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2009

1. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigo R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Camara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL Jr, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, More DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH Jr, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 324(5926):522-8. (2009).
    [View Abstract - PubMed 19390049]  Request Paper

2. Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 19(4):657-66. Epub 2009 Jan 30. (2009).
    [View Abstract - PubMed 19181841]  Request Paper

3. Hirst M, Marra MA. Epigenetics and human disease. Int J Biochem Cell Biol. 41(1):136-46. Epub 2008 Sep 24. (2009).
    [View Abstract - PubMed 18852064]  Request Paper

4. Kent DG, Copley MR, Benz C, Wohrer S, Dykstra BJ, Ma E, Cheyne J, Zhao Y, Bowie MB, Zhao Y, Gasparetto M, Delaney A, Smith C, Marra M, Eaves CJ. Prospective isolation and molecular characterization of hematopoietic stem cells with durable self-renewal potential. Blood. 2009 Apr 17. (2009).
    [View Abstract - PubMed 19377048]  Request Paper

5. McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, Gaudet J, Kohara Y, Bossinger O, Zhao Y, Khattra J, Hirst M, Jones SJ, Marra MA, Ruzanov P, Warner A, Zapf R, Moerman DG, Kalb JM. ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev Biol. 327(2):551-65. Epub 2008 Dec 9. (2009).
    [View Abstract - PubMed 19111532]  Request Paper

6. 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. 149A(6):1257-62. (2009).
    [View Abstract - PubMed 19449402]  Request Paper

2008

7. D'Souza CA, Chopra V, Varhol R, Xie Y, Bohacec S, Zhao Y, Lee LL, Bilenky M, Portales-Casamar E, He A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJ. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neurosci. 9(1):66. (2008).
    [View Abstract - PubMed 18625066]  Request Paper

8. Griffith M, Tang MJ, Griffith OL, Morin RD, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Hirst M, Jones SJ, Morin GB, Tai IT, Marra MA. ALEXA: a microarray design platform for alternative expression analysis. Nat Methods. 5(2):118. (2008).
    [View Abstract - PubMed 18235430]  Request Paper

9. Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Beach M, Hoodless PA, Jones SJ, Marra MA, Helgason CD. Identification of transcripts with enriched expression in the developing and adult pancreas. Genome Biol. 9(6):R99. (2008).
    [View Abstract - PubMed 18554416]  Request Paper

10. Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu AL, 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. 18(11):1787-97. Epub 2008 Oct 10. (2008).
     [View Abstract - PubMed 18849523]  Request Paper

11. McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, Gaudet J, Kohara Y, Bossinger O, Zhao Y, Khattra J, Hirst M, Jones SJ, Marra MA, Ruzanov P, Warner A, Zapf R, Moerman DG, Kalb JM. ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult. Dev Biol. 2008 Dec 9. (2008).
     [View Abstract - PubMed 19111532]  Request Paper

12. Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques. 45(1):81-94. (2008).
     [View Abstract - PubMed 18611170]  Request Paper

13. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, 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).
     [View Abstract - PubMed 18285502]  Request Paper

14. Morozova O, Marra MA. From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors. Biochem Cell Biol. 86(2):81-91. (2008).
     [View Abstract - PubMed 18443621]  Request Paper

15. Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics. 92(5):255-64. Epub 2008 Aug 24. (2008).
     [View Abstract - PubMed 18703132]  Request Paper

16. Morozova O, Morozov V, Hoffman BG, Helgason CD, Marra MA. A seriation approach for visualization-driven discovery of co-expression patterns in Serial Analysis of Gene Expression (SAGE) data. PLoS ONE. 2008 Sep 12;3(9):e3205. (2008).
     [View Abstract - PubMed 18787709]  Request Paper

17. Pugh TJ, Delaney AD, Farnoud N, Flibotte S, Griffith M, Li HI, Qian H, Farinha P, Gascoyne RD, Marra MA. Impact of whole genome amplification on analysis of copy number variants. Nucleic Acids Res. 36(13):e80. Epub 2008 Jun 17. (2008).
     [View Abstract - PubMed 18559357]  Request Paper

18. Ralph SG, Chun HJ, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJ, Marra MA, Bohlmann J. Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics. 9(1):57. (2008).
     [View Abstract - PubMed 18230180]  Request Paper

19. Ralph SG, Chun HJ, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Moore R, Barber S, Holt RA, Jones SJ, Marra MA, Douglas CJ, Ritland K, Bohlmann J. A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics. 2008 Oct 14;9:484. (2008).
     [View Abstract - PubMed 18854048]  Request Paper

20. Raouf A, Zhao Y, To K, Stingl J, 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. 3(1):109-18. (2008).
     [View Abstract - PubMed 18593563]  Request Paper

21. Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res. 18(12):1906-17. Epub 2008 Sep 11. (2008).
     [View Abstract - PubMed 18787082]  Request Paper

22. Salvagiotto G, Zhao Y, Vodyanik M, Ruotti V, Stewart R, Marra M, Thomson J, Eaves C, 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. 36(10):1377-89. (2008).
     [View Abstract - PubMed 18922365]  Request Paper

23. Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL, Jones SJ. Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags. BMC Biol. 2008 Jul 8;6:30. (2008).
     [View Abstract - PubMed 18611272]  Request Paper

24. 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 Jul 8. (2008).
     [View Abstract - PubMed 18611952]  Request Paper

25. Zahir FR, Baross A, Delaney AD, Eydoux P, Fernandes ND, Pugh T, Marra MA, Friedman JM. A patient with vertebral, cognitive and behavioural abnormalities and a de novo deletion of NRXN1alpha. J Med Genet. 45(4):239-43. Epub 2007 Dec 5. (2008).
     [View Abstract - PubMed 18057082]  Request Paper

2007

26. 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. 8(1):368. (2007).
     [View Abstract - PubMed 17910767]  Request Paper

27. Etchberger JF, Lorch A, Sleumer MC, 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. 21(13):1653-74. (2007).
     [View Abstract - PubMed 17606643]  Request Paper

28. Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csuros M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prufer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 316(5822):222-34. (2007).
     [View Abstract - PubMed 17431167]  Request Paper

29. Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O'connor MD, Zeng T, Moksa M, Fichter K, Mah D, Go A, Morin RD, Baross A, Zhao Y, Khattra J, Prabhu AL, Pandoh P, McDonald H, Asano J, Dhalla N, Ma K, Lee S, Ally A, Chahal N, Menzies S, Siddiqui A, Holt R, Jones S, Gerhard DS, Thomson JA, Eaves CJ, Marra MA. LongSAGE profiling of nine human embryonic stem cell lines. Genome Biol. 8(6):R113. (2007).
     [View Abstract - PubMed 17570852]  Request Paper

30. Hou J, Charters AM, Lee SC, Zhao Y, Wu MK, Jones SJ, Marra MA, Hoodless PA. A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE). BMC Dev Biol. 7(1):92. (2007).
     [View Abstract - PubMed 17683524]  Request Paper

31. 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. 17(10):1478-85. Epub 2007 Aug 21. (2007).
     [View Abstract - PubMed 17712020]  Request Paper

32. Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastas D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, McKay S, Okada HM, Pan J, Schulz 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 Caenorhabditis elegans. PLoS Biol. 5(9):e237. (2007).
     [View Abstract - PubMed 17850180]  Request Paper

33. Kelleher CT, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin T, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O'connor K, Prabhu AL, 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 SJ, 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. 50(6):1063-78. Epub 2007 May 3. (2007).
     [View Abstract - PubMed 17488239]  Request Paper

34. 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 M. A BAC clone fingerprinting approach to the detection of human genome rearrangements. Genome Biol. 8(10):R224. (2007).
     [View Abstract - PubMed 17953769]  Request Paper

35. Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor 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, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17(6):760-74. (2007).
     [View Abstract - PubMed 17567995]  Request Paper

36. 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 SJ, Moerman DG, Robertson AG. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol. 302(2):627-45. Epub 2006 Oct 21. (2007).
     [View Abstract - PubMed 17113066]  Request Paper

37. 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. J Med Genet. 44(4):264-8. Epub 2007 Jan 12. (2007).
     [View Abstract - PubMed 17220210]  Request Paper

38. 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 SM, 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, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Bloom T, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, MacCallum I, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 447(7141):167-77. (2007).
     [View Abstract - PubMed 17495919]  Request Paper

39. Peng FY, Reid KE, Liao N, Schlosser J, Lijavetzky D, Holt R, Martinez 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 potential roles in berry development. Gene. 402(1-2):40-50. Epub 2007 Jul 31. (2007).
     [View Abstract - PubMed 17761391]  Request Paper

40. 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 HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients. BMC Cancer. 7(1):128. (2007).
     [View Abstract - PubMed 17626639]  Request Paper

41. Quayle SN, Hare H, Delaney AD, Hirst M, Hwang D, Schein JE, Jones SJ, Marra MA, Sadar MD. Novel expressed sequences identified in a model of androgen independent prostate cancer. BMC Genomics. 2007 Jan 26;8:32. (2007).
     [View Abstract - PubMed 17257419]  Request Paper

42. 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. 4(8):651-7. Epub 2007 Jun 11. (2007).
     [View Abstract - PubMed 17558387]  Request Paper

43. Robertson N, Oveisi-Fordorei M, Zuyderduyn SD, Varhol RJ, Fjell C, Marra M, Jones S, Siddiqui A. DiscoverySpace: an interactive data analysis application. Genome Biol. 8(1):R6. (2007).
     [View Abstract - PubMed 17210078]  Request Paper

44. Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Aerts J, 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, Jann O, Jones SJ, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas FW, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TP, Sonstegard TS, Taylor JF, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biol. 8(8):R165. (2007).
     [View Abstract - PubMed 17697342]  Request Paper

45. 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. 9(5):R61. (2007).
     [View Abstract - PubMed 17875215]  Request Paper

46. Zahir F, Firth H, Baross A, Delaney A, Eydoux P, Gibson W, Langlois S, Martin H, Willat L, Marra M, Friedman JM. Novel deletions of 14q11.2 associated with developmental delay, cognitive impairment and similar minor anomalies in three children. J Med Genet. . (2007).
     [View Abstract - PubMed 17545556]  Request Paper

47. Zahir FR, Baross A, Delaney AD, Eydoux P, Fernandes ND, Pugh T, Marra MM, Friedman JM. A patient with vertebral, cognitive and behavioural abnormalities and a de novo deletion of NRXN1{alpha} J Med Genet. . (2007).
     [View Abstract - PubMed 18057082]  Request Paper

48. Zhao Y, Raouf A, Kent D, Khattra J, Delaney A, Schnerch A, Asano J, McDonald 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).
     [View Abstract - PubMed 17412892]  Request Paper

2006

49. Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, Jones SJ. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics. 2006 Sep 29;7:246. (2006).
     [View Abstract - PubMed 17010196]  Request Paper

50. Bakkeren G, Jiang G, Warren RL, 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).
     [View Abstract - PubMed 16793293]  Request Paper

51. Chen N, Mah A, Blacque OE, Chu J, Phgora K, Bakhoum MW, Newbury CR, 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. 7(12):R126. (2006).
     [View Abstract - PubMed 17187676]  Request Paper

52. 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 SJ, 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, Zahir F, Eydoux P, Marra MA. Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet. 79(3):500-13. Epub 2006 Jul 25. (2006).
     [View Abstract - PubMed 16909388]  Request Paper

53. Khattra J, Delaney AD, Zhao Y, Siddiqui A, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Eaves C, Jones S, Holt R, Hirst M, Hoodless PA, Marra MA. Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. Genome Res. . (2006).
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54. Lonergan KM, Chari R, Deleeuw RJ, Shadeo A, Chi B, Tsao MS, 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).
     [View Abstract - PubMed 16809635]  Request Paper

55. 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 SJ, Moerman DG, Robertson AG. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol. . (2006).
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56. McLeod MP, Warren RL, Hsiao WW, 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 SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A. 103(42):15582-7. Epub 2006 Oct 9. (2006).
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57. Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley CP 3rd, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Klein SL, Blakesley RW, Zeeberg BR, Narasimhan S, Weinstein JN, Pennacchio CP, Myers RM, Green ED, Wagner L, Gerhard DS, Marra MA, Jones SJ, Holt RA. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res. 16(6):796-803. Epub 2006 May 3. (2006).
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58. Ralph S, Oddy C, Cooper D, Yueh H, Jancsik S, Kolosova N, Philippe RN, Aeschliman D, White R, Huber D, Ritland CE, Benoit F, Rigby T, Nantel A, Butterfield YS, Kirkpatrick R, Chun E, Liu J, Palmquist D, Wynhoven B, Stott J, Yang G, Barber S, Holt RA, Siddiqui A, Jones SJ, Marra MA, Ellis BE, Douglas CJ, Ritland K, Bohlmann J. Genomics of hybrid poplar (Populus trichocarpax deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences in poplar. Mol Ecol. 15(5):1275-97. (2006).
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59. Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YS, Kirkpatrick R, Liu J, Jones SJ, Marra MA, Douglas CJ, Ritland K, Bohlmann J. Conifer defence against insects: 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. 29(8):1545-70. (2006).
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60. Siddiqui AS, Delaney AD, Schnerch A, Griffith OL, Jones SJ, Marra MA. Sequence biases in large scale gene expression profiling data. Nucleic Acids Res. 2006 Jul 13;34(12):e83. (2006).
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61. Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Belle R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Geneviere AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallbook F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Rottinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning FG, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 314(5801):941-52. (2006).
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62. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 313(5793):1596-604. (2006).
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63. Wang G, Jones SJ, Marra MA, Sadar MD. Identification of genes targeted by the androgen and PKA signaling pathways in prostate cancer cells. Oncogene. 25(55):7311-23. Epub 2006 Jun 5. (2006).
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64. Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang SP, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AS, Marra MA, Wilson RK, Jones SJ. Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res. 16(6):768-75. (2006).
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65. Wilson GM, 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. 16(2):173-81. Epub 2005 Dec 19. (2006).
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2005

66. Blacque OE, Perens EA, Boroevich KA, Inglis PN, Li C, Warner A, Khattra J, Holt RA, Ou G, Mah AK, McKay SJ, Huang P, Swoboda P, Jones SJ, Marra MA, Baillie DL, Moerman DG, Shaham S, Leroux MR. Functional genomics of the cilium, a sensory organelle. Curr Biol. 15(10):935-41. (2005).
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67. 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 details of mammalian chromosome evolution. Proc Natl Acad Sci U S A. 102(51):18526-31. Epub 2005 Dec 9. (2005).
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68. Halaschek-Wiener J, Khattra JS, McKay S, Pouzyrev A, Stott JM, Yang GS, Holt RA, Jones SJ, Marra MA, Brooks-Wilson AR, Riddle DL. Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Res. 15(5):603-15. Epub 2005 Apr 18. (2005).
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69. Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature. 434(7034):724-31. (2005).
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70. Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E, Aert R, Anupama A, Apostolou Z, Attipoe P, Bason N, Bauser C, Beck A, Beverley SM, Bianchettin G, Borzym K, Bothe G, Bruschi CV, Collins M, Cadag E, Ciarloni L, Clayton C, Coulson RM, Cronin A, Cruz AK, Davies RM, De Gaudenzi J, Dobson DE, Duesterhoeft A, Fazelina G, Fosker N, Frasch AC, Fraser A, Fuchs M, Gabel C, Goble A, Goffeau A, Harris D, Hertz-Fowler C, Hilbert H, Horn D, Huang Y, Klages S, Knights A, Kube M, Larke N, Litvin L, Lord A, Louie T, Marra M, Masuy D, Matthews K, Michaeli S, Mottram JC, Muller-Auer S, Munden H, Nelson S, Norbertczak H, Oliver K, O'neil S, Pentony M, Pohl TM, Price C, Purnelle B, Quail MA, Rabbinowitsch E, Reinhardt R, Rieger M, Rinta J, Robben J, Robertson L, Ruiz JC, Rutter S, Saunders D, Schafer M, Schein J, Schwartz DC, Seeger K, Seyler A, Sharp S, Shin H, Sivam D, Squares R, Squares S, Tosato V, Vogt C, Volckaert G, Wambutt R, Warren T, Wedler H, Woodward J, Zhou S, Zimmermann W, Smith DF, Blackwell JM, Stuart KD, Barrell B, Myler PJ. The genome of the kinetoplastid parasite, Leishmania major. Science. 309(5733):436-42. (2005).
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71. Larraya LM, Boyce KJ, So A, Steen BR, Jones S, Marra M, Kronstad JW. Serial analysis of gene expression reveals conserved links between protein kinase A, ribosome biogenesis, and phosphate metabolism in Ustilago maydis. Eukaryot Cell. 4(12):2029-43. (2005).
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72. Lian T, Simmer MI, D'Souza CA, Steen BR, Zuyderduyn SD, Jones SJ, Marra MA, Kronstad JW. Iron-regulated transcription and capsule formation in the fungal pathogen Cryptococcus neoformans. Mol Microbiol 55(5):1452-72. (2005).
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73. Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science. 307(5713):1321-4. Epub 2005 Jan 13. (2005).
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74. Ng SH, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJ, 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. 86(4):396-404. (2005).
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75. Pavy N, Paule C, Parsons L, Crow JA, Morency MJ, 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. 6:144. (2005).
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76. Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, Brown-John M, Chand S, Charest D, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA, Hou J, Kuo BY, Lee LL, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu AL, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie YY, Yang G, Zhang I, Hirst M, Jones SJ, Helgason CD, Simpson EM, Hoodless PA, Marra MA. A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A. 102(51):18485-90. Epub 2005 Dec 13. (2005).
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77. Smailus DE, Marziali A, Dextras P, Marra MA, Holt RA. Simple, robust methods for high-throughput nanoliter-scale DNA sequencing. Genome Res. 15(10):1447-50. Epub 2005 Sep 16. (2005).
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78. Warren RL, Butterfield YS, Morin RD, Siddiqui AS, Marra MA, Jones SJ. Management and visualization of whole genome shotgun assemblies using SAM. Biotechniques. 38(5):715-6, 718, 720. (2005).
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79. Yang GS, Stott JM, Smailus D, Barber SA, Balasundaram M, Marra MA, Holt RA. High-throughput sequencing: a failure mode analysis. BMC Genomics 6(1):2. (2005).
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2004

80. Anglesio MS, Evdokimova V, Melnyk N, Zhang L, Fernandez CV, Grundy PE, Leach S, Marra MA, Brooks-Wilson AR, Penninger J, Sorensen PH. Differential expression of a novel ankyrin containing E3 ubiquitin-protein ligase, Hace1, in sporadic Wilms' tumour versus normal kidney. Hum Mol Genet . (2004).
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81. Baross A, Butterfield YS, Coughlin SM, Zeng T, Griffith M, Griffith OL, Petrescu AS, Smailus DE, Khattra J, McDonald HL, McKay SJ, Moksa M, Holt RA, Marra MA. Systematic recovery and analysis of full-ORF human cDNA clones. Genome Res 14(10B):2083-92. (2004).
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82. Baross A, Schertzer M, Zuyderduyn SD, Jones SJ, Marra MA, Lansdorp PM. Effect of TERT and ATM on gene expression profiles in human fibroblasts. Genes Chromosomes Cancer 39(4):298-310. (2004).
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83. Flibotte S, Chiu R, Fjell C, Krzywinski M, Schein JE, Shin H, Marra MA. Automated ordering of fingerprinted clones. Bioinformatics 20(8):1264-71. Epub 2004 Feb 10. (2004).
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84. Henderson LJ, Okamoto I, Lestou VS, Ludkovski O, 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 bacterial artificial chromosome contig spanning a 6-megabase region of 6q16-q21. Genes Chromosomes Cancer 40(1):60-5. (2004).
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85. Hirst M, Astell CR, 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 SA, Goh S, Brunham RC, Robinson J, Bowes V, Sojonky K, Byrne SK, Li Y, Kobasa D, Booth T, Paetzel M. Novel avian influenza H7N3 strain outbreak, British Columbia. Emerg Infect Dis. 10(12):2192-5. (2004).
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86. Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Ling V, MacAulay C, Lam WL. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36(3):299-303. Epub 2004 Feb 15. (2004).
     [View Abstract - PubMed 14981516]  Request Paper

87. Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Girn N, Lee D, Masson A, Mayo M, Olson T, Pandoh P, Prabhu AL, Schoenmakers E, Tsai M, Albertson D, Lam W, Choy CO, Osoegawa K, Zhao S, de Jong PJ, Schein J, Jones S, Marra MA. A set of BAC clones spanning the human genome. Nucleic Acids Res 2004 Jul 9;32(12):3651-60. Print 2004. (2004).
     [View Abstract - PubMed 15247347]  Request Paper

88. Krzywinski M, Wallis J, Gosele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, Albracht D, Asano J, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Davito J, Fjell C, Gaige T, Ganten D, Girn N, Guggenheimer K, Himmelbauer H, Kreitler T, Leach S, Lee D, Lehrach H, Mayo M, Mead K, Olson T, Pandoh P, Prabhu AL, Shin H, Tanzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, Zimdahl H, Marziali A, Osoegawa K, Zhao S, Siddiqui A, de Jong PJ, Warren W, Mardis E, McPherson JD, Wilson R, Hubner N, Jones S, Marra M, Schein J. Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res. 14(4):766-79. (2004).
     [View Abstract - PubMed 15060021]  Request Paper

89. 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. 125(5 Suppl):97S. (2004).
     [View Abstract - PubMed 15136435]  Request Paper

90. Rat Genome Sequencing Project Consortium (including Marra M). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982):493-521. (2004).
     [View Abstract - PubMed 15057822]  Request Paper

91. 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 SR, Smailus DE, Jones SJ, Schein JE, Marra MA, Butterfield YS, Stott JM, Ng SH, Davidson WS, Koop BF. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res. 14(3):478-90. Epub 2004 Feb 12. (2004).
     [View Abstract - PubMed 14962987]  Request Paper

92. Schein J, Kucaba T, Sekhon M, Smailus D, Waterston R, Marra M. High-throughput BAC fingerprinting. Methods Mol Biol. 255:143-56. (2004).
     [View Abstract - PubMed 15020821]  Request Paper

93. The ENCODE Project Consortium (including Marra M). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306(5696):636-40. (2004).
     [View Abstract - PubMed 15499007]  Request Paper

94. The MGC Project Team (including Marra M). The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res 14(10B):2121-7. (2004).
     [View Abstract - PubMed 15489334]  Request Paper

95. Warren R, Hsiao WW, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield YS, Siddiqui A, Holt R, Marra MA, Jones SJ, Mohn WW, Brinkman FS, Fukuda M, Davies J, Eltis LD. Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. J Bacteriol. 186(22):7783-95. (2004).
     [View Abstract - PubMed 15516593]  Request Paper

2003

96. Boon K, Edwards JB, Siu IM, 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. 22(48):7687-94. (2003).
     [View Abstract - PubMed 14576832]  Request Paper

97. Fjell CD, Bosdet I, Schein JE, Jones SJ, Marra MA. Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps. Genome Res 13(6A):1244-9. (2003).
     [View Abstract - PubMed 12799356]  Request Paper

98. Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LW, Waterston RH, McPherson JD, Jones SJ, Marra MA. Software for automated analysis of DNA fingerprinting gels. Genome Res 13(5):940-53. (2003).
     [View Abstract - PubMed 12727910]  Request Paper

99. Gorski SM, Chittaranjan S, Pleasance ED, Freeman JD, Anderson CL, Varhol RJ, Coughlin SM, Zuyderduyn SD, Jones SJ, Marra MA. A SAGE approach to discovery of genes involved in autophagic cell death. Curr Biol 13(4):358-63. (2003).
     [View Abstract - PubMed 12593804]  Request Paper

100. Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK. The DNA sequence of human chromosome 7. Nature. 424(6945):157-64. (2003).
      [View Abstract - PubMed 12853948]  Request Paper

101. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, Khattra J, Asano JK, Barber SA, Chan SY, Cloutier A, Coughlin SM, Freeman D, Girn N, Griffith OL, Leach SR, Mayo M, McDonald H, Montgomery SB, Pandoh PK, Petrescu AS, Robertson AG, Schein JE, Siddiqui A, Smailus DE, Stott JM, Yang GS, Plummer F, Andonov A, Artsob H, Bastien N, Bernard K, Booth TF, Bowness D, Czub M, Drebot M, Fernando L, Flick R, Garbutt M, Gray M, Grolla A, Jones S, Feldmann H, Meyers A, Kabani A, Li Y, Normand S, Stroher U, Tipples GA, Tyler S, Vogrig R, Ward D, Watson B, Brunham RC, Krajden M, Petric M, Skowronski DM, Upton C, Roper RL. The Genome sequence of the SARS-associated coronavirus. Science 300(5624):1399-404. Epub 2003 May 1. (2003).
      [View Abstract - PubMed 12730501]  Request Paper

102. 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 SJ, Kai H, Li D, Mah A, Marra M, McGhee J, Newbury R, Pouzyrev A, Riddle DL, Sonnhammer E, Tian H, Tu D, Tyson JR, Vatcher G, Warner A, Wong K, Zhao Z, Moerman DG. Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans. Cold Spring Harb Symp Quant Biol. 68:159-69. (2003).
      [View Abstract - PubMed 15338614]  Request Paper

103. Moore SS, Hansen C, Williams JL, Fu A, Meng Y, Li C, Zhang Y, Urquhart BS, Marra M, Schein J, Benkel B, de Jong PJ, Osoegawa K, Kirkpatrick BW, Gill CA. 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 102(1-4):32-8. (2003).
      [View Abstract - PubMed 14970675]  Request Paper

104. Pleasance ED, Marra MA, Jones SJ. Assessment of SAGE in transcript identification. Genome Res 13(6A):1203-15. Epub 2003 May 12. (2003).
      [View Abstract - PubMed 12743019]  Request Paper

105. Steen BR, Zuyderduyn S, Toffaletti DL, Marra M, Jones SJ, Perfect JR, Kronstad J. Cryptococcus neoformans gene expression during experimental cryptococcal meningitis. Eukaryot Cell 2(6):1336-49. (2003).
      [View Abstract - PubMed 14665467]  Request Paper

106. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 1(2):E45. Epub 2003 Nov 17. (2003).
      [View Abstract - PubMed 14624247]  Request Paper

2002

107. Butterfield YS, Marra MA, Asano JK, Chan SY, Guin R, Krzywinski MI, Lee SS, MacDonald KW, Mathewson CA, Olson TE, Pandoh PK, Prabhu AL, Schnerch A, Skalska U, Smailus DE, Stott JM, Tsai MI, Yang GS, Zuyderduyn SD, Schein JE, Jones SJ. An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones. Nucleic Acids Res 30(11):2460-8. (2002).
      [View Abstract - PubMed 12034834]  Request Paper

108. Gorski S, Marra M. Programmed cell death takes flight: genetic and genomic approaches to gene discovery in Drosophila. Physiol Genomics 9(2):59-69. (2002).
      [View Abstract - PubMed 12006672]  Request Paper

109. Gregory SG, Sekhon M, Marra M, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Schein J, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee S, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu A, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, McPherson JD, and Bentley DR.. A physical map of the mouse genome. Nature, 2002;418:743-50. (2002).
      Request Paper

110. 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;100-1075-7. (2002).
      Request Paper

111. Ness SR, Terpstra W, Krzywinski M, Marra MA, Jones SJ. Assembly of fingerprint contigs: parallelized FPC. Bioinformatics 18(3):484-5. (2002).
      [View Abstract - PubMed 11934749]  Request Paper

112. 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 Research, 2002;12:1445-53. (2002).
      Request Paper

113. Shevchenko Y, Bouffard GG, Butterfield YS, Blakesley RW, Hartley JL, Young AC, Marra MA, Jones SJ, Touchman JW, Green ED. Systematic sequencing of cDNA clones using the transposon Tn5. Nucleic Acids Res 30(11):2469-77. (2002).
      [View Abstract - PubMed 12034835]  Request Paper

114. Steen BR, Lian T, Zuyderduyn S, MacDonald K, Marra M, Jones SJM, Kronstad JW. Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Research, 2002;12:1386-400. (2002).
      Request Paper

115. Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Marra MA. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A. 99(26):16899-903. Epub 2002 Dec 11. (2002).
      [View Abstract - PubMed 12477932]  Request Paper

116. 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, and 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, 538-9. (2002).
      Request Paper

2001

117. Cai WW, Chow CW, Damani S, Gregory SG, Marra M, Bradley A. An SSLP marker-anchored BAC framework map of the mouse genome. Nat Genet 29(2):133-4. (2001).
      [View Abstract - PubMed 11586294]  Request Paper

118. Clark MD, Hennig S, Herwig R, Clifton SW, Marra MA, Lehrach H, Johnson SL, Group tW. An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library. Genome Res 11(9):1594-602. (2001).
      [View Abstract - PubMed 11544204]  Request Paper

119. Gower NJ, 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 306(2):145-57. (2001).
      [View Abstract - PubMed 11237590]  Request Paper

120. Jones SJ, Riddle DL, 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 Caenorhabditis elegans. Genome Res 11(8):1346-52. (2001).
      [View Abstract - PubMed 11483575]  Request Paper

121. McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, et al. A physical map of the human genome. Nature 409(6822):934-41. (2001).
      [View Abstract - PubMed 11237014]  Request Paper

122. The International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409(6822):860-921. (2001).
      [View Abstract - PubMed 11237011]  Request Paper

123. Wendl MC, Marra MA, Hillier LW, Chinwalla AT, Wilson RK, Waterston RH. Theories and applications for sequencing randomly selected clones. Genome Res 11(2):274-80. (2001).
      [View Abstract - PubMed 11157790]  Request Paper

2000

124. Aamodt E, Shen L, Marra M, Schein J, Rose B, McDermott JB. Conservation of sequence and function of the pag-3 genes from C. elegans and C. briggsae. Gene 243(1-2):67-74. (2000).
      [View Abstract - PubMed 10675614]  Request Paper

125. 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 156(4):1109-15. (2000).
      [View Abstract - PubMed 10751334]  Request Paper

126. 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 408(6814):823-6. (2000).
      [View Abstract - PubMed 11130714]  Request Paper

127. 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 10(9):1393-402. (2000).
      [View Abstract - PubMed 10984457]  Request Paper

128. Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T, Hosouchi T, Kawashima K, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Naruo K, Okumura S, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Sato S, de la Bastide M, Huang E, Spiegel L, Gnoj L, O'Shaughnessy A, Preston R, Habermann K, Murray J, Johnson D, Rohlfing T, Nelson J, Stoneking T, Pepin K, Spieth J, Sekhon M, Armstrong J, Becker M, Belter E, Cordum H, Cordes M, Courtney L, Courtney W, Dante M, Du H, Edwards J, Fryman J, Haakensen B, Lamar E, Latreille P, Leonard S, Meyer R, Mulvaney E, Ozersky P, Riley A, Strowmatt C, Wagner-McPherson C, Wollam A, Yoakum M, Bell M, Dedhia N, Parnell L, Shah R, Rodriguez M, See LH, Vil D, Baker J, Kirchoff K, Toth K, King L, Bahret A, Miller B, Marra M, Martienssen R, McCombie WR, Wilson RK, Murphy G, Bancroft I, Volckaert G, Wambutt R, Dusterhoft A, Stiekema W, Pohl T, Entian KD, Terryn N, Hartley N, Bent E, Johnson S, Langham SA, McCullagh B, Robben J, Grymonprez B, Zimmermann W, Ramsperger U, Wedler H, Balke K, Wedler E, Peters S, van Staveren M, Dirkse W, Mooijman P, Lankhorst RK, Weitzenegger T, Bothe G, Rose M, Hauf J, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Villarroel R, Gielen J, Ardiles W, Bents O, Lemcke K, Kolesov G, Mayer K, Rudd S, Schoof H, Schueller C, Zaccaria P, Mewes HW, Bevan M, Fransz P. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature. 408(6814):823-6. (2000).
      [View Abstract - PubMed 11130714]  Request Paper

129. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796-815. (2000).
      [View Abstract - PubMed 11130711]  Request Paper

130. 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 100(3):377-86. (2000).
      [View Abstract - PubMed 10676819]  Request Paper

1999

131. Copenhaver GP, Nickel K, Kuromori T, Benito MI, 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 286(5449):2468-74. (1999).
      [View Abstract - PubMed 10617454]  Request Paper

132. Ellsworth RE, Ionasescu V, Searby C, Sheffield VC, Braden VV, Kucaba TA, McPherson JD, Marra MA, Green ED. The CMT2D locus: refined genetic position and construction of a bacterial clone-based physical map. Genome Res 9(6):568-74. (1999).
      [View Abstract - PubMed 10400924]  Request Paper

133. Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE, Marra MA, Prange C, Morin PJ, Polyak K, Papadopoulos N, Vogelstein B, Kinzler KW, Strausberg RL, Riggins GJ. A public database for gene expression in human cancers. Cancer Res 59(21):5403-7. (1999).
      [View Abstract - PubMed 10554005]  Request Paper

134. Marra M, Hillier L, Kucaba T, Allen M, Barstead R, Beck C, Blistain A, Bonaldo M, Bowers Y, Bowles L, Cardenas M, Chamberlain A, Chappell J, Clifton S, Favello A, Geisel S, Gibbons M, Harvey N, Hill F, Jackson Y, Kohn S, Lennon G, Mardis E, Martin J, Waterston R, et al.. An encyclopedia of mouse genes. Nat Genet 21(2):191-4. (1999).
      [View Abstract - PubMed 9988271]  Request Paper

135. Marra M, Kucaba T, Sekhon M, Hillier L, Martienssen R, Chinwalla A, Crockett J, Fedele J, Grover H, Gund 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 22(3):265-70. (1999).
      [View Abstract - PubMed 10391214]  Request Paper

136. Marra MA, Kucaba TA, Hillier LW, Waterston RH. High-throughput plasmid DNA purification for 3 cents per sample. Nucleic Acids Res 27(24):e37. (1999).
      [View Abstract - PubMed 10572189]  Request Paper

137. Mozo T, Dewar K, Dunn P, Ecker JR, 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 22(3):271-5. (1999).
      [View Abstract - PubMed 10391215]  Request Paper

138. 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 152(4):1573-84. (1999).
      [View Abstract - PubMed 10430584]  Request Paper

139. 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 9(4):348-59. (1999).
      [View Abstract - PubMed 10207157]  Request Paper

140. 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 15(2):51-8. (1999).
      [View Abstract - PubMed 10098407]  Request Paper

141. 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 230(2):137-44. (1999).
      [View Abstract - PubMed 10216251]  Request Paper

1998

142. Ajioka JW, Boothroyd JC, Brunk BP, Hehl A, Hillier L, Manger ID, Marra M, Overton GC, Roos DS, Wan KL, Waterston R, Sibley LD. Gene discovery by EST sequencing in Toxoplasma gondii reveals sequences restricted to the Apicomplexa. Genome Res 8(1):18-28. (1998).
      [View Abstract - PubMed 9445484]  Request Paper

143. Manger ID, Hehl A, Parmley S, Sibley LD, Marra M, Hillier L, Waterston R, Boothroyd JC. Expressed sequence tag analysis of the bradyzoite stage of Toxoplasma gondii: identification of developmentally regulated genes. Infect Immun 66(4):1632-7. (1998).
      [View Abstract - PubMed 9529091]  Request Paper

144. Marra MA, Hillier L, Waterston RH. Expressed sequence tags--ESTablishing bridges between genomes. Trends Genet. 14(1):4-7. (1998).
      [View Abstract - PubMed 9448457]  Request Paper

145. The C. elegans Genome Sequencing Consortium, Washington University Genome Sequencing Center, St. Louis, U.S.A. and the Sanger Centre, Hinxton, U.K. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282(5396):2012-18. (1998).
      [View Abstract - PubMed 9851916]  Request Paper

146. The Sanger Centre and the Washington University Genome Sequencing Center. Toward a complete human genome sequence. Genome Res 8(11):1097-108. (1998).
      [View Abstract - PubMed 9847074]  Request Paper

1997

147. Chissoe SL, Marra MA, Hillier L, Brinkman R, Wilson RK, Waterston RH. Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution. Nucleic Acids Res 25(15):2960-6. (1997).
      [View Abstract - PubMed 9224593]  Request Paper

148. Marra MA, Kucaba TA, 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 7(11):1072-84. (1997).
      [View Abstract - PubMed 9371743]  Request Paper

1996

149. Hillier LD, 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, Marra M, et al.. Generation and analysis of 280,000 human expressed sequence tags. Genome Res 6(9):807-28. (1996).
      [View Abstract - PubMed 8889549]  Request Paper

150. Marra M, Weinstock LA, Mardis ER. End sequence determination from large insert clones using energy transfer fluorescent primers. Genome Res 6(11):1118-22. (1996).
      [View Abstract - PubMed 8938436]  Request Paper

1994

151. Marra MA, Baillie DL. Recovery of duplications by drug resistance selection in Caenorhabditis elegans. Genome 37(4):701-5. (1994).
      [View Abstract - PubMed 7958827]  Request Paper

152. McKim KS, Matheson 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 242(3):346-57. (1994).
      [View Abstract - PubMed 8107682]  Request Paper

1993

153. Marra MA, Prasad SS, Baillie DL. Molecular analysis of two genes between let-653 and let-56 in the unc-22(IV) region of Caenorhabditis elegans. Mol Gen Genet 236(2-3):289-98. (1993).
      [View Abstract - PubMed 8382340]  Request Paper

154. Schein JE, Marra MA, Benian 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 36(6):1148-56. (1993).
      [View Abstract - PubMed 8112575]  Request Paper

155. . ().
      [View Abstract - PubMed 19111532]  Request Paper

2008

1. 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. Chapter 8:Unit 8.13. (2008).
    [View Abstract - PubMed 18972373]  Request Paper