Publications by authors named "Steven J M Jones"

100Publications

Matching methods in precision oncology: An introduction and illustrative example.

Mol Genet Genomic Med 2020 Nov 25:e1554. Epub 2020 Nov 25.

Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer, Vancouver, BC, Canada.

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http://dx.doi.org/10.1002/mgg3.1554DOI Listing
November 2020

-associated neurodevelopmental disorder.

J Med Genet 2020 Jun 16. Epub 2020 Jun 16.

Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1136/jmedgenet-2019-106756DOI Listing
June 2020

LIST-S2: taxonomy based sorting of deleterious missense mutations across species.

Nucleic Acids Res 2020 07;48(W1):W154-W161

Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.

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http://dx.doi.org/10.1093/nar/gkaa288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319545PMC
July 2020

Patient selection for a developmental therapeutics program using whole genome and Transcriptome analysis.

Invest New Drugs 2020 Oct 6;38(5):1601-1604. Epub 2020 Jan 6.

Department of Medical Oncology, BC Cancer, 600 West 10th Avenue, Vancouver, BC, V5Z 4E6, Canada.

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http://dx.doi.org/10.1007/s10637-020-00892-8DOI Listing
October 2020

The pivotal role of sampling recurrent tumors in the precision care of patients with tumors of the central nervous system.

Cold Spring Harb Mol Case Stud 2019 08 1;5(4). Epub 2019 Aug 1.

Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.

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http://dx.doi.org/10.1101/mcs.a004143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6672021PMC
August 2019

CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer.

Nat Methods 2019 06 20;16(6):505-507. Epub 2019 May 20.

Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1038/s41592-019-0422-yDOI Listing
June 2019

Improved measures for evolutionary conservation that exploit taxonomy distances.

Nat Commun 2019 04 5;10(1):1556. Epub 2019 Apr 5.

Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.

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http://dx.doi.org/10.1038/s41467-019-09583-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450959PMC
April 2019

Mutations in ILK, encoding integrin-linked kinase, are associated with arrhythmogenic cardiomyopathy.

Transl Res 2019 06 15;208:15-29. Epub 2019 Feb 15.

Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada; Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.trsl.2019.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7412573PMC
June 2019

Temporal Dynamics of Genomic Alterations in a Germline-Mutated Pancreatic Cancer With Low Genomic Instability Burden but Exceptional Response to Fluorouracil, Oxaliplatin, Leucovorin, and Irinotecan.

JCO Precis Oncol 2018 19;2. Epub 2018 Oct 19.

, , , , , , , , , , , , and , British Columbia Cancer Agency; , , , , and , Pancreas Centre BC; and , Simon Fraser University; , , , , , and , University of British Columbia; and , Vancouver General Hospital, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1200/PO.18.00057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7446469PMC
October 2018

Whole-Genome Sequencing in Cancer.

Cold Spring Harb Perspect Med 2019 03 1;9(3). Epub 2019 Mar 1.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada.

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http://dx.doi.org/10.1101/cshperspect.a034579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396343PMC
March 2019

Opposing Effects of CREBBP Mutations Govern the Phenotype of Rubinstein-Taybi Syndrome and Adult SHH Medulloblastoma.

Dev Cell 2018 03 15;44(6):709-724.e6. Epub 2018 Mar 15.

Center for Neuropathology, Ludwig-Maximilians-University, 81377 Munich, Germany; Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), Hamburg 20251, Germany; Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, 20246 Hamburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2018.02.012DOI Listing
March 2018

A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases.

Cell 2018 02;172(5):1050-1062.e14

Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.01.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346737PMC
February 2018

Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis.

J Inherit Metab Dis 2018 05 16;41(3):555-562. Epub 2018 Jan 16.

Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Room 3109, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.

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http://dx.doi.org/10.1007/s10545-017-0125-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5959948PMC
May 2018

A collaborative filtering-based approach to biomedical knowledge discovery.

Bioinformatics 2018 02;34(4):652-659

Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btx613DOI Listing
February 2018

Detection and genomic characterization of a mammary-like adenocarcinoma.

Cold Spring Harb Mol Case Stud 2017 Nov 21;3(6). Epub 2017 Nov 21.

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.

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http://dx.doi.org/10.1101/mcs.a002170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701302PMC
November 2017

Characterization of the human thyroid epigenome.

J Endocrinol 2017 Nov 14;235(2):153-165. Epub 2017 Aug 14.

Canada's Michael Smith Genome Sciences CentreBC Cancer Agency, Vancouver, Canada

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http://dx.doi.org/10.1530/JOE-17-0145DOI Listing
November 2017

The whole-genome landscape of medulloblastoma subtypes.

Nature 2017 07;547(7663):311-317

Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature22973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905700PMC
July 2017

Hypermutation signature reveals a slippage and realignment model of translesion synthesis by Rev3 polymerase in cisplatin-treated yeast.

Proc Natl Acad Sci U S A 2017 03 21;114(10):2663-2668. Epub 2017 Feb 21.

Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada V5Z1L3;

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http://dx.doi.org/10.1073/pnas.1618555114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5347559PMC
March 2017

Differential roles of RET isoforms in medullary and papillary thyroid carcinomas.

Endocr Relat Cancer 2017 01 21;24(1):53-69. Epub 2016 Nov 21.

Division of Cancer Biology and GeneticsCancer Research Institute, Queen's University, Kingston, Ontario, Canada

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http://dx.doi.org/10.1530/ERC-16-0393DOI Listing
January 2017

ChAsE: chromatin analysis and exploration tool.

Bioinformatics 2016 11 4;32(21):3324-3326. Epub 2016 Jul 4.

Graphics Usability and Visualization Lab, Simon Fraser University, Burnaby, Canada Visualization and Data Analysis Lab, Faculty of Computer Science, University of Vienna, Wien, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btw382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079470PMC
November 2016

Genome sequences of six species threatening forest ecosystems.

Genom Data 2016 Dec 3;10:85-88. Epub 2016 Oct 3.

Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Institut de Biologie Intégrative des Systèmes, Université Laval, Québec, Canada.

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http://dx.doi.org/10.1016/j.gdata.2016.09.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5061060PMC
December 2016

Putative BRAF activating fusion in a medullary thyroid cancer.

Cold Spring Harb Mol Case Stud 2016 Mar;2(2):a000729

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada;; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.

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http://dx.doi.org/10.1101/mcs.a000729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849853PMC
March 2016

Divergent clonal selection dominates medulloblastoma at recurrence.

Authors:
A Sorana Morrissy Livia Garzia David J H Shih Scott Zuyderduyn Xi Huang Patryk Skowron Marc Remke Florence M G Cavalli Vijay Ramaswamy Patricia E Lindsay Salomeh Jelveh Laura K Donovan Xin Wang Betty Luu Kory Zayne Yisu Li Chelsea Mayoh Nina Thiessen Eloi Mercier Karen L Mungall Yusanne Ma Kane Tse Thomas Zeng Karey Shumansky Andrew J L Roth Sohrab Shah Hamza Farooq Noriyuki Kijima Borja L Holgado John J Y Lee Stuart Matan-Lithwick Jessica Liu Stephen C Mack Alex Manno K A Michealraj Carolina Nor John Peacock Lei Qin Juri Reimand Adi Rolider Yuan Y Thompson Xiaochong Wu Trevor Pugh Adrian Ally Mikhail Bilenky Yaron S N Butterfield Rebecca Carlsen Young Cheng Eric Chuah Richard D Corbett Noreen Dhalla An He Darlene Lee Haiyan I Li William Long Michael Mayo Patrick Plettner Jenny Q Qian Jacqueline E Schein Angela Tam Tina Wong Inanc Birol Yongjun Zhao Claudia C Faria José Pimentel Sofia Nunes Tarek Shalaby Michael Grotzer Ian F Pollack Ronald L Hamilton Xiao-Nan Li Anne E Bendel Daniel W Fults Andrew W Walter Toshihiro Kumabe Teiji Tominaga V Peter Collins Yoon-Jae Cho Caitlin Hoffman David Lyden Jeffrey H Wisoff James H Garvin Duncan S Stearns Luca Massimi Ulrich Schüller Jaroslav Sterba Karel Zitterbart Stephanie Puget Olivier Ayrault Sandra E Dunn Daniela P C Tirapelli Carlos G Carlotti Helen Wheeler Andrew R Hallahan Wendy Ingram Tobey J MacDonald Jeffrey J Olson Erwin G Van Meir Ji-Yeoun Lee Kyu-Chang Wang Seung-Ki Kim Byung-Kyu Cho Torsten Pietsch Gudrun Fleischhack Stephan Tippelt Young Shin Ra Simon Bailey Janet C Lindsey Steven C Clifford Charles G Eberhart Michael K Cooper Roger J Packer Maura Massimino Maria Luisa Garre Ute Bartels Uri Tabori Cynthia E Hawkins Peter Dirks Eric Bouffet James T Rutka Robert J Wechsler-Reya William A Weiss Lara S Collier Adam J Dupuy Andrey Korshunov David T W Jones Marcel Kool Paul A Northcott Stefan M Pfister David A Largaespada Andrew J Mungall Richard A Moore Nada Jabado Gary D Bader Steven J M Jones David Malkin Marco A Marra Michael D Taylor

Nature 2016 Jan 13;529(7586):351-7. Epub 2016 Jan 13.

Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.

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http://dx.doi.org/10.1038/nature16478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936195PMC
January 2016