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Issue Date	Title	Author(s)
2012	The metagenome of the marine anammox bacterium 'Candidatus scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium	Vossenberg, J.L.C.M. van de; Woebken, D.; Maalcke, W.J.; Wessels, H.J.C.T.; Dutilh, B.E.; Kartal, B.; Janssen-Megens, E.M.; Roeselers, G.; Yan, J; Speth, D.; Gloerich, J.; Geerts, W.; Biezen, E. Van Der; Pluk, W.; Francoijs, K.J.; Russ, L.; Lam, P.; Malfatti, S.A.; Tringe, S.G.; Haaijer, S.C.M.; Camp, H.J.M. op den; Stunnenberg, H.G.; Amann, R.; Kuypers, M.M.M.; Jetten, M.S.M.
2011	The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis	Graaf, R.M. de; Ricard, G.N.S.; Alen, T.A. van; Duarte, I.; Dutilh, B.E.; Burgtorf, C.; Kuiper, J.W.; Staay, G.W.M. van der; Tielens, A.G.; Huynen, M.A.; Hackstein, J.H.
2011	Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.)	Kessel, M.A. van; Dutilh, B.E.; Neveling, K.; Kwint, M.P.; Veltman, J.A.; Flik, G.; Jetten, M.S.M.; Klaren, P.H.M.; Camp, H.J.M. op den
2011	FACIL: Fast and Accurate Genetic Code Inference and Logo	Dutilh, B.E.; Jurgelenaite, R.; Szklarczyk, R.J.; van Hijum, S.A.; Harhangi, H.R.; Schmid, M.; Wild, B. de; Francoijs, K.J.; Stunnenberg, H.G.; Strous, M.; Jetten, M.S.M.; Camp, H.J.M. op den; Huynen, M.A.
2011	Genome sequence of the human pathogen Vibrio cholerae Amazonia.	Thompson, C.C.; Marin, M.A.; Dias, G.M.; Dutilh, B.E.; Edwards, R.A.; Iida, T.; Thompson, F.L.; Vicente, A.C.
2011	Mass spectrometry analysis of hepcidin peptides in experimental mouse models	Tjalsma, H.; Laarakkers, C.M.; van Swelm, R.P.; Theurl, M.; Theurl, I.; Kemna, E.H.J.M.; Burgt, Y.E. van der; Venselaar, H.; Dutilh, B.E.; Russel, F.G.M.; Weiss, G.; Masereeuw, R.; Fleming, R.E.; Swinkels, D.W.
2011	Towards the human colorectal cancer microbiome	Marchesi, J.R.; Dutilh, B.E.; Hall, N.; Peters, W.H.M.; Roelofs, R.; Boleij, A.; Tjalsma, H.
2011	Genome-wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation.	Emons, J.; Dutilh, B.E.; Decker, E.; Pirzer, H.; Sticht, C.; Gretz, N.; Rappold, G.; Cameron, E.R.; Neil, J.C.; Stein, G.S.; Wijnen, A.J. van; Wit, J.M.; Post, J.N.; Karperien, M.
2010	Nitrite-driven anaerobic methane oxidation by oxygenic bacteria	Ettwig, K.F.; Butler, M.K.; Paslier, D. Le; Pelletier, E.; Mangenot, S.; Kuypers, M.M.M.; Schreiber, F.; Dutilh, B.E.; Zedelius, J.; Beer, D. de; Gloerich, J.; Wessels, H.; Alen, T. van; Luesken, F.A.; Wu, M.L.; Pas-Schoonen, K.T. Van de; Camp, H. den; Janssen-Megens, E.M.; Francoijs, K.J.; Stunnenberg, H.; Weissenbach, J.; Jetten, M.S.M.; Strous, M.
2010	Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.	Kouwenhoven, E.N.; Heeringen, S.J. van; Tena, J.J.; Oti, M.O.; Dutilh, B.E.; Alonso, M.E.; Calle-Mustienes, E. de la; Smeenk, L.; Rinne, T.K.; Parsaulian, L.; Bolat, E.; Jurgelenaite, R.; Huynen, M.A.; Hoischen, A.; Veltman, J.A.; Brunner, H.G.; Roscioli, T.; Oates, E.; Wilson, M.; Manzanares, M.; Gomez-Skarmeta, J.L.; Stunnenberg, H.G.; Lohrum, M.A.E.; Bokhoven, J.H.L.M. van; Zhou, H.
2009	Asymmetric relationships between proteins shape genome evolution.	Notebaart, R.A.; Kensche, P.R.; Huynen, M.A.; Dutilh, B.E.
2009	Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.	Dutilh, B.E.; Huynen, M.A.; Strous, M.
2009	The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus.	Graaf, R.M. de; Alen, T.A. van; Dutilh, B.E.; Kuiper, J.W.P.; Zoggel, H.J. van; Huynh, M.B.; Gortz, H.D.; Huynen, M.A.; Hackstein, J.H.P.
2008	Macronuclear genome structure of the ciliate Nyctotherus ovalis : single-gene chromosomes and tiny introns	Ricard, G.; Graaf, R.M. de; Dutilh, B.E.; Duarte, I.; Alen, T.A. van; Hoek, A.H. van; Boxma, B.; Staay, G.W.M. van der; Moon-van der Staay, S.Y.; Chang, W.; Landweber, L.F.; Hackstein, J.H.P.; Huijnen, M.A.
2008	Conservation of divergent transcription in fungi.	Kensche, P.R.; Oti, M.O.; Dutilh, B.E.; Huynen, M.A.
2008	Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.	Kensche, P.R.; Noort, V. van; Dutilh, B.E.; Huynen, M.A.
2008	Signature genes as a phylogenomic tool.	Dutilh, B.E.; Snel, B.; Ettema, T.J.G.; Huynen, M.A.
2008	Signature, a web server for taxonomic characterization of sequence samples using signature genes.	Dutilh, B.E.; He, Y.; Hekkelman, M.L.; Huynen, M.A.
2007	Assessment of phylogenomic and orthology approaches for phylogenetic inference.	Dutilh, B.E.; Noort, V. van; Heijden, R.T.J.M. van der; Boekhout, T.; Snel, B.; Huynen, M.A.
2007	Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution	Kensche, P.R.; Noort, V. van; Dutilh, B.E.; Huynen, M.A.
2007	Assessment of phylogenomic and orthology approaches for phylogenetic inference	Dutilh, B.E.; Noort, V. van; Heijden, R.T.J.M. van der; Boekhout, T.; Snel, B.; Huynen, M.A.
2007	Extracting the evolutionary signal from genomes	Dutilh, Bas E.
2007	Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate	Datson, N.A.; Morsink, M.C.; Atanasova, S.; Armstrong, V.W.; Zischler, H.; Schlumbohm, C.; Dutilh, B.E.; Huynen, M.A.; Waegele, B.; Ruepp, A.; Kloet, E.R. de; Fuchs, E.
2006	A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation	Dutilh, B.E.; Huijnen, M.A.; Snel, B.
2006	Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment	Ricard, G.; McEwan, N.R.; Dutilh, B.E.; Jouany, J.P.; Macheboeuf, D.; Mitsumori, M.; McIntosh, F.M.; Michalowski, T.; Nagamine, T.; Nelson, N.; Newbold, C.J.; Nsabimana, E.; Takenaka, A.; Thomas, N.A.; Ushida, K.; Hackstein, J.H.P.; Huynen, M.A.
2006	Deciphering the evolution and metabolism of an anammox bacterium from a community genome.	Strous, M.; Pelletier, E.; Mangenot, S.; Rattei, T.; Lehner, A.; Taylor, M.W.; Horn, M.; Daims, H.; Bartol-Mavel, D.; Wincker, P.; Barbe, V.; Fonknechten, N.; Vallenet, D.; Segurens, B.; Schenowitz-Truong, C.; Medigue, C.; Collingro, A.; Snel, B.; Dutilh, B.E.; Camp, H.J.M. op den; Drift, C. van der; Cirpus, I.E.Y.; Pas-Schoonen, K.T. van de; Harhangi, R.H.; Niftrik, L.A.M.P. van; Schmid, M.; Keltjens, J.T.M.; Vossenberg, J.L.C.M. van de; Kartal, M.B.; Meier, H.; Frishman, D.; Huynen, M.A.; Mewes, H.W.; Weissenbach, J.; Jetten, M.S.M.; Wagner, M.; Paslier, D. Le
2005	Genome trees and the nature of genome evolution	Snel, B.; Huynen, M.A.; Dutilh, B.E.
2004	The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise	Dutilh, B.E.; Huynen, M.A.; Bruno, W.J.; Snel, B.
2004	The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise.	Dutilh, B.E.; Huynen, M.A.; Bruno, W.J.; Snel, B.