Steven Jm Jones

Summary

Affiliation: British Columbia
Country: Canada

Publications

  1. pmc Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans
    Monica C Sleumer
    Canada s Michael Smith Genome Sciences Centre, BC Cancer Agency, 570 W 7th Ave Suite 100, Vancouver, BC, Canada
    Nucleic Acids Res 38:2990-3004. 2010
  2. pmc Recurrent targets of aberrant somatic hypermutation in lymphoma
    Alireza Hadj Khodabakhshi
    Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
    Oncotarget 3:1308-19. 2012
  3. pmc Perturbation of interaction networks for application to cancer therapy
    Adrian P Quayle
    Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
    Cancer Inform 5:45-65. 2007
  4. pmc Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel
    Marieke Simonis
    Genome Biology Group, Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Genome Biol 13:r31. 2012
  5. pmc Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells
    Irina A Maksakova
    Department of Medical Genetics, Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
    Epigenetics Chromatin 6:15. 2013
  6. pmc Transcriptome resources and functional characterization of monoterpene synthases for two host species of the mountain pine beetle, lodgepole pine (Pinus contorta) and jack pine (Pinus banksiana)
    Dawn E Hall
    Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
    BMC Plant Biol 13:80. 2013
  7. pmc Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline
    Alireza Hadj Khodabakhshi
    Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Ave, Vancouver, British Columbia, V5Z 4S6, Canada
    BMC Bioinformatics 14:167. 2013
  8. pmc Identification of transcripts with enriched expression in the developing and adult pancreas
    Brad G Hoffman
    Department of Cancer Endocrinology, BC Cancer Research Center, West 10th Ave, Vancouver, BC V5Z 1L3, Canada
    Genome Biol 9:R99. 2008
  9. pmc A physical map of the bovine genome
    Warren M Snelling
    USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
    Genome Biol 8:R165. 2007
  10. pmc Text-mining assisted regulatory annotation
    Stein Aerts
    Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B 3000, Belgium
    Genome Biol 9:R31. 2008

Detail Information

Publications109 found, 100 shown here

  1. pmc Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans
    Monica C Sleumer
    Canada s Michael Smith Genome Sciences Centre, BC Cancer Agency, 570 W 7th Ave Suite 100, Vancouver, BC, Canada
    Nucleic Acids Res 38:2990-3004. 2010
    ..elegans trans-splice acceptor site. One motif group was tested for regulatory function in a series of green fluorescent protein expression experiments and was shown to be involved in pharyngeal expression...
  2. pmc Recurrent targets of aberrant somatic hypermutation in lymphoma
    Alireza Hadj Khodabakhshi
    Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
    Oncotarget 3:1308-19. 2012
    ..In particular, we have identified 32 novel targets that show same or higher level of aSHM activity than genes previously reported. Amongst these novel targets, 22 genes showed a significant correlation between mRNA abundance and aSHM...
  3. pmc Perturbation of interaction networks for application to cancer therapy
    Adrian P Quayle
    Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
    Cancer Inform 5:45-65. 2007
    ..The approach developed can potentially be applied to many other diseased cell types...
  4. pmc Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel
    Marieke Simonis
    Genome Biology Group, Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Genome Biol 13:r31. 2012
    ..Recombinant inbred panels are powerful tools to study the cis and trans effects of genetic variation on molecular phenotypes such as gene expression...
  5. pmc Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells
    Irina A Maksakova
    Department of Medical Genetics, Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
    Epigenetics Chromatin 6:15. 2013
    ..Intriguingly, MERVL retroelements are actively transcribed exclusively in the two-cell (2C) embryo, but the molecular basis of silencing of these class III ERVs at later developmental stages has not been systematically addressed...
  6. pmc Transcriptome resources and functional characterization of monoterpene synthases for two host species of the mountain pine beetle, lodgepole pine (Pinus contorta) and jack pine (Pinus banksiana)
    Dawn E Hall
    Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
    BMC Plant Biol 13:80. 2013
    ..Volatile monoterpenes also serve as host recognition cues for MPB and as precursors for MPB pheromones. The genes responsible for terpene biosynthesis in jack pine and lodgepole pine were previously unknown...
  7. pmc Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline
    Alireza Hadj Khodabakhshi
    Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Ave, Vancouver, British Columbia, V5Z 4S6, Canada
    BMC Bioinformatics 14:167. 2013
    ....
  8. pmc Identification of transcripts with enriched expression in the developing and adult pancreas
    Brad G Hoffman
    Department of Cancer Endocrinology, BC Cancer Research Center, West 10th Ave, Vancouver, BC V5Z 1L3, Canada
    Genome Biol 9:R99. 2008
    ....
  9. pmc A physical map of the bovine genome
    Warren M Snelling
    USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
    Genome Biol 8:R165. 2007
    ..The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project...
  10. pmc Text-mining assisted regulatory annotation
    Stein Aerts
    Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B 3000, Belgium
    Genome Biol 9:R31. 2008
    ....
  11. pmc DiscoverySpace: an interactive data analysis application
    Neil Robertson
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
    Genome Biol 8:R6. 2007
    ..DiscoverySpace is of broad utility and its particular strength is in the analysis of serial analysis of gene expression (SAGE) data. The application is freely available online...
  12. pmc LongSAGE profiling of nine human embryonic stem cell lines
    Martin Hirst
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
    Genome Biol 8:R113. 2007
    ....
  13. pmc A BAC clone fingerprinting approach to the detection of human genome rearrangements
    Martin Krzywinski
    BC Cancer Agency Genome Sciences Centre, West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6
    Genome Biol 8:R224. 2007
    ..Our method has compelling potential for use as a whole-genome method for the identification and characterization of human genome rearrangements...
  14. pmc Identification of a set of genes showing regionally enriched expression in the mouse brain
    Cletus A D'Souza
    Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave Suite 100, Vancouver, BC, V5Z 4E6, Canada
    BMC Neurosci 9:66. 2008
    ....
  15. pmc Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees
    Queenie W T Chan
    Department of Biochemistry Ž Molecular Biology, Centre for High Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia, V6T 1Z4 Canada
    BMC Genomics 12:450. 2011
    ..However, the power of these methodologies is severely limited without a complete genome; we undertake to address that deficiency here...
  16. pmc Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera
    Uljana Hesse-Orce
    Department of Wood Science, University of British Columbia, Vancouver, Canada
    BMC Genomics 11:536. 2010
    ..Trees respond to attacks from beetles and associated fungi by releasing terpenoid and phenolic defense compounds. It is unclear which genes are important for G. clavigera's ability to overcome antifungal pine terpenoids and phenolics...
  17. pmc Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE
    Xin Wang
    Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
    BMC Genomics 10:213. 2009
    ..To increase our understanding of the genes that might be necessary for the formation and function of the germ line, we have constructed a SAGE library from hand dissected C. elegans hermaphrodite gonads...
  18. pmc Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries
    Tammy L Romanuik
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    BMC Genomics 10:476. 2009
    ..The androgen pathway continues to be important in prostate cancer. Here, we evaluated the transcriptome of prostate cancer cells in response to androgen using long serial analysis of gene expression (LongSAGE) libraries...
  19. pmc Novel expressed sequences identified in a model of androgen independent prostate cancer
    Steven N Quayle
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
    BMC Genomics 8:32. 2007
    ..The molecular changes that occur to allow prostate cells to proliferate in the absence of androgens are not fully understood...
  20. pmc Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern
    Ann M Rose
    Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
    BMC Genomics 11:131. 2010
    ..Sequencing of this strain provides an opportunity to examine the consequences on the genome of altering the distribution of meiotic recombination events...
  21. pmc 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)
    Steven G Ralph
    Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
    BMC Genomics 9:484. 2008
    ..Sequence-finished full-length (FL)cDNAs and large collections of expressed sequence tags (ESTs) are essential for gene discovery, functional genomics, and for future efforts of conifer genome annotation...
  22. pmc Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data
    Peter Ruzanov
    Michael Smith Laboratories University of British Columbia, Vancouver BC V6T 1Z4, Canada
    BMC Genomics 8:447. 2007
    ..These isoforms may have specialized functions, and may be tissue- or stage-specific. Our aim was to use computational analysis of SAGE and genomic data to predict alternatively spliced transcripts expressed in C. elegans...
  23. pmc Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome
    Jong S Leong
    Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada
    BMC Genomics 11:279. 2010
    ....
  24. pmc 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
    Steven G Ralph
    Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
    BMC Genomics 9:57. 2008
    ..Poplar has been established as a model system for genomics studies of growth, development, and adaptation of woody perennial plants including secondary xylem formation, dormancy, adaptation to local environments, and biotic interactions...
  25. pmc A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE)
    Juan Hou
    Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
    BMC Dev Biol 7:92. 2007
    ..However, investigation into the molecular mechanisms of DE differentiation has been hindered by the lack of early DE-specific markers...
  26. pmc Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags
    Heesun Shin
    Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
    BMC Biol 6:30. 2008
    ..This work also demonstrates the successful and efficient application of a next generation sequencing methodology...
  27. pmc An approach to large scale identification of non-obvious structural similarities between proteins
    Artem Cherkasov
    Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
    BMC Bioinformatics 5:61. 2004
    ..When applied to the testing set of proteins with known three dimensional structures the developed approach was able to recognize structurally similar proteins with high accuracy...
  28. pmc Structural characterization of genomes by large scale sequence-structure threading
    Artem Cherkasov
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    BMC Bioinformatics 5:37. 2004
    ..Using sequence-structure threading we have conducted structural characterization of complete proteomes of 37 archaeal, bacterial and eukaryotic organisms (including worm, fly, mouse and human) totaling 167,888 genes...
  29. pmc Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics
    Artem Cherkasov
    Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    BMC Bioinformatics 5:101. 2004
    ..For instance, Weibull distributions are widely used in reliability, maintainability and safety work to model time-to-failure of mechanical devices, mechanisms, building constructions and equipment...
  30. pmc CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes
    Chris D Bajdik
    Cancer Control Research Program, BC Cancer Agency, 600 West 10th Avenue, Vancouver BC, V5Z 4E6, Canada
    BMC Bioinformatics 6:78. 2005
    ..We developed the computer program CGMIM to search for entries in OMIM that are related to one or more cancer types. We performed manual searches of OMIM to verify the program results...
  31. pmc A knowledge discovery object model API for Java
    Scott D Zuyderduyn
    Canada s Michael Smith Genome Sciences Centre, BC Cancer Agency, 600 West 10th Ave, Vancouver, Canada
    BMC Bioinformatics 4:51. 2003
    ..Although efforts are underway to create a standard format for the transmission and storage of biological data, this objective has yet to be fully realized...
  32. ncbi request reprint Prediction of genomic functional elements
    Steven J M Jones
    Genome Sciences Centre, British Columbia Cancer Research Center, Vancouver, British Columbia, V5Z 1L3, Canada
    Annu Rev Genomics Hum Genet 7:315-38. 2006
    ..Recent methodologies for predicting noncoding RNA genes, including microRNA genes and their targets, are also reviewed...
  33. pmc Gene expression profiling of oxidative stress response of C. elegans aging defective AMPK mutants using massively parallel transcriptome sequencing
    Heesun Shin
    Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6
    BMC Res Notes 4:34. 2011
    ..abstract:..
  34. pmc Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach
    Matthew N Bainbridge
    British Columbia Cancer Agency BCCA Genome Sciences Centre, Vancouver, British Columbia, Canada
    BMC Genomics 7:246. 2006
    ..Although the sequence reads are short, they can readily be used for re-sequencing. By re-sequencing the mRNA products of a cell, one may rapidly discover polymorphisms and splice variants particular to that cell...
  35. pmc Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors
    Steven Jm Jones
    Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
    Genome Biol 11:R82. 2010
    ..We investigated the utility of massively parallel sequencing to characterize an adenocarcinoma of the tongue, before and after treatment...
  36. ncbi request reprint AcePrimer: automation of PCR primer design based on gene structure
    Sheldon J McKay
    Genome Sciences Centre, British Columbia Cancer Agency, 600 W 10th Avenue, Vancouver, BC, Canada V5Z 4E6
    Bioinformatics 18:1538-9. 2002
    ....
  37. pmc Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding
    A Gordon Robertson
    BC Cancer Agency Genome Sciences Centre, Vancouver, Canada
    Genome Res 18:1906-17. 2008
    ....
  38. doi request reprint Alternative expression analysis by RNA sequencing
    Malachi Griffith
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
    Nat Methods 7:843-7. 2010
    ..Alternative expression annotation databases, source code, a data viewer and other resources to facilitate analysis are available at http://www.alexaplatform.org/alexa_seq/...
  39. ncbi request reprint Management and visualization of whole genome shotgun assemblies using SAM
    Rene L Warren
    Genome Sciences Centre, Vancouver, BC, Canada
    Biotechniques 38:715-6, 718, 720. 2005
    ..RHAI and Cryptococcus neoformans WM276 genomes...
  40. pmc ABySS: a parallel assembler for short read sequence data
    Jared T Simpson
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 19:1117-23. 2009
    ..Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes...
  41. pmc Sockeye: a 3D environment for comparative genomics
    Stephen B Montgomery
    Canada s Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 14:956-62. 2004
    ..By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization...
  42. pmc Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer
    Chunxiao Wu
    Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
    J Pathol 227:53-61. 2012
    ..Overall, this work highlights the importance of integrated analyses of genome, exome and transcriptome sequences for basic tumour biology, sequence-based molecular pathology and personalized oncology...
  43. doi request reprint High quality SNP calling using Illumina data at shallow coverage
    Nawar Malhis
    Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada
    Bioinformatics 26:1029-35. 2010
    ....
  44. doi request reprint The new paradigm of flow cell sequencing
    Robert A Holt
    British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 18:839-46. 2008
    ..Given the ever increasing demand for DNA sequence information, we can expect continuous improvement of this new generation of instruments and their eventual replacement by even more powerful technology...
  45. pmc FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
    Anthony P Fejes
    Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada
    Bioinformatics 24:1729-30. 2008
    ..Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads...
  46. doi request reprint Biomarker panel diagnosis of thyroid cancer: a critical review
    Obi L Griffith
    Department of Medical Genetics, University of British Columbia and Michael Smith Genome, Sciences Center, British Columbia Cancer Research Centre, 100 570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada
    Expert Rev Anticancer Ther 8:1399-413. 2008
    ..In the future, studies evaluating larger numbers of biomarkers in large patient cohorts are required for the development and validation of a clinically applicable test...
  47. pmc Slider--maximum use of probability information for alignment of short sequence reads and SNP detection
    Nawar Malhis
    Genome Sciences Centre, BC Cancer Agency, Vancouver and School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
    Bioinformatics 25:6-13. 2009
    ..In this article, we will introduce a new alignment approach (Slider) that reduces the alignment problem space by utilizing each read base's probabilities given in the prb files...
  48. doi request reprint Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing
    Brad G Hoffman
    Department of Cancer Endocrinology, BC Cancer Research Center, 675 West 10th Avenue, Vancouver, BC, Canada
    J Endocrinol 201:1-13. 2009
    ..However, to date, this technology has been applied only to a small number of cell types, and even fewer tissues, suggesting a huge potential for novel discovery in this field...
  49. pmc Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements
    Monica C Sleumer
    Canada s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
    Nucleic Acids Res 37:1323-34. 2009
    ..The annotated motifs provide novel binding site candidates for both characterized transcription factors and orthologues of characterized mammalian transcription factors...
  50. doi request reprint De novo transcriptome assembly with ABySS
    Inanc Birol
    Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
    Bioinformatics 25:2872-7. 2009
    ..One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable...
  51. ncbi request reprint ABySS-Explorer: visualizing genome sequence assemblies
    Cydney B Nielsen
    BC Cancer Agency, Genome Sciences Centre
    IEEE Trans Vis Comput Graph 15:881-8. 2009
    ..Finally, we touch on applications of this representation not initially considered in our design phase, suggesting the generality of this encoding for DNA sequence data...
  52. pmc ORegAnno: an open-access community-driven resource for regulatory annotation
    Obi L Griffith
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
    Nucleic Acids Res 36:D107-13. 2008
    ..All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org...
  53. ncbi request reprint Genomics of hybrid poplar (Populus trichocarpax deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences
    Steven Ralph
    Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
    Mol Ecol 15:1275-97. 2006
    ..This study provides the first genome-scale approach to characterize insect-induced defences in a woody perennial providing a solid platform for functional investigation of plant-insect interactions in poplar...
  54. ncbi request reprint Assembling millions of short DNA sequences using SSAKE
    Rene L Warren
    British Columbia Cancer Agency, Genome Sciences Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
    Bioinformatics 23:500-1. 2007
    ..Availability: http://www.bcgsc.ca/bioinfo/software/ssake...
  55. ncbi request reprint A large-scale computational approach to drug repositioning
    Yvonne Y Li
    Canada s Michael Smith Genome Sciences Centre, 570 West 7th Avenue, Vancouver, British Columbia, V5Z 4S6, Canada
    Genome Inform 17:239-47. 2006
    ..Our results highlight the promising nature of the inverse docking method for identifying potential novel therapeutic uses for existing drugs...
  56. pmc A regulatory toolbox of MiniPromoters to drive selective expression in the brain
    Elodie Portales-Casamar
    Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z4H4
    Proc Natl Acad Sci U S A 107:16589-94. 2010
    ..The publicly available Pleiades MiniPromoter Project is a key resource to facilitate research on brain development and therapies...
  57. ncbi request reprint Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers
    Obi L Griffith
    Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
    J Clin Oncol 24:5043-51. 2006
    ..However, researchers are faced with an overwhelming number of potential markers from numerous thyroid cancer expression profiling studies...
  58. ncbi request reprint Selective targeting of indel-inferred differences in spatial structures of homologous proteins
    Yvonne Y Li
    CIHR MSFHR Strategic Training Program in Bioinformatics, University of British Columbia, 570 West 7th Avenue, Vancouver, British Columbia, V5Z 4S6, Canada
    J Bioinform Comput Biol 4:403-14. 2006
    ..While experimental evidence is required to verify our results, our findings thus far appear to support this approach as a new strategy for the development of antagonists against pathogenic targets having close human homologs...
  59. ncbi request reprint THOR: targeted high-throughput ortholog reconstructor
    Matthew N Bainbridge
    British Columbia Cancer Agency BCCA Genome Sciences Centre, 675 West 10th Avenue, Vancouver, BC, Canada
    Bioinformatics 23:2622-4. 2007
    ..3 min/promoter. THOR's reconstruction rate improves markedly with both higher-coverage, and less divergent target species...
  60. pmc An interactive tool for visualization of relationships between gene expression profiles
    Peter Ruzanov
    Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC V5Z 4S6, Canada
    BMC Bioinformatics 7:193. 2006
    ..Application of phenetic methods to gene expression analysis proved to be a successful approach. Visualizing the results in a 3-dimentional space may further enhance these techniques...
  61. pmc De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
    Scott DiGuistini
    Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
    Genome Biol 10:R94. 2009
    ..Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data...
  62. pmc Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers
    Stephen Yip
    Department of Pathology and Laboratory Medicine, BC Cancer Agency, BC, Canada
    J Pathol 226:7-16. 2012
    ..Our detailed study of genetic aberrations in oligodendroglioma suggests a functional interaction between CIC mutation, IDH1/2 mutation, and 1p/19q co-deletion...
  63. pmc Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast
    Fiona S L Brinkman
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
    Genome Res 12:1159-67. 2002
    ....
  64. ncbi request reprint Effect of TERT and ATM on gene expression profiles in human fibroblasts
    Agnes Baross
    Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    Genes Chromosomes Cancer 39:298-310. 2004
    ..Supplementary material for this article can be found on the Genes, Chromosomes and Cancer website at http://www.interscience.wiley.com/jpages/1045-2257/suppmat/index.html...
  65. pmc Physical map-assisted whole-genome shotgun sequence assemblies
    Rene L Warren
    British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
    Genome Res 16:768-75. 2006
    ..A 6.5-fold coverage draft DNA sequence of the Pan troglodytes (chimpanzee) genome was assembled using map-derived constraints and resulted in a 26.1% increase in scaffold contiguity...
  66. pmc ARID1A mutations in endometriosis-associated ovarian carcinomas
    Kimberly C Wiegand
    British Columbia Cancer Agency, Vancouver, Canada
    N Engl J Med 363:1532-43. 2010
    ..Ovarian clear-cell and endometrioid carcinomas may arise from endometriosis, but the molecular events involved in this transformation have not been described...
  67. pmc Assessment of SAGE in transcript identification
    Erin D Pleasance
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver V5Z 4E6, Canada
    Genome Res 13:1203-15. 2003
    ..This work identifies and quantifies genes not amenable to SAGE analysis, in addition to providing tag-to-gene mappings for two model organisms...
  68. pmc A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells
    Asim S Siddiqui
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 4S6
    Proc Natl Acad Sci U S A 102:18485-90. 2005
    ..The visual cortex, pancreas, mammary gland, preimplantation embryo, and placenta contain the largest number of differentially expressed transcripts, 25% of which are previously undescribed loci...
  69. pmc A survey of genomic properties for the detection of regulatory polymorphisms
    Stephen B Montgomery
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    PLoS Comput Biol 3:e106. 2007
    ..Using a 10-fold cross-validation approach, we were able to achieve a sensitivity and specificity of 0.82 and 0.71, respectively, and we show that this performance is strongly influenced by the distance to the transcription start site...
  70. doi request reprint De novo assembly and analysis of RNA-seq data
    Gordon Robertson
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
    Nat Methods 7:909-12. 2010
    ....
  71. pmc Sequence biases in large scale gene expression profiling data
    Asim S Siddiqui
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
    Nucleic Acids Res 34:e83. 2006
    ..The bias in the Affymetrix data primarily impacts genes expressed at lower levels. Despite the larger sampling of the MPSS library, SAGE identifies significantly more genes (60% more RefSeq genes in a single comparison)...
  72. pmc Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans
    Jacqueline E Schein
    Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 12:1445-53. 2002
    ..The physical maps also serve as a link between map-based and sequence-based data, providing a powerful resource for continued genomic studies..
  73. ncbi request reprint 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
    Steven G Ralph
    Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
    Plant Cell Environ 29:1545-70. 2006
    ..Induction of spruce genes of octadecanoid and ethylene signalling, terpenoid biosynthesis, and phenolic secondary metabolism are discussed in more detail...
  74. pmc Diagnostic utility of galectin-3 in thyroid cancer
    Connie G Chiu
    Department of Surgery, St Paul s Hospital and University of British Columbia, Vancouver, British Columbia, Canada
    Am J Pathol 176:2067-81. 2010
    ....
  75. pmc An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones
    Yaron S N Butterfield
    Genome Sciences Centre, BC Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
    Nucleic Acids Res 30:2460-8. 2002
    ....
  76. pmc Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression
    Julius Halaschek-Wiener
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
    Genome Res 15:603-15. 2005
    ..Comparison of our results to recent microarray studies highlights sets of overlapping genes that are highly conserved throughout evolution and thus represent strong candidate genes that control aging and longevity...
  77. pmc Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps
    Christopher D Fjell
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada
    Genome Res 13:1244-9. 2003
    ..We are also using iCE as part of the Rat Genome Sequencing Project to manage our provision of rat BAC clones for sequencing at the Human Genome Sequencing Center at the Baylor College of Medicine...
  78. doi request reprint Meta-analysis of colorectal cancer gene expression profiling studies identifies consistently reported candidate biomarkers
    Simon K Chan
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Suite 100, 570 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 4S6
    Cancer Epidemiol Biomarkers Prev 17:543-52. 2008
    ..One solution is to take the intersection of the lists from independent studies. However, often times, the statistical significance of the observed intersection are not assessed...
  79. pmc Identification and analysis of internal promoters in Caenorhabditis elegans operons
    Peiming Huang
    Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
    Genome Res 17:1478-85. 2007
    ..Our work suggests that hybrid operons are common in the C. elegans genome and that internal promoters influence not only gene organization and expression but also operon evolution...
  80. doi request reprint Complete genomic landscape of a recurring sporadic parathyroid carcinoma
    Katayoon Kasaian
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    J Pathol 230:249-60. 2013
    ..The key somatic mutations identified in this study can serve as novel diagnostic markers as well as therapeutic targets...
  81. ncbi request reprint Hive plots--rational approach to visualizing networks
    Martin Krzywinski
    BC Cancer Research Center, Vancouver, Canada
    Brief Bioinform 13:627-44. 2012
    ..The method is computationally straightforward, scales well and is amenable to a plugin for existing tools...
  82. doi request reprint Coordinated expression of galectin-3 and caveolin-1 in thyroid cancer
    Jay Shankar
    Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
    J Pathol 228:56-66. 2012
    ..Co-expression of Gal3 and Cav1 in the T238 anaplastic cell line stabilized FAK-GFP in focal adhesions. Gal3 and Cav1 therefore function synergistically to promote focal adhesion signalling, migration and progression of DTC...
  83. doi request reprint A new frontier in personalized cancer therapy: mapping molecular changes
    Katayoon Kasaian
    Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    Future Oncol 7:873-94. 2011
    ..This article provides an overview of advances in the molecular characterization of cancers and their applications in therapy...
  84. doi request reprint Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities
    Kasmintan A Schrader
    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
    J Pathol 225:12-8. 2011
    ..The diagnosis was confirmed by biochemical studies and both broadens the mucolipidosis type III phenotype and demonstrates the clinical utility of next-generation sequencing to diagnose rare genetic diseases...
  85. pmc Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver
    Brad G Hoffman
    Department of Cancer Endocrinology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
    Genome Res 20:1037-51. 2010
    ..Finally, we apply these approaches to generate novel insights into how FOXA2, PDX1, and HNF4A cooperate to drive islet- and liver-specific gene expression...
  86. ncbi request reprint Anaplastic thyroid carcinoma exhibits intratumoral molecular homogeneity for a therapeutic target panel
    Shaun Deen
    Department of Surgery, St Paul s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
    Anticancer Res 29:2437-44. 2009
    ..The objective of this work was to determine if molecular heterogeneity exists between different intratumoral histological subtype foci of anaplastic thyroid carcinoma (ATC)...
  87. doi request reprint Molecular phenotyping of thyroid tumors identifies a marker panel for differentiated thyroid cancer diagnosis
    Sam M Wiseman
    Department of Surgery, St Paul s Hospital, University of British Columbia, C303 1081 Burrard Street, Vancouver, BC, Canada
    Ann Surg Oncol 15:2811-26. 2008
    ..The objective of this work was to evaluate the molecular phenotype of differentiated thyroid cancer (DTC) and benign thyroid lesions to identify molecular markers that allow for accurate thyroid cancer diagnosis...
  88. ncbi request reprint Identification of molecular markers altered during transformation of differentiated into anaplastic thyroid carcinoma
    Sam M Wiseman
    Department of Surgery, St Paul s Hospital, University of British Columbia, C303 1081 Burrard St, Vancouver, BC, Canada V6Z 1Y6
    Arch Surg 142:717-27; discussion 727-9. 2007
    ..A change in tumor expression profile will be observed during the transformation of differentiated into anaplastic thyroid carcinoma...
  89. ncbi request reprint The Genome sequence of the SARS-associated coronavirus
    Marco A Marra
    British Columbia Cancer Agency BCCA Genome Sciences Centre, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada
    Science 300:1399-404. 2003
    ....
  90. pmc The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
    Brendan J Loftus
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:1321-4. 2005
    ..neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes...
  91. pmc The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)
    Daniela S Gerhard
    Genome Res 14:2121-7. 2004
    ..Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline...
  92. pmc Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics
    Matthew L Rise
    Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5 Canada
    Genome Res 14:478-90. 2004
    ..A microarray is described, containing 7356 salmonid elements representing 3557 different cDNAs. Analyses of cross-species hybridizations to this cDNA microarray indicate that this resource may be used for studies involving all salmonids...
  93. pmc Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling
    Ryan D Morin
    British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
    Genome Res 16:796-803. 2006
    ..Approximately 14% of the paralogous pairs analyzed here also show differential expression indicative of subfunctionalization...
  94. pmc Software for automated analysis of DNA fingerprinting gels
    Daniel R Fuhrmann
    Department of Electrical Engineering, Washington University, St Louis, Missouri 63130, USA
    Genome Res 13:940-53. 2003
    ..Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects...
  95. pmc Mapping segmental and sequence variations among laboratory mice using BAC array CGH
    Antoine M Snijders
    Cancer Research Institute, University of California San Francisco, San Francisco, California 94143, USA
    Genome Res 15:302-11. 2005
    ..1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses...
  96. ncbi request reprint Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques
    Laura Elnitski
    Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20878, USA
    Genome Res 16:1455-64. 2006
    ..A variety of techniques useful for localized- and high-throughput analyses are discussed here, with emphasis on aspects of data generation and verification...
  97. pmc Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences
    Robert L Strausberg
    National Cancer Institute, Bethessda, MD 20892 2580, USA
    Proc Natl Acad Sci U S A 99:16899-903. 2002
    ..All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov)...
  98. doi request reprint ALEXA: a microarray design platform for alternative expression analysis
    Malachi Griffith
    Nat Methods 5:118. 2008
  99. pmc Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans
    Barbara R Steen
    Biotechnology Laboratory, Department of Microbiology and Immunology, and Faculty of Agricultural Sciences, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
    Genome Res 12:1386-400. 2002
    ..Overall, this work provides the most comprehensive gene expression data available for C. neoformans; this information will be a critical resource both for gene discovery and genome annotation in this pathogen...
  100. ncbi request reprint A SAGE approach to discovery of genes involved in autophagic cell death
    Sharon M Gorski
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
    Curr Biol 13:358-63. 2003
    ..Our analyses strongly support both the emerging notion that there is overlap with respect to the molecules involved in autophagic cell death and apoptosis, and that there are important differences...
  101. ncbi request reprint A physical map of the genome of Atlantic salmon, Salmo salar
    Siemon H S Ng
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
    Genomics 86:396-404. 2005
    ....