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Felipe H. Coutinho, Bas E. Dutilh, Cristiane C. Thompson, and Fabiano L. Thompson (2016), "Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features", Archives of Microbiology.   
Daan R. Speth, Michiel H. in ’t Zandt, Simon Guerrero-Cruz, Bas E. Dutilh*, and Mike S.M. Jetten* (*contributed equally) (2016), "Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system", Nature Communications 7: 11172.    
Guus A.M. Kortman, Bas E. Dutilh, Annet J.H. Maathuis, Udo F. Engelke, Jos Boekhorst, Kevin P. Keegan, Fiona G.G. Nielsen, Jason Betley, Jacqueline C. Weir, Zoya Kingsbury, Leo A.J. Kluijtmans, Dorine W. Swinkels, Koen Venema, and Harold Tjalsma (2016), "Microbial metabolism shifts towards an adverse profile with supplementary iron in the TIM-2 in vitro model of the human colon", Frontiers in Microbiology 6: 1481.    
Mart Krupovic, Bas E. Dutilh, Evelien M. Adriaenssens, Johannes Wittmann, Finn K. Vogensen, Mathew B. Sullivan, Janis Rumnieks, David Prangishvili, Rob Lavigne, Andrew M. Kropinski, Jochen Klumpp, Annika Gillis, Francois Enault, Rob A. Edwards, Siobain Duffy, Martha R.C. Clokie, Jakub Barylski, Hans-Wolfgang Ackermann, and Jens H. Kuhn (2016), "Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee", Archives of Virology 161: 1095-1099.   
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Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2016 ), "Computational approaches to predict bacteriophage-host relationships ", FEMS Microbiology Reviews 40 : 258-272 .    
Daniela Bezemer, Anne Cori, Oliver Ratmann, Ard van Sighem, Hillegonda S. Hermanides, Bas E. Dutilh, Luuk Gras, Nuno Rodrigues Faria, Rob van den Hengel, Ashley J. Duits, Peter Reiss, Frank de Wolf, Christophe Fraser, and ATHENA observational cohort (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 Medicine 12: e1001898.     
Genivaldo Gueiros Z. Silva, Kevin T. Green, Bas E. Dutilh, and Robert A. Edwards "SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data", Bioinformatics.    
Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, and K. Anton Feenstra (2015), "Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case", BMC Bioinformatics 16: 325.     
Jeremy J. Barr, Bas E. Dutilh, Connor T. Skennerton, Toshikazu Fukushima, Marcus L. Hastie, Jeffrey J. Gorman, Gene W. Tyson, and Philip L. Bond (2015), "Metagenomic and metaproteomic analyses of Accumulibacter phosphatis enriched floccular and granular biofilm", Environmental Microbiology.   
Daniel R. Garza and Bas E. Dutilh (2015), "From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems", Cellular and Molecular Life Sciences.    
Felipe H. Coutinho, Pedro M. Meirelles, Ana Paula B. Moreira, Rodolfo P. Paranhos, Bas E. Dutilh, and Fabiano L. Thompson (2015), "Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review", PeerJ 3: e1008.    
T. David Matthews, Robert Schmieder, Genivaldo G. Z. Silva, Julia Busch, Noriko Cassman, Bas E. Dutilh, Dawn Green, Brian Matlock, Brian Heffernan, Gary J. Olsen, Leigh Farris Hanna, Dieter M, Schifferli, Stanley Maloy, Elizabeth A. Dinsdale, and Robert A. Edwards (2015), "Genomic comparison of the closely-related Salmonella enterica serovars Enteritidis, Dublin and Gallinarum", PLoS ONE 10: e0126883.   
Julia Busch, Juliana R. Nascimento, Ana Carolina Magalhães, Bas E. Dutilh, and Elizabeth Dinsdale (2015), "Copper tolerance and distribution of epibiotic bacteria associated with giant kelp Macrocystis pyrifera in southern California", Ecotoxicology 24: 1131-1140.    
Silke Appenzeller, Christian Gilissen, Jos Rijntjes, Bastiaan B.J. Tops, Annemiek Kastner-van Raaij, Konnie M. Hebeda, Loes Nissen, Bas E. Dutilh, J. Han J.M. van Krieken, and Patricia J.T.A. Groenen (2015), "Immunoglobulin rearrangement analysis from multiple lesions in the same patient using Next Generation Sequencing", Histopathology.    
Richard J. Hall, Jenny L. Draper, Fiona G.G. Nielsen, and Bas E. Dutilh (2015), "Beyond research: a primer for considerations on using viral metagenomics in the field and clinic", Frontiers in Microbiology 6: 224.    
Daan R. Speth, Lina Russ, Boran Kartal, Huub J.M. Op den Camp, Bas E. Dutilh, and Mike S.M. Jetten (2015), "Draft genome sequence of anammox bacterium "Candidatus Scalindua brodae", obtained using differential coverage binning of sequencing data from two reactor enrichments", Genome Announcements 3: e01415-14.    
Cristiane C. Thompson, Gilda R. Amaral, Robert A. Edwards, Martin F. Polz, Bas E. Dutilh, David W. Ussery, Erko Stackebrandt, Jean Swings, and Fabiano L. Thompson (2015), "Microbial taxonomy in the post-genomic era: Rebuilding from scratch?", Archives of Microbiology 197: 359-370.    
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Nelson Alves Junior, Pedro Milet Meirelles, Eidy de Oliveira Santos, Bas Dutilh, Genivaldo G.Z. Silva, Rodolfo Paranhos, Anderson S. Cabral, Carlos Rezende, Tetsuya Iida, Rodrigo L. de Moura, Ricardo Henrique Kruger, Renato C. Pereira, Rogério Valle, Tomoo Sawabe, Cristiane Thompson, and Fabiano Thompson (2014), "Microbial community diversity and physical-chemical features of the Southwestern Atlantic Ocean", Archives of Microbiology 197: 165-179.    
Yan Wei Lim, Daniel Cuevas, Genivaldo G.Z. Silva, Kristen Aguinaldo, Elizabeth Dinsdale, Andreas Haas, Mark Hatay, Savannah Sanchez, Linda Wegley-Kelly, Bas E. Dutilh, Timothy Harkins, Clarence Lee, Warren Tom, Stuart Sandin, Jennifer E. Smith, Brian Zgliczynski, Mark J.A. Vermeij, Forest Rohwer, and Robert A. Edwards (2014), "Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands research expedition", PeerJ 2: e520.    
Bas E. Dutilh, Cristiane C. Thompson, Ana C.P. Vicente, Michel A. Marin, Clarence Lee, Genivaldo G.Z. Silva, Robert Schmieder, Bruno G.N. Andrade, Luciane Chimetto, Daniel Cuevas, Daniel Garza, Iruka N. Okeke, A. Oladipo Aboderin, Jessica Spangler, Tristen Ross, Elizabeth A. Dinsdale, Fabiano L. Thompson, Timothy T. Harkins, and Robert A. Edwards (2014), "Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions", BMC Genomics 15: 654.     
Bas E. Dutilh, Noriko Cassman, Katelyn McNair, Savannah E. Sanchez, Genivaldo G.Z. Silva, Lance Boling, Jeremy J. Barr, Daan R. Speth, Victor Seguritan, Ramy K. Aziz, Ben Felts, Elizabeth A. Dinsdale, John L. Mokili, and Robert A. Edwards (2014), "A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes", Nature Communications 5: 4498.    
Sarah Ghamrawi, Gilles Rénier, Patrick Saulnier, Stéphane Cuenot, Agata Zykwinska, Bas E. Dutilh, Christopher Thornton, Sébastien Faure, and Jean-Philippe Bouchara (2014), "Cell wall modifications during conidial maturation of the human pathogenic fungus Pseudallescheria boydii", PLoS ONE 9: e100290.     
Genivaldo G.Z. Silva, Daniel A. Cuevas, Bas E. Dutilh, and Robert A. Edwards (2014), "FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares", PeerJ 2: e425.    
Marwa ElRakaiby, Bas E. Dutilh, Mariam R. Rizkallah, Annemarie Boleij, Jason N. Cole, and Ramy K. Aziz (2014), "Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics", OMICS: A Journal of Integrative Biology 18: 402-414.    
Harold Tjalsma, Bas E. Dutilh, Annemarie Boleij, and Julian R. Marchesi (2014), "Colorectal cancer associated microbiota", Encyclopedia of Metagenomics III: Human Metagenomics: Eds. Sarah Highlander and Karen E. Nelson.  
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Genivaldo G.Z. Silva, Bas E. Dutilh, T. David Matthews, Keri Elkins, Robert Schmieder, Elizabeth A. Dinsdale, and Robert A. Edwards (2013), "Combining de novo and reference-guided assembly with Scaffold_builder", Source Code for Biology and Medicine 8: 23.    
Bas E. Dutilh, Lennart Backus, Sacha A.F.T. van Hijum, and Harold Tjalsma (2013), "Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer", Best Practice & Research: Clinical Gastroenterology 27: 85-99.    
Bas E. Dutilh, Lennart Backus, Robert A. Edwards, Michiel Wels, Jumamurat R. Bayjanov, and Sacha A.F.T. van Hijum (2013), "Explaining microbial phenotypes on a genomic scale: GWAS for microbes", Briefings in Functional Genomics 12: 366-380.    
John L. Mokili, Bas E. Dutilh, Yan Wei Lim, Bradley S. Schneider, Travis Taylor, Matthew R. Haynes, David Metzgar, Christopher A. Myers, Patrick J. Blair, Bahador Nosrat, Nathan D. Wolfe, and Forest Rohwer (2013), "Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness", PLoS ONE 8: e58404.     
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Simone M.T. Camps*, Bas E. Dutilh*, Maiken C. Arendrup, Antonius J.M.M. Rijs, Eveline Snelders, Martijn A. Huynen, Paul E. Verweij, and Willem J.G. Melchers (*contributed equally) (2012), "Discovery of a hapE mutation that causes azole resistance in Aspergillus fumigatus through whole genome sequencing and sexual crossing", PLoS ONE 7: e50034.     
Bas E. Dutilh, Robert Schmieder, Jim Nulton, Ben Felts, Peter Salamon, Robert A. Edwards, and John L. Mokili (2012), "Reference-independent comparative metagenomics using cross-assembly: crAss", Bioinformatics 28: 3225-3231.    
Noriko Cassman*, Alejandra Prieto-Davó*, Kevin Walsh, Genivaldo G. Z. Silva, Florent Angly, Sajia Akhter, Katie Barott, Julia Busch, Tracey McDole, J. Matthew Haggerty, Dana Willner, Gadiel Alarcón, Osvaldo Ulloa, Edward F. DeLong, Bas E. Dutilh, Forest Rohwer, and Elizabeth A. Dinsdale (*contributed equally) (2012), "Oxygen minimum zones harbour novel viral communities with low diversity", Environmental Microbiology 14: 3043-3065.    
Amaro E. Trindade-Silva, Cintia Rua, Genivaldo G. Z. Silva, Bas E. Dutilh, Ana Paula B. Moreira, Robert A. Edwards, Eduardo Hajdu, Gisele Lobo-Hajdu, Ana Tereza Vasconcelos, Roberto G. S. Berlinck, and Fabiano L. Thompson (2012), "Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis", PLoS ONE 7: e39905.     
Harold Tjalsma, Annemarie Boleij, Julian R Marchesi, and Bas E Dutilh (2012), "A bacterial driver-passenger model for colorectal cancer: beyond the usual suspects", Nature Reviews Microbiology 10: 575-582.    
Annemarie Boleij, Bas E Dutilh, Guus Kortman, Rian Roelofs, Coby M. Laarakkers, Udo F. Engelke, and Harold Tjalsma (2012), "Bacterial responses to a simulated colon tumor microenvironment", Molecular and Cellular Proteomics 11: 851-862.    
Daniel R. Garza, Cristiane C. Thompson, Edvaldo C.B. Loureiro, Bas E. Dutilh, Davi T. Inada, Edivaldo C. Sousa Jr, Jedson F. Cardoso, Márcio R.T. Nunes, Clayton Pereira Silva de Lima, Rodrigo V.D. Silvestre, Keley N.B. Nunes, Elisabeth C.O. Santos, Robert A. Edwards, Ana C.P. Vicente, and Lena L. Canto de Sá Morais (2012), "Genome-wide study of the defective sucrose fermenter strain of Vibrio cholerae from the Latin American cholera epidemic", PLoS ONE 7: e37283.     
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, and 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 15: 1275-1289.    
John L. Mokili, Forest Rohwer, and Bas E. Dutilh (2012), "Metagenomics and future perspectives in virus discovery", Current Opinion in Virology 2: 63-77.   
Bas E. Dutilh and Ramy K. Aziz (2012 ), "Genomes, metagenomes, and microbiomes: a new biology for a new millennium ", New Life Sciences: Linking Science to Society, BioVisionAlexandria 2012 Proceedings : 105-116 .   
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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.    
Cristiane C. Thompson, Michel Abanto Marin, Graciela Maria Dias, Bas E. Dutilh, Rob Edwards, Tetsuya Iida, and 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.    
Julian R. Marchesi, Bas E. Dutilh, Neil Hall, Wilbert H. M. Peters, Rian Roelofs, Annemarie Boleij, and Harold Tjalsma (2011), "Towards the human colorectal cancer microbiome", PLoS ONE 6: e20447.      
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, and Dorine W. Swinkels (*contributed equally) (2011), "Mass spectrometry analysis of hepcidin peptides in experimental mouse models", PLoS ONE 6: e16762.     
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 (*contributed equally) (2011), "The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis", Molecular Biology and Evolution 28: 2379-2391.    
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, and 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 .  
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.   
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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 (*contributed equally) (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 .     
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 (*contributed equally) (2010 ), "Nitrite-driven anaerobic methane oxidation by oxygenic bacteria ", Nature 464 : 543-548 .     
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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 .     
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 .    
Richard A. Notebaart*, Philip R. Kensche*, Martijn A. Huynen, and Bas E. Dutilh (*contributed equally) (2009 ), "Asymmetric relationships between proteins shape genome evolution ", Genome Biology 10 : R19 .    
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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 .     
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 .    
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 .    
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 .    
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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 .     
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 .    
Bas E. Dutilh (2007 ), "Extracting the evolutionary signal from genomes ", Ph.D. thesis. Email me to receive a printed copy. .   
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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 .     
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 .   
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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 .    
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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 .     
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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 .    
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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) .   
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Bas E. Dutilh and Paulien Hogeweg (1999 ), "Gene networks from microarray data ", report Binf.1999.11.01, Bioinformatics, Utrecht University .