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Steven Jones Publications

by Becky Gillespie — last modified Nov 24, 2009 10:26 AM
Steven Jones' Complete Bibliography
  1. Nielsen CB, Jackman SD, Birol I, Jones SJ. AbySS-Explorer: Visualizing Genome Sequence Assemblies. IEEE Trans Vis Comput. Graph. 2009 Nov-Dec; 15(6):881-8.
  2. The MGC Project Team including: Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJM, Holt RA, Marra MA. The Completion of the Mammilian Gene Collection (MGC). Genome Research. 2009 Oct. 28. [Epub ahead of print].
  3. Romanuik T, Wang G, Holt RA, Jones SJM, Marra MA, Sadar MD. Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries. BMC Genomics. 2009 Oct. 15;10:476.
  4. Shah SP, Morin R, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, Steidl C, Holt RA, Jones SJ, Sun M, Leung G, Moore R, Severson T, Taylor G, Teschendorff AE, Tse K, Turashvili G, Varhol R, Warren RL, Watson P, Zhao YJ, Caldas C, Huntsman D, Hirst M, Marra MA, Aparicio S. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009 Oct. 8;461(7265):809-13.
  5. DiGuistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJM. De novo assembly of a genome sequence for the filamentous fungus, Grosmannia clavigera, assembled using Sanger, 454 and Illumina sequence data. Genome Biology. 2009 Sep 11;10(9):R94. [Epub ahead of print]. PMID: 19747388.
  6. Deen S, Griffith OL, Masoudi H, Gown A, Jones SJ, Wiseman SM. Anaplastic thyroid carcinoma exhibits intratumoral molecular homogeneity for a therapeutic target panel. Anticancer Research. 2009 Jul;29(7):2437-44.
  7. Meissner B, Warner A, Wong K, Dube N, Lorch A, McKay SJ, Khattra J, Rogalski T, Somasiri A, Chaudhry I, Fox RM, Miller DM, Baillie DL, Holt RA, Jones SJM, Marra MA, Moerman DG. An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genetics. 2009 Jun;5 (6):e1000537. Epub 2009 Jun 26.
  8. Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Zhao YJ, Hirst M, Jones S, Marra MA. Next generation tag sequencing for cancer gene expression profiling. Genome Research. 2009 Oct;19(10):1825-35. Epub 2009 Jun 18.
  9. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra M. Circos: an Information Aesthetic for Comparative Genomics. Genome Research. 2009 Sep;19(9):1639-45. 2009 Jun 18. [Epub ahead of print].
  10. Birol I, Jackman SD, Nielsen C, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJ. De novo Transcriptome Assembly with ABySS. Bioinformatics. 2009 Nov 1;25(21):2872-7. 2009 Jun 15. [Epub ahead of print].
  11. Shah SP, Köbel M, Senz J, Morin RD, Clarke BA, Wiegand KC, Leung G, Zayed A, Mehl E, Kalloger SE, Sun M, Giuliany R, Yorida E, Jones S, Varhol R, Swenerton KD, Miller D, Clement PB, Crane C, Madore J, Provencher D, Leung P, DeFazio A, Khattra J, Turashvili G, Zhao Y, Zeng T, Glover JN, Vanderhyden B, Zhao C, Parkinson CA, Jimenez-Linan M, Bowtell DD, Mes-Masson AM, Brenton JD, Aparicio SA, Boyd N, Hirst M, Gilks CB, Marra M, Huntsman DG. Mutation of the FOXL2 Gene in Granulosa Cell Tumors of the Ovary. New England Journal of Medicine. 2009 June 10; 360(26): 2719-29. [Epub ahead of print].
  12. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: A parallel assembler for short read sequence data. Genome Research. 2009 Jun;19(6):1117-23. Epub 2009 Feb 27.
  13. An J, Lee DC, Law AH, Yang CL, Poon LL, Lau AS, Jones SJ. A novel small-molecule inhibitor of the avian influenza H5N1 virus determined through computational screening against the neuraminidase. Journal of Medicinal Chemistry. 2009 May 14;52(9):2667-72.
  14. Wang X, Zhao YJ, Wong K, Ehlers P, Kohara Y, Jones SJ, Marra MA, Holt RA, Moerman DG, Hansen D. Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE. BMC Genomics. 2009 May 9;10(1):213. [Epub ahead of print]
  15. Bovine Genome Sequencing and Analysis Consortium, et al, including Holt RA, Jones SJ, Marra MA, Moore R, Schein JE, The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24;324 (5926):522-8.
  16. Sleumer MC, Bilenky M, He A, Robertson AG, Jones SJM. C. elegans cisRED: A catalogue of conserved genomic elements. Nucleic Acids Research. 2009 Jan 16. [Epub ahead of print].
  17. Malhis N, Butterfield YS, Ester M, Jones SJ. Slider--maximum use of probability information for alignment of short sequence reads and SNP detection. Bioinformatics 2009 Jan 1;25(1):6-13.
  18. McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, Gaudet J, Kohara Y, Bossinger O, Zhao YJ, 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. Developmental Biology. 2008 Dec 9. [Epub ahead of print].
  19. Robertson GA, Bilenky M, Tam A, Zhao YJ, 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 SJM. Genome wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding. Genome Research. (18) 1906-1917 Sept. 2008.
  20. 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(1):484. [Epub ahead of print]
  21. Joshi B, Strugnell S, Goetz JG, Kojic LD, Cox ME, Griffith OL, Jones S, Leung S, Masoudi H, Leung S, Wiseman SM, Nabi IR. Phospho-caveolin-1 regulates Rho/ROCK-dependent focal adhesion dynamics and tumor cell migration. Cancer Research. 2008 Oct 15;68(20):8210-20.
  22. Morin RD, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh TJ, McDonald H, Varhol R, Jones SJM, Marra MA. (first 2 are first co-authors) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques. 2008 Jul ;45(1):81-94.
  23. D’Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao YJ, Lee LC, Bilenky M, Portales-Casamar E, he A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJM. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neuroscience. 2008 Jul 14; 9(1):66. [Epub ahead of print]
  24. Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL. Jones SJ. Transcriptome analysis for Caenorhabiditis elegans based on novel expressed sequence tags. BMC Biology. 2008 Jul 8;6:30.
  25. Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao YJ, 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 Research. 2008 Aug;36(14):4549-64. 2008 Jul 8. [Epub ahead of print]
  26. Raouf A, Zhao Y, 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. 2008 Jul 3; 3(1);109-18.
  27. Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJM. FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short read sequencing technology. Bioinformatics. 2008 Aug 1;24(15):1729-30. 2008 Jul 3. [Epub ahead of print].
  28. Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Beach M, Hoodless PA, Jones S, Marra MA, Helgason CD. Identification of Transcripts with Enriched Expression in the Developing and Adult Pancreas. Genome Biology. 2008 June 14;9(6):R99. [Epub ahead of print].
  29. Liang B, Luo M, Ball TB, Yao X, van Domselaar G, Cuff WR, Cheang M, Jones SJM, Plummer FA. Systematic Analysis of host immunological pressure on the envelope gene of human immunodeficiency virus type 1 by an immunological approach. Current HIV Research. 2008 Jun;6(4):370-9.
  30. Leung SP, Griffith OL, Masoudi H, Gown A, Jones SJ, Phang T, Wiseman SM. Clinical Utility of Type 1 Growth Factor Receptor Expression by Colon Cancer. The American Journal of Surgery. 2008 May;195(5):604-10.>
  31. Wiseman SM, Griffith OL, Melck A, Masoudi H, Gown A, Nabi IR, Jones SJM. Evaluation of type 1 growth factor receptor family expression in benign and malignant thyroid lesions. The American Journal of Surgery. 2008 May;195(5):667-73.
  32. Shivaswamy S, Bhinge A, Zhao Y, Jones SJM, Hirst M, Iyer VR. Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation. PLoS Biology. 2008 Mar 18;6(3):e65 [Epub ahead of print]
  33. Chan SK, Griffith OL, Tai IT, Jones SJM. Meta-Analysis of Colorectal Cancer Gene Expression Profiling Studies Identifies Consistently Reported Candidate Biomarkers. Cancer Epidemiol Biomarkers Prev. 2008 Mar;17(3):543–52.
  34. Aerts S, Haeussler M, Griffith OL, van Vooren S, Jones SJM, Montgomery SB, Bergman CM, The Open Regulatory Annotation Consortium. Text-mining assisted regulatory annotation. Genome Biology. 2008 Feb 13;9(2):R31 [Epub ahead of print].
  35. Griffith M, Tang MJ, Griffith OL, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Morin RD, Hirst M, Jones SJM, Morin GB, Tai IT and Marra MA. ALEXA – A microarray design platform for alternative expression analysis. Nature Methods. 2008 Feb;5(2):118.
  36. 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(1):57 [Epub ahead of print]
  37. Kneller JM, Ehlen T, Matisic JP, Miller D, van Niekerk D, Lam WL, Marra M, Richards-Kortum R, Follen M, MacAulay C, Jones SJM. Using longSAGE to detect biomarkers of cervical cancer potentially amenable to optical contrast agent labelling. Biomarker Insights. 2007 Dec 11;2:447-61.
  38. Griffith OL, Montgomery SB, Bernier B, Chu B, Aerts S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Mahony S, 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 SJM; The Open Regulatory Annotation Consortium. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research. 2008 Jan: 36(Database Issue):D107-13. Epub 2007 Nov. 15.
  39. Quayle AP, Siddiqui AS, Jones SJM. Perturbation of Interaction Networks for Application to Cancer Therapy. Cancer Informatics.(Edition: Systems Biology Special Issue) 2007: (2) 45-65.
  40. 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.
  41. 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 EST’s in Vitis vinifera Wine Grape (Cabernet Sauvingnon) and Table Grape (Muscat Hamburg) and discovery of new candidate genes with possible roles in berry development. Gene. 2007 Nov 1 ;402 (1-2) :40-50. Epub 2007 Jul 31.
  42. Krzywinski MI, Bosdet I, Mathewson C, Wye N, Brebner J, Chiu R, Corbett R, Field M, Lee D, Pugh T, Volik S, Siddiqui AS, Jones SJM, Schein JE, Collins C, Marra A. A BAC clone fingerprinting approach to the detection of human genome rearrangements. Genome Biology. 2007 Oct 22; 8(10):R224 [Epub ahead of print]
  43. Huang P, Pleasance ED, Maydan JS, Hunt-Newbury R, O’Neil NJ, Mah A, Baillie DL, Marra MA, Moerman DG, Jones SJ. Identification and analysis of internal promoters in Caenorhabditis elegans Operons. Genome Res. 2007 Oct; 17 (10): 1478-85. Epub 2007 Aug 21.
  44. Melck AL, Masoudi H, Griffith OL, Rajput A, Wilkins GE, Bugis S, Jones S, Wiseman SM. Cell Cycle Regulators Show Diagnostic and Prognostic Utility for Differentiated Thyroid Cancer. Annals of Surgical Oncology. 2007 Sep 20; 14(12):3403-3411.[Epub ahead of print]
  45. Hunt Newbury R, Viveiros R, Johnsen R, Mah A, Anastis D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, MacKay S, Okada M, Pan J, Shultz AK, Tu D, Wong K, Zhao Z, Aleeyenko A, Buerglin T, Sonnhammer E, Schnabel R, Jones SJ, Marra MA, Baillie DL, Moerman DG. High throughput in vivo analysis of gene expression in C elegans. PloS Biology. 2007 Sep; 5 (9) :e237.
  46. Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwaN JC, McKay S, McWilliam S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas F, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel R, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor J, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G and Zhao S. A physical map of the bovine genome. Genome Biology. 2007 Aug 14; 8(8):R165 [Epub ahead of print]
  47. Wiseman SM, Griffith OL, Deen S, Rajput A, Masoudi H, Gilks B, Goldstein L, Gown A, Jones SJM. Identification of Molecular Markers Altered during Transformation Of Differentiated Into Anaplastic Thyroid Carcinoma. Archives of Surgery. 2007 Aug. 142 (8): 717-729.
  48. Hou J, Charters AM, Lee SC, Zhou Y, Wu M, Jones SJM, Marra MA, Hoodless PA. A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE). BMC Developmental Biology. 2007 Aug 2;7:92.
  49. Etchberger JF, Lorch A, Sleumer M, Zapf R, Jones SJ, Marra MA, Holt RA, Moerman DG, Hobert O. The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron. Genes Development. 2007 Jul 1;21(13):1653-74.
  50. Zhao Y, Raouf A. Kent D, Khattra J, Delaney A, Schnerch A, Asano J, MacDonald H, Chan C, Jones S, Marra M, Eaves C. A modified polymerase chain reaction-long serial analysis of gene expression protocol identifies novel novel transcripts in human CD34+ bone marrow cells. Stem Cells. 2007 Jul; 25 (7): 1681-9. [Epub ahead of print] Apr 5.
  51. Hu G, Linning R, McCallum B, Banks T, Cloutier S, Butterfield Y, Liu J, Kirkpatrick R, Stott J, Yang G, Smailus D, Jones S, Marra M, Schein J, Bakkeren G. Generation of a wheat leaf rust, Puccinia triticina, EST database from stage-specific cDNA libraries. Molecular Plant Pathology. 2007 July 8 (4), 451-467.
  52. Montgomery SB, Griffith OG, Scheutz JM, Brooks-Wilson A, Jones SJM. A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms. PLoS, Computational Biology. 2007 Jun 8;3 (6) :e106 Epub 2007 Apr 25.
  53. 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. Nature Methods. 2007 Jun 11; [Epub ahead of print]
  54. 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 A-L, 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 Biology. 2007 Jun 14; 8(6):R113.
  55. 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 Journal. 2007 Jun;50(6):1063-78. Epub 2007 May 3.
  56. Ruzanov P, Riddle DL, Marra MA, McKay SJ, Jones SJM. Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults. Experimental Gerontol. 2007 Aug;42(8):825-39. Epub 2007 Apr 21.
  57. Rhesus Macaque Genome Sequencing and Analysis Consortium (incl. Schein, J, Jones, S). Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. Science. 2007 Apr 13. 316, 222.
  58. Warren RL, Sutton GG, Jones SJM and Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 2007 Feb 15;23(4):500-1. Epub 2006 Dec 8
  59. McGhee JD, Sleumer M, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJM, Moerman DG, Robertson AG. The ELT-2 GATA-Factor and the Global Regulation of Transcription in the C. Elegans Intestine. Development Biology. 2007 Feb 15: 302(2): 627-45.
  60. DiGuistini S, Ralph S, Lim Y, 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 Microbiology Letters. 2007, 267: 151-158
  61. 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 Research. 2007 Jan; 17(1) 108-116. Epub 2006 Nov 29.
  62. Robertson N, Oveisi-Fordorei M, Zuyderduyn S, Varhol R, Fjell C, Marra MA, Jones SJM, Siddiqui AS. DiscoverySpace: an interactive data analysis application. Genome Biology. 2007 Jan 8;8(1):R6.
  63. Quayle S, Hare H, Delaney A, Hwang D, Schein J, Jones S, Marco M, Sadar M. Novel expressed sequences identified in a model of androgen independent prostate cancer. BMC Genomics. 2007, 8:32.
  64. Elnitski L, Jin VX, Farnham PJ, Jones SJM. Locating Mammalian Transcription Factor Binding Sites: A Survey of Computational and Experimental Techniques. Genome Research. 2006 Dec;16(12):1455-64. Epub 2006 Oct 19.
  65. Lonergan K, Chari R, deLeeuw R, Shadeo A, Chi B, Tsao M-S, Jones S, Marra M, Ling V, Ng R, MacAulay C, Lam S, Lam W. Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression. American Journal of Respiratory Cell and Molecular Biology. 2006, Dec, 235 (6): 651-61.
  66. Wang G, Jones SJM, Marra MA, Sadar M. Identification of genes targeted by the androgen and PKA signaling pathways in prostate cancer cells. Oncogene. 2006, Nov. 25:7311-23.
  67. Griffith OL, Melck A, Jones SJM, Wiseman SM. A Meta-analysis and Meta-review of Thyroid Cancer Gene Expression Profiling Studies Identifies Important Diagnostic Biomarkers. Journal of Clinical Investigation. 2006 Nov 1;24 (31):5043-51
  68. Bainbridge M.N, Warren R.L, He A, Bilenky M, Robertson A.G, Jones S. THOR: Targeted High-throughput Ortholog Reconstructor. Bioinformatics. 2007 Oct 1;23(19):2622-4. 2006 Oct 11; [Epub ahead of print]
  69. McLeod MP, Warren RL, Araki N, Hsiao WWL, Miyazawa D, Myhre M, Fernandes C, Morin RD, Wong W, Lillquist AL, Wang D, Petrescu A, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield Y, Siddiqui AS, Marra MA, Jones SJM, Holt R, Brinkman FSL, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD. The complete genome of Rhodococcus sp. RHA1: insights into a catabolic powerhouse. Proceedings of the National Academy of Science. 2006 Oct 17;103(42):15582-7. Epub 2006 Oct 9
  70. Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delany A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, Jones SJM. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics. 2006, Sept. 7:246.
  71. Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Asano J, Bailey DK, Barber S, Birch P, Brown-John M, Cao M, Chan S, Charest DL, Farnoud N, Fernandes N, Flibotte S, Go A, Gibson WT, Holt RA, Jones SJM, Kennedy GC, Krzywinski M, Langlois S, Li HI, McGillivray BC, Nayar T, Pugh TJ, Rajcan-Separovic E, Schein JE, Schnerch A, Siddiqui A, Van Allen MI, Wilson G, Yong SL, Eydoux P, Marra MA. Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation. American Journal of Human Genetics. 2006 Sept. 79(3):500-13.
  72. Quayle AP, Siddiqui AS, Jones SJM. Preferential perturbation and network topology. Physica A. 2006 Sept. 371, 823-840.
  73. Tuskan G, DiFazio S, Bohlmann J, Grigoriev I, Hellsten U, Jansson S,. Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao R.R, Bhalerao R.P, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen G.-L, Cooper D, Coutinho P, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S,. Déjardin 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, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé J, Locascio P, Luo Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson D.R., Nelson C, Nieminen K, Nilsson O, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A., Sterky F, Terry A, Tsai C, Uberbache E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw) Science. 2006 Sep 15; 313(5793):1596-604.
  74. 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 Genetics & Biology. 2006 Sept 43: (9) 655-666.
  75. Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YSN, Kirkpatrick R, Liu J, Jones SJM, Marra M, 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 and Environment . Aug (2006) 29, 1545–1570.
  76. Gao BJ, Griffith OL, Ester M, Jones SJ. Discovering significant OPSM subspace clusters in massive gene expression data. Proceedings of the 12th ACM SIGKDD international Conference on Knowledge Discovery and Data Mining (Philadelphia, PA, USA, August 20 - 23, 2006). KDD '06. ACM Press, New York, NY, 922-928.
  77. Siddiqui A, Delaney A, Schnerch A, Griffith O, Jones S, Marra M. Sequence biases in large scale gene expression profiling data. Nucleic Acids Research. 2006 Jul 13;34(12):e83.
  78. 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 III CP, 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 SK, Blakesley RW, Prange C, Myers RM, Green ED, Wagner K, Gerhard DS, Marra MA, Jones SJM, Holt RA. Sequencing and analysis of 10967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis. Genome Research. Jun 2006; 16: 796 – 803.
  79. Quayle AP, Siddiqui AS, Jones SJM. Modeling network growth with assortative mixing. European Physical Journal B. 50(4), 617-630, 2006
  80. Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang S-P, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AA, Marra MA, Wilson RK, Jones SJM. Physical map-assisted whole-genome shotgun sequence assemblies. Genome Research. 2006 Jun.16 (6):768-775.
  81. 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 YSN, Kirkpatrick R, Chun E, Liu J, Palmquist D, Wynhoven B, Stott J, Yang G, Barber S, Holt RA, Siddiqui A, Jones SJM, Marra MA, Ellis BE, Douglas CJ, Ritland K, Bohlmann J. Genomics of hybrid poplar (Populus trichocarpa x deltoides) interacting with forest tent caterpillars (Malacosoma disstria): Normalized and full-length cDNA libraries, expressed sequence tags (ESTs), and a cDNA microarray for the study of insect-induced defenses in poplar. Molecular Ecology. Apr. 2006 15, 1275–1297.
  82. Li YY, Jones SJM, Cherkasov A. Selective Targeting of Indel-Inferred Differences in Spatial Structures of Homologous Proteins. Journal of Bioinformatics and Computational Biology. 2006 Apr;4(2):403-14.
  83. Ruzanov P, Jones SJM. An interactive tool for visualization of relationships between gene expression profiles. BMC Bioinformatics. 2006 Apr 6;7(1):193.
  84. Sundaram B, Chapman BM, Li B, Mayo M, Siddiqui A, Jones S. Sun Grid Engine Package for OSCAR – A Google Summer of Code 2005 Project. Proceedings of 4th Annual OSCAR Symposium (OSCAR 2006).
  85. 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. 2006 Mar 1; 22(5):637-40.
  86. 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 SJM. cisRED: A Database System for Genome Scale Computational Discovery of Regulatory Elements. Nucleic Acids Research. 2006 Jan 1;34(Database issue):D68-73.
  87. 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 Research. 2006 Feb;16(2):173-81.
  88. 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-L, Lee LLC, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu A-L, Pandoh P, Riggins GJ, Ruiz de Algara T, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, MK Wu, Xie Y-Y, Yang G, Zhang I, Hirst M, Jones SJM, 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. Proceedings of the National Academy of Science. 2005 102: 18485-18490; published online before print December 13 2005, 10.1073/pnas.0509455102.
  89. Cherkasov A, Shi Z, Li Y, Jones SM, 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. Chem Inf Model. 2005 Nov 28;45(6):1842-1853.
  90. Larraya LM, Boyce K, So A, Steen BR, Jones S, Marra M, Kronstad J. Serial Analysis of Gene Expression Reveals Conserved Links between Protein Kinase A, Ribosome Biogenesis, and Phosphate Metabolism in Ustilago maydis. Eukaryot Cell. 2005 Dec;4(12):2029-43.
  91. 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. 2005 Oct;86(4):476-488.
  92. 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. 2005 Oct;86(4):396-404.
  93. Montgomery SB, Fu T, Guan J, Lin K, Jones SJM. An application of peer-to-peer technology to the discovery, use and assessment of bioinformatics programs. Nature Methods. 2005 Aug;2(8):563.
  94. Blacque OE, Perens EA, Boroevich KA, Inglis PA, Li C, Warner A, Khattra J, Holt RA, Ou G, Mah AK, McKay SJ, Huang P, Swoboda P, Jones SJM, Marra MA, Baillie DL, Moerman DG, Shaham S, Leroux MR. Functional genomics of the cilium, a sensory organelle. Current Biology. 2005 May 24;15(10):935-41.
  95. Warren RL, Butterfield YS, Morin RD, Siddiqui AS, Marra MA, Jones SJM. Management and visualization of whole genome shotgun assemblies using SAM. Biotechniques. 2005 May;38(5):715-6, 718, 720.
  96. Halaschek-Wiener J, Khattra JS, McKay S, Pouzyrev A, Stott JM, Yang GS, Holt RA, Jones SJM, Marra MA, Brooks-Wilson AR, Riddle DL. Analysis of Long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Research. 2005 May;15(5):603-15. Epub 2005 Apr 18.
  97. 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. Molecular Microbiology. 2005 Mar: 55 (5): 1452-72.
  98. 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. 2005 Mar 24;434(7032):462-9. Citation: 139
  99. 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(1):78.
  100. Loftus B, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamethevan J, Miranda M, Anderson I, Fraser JA, Allen J, Bosdet I, Brent MR, Chiu R, Doering TL, Donlin, MJ, D’Souza C, Fox DS, Grinberg V, Fu J, Fukushima M, Haas B, Huang JC, Janbon G, Jones S, Krzywinski MI, Kwon-Chung J, Lengeler KB, Maiti R, Marra M, Marra RE, Mathewson C, Mitchell TG, Pertea M, Riggs F, Salzberg SL, Schein J, Shvartsbeyn, Shin H, Specht C, Suh B, Tenny A, Utterback T, Wickes BL, Wye N, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CW, Hyman RW. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science. 2005 Feb 25;307(5713):1321-4. Epub 2005 Jan 13. Citation: 111
  101. 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 Research. 2005 Feb;15(2):302-11.
  102. Sander J, Ng R, Sleumer MC, Yuen MS, Jones S. A Methodology for Analyzing SAGE Libraries For Cancer Profiling. ACM Transactions on Information and Systems. 2005 Jan; 23(1)35-60.
  103. Hirst M, Astell C, Griffith M, Coughlin SM, Moksa M, Zeng T, Smailus DE, Holt RA, Jones S, Marra MA, Petric M, Krajden M, Lawrence D, Mak A, Chow R, Skowronski DM, Tweed A, Goh S, Brunham RC, Robinson J, Bowes V, Sojonky K, Byrne SK, Paetzel M. A novel avian influenza H7N3 strain associated with an Avian Influenza Outbreak in British Columbia. Emerging Infectious Diseases. 2004 Dec;10(12):2192-2195.
  104. Warren R, Hsiao WW, Kudo H, Myhre M, Donsanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Holt R, Jones S, Mohn WW, Brinkman FSL, Fukuda M, Davies J, Eltis LD. Functional Characterization of a Catabolic Plasmid from PCB-Degrading Rhodococcus sp. RHA1. J Bacteriol. 2004 Nov;186(22):7783-95.
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  106. The MGC Project Team. The Status, Quality and Expansion of the NIH Full-length cDNA project (MGC). Genome Research. 2004 Oct;14(10B):2121-7.
  107. Baross A, Butterfield Y, Coughlin S, Zeng T, Griffith M, Griffith O, Petrescu A, Smailus D, Khattra J, McDonald H, McKay S, Moksa M, Siddiqui A, Jones S, Holt R, Marra M. Systematic Recovery and Analysis of Full-ORF Human cDNA Clones. Genome Research. 2004 Oct 14;(10B):2003-2092
  108. 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. 2004 Jul 26;5(1):101.
  109. Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Tsai M, Albertson D, Lam W, Choy C-O, Osoegawa K, Zhao S, de Jong P, Schein J, Jones S, Marra M. A Set of BAC Clones Spanning the Human Genome. Nucleic Acid Research. 2004 Jul 9; 32(12):3651-60.
  110. Cherkasov AR, Jones SJ. An approach to large scale identification of non-obvious structural similarities between proteins. BMC Bioinformatics. 2004 May 17;5(1):61.
  111. Montgomery SB, Astakhova T, Bilenky M, Birney E, Fu T, Hassel M, Melsopp C, Rak M, Robertson G, Sleumer M, Siddiqui AS, Jones SJM. Sockeye: A 3D Environment for Comparative Genomics. Genome Research. 2004 May; 14(5):956-62.
  112. MacAulayC, Lonergan K, Chi B, Zuyderduyn S, Schein J, Tsao M, LeRiche J, Jones S, Marra M, Lam S, Lam WL. Serial analysis of gene expression profiles of developmental stages in no-small cell lung carcinoma. Chest, 2004 May: 125 (5 Suppl): 97S
  113. Krzywinski M, Wallis J, Gösele 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 A-L, Shin H, Tänzer 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, P, Warren W, Mardis E, McPherson J, Wilson R, Hűbner N, Jones S, Marra M, Schein J. Integrated and Sequence-Ordered BAC and YAC-based Physical Maps for the Rat Genome. Genome Research. 2004 Apr;14(4):766-79.
  114. Cherkasov AR, Jones SJ. Structural characterization of genomes by large scale sequence-structure threading. BMC Bioinformatics. 2004 Apr 3;5(1):37.
  115. The Rat Genome Project Consortium. Genome Sequence of the Brown Norway Rat Yields Insights into Mammalian Evolution. Nature. 2004. Apr 1;428(6982):493-521.
  116. Baross A, Schertzer M, Zuyderduyn SD, Jones SJM, Marra MA, Lansdorp PL. Effect of TERT and ATM on gene expression profiles in human fibroblasts. Genes Chromosomes Cancer. 2004 Apr;39(4):298-310.
  117. Rise ML, von Schalburg KR, Brown GD, Mawer, MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SRM, Smailus DE, Jones SJM, Schein J, Marra MA, Butterfield YSN, Stott J, Ng SHS, Davidson WS, Koop BF. Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics. Genome Research, 2004 March:14:478-490. Citation: 92
  118. McKay SJ, Johnsen R, Khattra J, Asano J, Baillie DL, Chan S, Dube N, Fang L, Goszczynski B, Ha E, Halfnight E, Hollebakken R, Huang P, Hung K, Jensen V, Jones SJM, Kai H, Li D, Mah A, Marra M, McGhee J, Newbury R, Pouzyrev A, Riddle DL, Sonnhammer E, Tian H, Tu D, Tyson JR, Vatcher G, Warner A, Wong K, Zhao Z, and Moerman DG. Gene Expression Profiling of Cells, Tissues and Developmental Stages of the Nematode c. elegans. Cold Spring Harbor Symposia on Quantitative Biology. 2004 Jan: 159-169. Citation: 40
  119. Steen BR, Zuyderduyn S, Toffaletti DL, Marra M, Jones SJM, Perfect JR, Kronstad J. Analysis of Cryptococcus neoformans gene expression during experimental cryptococcal meningitis. Eukaryot Cell. 2003 Dec;2(6):1336-49.
  120. Kiger AA, Baum B, Jones S, Jones MR, Coulson A, Echeverri C, Perrimon N. A functional genomic analysis of cell morphology using RNA interference. Journal of Biology. 2003;2(4):27.
  121. Pleasance ED, Marra MA, Jones SJM. Assessment of SAGE in transcript identification. Genome Research. 2003;June13(6A):1203-15.
  122. Fjell CD, Bosdet I, Schein JE, Jones SJM, Marra MA. Internet Contig Explorer (iCE) - A tool for visualizing clone fingerprint maps. Genome Research. 2003 June;13(6A):1244-9.
  123. 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. 2003 May 30;300(5624):1399-1404. Citation: 772
  124. Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LW, Waterston RH, McPherson JD, Jones SJM, Marra MA. Software for automated analysis of DNA fingerprinting gels. Genome Research, 2003 May; 13(5):940-53.
  125. Gorski SM, Chittaranjan S, Pleasance ED, Freeman JD, Anderson CL, Varhol RJ, Coughlin SM, Jones SJM, Marra MA. A SAGE Approach to Discovery of Genes Involved in Autophagic Cell Death. Current Biology. 2003 Feb 18;13(4):358-63. Citation: 50
  126. Phan J, Ng R, Yuen M, Jones S. GEA: a Toolkit for Gene Expression Analysis. Proceedings of 2002 ACM SIGMOD, 2002: 628. (Longer version appears in: Proceedings of BIOKDD 2002 Workshop on Data Mining in Bioinformatics, August 2002.)
  127. Hsiao W, Wan I, Jones SJ, Brinkman FSL. IslandPath: Aiding detection of genomic islands in prokaryotes. Bioinformatics. 2002; 19(3):418-420.
  128. 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. Proceedings of the Nationall Academy of Science USA. 2002 Dec 24;99(26):16899-903. Citation: 600
  129. McKay SJ, Jones SJM. AcePrimer: automation of PCR primer design based on gene structure. Bioinformatics. 2002; 18(0):1-2.
  130. Guiliano DB, Hall N, Jones SJM, Clark LN, Corton CH, Barrell BG, Blaxter ML. Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes. Genome Biology. 2002; 3(10): research0057.1-0057.14.
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  132. Vatcher G, Smailus D, Krzywinski M, Guin R, Stott J, Tsai M, Chan S, Pandoh P, Yang G, Asano J, Olson T, Prabhu A, Coope R, Marziali A, Schein J, Jones S, Marra M. Resuspension of DNA sequencing reaction products in agarose increases sequence quality on the MegaBACE 1000 automated sequencer. Biotechniques. 2002; 33(3):532-539.
  133. Brinkman FSL, Blanchard JL, Cherkasov A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BFF, Keeling PJ, Hancock REW, Rose AM, Jones SJM. Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria and the chloroplast. Genome Research. 2002; 12(8):1159-1167.
  134. 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(3):1075-7.
  135. 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(9):1386-400.
  136. 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 Sep;12(9):1445-53.
  137. Butterfield YSN, Marra MA, Chan SY, Guin R, Kryzwinski MI, Lee SS, MacDonald KWK, Mathewson CA, Olson TE, Pandoh PK, Prabhu A, Schnerch A, Skalska U, Smailus DE, Stott JM, Tsai MI, Yang GS, Zuyderduyn SD, Schein JE, Jones SJM. An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones. Nucleic Acids Research. 2002 Jun 1; 30(11):2460-2468.
  138. Shevchenko Y, Bouffard GG, Butterfield YSN, Blakesley RW, Hartley JL, Young AC, Marra MA, Jones SJM, Touchman JW, Green ED. Systematic sequencing of cDNA clones using the transposon Tn5. Nucleic Acids Research. 2002 Jun 1;30(11):2469-2477.
  139. Ness SR, Terpstra W, Krzywinski M, Marra MA, Jones SJM. Assembly of fingerprint contigs: parallelized FPC. Bioinformatics. 2002 Mar;18(3):484-485.
  140. Jones SJM, 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 C. elegans. Genome Research. 2001; 11:1346-1352. Citation: 78
  141. Brinkman FSL, Wan I, Hancock REW, Rose AM, Jones SJ. PhyloBLAST: A tool facilitating phylogenetic analysis of BLAST results. Bioinformatics. 2001; 17(4):385-387.
  142. 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. 2001; 409:934-941.
  143. Gönczy P, Echeverri C, Oegema K, Coulson A, Jones SJM, 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, Özlü N, Bork P, Hyman AA. Functional genomic screen of cell division processes in C. elegans using RNAi: analysis of chromosome III. Nature. 2000; 408(6810):331-336. Citation: 441
  144. 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 expression in C. elegans. Molecular Cell. 2000; 6(3):605-616.
  145. de Koning AP, Brinkman F, Jones S, Keeling PJ. Evidence of a Laterally Transferred Gene in Trichomonas vaginalis. Molecular Biology and Evolution. 2000; 17(11):1769-1773.
  146. 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, Zhong F, Zhong W, Gibbs R, Venter JC, Adams MD, Lewis S. Comparative genomics of the eukaryotes. Science. 2000; 287(5461):2204-2215. Citation: 756>
  147. Johnsen R, Jones SJM, Rose A. Mutational accessibility of essential genes on chromasome l(left) in Caenorhabditis elegans. Molecular & General Genetics. 2000; 263(2):239-252.
  148. 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. 1999; 283(5405):1164-1167. Citation: 54
  149. The C. elegans Sequencing Consortium. How the worm was won: The C. elegans Sequencing Project. Trends in Genetics. 1999; 15:51-58.
  150. The C. elegans Sequencing Consortium. Genome Sequence of the Nematode C. elegans: A platform for Investigating Biology. Science. 1998; 282(5396):2012-2018.
  151. Simmen MW, Leitgeb S, Clark VH, Jones SJ, Bird A. Gene number in an invertebrate chordate, Ciona intestinalis. Proceedings of the National Academy of Science USA. 1998 Apr 14;95(8):4437-40. Citation: 88
  152. 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. Chemical Biology. 1998; 3:155-62. Citation: 148
  153. Jones SJM. An update and lessons from whole genome sequencing projects. Current Opinions in Genetics and Development. 1995; 5:349-353.
  154. Jones SJM, Baillie DL. Characterisation of the let-653 gene in Caenorhabditis elegans. Molecular and General Genetics. 1995; 248:719-726.

 

BOOK CHAPTERS AND REVIEW ARTICLES

 

  1. Griffith Ol, Melck A, Jones SJM, Wiseman SM. Thyroid Cancer: Identification of Gene Expression Markers for Diagnosis. Methods of Cancer Diagnosis, Therapy and Prognosis. Hyat MA, editor, Springer Publishing Company, New York, NY. Vol. 7. ISBN: 978-90-481-3185-3. Not yet published. Available: January 3, 2010.
  2. Hoffman BG, Jones SJM. Genome-wide identification of DNA-protein interactions using ChIP-Seq. Journal of Endocrinology. 2009 Jan 9. [Epub ahead of print].
  3. Fejes AP, Jones SJM. Chapter contribution to “Next generation genome sequencing – toward personalized medicine” Wiley-VCH. Ed. Janitz. 978-3-527-32090-5. Published Oct. 2008.
  4. Griffith OL, Chiu CG, Gown AM, Jones SJ, Wiseman SM. Biomarker panel diagnosis of thyroid cancer: a critical review. Expert Review of Anticancer Therapy. 2008 Sep;8(9):1399-413.
  5. Holt RA, Jones SJM. The new paradigm of flow cell sequencing. Genome Research. Invited review article. 2008 Jun;18(6):839-46
  6. Jones SJM. “Prediction of Genomic Functional Elements.” Annual Review of Genomics and Human Genetics: Vol 7. 2006;7:315-38.
  7. Pleasance ED, Jones SJM. “Evaluation of SAGE tags for transcriptome study”. SAGE Technologies: Current Technologies and Applications.Ed San Ming Wang. Norwich, UK: Horizon Bioscience, 2005.
  8. Siddiqui A, Jones S. “Contig Mapping and Analysis.” Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Ed. A Kuspa. Chichester, UK: John Wiley & Sons, Ltd, 2004.
  9. Astell CR, Holt RA, Jones SJM, Marra MA. “Genome Organization and Structural Aspects of the SARS-related Virus.” Birkhauser Advances in Infectious Diseases: Vol I. Eds A. Schmidt, M.H. Wolff, S.H.E. Kaufman. Basel, CHE: Birkhauser, 2004. 101-128pp.
  10. Bird D, Opperman CH, Jones SJM, Baillie DL. “The Caenorhabditis elegans genome: A guide in the post genomics age.” Annual Review of Phytopathology: Vol 37. Palo Alto, CA, 1999. 247-265pp.
  11. Jones SJM, Hodgson D. “Internet resources for invertebrates.” Internet for the Molecular Biologist. Eds S.R. Swindell, R.R. Miller, G.S.A. Myers. Norwich, UK: Horizon Scientific Press, 1996.
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