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Steven Jones
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42
Marra, Marco
17
Griffith, Obi
15
Schein, Jacqueline
12
Marra, Marco
11
Bilenky, Mikhail
10
Zuyderduyn, Scott
9
Hirst, Martin
9
Siddiqui, Asim
9
Holt, Robert
8
Khattra, Jaswinder
8
Krzywinski, Martin
8
Moerman, Donald
8
Baillie, David
8
Warren, Rene
7
Wiseman, Sam
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All Publications
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2009: Nielsen Cydney B; Jackman Shaun D; Birol Inanç; Jones Steven J M
ABySS-Explorer: visualizing genome sequence assemblies.
IEEE transactions on visualization and computer graphics 2009;15(6):881-8.
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2009: Birol Inanç; Jackman Shaun D; Nielsen Cydney B; Qian Jenny Q; Varhol Richard; Stazyk Greg; Morin Ryan D; Zhao Yongjun; Hirst Martin; Schein Jacqueline E; Horsman Doug E; Connors Joseph M; Gascoyne Randy D; Marra Marco A; Jones Steven J M
De novo transcriptome assembly with ABySS.
Bioinformatics (Oxford, England) 2009;25(21):2872-7.
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2009: Deen Shaun; Griffith Obi L; Masoudi Hamid; Gown Allen; Jones Steven J M; Wiseman Sam M
Anaplastic thyroid carcinoma exhibits intratumoral molecular homogeneity for a therapeutic target panel.
Anticancer research 2009;29(7):2437-44.
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2009: Meissner Barbara; Warner Adam; Wong Kim; Dube Nicholas; Lorch Adam; McKay Sheldon J; Khattra Jaswinder; Rogalski Teresa; Somasiri Aruna; Chaudhry Iasha; Fox Rebecca M; Miller David M; Baillie David L; Holt Robert A; Jones Steven J M; Marra Marco A; Moerman Donald G
An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans.
PLoS genetics 2009;5(6):e1000537.
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2009: Simpson Jared T; Wong Kim; Jackman Shaun D; Schein Jacqueline E; Jones Steven J M; Birol Inanç
ABySS: a parallel assembler for short read sequence data.
Genome research 2009;19(6):1117-23.
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2009: An Jianghong; Lee Davy C W; Law Anna H Y; Yang Cindy L H; Poon Leo L M; Lau Allan S Y; Jones Steven J M
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.
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2009: Hoffman Brad G; Jones Steven J M
Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing.
The Journal of endocrinology 2009;201(1):1-13.
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2009: Sleumer Monica C; Bilenky Mikhail; He An; Robertson Gordon; Thiessen Nina; Jones Steven J M
Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements.
Nucleic acids research 2009;37(4):1323-34.
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2009: McGhee James D; Fukushige Tetsunari; Krause Michael W; Minnema Stephanie E; Goszczynski Barbara; Gaudet Jeb; Kohara Yuji; Bossinger Olaf; Zhao Yongjun; Khattra Jaswinder; Hirst Martin; Jones Steven J M; Marra Marco A; Ruzanov Peter; Warner Adam; Zapf Richard; Moerman Donald G; Kalb John M
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.
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2008: Robertson A Gordon; Bilenky Mikhail; Tam Angela; Zhao Yongjun; Zeng Thomas; Thiessen Nina; Cezard Timothee; Fejes Anthony P; Wederell Elizabeth D; Cullum Rebecca; Euskirchen Ghia; Krzywinski Martin; Birol Inanc; Snyder Michael; Hoodless Pamela A; Hirst Martin; Marra Marco A; Jones Steven J M
Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.
Genome research 2008;18(12):1906-17.
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2008: Wiseman Sam M; Melck Adrienne; Masoudi Hamid; Ghaidi Fariba; Goldstein Lynn; Gown Allen; Jones Steven J M; Griffith Obi L
Molecular phenotyping of thyroid tumors identifies a marker panel for differentiated thyroid cancer diagnosis.
Annals of surgical oncology 2008;15(10):2811-26.
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2008: Griffith Obi L; Chiu Connie G; Gown Allen M; Jones Steven J M; Wiseman Sam M
Biomarker panel diagnosis of thyroid cancer: a critical review.
Expert review of anticancer therapy 2008;8(9):1399-413.
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2008: Fejes Anthony P; Robertson Gordon; Bilenky Mikhail; Varhol Richard; Bainbridge Matthew; Jones Steven J M
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.
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2008: Liang Binhua; Luo Ma; Ball T Blake; Yao Xiaojian; Van Domselaar Gary; Cuff Wilfred R; Cheang Mary; Jones Steven J M; Plummer Francis A
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.
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2008: Holt Robert A; Jones Steven J M
The new paradigm of flow cell sequencing.
Genome research 2008;18(6):839-46.
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2008: Wiseman Sam M; Griffith Obi L; Melck Adrienne; Masoudi Hamid; Gown Allen; Nabi Ivan R; Jones Steven J M
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.
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2008: Chan Simon K; Griffith Obi L; Tai Isabella T; Jones Steven J M
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.
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2008: Griffith Malachi; Tang Michelle J; Griffith Obi L; Morin Ryan D; Chan Susanna Y; Asano Jennifer K; Zeng Thomas; Flibotte Stephane; Ally Adrian; Baross Agnes; Hirst Martin; Jones Steven J M; Morin Gregg B; Tai Isabella T; Marra Marco A
ALEXA: a microarray design platform for alternative expression analysis.
Nature methods 2008;5(2):118.
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2008: Griffith Obi L; Montgomery Stephen B; Bernier Bridget; Chu Bryan; Kasaian Katayoon; Aerts Stein; Mahony Shaun; Sleumer Monica C; Bilenky Mikhail; Haeussler Maximilian; Griffith Malachi; Gallo Steven M; Giardine Belinda; Hooghe Bart; Van Loo Peter; Blanco Enrique; Ticoll Amy; Lithwick Stuart; Portales-Casamar Elodie; Donaldson Ian J; Robertson Gordon; Wadelius Claes; De Bleser Pieter; Vlieghe Dominique; Halfon Marc S; Wasserman Wyeth; Hardison Ross; Bergman Casey M; Jones Steven J M;
ORegAnno: an open-access community-driven resource for regulatory annotation.
Nucleic acids research 2008;36(Database issue):D107-13.
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2008: Ralph Steven G; Chun Hye Jung E; Kolosova Natalia; Cooper Dawn; Oddy Claire; Ritland Carol E; Kirkpatrick Robert; Moore Richard; Barber Sarah; Holt Robert A; Jones Steven J M; Marra Marco A; Douglas Carl J; Ritland Kermit; Bohlmann Jörg
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.
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2008: D'Souza Cletus A; Chopra Vikramjit; Varhol Richard; Xie Yuan-Yun; Bohacec Slavita; Zhao Yongjun; Lee Lisa L C; Bilenky Mikhail; Portales-Casamar Elodie; He An; Wasserman Wyeth W; Goldowitz Daniel; Marra Marco A; Holt Robert A; Simpson Elizabeth M; Jones Steven J M
Identification of a set of genes showing regionally enriched expression in the mouse brain.
BMC neuroscience 2008;9():66.
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2008: Shin Heesun; Hirst Martin; Bainbridge Matthew N; Magrini Vincent; Mardis Elaine; Moerman Donald G; Marra Marco A; Baillie David L; Jones Steven J M
Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.
BMC biology 2008;6():30.
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2008: Hoffman Brad G; Zavaglia Bogard; Witzsche Joy; Ruiz de Algara Teresa; Beach Mike; Hoodless Pamela A; Jones Steven J M; Marra Marco A; Helgason Cheryl D
Identification of transcripts with enriched expression in the developing and adult pancreas.
Genome biology 2008;9(6):R99.
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2008: Aerts Stein; Haeussler Maximilian; van Vooren Steven; Griffith Obi L; Hulpiau Paco; Jones Steven J M; Montgomery Stephen B; Bergman Casey M;
Text-mining assisted regulatory annotation.
Genome biology 2008;9(2):R31.
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2008: Ralph Steven G; Chun Hye Jung E; Cooper Dawn; Kirkpatrick Robert; Kolosova Natalia; Gunter Lee; Tuskan Gerald A; Douglas Carl J; Holt Robert A; Jones Steven J M; Marra Marco A; Bohlmann Jörg
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.
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2007: Melck Adrienne; Masoudi Hamid; Griffith Obi L; Rajput Ashish; Wilkins Graeme; Bugis Sam; Jones Steven J M; Wiseman Sam M
Cell cycle regulators show diagnostic and prognostic utility for differentiated thyroid cancer.
Annals of surgical oncology 2007;14(12):3403-11.
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2007: Peng Fred Y; Reid Karen E; Liao Nancy; Schlosser James; Lijavetzky Diego; Holt Robert; Martínez Zapater José M; Jones Steven; Marra Marco; Bohlmann Jörg; Lund Steven T
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.
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2007: Huang Peiming; Pleasance Erin D; Maydan Jason S; Hunt-Newbury Rebecca; O'Neil Nigel J; Mah Allan; Baillie David L; Marra Marco A; Moerman Donald G; Jones Steven J M
Identification and analysis of internal promoters in Caenorhabditis elegans operons.
Genome research 2007;17(10):1478-85.
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2007: Bainbridge Matthew N; Warren René L; He An; Bilenky Mikhail; Robertson A Gordon; Jones Steven J M
THOR: targeted high-throughput ortholog reconstructor.
Bioinformatics (Oxford, England) 2007;23(19):2622-4.
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2007: Hunt-Newbury Rebecca; Viveiros Ryan; Johnsen Robert; Mah Allan; Anastas Dina; Fang Lily; Halfnight Erin; Lee David; Lin John; Lorch Adam; McKay Sheldon; Okada H Mark; Pan Jie; Schulz Ana K; Tu Domena; Wong Kim; Zhao Z; Alexeyenko Andrey; Burglin Thomas; Sonnhammer Eric; Schnabel Ralf; Jones Steven J; Marra Marco A; Baillie David L; Moerman Donald G
High-throughput in vivo analysis of gene expression in Caenorhabditis elegans.
PLoS biology 2007;5(9):e237.
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2007: Wiseman Sam M; Griffith Obi L; Deen Shaun; Rajput Ashish; Masoudi Hamid; Gilks Blake; Goldstein Lynn; Gown Allen; Jones Steven J M
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.
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2007: Robertson Gordon; Hirst Martin; Bainbridge Matthew; Bilenky Misha; Zhao Yongjun; Zeng Thomas; Euskirchen Ghia; Bernier Bridget; Varhol Richard; Delaney Allen; Thiessen Nina; Griffith Obi L; He Ann; Marra Marco; Snyder Michael; Jones Steven
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
Nature methods 2007;4(8):651-7.
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2007: Ruzanov Peter; Riddle Donald L; Marra Marco A; McKay Sheldon J; Jones Steven M
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.
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2007: Trip S A; Schlottmann P G; Jones S J; Li W-Y; Garway-Heath D F; Thompson A J; Plant G T; Miller D H
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.
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2007: Etchberger John F; Lorch Adam; Sleumer Monica C; Zapf Richard; Jones Steven J; Marra Marco A; Holt Robert A; Moerman Donald G; Hobert Oliver
The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron.
Genes & development 2007;21(13):1653-74.
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2007: Zhao Yun; Raouf Afshin; Kent David; Khattra Jaswinder; Delaney Allen; Schnerch Angelique; Asano Jennifer; McDonald Helen; Chan Christina; Jones Steven; Marra Marco A; Eaves Connie J
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.
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2007: Montgomery Stephen B; Griffith Obi L; Schuetz Johanna M; Brooks-Wilson Angela; Jones Steven J M
A survey of genomic properties for the detection of regulatory polymorphisms.
PLoS computational biology 2007;3(6):e106.
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2007: DiGuistini Scott; Ralph Steven G; Lim Young W; Holt Robert; Jones Steven; Bohlmann Jörg; Breuil Colette
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.
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2007: Warren René L; Sutton Granger G; Jones Steven J M; Holt Robert A
Assembling millions of short DNA sequences using SSAKE.
Bioinformatics (Oxford, England) 2007;23(4):500-1.
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2007: McGhee James D; Sleumer Monica C; Bilenky Mikhail; Wong Kim; McKay Sheldon J; Goszczynski Barbara; Tian Helen; Krich Natisha D; Khattra Jaswinder; Holt Robert A; Baillie David L; Kohara Yuji; Marra Marco A; Jones Steven J M; Moerman Donald G; Robertson A Gordon
The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine.
Developmental biology 2007;302(2):627-45.
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2007: Khattra Jaswinder; Delaney Allen D; Zhao Yongjun; Siddiqui Asim; Asano Jennifer; McDonald Helen; Pandoh Pawan; Dhalla Noreen; Prabhu Anna-Liisa; Ma Kevin; Lee Stephanie; Ally Adrian; Tam Angela; Sa Danne; Rogers Sean; Charest David; Stott Jeff; Zuyderduyn Scott; Varhol Richard; Eaves Connie; Jones Steven; Holt Robert; Hirst Martin; Hoodless Pamela A; Marra Marco A
Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.
Genome research 2007;17(1):108-16.
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2007: Kneller Julie M; Ehlen Thomas; Matisic Jasenka P; Miller Dianne; Van Niekerk Dirk; Lam Wan L; Marra Marco; Richards-Kortum Rebecca; Follen Michelle; Macaulay Calum; Jones Steven J M
Using LongSAGE to Detect Biomarkers of Cervical Cancer Potentially Amenable to Optical Contrast Agent Labelling.
Biomarker insights 2007;2():447-61.
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2007: Quayle Adrian P; Siddiqui Asim S; Jones Steven J M
Perturbation of interaction networks for application to cancer therapy.
Cancer informatics 2007;5():45-65.
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2007: Ruzanov Peter; Jones Steven J; Riddle Donald L
Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data.
BMC genomics 2007;8():447.
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2007: Krzywinski Martin; Bosdet Ian; Mathewson Carrie; Wye Natasja; Brebner Jay; Chiu Readman; Corbett Richard; Field Matthew; Lee Darlene; Pugh Trevor; Volik Stas; Siddiqui Asim; Jones Steven; Schein Jacquie; Collins Collin; Marra Marco
A BAC clone fingerprinting approach to the detection of human genome rearrangements.
Genome biology 2007;8(10):R224.
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2007: Hou Juan; Charters Anita M; Lee Sam C; Zhao Yongjun; Wu Mona K; Jones Steven J M; Marra Marco A; Hoodless Pamela A
A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE).
BMC developmental biology 2007;7():92.
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2007: Quayle Steven N; Hare Heidi; Delaney Allen D; Hirst Martin; Hwang Dorothy; Schein Jacqueline E; Jones Steven J M; Marra Marco A; Sadar Marianne D
Novel expressed sequences identified in a model of androgen independent prostate cancer.
BMC genomics 2007;8():32.
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2007: Robertson Neil; Oveisi-Fordorei Mehrdad; Zuyderduyn Scott D; Varhol Richard J; Fjell Christopher; Marra Marco; Jones Steven; Siddiqui Asim
DiscoverySpace: an interactive data analysis application.
Genome biology 2007;8(1):R6.
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2006: Elnitski Laura; Jin Victor X; Farnham Peggy J; Jones Steven J M
Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques.
Genome research 2006;16(12):1455-64.
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2006: Lonergan Kim M; Chari Raj; Deleeuw Ronald J; Shadeo Ashleen; Chi Bryan; Tsao Ming-Sound; Jones Steven; Marra Marco; Ling Victor; Ng Raymond; Macaulay Calum; Lam Stephen; Lam Wan L
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.
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2006: Griffith Obi L; Melck Adrienne; Jones Steven J M; Wiseman Sam M
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.
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2006: Wang G; Jones S J M; Marra M A; Sadar M D
Identification of genes targeted by the androgen and PKA signaling pathways in prostate cancer cells.
Oncogene 2006;25(55):7311-23.
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2006: McLeod Michael P; Warren René L; Hsiao William W L; Araki Naoto; Myhre Matthew; Fernandes Clinton; Miyazawa Daisuke; Wong Wendy; Lillquist Anita L; Wang Dennis; Dosanjh Manisha; Hara Hirofumi; Petrescu Anca; Morin Ryan D; Yang George; Stott Jeff M; Schein Jacqueline E; Shin Heesun; Smailus Duane; Siddiqui Asim S; Marra Marco A; Jones Steven J M; Holt Robert; Brinkman Fiona S L; Miyauchi Keisuke; Fukuda Masao; Davies Julian E; Mohn William W; Eltis Lindsay D
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.
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2006: Bakkeren Guus; Jiang Guoqiao; Warren René L; Butterfield Yaron; Shin Heesun; Chiu Readman; Linning Rob; Schein Jacqueline; Lee Nancy; Hu Guanggan; Kupfer Doris M; Tang Yuhong; Roe Bruce A; Jones Steven; Marra Marco; Kronstad James W
Mating factor linkage and genome evolution in basidiomycetous pathogens of cereals.
Fungal genetics and biology : FG & B 2006;43(9):655-66.
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2006: Ralph Steven G; Yueh Hesther; Friedmann Michael; Aeschliman Dana; Zeznik Jeffrey A; Nelson Colleen C; Butterfield Yaron S N; Kirkpatrick Robert; Liu Jerry; Jones Steven J M; Marra Marco A; Douglas Carl J; Ritland Kermit; Bohlmann Jörg
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.
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2006: Warren René L; Varabei Dmitry; Platt Darren; Huang Xiaoqiu; Messina David; Yang Shiaw-Pyng; Kronstad James W; Krzywinski Martin; Warren Wesley C; Wallis John W; Hillier LaDeana W; Chinwalla Asif T; Schein Jacqueline E; Siddiqui Asim S; Marra Marco A; Wilson Richard K; Jones Steven J M
Physical map-assisted whole-genome shotgun sequence assemblies.
Genome research 2006;16(6):768-75.
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2006: Li Yvonne Y; Jones Steven J M; Cherkasov Artem
Selective targeting of indel-inferred differences in spatial structures of homologous proteins.
Journal of bioinformatics and computational biology 2006;4(2):403-14.
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2006: Montgomery S B; Griffith O L; Sleumer M C; Bergman C M; Bilenky M; Pleasance E D; Prychyna Y; Zhang X; Jones S J M
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.
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2006: Wilson Gary M; Flibotte Stephane; Missirlis Perseus I; Marra Marco A; Jones Steven; Thornton Kevin; Clark Andrew G; Holt Robert A
Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla.
Genome research 2006;16(2):173-81.
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2006: Robertson G; Bilenky M; Lin K; He A; Yuen W; Dagpinar M; Varhol R; Teague K; Griffith O L; Zhang X; Pan Y; Hassel M; Sleumer M C; Pan W; Pleasance E D; Chuang M; Hao H; Li Y Y; Robertson N; Fjell C; Li B; Montgomery S B; Astakhova T; Zhou J; Sander J; Siddiqui A S; Jones S J M
cisRED: a database system for genome-scale computational discovery of regulatory elements.
Nucleic acids research 2006;34(Database issue):D68-73.
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2006: Li Yvonne Y; An Jianghong; Jones Steven J M
A large-scale computational approach to drug repositioning.
Genome informatics. International Conference on Genome Informatics 2006;17(2):239-47.
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2006: Bainbridge Matthew N; Warren René L; Hirst Martin; Romanuik Tammy; Zeng Thomas; Go Anne; Delaney Allen; Griffith Malachi; Hickenbotham Matthew; Magrini Vincent; Mardis Elaine R; Sadar Marianne D; Siddiqui Asim S; Marra Marco A; Jones Steven J M
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.
BMC genomics 2006;7():246.
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2006: Siddiqui Asim S; Delaney Allen D; Schnerch Angelique; Griffith Obi L; Jones Steven J M; Marra Marco A
Sequence biases in large scale gene expression profiling data.
Nucleic acids research 2006;34(12):e83.
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2006: Jones Steven J M
Prediction of genomic functional elements.
Annual review of genomics and human genetics 2006;7():315-38.
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2006: Ruzanov Peter; Jones Steven J M
An interactive tool for visualization of relationships between gene expression profiles.
BMC bioinformatics 2006;7():193.
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2005: Larraya Luis M; Boyce Kylie J; So Austin; Steen Barbara R; Jones Steven; Marra Marco; Kronstad James W
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.
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2005: Cherkasov Artem; Shi Zheng; Li Yvonne; Jones Steven J M; Fallahi Magid; Hammond Geoffrey L
'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.
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2005: Griffith Obi L; Pleasance Erin D; Fulton Debra L; Oveisi Mehrdad; Ester Martin; Siddiqui Asim S; Jones Steven J M
Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses.
Genomics 2005;86(4):476-88.
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2005: Ng Siemon H S; Artieri Carlo G; Bosdet Ian E; Chiu Readman; Danzmann Roy G; Davidson William S; Ferguson Moira M; Fjell Christopher D; Hoyheim Bjorn; Jones Steven J M; de Jong Pieter J; Koop Ben F; Krzywinski Martin I; Lubieniecki Krzysztof; Marra Marco A; Mitchell Leslie A; Mathewson Carrie; Osoegawa Kazutoyo; Parisotto Sarah E; Phillips Ruth B; Rise Matthew L; von Schalburg Kristian R; Schein Jacqueline E; Shin Heesun; Siddiqui Asim; Thorsen Jim; Wye Natasja; Yang George; Zhu Baoli
A physical map of the genome of Atlantic salmon, Salmo salar.
Genomics 2005;86(4):396-404.
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2005: Montgomery Stephen B; Fu Tony; Guan Jun; Lin Keven; Jones Steven J M
An application of peer-to-peer technology to the discovery, use and assessment of bioinformatics programs.
Nature methods 2005;2(8):563.
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2005: Warren René L; Butterfield Yaron S; Morin Ryan D; Siddiqui Asim S; Marra Marco A; Jones Steven J M
Management and visualization of whole genome shotgun assemblies using SAM.
BioTechniques 2005;38(5):715-6, 718, 720.
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2005: Blacque Oliver E; Perens Elliot A; Boroevich Keith A; Inglis Peter N; Li Chunmei; Warner Adam; Khattra Jaswinder; Holt Rob A; Ou Guangshuo; Mah Allan K; McKay Sheldon J; Huang Peter; Swoboda Peter; Jones Steve J M; Marra Marco A; Baillie David L; Moerman Donald G; Shaham Shai; Leroux Michel R
Functional genomics of the cilium, a sensory organelle.
Current biology : CB 2005;15(10):935-41.
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2005: Halaschek-Wiener Julius; Khattra Jaswinder S; McKay Sheldon; Pouzyrev Anatoli; Stott Jeff M; Yang George S; Holt Robert A; Jones Steven J M; Marra Marco A; Brooks-Wilson Angela R; Riddle Donald L
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression.
Genome research 2005;15(5):603-15.
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2005: Lian Tianshun; Simmer Megan I; D'Souza Cletus A; Steen Barbara R; Zuyderduyn Scott D; Jones Steven J M; Marra Marco A; Kronstad James W
Iron-regulated transcription and capsule formation in the fungal pathogen Cryptococcus neoformans.
Molecular microbiology 2005;55(5):1452-72.
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2005: Snijders Antoine M; Nowak Norma J; Huey Bing; Fridlyand Jane; Law Sindy; Conroy Jeffrey; Tokuyasu Taku; Demir Kubilay; Chiu Readman; Mao Jian-Hua; Jain Ajay N; Jones Steven J M; Balmain Allan; Pinkel Daniel; Albertson Donna G
Mapping segmental and sequence variations among laboratory mice using BAC array CGH.
Genome research 2005;15(2):302-11.
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2004: Hirst Martin; Astell Caroline R; Griffith Malachi; Coughlin Shaun M; Moksa Michelle; Zeng Thomas; Smailus Duane E; Holt Robert A; Jones Steven; Marra Marco A; Petric Martin; Krajden Mel; Lawrence David; Mak Annie; Chow Ron; Skowronski Danuta M; Tweed S Aleina; Goh SweeHan; Brunham Robert C; Robinson John; Bowes Victoria; Sojonky Ken; Byrne Sean K; Li Yan; Kobasa Darwyn; Booth Tim; Paetzel Mark
Novel avian influenza H7N3 strain outbreak, British Columbia.
Emerging infectious diseases 2004;10(12):2192-5.
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2004: Warren René; Hsiao William W L; Kudo Hisashi; Myhre Matt; Dosanjh Manisha; Petrescu Anca; Kobayashi Hiroyuki; Shimizu Satoru; Miyauchi Keisuke; Masai Eiji; Yang George; Stott Jeff M; Schein Jacquie E; Shin Heesun; Khattra Jaswinder; Smailus Duane; Butterfield Yaron S; Siddiqui Asim; Holt Robert; Marra Marco A; Jones Steven J M; Mohn William W; Brinkman Fiona S L; Fukuda Masao; Davies Julian; Eltis Lindsay D
Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.
Journal of bacteriology 2004;186(22):7783-95.
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2004: Cherkasov Artem; Ho Sui Shannan J; Brunham Robert C; Jones Steven J M
Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics.
BMC bioinformatics 2004;5():101.
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2004: Cherkasov Artem; Jones Steven J M
An approach to large scale identification of non-obvious structural similarities between proteins.
BMC bioinformatics 2004;5():61.
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2004: MacAulay Calum; Lonergan Kim; Chi Bryan; Zuyderduyn Scott; Shein Jaquie; Tsao Ming; LeRiche Jean; Jones Steven; Marra Marco; Lam Stephen; Lam Wan L
Serial analysis of gene expression profiles of developmental stages in non-small cell lung carcinoma.
Chest 2004;125(5 Suppl):97S.
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2004: Montgomery Stephen B; Astakhova Tamara; Bilenky Mikhail; Birney Ewan; Fu Tony; Hassel Maik; Melsopp Craig; Rak Marcin; Robertson A Gordon; Sleumer Monica; Siddiqui Asim S; Jones Steven J M
Sockeye: a 3D environment for comparative genomics.
Genome research 2004;14(5):956-62.
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2004: Cherkasov Artem; Jones Steven J M
Structural characterization of genomes by large scale sequence-structure threading.
BMC bioinformatics 2004;5():37.
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2004: Baross Agnes; Schertzer Mike; Zuyderduyn Scott D; Jones Steven J M; Marra Marco A; Lansdorp Peter M
Effect of TERT and ATM on gene expression profiles in human fibroblasts.
Genes, chromosomes & cancer 2004;39(4):298-310.
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2004: Rise Matthew L; von Schalburg Kristian R; Brown Gordon D; Mawer Melanie A; Devlin Robert H; Kuipers Nathanael; Busby Maura; Beetz-Sargent Marianne; Alberto Roberto; Gibbs A Ross; Hunt Peter; Shukin Robert; Zeznik Jeffrey A; Nelson Colleen; Jones Simon R M; Smailus Duane E; Jones Steven J M; Schein Jacqueline E; Marra Marco A; Butterfield Yaron S N; Stott Jeff M; Ng Siemon H S; Davidson William S; Koop Ben F
Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics.
Genome research 2004;14(3):478-90.
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2004: Krzywinski Martin; Bosdet Ian; Smailus Duane; Chiu Readman; Mathewson Carrie; Wye Natasja; Barber Sarah; Brown-John Mabel; Chan Susanna; Chand Steve; Cloutier Alison; Girn Noreen; Lee Darlene; Masson Amara; Mayo Michael; Olson Teika; Pandoh Pawan; Prabhu Anna-Liisa; Schoenmakers Eric; Tsai Miranda; Albertson Donna; Lam Wan; Choy Chik-On; Osoegawa Kazutoyo; Zhao Shaying; de Jong Pieter J; Schein Jacqueline; Jones Steven; Marra Marco A
A set of BAC clones spanning the human genome.
Nucleic acids research 2004;32(12):3651-60.
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2003: Steen B R; Zuyderduyn S; Toffaletti D L; Marra M; Jones S J M; Perfect J R; Kronstad J
Cryptococcus neoformans gene expression during experimental cryptococcal meningitis.
Eukaryotic cell 2003;2(6):1336-49.
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2003: Zuyderduyn Scott D; Jones Steven J M
A knowledge discovery object model API for Java.
BMC bioinformatics 2003;4():51.
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2003: Fjell Christopher D; Bosdet Ian; Schein Jacqueline E; Jones Steven J M; Marra Marco A
Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps.
Genome research 2003;13(6A):1244-9.
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2003: Pleasance Erin D; Marra Marco A; Jones Steven J M
Assessment of SAGE in transcript identification.
Genome research 2003;13(6A):1203-15.
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2003: Fuhrmann Daniel R; Krzywinski Martin I; Chiu Readman; Saeedi Parvaneh; Schein Jacqueline E; Bosdet Ian E; Chinwalla Asif; Hillier LaDeana W; Waterston Robert H; McPherson John D; Jones Steven J M; Marra Marco A
Software for automated analysis of DNA fingerprinting gels.
Genome research 2003;13(5):940-53.
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2003: Gorski Sharon M; Chittaranjan Suganthi; Pleasance Erin D; Freeman J D; Anderson Carrie L; Varhol Richard J; Coughlin Shaun M; Zuyderduyn Scott D; Jones Steven J M; Marra Marco A
A SAGE approach to discovery of genes involved in autophagic cell death.
Current biology : CB 2003;13(4):358-63.
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2003: Hsiao William; Wan Ivan; Jones Steven J; Brinkman Fiona S L
IslandPath: aiding detection of genomic islands in prokaryotes.
Bioinformatics (Oxford, England) 2003;19(3):418-20.
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2002: McKay Sheldon J; Jones Steven J M
AcePrimer: automation of PCR primer design based on gene structure.
Bioinformatics (Oxford, England) 2002;18(11):1538-9.
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2002: Vatcher G; Smailus D; Krzywinski M; Guin R; Stott J; Tsai M; Chan S; Pandoh P; Yang G; Asano J; Olson T; Prabhu A L; Coope R; Marziali A; Schein J; Jones S; Marra M
Resuspension of DNA sequencing reaction products in agarose increases sequence quality on an automated sequencer.
BioTechniques 2002;33(3):532-4, 536, 538-9.
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2002: Schein Jacqueline E; Tangen Kristin L; Chiu Readman; Shin Heesun; Lengeler Klaus B; MacDonald William Kim; Bosdet Ian; Heitman Joseph; Jones Steven J M; Marra Marco A; Kronstad James W
Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans.
Genome research 2002;12(9):1445-53.
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2002: Steen Barbara R; Lian Tian; Zuyderduyn Scott; MacDonald William Kim; Marra Marco; Jones Steven J M; Kronstad James W
Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans.
Genome research 2002;12(9):1386-400.
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2002: Brinkman Fiona S L; Blanchard Jeffrey L; Cherkasov Artem; Av-Gay Yossef; Brunham Robert C; Fernandez Rachel C; Finlay B Brett; Otto Sarah P; Ouellette B F Francis; Keeling Patrick J; Rose Ann M; Hancock Robert E W; Jones Steven J M; Greberg Hans
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.
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2002: Mattman Andre; Huntsman David; Lockitch Gillian; Langlois Sylvie; Buskard Noel; Ralston Diana; Butterfield Yaron; Rodrigues Pedro; Jones Steven; Porto Graça; Marra Marco; De Sousa Maria; Vatcher Greg
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.
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2002: Shevchenko Yuriy; Bouffard Gerard G; Butterfield Yaron S N; Blakesley Robert W; Hartley James L; Young Alice C; Marra Marco A; Jones Steven J M; Touchman Jeffrey W; Green Eric D
Systematic sequencing of cDNA clones using the transposon Tn5.
Nucleic acids research 2002;30(11):2469-77.
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2002: Butterfield Yaron S N; Marra Marco A; Asano Jennifer K; Chan Susanna Y; Guin Ranabir; Krzywinski Martin I; Lee Soo Sen; MacDonald Kim W K; Mathewson Carrie A; Olson Teika E; Pandoh Pawan K; Prabhu Anna-Liisa; Schnerch Angelique; Skalska Ursula; Smailus Duane E; Stott Jeff M; Tsai Miranda I; Yang George S; Zuyderduyn Scott D; Schein Jacqueline E; Jones Steven J M
An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones.
Nucleic acids research 2002;30(11):2460-8.
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2002: Ness S R; Terpstra W; Krzywinski M; Marra M A; Jones S J M
Assembly of fingerprint contigs: parallelized FPC.
Bioinformatics (Oxford, England) 2002;18(3):484-5.
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2001: Jones S J; Riddle D L; Pouzyrev A T; Velculescu V E; Hillier L; Eddy S R; Stricklin S L; Baillie D L; Waterston R; Marra M A
Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans.
Genome research 2001;11(8):1346-52.
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2001: Brinkman F S; Wan I; Hancock R E; Rose A M; Jones S J
PhyloBLAST: facilitating phylogenetic analysis of BLAST results.
Bioinformatics (Oxford, England) 2001;17(4):385-7.
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2000: Gönczy P; Echeverri C; Oegema K; Coulson A; Jones S J; Copley R R; Duperon J; Oegema J; Brehm M; Cassin E; Hannak E; Kirkham M; Pichler S; Flohrs K; Goessen A; Leidel S; Alleaume A M; Martin C; Ozlü N; Bork P; Hyman A A
Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III.
Nature 2000;408(6810):331-6.
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2000: de Koning A P; Brinkman F S; Jones S J; Keeling P J
Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis.
Molecular biology and evolution 2000;17(11):1769-73.
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2000: Reinke V; Smith H E; Nance J; Wang J; Van Doren C; Begley R; Jones S J; Davis E B; Scherer S; Ward S; Kim S K
A global profile of germline gene expression in C. elegans.
Molecular cell 2000;6(3):605-16.
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2000: Johnsen R C; Jones S J; Rose A M
Mutational accessibility of essential genes on chromosome I(left) in Caenorhabditis elegans.
Molecular & general genetics : MGG 2000;263(2):239-52.
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1999: Simmen M W; Leitgeb S; Charlton J; Jones S J; Harris B R; Clark V H; Bird A
Nonmethylated transposable elements and methylated genes in a chordate genome.
Science (New York, N.Y.) 1999;283(5405):1164-7.
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1998: Simmen M W; Leitgeb S; Clark V H; Jones S J; Bird A
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.
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1998: van Wageningen A M; Kirkpatrick P N; Williams D H; Harris B R; Kershaw J K; Lennard N J; Jones M; Jones S J; Solenberg P J
Sequencing and analysis of genes involved in the biosynthesis of a vancomycin group antibiotic.
Chemistry & biology 1998;5(3):155-62.
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1995: Jones S J; Baillie D L
Characterization of the let-653 gene in Caenorhabditis elegans.
Molecular & general genetics : MGG 1995;248(6):719-26.
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1995: Jones S J
An update and lessons from whole-genome sequencing projects.
Current opinion in genetics & development 1995;5(3):349-53.
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