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Steven Jones

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Diane L Trinh; Yongjun Zhao; Jianghong An; Joseph M Connors; Randy D Gascoyne; Steven J M Jones; Maria Mendez-Lago; Ryan D Morin; Andrew J Mungall; Jacqueline Schein; David W Scott; Christian Steidl; Marco A Marra
Analysis of FOXO1 mutations in diffuse large B-cell lymphoma.
Amy M Clemons; Monica P Colaiácovo; Steven J M Jones; Bhavatharini Kasinathan; Heather M Brockway; Yaron S Butterfield; Yizhi Yin; Sarit Smolikove
akirin is required for diakinesis bivalent structure and synaptonemal complex disassembly at meiotic prophase I.
Adrian M Dubuc; Charles G Eberhart; Cynthia Hawkins; Thomas Hielscher; David T W Jones; Steven J M Jones; Marcel Kool; Andrey Korshunov; Marco A Marra; Maria Mendez-Lago; A Sorana Morrissy; Paul A Northcott; John Peacock; Stefan M Pfister; Vijay Ramaswamy; Marc Remke; Adi Rolider; James T Rutka; David Shih; Alexander Unterberger; Rajeev Vibhakar; Xin Wang; William A Weiss; Hendrik Witt; Shing H Zhan; Sidney Croul; Michael D Taylor
Aberrant patterns of H3K4 and H3K27 histone lysine methylation occur across subgroups in medulloblastoma.

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2013: Diane L Trinh; Yongjun Zhao; Jianghong An; Joseph M Connors; Randy D Gascoyne; Steven J M Jones; Maria Mendez-Lago; Ryan D Morin; Andrew J Mungall; Jacqueline Schein; David W Scott; Christian Steidl; Marco A Marra
Analysis of FOXO1 mutations in diffuse large B-cell lymphoma.
Blood 2013;121(18):3666-74.
2013: Amy M Clemons; Monica P Colaiácovo; Steven J M Jones; Bhavatharini Kasinathan; Heather M Brockway; Yaron S Butterfield; Yizhi Yin; Sarit Smolikove
akirin is required for diakinesis bivalent structure and synaptonemal complex disassembly at meiotic prophase I.
Molecular biology of the cell 2013;24(7):1053-67.
2013: Adrian M Dubuc; Charles G Eberhart; Cynthia Hawkins; Thomas Hielscher; David T W Jones; Steven J M Jones; Marcel Kool; Andrey Korshunov; Marco A Marra; Maria Mendez-Lago; A Sorana Morrissy; Paul A Northcott; John Peacock; Stefan M Pfister; Vijay Ramaswamy; Marc Remke; Adi Rolider; James T Rutka; David Shih; Alexander Unterberger; Rajeev Vibhakar; Xin Wang; William A Weiss; Hendrik Witt; Shing H Zhan; Sidney Croul; Michael D Taylor
Aberrant patterns of H3K4 and H3K27 histone lysine methylation occur across subgroups in medulloblastoma.
Acta neuropathologica 2013;125(3):373-84.
2013: Kristen M Reipas; Amarpal S Cheema; Artem Cherkasov; Nicole Couto; John A Hassell; Sumaiya Islam; Steven J M Jones; Karen Jung; Jennifer H Law; Huifang Li; Yvonne Li; Sandra E Dunn
Luteolin is a novel p90 ribosomal S6 kinase (RSK) inhibitor that suppresses Notch4 signaling by blocking the activation of Y-box binding protein-1 (YB-1).
Oncotarget 2013;4(2):329-45.
2013: Zhaohui S Qin; Gang Su; Misha Bilenky; Steven J M Jones
MotifOrganizer: a scalable model-based motif clustering tool for mammalian genomes.
Frontiers in bioscience (Elite edition) 2013;5():785-97.
2012: Weishi Zhang; Yue Gong; Steven J M Jones; Stefan Knapp; Jeffrey J T Kwok; Yinghui Li; Sven Pettersson; Celine Prakash; Calvin Sum; Nina Thiessen; Henry Yang; Keh-Chuang Chin
Bromodomain-containing protein 4 (BRD4) regulates RNA polymerase II serine 2 phosphorylation in human CD4+ T cells.
The Journal of biological chemistry 2012;287(51):43137-55.
2012: Alireza Hadj Khodabakhshi; Marco A Marra; Ryan D Morin; Andrew J Mungall; Karen L Mungall; Inanc Birol; Madison Bolger-Munro; Joseph Michael Connors; Anthony P Fejes; Randy D Gascoyne; Nathalie A Johnson; Steven J M Jones
Recurrent targets of aberrant somatic hypermutation in lymphoma.
Oncotarget 2012;3(11):1308-19.
2012: Cydney B Nielsen; Henriette O'Geen; Ting Wang; Xiaoqin Xu; Hamid Younesy; Joseph F Costello; Peggy J Farnham; Martin Hirst; Andrew R Jackson; Aleksandar Milosavljevic; Steven J M Jones
Spark: a navigational paradigm for genomic data exploration.
Genome research 2012;22(11):2262-9.
2012: Christopher I Keeling; Maria Li; Nancy Y Liao; Diana Palmquist; Greg A Taylor; Mack Yuen; T Roderick Docking; Simon K Chan; Erin L Clark; Jordie D Fraser; Hannah Henderson; Dezene P W Huber; Steven J M Jones; Inanc Birol; Jörg Bohlmann
Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests.
Insect biochemistry and molecular biology 2012;42(8):525-36.
2012: Dan Doherty; Anthony P Fejes; A Micheil Innes; Gisele E Ishak; Steven J M Jones; Moien Kanaan; Edmond G Lemire; Aizeddin A Mhanni; Ian G Phelps; R Curtis Rogers; Hashem Shahin; Mustafa Tekin; Barbara L Triggs-Raine; Hatice Akay; Albert E Chudley; Gail Coghlan; Shing H Zhan; Teresa Zelinski
GPSM2 mutations cause the brain malformations and hearing loss in Chudley-McCullough syndrome.
American journal of human genetics 2012;90(6):1088-93.
2012: Connie G Chiu; Z Amy Fang; Blake Gilks; Steven J M Jones; Janessa Laskin; Hamid Masoudi; Simon K Chan; Richard Wood-Baker; Sam M Wiseman
Beta-catenin expression is prognostic of improved non-small cell lung cancer survival.
American journal of surgery 2012;203(5):654-9.
2012: Jeffrey S-C Chu; Shu Yi Chua; Mark Dennison; Robert C Johnsen; Steven J M Jones; Marco Marra; David L Baillie; Domena Tu; Ann M Rose
Allelic ratios and the mutational landscape reveal biologically significant heterozygous SNVs.
Genetics 2012;190(4):1225-33.
2012: Olexandr Ya Yakovenko; Volodymyr G Bdzhola; Yvonne Y Li; Alexander A Oliferenko; Ganna M Vashchenko; Steven J M Jones
Ab initio parameterization of YFF1, a universal force field for drug-design applications.
Journal of molecular modeling 2012;18(2):663-73.
2012: Cheng-Han Lee; Adrian Mariño-Enriquez; Marco A Marra; Mark Mayeda; Jessica N McAlpine; Andrew McPherson; Marisa R Nucci; Wen-Bin Ou; Leah M Prentice; Sohrab P Shah; Matt van de Rijn; Yuexiang Wang; Robert B West; Michael B Yaffe; Meijun Zhu; Frederic Amant; Alayne L Brunner; Paola Dal Cin; Maria Debiec-Rychter; Christopher A French; C Blake Gilks; Xiangqian Guo; David G Huntsman; Steven J M Jones; Jonathan A Fletcher
14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(3):929-34.
2012: William T Gibson; Rebecca L Hood; Jianghong An; Riyana Babul-Hirji; Kym M Boycott; Dennis E Bulman; David Chitayat; Patrice Eydoux; Anthony P Fejes; Marco A Marra; Richard Moore; Andrew J Mungall; David D Weaver; Shing Hei Zhan; Steven J M Jones
Mutations in EZH2 cause Weaver syndrome.
American journal of human genetics 2012;90(1):110-8.
2012: Pavle Vrljicak; Elizabeth D Wederell; Eric Xu; Steven J M Jones; Aly Karsan; Marco A Marra; Mikhail Bilenky; Alex C Y Chang; Rebecca Cullum; Pamela A Hoodless
Twist1 transcriptional targets in the developing atrio-ventricular canal of the mouse.
PloS one 2012;7(7):e40815.
2011: Yvonne Y Li; Jianghong An; Steven J M Jones
A computational approach to finding novel targets for existing drugs.
PLoS computational biology 2011;7(9):e1002139.
2011: Amanda Johner; Steven J M Jones; Hannah Piper; Blair Walker; Graeme Wilkins; Christopher R Baliski; Obi L Griffith; Leanne Wood; Sam M Wiseman
Detection and management of hypothyroidism following thyroid lobectomy: evaluation of a clinical algorithm.
Annals of surgical oncology 2011;18(9):2548-54.
2011: Sam M Wiseman; Obi L Griffith; Allen Gown; Blair Walker; Steven J M Jones
Immunophenotyping of thyroid tumors identifies molecular markers altered during transformation of differentiated into anaplastic carcinoma.
American journal of surgery 2011;201(5):580-6.
2011: Anthony P Fejes; Alireza Hadj Khodabakhshi; Inanc Birol; Steven J M Jones
Human variation database: an open-source database template for genomic discovery.
Bioinformatics (Oxford, England) 2011;27(8):1155-6.
2011: Armando Geraldes; Johnson Pang; Nina Thiessen; Timothee Cezard; Richard Moore; Yongjun Zhao; Angela Tam; Shucai Wang; Michael Friedmann; Inanc Birol; Steven J M Jones; Quentin C B Cronk; Carl J Douglas
SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing.
Molecular ecology resources 2011;11 Suppl 1():81-92.
2011: Jennifer L Gardy; James C Johnston; Shannan J Ho Sui; Victoria J Cook; Lena Shah; Elizabeth Brodkin; Shirley Rempel; Richard Moore; Yongjun Zhao; Robert Holt; Richard Varhol; Inanc Birol; Marcus Lem; Meenu K Sharma; Kevin Elwood; Steven J M Jones; Fiona S L Brinkman; Robert brunham; Patrick Tang
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.
The New England journal of medicine 2011;364(8):730-9.
2011: Scott DiGuistini; Ye Wang; Nancy Y Liao; Greg Taylor; Philippe Tanguay; Nicolas Feau; Bernard Henrissat; Simon K Chan; Uljana Hesse-Orce; Sepideh Massoumi Alamouti; Clement Tsui; Roderick T Docking; Anthony Levasseur; Sajeet Haridas; Gordon Robertson; Inanc Birol; Robert A Holt; Marco A Marra; Richard C Hamelin; Martin Hirst; Steven J M Jones; Jörg Bohlmann; Colette Breuil
Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(6):2504-9.
2011: Binhua Liang; Ma Luo; Mark Mendoza; Blake T Ball; Rupert Capina; Morag Graham; Hezhao Ji; Steven J M Jones; Joshua Kimani; Joel Scott-Herridge; Christina Semeniuk; Brent Sheardown; Shane Tyler; Gary H Van Domselaar; Francis A Plummer
A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1.
PloS one 2011;6(10):e26745.
2010: Gordon Robertson; Jacqueline Schein; Readman Chiu; Richard Corbett; Matthew Field; Shaun D Jackman; Karen Mungall; Sam Lee; Hisanaga Mark Okada; Jenny Q Qian; Malachi Griffith; Anthony Raymond; Nina Thiessen; Timothee Cezard; Yaron S Butterfield; Richard Newsome; Simon K Chan; Rong She; Richard J Varhol; Baljit Kamoh; Anna-Liisa Prabhu; Angela Tam; Yongjun Zhao; Richard A Moore; Martin Hirst; Marco A Marra; Steven J M Jones; Pamela A Hoodless; Inanc Birol
De novo assembly and analysis of RNA-seq data.
Nature methods 2010;7(11):909-12.
2010: Malachi Griffith; Obi L Griffith; Jill Mwenifumbo; Rodrigo Goya; A Sorana Morrissy; Ryan D Morin; Richard Corbett; Michelle J Tang; Ying-Chen Hou; Trevor J Pugh; Gordon Robertson; Suganthi Chittaranjan; Adrian Ally; Jennifer K Asano; Susanna Y Chan; Haiyan I Li; Helen McDonald; Kevin Teague; Yongjun Zhao; Thomas Zeng; Allen D Delaney; Martin Hirst; Gregg B Morin; Steven J M Jones; Isabella T Tai; Marco A Marra
Alternative expression analysis by RNA sequencing.
Nature methods 2010;7(10):843-7.
2010: Binhua Liang; Ma Luo; T Blake Ball; Steven J M Jones; Francis A Plummer
QUASI analysis of host immune responses to Gag polyproteins of human immunodeficiency virus type 1 by a systematic bioinformatics approach.
Biochemistry and cell biology = Biochimie et biologie cellulaire 2010;88(4):671-81.
2010: Brad G Hoffman; Gordon Robertson; Bogard Zavaglia; Mike Beach; Rebecca Cullum; Sam Lee; Galina Soukhatcheva; Leping Li; Elizabeth D Wederell; Nina Thiessen; Mikhail Bilenky; Timothee Cezard; Angela Tam; Baljit Kamoh; Inanc Birol; Derek Dai; Yongjun Zhao; Martin Hirst; C Bruce Verchere; Cheryl D Helgason; Marco A Marra; Steven J M Jones; Pamela A Hoodless
Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver.
Genome research 2010;20(8):1037-51.
2010: Alika K Maunakea; Raman P Nagarajan; Mikhail Bilenky; Tracy J Ballinger; Cletus D'Souza; Shaun D Fouse; Brett E Johnson; Chibo Hong; Cydney Nielsen; Yongjun Zhao; Gustavo Turecki; Allen Delaney; Richard Varhol; Nina Thiessen; Ksenya Shchors; Vivi M Heine; David H Rowitch; Xiaoyun Xing; Chris Fiore; Maximiliaan Schillebeeckx; Steven J M Jones; David Haussler; Marco A Marra; Martin Hirst; Ting Wang; Joseph F Costello
Conserved role of intragenic DNA methylation in regulating alternative promoters.
Nature 2010;466(7303):253-7.
2010: Santosh S Atanur; Inanç Birol; Victor Guryev; Martin Hirst; Oliver Hummel; Catherine Morrissey; Jacques Behmoaras; Xose M. Fernandez; Michelle D Johnson; William M McLaren; Giannino Patone; Enrico Petretto; Charles Plessy; Kathleen S Rockland; Charles Rockland; Kathrin Saar; Yongjun Zhao; piero carninci; Paul Flicek; Ted Kurtz; Edwin Cuppen; Michal Pravenec; Norbert Hubner; Steven J M Jones; Ewan Birney; Timothy J Aitman
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Genome research 2010;20(6):791-803.
2010: Connie G Chiu; Scott S Strugnell; Obi L Griffith; Steven J M Jones; Allen M Gown; Blair Walker; Ivan R Nabi; Sam M Wiseman
Diagnostic utility of galectin-3 in thyroid cancer.
The American journal of pathology 2010;176(5):2067-81.
2010: Monica Sleumer; Allan K Mah; David L Baillie; Steven J M Jones
Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans.
Nucleic acids research 2010;38(9):2990-3004.
2010: Nawar Malhis; Steven J M Jones
High quality SNP calling using Illumina data at shallow coverage.
Bioinformatics (Oxford, England) 2010;26(8):1029-35.
2010: Jennifer H Law; Yvonne Li; Karen To; Michelle Wang; Arezoo Astanehe; K Lambie; Jaspreet Dhillon; Steven J M Jones; Martin E Gleave; Connie J Eaves; Sandra E Dunn
Molecular decoy to the Y-box binding protein-1 suppresses the growth of breast and prostate cancer cells whilst sparing normal cell viability.
PloS one 2010;5(9):.
2010: Stephen B Montgomery; Katayoon Kasaian; Steven J M Jones; Obi L Griffith
Annotating the regulatory genome.
Methods in molecular biology (Clifton, N.J.) 2010;674():313-49.
2009: Cydney B Nielsen; Shaun D Jackman; Inanç Birol; Steven J M Jones
ABySS-Explorer: visualizing genome sequence assemblies.
IEEE transactions on visualization and computer graphics 2009;15(6):881-8.
2009: Inanç Birol; Shaun D Jackman; Cydney B Nielsen; Jenny Q Qian; Richard Varhol; Greg Stazyk; Ryan D Morin; Yongjun Zhao; Martin Hirst; Jacqueline E Schein; Doug E Horsman; Joseph Michael Connors; Randy D Gascoyne; Marco A Marra; Steven J M Jones
De novo transcriptome assembly with ABySS.
Bioinformatics (Oxford, England) 2009;25(21):2872-7.
2009: Shaun Deen; Obi L Griffith; Hamid Masoudi; Allen Gown; Steven J M Jones; Sam M Wiseman
Anaplastic thyroid carcinoma exhibits intratumoral molecular homogeneity for a therapeutic target panel.
Anticancer research 2009;29(7):2437-44.
2009: Barbara Meissner; Adam Warner; Kim Wong; Nicholas Dube; Adam Lorch; Sheldon J McKay; Jaswinder Khattra; Teresa Rogalski; Aruna Somasiri; Iasha Chaudhry; Rebecca M Fox; David M Miller; David Baillie; Robert A Holt; Steven J M Jones; Marco A Marra; Donald G Moerman
An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans.
PLoS genetics 2009;5(6):e1000537.
2009: Jared T Simpson; Kim Wong; Shaun D Jackman; Jacqueline E Schein; Steven J M Jones; Inanç Birol
ABySS: a parallel assembler for short read sequence data.
Genome research 2009;19(6):1117-23.
2009: Jianghong An; Davy C W Lee; Anna H Y Law; Cindy L H Yang; Leo L M Poon; Allan S Y Lau; Steven J M Jones
A novel small-molecule inhibitor of the avian influenza H5N1 virus determined through computational screening against the neuraminidase.
Journal of medicinal chemistry 2009;52(9):2667-72.
2009: Brad G Hoffman; Steven J M Jones
Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing.
The Journal of endocrinology 2009;201(1):1-13.
2009: James D McGhee; Tetsunari Fukushige; Michael W Krause; Stephanie E Minnema; Barbara Goszczynski; Jeb Gaudet; Yuji Kohara; Olaf Bossinger; Yongjun Zhao; Jaswinder Khattra; Martin Hirst; Steven J M Jones; Marco A Marra; Peter Ruzanov; Adam Warner; Richard Zapf; Donald G Moerman; John M Kalb
ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult.
Developmental biology 2009;327(2):551-65.
2009: Monica Sleumer; Mikhail Bilenky; Ann He; Gordon Robertson; Nina Thiessen; Steven J M Jones
Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements.
Nucleic acids research 2009;37(4):1323-34.
2008: A Gordon Robertson; Mikhail Bilenky; Angela Tam; Yongjun Zhao; Thomas Zeng; Nina Thiessen; Timothee Cezard; Anthony P Fejes; Elizabeth D Wederell; Rebecca Cullum; Ghia Euskirchen; Martin Krzywinski; Inanc Birol; Michael Snyder; Pamela A Hoodless; Martin Hirst; Marco A Marra; Steven J M Jones
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.
Genome research 2008;18(12):1906-17.
2008: Sam M Wiseman; Adrienne Melck; Hamid Masoudi; Fariba Ghaidi; Lynn Goldstein; Allen M Gown; Steven J M Jones; Obi L Griffith
Molecular phenotyping of thyroid tumors identifies a marker panel for differentiated thyroid cancer diagnosis.
Annals of surgical oncology 2008;15(10):2811-26.
2008: Obi L Griffith; Connie G Chiu; Allen M Gown; Steven J M Jones; Sam M Wiseman
Biomarker panel diagnosis of thyroid cancer: a critical review.
Expert review of anticancer therapy 2008;8(9):1399-413.
2008: Anthony P Fejes; Gordon Robertson; Mikhail Bilenky; Richard Varhol; Matthew Bainbridge; Steven J M Jones
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology.
Bioinformatics (Oxford, England) 2008;24(15):1729-30.
2008: Binhua Liang; Ma Luo; T Blake Ball; Xiaojian Yao; Gary Van Domselaar; Wilfred R Cuff; Mary Cheang; Steven J M Jones; Francis A Plummer
Systematic analysis of host immunological pressure on the envelope gene of human immunodeficiency virus type 1 by an immunobioinformatics approach.
Current HIV research 2008;6(4):370-9.
2008: Robert A Holt; Steven J M Jones
The new paradigm of flow cell sequencing.
Genome research 2008;18(6):839-46.
2008: Sam M Wiseman; Obi L Griffith; Adrienne Melck; Hamid Masoudi; Allen M Gown; Ivan R Nabi; Steven J M Jones
Evaluation of type 1 growth factor receptor family expression in benign and malignant thyroid lesions.
American journal of surgery 2008;195(5):667-73; discussion 673.
2008: Simon K Chan; Obi L Griffith; Isabella T Tai; Steven J M Jones
Meta-analysis of colorectal cancer gene expression profiling studies identifies consistently reported candidate biomarkers.
Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2008;17(3):543-52.
2008: Malachi Griffith; Michelle J Tang; Obi L Griffith; Ryan D Morin; Susanna Y Chan; Jennifer K Asano; Thomas Zeng; Stephane Flibotte; Adrian Ally; Agnes Baross; Martin Hirst; Steven J M Jones; Gregg B Morin; Isabella T Tai; Marco A Marra
ALEXA: a microarray design platform for alternative expression analysis.
Nature methods 2008;5(2):118.
2008: Steven G Ralph; Hye Jung E Chun; Natalia Kolosova; Dawn Cooper; Claire Oddy; Carol Ritland; Robert Kirkpatrick; Richard Moore; Sarah Barber; Robert A Holt; Steven J M Jones; Marco A Marra; Carl J Douglas; Kermit Ritland; Jörg Bohlmann
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;9():484.
2008: Cletus A D'Souza; Vikramjit Chopra; Richard Varhol; Yuan-Yun Xie; Slavita Bohacec; Yongjun Zhao; Lisa L C Lee; Mikhail Bilenky; Elodie Portales-Casamar; An He; Wyeth W Wasserman; Daniel Goldowitz; Marco A Marra; Robert A Holt; Elizabeth M Simpson; Steven J M Jones
Identification of a set of genes showing regionally enriched expression in the mouse brain.
BMC neuroscience 2008;9():66.
2008: Heesun Shin; Martin Hirst; Matthew N Bainbridge; vincent magrini; Elaine Mardis; Donald G Moerman; Marco A Marra; David Baillie; Steven J M Jones
Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.
BMC biology 2008;6():30.
2008: Brad G Hoffman; Bogard Zavaglia; Joy Witzsche; Teresa Ruiz de Algara; Mike Beach; Pamela A Hoodless; Steven J M Jones; Marco A Marra; Cheryl D Helgason
Identification of transcripts with enriched expression in the developing and adult pancreas.
Genome biology 2008;9(6):R99.
2008: Stein Aerts; Maximilian Haeussler; Steven van Vooren; Obi L Griffith; Paco Hulpiau; Steven J M Jones; Stephen B Montgomery; Casey M Bergman
Text-mining assisted regulatory annotation.
Genome biology 2008;9(2):R31.
2008: Steven G Ralph; Hye Jung E Chun; Dawn Cooper; Robert Kirkpatrick; Natalia Kolosova; Lee Gunter; Gerald A Tuskan; Carl J Douglas; Robert A Holt; Steven J M Jones; Marco A Marra; Jörg Bohlmann
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;9():57.
2008: Obi L Griffith; Stephen B Montgomery; Bridget Bernier; Bryan Chu; Katayoon Kasaian; Stein Aerts; Shaun Mahony; Monica Sleumer; Mikhail Bilenky; Maximilian Haeussler; Malachi Griffith; Steven M Gallo; Belinda Giardine; Bart Hooghe; Peter Van Loo; Enrique Blanco; Amy Ticoll; Stuart Lithwick; Elodie Portales-Casamar; Ian J Donaldson; Gordon Robertson; Claes Wadelius; Pieter De Bleser; Dominique Vlieghe; Marc S. Halfon; Wyeth W Wasserman; Ross C Hardison; Casey M Bergman; Steven J M Jones
ORegAnno: an open-access community-driven resource for regulatory annotation.
Nucleic acids research 2008;36(Database issue):D107-13.
2007: Adrienne Melck; Hamid Masoudi; Obi L Griffith; Ashish Rajput; Graeme Wilkins; Samuel P Bugis; Steven J M Jones; Sam M Wiseman
Cell cycle regulators show diagnostic and prognostic utility for differentiated thyroid cancer.
Annals of surgical oncology 2007;14(12):3403-11.
2007: Fred Y Peng; Karen E Reid; Nancy Liao; James Schlosser; Diego Lijavetzky; Robert Holt; José M Martínez-Zapater; Steven J M Jones; Marco Marra; Jörg Bohlmann; Steven T Lund
Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development.
Gene 2007;402(1-2):40-50.
2007: Peiming Huang; Erin D Pleasance; Jason S Maydan; Rebecca Hunt-Newbury; Nigel J O'Neil; Allan K Mah; David Baillie; Marco A Marra; Donald G Moerman; Steven J M Jones
Identification and analysis of internal promoters in Caenorhabditis elegans operons.
Genome research 2007;17(10):1478-85.
2007: Matthew N Bainbridge; Rene Warren; Ann He; Mikhail Bilenky; A Gordon Robertson; Steven J M Jones
THOR: targeted high-throughput ortholog reconstructor.
Bioinformatics (Oxford, England) 2007;23(19):2622-4.
2007: Rebecca Hunt-Newbury; Ryan Viveiros; Robert C Johnsen; Allan K Mah; Dina Anastas; Lily Fang; Erin Halfnight; David Lee; John Lin; Adam Lorch; Sheldon McKay; H Mark Okada; Jie Pan; Ana K Schulz; Domena Tu; Kim Wong; Z Zhao; Andrey Alexeyenko; Thomas Burglin; Eric Sonnhammer; Ralf Schnabel; Steven J M Jones; Marco A Marra; David Baillie; Donald G Moerman
High-throughput in vivo analysis of gene expression in Caenorhabditis elegans.
PLoS biology 2007;5(9):e237.
2007: Sam M Wiseman; Obi L Griffith; Shaun Deen; Ashish Rajput; Hamid Masoudi; Blake Gilks; Lynn Goldstein; Allen M Gown; Steven J M Jones
Identification of molecular markers altered during transformation of differentiated into anaplastic thyroid carcinoma.
Archives of surgery (Chicago, Ill. : 1960) 2007;142(8):717-27; discussion 727-9.
2007: Gordon Robertson; Martin Hirst; Matthew N Bainbridge; Mikhail Bilenky; Yongjun Zhao; Thomas Zeng; Ghia Euskirchen; Bridget Bernier; Richard J Varhol; Allen D Delaney; Nina Thiessen; Obi L Griffith; Ann He; Marco Marra; Michael Snyder; Steven J M Jones
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
Nature methods 2007;4(8):651-7.
2007: Peter Ruzanov; Donald L Riddle; Marco A Marra; Sheldon J McKay; Steven J M Jones
Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults.
Experimental gerontology 2007;42(8):825-39.
2007: S Anand Trip; Patricio Schlottmann; Steven J M Jones; Wai-Yung Li; David F Garway-Heath; Alan J Thompson; Gordon T Plant; David H Miller
Optic nerve magnetization transfer imaging and measures of axonal loss and demyelination in optic neuritis.
Multiple sclerosis (Houndmills, Basingstoke, England) 2007;13(7):875-9.
2007: John F Etchberger; Adam Lorch; Monica C Sleumer; Richard Zapf; Steven J M Jones; Marco A Marra; Robert A Holt; Donald G Moerman; Oliver Hobert
The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron.
Genes & development 2007;21(13):1653-74.
2007: Yun Zhao; Afshin Raouf; David Kent; Jaswinder Khattra; Allen D Delaney; Angelique Schnerch; Jennifer Asano; Helen McDonald; Christina Chan; Steven J M Jones; Marco A Marra; Connie J Eaves
A modified polymerase chain reaction-long serial analysis of gene expression protocol identifies novel transcripts in human CD34+ bone marrow cells.
Stem cells (Dayton, Ohio) 2007;25(7):1681-9.
2007: Stephen B Montgomery; Obi L Griffith; Johanna M Schuetz; Angela R Brooks-Wilson; Steven J M Jones
A survey of genomic properties for the detection of regulatory polymorphisms.
PLoS computational biology 2007;3(6):e106.
2007: Rene Warren; Granger Sutton; Steven J M Jones; Robert A Holt
Assembling millions of short DNA sequences using SSAKE.
Bioinformatics (Oxford, England) 2007;23(4):500-1.
2007: James D McGhee; Monica C Sleumer; Mikhail Bilenky; Kim Wong; Sheldon J McKay; Barbara Goszczynski; Helen Tian; Natisha D Krich; Jaswinder Khattra; Robert A Holt; David Baillie; Yuji Kohara; Marco A Marra; Steven J M Jones; Donald G Moerman; A Gordon Robertson
The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine.
Developmental biology 2007;302(2):627-45.
2007: Scott DiGuistini; Steven G Ralph; Young Woon Lim; Robert Holt; Steven J M Jones; Jörg Bohlmann; Colette Breuil
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(2):151-8.
2007: Julie M Kneller; Thomas G Ehlen; Jasenka Matisic; Dianne Miller; Dirk Van Niekerk; Wan L Lam; Marco Marra; Rebecca Richards-Kortum; Michele Follen; Calum MacAulay; Steven J M Jones
Using LongSAGE to Detect Biomarkers of Cervical Cancer Potentially Amenable to Optical Contrast Agent Labelling.
Biomarker insights 2007;2():447-61.
2007: Adrian P Quayle; Asim S Siddiqui; Steven J M Jones
Perturbation of interaction networks for application to cancer therapy.
Cancer informatics 2007;5():45-65.
2007: Peter Ruzanov; Steven J M Jones; Donald L Riddle
Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data.
BMC genomics 2007;8():447.
2007: Martin I Krzywinski; Ian Bosdet; Carrie Mathewson; Natasja Wye; Jay Brebner; Readman Chiu; Richard Corbett; Matthew Field; Darlene Lee; Trevor Pugh; Stanislav V Volik; Asim Siddiqui; Steven J M Jones; Jacqueline E Schein; Collin Collins; Marco Marra
A BAC clone fingerprinting approach to the detection of human genome rearrangements.
Genome biology 2007;8(10):R224.
2007: Juan Hou; Anita M Charters; Sam C Lee; Yongjun Zhao; Mona K Wu; Steven J M Jones; Marco A Marra; Pamela A Hoodless
A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE).
BMC developmental biology 2007;7():92.
2007: Steven N Quayle; Heidi Hare; Allen D Delaney; Martin Hirst; Dorothy Hwang; Jacqueline E Schein; Steven J M Jones; Marco A Marra; Marianne D Sadar
Novel expressed sequences identified in a model of androgen independent prostate cancer.
BMC genomics 2007;8():32.
2007: Neil Robertson; Mehrdad Oveisi-Fordorei; Scott D Zuyderduyn; Richard J Varhol; Christopher Fjell; Marco Marra; Steven J M Jones; Asim Siddiqui
DiscoverySpace: an interactive data analysis application.
Genome biology 2007;8(1):R6.
2007: Jaswinder Khattra; Allen D Delaney; Yongjun Zhao; Asim Siddiqui; Jennifer Asano; Helen McDonald; Pawan Pandoh; Noreen Dhalla; Anna-Liisa Prabhu; Kevin Ma; Stephanie Lee; Adrian Ally; Angela Tam; Danne Sa; Sean Rogers; David Charest; Jeff M Stott; Scott D Zuyderduyn; Richard J Varhol; Connie Eaves; Steven J M Jones; Robert Holt; Martin Hirst; Pamela A Hoodless; Marco A Marra
Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.
Genome research 2007;17(1):108-16.
2006: Laura Elnitski; Victor X Jin; Peggy J Farnham; Steven J M Jones
Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques.
Genome research 2006;16(12):1455-64.
2006: Kim M Lonergan; Raj Chari; Ronald deLeeuw; Ashleen Shadeo; Bryan Chi; Ming Tsao; Steven J M Jones; Marco Marra; Victor Ling; Raymond Ng; Calum MacAulay; Stephen Lam; Wan L Lam
Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression.
American journal of respiratory cell and molecular biology 2006;35(6):651-61.
2006: G Wang; Steven J M Jones; Marco A Marra; Marianne D Sadar
Identification of genes targeted by the androgen and PKA signaling pathways in prostate cancer cells.
Oncogene 2006;25(55):7311-23.
2006: Obi L Griffith; Adrienne Melck; Steven J M Jones; Sam M Wiseman
Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers.
Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2006;24(31):5043-51.
2006: Michael P McLeod; Rene Warren; William WL Hsiao; Naoto Araki; Matthew Myhre; Clinton Fernandes; Daisuke Miyazawa; Wendy Wong; Anita L Lillquist; Dennis Wang; Manisha Dosanjh; Hirofumi Hara; Anca Petrescu; Ryan D Morin; George Yang; Jeff M Stott; Jacqueline E Schein; Heesun Shin; Duane E Smailus; Asim S Siddiqui; Marco A Marra; Steven J M Jones; Robert Holt; Fiona S L Brinkman; Keisuke Miyauchi; Masao Fukuda; Julian E Davies; William W Mohn; Lindsay D Eltis
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(42):15582-7.
2006: Guus Bakkeren; Guoqiao Jiang; Rene Warren; Yaron S N Butterfield; Heesun Shin; Readman Chiu; Rob Linning; Jacqueline E Schein; Nancy Lee; Guanggan Hu; Doris M Kupfer; Yuhong Tang; Bruce A Roe; Steven J M Jones; Marco Marra; James W Kronstad
Mating factor linkage and genome evolution in basidiomycetous pathogens of cereals.
Fungal genetics and biology : FG & B 2006;43(9):655-66.
2006: Steven G Ralph; Hesther Yueh; Michael Friedmann; Dana Aeschliman; Jeffrey A Zeznik; Colleen C Nelson; Yaron S N Butterfield; Robert Kirkpatrick; Jerry Liu; Steven J M Jones; Marco A Marra; Carl J Douglas; Kermit Ritland; Jörg Bohlmann
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 & environment 2006;29(8):1545-70.
2006: Rene Warren; Dmitry Varabei; Darren Platt; Xiaoqiu Huang; David Messina; Shiaw-Pyng Yang; James W Kronstad; Martin I Krzywinski; Wesley C Warren; John W Wallis; LaDeana W Hillier; Asif T Chinwalla; Jacqueline E Schein; Asim S Siddiqui; Marco A Marra; Richard K Wilson; Steven J M Jones
Physical map-assisted whole-genome shotgun sequence assemblies.
Genome research 2006;16(6):768-75.
2006: Yvonne Y Li; Steven J M Jones; Artem Cherkasov
Selective targeting of indel-inferred differences in spatial structures of homologous proteins.
Journal of bioinformatics and computational biology 2006;4(2):403-14.
2006: Stephen B Montgomery; Obi L Griffith; Monica Sleumer; C M Bergman; Mikhail Bilenky; Erin D Pleasance; Y Prychyna; X Zhang; Steven J M Jones
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.
Bioinformatics (Oxford, England) 2006;22(5):637-40.
2006: Gary M Wilson; Stephane Flibotte; Perseus I Missirlis; Marco A Marra; Steven J M Jones; Kevin Thornton; andrew clark; Robert A Holt
Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla.
Genome research 2006;16(2):173-81.
2006: Yvonne Y Li; Jianghong An; Steven J M Jones
A large-scale computational approach to drug repositioning.
Genome informatics. International Conference on Genome Informatics 2006;17(2):239-47.
2006: Matthew N Bainbridge; Rene Warren; Martin Hirst; Tammy Romanuik; Thomas Zeng; Anne Go; Allen D Delaney; Malachi Griffith; Matthew Hickenbotham; vincent magrini; Elaine R Mardis; Marianne D Sadar; Asim S Siddiqui; Marco A Marra; Steven J M Jones
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.
BMC genomics 2006;7():246.
2006: Asim S Siddiqui; Allen D Delaney; Angelique Schnerch; Obi L Griffith; Steven J M Jones; Marco A Marra
Sequence biases in large scale gene expression profiling data.
Nucleic acids research 2006;34(12):e83.
2006: Steven J M Jones
Prediction of genomic functional elements.
Annual review of genomics and human genetics 2006;7():315-38.
2006: Peter Ruzanov; Steven J M Jones
An interactive tool for visualization of relationships between gene expression profiles.
BMC bioinformatics 2006;7():193.
2006: G Robertson; Mikhail Bilenky; K Lin; Ann He; W Yuen; M Dagpinar; Richard J Varhol; K Teague; Obi L Griffith; X Zhang; Y Pan; M Hassel; Monica Sleumer; W Pan; Erin D Pleasance; M Chuang; H Hao; Y Y Li; N Robertson; C Fjell; B Li; Stephen B Montgomery; T Astakhova; J Zhou; J Sander; Asim S Siddiqui; Steven J M Jones
cisRED: a database system for genome-scale computational discovery of regulatory elements.
Nucleic acids research 2006;34(Database issue):D68-73.
2005: Luis M Larraya; Kylie J Boyce; Austin So; Barbara R Steen; Steven J M Jones; Marco Marra; James W Kronstad
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):2029-43.
2005: Artem Cherkasov; Zheng Shi; Yvonne Li; Steven J M Jones; Magid Fallahi; Geoffrey L Hammond
'Inductive' charges on atoms in proteins: comparative docking with the extended steroid benchmark set and discovery of a novel SHBG ligand.
Journal of chemical information and modeling 2005;45(6):1842-53.
2005: Obi L Griffith; Erin D Pleasance; Debra L Fulton; Mehrdad Oveisi; Martin Ester; Asim S Siddiqui; Steven J M Jones
Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses.
Genomics 2005;86(4):476-88.
2005: Siemon H S Ng; Carlo G Artieri; Ian Bosdet; Readman Chiu; Roy G Danzmann; William S Davidson; Moira M Ferguson; Christopher D Fjell; Bjorn Hoyheim; Steven J M Jones; Pieter J de Jong; Ben F Koop; Martin I Krzywinski; Krzysztof Lubieniecki; Marco A Marra; Leslie A Mitchell; Carrie Mathewson; Kazutoyo Osoegawa; Sarah E Parisotto; Ruth B Phillips; Matthew L Rise; Kristian R Von Schalburg; Jacqueline E Schein; Heesun Shin; Asim Siddiqui; Jim Thorsen; Natasja Wye; George Yang; Baoli Zhu
A physical map of the genome of Atlantic salmon, Salmo salar.
Genomics 2005;86(4):396-404.
2005: Stephen B Montgomery; Tony Fu; Jun Guan; Keven Lin; Steven J M Jones
An application of peer-to-peer technology to the discovery, use and assessment of bioinformatics programs.
Nature methods 2005;2(8):563.
2005: Oliver E Blacque; Elliot A Perens; Keith A Boroevich; Peter N Inglis; Chunmei Li; Adam Warner; Jaswinder Khattra; Rob A Holt; Guangshuo Ou; Allan K Mah; Sheldon J McKay; Peter Huang; Peter Swoboda; Steven J M Jones; Marco A Marra; David Baillie; Donald G Moerman; Shai Shaham; Michel R Leroux
Functional genomics of the cilium, a sensory organelle.
Current biology : CB 2005;15(10):935-41.
2005: Rene Warren; Yaron S N Butterfield; Ryan D Morin; Asim S Siddiqui; Marco A Marra; Steven J M Jones
Management and visualization of whole genome shotgun assemblies using SAM.
BioTechniques 2005;38(5):715-6, 718, 720.
2005: Julius Halaschek-Wiener; Jaswinder Khattra; Sheldon McKay; Anatoli Pouzyrev; Jeff M Stott; George S Yang; Robert A Holt; Steven J M Jones; Marco A Marra; Angela R Brooks-Wilson; Donald L Riddle
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression.
Genome research 2005;15(5):603-15.
2005: Tianshun Lian; Megan I Simmer; Cletus A D'Souza; Barbara R Steen; Scott D Zuyderduyn; Steven J M Jones; Marco A Marra; James W Kronstad
Iron-regulated transcription and capsule formation in the fungal pathogen Cryptococcus neoformans.
Molecular microbiology 2005;55(5):1452-72.
2005: Antoine M Snijders; Norma J Nowak; Bing Huey; Jane Fridlyand; Sindy Law; Jeffrey Conroy; Taku Tokuyasu; Kubilay Demir; Readman Chiu; Jian-Hua Mao; Ajay N Jain; Steven J M Jones; Allan Balmain; Daniel Pinkel; Donna G Albertson
Mapping segmental and sequence variations among laboratory mice using BAC array CGH.
Genome research 2005;15(2):302-11.
2004: Martin Hirst; Caroline R Astell; Malachi Griffith; Shaun M Coughlin; Michelle Moksa; Thomas Zeng; Duane E Smailus; Robert A Holt; Steven J M Jones; Marco A Marra; Martin Petric; Mel Krajden; David Lawrence; Annie Mak; Ron Chow; Danuta M Skowronski; S Aleina Tweed; SweeHan Goh; Robert brunham; John Robinson; Victoria Bowes; Ken Sojonky; Sean K Byrne; Yan Li; Darwyn Kobasa; Timothy F Booth; Mark Paetzel
Novel avian influenza H7N3 strain outbreak, British Columbia.
Emerging infectious diseases 2004;10(12):2192-5.
2004: René Warren; Rene Warren; Hisashi Kudo; Matt Myhre; Manisha Dosanjh; Anca Petrescu; Hiroyuki Kobayashi; Satoru Shimizu; Keisuke Miyauchi; Eiji Masai; George Yang; Jeff M Stott; Jacqueline E Schein; Heesun Shin; Jaswinder Khattra; Duane E Smailus; Yaron S N Butterfield; Asim Siddiqui; Robert Holt; Marco A Marra; Steven J M Jones; William W Mohn; Fiona S L Brinkman; Masao Fukuda; Julian Davies; Lindsay D Eltis
Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.
Journal of bacteriology 2004;186(22):7783-95.
2004: Artem Cherkasov; Shannan J Ho Sui; Robert brunham; Steven J M Jones
Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics.
BMC bioinformatics 2004;5():101.
2004: Artem Cherkasov; Steven J M Jones
An approach to large scale identification of non-obvious structural similarities between proteins.
BMC bioinformatics 2004;5():61.
2004: Calum MacAulay; Kim Lonergan; Bryan Chi; Scott D Zuyderduyn; Jaquie Shein; Ming Tsao; Jean C leRiche; Steven J M Jones; Marco Marra; Stephen Lam; Wan L Lam
Serial analysis of gene expression profiles of developmental stages in non-small cell lung carcinoma.
Chest 2004;125(5 Suppl):97S.
2004: Stephen B Montgomery; Tamara Astakhova; Mikhail Bilenky; Ewan Birney; Tony Fu; Maik Hassel; Craig Melsopp; Marcin Rak; A Gordon Robertson; Monica Sleumer; Asim S Siddiqui; Steven J M Jones
Sockeye: a 3D environment for comparative genomics.
Genome research 2004;14(5):956-62.
2004: Artem Cherkasov; Steven J M Jones
Structural characterization of genomes by large scale sequence-structure threading.
BMC bioinformatics 2004;5():37.
2004: Agnes Baross; Mike Schertzer; Scott D Zuyderduyn; Steven J M Jones; Marco A Marra; Peter M Lansdorp
Effect of TERT and ATM on gene expression profiles in human fibroblasts.
Genes, chromosomes & cancer 2004;39(4):298-310.
2004: Matthew L Rise; Kristian R Von Schalburg; Gordon D Brown; Melanie A Mawer; Robert H Devlin; Nathanael Kuipers; Maura Busby; Marianne Beetz-Sargent; Roberto Alberto; A Ross Gibbs; Peter Hunt; Robert Shukin; Jeffrey A Zeznik; Colleen Nelson; Simon R M Jones; Duane E Smailus; Steven J M Jones; Jacqueline E Schein; Marco A Marra; Yaron S N Butterfield; Jeff M Stott; Siemon H S Ng; William S Davidson; Ben F Koop
Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics.
Genome research 2004;14(3):478-90.
2004: Martin I Krzywinski; Ian Bosdet; Duane E Smailus; Readman Chiu; Carrie Mathewson; Natasja Wye; Sarah Barber; Mabel Brown-John; Susanna Chan; Steve Chand; Alison Cloutier; Noreen Girn; Darlene Lee; Amara Masson; Michael Mayo; Teika Olson; Pawan Pandoh; Anna-Liisa Prabhu; Eric F P M Schoenmakers; Miranda Tsai; Donna G Albertson; Wan Lam; Chik On Choy; Kazutoyo Osoegawa; Shaying Zhao; Pieter J de Jong; Jacqueline E Schein; Steven J M Jones; Marco A Marra
A set of BAC clones spanning the human genome.
Nucleic acids research 2004;32(12):3651-60.
2003: Barbara R Steen; Scott D Zuyderduyn; D L Toffaletti; Marco Marra; Steven J M Jones; J R Perfect; James W Kronstad
Cryptococcus neoformans gene expression during experimental cryptococcal meningitis.
Eukaryotic cell 2003;2(6):1336-49.
2003: Scott D Zuyderduyn; Steven J M Jones
A knowledge discovery object model API for Java.
BMC bioinformatics 2003;4():51.
2003: Christopher D Fjell; Ian Bosdet; Jacqueline E Schein; Steven J M Jones; Marco A Marra
Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps.
Genome research 2003;13(6A):1244-9.
2003: Erin D Pleasance; Marco A Marra; Steven J M Jones
Assessment of SAGE in transcript identification.
Genome research 2003;13(6A):1203-15.
2003: Daniel R Fuhrmann; Martin I Krzywinski; Readman Chiu; Parvaneh Saeedi; Jacqueline E Schein; Ian Bosdet; Asif T Chinwalla; LaDeana W Hillier; Robert H Waterston; John D McPherson; Steven J M Jones; Marco A Marra
Software for automated analysis of DNA fingerprinting gels.
Genome research 2003;13(5):940-53.
2003: Sharon M Gorski; Suganthi Chittaranjan; Erin D Pleasance; J D Freeman; Carrie L Anderson; Richard J Varhol; Shaun M Coughlin; Scott D Zuyderduyn; Steven J M Jones; Marco A Marra
A SAGE approach to discovery of genes involved in autophagic cell death.
Current biology : CB 2003;13(4):358-63.
2003: William WL Hsiao; Ivan Wan; Steven J M Jones; Fiona S L Brinkman
IslandPath: aiding detection of genomic islands in prokaryotes.
Bioinformatics (Oxford, England) 2003;19(3):418-20.
2002: Sheldon J McKay; Steven J M Jones
AcePrimer: automation of PCR primer design based on gene structure.
Bioinformatics (Oxford, England) 2002;18(11):1538-9.
2002: G Vatcher; Duane E Smailus; Martin I Krzywinski; R Guin; Jeff M Stott; M Tsai; S Chan; Pawan Pandoh; G Yang; Jennifer Asano; T Olson; Anna-Liisa Prabhu; Robin J N Coope; A Marziali; Jacqueline E Schein; Steven J M Jones; Marco Marra
Resuspension of DNA sequencing reaction products in agarose increases sequence quality on an automated sequencer.
BioTechniques 2002;33(3):532-4, 536, 538-9.
2002: Jacqueline E Schein; Kristin L Tangen; Readman Chiu; Heesun Shin; Klaus B Lengeler; William Kim MacDonald; Ian Bosdet; Joseph Heitman; Steven J M Jones; Marco A Marra; James W Kronstad
Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans.
Genome research 2002;12(9):1445-53.
2002: Barbara R Steen; Tianshun Lian; Scott D Zuyderduyn; William Kim MacDonald; Marco Marra; Steven J M Jones; James W Kronstad
Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans.
Genome research 2002;12(9):1386-400.
2002: Fiona S L Brinkman; Jeffrey L Blanchard; Artem Cherkasov; Yossef Av-Gay; Robert brunham; Rachel C Fernandez; B Brett Finlay; Sarah P Otto; B F Francis Ouellette; Patrick J Keeling; Ann M Rose; Robert E W Hancock; Steven J M Jones; Hans Greberg
Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast.
Genome research 2002;12(8):1159-67.
2002: Andre Mattman; David Huntsman; Gillian Lockitch; Sylvie Langlois; Noel Buskard; Diana Ralston; Yaron Butterfield; Pedro Rodrigues; Steven J M Jones; Graça Porto; Marco Marra; Maria de Sousa; Greg Vatcher
Transferrin receptor 2 (TfR2) and HFE mutational analysis in non-C282Y iron overload: identification of a novel TfR2 mutation.
Blood 2002;100(3):1075-7.
2002: Yuriy Shevchenko; Gerald Bouffard; Yaron S N Butterfield; Robert W Blakesley; James L Hartley; Alice C Young; Marco A Marra; Steven J M Jones; Jeffrey W Touchman; Eric Green
Systematic sequencing of cDNA clones using the transposon Tn5.
Nucleic acids research 2002;30(11):2469-77.
2002: Yaron S N Butterfield; Marco A Marra; Jennifer Asano; Susanna Y Chan; Ranabir Guin; Martin I Krzywinski; Soo Sen Lee; Kim W K MacDonald; Carrie Mathewson; Teika E Olson; Pawan Pandoh; Anna-Liisa Prabhu; Angelique Schnerch; Ursula Skalska; Duane E Smailus; Jeff M Stott; Miranda I Tsai; George S Yang; Scott D Zuyderduyn; Jacqueline E Schein; Steven J M Jones
An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones.
Nucleic acids research 2002;30(11):2460-8.
2002: S R Ness; W Terpstra; Martin I Krzywinski; Marco A Marra; Steven J M Jones
Assembly of fingerprint contigs: parallelized FPC.
Bioinformatics (Oxford, England) 2002;18(3):484-5.
2001: Steven J M Jones; D L Riddle; A T Pouzyrev; Victor E Velculescu; LaDeana W Hillier; Sean R Eddy; S L Stricklin; David Baillie; Robert H Waterston; Marco A Marra
Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans.
Genome research 2001;11(8):1346-52.
2001: Fiona S L Brinkman; I Wan; Robert E W Hancock; Ann M Rose; Steven J M Jones
PhyloBLAST: facilitating phylogenetic analysis of BLAST results.
Bioinformatics (Oxford, England) 2001;17(4):385-7.
2000: Pierre Gönczy; Christophe Echeverri; Karen Oegema; A Coulson; Steven J M Jones; R R Copley; J Duperon; J Oegema; M Brehm; E Cassin; Eva Hannak; Matthew Kirkham; S Pichler; K Flohrs; A Goessen; Sebastian Leidel; A M Alleaume; C Martin; Nurhan Ozlü; P Bork; Anthony A Hyman
Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III.
Nature 2000;408(6810):331-6.
2000: Audrey P de Koning; Fiona S L Brinkman; Steven J M Jones; Patrick J Keeling
Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis.
Molecular biology and evolution 2000;17(11):1769-73.
2000: Valerie Reinke; H E Smith; Jeremy Nance; John Wang; C Van Doren; Rebecca Begley; Steven J M Jones; E B Davis; S Scherer; Samuel Ward; Stuart K Kim
A global profile of germline gene expression in C. elegans.
Molecular cell 2000;6(3):605-16.
2000: Robert C Johnsen; Steven J M Jones; Ann M Rose
Mutational accessibility of essential genes on chromosome I(left) in Caenorhabditis elegans.
Molecular & general genetics : MGG 2000;263(2):239-52.
1999: Martin W Simmen; S Leitgeb; J Charlton; Steven J M Jones; B R Harris; VH Clark; Adrian Bird
Nonmethylated transposable elements and methylated genes in a chordate genome.
Science (New York, N.Y.) 1999;283(5405):1164-7.
1998: Martin W Simmen; S Leitgeb; VH Clark; Steven J M Jones; Adrian Bird
Gene number in an invertebrate chordate, Ciona intestinalis.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(8):4437-40.
1998: A M van Wageningen; P N Kirkpatrick; Dudley H Williams; B R Harris; J K Kershaw; N J Lennard; M Jones; Steven J M Jones; P J Solenberg
Sequencing and analysis of genes involved in the biosynthesis of a vancomycin group antibiotic.
Chemistry & biology 1998;5(3):155-62.
1995: Steven J M Jones; David Baillie
Characterization of the let-653 gene in Caenorhabditis elegans.
Molecular & general genetics : MGG 1995;248(6):719-26.
1995: Steven J M Jones
An update and lessons from whole-genome sequencing projects.
Current opinion in genetics & development 1995;5(3):349-53.