Publications by authors named "Andrew Stubbs"

67Publications

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy.

Gigascience 2020 Oct;9(10)

Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Centre, Wytemaweg 80, 3015 CN, Rotterdam, the Netherlands.

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http://dx.doi.org/10.1093/gigascience/giaa105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7568507PMC
October 2020

Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota.

Genes (Basel) 2020 Sep 21;11(9). Epub 2020 Sep 21.

Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center (Erasmus MC), 3015 CN Rotterdam, The Netherlands.

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http://dx.doi.org/10.3390/genes11091105DOI Listing
September 2020

The tissue-specific aspect of genome-wide DNA methylation in newborn and placental tissues: implications for epigenetic epidemiologic studies.

J Dev Orig Health Dis 2020 Apr 24:1-11. Epub 2020 Apr 24.

Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Centre Rotterdam, Postbus 2040, 3000 CARotterdam, The Netherlands.

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http://dx.doi.org/10.1017/S2040174420000136DOI Listing
April 2020

Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur.

Gigascience 2019 02;8(2)

Erasmus University Medical Center Rotterdam, Department of Pathology, Bioinformatics group, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.

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https://academic.oup.com/gigascience/article/doi/10.1093/gig
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http://dx.doi.org/10.1093/gigascience/giy166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377400PMC
February 2019

KREAP: an automated Galaxy platform to quantify in vitro re-epithelialization kinetics.

Gigascience 2018 07;7(7)

Department of Bioinformatics, Erasmus University Medical Centre, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1093/gigascience/giy078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048990PMC
July 2018

Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics.

Eur J Clin Microbiol Infect Dis 2018 Jun 16;37(6):1081-1089. Epub 2018 Mar 16.

Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre Rotterdam (Erasmus MC), Wytemaweg 80, 3015 CN, Rotterdam, the Netherlands.

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http://dx.doi.org/10.1007/s10096-018-3220-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5948305PMC
June 2018

Early- and late-onset preeclampsia and the tissue-specific epigenome of the placenta and newborn.

Placenta 2017 Oct 30;58:122-132. Epub 2017 Aug 30.

Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Centre Rotterdam, Postbus 2040, 3000 CA Rotterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.placenta.2017.08.070DOI Listing
October 2017

Identification of Associated Genes and Diseases in Patients With Congenital Upper-Limb Anomalies: A Novel Application of the OMT Classification.

J Hand Surg Am 2017 Jul;42(7):533-545.e4

Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.jhsa.2017.03.043DOI Listing
July 2017

Reduced bioavailable manganese causes striatal urea cycle pathology in Huntington's disease mouse model.

Biochim Biophys Acta Mol Basis Dis 2017 06 16;1863(6):1596-1604. Epub 2017 Feb 16.

Department of Pediatrics, Vanderbilt University (VU), Vanderbilt University Medical Center (VUMC), Nashville, TN, USA; Department of Neurology, Vanderbilt University (VU), Vanderbilt University Medical Center (VUMC), Nashville, TN, USA; Department of Biochemistry, Vanderbilt University (VU), Nashville, TN, USA; Vanderbilt Brain Institute, VU. Electronic address:

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http://dx.doi.org/10.1016/j.bbadis.2017.02.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515276PMC
June 2017

Evaluation of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and Adults.

Front Immunol 2016 17;7:410. Epub 2016 Oct 17.

Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands.

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http://dx.doi.org/10.3389/fimmu.2016.00410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086PMC
October 2016

Whole genome sequencing of a dizygotic twin suggests a role for the serotonin receptor HTR7 in autism spectrum disorder.

Am J Med Genet B Neuropsychiatr Genet 2016 12 6;171(8):1049-1056. Epub 2016 Jul 6.

Department of Bioinformatics, Erasmus MC, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1002/ajmg.b.32473DOI Listing
December 2016

A contribution for cost models in biobanking.

Technol Health Care 2016 ;24(1):93-8

Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands.

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http://dx.doi.org/10.3233/THC-151110DOI Listing
January 2017

An International Ki67 Reproducibility Study in Adrenal Cortical Carcinoma.

Am J Surg Pathol 2016 Apr;40(4):569-76

Departments of *Pathology ∥Bioinformatics ¶¶¶Medical Oncology ∥∥∥Internal Medicine, Division of Endocrinology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam ††Laboratory for Pathology, PAL Dordrecht, Dordrecht ###Department of Pathology, Reinier de Graaf Hospital, Delft ****Department of Pathology, University Medical Center Utrecht, Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands †Department of Histopathology, King's College Hospital, London ***Department of Pathology, University Hospitals Birmingham, Birmingham †††Department of Histopathology, Royal Hallamshire Hospital, Sheffield, UK ‡Department of Clinical and Molecular Medicine, Pathology Unit, Sant' Andrea Hospital, Sapienza University, Rome ¶Department of Oncology, University of Turin at San Luigi Hospital, Orbassano, Italy §Department of Pathology, Department of Internal Medicine, University of Michigan Comprehensive Cancer Center, University of Michigan Health System, Ann Arbor, MI #Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI **Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine ‡‡Department of Pathology, Massachusetts General Hospital, Boston, MA §§Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN ∥∥Department of Pathology, University Health Network, University of Toronto, Toronto, ON, Canada ¶¶Department of Anatomical Pathology, Royal North Shore Hospital and University of Sydney, Sydney, NSW, Australia ##Department of Pathology and Molecular Genetics and Research Laboratory, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, University of Lleida, Lleida, Spain ‡‡‡INSERM U1016 CNRS UMR8104, Institut Cochin, Paris Descartes University, Sorbonne Paris Cité §§§Department of Pathology, Pitié-Salpetrière Hospital, APHP, Pierre and Marie Curie Univers

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http://dx.doi.org/10.1097/PAS.0000000000000574DOI Listing
April 2016

FuMa: reporting overlap in RNA-seq detected fusion genes.

Bioinformatics 2016 04 10;32(8):1226-8. Epub 2015 Dec 10.

Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3000 CA, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btv721DOI Listing
April 2016

Platelet density per monocyte predicts adverse events in patients after percutaneous coronary intervention.

Thromb Haemost 2016 Jan 1;115(2):353-60. Epub 2015 Oct 1.

Dr. Bert Rutten, Department of Clinical Chemistry and Haematology, UMC Utrecht, Utrecht, the Netherlands, E-mail:

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http://dx.doi.org/10.1160/TH15-03-0227DOI Listing
January 2016

Discriminating somatic and germline mutations in tumor DNA samples without matching normals.

Genome Res 2015 Sep 24;25(9):1382-90. Epub 2015 Jul 24.

Department of Bioinformatics, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands;

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http://dx.doi.org/10.1101/gr.183053.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561496PMC
September 2015

iReport: a generalised Galaxy solution for integrated experimental reporting.

Gigascience 2014 13;3:19. Epub 2014 Oct 13.

Department of Bioinformatics, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.

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http://dx.doi.org/10.1186/2047-217X-3-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220639PMC
November 2014

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy.

Gigascience 2014 Jan 24;3(1). Epub 2014 Jan 24.

Department of Bioinformatics, Erasmus MC, Dr, Molewaterplein 5, 3015 GE Rotterdam, The Netherlands.

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http://dx.doi.org/10.1186/2047-217X-3-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905657PMC
January 2014

NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data.

Bioinformatics 2013 Nov 4;29(22):2946-7. Epub 2013 Sep 4.

Department of Bioinformatics, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands, Department of Mathematics and Computer Science, Metropolitan State University of Denver, Colorado, USA, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands, Netherlands Proteomics Centre, H.R. Kruytgebouw, Padualaan 8, 3584CH Utrecht, The Netherlands and Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btt513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810856PMC
November 2013

iFUSE: integrated fusion gene explorer.

Bioinformatics 2013 Jul 9;29(13):1700-1. Epub 2013 May 9.

Department of Urology, Erasmus MC, 3015 GE Rotterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btt252DOI Listing
July 2013

Gene fusions by chromothripsis of chromosome 5q in the VCaP prostate cancer cell line.

Hum Genet 2013 Jun 25;132(6):709-13. Epub 2013 Apr 25.

Department of Urology, Josephine Nefkens Institute, Erasmus University Medical Center, Be 362a, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1007/s00439-013-1308-1DOI Listing
June 2013

Deep proteome profiling of circulating granulocytes reveals bactericidal/permeability-increasing protein as a biomarker for severe atherosclerotic coronary stenosis.

J Proteome Res 2012 Nov 11;11(11):5235-44. Epub 2012 Oct 11.

Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands.

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http://pubs.acs.org/doi/10.1021/pr3004375
Publisher Site
http://dx.doi.org/10.1021/pr3004375DOI Listing
November 2012

Comprehensive investigation of parameter choice in viral integration site analysis and its effects on the gene annotations produced.

Hum Gene Ther 2012 Nov 27;23(11):1209-19. Epub 2012 Sep 27.

Department of Hematology, Erasmus University Medical Center, GE Rotterdam, The Netherlands.

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http://dx.doi.org/10.1089/hum.2011.037DOI Listing
November 2012

Recombinant yeast as a vaccine vector for the induction of cytotoxic T-lymphocyte responses.

Curr Opin Mol Ther 2002 Feb;4(1):35-40

Department of Medicine, University of Colorado Health Sciences Center, Denver 80262, USA.

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February 2002