerhouse. Proc Natl Acad Sci USA. 2006;103(42):15582-15587. Bainbridge M, Warren R, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis E, Sadar M, Siddiqui A, Marra M, Jones S. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics. 2006;7:246. Menten B, Buysse K, Zahir F, Hellemans J, Hamilton SJ, Costa T, Fagerstrom C, Anadiotis G, Kingsbury D, McGillivray BC, Marra MA, Friedman JM, Speleman F, Mortier G. Osteopoikilosis, short stature and mental retardation as key features of a new microdeletion syndrome on 12q14. BJ Med Genet. 2007 Jan 12. Robertson N, Oveisi-Fordorei M, Zuyderduyn S, Varhol R, Fjell C, Marra MA, Jones SJM, Siddiqui AS. DiscoverySpace: an interactive data analysis application. Genome Biol. 2007;8(1):R6. Khattra J, Delaney AD, Zhao Y, Siddiqui A, Hirst M, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu A, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Jones S, Holt R, Hoodless P, Marra MA. Large scale production of SAGE libraries from microdissected tissues, flow-sorted cells and cell lines. Genome Res. 2006 Dec 22;7(12):R126. Chen N, Mah A, Blacque OE, Chu J, Phgora K, Bakhoum MW, Newbury CRH, Khattra J, Chan S, Go A, Efimenko E, Johnsen R, Phirke P, Swoboda P, Marra M, Moerman DG, Leroux MR, Baillie DL, Stein LD. Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics. Genome Biol. 2006;7(12):R126. Lonergan KM, Chari R, deLeeuw RJ, Shadeo A, Chi B, Tsao M-S, Jones S, Marra M, Ling V, Ng R, MacAulay C, Lam S, Lam WL. Identification of Novel Lung Genes in Bronchial Epithelium by Serial Analysis of Gene Expression. Am J Respir Cell Mol Biol. 2006;35(6):651-661. Sea Urchin Genome Sequencing Consortium (incl. I. Bosdet, Shin H, Schein J and Marra MA). The Genome of the Sea Urchin Strongylocentrotus purpuratus. Science. 2006;314(5801):941-952. Tuskan GA, DiFazio SP, Hessten U, Jansson S, Rombauts S, Putnam N, Sterck L, Bohlmann J, Schein J, Ralph S, Aets A, Bhalerao R, Bhalerao P, Blaudez D, 85 other authors, Marra M, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006;313(5793):1596-1604. Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Asano J, Bailey DK, Barber S, Birch P, Brown-John M, Cao M, Chan S, Charest DL, Farnoud N, Fernandes N, Flibotte S, Go A, Gibson WT, Holt RA, Jones SJM, Kennedy GC, Krzywinski M, Langlois S, Li HI, McGillivray BC, Nayar T, Pugh TJ, Rajcan-Separovic E, Schein JE, Schnerch A, Siddiqui A, Van Allen MI, Wilson G, Yong SL, Eydoux P, Marra MA. Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet. 2006;79(3):500-513. Bakkeren G, Jiang G, Warren R, Butterfield Y, Shin H, Chiu R, Linning R, Schein J, Lee N, Hu G, Kupfer DM, Tang Y, Roe BA, Jones S, Marra M, Kronstad JW. Mating factor linkage and genome evolution in basidiomycetous pathogens of cereals. Fungal Genet Biol. 2006;43(9):655-666. Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YSN, Kirkpatrick R, Liu J, Jones SJM, Marra MA, Douglas CJ, Ritland K, Bohlmann J. Conifer defense against iInsects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-scale changes of the host transcriptome. Plant Cell Environ. 2006;29(8):1545-1570. Siddiqui AS, Delaney AD, Schnerch A, Griffith OL, Jones SJM, Marra MA. Sequence biases in large scale gene expression profiling data. Nucleic Acids Res. 2006;34(12):e83. Wang G, Jones SJM, Marra MA, Sadar MD. Identification of genes targeted by the androgen and PKA signaling pathways in prostate cancer cells. Oncogene. 2006 Jun 5;7311-7323. Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, 35 other authors, Marra MA, Jones SJM, Holt RA. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis. Genome Res. 2006;16(6):796-803. Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang S-P, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AS, Marra MA, Wilson RK, Jones SJM. Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res. 2006;16:768-775. Ralph S, Oddy C, Cooper D, Yueh H, Jancsik S, Kolosova N, Philippe RN, Aeschliman D, White R, Huber D, Ritland CE, 15 other authors, Marra MA, Ellis BE, Douglas CJ, Ritland K, Bohlmann J. Genomics of hybrid poplar (Populus trichocarpa x deltoids) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags (ESTs), and a cDNA microarray for the study of insect-induced defenses in poplar. Mol Ecol. 2006;15(5):1275-1297. Wilson GE, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG, Holt RA. Identification by full coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res. 2006;16(2):173-182. Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, 38 other authors, Marra M. A mouse altas of gene expression: Large-scale digital gene expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci USA. 2005;102(51):18485-18490. Everts-van der Wind A, Larkin DM, Green CA, Elliott JS, Olmstead CA, Chiu R, Schein JE, Marra MA, Womack JE, Lewin HA. A high-resolution whole-genome cattle-human comparative map reveals new details of mammalian chromosome evolution. Proc Natl Acad Sci USA. 2005;102(51):18526-18531. Larraya LM, Boyce K, So A, Steen BR, Jones S, Marra M, Kronstad J. Serial Analysis of Gene Expression Reveals Conserved Links Between Protein Kinase A, Ribosome Biogenesis and Phosphate Metabolism in Ustilago maydis. Eukaryot Cell. 2005;4(12):2029-2043. Pavy N, Paule C, Parsons L, Crow JA, Morency M-J, Cooke J, Johnson JE, Noumen E, Guillet-Claude C, Butterfield Y, Barber S, Yang G, Liu J, Stott J, Kirkpatrick R, Siddiqui A, Holt R, Marra M, Seguin A, Retzel E, Bousquet J, MacKay J. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics. 2005;6:144. Smailus DE, Marziali A, Dextras P, Marra MA, Holt RA. Simple, robust methods for high-throughput nanoliter-scale DNA sequencing. Genome Res. 2005;15:1447-1450. Ng SHS, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJM, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddiqui A, Thorsen J, Wye N, Yang G, Zhu B. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics. 2005;86(4):396-404. Ivens AC, Peacock C, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Marra M et al. The Genome of the Kinetoplastid parasite, Leishmania major. Science. 2005;309(5733):436-442. Halaschek-Wiener J, Khattra JS, McKay S, Pouzyrev A, Stott JM, Yang GS, Holt RA, Jones SJM, Marra MA, Brooks-Wilson AR, Riddle DL. Analysis of Long-lived C. elegans daf-2 Mutants using Serial Analysis of Gene Expression. Genome Res. 2005;15(5)603-615. Blacque OE, Boroevich KA, Inglis PN, Li C, Warner A, Khattra J, Holt RA, Mah AK, McKay SJ, Huang P, Swoboda P, Jones SJM, Marra MA, Baillie DL, Moerman DG, Shaham S, Leroux MR. Functional Genomics of the Cilium, A Sensory Organelle. Curr Biol. 2005;15(10):935-941. Warren RL, Butterfield YS, Morin RD, Siddiqui AS, Marra MA, Jones SJM. Management and Visualization of Whole Genome Shotgun Assemblies using SAM. Biotechiques. 2005;38:715-720. Hillier LW, Graves TA, 110 other authors, Marra MA et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature. 2005;434(7034):724-731. Lian TS, Simmer M, D’Souza CD, Steen BR, Zuyderduyn S, Jones S, Marra M, Kronstad J. Iron-regulated transcription and capsule formation in the fungal pathogen Cryptococcus neoformans. Mol Microbiol. 2005;55(5):1452-1472>. Loftus B, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamethevan J, Miranda M, Anderson I, Fraser JA, Allen J, Bosdet I, Brent MR, Chiu R, Doering TL, Donlin, MJ, D’Souza C. Fox DS, Grinberg V, Fu J, Fukushima M, Haas B, Huang JC, Janbon G, Jones S, Krzywinski MI, Kwon-Chung J, Lengeler KB, Maiti R, Marra M et al. The genome and transcriptone of Cryptococcus neoformans, a basidiomycetous fungal pathogen of humans. Science. 2005;307(5713):1321-1324. Yang GS, Stott JM, Smailus D, Barber SA, Balasundaram M, Marra MA, Holt RA. High-throughput Sequencing: A Failure Mode Analysis. BMC Genomics. 2005;6(1):2. Hirst M, Astell C, Griffith M, Coughlin SM, Moksa M, Zeng T, Smailus DE, Holt RA, Jones S, Marra MA, Petric M, Krajden M, Lawrence D, Mak A, Chow R, Skowronski DM, Tweed A, Goh S, Brunham RC, Robinson J, Bowes V, Sojonky K, Byrne SK, Paetzel M. A novel avian influenza H7N3 strain associated with an Avian Influenza Outbreak in British Columbia. Emerg Infect Dis. 2004;10(12):2192-2195. Warren R, Hsiao WWL, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Butterfield Y, Schein JE, Shin H, Khattra J, Smailus D, Holt R, Siddiqui A, Jones S, Marra M, Mohn WW, Brinkman FSL, Fukuda M, Davies J, Eltis LD. Functional characterization of catabolic plasmid from PCB-degrading Rhodococcus sp. RHA1. J Bacteriol. 2004;186(22)7783-7795. The ENCODE Project Consortium (including Marra M). The ENCODE (ENCyclopedia of DNA Elements) Project. Science. 2004;306(5696):636-640. The MGC Project Team (including Marra M). The Status, Quality and Expansion of the NIH Full-length cDNA project (MGC). Genome Res. 2004;(10B):2121-2127. Baross A, Butterfield Y, Coughlin S, Zeng T, Griffith M, Griffith O, Petrescu A, Smailus D, Khattra J, McDonald H, McKay S, Moksa M, Siddiqui A, Jones S, Holt R, Marra M. Systematic Recovery and Analysis of Full-ORF Human cDNA Clones. Genome Res. 2004(10B):2083-2092. Anglesio MS, Evdokimova V, Melnyk N, Zhang L, Fernandez CV, Grundy PE, Leach S, Marra MA, Brooks-Wilson AR, Penninger J, Sorensen PHB. Differential expression of a novel ankyrin containing E3 ubiquitin-protein ligase, Hace1, in sporadic Wilm’s tumor versus normal kidney. Hum Mol Genet. 2004;13(18):2061-2074. Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Tsai M, Albertson D, Lam W, Choy C-O, Osoegawa K, Zhao S, de Jong P, Schein J, Jones S, Marra M. A Set of BAC Clones Spanning the Human Genome. Nucleic Acids Res. 2004;32(12):3651-3660. Flibotte S, Chiu R, Fjell C, Krzywinski M, Schein JE, Shin Heesun, Marra MA. Automated ordering of fingerprinted clones. Bioinformatics. 2004;20(8):1264-1271. MacAulay C, Lonergan K, Chi B, Zuyderduyn S, Shein J, Tsao M, LeRiche J, Jones S, Marra M, Lam S, Lam WL. Serial analysis of gene expression profiles of developmental stages in non-small cell lung carcinoma. Chest. 2004;125(5 Suppl):97S. Henderson L-J, Okamoto I, Lestou VS, Robichaud M, Chhanabhai M, Gascoyne RD, Klasa RJ, Connors JM, Marra MA, Horsman DE, Lam WL. Delineation of a minimal region of deletion at 6q16.3 in follicular lymphoma and construction of a BAC contig spanning a 6 megabase region of 6q16-q22. Genes Chromosomes Cancer. 2004;40:60-65. Krzywinski M, Wallis J, Gösele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, 39 other authors, Marra M, Schein J. Integrated and Sequence-Ordered BAC and YAC-based Physical Maps for the Rat Genome. Genome Res. 2004;14(4):766-779. Baross A, Schertzer M, Zuyderduyn SD, Jones SJM, Marra MA, Lansdorp PM. Effect of TERT and ATM on gene expression profiles in human fibroblasts. Genes Chromosomes Cancer. 2004 Apr;39(4):298-310. Rat Genome Sequencing Project Consortium (including Marra M). Genome Sequence of the Brown Norway Rat Yields Insights into Mammalian Evolution. Nature. 2004;428(6982):493-521. Ishkanian AS, Malloff C, Watson S, deLeeuw R, Chi B, Coe B, Albertson DG, Pinkel D, Marra M , Ling V, MacAulay C, Lam WL. A tiling resolution DNA Microarray with complete coverage of the human genome. Nat Genet. 2004;36(3):299-303. Rise ML, von Schalburg KR, Brown GD, Mawer, MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SRM, Smailus DE, Jones SJM, Schein J, Marra MA, Butterfield YSN, Stott J, Ng SHS, Davidson WS, Koop BF. Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Intespecific Hybridization Characteristics. Genome Res. 2004;14:478-490. McKay SJ, Johnsen R, Khattra J, Asano J, Baillie DL, Chan S, Dube N, Fang L, Goszczynski B, Ha E, Halfnight E, Hollebakken R, Huang P, Hung K, Jensen V, Jones SJM, Kai H, Li D, Mah A, Marra M et al. Gene Expression Profiling of Cells, Tissues and Developmental Stages of the Nematode C. elegans. Cold Spring Harb Symp Quant Biol. 2004;159-169. Kingsley D, Zhu B, DeJong P, Schein J, Marra M, Peichel K, Amemiya C, Schluter D, Balabhadra S, Friedlander B, Cha YM, Dickson M, Grimwood J, Schmutz J, Talbot WS, Myers R. New genomic tools for molecular studies of evolutionary change in sticklebacks. Behavior. 2004;141:1331-1344. Steen BR, Zuyderduyn S, Toffaletti DL, Marra M, Jones SJM, Perfect JR, Kronstad J. Analysis of Cryptococcus neoformans gene expression during experimental cryptococcal meningitis. Eukaryot Cell. 2003;2(6):1336-1349. Stein LD, Bao Z, Blasier D, Blumenthal T, Brent M, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D’Eustachio P, Fulton L, Fulton R, Griffiths-Jones S, Harris T, Hillier L, Kamath R, Kuwabara P, Marra M et al. The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics. PLoS Biol. 2003;1(2):E45. Boon K, Edwards JB, Siu I-M, Olschner D, Eberhart CG, Marra MA, Strausberg RL, Riggins GJ. Comparison of Medulloblastoma and Normal Neural Transcriptomes Identifies a Restricted Set of Activated Genes. Oncogene. 2003;22(48):7687-7694. Hillier LW, Fulton RS, 72 other authors, Marra MA et al. The DNA sequence of human chromosome 7. Nature. 2003;424(6945):157-164. Fjell CD, Bosdet I, Schein JE, Jones SJM, Marra MA. Internet Contig Explorer (iCE) - A tool for visualizing clone fingerprint maps. Genome Res. 2003;13(6):1244-1249. Pleasance ED, Marra MA, Jones SJM. Assessment of SAGE in transcript identification based on a new method of tag-to-gene mapping. Genome Res. 2003;13(6):1203-1215. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A et al. The genome sequence of the SARS-associated coronavirus. Science. 2003;300(5624):1399-1404. Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LW, Waterston RH, McPherson JD, Jones SJM, Marra MA. Software for automated analysis of DNA fingerprinting gels. Genome Res. 2003;13(5)940-953. S.S. Moore, C. Hansen, J.L. Willimans, A. Fu, Y. Meng, C. Li, Y Zhang, B.S.D. Urquhart, Marra M, J Schein, B. Benkel, P. J. de Jong, K. Osoegawa, B.W. Kirkpatrick and C.A. Gill. A comparative map of bovine chromosome 19 based on a combination of mapping on a bacterial artificial chromosome scaffold map, a whole genome radiation hybrid panel and the human draft sequence. Cytogenet Genome Res. 2003;102:32-38. Mammalian Gene Collection Program Consortium (including Marra M). Generation and initial analysis of more than 14,000 non-redundant, full-length human and mouse cDNA sequences by the NIH Mammalian Gene Collection Program. Proc Natl Acad Sci USA. 2002;99(26):16899-16903. Vatcher G, Smailus D, Krzywinski M, Guin R, Stott J, Tsai M, Chan S, Pandoh P, Yang G, Asano J, Olson T, Prabhu A, Coope R, Marziali A, Schein J, Jones S, Marra M. Resuspension of DNA sequencing reaction products in agarose increases sequence quality on the MegaBACE 1000 automated sequencer. Biotechniques. 2002;33:532-4,536,538-539. Steen BR, Lian T, Zuyderduyn S, MacDonald K, Marra M, Jones SJM, Kronstad JW. Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Res. 2002;12:1386-1400. Schein J, Tangen K, Chiu R, Shin H, Lengeler KB, MacDonald K, Bosdet I, Heitman J, Jones SJM, Marra M, Kronstad JW. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res. 2002;12:1445-53. Gregory SG, Sekhon M, 83 other authors, Marra M, McPherson JD, Bentley DR. A physical map of the mouse genome. Nature. 2002; 418:743-750. Mattman A, Huntsman D, Lockitch G, Langlois S, Buskard N, Ralston D, Butterfield Y, Rodrigues P, Jones S, Porto G, Marra M, De Sousa M, Vatcher G. Transferrin Receptor 2 (TFR2) and HFE Mutational Analysis in Non-C282Y Iron Overload:Identification of a Novel TfR2 mutation associated with Iron Overload and Leukopenia. Blood. 2002;100:1075-1077. Butterfield YSN, Marra MA, Asano JK, Chan SY, Guin R, Kryzwinski MI, Lee SS, MacDonald KWK, Mathewson CA, Olson TE, Pandoh PK, Prabhu A, Schnerch A, Skalska U, Smailus DE, Stott JM, Tsai MI, Yang GS, Zuyderduyn SD, Schein JE, Jones SJM. An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones. Nucleic Acids Res. 2002;30:2460-2468. Shevchenko Y, Bouffard GG, Butterfield YSN, Blakesley RW, Hartley JL, Young AC, Marra MA, Jones SJM, Touchman JW, Green ED. Systematic sequencing of cDNA clones using the transposon Tn5. Nucleic Acids Res. 2002;1;30:2469-2477. Ness SR, Terpstra W, Krzywinski M, Marra MA, Jones SJM. Assembly of fingerprint contigs: parallelized FPC. Bioinformatics. 2002;18:484-485. Gorski S, Marra M. Programmed cell death takes flight: Genetic and genomic approaches to gene discovery in Drosophila. Physiol Genomics. 2002; 9:59-69. Cai W-W, Chow C-W, Damani S, Gregory SG, Marra M, Bradley A. An SSLP marker-anchored BAC framework map of the mouse genome. Communication. Nat Genet. 2001;29:133-134. Clark MD, Herwig R, Clifton SW, Marra MA, Lehrach H, Johnson, SL. An oligonucleotide fingerprint normalised and Expressed Sequence Tag characterised zebrafish cDNA library. Genome Res. 2001;11:1594-1602. Jones SJM, Riddle D, Pouzyrev AT, Velculescu VE, Hillier L, Eddy SR, Stricklin SL, Baillie DL, Waterston R, Marra MA. Changes in gene expression associated with developmental arrest and longevity in C. elegans. Genome Res. 2001;11:1346-1352. Gower NJD, Temple GR, Schein JE, Marra M, Walker DS, Baylis HA. Dissection of the promoter region of the inositol 1,4,5-trisphosphate receptor gene, itr-1, in C. elegans: A molecular basis for cell-specific expression of IP3R isoforms. J Mol Biol. 2001;306(2):145-157. McPherson JD, Marra M et al. A physical map of the human genome. Nature. 2001; 409:934-941. The International Human Genome Sequencing Consortium (including Marra M). Initial sequencing and analysis of the human genome. Nature. 2001;409:860-921. Wendl MC, Marra MA, Hillier LW, Chinwalla AT, Wilson RK, Waterston RH. Theories and applications for sequencing randomly selected clones. Genome Res. 2001;11:274-280. The Arabidopsis Genome Initiative (including Marra M). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408:796-815. Kazusa DNA Research Institute, the Cold Spring Harbor and Washington University Sequencing Consortium, the European Union Arabidopsis Genome Sequencing Consortium and Institute of Plant Genetics and Crop Plant Research (IPK). Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature. 2000;408:823-826. Loging WT, Lal A, Siu IM, Loney TL, Wikstrand CJ, Marra MA, Prange C, Bigner DD, Strausberg RL, Riggins GJ. Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening. Genome Res. 2000;10(9):1393-1402. Emmert-Buck MR, Strausberg RL, Krizman DB, Bonaldo MF, Bonner RF, Bostwick DG, Brown MR, Buetow KH, Chuaqui RF, Cole KA, Duray PH, Englert CR, Gillespie JW, Greenhut S, Grouse L, Hillier LW, Katz KS, Klausner RD, Kuznetzov V, Lash AE, Lennon G, Linehan WM, Liotta LA, Marra MA, Munson PJ, Ornstein DK, Prabhu VV, Prange C, Schuler GD, Soares MB, Tolstoshev CM, Vocke CD, Waterston RH. Molecular Profiling of Clinical Tissue Specimens: Feasibility and Applications. Am J Pathol. 2000;156(4):1109-1115. Aamodt E, Shen L, Marra M, Schein J, Rose B and McDermott J. Conservation of sequence and function of the pag-3 genes from C. elegans and C. briggsae. Gene 2000;243:67-74. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium. The complete sequence of a heterochromatic island from a higher eukaryote. Cell 2000;100:377-386. The European Union Arabidopsis Genome Sequencing Consortium, The Cold Spring Harbor, Washington University in St. Louis, and PE Biosystems Arabidopsis Sequencing Consortium. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature. 1999;402:769-776. Copenhaver GP, Nickel K, Kuromori T, Benito M-I, Kaul S, Lin X, Bevan M, Murphy G, Harris B, Parnell LD, McCombie WR, Martienssen RA, Marra M, Preuss D. Genetic definition and sequence analysis of Arabidopsis centromeres. Science. 1999;286:2468-2474. Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE, Marra MA, Prange C, Morin PJ, Polyak N, Papadopoulos N, Vogelstein B, Kinzler KW, Strausberg RL, Riggins GJ. A Public Database for Gene Expression in Human Cancers. Cancer Res. 1999;59: 5403-5407. Ellsworth RE, Ionasescu V, Searby C, Sheffield VC, Braden VV, Kucaba TA, McPherson JD, Marra MA, Green ED. The CMT2D Locus: Refined genetic position, construction of a bacterial-based physical map, and evidence of allelic heterogeneity with distal spinal muscular atrophy. Genome Res. 1999;9:568-574. Marra M, Kucaba T, Sekhon M, Hillier L, Martienssen R, Chinwalla A, Crockett J, Fedele J, Grover H, Gun C, McCombie WR, McDonald K, McPherson J, Mudd N, Parnell L, Schein J, Seim R, Shelby P, Waterston R, Wilson R. A map for sequence analysis of the Arabidopsis thaliana genome. Nat Genet. 1999;22:265-270. Mozo T, Dewar K, Dunn P, Ecker J, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S, Altmann T. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet. 1999;22:271-275. The C. elegans Genome Sequencing Consortium, Washington University Genome Sequencing Center, St. Louis U.S.A. and the Sanger Centre, Hinxton, U.K. How the worm was won: The C. elegans genome sequencing project. Trends Genet. 1999;15:51-58. Marra M, Hillier L, K et al. An encyclopedia of mouse genes. Nat Genet. 1999;21:191-194. Marra MA, Kucaba TA, Hillier LW, Waterston RH. High-throughput plasmid DNA purification for three cents per sample. Nucleic Acids Res. 1999;27:e37 (1-6). Thacker C, Marra MA, Jones A, Baillie DL, Rose AM. Functional genomics in Caenorhabditis elegans: an approach involving comparisons of sequences from related nematodes. Genome Res. 1999;9:348-359. Streit A, Li W, Robertson B, Schein J, Kamal IH, Marra M, Wood WB. Homologs of the Caenorhabditis elegans Masculinizing Gene her-1 in C. briggsae and the Filarial Parasite Brugia malayi. Genetics. 1999;152:1573-1584. Vatcher GP, Barbazuk WB, O'Neil NJ, Marra MA, Ha T, Baillie DL. Identification and characterization of a serine hydroxymethyltransferase isoform in Caenorhabditis briggsae. Gene. 1999;230:137-144. The Sanger Centre and the Washington University Genome Sequencing Center. Toward a complete human genome sequence. Genome Res. 1998; 8:1097-1108. The C. elegans Genome Sequencing Consortium (incl Marra M), Washington University Genome Sequencing Center, St. Louis U.S.A., and the Sanger Center, Hinxton, U.K. Genome sequence of the nematode Caenorhabditis elegans. A platform for investigating biology. Science. 1998;282:2012-2018. Manger ID, Hehl A, Parmley S, Sibley LD, Marra MA. Hillier L, Waterston RH, Boothroyd JC. Expressed sequence tag analysis of the bradyzoite stage of toxoplasma gondii: Identification of developmentally regulated gene. Infect Immun. 1998;66:1632-1637. Ajioka J, Boothroyd JC, Brunk BP, Hehl L, Manger ID, Overton GC, Marra MA. Roos D, Wan KL, Waterston RH, Sibley LD. Gene discovery by EST sequencing to toxoplasma gondii reveals sequences restricted to the apicomplexa. Genome Res. 1998;8:18-28. Marra MA, Hillier L, Waterston RH. Expressed sequence tags - ESTablishing bridges between genomes. Trends Genet. 1998;14:4-7. Marra MA, Kucaba TK, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterston RH. High throughput fingerprint analysis of large-insert clones. Genome Res. 1997;7:1072-1084. Chissoe SL, Marra MA, Hillier L, Brinkman R, Wilson RK, Waterston RH. Representation of cloned genomic sequences in two sequencing vectors: Colleration of DNA sequence and subclone distribution. Nucleic Acids Res. 1997;25:2960-2966. Marra MA, Weinstock LA, Mardis ER. End sequence determination from large insert clones using energy transfer fluorescent primers. Genome Res. 1996;6:1118-1122. Hillier L, Lennon G, Becker M, Bonaldo MF, Chiapelli B, Chissoe S, Dietrich N, DuBuque T, Favello A, Gish W, Hawkins M, Hultman M, Kucaba T, Lacy M, Le M, Le N, Mardis E, Moore B, Morris M, Parsons J, Prange C, Rifkin L, Rohlfing T, Schellenberg K, Soares MB, Tan F, Thierry-Mieg J, Trevaskis E, Underwood K, Wohldman P, Waterston R, Wilson RK, Marra MA. Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 1996 Sep;(6)9:807-828. Marra MA, Baillie DL. Recovery of duplications by drug resistance selection in Caenorhabditis elegans. Genome. 1994;37:701-705. McKim KS. Mathewson C, Marra MA, Wakarchuk MF, Baillie DL. The Caenorhabditis elegans unc-60 gene encodes proteins homologous to a family of actin-binding proteins. Mol Gen Genet. 1994;242:346-357. Schein JE, Marra MA, Benien GM, Fields C, Baillie DL. The use of deficiencies to determine essential gene content in the let-56 - unc-22 region of Caenorhabditis elegans. Genome. 1993;36:1148-1156. Marra MA, Prasad SS, Baillie DL, Molecular analysis of two genes between let-653 in the unc-22(IV) region of C. elegans. Mol Gen Genet. 1993;236:289-298. 2009
2008
2007
2006
2005
2004
2003
2002
2001
2000
1999
1998
1997
1996
1994
1993
Book Chapters
Tucker T, Marra M, Friedman, JM. Massively Parallel Sequencing. Molecular Analysis & Genome Discovery, Second Edition. Edited by Ralph Rapley and Stuart Harbron. 2012 John Wiley & Sons, Ltd. Published 2012 by John Wiley & Sons, Ltd.
Morrissy AS, Zhao YJ, Delaney A, Asano J, Dhalla N, Li I, McDonald H, Pandoh P, Pradhu A-L, Tam A, Hirst M, Marra M. Tag-seq: Next generation tag sequencing for gene expression profiling. 2010. Tag-based Approaches for Next Generation Sequencing. Part 1. Chapter 14. Wiley-VCH, Germany. In press
Morin RD, Zhao YJ, Prabhu AL, Dhalla N, McDonald H, Pandoh P, Tam A, Zeng T, Hirst M, Marra MA. Preparation and Analysis of MicroRNA Libraries Using the Illumina Massively Parallel Sequencing Technology. RNAi and microRNA-Mediated Gene Regulation in Stem Cells. Methods in Molecular Biology, Zhang, Baohong, Stellwag, Edmund J. (Eds.). 1st Edition. 2010 Sep. Vol 650 Section III, pp 173-199.
Morrissy SA, Zhao YJ, Delaney A, Asano J, Dhalla N, Li I, McDonald H, Pandoh P, Prabhu A-L, Tam A, Hirst M, Marra MA. Digital Gene Expression by Tag Sequencing on the Illumina Genome Analyzer. Curr Protoc Hum Genet. 2010 Apr; Chapter 11:Unit 11.11.1-36.
Pugh TJ and Marra MA. Trisomy 9. Encyclopedia of Molecular Mechanisms of Disease. 2008.
Petrescu AS and Marra MA. Genomic approaches for identifying mammalian cis-encoded antisense transcripts. Res Adv Nucleic Acids Res. 2, 2008.
Delaney AD, Qian H, Friedman JM, Marra MA. Use of Affymetrix mapping arrays in the diagnosis of gene copy number variation. Curr Protoc Hum Genet. 2008 Oct; Chapter 8: Unit 8:13.
Griffith M and Marra MA. Alternative expression analysis: Experimental and bioinformatic approaches for the analysis of transcript diversity. Genes, Genomes and Genomics. Thangadurai D, Tang W, Papavassiliou AG, Anupama M (eds), Regency Publications New Delhi, India, 2007; Vol 2, pp. 199-250.
Mathewson CA, Schein JE, Marra MA. Large-scale BAC clone restriction digest fingerprinting. Curr Prot Human Genet. D. Smith (ed) John Wiley and Sons, Inc., Hoboken, NJ, 26 Apr 2007;pp. 5.19.1-5.19.21.
Halaschek-Weiner JV, Marra MA, Brooks-Wilson AR. (2005) Gene Expression Analysis in Pharmacogenetics and Pharmacogenomics. Pharmacogenomics 2nd Edition. Kalow W, Meyer UA, Tyndale RF (eds) Marcel Dekker Inc. New York, USA, Vol. 156, pp. 389-406.
Astell CR, Holt RA, Jones SJM, Marra MA.(2005) Genome Organization and Structural Aspects of the SARS-related Virus. Adv Infect Dis. Schmidt A, Wolff MH, Weber O (eds), Birkhauser Verlag, Basel, Switzerland, Vol. I, pp. 101-128.
Schein J, Kucaba T, Sekhon M, Smailus D, Waterston R, Marra M.(2004) High throughput BAC fingerprinting. Meth Mol Biol. Zhao S, Stodolsky M (eds), Humana Press, Clifton, NJ, Vol. 255, pp. 143-156.