Bas E Dutilh

Bas E Dutilh

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Bas E Dutilh

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Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Authors:
Robert A Edwards Alejandro A Vega Holly M Norman Maria Ohaeri Kyle Levi Elizabeth A Dinsdale Ondrej Cinek Ramy K Aziz Katelyn McNair Jeremy J Barr Kyle Bibby Stan J J Brouns Adrian Cazares Patrick A de Jonge Christelle Desnues Samuel L Díaz Muñoz Peter C Fineran Alexander Kurilshikov Rob Lavigne Karla Mazankova David T McCarthy Franklin L Nobrega Alejandro Reyes Muñoz German Tapia Nicole Trefault Alexander V Tyakht Pablo Vinuesa Jeroen Wagemans Alexandra Zhernakova Frank M Aarestrup Gunduz Ahmadov Abeer Alassaf Josefa Anton Abigail Asangba Emma K Billings Vito Adrian Cantu Jane M Carlton Daniel Cazares Gyu-Sung Cho Tess Condeff Pilar Cortés Mike Cranfield Daniel A Cuevas Rodrigo De la Iglesia Przemyslaw Decewicz Michael P Doane Nathaniel J Dominy Lukasz Dziewit Bashir Mukhtar Elwasila A Murat Eren Charles Franz Jingyuan Fu Cristina Garcia-Aljaro Elodie Ghedin Kristen M Gulino John M Haggerty Steven R Head Rene S Hendriksen Colin Hill Heikki Hyöty Elena N Ilina Mitchell T Irwin Thomas C Jeffries Juan Jofre Randall E Junge Scott T Kelley Mohammadali Khan Mirzaei Martin Kowalewski Deepak Kumaresan Steven R Leigh David Lipson Eugenia S Lisitsyna Montserrat Llagostera Julia M Maritz Linsey C Marr Angela McCann Shahar Molshanski-Mor Silvia Monteiro Benjamin Moreira-Grez Megan Morris Lawrence Mugisha Maite Muniesa Horst Neve Nam-Phuong Nguyen Olivia D Nigro Anders S Nilsson Taylor O'Connell Rasha Odeh Andrew Oliver Mariana Piuri Aaron J Prussin Ii Udi Qimron Zhe-Xue Quan Petra Rainetova Adán Ramírez-Rojas Raul Raya Kim Reasor Gillian A O Rice Alessandro Rossi Ricardo Santos John Shimashita Elyse N Stachler Lars C Stene Ronan Strain Rebecca Stumpf Pedro J Torres Alan Twaddle MaryAnn Ugochi Ibekwe Nicolás Villagra Stephen Wandro Bryan White Andy Whiteley Katrine L Whiteson Cisca Wijmenga Maria M Zambrano Henrike Zschach Bas E Dutilh

Nat Microbiol 2019 Oct 8;4(10):1727-1736. Epub 2019 Jul 8.

Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/s41564-019-0494-6DOI Listing
October 2019

A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion.

Cell Host Microbe 2019 10 24;26(4):542-550.e5. Epub 2019 Sep 24.

GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Symbioses, 24105 Kiel, Germany; Christian-Albrechts-University of Kiel, 24105 Kiel, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2019.08.019DOI Listing
October 2019

Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia.

J Glob Antimicrob Resist 2019 Mar 29;16:170-177. Epub 2018 Aug 29.

Infectious Disease Research Center, Faculty of Medicine, Universitas Padjadjaran, Eijkman 38, Bandung 40161, Indonesia; Faculty of Medicine, Universitas Padjadjaran/Hasan Sadikin Hospital, Pasir Kaliki 38, Bandung 40161, Indonesia.

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http://dx.doi.org/10.1016/j.jgar.2018.08.018DOI Listing
March 2019

Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients.

Front Cell Infect Microbiol 2018 6;8:25. Epub 2018 Feb 6.

Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, Rome, Italy.

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http://dx.doi.org/10.3389/fcimb.2018.00025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808120PMC
January 2019

Molecular and Evolutionary Determinants of Bacteriophage Host Range.

Trends Microbiol 2019 01 1;27(1):51-63. Epub 2018 Sep 1.

Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525GA Nijmegen, The Netherlands; These authors made equal contributions. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0966842X183017
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http://dx.doi.org/10.1016/j.tim.2018.08.006DOI Listing
January 2019

Targeting mechanisms of tailed bacteriophages.

Nat Rev Microbiol 2018 12;16(12):760-773

Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands.

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http://dx.doi.org/10.1038/s41579-018-0070-8DOI Listing
December 2018

Phage Genome Annotation Using the RAST Pipeline.

Methods Mol Biol 2018 ;1681:231-238

Computational Sciences Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.

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http://dx.doi.org/10.1007/978-1-4939-7343-9_17DOI Listing
June 2018

Towards predicting the environmental metabolome from metagenomics with a mechanistic model.

Nat Microbiol 2018 04 12;3(4):456-460. Epub 2018 Mar 12.

Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/s41564-018-0124-8DOI Listing
April 2018

Temporal dynamics of uncultured viruses: a new dimension in viral diversity.

ISME J 2018 01 13;12(1):199-211. Epub 2017 Oct 13.

School of Biological Sciences, The Queen's University of Belfast, Belfast, UK.

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http://dx.doi.org/10.1038/ismej.2017.157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739013PMC
January 2018

Ecogenomics and Taxonomy of Cyanobacteria Phylum.

Front Microbiol 2017 14;8:2132. Epub 2017 Nov 14.

Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.

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http://dx.doi.org/10.3389/fmicb.2017.02132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694629PMC
November 2017

Editorial: Virus Discovery by Metagenomics: The (Im)possibilities.

Front Microbiol 2017 8;8:1710. Epub 2017 Sep 8.

Department of Molecular Biology and Biochemistry, University of California, IrvineIrvine, CA, United States.

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http://dx.doi.org/10.3389/fmicb.2017.01710DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596103PMC
September 2017

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans.

Nat Commun 2017 07 5;8:15955. Epub 2017 Jul 5.

Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21944970, Brazil.

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http://dx.doi.org/10.1038/ncomms15955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5504273PMC
July 2017

Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses.

Viruses 2017 06 2;9(6). Epub 2017 Jun 2.

Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and University of Utrecht, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.

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http://dx.doi.org/10.3390/v9060134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490811PMC
June 2017

Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses.

Front Microbiol 2017 3;8:352. Epub 2017 Mar 3.

Department of Civil and Environmental Engineering, University of Utah Salt Lake, UT, USA.

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http://dx.doi.org/10.3389/fmicb.2017.00352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5334351PMC
March 2017

Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Bioreactor Enrichment Culture.

Front Microbiol 2016 8;7:1740. Epub 2016 Nov 8.

Department of Microbiology, Faculty of Science, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands.

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http://dx.doi.org/10.3389/fmicb.2016.01740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5099504PMC
November 2016

Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee.

Arch Virol 2016 Apr 5;161(4):1095-9. Epub 2016 Jan 5.

Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA.

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http://dx.doi.org/10.1007/s00705-015-2728-0DOI Listing
April 2016

Computational approaches to predict bacteriophage-host relationships.

FEMS Microbiol Rev 2016 Mar 9;40(2):258-72. Epub 2015 Dec 9.

Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands

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http://dx.doi.org/10.1093/femsre/fuv048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831537PMC
March 2016

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system.

Nat Commun 2016 Mar 31;7:11172. Epub 2016 Mar 31.

Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/ncomms11172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821891PMC
March 2016

Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum.

PLoS One 2015 3;10(6):e0126883. Epub 2015 Jun 3.

Department of Biology, San Diego State University, San Diego, California, 92182, United States of America; Department of Computer Science, San Diego State University, San Diego, California, 92182, United States of America; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Argonne National Laboratory, 9700 S. Cass Ave, Argonne, Illinois, 60349, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126883PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454671PMC
February 2016

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.

Bioinformatics 2016 Feb 9;32(3):354-61. Epub 2015 Oct 9.

Computational Science Research Center Department of Biology, San Diego State University, San Diego, CA 92182, USA Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Brazil Department of Computer Science, San Diego State University, San Diego, CA 92182, USA Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, IL 60439, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734042PMC
February 2016

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm.

Environ Microbiol 2016 Jan 21;18(1):273-87. Epub 2015 Oct 21.

Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Qld, Australia.

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http://dx.doi.org/10.1111/1462-2920.13019DOI Listing
January 2016

Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon.

Front Microbiol 2015 6;6:1481. Epub 2016 Jan 6.

Department of Laboratory Medicine - Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Netherlands.

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http://dx.doi.org/10.3389/fmicb.2015.01481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4701948PMC
January 2016

From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.

Cell Mol Life Sci 2015 Nov 9;72(22):4287-308. Epub 2015 Aug 9.

Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1007/s00018-015-2004-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4611022PMC
November 2015

Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis.

PLoS Med 2015 Nov 3;12(11):e1001898; discussion e1001898. Epub 2015 Nov 3.

Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom.

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https://dx.plos.org/10.1371/journal.pmed.1001898
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http://dx.doi.org/10.1371/journal.pmed.1001898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631366PMC
November 2015

Sequence specificity between interacting and non-interacting homologs identifies interface residues--a homodimer and monomer use case.

BMC Bioinformatics 2015 Oct 8;16:325. Epub 2015 Oct 8.

Center for Integrative Bioinformatics VU (IBIVU), Vrije University Amsterdam, De Boelelaan 1081A, 1081 HV, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/s12859-015-0758-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4599308PMC
October 2015

Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review.

PeerJ 2015 16;3:e1008. Epub 2015 Jun 16.

Universidade Federal do Rio de Janeiro (UFRJ)/Instituto de Biologia (IB) , Rio de Janeiro , Brazil ; Universidade Federal do Rio de Janeiro (UFRJ)/COPPE, SAGE , Rio de Janeiro , Brazil.

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https://peerj.com/articles/1008.pdf
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https://peerj.com/articles/1008
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http://dx.doi.org/10.7717/peerj.1008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476133PMC
July 2015

Microbial taxonomy in the post-genomic era: rebuilding from scratch?

Arch Microbiol 2015 Apr 23;197(3):359-70. Epub 2014 Dec 23.

Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil,

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http://dx.doi.org/10.1007/s00203-014-1071-2DOI Listing
April 2015

Beyond research: a primer for considerations on using viral metagenomics in the field and clinic.

Front Microbiol 2015 25;6:224. Epub 2015 Mar 25.

Theoretical Biology and Bioinformatics, Utrecht University, Utrecht Netherlands ; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen Netherlands ; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro Brazil.

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http://dx.doi.org/10.3389/fmicb.2015.00224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4373370PMC
April 2015

Cell wall modifications during conidial maturation of the human pathogenic fungus Pseudallescheria boydii.

PLoS One 2014 20;9(6):e100290. Epub 2014 Jun 20.

L'UNAM Université, Université d'Angers, Groupe d'Etude des Interactions Hôte-Pathogène EA 3142, Angers, France; Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire, Angers, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100290PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4065047PMC
February 2015

Metagenomic ventures into outer sequence space.

Authors:
Bas E Dutilh

Bacteriophage 2014;4(4):e979664. Epub 2014 Dec 15.

Theoretical Biology and Bioinformatics; Utrecht University ; Utrecht, The Netherlands ; Centre for Molecular and Biomolecular Informatics; Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre ; Nijmegen, The Netherlands ; Department of Marine Biology, Institute of Biology; Federal University of Rio de Janeiro ; Rio de Janeiro, Brazil.

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http://dx.doi.org/10.4161/21597081.2014.979664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588555PMC
December 2014

Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.

PeerJ 2014 19;2:e520. Epub 2014 Aug 19.

Department of Biology, San Diego State University , San Diego, CA , USA ; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro , Brazil ; Division of Mathematics and Computer Science, Argonne National Laboratory , Argonne, IL , USA.

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http://dx.doi.org/10.7717/peerj.520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145072PMC
September 2014

Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics.

OMICS 2014 Jul 2;18(7):402-14. Epub 2014 May 2.

1 Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University , Cairo, Egypt .

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http://dx.doi.org/10.1089/omi.2014.0018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086029PMC
July 2014

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes.

Nat Commun 2014 Jul 24;5:4498. Epub 2014 Jul 24.

1] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo. 373, Prédio Anexo ao Bloco A do Centro de Ciências da Saúde, Ilha do Fundão, CEP 21941-902 Rio de Janeiro, Brazil [3] Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [4] Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S Cass Ave B109, Argonne, Illinois 60439, USA.

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http://dx.doi.org/10.1038/ncomms5498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111155PMC
July 2014

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.

PeerJ 2014 5;2:e425. Epub 2014 Jun 5.

Computational Science Research Center, San Diego State University , San Diego, CA , USA ; Department of Computer Science, San Diego State University , San Diego, CA , USA ; Department of Biology, San Diego State University , San Diego, CA , USA ; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro , Brazil ; Division of Mathematics and Computer Science, Argonne National Laboratory , Argonne, IL , USA.

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http://dx.doi.org/10.7717/peerj.425DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060023PMC
June 2014

Combining de novo and reference-guided assembly with scaffold_builder.

Source Code Biol Med 2013 Nov 22;8(1):23. Epub 2013 Nov 22.

Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA.

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http://dx.doi.org/10.1186/1751-0473-8-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177539PMC
November 2013

Explaining microbial phenotypes on a genomic scale: GWAS for microbes.

Brief Funct Genomics 2013 Jul 26;12(4):366-80. Epub 2013 Apr 26.

CMBI, NCMLS, Radboud University Medical Centre. Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bfgp/elt008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743258PMC
July 2013

Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer.

Best Pract Res Clin Gastroenterol 2013 Feb;27(1):85-99

Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands.

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https://linkinghub.elsevier.com/retrieve/pii/S15216918130006
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http://dx.doi.org/10.1016/j.bpg.2013.03.008DOI Listing
February 2013

Reference-independent comparative metagenomics using cross-assembly: crAss.

Bioinformatics 2012 Dec 16;28(24):3225-31. Epub 2012 Oct 16.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bts613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3519457PMC
December 2012

Bacterial responses to a simulated colon tumor microenvironment.

Mol Cell Proteomics 2012 Oct 19;11(10):851-62. Epub 2012 Jun 19.

Department of Laboratory Medicine/830, Radboud University Medical Centre, 6500 HB Nijmegen, the Netherlands.

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http://dx.doi.org/10.1074/mcp.M112.019315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494137PMC
October 2012

A bacterial driver-passenger model for colorectal cancer: beyond the usual suspects.

Nat Rev Microbiol 2012 06 25;10(8):575-82. Epub 2012 Jun 25.

Department of Laboratory Medicine, Nijmegen Institute for Infection, Inflammation and Immunity (N4i) & Radboud University Centre for Oncology (RUCO), Geert Grooteplein 10 (830), 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/nrmicro2819DOI Listing
June 2012

Metagenomics and future perspectives in virus discovery.

Curr Opin Virol 2012 Feb 20;2(1):63-77. Epub 2012 Jan 20.

Department of Biology, San Diego State University, San Diego, CA 92182, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S187962571100190
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http://dx.doi.org/10.1016/j.coviro.2011.12.004DOI Listing
February 2012

Ultra-deep pyrosequencing of pmoA amplicons confirms the prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog.

Environ Microbiol Rep 2011 Dec 9;3(6):667-73. Epub 2011 May 9.

Radboud University Nijmegen, Institute for Water and Wetland Research (IWWR), Department of Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands. Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands. Department of Bioresources, AIT, Austrian Institute of Technology GmbH, 2444 Seibersdorf, Austria. Department of Human Genetics, Radboud University Nijmegen Medical Centre, Geert Grooteplein 10, 6525 GA Nijmegen, the Netherlands.

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http://dx.doi.org/10.1111/j.1758-2229.2011.00260.xDOI Listing
December 2011

Genome sequence of the human pathogen Vibrio cholerae Amazonia.

J Bacteriol 2011 Oct;193(20):5877-8

Laboratory of Molecular Genetics of Microrganims, Oswaldo Cruz Institute, Rio de Janeiro, Brazil.

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http://dx.doi.org/10.1128/JB.05643-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187201PMC
October 2011

The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis.

Mol Biol Evol 2011 Aug 4;28(8):2379-91. Epub 2011 Mar 4.

Department of Evolutionary Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/molbev/msr059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144386PMC
August 2011

FACIL: Fast and Accurate Genetic Code Inference and Logo.

Bioinformatics 2011 Jul 8;27(14):1929-33. Epub 2011 Jun 8.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129529PMC
July 2011

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.

Bioinformatics 2009 Nov 19;25(21):2878-81. Epub 2009 Jun 19.

Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btp377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781756PMC
November 2009

Asymmetric relationships between proteins shape genome evolution.

Genome Biol 2009 Feb 12;10(2):R19. Epub 2009 Feb 12.

Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/gb-2009-10-2-r19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688278PMC
February 2009

Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns.

BMC Genomics 2008 Dec 5;9:587. Epub 2008 Dec 5.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Nijmegen, the Netherlands.

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http://dx.doi.org/10.1186/1471-2164-9-587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633312PMC
December 2008

Signature genes as a phylogenomic tool.

Mol Biol Evol 2008 Aug 19;25(8):1659-67. Epub 2008 May 19.

Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/molbev/msn115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2464742PMC
August 2008

Signature, a web server for taxonomic characterization of sequence samples using signature genes.

Nucleic Acids Res 2008 Jul 17;36(Web Server issue):W470-4. Epub 2008 May 17.

Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkn277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447722PMC
July 2008

Conservation of divergent transcription in fungi.

Trends Genet 2008 May 28;24(5):207-11. Epub 2008 Mar 28.

Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1016/j.tig.2008.02.003DOI Listing
May 2008

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.

J R Soc Interface 2008 Feb;5(19):151-70

Centre for Molecular and Biomolecular Informatics/Nijmegen, Centre for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands.

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http://rsif.royalsocietypublishing.org/cgi/doi/10.1098/rsif.
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http://dx.doi.org/10.1098/rsif.2007.1047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2405902PMC
February 2008

Genome trees and the nature of genome evolution.

Annu Rev Microbiol 2005 ;59:191-209

Center for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1146/annurev.micro.59.030804.121233DOI Listing
January 2006

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

BMC Genomics 2006 Jan 19;7:10. Epub 2006 Jan 19.

Center for Molecular and Biomolecular Informatics / Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-7-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1382217PMC
January 2006

The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise.

J Mol Evol 2004 May;58(5):527-39

Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, University of Nijmegen, Nijmegen, The Netherlands.

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http://link.springer.com/10.1007/s00239-003-2575-6
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http://dx.doi.org/10.1007/s00239-003-2575-6DOI Listing
May 2004

Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells.

J Theor Biol 2003 Oct;224(3):351-8

Theoretical Biology and Bioinformatics Group, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

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http://dx.doi.org/10.1016/s0022-5193(03)00172-3DOI Listing
October 2003