Department of Medical Genetics, University of British Columbia
Associate Director/Head Bioinformatics, Genome Sciences Centre, BC Cancer Research Centre
Director, CIHR/MSFHR Bioinformatics Training Program for Health Research

Research interests: Bioinformatics, gene expression, gene regulation, genome sequence analysis and genome assembly.

Selected publications:
D’Souza CA, Chopra V, Varhol R, Xie Y, Bohacec S, Zhao Y, Lee LLC, 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 Neurosci. 2008;9(1):66.

Shin H, Hirst M, Bainbridge M, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL, Jones SJM. Transcriptome Analysis for C. elegans based on Novel Expressed Sequence Tags (ESTs). BMC Biology. 2008;6(1):30.

Wederell1 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

Raouf A, Zhao Y, To K, Stingl HJ, Delaney A, Barbara M, Iscove N, Jones S, McKinney S, Emerman J, Aparicio S, Marra M, Eaves C. Transcriptome analysis of the normal human mammary cell commitment and differentiation process. Cell Stem Cell. 2008;3(1):109-18.

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;45(1): 81-94.

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. Application note – Bioinformatics. 2008

Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Hoodless PA, Jones S, Marra MA, Helgason CD. Identification of Transcripts with Enriched Expression in the Developing and Adult Pancreas. Genome Biol. 2008;9(6):R99.

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. Am J Surg. 2008;195(5):604-10.

Holt RA, Jones SJM. The new paradigm of flow cell sequencing. Genome Res. Invited review article.2008;18(6):839-46

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. Am J Surg. 2008;195(5):667-73.

Shivaswamy S, Bhingel A, Zhao YJ, Jones SJM, Hirst M, Iyer VR. Precise positioning of individual nucleosomes and remodeling across a eukaryotic genome.Plos Biology. 2008;6(3):e65.

Griffith M. Tang MJ, Griffith OL, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Morin RD, Hirst M, Jones SJM, Morin GB, Tai IT, Marra M. ALEXA – A microarray design platform for alternative expression analysis. Nat Methods. 2008;5(2):118.

Aerts S, Haeussler M, Griffith OL, van Vooren S, Jones SJM, Montgomery SB, Bergman CM. The Open Regulatory Annotation Vonsortium. Text-mining assisted regulatory annotation. Genome Biol. 2008;9(2):R31.

Ralph SG, Chun HJE, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJM, Marra MA, Bohlmann J. Analysis of 6,464 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics. 2008;(1):57

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, Donalson 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 Res. 2008:36(Datatbase Issue):D107-13. Epub 2007 Nov. 15.

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;17(3):543-52

Ruzanov P, Jones SJ, Riddle DL. Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data. BMC Genomics. 2007;8:447.

Peng FY, Reid KE, Liao N, Schlosser J, Lijavetzky D, Holt R, Martínez Zapater JM, Jones S, Marra M, Bohlmann J, Lund ST. Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table Grape (Muscat Hamburg) and discovery of new candidate genes with possible roles in berry development.Gene. 2007;402(1-2):40-50. Epub 2007.

Krzywinski M, Bosdet I, Mathewson C, Wye N, Brebner J, Chiu R, Corbett R, Field M, Lee D, Pugh T, Volik S, Siddiqui A, Jones S, Schein J, Collins C, Marra A. A BAC clone fingerprinting approach to the detection of human genome rearrangements. Genome Biol. 2007;8(10):R224.

Huang P, Pleasance ED, Maydan JS, Hunt-Newbury R, O’Neil NJ, Mah A, Baillie DL, Marra MA, Moerman DG, Jones SJ. Identification and analysis of internal promoters in Caenorhabditis elegans operons. Genome Res. 2007;17(10):1478-1485. Epub 2007 Aug 21.

Melk 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. Ann Surg Oncol. 2007;14(12):3403-3411.

Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastis D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, Mckay S, Okada HM, Pan J, Shultz AK, Tu D, Wong K, Zhao Z, Alexeyenko A, Burglin T, Sonnhammer E, Schnabel R, Jones SJ, Marra MA, Baillie DL, Moerman DG. High Throughput In Vivo Analysis of Gene Expression in C. Elegans. PloS Biology. 2007;5(9):e237.

Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, McWilliam S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas F, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel R, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor J, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biol. 2007;8(8):R165.

Ruzanov P, Riddle DL, Marra MA, McKay SJ, Jones SM. Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults. Exp Gerontol. 2007;42(8):825-839.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Pandoh P, Fichter K, Tam A, Ma K, Prabhu A, Moksa M, Lee S, Mah D, Sa D, McDonald H, Delaney A, Thiessen N, Bernier B, Griffith OL, He A, Varhol R, Euskirchen G, Snyder M, Marra M, Jones S. Genome-wide profiles of STAT1 DNA association in HeLa S3 cells using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007;4(8):651-7.

Hou J, Charters AM, Lee SC, Zhao Y, Wu MK, Jones SJM, Marra MA, Hoodless PA. A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE). BMC Dev. Biol. 2007;7(1):92.

Wiseman SM, Girffith 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. Arch Surg. 2007;7:92

Hu G, Linning R, Joseph C, McCallum B, Banks T, Cloutier S, Butterfield Y, Liu J, Kirkpatrick R, Stott J, Yang G, Smailus D, Jones S, Marra M, Schein J, Bakkeren G. Generation of a wheat leaf rust, Puccinia triticina, EST database from stage-specific cDNA libraries. Mol Plant Pathol. 2007;8(4):451-467.

Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O’Connor MD, Zeng T, 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 CJMarra MA. LongSAGE transcriptome analysis of nine human embryonic stem cell lines reveals novel transcripts and an over-representation of binding proteins. Genome Biol. 2007;8(6):R113.

Montgomery SB, Griffith OG, Scheutz JM, Brooks-Wilson A, Jones SJM. A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms. PLoS, Comput Biol. 2007;3(6):e106 Epub 2007 Apr 25.

Kelleher CT, Chiu R. Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin TM, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O’Connor K, Pradhu A-L, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJM, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ, Schein JE. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant J. 2007;50(6):1063-1078. Epub 2007 May 3.

Rhesus Macaque Genome Sequencing and Analysis Consortium (incl Jones SM, Marra MA, and Schein JE). Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316(5822):222-234.

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 Microbiol Lett. 2007; 267: 151-158

McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJM, Moerman DG, Robertson AG. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol. 2007; 302(2): 627-645. Epub 2006 Oct 21.

Warren RL, Sutton GG, Jones SJM, Holt RA. Assembling millions of short sequences using SSAKE. Bioinformatics. 2007;23(4):500-1. Epub 2006 Dec 8.

Quayle SN, Hare HA, Delaney AD, Hirst M, Hwang D, Schein JE, Jones SJM, Marra MA, Sadar MD. Novel expressed sequences identified in a model of androgen independent prostate cancer.BMC Genomics. 2007;8:32

Robertson N, Oveisi-Fordorei M, Zuyderduyn S, Varhol R, Fjell C, Marra MA, Jones SJM, Siddiqui AS. DiscoverySpace: an interactive data analysis application. Genome Biol. 2007;8(1):R6.

Khattra J, Delaney AD, Zhao Y, Siddiqui A, Hirst M, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu A, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Jones S, Holt R, Hoodless P, Marra MA. Large scale production of SAGE libraries from microdissected tissues, flow-sorted cells and cell lines. Genome Res. 2007;17(1) 108-116. Epub 2006 Nov 29.

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 labeling. Biomedical Insights 2007:2 447-461.

Quayle AP, Siddiqui AS, Jones SJM. Perturbation of Interaction Networks for Applicationto Cancer Therapy. Cancer Informatics. (Edition: Systems Biology Special Issue) 2007:(2)45-65.

Lonergan KM, Chari R, deLeeuw RJ, Shadeo A, Chi B, Tsao M-S, Jones S, Marra M, Ling V, Ng R, MacAulay C, Lam S, Lam WL. Identification of Novel Lung Genes in Bronchial Epithelium by Serial Analysis of Gene Expression. Am J Respir Cell Mol Biol. 2006;35(6):651-661. 2006 (Epub).

McLeod MP, Warren RL, Hsiao WWL, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE. Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJM, Holt R, Brinkman FSL, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD. The complete genome of Rhodococcus sp. RHA1: insights into a catabolic powerhouse. Proc Natl Acad Sci.2006;103(42):15582-15587.

Bainbridge M, Warren R, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis E, Sadar M, Siddiqui A, Marra M, Jones S. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics. 2006;7:246.

Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Asano J, Bailey DK, Barber S, Birch P, Brown-John M, Cao M, Chan S, Charest DL, Farnoud N, Fernandes N, Flibotte S, Go A, Gibson WT, Holt RA, Jones SJM, Kennedy GC, Krzywinski M, Langlois S, Li HI, McGillivray BC, Nayar T, Pugh TJ, Rajcan-Separovic E, Schein JE, Schnerch A, Siddiqui A, Van Allen MI, Wilson G, Yong SL, Eydoux P, Marra MA. Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Human Genet. 2006;79(3):500-513. Epub 2006 Jul 25.

Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YSN, Kirkpatrick R, Liu J, Jones SJM, Marra MA, Douglas CJ, Ritland K, Bohlmann J. Conifer defense against iInsects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils ( Pissodes strobi) reveals large-scale changes of the host transcriptome. Plant Cell Environ. 2006;29(8):1545-1570.

Bakkeren G, Jiang G, Warren R, Butterfield Y, Shin H, Chiu R, Linning R, Schein J, Lee N, Hu G, Kupfer DM, Tang Y, Roe BA, Jones S, Marra M, Kronstad JW. Mating factor linkage and genome evolution in basidiomycetous pathogens of cereals. Fungal Genetics Biology. 2006;43(9):655-666. Epub 2006.

Siddiqui AS, Delaney AD, Schnerch A, Griffith OL, Jones SJM, Marra MA. Sequence biases in large scale gene expression profiling data. Nucleic Acids Res. 2006;34(12):e83.

Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley CP 3rd, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang M, 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. 2006;16(6):796-803.

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 deltoids) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags (ESTs), and a cDNA microarray for the study of insect-induced defenses in poplar. Mol Ecol. 2006;15(5):1275-1297.

Ruzanov P, Jones SJM. An interactive tool for visualization of relationships between gene expression profiles. BMC Bioinformatics 2006;7(1):193.

Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Jones SJ et al. ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 20061;22(5):637-40.

Wilson GE, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG, Holt RA. Identification by full coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res. 2006;16(2):173-181.

Robertson G, Bilenky M., Lin K, He A, Yuen W, Jones SJM et al. cisRED: A Database System for Genome Scale Computational Discovery of Regulatory Elements. Nucleic Acids Res. 2006;34(Database issue):D68-73.

Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang S-P, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AS, Marra MA, Wilson RK, Jones SJM. Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res. 2006;16(6):768-775.

Quayle AP, Siddiqui A, Jones SJM. Modeling network growth with assortative mixing. European Physical Journal. 2006;50(4), 617-630.

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, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt R, Hou J, Kuo BY-L, Lee LLC, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Pradhu A, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie Y-Y, Yang G, Zhang I, Hirst M, Jones SJM, Helgason CD, Simpson EM, Hoodless PA, Marra M. A mouse altas of gene expression: Large-scale digital gene expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci. 2005;102(51):18485-18490.

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. Eukaryotic Cell. 2005;4(12):2029-2043.

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. J Chem Inf Model. 2005;45(6:1842-53.

Ng SHS, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJM, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddiqui A, Thorsen J, Wye N, Yang G, Zhu B. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics. 2005;86(4):396-404.

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;86(4):476-488.

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. Nat Methods. 2005;2(8):563.

Lian T, Simmer MD, 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. 2005;55(5):1452-1472.

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. Curr Biol. 2005 May 24;15(10):935-41.

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;38:715-720

Halaschek-Wiener J, Khattra JS, McKay S, Pouzyrev A, Stott JM, Yang GS, Holt RA, Jones SJM, Marra MA, Brooks-Wilson AR, Riddle DL. Analysis of Long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Res. Epub 2005 April 18; 10.1101/gr.3274805.

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.

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.

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.

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. 2005 Feb;15(2):302-11.

Sander J, Ng R, Sleumer MC, Yuen MS, Jones S. A Methodology for Analyzing SAGE Libraries For Cancer Profiling. ACM Trans. Inf. Syst. 2005 Jan; 23(1)35-60.

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.

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.

ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40.

The MGC Project Team. The Status, Quality and Expansion of the NIH Full-length cDNA project (MGC). Genome Res. 2004 Oct;14(10B):2121-7.

Baross A, Butterfield Y, Coughlin S, Zeng T, Griffith M, Griffith O, Petrescu A, Smailus D, Khattra J, McDonald H, McKay S, Moksa M, Siddiqui A, Jones S, Holt R, Marra M. Systematic Recovery and Analysis of Full-ORF Human cDNA Clones. Genome Res. 2004;(10B): 2083-2092.

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.

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.

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.

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 Res. 2004 May; 14(5):956-62.

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, H?bner N, Jones S, Marra M, Schein J. Integrated and Sequence-Ordered BAC and YAC-based Physical Maps for the Rat Genome. Genome Res. 2004 Apr;14(4):766-79.

Cherkasov AR, Jones SJ. Structural characterization of genomes by large scale sequence-structure threading. BMC Bioinformatics. 2004 Apr 3;5(1):37.

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.

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.

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 Res, 2004 March:14:478-490.

McKay SJ, Johnsen R, Khattra J, Asano J, Baillie DL, Chan S, Dube N, Fang L, Goszczynski B, Ha E, Halfnight E, Hollebakken R, Huang P, Hung K, Jensen V, Jones SJM, Kai H, Li D, Mah A, Marra M, 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. 2003 Jan: 159-169.

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.

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. 2003;2(4):27.

Pleasance ED, Marra MA, Jones SJM. Assessment of SAGE in transcript identification. Genome Res. 2003;June13(6A):1203-15.

Fjell CD, Bosdet I, Schein JE, Jones SJM, Marra MA. Internet Contig Explorer (iCE) – A tool for visualizing clone fingerprint maps. Genome Res. 2003 June;13(6A):1244-9.

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.

Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LW, Waterston RH, McPherson JD, Jones SJM, Marra MA. Software for automated analysis of DNA fingerprinting gels. Genome Res, 2003 May; 13(5):940-53.

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. Curr Biol. 2003 Feb 18;13(4):358-63.

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, Moerman DG. Gene Expression Profiling of Cells, Tissues and Developmental Stages of the Nematode C. elegans. Cold Spring Harb Symp Quant Biol. 2003;159-169.

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.)

Hsiao W, Wan I, Jones SJ, Brinkman FSL. IslandPath: Aiding detection of genomic islands in prokaryotes. Bioinformatics. 2002; 19(3):418-420.

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 USA. 2002 Dec 24;99(26):16899-903.

McKay SJ, Jones SJM. AcePrimer: automation of PCR primer design based on gene structure. Bioinformatics. 2002; 18(0):1-2.

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.

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. 2002; 418(6899):743-50.

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):532-4, 536, 538-9.

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 Res. 2002; 12(8):1159-1167.

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.

Steen BR, Lian T, Zuyderduyn S, MacDonald K, Marra M, Jones SJM, Kronstad JW. Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Res. 2002; 12(9):1386-400; 12(9):1386-400.

Schein J, Tangen K, Chiu R, Shin H, Lengeler KB, MacDonald K, Bosdet I, Heitman J, Jones SJM, Marra M, Kronstad JW. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res. 2002Sep;12(9):1445-53.

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 Res. 2002 Jun 1; 30(11):2460-2468

Shevchenko Y, Bouffard GG, Butterfield YSN, Blakesley RW, Hartley JL, Young AC, Marra MA, Jones SJM, Touchman JW, Green ED. Systematic sequencing of cDNA clones using the transposon Tn5. Nucleic Acids Res. 2002 Jun 1;30(11):2469-2477

Ness SR, Terpstra W, Krzywinski M, Marra MA, Jones SJM. Assembly of fingerprint contigs: parallelized FPC. Bioinformatics. 2002 Mar;18(3):484-485.

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.

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.

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.

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.

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.

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.

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.

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.

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.

The C. elegans Sequencing Consortium. How the worm was won: The C. elegans Sequencing Project. Trends in Genetics. 1999; 15:51-58.

The C. elegans Sequencing Consortium. Genome Sequence of the Nematode C. elegans: A platform for Investigating Biology. Science. 1998; 282(5396):2012-2018.

Simmen MW, Leitgeb S, Clark VH, Jones SJ, Bird A. Gene number in an invertebrate chordate, Ciona intestinalis. Proc Natl ACAD Sci U S A. 1998 Apr 14;95(8):4437-40.

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.

Jones SJM. An update and lessons from whole genome sequencing projects. Current Opinions in Genetics and Development. 1995; 5:349-353.

Jones SJM, Baillie DL. Characterisation of the let-653 gene in Caenorhabditis elegans. Molecular and General Genetics. 1995; 248:719-726.