Bas E. Dutilh - Publications

2012

2011

2010

2009

Brigida T. Luckwu de Lucena, Genivaldo G.Z. Silva, Billy Manoel dos Santos, Graciela M. Dias, Gilda R. Amaral, Ana P. Moreira, Marcos A. de Morais Júnior, Bas E. Dutilh, Robert A. Edwards, Valdir Balbino, Cristiane C. Thompson and Fabiano L. Thompson (2012), "Genome sequence of the ethanol tolerant Lactobacillus vini strains LMG23202T and JP7.8.9", Journal of Bacteriology 194: 3018.

Jack van de Vossenberg, Dagmar Woebken, Wouter J. Maalcke, Hans J.C.T. Wessels, Bas E. Dutilh, Boran Kartal, Eva M. Janssen-Megens, Guus Roeselers, Jia Yan, Daan Speth, Jolein Gloerich, Wim Geerts, Erwin van der Biezen, Wendy Pluk, Kees-Jan Françoijs, Lina Russ, Phyllis Lam, Stefanie A. Malfatti, Susannah Green Tringe, Suzanne C.M. Haaijer, Huub J.M. Op den Camp, Henk G. Stunnenberg, Rudi Amann, Marcel M.M. Kuypers, Mike S.M. Jetten (2012), "The metagenome of the marine anammox bacterium "Candidatus Scalindua profunda" illustrates the versatility of this globally important nitrogen cycle bacterium", Environmental Microbiology.

DOI, supplements.

John L. Mokili, Forest Rohwer and Bas E. Dutilh (2012), "Metagenomics and future perspectives in virus discovery", Current Opinion in Virology 2: 1-15.

DOI

Maartje A.H.J. van Kessel, Bas E. Dutilh, Kornelia Neveling, Michael P. Kwint, Joris A. Veltman, Gert Flik, Mike S.M. Jetten, Peter H.M. Klaren and Huub J.M. Op den Camp (2011), "Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.)", AMB Express 1: 41.

Supplements: Figure, Table.

Cristiane C. Thompson, Michel Abanto Marin, Graciela Maria Dias, Bas E. Dutilh, Rob Edwards, Tetsuya Iida, Fabiano L. Thompson (2011), "Genome sequence of the human pathogen Vibrio cholerae Amazonia", Journal of Bacteriology 193: 5877-5878.

Bas E. Dutilh, Rasa Jurgelenaite, Radek Szklarczyk, Sacha A.F.T. van Hijum, Harry R. Harhangi, Markus Schmid, Bart de Wild, Kees-Jan Françoijs, Hendrik G. Stunnenberg, Marc Strous, Mike S.M. Jetten, Huub J.M. Op den Camp and Martijn A. Huynen (2011), "FACIL: fast and accurate genetic code inference and logo", Bioinformatics 27: 1929-1933.

Supplements

Julian R. Marchesi, Bas E. Dutilh, Neil Hall, Wilbert H. M. Peters, Rian Roelofs, Annemarie Boleij, Harold Tjalsma (2011), "Towards the human colorectal cancer microbiome", PLoS ONE 6: e20447.

Supplements

Harold Tjalsma*, Coby M.M. Laarakkers*, Rachel P.S. van Swelm, Milan Theurl, Igor Theurl, Erwin H. Kemna, Yuri E.M. van der Burgt, Hanka Venselaar, Bas E. Dutilh, Frans G.M. Russel, Günter Weiss, Rosalinde Masereeuw, Robert E. Fleming, Dorine W. Swinkels (2011), "Mass spectrometry analysis of hepcidin peptides in experimental mouse models", PLoS ONE 6: e16762.

*Authors contributed equally.
Supplements

Rob M. de Graaf*, Guenola Ricard*, Theo A. van Alen, Isabel Duarte, Bas E. Dutilh, Carola Burgtorf, Jan W.P. Kuiper, Georg W.M. van der Staay, Aloysius G.M. Tielens, Martijn A. Huynen and Johannes H.P. Hackstein (2011), "The organellar genome and metabolic potential of the hydrogen- producing mitochondrion of Nyctotherus ovalis", Molecular Biology and Evolution 28: 2379-2391.

*Authors contributed equally.

Joyce Emons, Bas E. Dutilh, Eva Decker, Heide Pirzer, Carsten Sticht, Norbert Gretz, Gudrun Rappold, Ewen R. Cameron, James C. Neil, Gary S. Stein, Andre J. van Wijnen, Jan Maarten Wit, Janine N. Post, Marcel Karperien (2011), "Genome wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation", Journal of Endocrinology 209: 245-254.

Bas E. Dutilh, Martijn A. Huynen, Jolein Gloerich and Marc Strous (2011), "Iterative read mapping and assembly allows the use of a more distant reference in metagenome assembly", Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches: Ed. Frans J. De Bruijn. Wiley-Blackwell.

Wiley-Blackwell

Nardy Kip, Bas E. Dutilh, Yao Pan, Levente Bodrossy, Kornelia Neveling, Michael P. Kwint, Mike S.M. Jetten and Huub J.M. Op den Camp (2011), "Ultra-deep pyrosequencing of pmoA amplicons confirms prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog", Environmental Microbiology Reports 3: no. doi: 10.1111/j.1758-2229.2011.00260.x.

DOI, supplements.

Evelyn N. Kouwenhoven*, Simon J. van Heeringen*, Juan J. Tena*, Martin Oti, Bas E. Dutilh, M. Eva Alonso, Elisa de la Calle-Mustienes, Leonie Smeenk, Tuula Rinne, Lilian Parsaulian, Emine Bolat, Rasa Jurgelenaite, Martijn A. Huynen, Alexander Hoischen, Joris A. Veltman, Han G. Brunner, Tony Roscioli, Emily Oates, Meredith Wilson, Miguel Manzanares, José Luis Gómez-Skarmeta, Hendrik G. Stunnenberg, Marion Lohrum, Hans van Bokhoven and Huiqing Zhou (2010), "Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus", PLoS Genetics 6: e1001065.

*Authors contributed equally.
Supplement

Katharina F. Ettwig*, Margaret K. Butler*, Denis Le Paslier, Eric Pelletier, Sophie Mangenot, Marcel M.M. Kuypers, Frank Schreiber, Bas E. Dutilh, Johannes Zedelius, Dirk de Beer, Jolein Gloerich, Hans J.C.T. Wessels, Theo A. van Alen, Francisca Luesken, Ming L. Wu, Katinka T. van de Pas-Schoonen, Huub J.M. Op den Camp, Eva M. Janssen-Megens, Kees-Jan Francoijs, Henk Stunnenberg, Jean Weissenbach, Mike S.M. Jetten and Marc Strous (2010), "Nitrite-driven anaerobic methane oxidation by oxygenic bacteria", Nature 464: 543-548.

*Authors contributed equally.
Supplement
Entrez Genomes

Rob M. de Graaf, Theo A. van Alen, Bas E. Dutilh, Jan W.P. Kuiper, Hanneke J.A.A. van Zoggel, Minh Bao Huynh, Hans-Dieter Görtz, Martijn A. Huynen and Johannes H.P. Hackstein (2009), "The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus", BMC Genomics 10: 514.

Supplement: Figures 1/2/3, Table.

Bas E. Dutilh, Martijn A. Huynen and Marc Strous (2009), "Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly", Bioinformatics 25: 2878-2881.

Supplement

Richard A. Notebaart*, Philip R. Kensche*, Martijn A. Huynen and Bas E. Dutilh (2009), "Asymmetric relationships between proteins shape genome evolution", Genome Biology 10: R19.

*Authors contributed equally.
Supplements: 1/2/3/4

Guénola Ricard, Rob M. de Graaf, Bas E. Dutilh, Isabel Duarte, Theo A. van Alen, Angela H.A.M. van Hoek, Brigitte Boxma, Georg W.M. van der Staay, Seung Yeo Moon van der Staay, Wei-Jen Chang, Laura F. Landweber, Johannes H.P. Hackstein and Martijn A. Huynen (2008), "Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns", BMC Genomics 9: 587.

Supplements: 1/2

Bas E. Dutilh, Berend Snel, Thijs J.G. Ettema and Martijn A. Huynen (2008), "Signature genes as a phylogenomic tool", Molecular Biology and Evolution 25: 1659-1667.

Supplements: Figure, Tables 1/2

Bas E. Dutilh, Ying He, Maarten L. Hekkelman and Martijn A. Huynen (2008), "Signature, a web server for taxonomic characterization of sequence samples using signature genes", Nucleic Acids Research 36 (Web Server issue): W470-W474.

Philip R. Kensche, Martin Oti, Bas E. Dutilh and Martijn A. Huynen (2008), "Conservation of divergent transcription in fungi", Trends in Genetics 24: 207-211.

Supplements: PDF, XLS

Philip R. Kensche, Vera van Noort, Bas E. Dutilh and Martijn A. Huynen (2008), "Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution", Journal of the Royal Society Interface 5: 151-170.

Supplement

Nicole A. Datson, Maarten C. Morsink, Srebrena Atanasova, Victor W. Armstrong, Hans Zischler, Christina Schlumbohm, Bas E. Dutilh, Martijn A. Huynen, Brigitte Waegele, Andreas Ruepp, E. Ronald de Kloet and Eberhard Fuchs (2007), "Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate", BMC Genomics 8: 190.

Supplements: 1/2/3
Entrez: Nucleotide, EST, Protein

Bas E. Dutilh, Vera van Noort, René T.J.M. van der Heijden, Teun Boekhout, Berend Snel and Martijn A. Huynen (2007), "Assessment of phylogenomic and orthology approaches for phylogenetic inference", Bioinformatics 23: 815-824.

Supplement, orthologies and trees

Bas E. Dutilh (2007), "Extracting the evolutionary signal from genomes", Ph.D. thesis.

Email me to receive a printed copy.

Marc Strous, Eric Pelletier, Sophie Mangenot, Thomas Rattei, Angelika Lehner, Michael W. Taylor, Matthias Horn, Holger Daims, Delphine Bartol-Mavel, Patrick Wincker, Valérie Barbe, Nuria Fonknechten, David Vallenet, Béatrice Segurens, Chantal Schenowitz-Truong, Claudine Médigue, Astrid Collingro, Berend Snel, Bas E. Dutilh, Huub J. M. Op den Camp, Chris van der Drift, Irina Cirpus, Katinka T. van de Pas-Schoonen, Harry R. Harhangi, Laura van Niftrik, Markus Schmid, Jan Keltjens, Jack van de Vossenberg, Boran Kartal, Harald Meier, Dmitrij Frishman, Martijn A. Huynen, Hans-Werner Mewes, Jean Weissenbach, Mike S. M. Jetten, Michael Wagner and Denis Le Paslier (2006), "Deciphering the evolution and metabolism of an anammox bacterium from a community genome", Nature 440: 790-794.

Supplement
Entrez Genome

Guenola Ricard, Neil R. McEwan, Bas E. Dutilh, Jean-Pierre Jouany, Didier Macheboeuf, Makoto Mitsumori, Freda M. McIntosh, Tadeusz Michalowski, Takafumi Nagamine, Nancy Nelson, Charles J. Newbold, Eli Nsabimana, Akio Takenaka, Nadine A. Thomas, Kazunari Ushida, Johannes H.P. Hackstein and Martijn A. Huynen (2006), "Horizontal Gene Transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic carbohydrates rich environment", BMC Genomics 7: 22.

Bas E. Dutilh, Martijn A. Huynen and Berend Snel (2006), "A global definition of expression context is conserved between orthologs but does not correlate with sequence conservation", BMC Genomics 7: 10.

Augustinus R. Uria, Ronnie Machielsen, Bas E. Dutilh, Martijn A. Huynen and John van der Oost (2006), "Alcohol dehydrogenases from marine hyperthermophilic microorganisms and their importance to the pharmaceutical industry", Presented at "International seminar and workshop on marine biodiversity and their potential for developing bio-pharmaceutical industry", May 2006, Jakarta.

Berend Snel, Martijn A. Huynen and Bas E. Dutilh (2005), "Genome trees and the nature of genome evolution", Annual Review of Microbiology 59: 191-209.

Bas E. Dutilh, Martijn A. Huynen, William J. Bruno and Berend Snel (2004), "The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise", Journal of Molecular Evolution 58: 527-539.

Bas E. Dutilh and Rob J. de Boer (2003), "Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells", Journal of Theoretical Biology 224: 351-358.

Bas E. Dutilh, Chris E. Dutilh and Willem H.M.M. van Laarhoven (2001), "Initiatives on sustainable development in the food sector worldwide", Foundation for Sustainability in the Food Chain (DuVo).