Publications by authors named "Peter Dawyndt"

62Publications

Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool.

J Proteome Res 2021 Jan 5. Epub 2021 Jan 5.

Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium.

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January 2021

Unipept CLI 2.0: adding support for visualizations and functional annotations.

Bioinformatics 2020 Aug;36(14):4220-4221

Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium.

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August 2020

Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis.

J Proteome Res 2020 08 11;19(8):3562-3566. Epub 2020 Jun 11.

Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.

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August 2020

Unipept 4.0: Functional Analysis of Metaproteome Data.

J Proteome Res 2019 02 4;18(2):606-615. Epub 2018 Dec 4.

Department of Applied Mathematics, Computer Science and Statistics , Ghent University , Ghent B-9000 , Belgium.

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February 2019

Multifunctional sequence-defined macromolecules for chemical data storage.

Nat Commun 2018 10 26;9(1):4451. Epub 2018 Oct 26.

Department of Organic and Macromolecular Chemistry, Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Ghent University, Krijgslaan 281 S4bis, 9000, Ghent, Belgium.

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October 2018

Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea.

Environ Sci Technol 2017 Jul 19;51(13):7350-7360. Epub 2017 Jun 19.

Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium.

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July 2017

High-throughput metaproteomics data analysis with Unipept: A tutorial.

J Proteomics 2018 01 24;171:11-22. Epub 2017 May 24.

Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.

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January 2018

Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Leaf Infection.

Front Microbiol 2016 22;7:2062. Epub 2016 Dec 22.

Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries Research Merelbeke, Belgium.

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December 2016

Global alternans instability and its effect on non-linear wave propagation: dynamical Wenckebach block and self terminating spiral waves.

Sci Rep 2016 07 7;6:29397. Epub 2016 Jul 7.

Department of Physics and Astronomy, Ghent University, Krijgslaan 281, S9, 9000 Ghent, Belgium.

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July 2016

The unique peptidome: Taxon-specific tryptic peptides as biomarkers for targeted metaproteomics.

Proteomics 2016 09 16;16(17):2313-8. Epub 2016 Aug 16.

Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium.

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September 2016

Unipept web services for metaproteomics analysis.

Bioinformatics 2016 06 27;32(11):1746-8. Epub 2016 Jan 27.

Department of Applied Mathematics, Computer Science and Statistics.

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June 2016

Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis.

J Cyst Fibros 2016 Mar 30;15(2):242-50. Epub 2015 Aug 30.

Ghent University, Department of Biochemistry and Microbiology, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

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March 2016

Bacterial Community Profiling of Plastic Litter in the Belgian Part of the North Sea.

Environ Sci Technol 2015 Aug 6;49(16):9629-38. Epub 2015 Aug 6.

§Department of Applied Mathematics, Computer Sciences and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Ghent, Belgium.

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August 2015

A Long Fragment Aligner called ALFALFA.

BMC Bioinformatics 2015 May 15;16:159. Epub 2015 May 15.

Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 Building S9, Ghent, B-9000, Belgium.

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May 2015

The Unipept metaproteomics analysis pipeline.

Proteomics 2015 Apr 11;15(8):1437-42. Epub 2015 Feb 11.

Faculty of Sciences, Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.

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April 2015

Small size ionic heterogeneities in the human heart can attract rotors.

Am J Physiol Heart Circ Physiol 2014 Nov 12;307(10):H1456-68. Epub 2014 Sep 12.

Department of Physics and Astronomy, Ghent University, Ghent, Belgium; Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russia

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November 2014

Initiation and dynamics of a spiral wave around an ionic heterogeneity in a model for human cardiac tissue.

Phys Rev E Stat Nonlin Soft Matter Phys 2013 Dec 3;88(6):062703. Epub 2013 Dec 3.

Department of Physics and Astronomy, Ghent University, Ghent, Belgium.

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December 2013

StrainInfo introduces electronic passports for microorganisms.

Syst Appl Microbiol 2014 Feb 8;37(1):42-50. Epub 2013 Dec 8.

Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium. Electronic address:

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February 2014

Filtering and ranking techniques for automated selection of high-quality 16S rRNA gene sequences.

Syst Appl Microbiol 2013 Dec 22;36(8):549-59. Epub 2013 Oct 22.

Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium. Electronic address:

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December 2013

essaMEM: finding maximal exact matches using enhanced sparse suffix arrays.

Bioinformatics 2013 Mar 24;29(6):802-4. Epub 2013 Jan 24.

Department of Applied Mathematics and Computer Science and Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium.

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March 2013

Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples.

J Proteome Res 2012 Dec 26;11(12):5773-80. Epub 2012 Nov 26.

Department of Applied Mathematics and Computer Science, Laboratory for Protein Biochemistry and Biomolecular Engineering, Faculty of Sciences, Ghent University, Krijgslaan 281, B-9000 Ghent, Belgium.

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December 2012

Prospects and limitations of full-text index structures in genome analysis.

Nucleic Acids Res 2012 Aug 13;40(15):6993-7015. Epub 2012 May 13.

Department of Applied Mathematics and Computer Science, Ghent University, Building S9, 281 Krijgslaan, Belgium.

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August 2012

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Authors:
Pelin Yilmaz Renzo Kottmann Dawn Field Rob Knight James R Cole Linda Amaral-Zettler Jack A Gilbert Ilene Karsch-Mizrachi Anjanette Johnston Guy Cochrane Robert Vaughan Christopher Hunter Joonhong Park Norman Morrison Philippe Rocca-Serra Peter Sterk Manimozhiyan Arumugam Mark Bailey Laura Baumgartner Bruce W Birren Martin J Blaser Vivien Bonazzi Tim Booth Peer Bork Frederic D Bushman Pier Luigi Buttigieg Patrick S G Chain Emily Charlson Elizabeth K Costello Heather Huot-Creasy Peter Dawyndt Todd DeSantis Noah Fierer Jed A Fuhrman Rachel E Gallery Dirk Gevers Richard A Gibbs Inigo San Gil Antonio Gonzalez Jeffrey I Gordon Robert Guralnick Wolfgang Hankeln Sarah Highlander Philip Hugenholtz Janet Jansson Andrew L Kau Scott T Kelley Jerry Kennedy Dan Knights Omry Koren Justin Kuczynski Nikos Kyrpides Robert Larsen Christian L Lauber Teresa Legg Ruth E Ley Catherine A Lozupone Wolfgang Ludwig Donna Lyons Eamonn Maguire Barbara A Methé Folker Meyer Brian Muegge Sara Nakielny Karen E Nelson Diana Nemergut Josh D Neufeld Lindsay K Newbold Anna E Oliver Norman R Pace Giriprakash Palanisamy Jörg Peplies Joseph Petrosino Lita Proctor Elmar Pruesse Christian Quast Jeroen Raes Sujeevan Ratnasingham Jacques Ravel David A Relman Susanna Assunta-Sansone Patrick D Schloss Lynn Schriml Rohini Sinha Michelle I Smith Erica Sodergren Aymé Spo Jesse Stombaugh James M Tiedje Doyle V Ward George M Weinstock Doug Wendel Owen White Andrew Whiteley Andreas Wilke Jennifer R Wortman Tanya Yatsunenko Frank Oliver Glöckner

Nat Biotechnol 2011 May;29(5):415-20

Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

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May 2011

Make Histri: reconstructing the exchange history of bacterial and archaeal type strains.

Syst Appl Microbiol 2011 Jul 22;34(5):328-36. Epub 2011 Apr 22.

Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.

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July 2011

Classification and identification of the Burkholderia cepacia complex: Past, present and future.

Syst Appl Microbiol 2011 Apr 22;34(2):87-95. Epub 2011 Jan 22.

Laboratory of Microbiology, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

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April 2011

Microbiological Common Language (MCL): a standard for electronic information exchange in the Microbial Commons.

Res Microbiol 2010 Jul-Aug;161(6):439-45. Epub 2010 Mar 6.

Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.

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November 2010

Towards large-scale FAME-based bacterial species identification using machine learning techniques.

Syst Appl Microbiol 2009 May 23;32(3):163-76. Epub 2009 Feb 23.

Research Unit Knowledge-based Systems, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Ghent, Belgium.

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May 2009

Bayesian clustering of fuzzy feature vectors using a quasi-likelihood approach.

IEEE Trans Pattern Anal Mach Intell 2009 Jan;31(1):74-85

Departement of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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January 2009

Genus-wide Bacillus species identification through proper artificial neural network experiments on fatty acid profiles.

Antonie Van Leeuwenhoek 2008 Aug 6;94(2):187-98. Epub 2008 Mar 6.

Research Unit Knowledge-based Systems, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent 9000, Belgium.

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August 2008

Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium).

Int J Syst Evol Microbiol 2008 Jan;58(Pt 1):200-14

Laboratorium voor Microbiologie (WE10), Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium.

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January 2008

Identification of lactobacilli by pheS and rpoA gene sequence analyses.

Int J Syst Evol Microbiol 2007 Dec;57(Pt 12):2777-2789

BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium.

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December 2007

Ecological diversification in the Bacillus cereus Group.

Environ Microbiol 2008 Apr 25;10(4):851-65. Epub 2007 Nov 25.

Institut National de Recherche Agronomique, UMR A408 Sécurité et Qualité des Produits d'Origine Végétale, INRA, Domaine Saint-Paul, Site Agroparc, F-84914 Avignon Cedex 9, France.

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April 2008

Fame-based Bacillus species identification using artificial neural networks.

Commun Agric Appl Biol Sci 2006 ;71(1):259-62

Research Unit Knowledge-based Systems, Ghent University Coupure Links 653, BE-9000 Gent, Belgium.

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January 2007

Stepping stones towards a new prokaryotic taxonomy.

Philos Trans R Soc Lond B Biol Sci 2006 Nov;361(1475):1911-6

Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.

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November 2006

Raman microspectroscopy as an identification tool within the phylogenetically homogeneous 'Bacillus subtilis' group.

Syst Appl Microbiol 2006 Dec 24;29(8):650-60. Epub 2006 Mar 24.

Department of Analytical Chemistry, Ghent University, Proeftuinstraat 86, Ghent, Belgium.

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December 2006

Mining fatty acid databases for detection of novel compounds in aerobic bacteria.

J Microbiol Methods 2006 Sep 7;66(3):410-33. Epub 2006 Mar 7.

Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium.

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September 2006

Improving interoperability between microbial information and sequence databases.

BMC Bioinformatics 2005 Dec 1;6 Suppl 4:S23. Epub 2005 Dec 1.

Bioinformatics and Structural Proteomics, National Cancer Research Institute, Largo Rosanna Benzi 10, I-16132, Genova, Italy.

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December 2005

Staphylococcus pseudintermedius sp. nov., a coagulase-positive species from animals.

Int J Syst Evol Microbiol 2005 Jul;55(Pt 4):1569-1573

Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium.

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July 2005

Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes.

Microbiology (Reading) 2005 Jul;151(Pt 7):2141-2150

BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium.

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July 2005

Grouping of streptomycetes using 16S-ITS RFLP fingerprinting.

Res Microbiol 2005 Jun-Jul;156(5-6):755-62. Epub 2005 Feb 26.

BCCM/LMG Bacteria Collection and Laboratorium voor Microbiologie, University Gent, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium. Benjamin.Lanoot

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October 2005

Diversity of 746 heterotrophic bacteria isolated from microbial mats from ten Antarctic lakes.

Syst Appl Microbiol 2002 Dec;25(4):603-10

Laborarorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, Belgium.

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December 2002