Publications by authors named "Mark D Wilkinson"

59Publications

Data-driven classification of the certainty of scholarly assertions.

PeerJ 2020 21;8:e8871. Epub 2020 Apr 21.

Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcon, Madrid, Spain.

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http://dx.doi.org/10.7717/peerj.8871DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182025PMC
April 2020

A Biosynthetic Platform for Antimalarial Drug Discovery.

Antimicrob Agents Chemother 2020 04 21;64(5). Epub 2020 Apr 21.

Department of Life Sciences, Imperial College London, London, United Kingdom

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http://dx.doi.org/10.1128/AAC.02129-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7179595PMC
April 2020

Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa.

Gigascience 2019 12;8(12)

Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón (Madrid), Spain.

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http://dx.doi.org/10.1093/gigascience/giz147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892454PMC
December 2019

Robust and automatic definition of microbiome states.

PeerJ 2019 26;7:e6657. Epub 2019 Mar 26.

Centro de Biotecnología y Genómica de Plantas UPM-INIA, Universidad Politécnica de Madrid, Madrid, Spain.

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http://dx.doi.org/10.7717/peerj.6657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6440462PMC
March 2019

MDPbiome: microbiome engineering through prescriptive perturbations.

Bioinformatics 2018 09;34(17):i838-i847

Center for Plant Biotechnology and Genomics UPM - INIA, Universidad Politecnica de Madrid, Madrid, Spain.

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https://academic.oup.com/bioinformatics/article/34/17/i838/5
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http://dx.doi.org/10.1093/bioinformatics/bty562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129268PMC
September 2018

Virulence- and signaling-associated genes display a preference for long 3'UTRs during rice infection and metabolic stress in the rice blast fungus.

New Phytol 2019 01 31;221(1):399-414. Epub 2018 Aug 31.

Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain.

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http://dx.doi.org/10.1111/nph.15405DOI Listing
January 2019

A design framework and exemplar metrics for FAIRness.

Sci Data 2018 06 26;5:180118. Epub 2018 Jun 26.

Institute of Data Science, Maastricht University, Maastricht, The Netherlands.

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http://dx.doi.org/10.1038/sdata.2018.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018520PMC
June 2018

Preparing Data at the Source to Foster Interoperability across Rare Disease Resources.

Adv Exp Med Biol 2017 ;1031:165-179

Centro de Biotecnología y Genómica de Plantas UPM-INIA, Universidad Politécnica de Madrid, Madrid, Spain.

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http://dx.doi.org/10.1007/978-3-319-67144-4_9DOI Listing
June 2018

Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae.

Arch Virol 2017 Mar 17;162(3):891-895. Epub 2016 Nov 17.

Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA Campus Montegancedo UPM), Pozuelo de Alarcón, 28223, Madrid, Spain.

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http://dx.doi.org/10.1007/s00705-016-3144-9DOI Listing
March 2017

Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base.

Front Plant Sci 2016 12;7:641. Epub 2016 May 12.

Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid Madrid, Spain.

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http://dx.doi.org/10.3389/fpls.2016.00641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4922217PMC
July 2016

Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.

Gigascience 2015 3;4:59. Epub 2015 Dec 3.

Biological Informatics, Centre for Plant Biotechnology and Genomics (CBGP), Technical University of Madrid (UPM), Campus of Montegancedo, Pozuelo de Alarcón, 28223 Spain.

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http://dx.doi.org/10.1186/s13742-015-0092-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669641PMC
July 2016

VPS13D Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock.

J Innate Immun 2015 17;7(5):545-53. Epub 2015 Apr 17.

Critical Care Research Laboratories, Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, B.C., Canada.

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http://dx.doi.org/10.1159/000381265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6738836PMC
June 2016

Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples.

Anal Bioanal Chem 2015 Mar 11;407(7):1841-8. Epub 2015 Jan 11.

Genetics, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain.

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http://dx.doi.org/10.1007/s00216-014-8435-yDOI Listing
March 2015

The relationship between host lifespan and pathogen reservoir potential: an analysis in the system Arabidopsis thaliana--cucumber mosaic virus.

PLoS Pathog 2014 Nov 6;10(11):e1004492. Epub 2014 Nov 6.

Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain.

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http://dx.doi.org/10.1371/journal.ppat.1004492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223077PMC
November 2014

Executing SADI services in Galaxy.

J Biomed Semantics 2014 22;5(1):42. Epub 2014 Sep 22.

Biological Informatics, Centre for Plant Biotechnology and Genomics (CBGP), Technical University of Madrid (UPM), Campus of Montegancedo, 28223 Pozuelo de Alarcón, Spain.

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http://dx.doi.org/10.1186/2041-1480-5-42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193140PMC
October 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

Automatically exposing OpenLifeData via SADI semantic Web Services.

J Biomed Semantics 2014 19;5:46. Epub 2014 Nov 19.

Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain.

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http://dx.doi.org/10.1186/2041-1480-5-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417525PMC
May 2015

The emergent discipline of health web science.

J Med Internet Res 2013 Aug 22;15(8):e166. Epub 2013 Aug 22.

Web Science Research Center, Tetherless World Constellation, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.

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http://dx.doi.org/10.2196/jmir.2499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758025PMC
August 2013

The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions.

JMIR Res Protoc 2013 Apr 5;2(1):e14. Epub 2013 Apr 5.

James Hogg Research Centre, Heart & Lung Institute, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.2196/resprot.2315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628156PMC
April 2013

Analysis of a multilevel diagnosis decision support system and its implications: a case study.

Comput Math Methods Med 2012 23;2012:367345. Epub 2012 Dec 23.

Centre for Plant Biotechnology and Genomics UPM-INIA, Polytechnic University of Madrid, Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain.

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http://dx.doi.org/10.1155/2012/367345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540781PMC
March 2013

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows.

J Biomed Semantics 2013 Jan 4;4(1). Epub 2013 Jan 4.

Ontology Engineering Group, School of Computer Science, Technical University of Madrid (UPM), Boadilla del Monte, 28660, Spain.

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http://dx.doi.org/10.1186/2041-1480-4-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3643862PMC
January 2013

Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web.

J Biomed Semantics 2012 Jul 20;3(1). Epub 2012 Jul 20.

NCE CECR Center of Excellence for the Prevention of Organ Failure (PROOF Centre), St, Paul's Hospital, Room 166, Burrard Building 1081 Burrard Street, Vancouver, BC, Canada, V6Z 1Y6.

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http://jbiomedsem.biomedcentral.com/articles/10.1186/2041-14
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http://dx.doi.org/10.1186/2041-1480-3-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639885PMC
July 2012

Genomics data resources: frameworks and standards.

Authors:
Mark D Wilkinson

Methods Mol Biol 2012 ;856:489-511

Department of Medical Genetics, University of British Columbia and PI Bioinformatics, Heart + Lung Institute at St. Paul's Hospital, Vancouver, BC, Canada.

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http://dx.doi.org/10.1007/978-1-61779-585-5_20DOI Listing
July 2012

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

J Biomed Semantics 2011 Oct 24;2(1). Epub 2011 Oct 24.

Department of Medical Genetics, Heart + Lung Institute at St, Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/2041-1480-2-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212890PMC
October 2011

SADI, SHARE, and the in silico scientific method.

BMC Bioinformatics 2010 Dec 21;11 Suppl 12:S7. Epub 2010 Dec 21.

Heart + Lung Institute at St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.

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http://link.springer.com/content/pdf/10.1186%2F1471-2105-11-
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http://www.biomedcentral.com/1471-2105/11/S12/S7
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http://dx.doi.org/10.1186/1471-2105-11-S12-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040533PMC
December 2010

OWL2Perl: creating Perl modules from OWL class definitions.

Bioinformatics 2010 Sep 13;26(18):2357-8. Epub 2010 Jul 13.

Heart + Lung Institute at St. Paul's Hospital, Vancouver, BC, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btq416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935399PMC
September 2010

Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics.

BMC Bioinformatics 2009 Sep 25;10:313. Epub 2009 Sep 25.

Heart + Lung Institute at St, Paul's Hospital, University of British Columbia, Vancouver, Canada.

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http://dx.doi.org/10.1186/1471-2105-10-313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760536PMC
September 2009

Transgenic approach to improve wheat (Triticum aestivum L.) nutritional quality.

Plant Cell Rep 2009 Jul 24;28(7):1085-94. Epub 2009 May 24.

Agricultural Research Institute of the Hungarian Academy of Sciences, 2462, Martonvásár, Hungary.

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http://dx.doi.org/10.1007/s00299-009-0716-0DOI Listing
July 2009

Moby and Moby 2: creatures of the deep (web).

Brief Bioinform 2009 Mar 16;10(2):114-28. Epub 2009 Jan 16.

Department of Medical Genetics, The Providence Heart + Lung Research Institute at St Paul's Hospital, University of British Columbia, Vancouver, British Columbia V6Z 1Y6, Canada.

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http://dx.doi.org/10.1093/bib/bbn051DOI Listing
March 2009

DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs.

Bioinformatics 2007 Mar 18;23(6):780-2. Epub 2007 Jan 18.

James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btl648DOI Listing
March 2007

Vcsa1 gene peptides for the treatment of inflammatory and allergic reactions.

Recent Pat Inflamm Allergy Drug Discov 2007 Jun;1(2):124-32

Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, 550A Heritage Medical Research Centre, Edmonton, Alberta, Canada.

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http://dx.doi.org/10.2174/187221307780979892DOI Listing
June 2007

iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website.

BMC Bioinformatics 2006 Dec 15;7:534. Epub 2006 Dec 15.

The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, Providence Health Care/University of British Columbia, St, Paul's Hospital, Rm, 166, 1081 Burrard St, Vancouver, British Columbia, V6Z 1Y6, Canada.

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http://dx.doi.org/10.1186/1471-2105-7-534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764905PMC
December 2006

BioMoby extensions to the Taverna workflow management and enactment software.

BMC Bioinformatics 2006 Nov 30;7:523. Epub 2006 Nov 30.

James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St, Paul's Hospital, Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6Z 1Y6, Canada.

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http://dx.doi.org/10.1186/1471-2105-7-523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693925PMC
November 2006

Fast, cheap and out of control: a zero curation model for ontology development.

Pac Symp Biocomput 2006 :128-39

James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia V6Z1 Y6, Canada.

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January 2007

The Life Sciences Semantic Web is full of creeps!

Brief Bioinform 2006 Sep 9;7(3):275-86. Epub 2006 Aug 9.

James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, Vancouver, BC.

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http://dx.doi.org/10.1093/bib/bbl025DOI Listing
September 2006

Comparison of ESTs from juvenile and adult phases of the giant unicellular green alga Acetabularia acetabulum.

BMC Plant Biol 2004 Mar 12;4. Epub 2004 Mar 12.

Department of Biology, University of Washington, Box 355325, 1521 NE Pacific Street, Seattle, WA 98195-5325, USA.

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http://dx.doi.org/10.1186/1471-2229-4-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC385229PMC
March 2004

FDG PET imaging of metastatic gastrointestinal stromal tumor.

Clin Nucl Med 2003 Sep;28(9):780-1

Department of PET and Nuclear Medicine, Royal Prince Alfred Hospital, Camperdown, Australia.

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http://dx.doi.org/10.1097/01.rlu.0000082674.73719.70DOI Listing
September 2003

Differentiation of synchronous tumors using FDG positron emission tomography.

Clin Nucl Med 2003 Jun;28(6):489-91

Department of PET and Nuclear Medicine, Royal Prince Alfred Hospital, Camperdown, Australia.

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http://dx.doi.org/10.1097/00003072-200306000-00009DOI Listing
June 2003

Invasive aspergillosis mimicking stage IIIA non-small-cell lung cancer on FDG positron emission tomography.

Clin Nucl Med 2003 Mar;28(3):234-5

Departments of PET and Nuclear Medicine, Royal Prince Alfred Hospital, Caperdown, New South Wales, Austrlia.

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http://dx.doi.org/10.1097/01.RLU.0000053535.03453.D9DOI Listing
March 2003

Neuroimaging findings in a suprasellar granular cell tumor.

J Comput Assist Tomogr 2003 Jan-Feb;27(1):26-9

Department of Positron Emission Tomography, Royal Prince Alfred Hospital, Sydney, Australia.

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http://dx.doi.org/10.1097/00004728-200301000-00005DOI Listing
February 2003

FDG positron emission tomographic imaging of a large abdominal aortic aneurysm.

Clin Nucl Med 2003 Feb;28(2):130-1

Department of PET and Nuclear Medicine, Royal Prince Alfred Hospital, Camperdown, Sydney, Australia.

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http://dx.doi.org/10.1097/01.RLU.0000048511.49315.69DOI Listing
February 2003

BioMOBY: an open source biological web services proposal.

Brief Bioinform 2002 Dec;3(4):331-41

BioMOBY Project, Plant Biotechnology Institute, National Research Council Canada, Saskatoon, Saskatchewan.

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http://dx.doi.org/10.1093/bib/3.4.331DOI Listing
December 2002

Transcripts of Vp-1 homeologues are misspliced in modern wheat and ancestral species.

Proc Natl Acad Sci U S A 2002 Jul 15;99(15):10203-8. Epub 2002 Jul 15.

Institute of Arable Crops Research-Long Ashton Research Station, Department of Agricultural Sciences, University of Bristol, Long Ashton, Bristol BS41 9AF, United Kingdom.

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http://dx.doi.org/10.1073/pnas.152318599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126648PMC
July 2002