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2008

1. Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM. Text-mining assisted regulatory annotation. Genome Biol. 9(2):R31. Epub 2008 Feb 13. (2008).
    [View Abstract - PubMed 18271954]  Request Paper

2. Chan SK, Griffith OL, Tai IT, Jones SJ. Meta-analysis of colorectal cancer gene expression profiling studies identifies consistently reported candidate biomarkers. Cancer Epidemiol Biomarkers Prev. 17(3):543-52. (2008).
    [View Abstract - PubMed 18349271]  Request Paper

3. 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

4. Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics. 24(15):1729-30. Epub 2008 Jul 3. (2008).
    [View Abstract - PubMed 18599518]  Request Paper

5. 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

6. Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 36(Database issue):D107-13. Epub 2007 Nov 15. (2008).
    [View Abstract - PubMed 18006570]  Request Paper

7. 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

8. Holt RA, Jones SJ. The new paradigm of flow cell sequencing. Genome Res. 18(6):839-46. (2008).
    [View Abstract - PubMed 18519653]  Request Paper

9. Leung SP, Griffith OL, Masoudi H, Gown A, Jones S, Phang T, Wiseman SM. Clinical utility of type 1 growth factor receptor expression in colon cancer. Am J Surg. 195(5):604-10. (2008).
    [View Abstract - PubMed 18424279]  Request Paper

10. 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

11. 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. 2008 Jan 29;9:57. (2008).
     [View Abstract - PubMed 18230180]  Request Paper

12. 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

13. 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

14. Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol. 6(3):e65. (2008).
     [View Abstract - PubMed 18351804]  Request Paper

15. 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).
     [View Abstract - PubMed 18611952]  Request Paper

16. Wiseman SM, Griffith OL, Melck A, Masoudi H, Gown A, Nabi IR, Jones SJ. Evaluation of type 1 growth factor receptor family expression in benign and malignant thyroid lesions. Am J Surg. 195(5):667-73; discussion 673. (2008).
     [View Abstract - PubMed 18424286]  Request Paper

2007

17. DiGuistini S, Ralph SG, Lim YW, Holt R, Jones S, Bohlmann J, Breuil C. Generation and annotation of lodgepole pine and oleoresin-induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a Mountain Pine Beetle-associated pathogen. FEMS Microbiol Lett. 267(2):151-8. (2007).
     [View Abstract - PubMed 17328114]  Request Paper

18. 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

19. 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

20. 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

21. 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. 2007 Aug 2;7:92. (2007).
     [View Abstract - PubMed 17683524]  Request Paper

22. 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

23. 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

24. 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

25. 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. 17(1):108-16. Epub 2006 Nov 29. (2007).
     [View Abstract - PubMed 17135571]  Request Paper

26. 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

27. 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

28. Melck A, Masoudi H, Griffith OL, Rajput A, Wilkins G, Bugis S, Jones SJ, Wiseman SM. Cell cycle regulators show diagnostic and prognostic utility for differentiated thyroid cancer. Ann Surg Oncol. 14(12):3403-11. Epub 2007 Sep 20. (2007).
     [View Abstract - PubMed 17882495]  Request Paper

29. Montgomery SB, Griffith OL, Schuetz JM, Brooks-Wilson A, Jones SJ. A survey of genomic properties for the detection of regulatory polymorphisms. PLoS Comput Biol. 3(6):e106. Epub 2007 Apr 25. (2007).
     [View Abstract - PubMed 17559298]  Request Paper

30. 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

31. 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

32. 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

33. 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

34. Ruzanov P, Jones SJ, Riddle DL. Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data. BMC Genomics. 2007 Nov 30;8:447. (2007).
     [View Abstract - PubMed 18053145]  Request Paper

35. 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. 42(8):825-39. Epub 2007 Apr 21. (2007).
     [View Abstract - PubMed 17543485]  Request Paper

36. 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

37. Warren RL, Sutton GG, Jones SJ, Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 23(4):500-1. Epub 2006 Dec 8. (2007).
     [View Abstract - PubMed 17158514]  Request Paper

38. Wiseman SM, Griffith OL, Deen S, Rajput A, Masoudi H, Gilks B, Goldstein L, Gown A, Jones SJ. Identification of molecular markers altered during transformation of differentiated into anaplastic thyroid carcinoma. Arch Surg. 142(8):717-27; discussion 727-9. (2007).
     [View Abstract - PubMed 17709725]  Request Paper

39. 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 polymerase chain reaction-long serial analysis of gene expression protocol identifies novel transcripts in human CD34+ bone marrow cells. Stem Cells. 25(7):1681-9. Epub 2007 Apr 5. (2007).
     [View Abstract - PubMed 17412892]  Request Paper

2006

40. 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

41. 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. 43(9):655-66. Epub 2006 Jun 21. (2006).
     [View Abstract - PubMed 16793293]  Request Paper

42. Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Armstrong 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

43. 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. 35(6):651-61. Epub 2006 Jun 29. (2006).
     [View Abstract - PubMed 16809635]  Request Paper

44. 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).
     [View Abstract - PubMed 17030794]  Request Paper

45. Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics. 22(5):637-40. Epub 2006 Jan 5. (2006).
     [View Abstract - PubMed 16397004]  Request Paper

46. Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Chow W, 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).
     [View Abstract - PubMed 16672307]  Request Paper

47. 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).
     [View Abstract - PubMed 16626454]  Request Paper

48. 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).
     [View Abstract - PubMed 16898017]  Request Paper

49. Robertson G, Bilenky M, Lin K, He A, Yuen W, Dagpinar M, Varhol R, Teague K, Griffith OL, Zhang X, Pan Y, Hassel M, Sleumer MC, Pan W, Pleasance ED, Chuang M, Hao H, Li YY, Robertson N, Fjell C, Li B, Montgomery SB, Astakhova T, Zhou J, Sander J, Siddiqui AS, Jones SJ. cisRED: a database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res. 34(Database issue):D68-73. (2006).
     [View Abstract - PubMed 16381958]  Request Paper

50. Ruzanov P, Jones SJ. An interactive tool for visualization of relationships between gene expression profiles. BMC Bioinformatics. 2006 Apr 6;7:193. (2006).
     [View Abstract - PubMed 16600045]  Request Paper

51. 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).
     [View Abstract - PubMed 16840527]  Request Paper

52. 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).
     [View Abstract - PubMed 16751804]  Request Paper

53. 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).
     [View Abstract - PubMed 16741162]  Request Paper

54. 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).
     [View Abstract - PubMed 16365383]  Request Paper

2005

55. Bajdik CD, Kuo B, Rusaw S, Jones S, Brooks-Wilson A. CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes. BMC Bioinformatics. 2005 Mar 29;6:78. (2005).
     [View Abstract - PubMed 15796777]  Request Paper

56. 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).
     [View Abstract - PubMed 15916950]  Request Paper

57. Cherkasov A, Shi Z, Li Y, Jones SJ, Fallahi M, Hammond GL. 'Inductive' charges on atoms in proteins: comparative docking with the extended steroid benchmark set and discovery of a novel SHBG ligand. J Chem Inf Model. 45(6):1842-53. (2005).
     [View Abstract - PubMed 16309292]  Request Paper

58. Griffith OL, Pleasance ED, Fulton DL, Oveisi M, Ester M, Siddiqui AS, Jones SJ. Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses. Genomics. 86(4):476-88. (2005).
     [View Abstract - PubMed 16098712]  Request Paper

59. 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).
     [View Abstract - PubMed 15837805]  Request Paper

60. 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).
     [View Abstract - PubMed 16339721]  Request Paper

61. 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).
     [View Abstract - PubMed 15720553]  Request Paper

62. 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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63. Montgomery SB, Fu T, Guan J, Lin K, Jones SJ. An application of peer-to-peer technology to the discovery, use and assessment of bioinformatics programs. Nat Methods. 2(8):563. (2005).
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64. 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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65. 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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66. Snijders AM, Nowak NJ, Huey B, Fridlyand J, Law S, Conroy J, Tokuyasu T, Demir K, Chiu R, Mao JH, Jain AN, Jones SJ, Balmain A, Pinkel D, Albertson DG. Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res. 15(2):302-11. (2005).
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67. Sonnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, Brehm M, Alleaume AM, Artelt J, Bettencourt P, Cassin E, Hewitson M, Holz C, Khan M, Lazik S, Martin C, Nitzsche B, Ruer M, Stamford J, Winzi M, Heinkel R, Roder M, Finell J, Hantsch H, Jones SJ, Jones M, Piano F, Gunsalus KC, Oegema K, Gonczy P, Coulson A, Hyman AA, Echeverri CJ. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature. 434(7032):462-9. (2005).
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68. 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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2004

69. 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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70. 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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71. Cherkasov A, Ho Sui SJ, Brunham RC, Jones SJ. Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics. BMC Bioinformatics. 5:101. (2004).
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72. Cherkasov A, Jones SJ. Structural characterization of genomes by large scale sequence-structure threading. BMC Bioinformatics. 5:37. (2004).
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73. Cherkasov A, Jones SJ. An approach to large scale identification of non-obvious structural similarities between proteins. BMC Bioinformatics. 5:61. (2004).
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74. 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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75. 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).
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76. 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).
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77. 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).
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78. Montgomery SB, Astakhova T, Bilenky M, Birney E, Fu T, Hassel M, Melsopp C, Rak M, Robertson AG, Sleumer M, Siddiqui AS, Jones SJ. Sockeye: a 3D environment for comparative genomics. Genome Res. 14(5):956-62. (2004).
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79. 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).
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80. 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).
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2003

81. 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).
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82. 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).
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83. 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).
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84. Kiger AA, Baum B, Jones S, Jones MR, Coulson A, Echeverri C, Perrimon N. A functional genomic analysis of cell morphology using RNA interference. J Biol. 2(4):27. Epub 2003 Oct 1. (2003).
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85. 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).
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86. 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).
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87. Pleasance ED, Marra MA, Jones SJ. Assessment of SAGE in transcript identification. Genome Res. 13(6A):1203-15. Epub 2003 May 12. (2003).
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88. 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).
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2002

89. Brinkman FS, Blanchard JL, Cherkasov A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BF, Keeling PJ, Rose AM, Hancock RE, Jones SJ, Greberg H. Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Genome Res. 12(8):1159-67. (2002).
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90. 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).
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91. Gregory SG, Sekhon M, Schein J, 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, 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 SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu AL, 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, Marra M, McPherson JD, Bentley DR. A physical map of the mouse genome. Nature. 418(6899):743-50. Epub 2002 Aug 4. (2002).
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92. Guiliano DB, Hall N, Jones SJ, Clark LN, Corton CH, Barrell BG, Blaxter ML. Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes. Genome Biol. 3(10):RESEARCH0057. Epub 2002 Sep 26. (2002).
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93. Hsiao W, Wan I, Jones SJ, Brinkman FS. IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics. 19(3):418-20. (2002).
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94. 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. Blood. 100(3):1075-7. (2002).
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95. McKay SJ, Jones SJ. AcePrimer: automation of PCR primer design based on gene structure. Bioinformatics. 18(11):1538-9. (2002).
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96. Ness SR, Terpstra W, Krzywinski M, Marra MA, Jones SJ. Assembly of fingerprint contigs: parallelized FPC. Bioinformatics. 18(3):484-5. (2002).
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97. Schein JE, Tangen KL, Chiu R, Shin H, Lengeler KB, MacDonald WK, Bosdet I, Heitman J, Jones SJ, Marra MA, Kronstad JW. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res. 12(9):1445-53. (2002).
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98. 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).
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99. Steen BR, Lian T, Zuyderduyn S, MacDonald WK, Marra M, Jones SJ, Kronstad JW. Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Res. 12(9):1386-400. (2002).
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100. 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).
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101. Vatcher G, Smailus D, Krzywinski M, Guin R, Stott J, Tsai M, Chan S, Pandoh P, Yang G, Asano J, Olson T, Prabhu AL, Coope R, Marziali A, Schein J, Jones S, Marra M. Resuspension of DNA sequencing reaction products in agarose increases sequence quality on an automated sequencer. Biotechniques. 33(3):532-4, 536, 538-9. (2002).
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2001

102. Brinkman FS, Wan I, Hancock RE, Rose AM, Jones SJ. PhyloBLAST: facilitating phylogenetic analysis of BLAST results. Bioinformatics. 17(4):385-7. (2001).
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103. 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).
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104. 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, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Kucherlapati, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, Asakawa S, Kawasaki K, Sasaki T, Shintani A, Shimizu A, Shibuya K, Kudoh J, Minoshima S, Ramser J, Seranski P, Hoff C, Poustka A, Reinhardt R, Lehrach H. A physical map of the human genome. Nature. 409(6822):934-41. (2001).
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105. The International Human Genome Mapping Consortium. A physical map of the human genome. Nature 409(6822):934-41. (2001).
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2000

106. Gonczy P, Echeverri G, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume AM, Martin C, Ozlu N, Bork P, Hyman AA. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408(6810):331-6. (2000).
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107. Johnsen RC, Jones SJ, Rose AM. Mutational accessibility of essential genes on chromosome I(left) in Caenorhabditis elegans. Mol Gen Genet 263(2):239-52. (2000).
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108. Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, Kim SK. A global profile of germline gene expression in C. elegans. Mol Cell 6(3):605-16. (2000).
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109. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S. Comparative genomics of the eukaryotes. Science 287(5461):2204-15. (2000).
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110. de Koning AP, Brinkman FS, Jones SJ, Keeling PJ. Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis. Mol Biol Evol 17(11):1769-73. (2000).
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1999

111. Simmen MW, Leitgeb S, Charlton J, Jones SJ, Harris BR, Clark VH, Bird A. Nonmethylated transposable elements and methylated genes in a chordate genome. Science 283(5405):1164-7. (1999).
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112. The C. elegans Sequencing Consortium. . How the worm was won: The C. elegans Sequencing Project. Trends in Genetics 15:51-58 (1999).
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1998

113. The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282(5396):2012-8. (1998).
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114. van Wageningen AM, Kirkpatrick PN, Williams DH, Harris BR, Kershaw JK, Lennard NJ, Jones M, Jones SJ, Solenberg PJ. Sequencing and analysis of genes involved in the biosynthesis of a vancomycin group antibiotic. Chem Biol 5(3):155-62. (1998).
      [View Abstract - PubMed 9545426]  Request Paper

1995

115. Jones SJ. An update and lessons from whole-genome sequencing projects. Curr Opin Genet Dev 5(3):349-53. (1995).
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116. Jones SJ, Baillie DL. Characterization of the let-653 gene in Caenorhabditis elegans. Mol Gen Genet 248(6):719-26. (1995).
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