Dr. Steven Jones

Titles and Education

Titles

Head, Bioinformatics, Genome Sciences Centre, BC Cancer Agency
Associate Director, Genome Sciences Centre, BC Cancer Agency
Director Bioinformatics, Genome BC Bioinformatics Platform, Genome BC
Founding Director, CIHR/MSFHR Bioinformatics Training Program
Professor, Molecular Biology & Biochemistry, Simon Fraser University
Director, Bioinformatics Graduate Program, University of British Columbia
Adjunct Professor, Medical Microbiology & Infectious Diseases, University of Manitoba
Associate Professor, Medical Genetics, University of British Columbia
Adjunct Professor, Genetics Graduate Program, University of British Columbia
Associate Member, Peter Wall Institute for Advanced Studies
Associate Member, Michael Smith Laboratories, University of British Columbia

Education

B.Sc., Biochemistry (honours), Bristol University, Bristol, UK
M.Sc., Genetics, Simon Fraser University
Ph.D., Bioinformatics, Sanger Institute, Cambridge, UK

Research

The Bioinformatics group at Canada's Michael Smith Genome Sciences Centre is developing computational approaches to analyse DNA sequence information, especially deriving from the next-generation DNA sequencing technology.  Studies are ongoing which will provide insights to the mutations and other DNA re-arrangements which occur and accrue within the oncogenic process which give rise to cancer.  

     The group has a long established interest  in the understanding the mechanisms by which DNA sequence changes can give rise to altered gene expression. To this end, investigating computational approaches to detect regulatory elements within genomic sequences as well as methods to map transcription factor binding events such as described in Nat. Methods. 2007 Aug;4(8):613-4.

     Previously, Steven Jones was a researcher at the Sanger Institute, Cambridge, UK. , 1994-1998. During this time he participated in the computational analysis of the 45 MB of Caenorhabditis elegans sequence generated at the Sanger Centre as part of the C. elegans Genome Project [Science (1998) 282:2012-2018]. This project resulted in the derivation of the first complete genome of a multi-cellular organism. Another contribution also includes the invention of the web-based blast server, which currently is now the most common interface through which DNA and protein sequence searches are now performed. The original concept was developed to serve the needs of the C. elegans genome sequencing project but it was rapidly adopted by other groups, including both NCBI and EMBL, as a generic way of searching DNA and Protein databases. See here and here my original postings to the C. elegans newsgroup back in the heady days of 1995.

In 2005 Steven Jones was nominated as one of Canada's top 40 professional under 40. He also received the Spencer Award for IT innovation as well as the 2007 Medical Genetics teaching award for UBC. Further contributions include his involvment as the founding director of the CIHR/MSFHR Bioinformatics Training Program as well as director of the University of British Columbia Bioinformatics Graduate Program.

To learn about more events for Bioinformatics in the Vancouver area, check out VanBug.

Select Publications

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.

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 Jun 15. [Epub ahead of print].

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.

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.

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.

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 Aug 1;24(15):1729-30. 2008 Jul 3. [Epub ahead of print].

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.

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 Research. 2007 Oct; 17 (10): 1478-85. Epub 2007 Aug 21.

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.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug;4(8):651-7. [Epub ahead of print] 2007 Jun 11.

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 Res. 2006 Jan 1;34(Database issue):D68-73.

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.

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

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

Steven Jones' Complete Publications List including selected links to full text articles.