Bastiaan Elie Dutilh

  • Endereço para acessar este CV: http://lattes.cnpq.br/3434344864605631
  • Última atualização do currículo em 21/02/2014


My field of expertise is bioinformatics, including sequence analysis (genetics, genomics and metagenomics*), biostatistics and tool development. As a biologist, I see the computer as a tool to answer biological questions. The reciprocal exchange of ideas and results between bioinformatics and laboratory or field studies is the fastest way to obtain new biological knowledge.
I have studied most taxonomic groups and several biological and medical systems, but my emphasis has been on microbes. I am fascinated by the dynamics in their genome evolution and in the interactions with each other and with their environment. Phenomena like horizontal gene transfer and micro-diversity are of great importance not only in microbial genome evolution, but also in microbial ecology and medicine. To understand these phenomena requires new tools and technologies, as well as well-designed experiments. My daily work consists of the development of bioinformatic tools to study these phenomena from different angles, the analysis of large-scale datasets, as well as collaborating with microbial ecologists, evolutionary and medical microbiologists to interpret our results.
I obtained my PhD in Bioinformatics for Medical Sciences at Radboud University Nijmegen in 2007.

* Yes, I have also worked on metagenetics, a.k.a. environmental amplicon sequencing. (Texto informado pelo autor)


Identificação


Nome
Bastiaan Elie Dutilh
Nome em citações bibliográficas
DUTILH, B. E.;Bas E. Dutilh;Dutilh, Bas E.;B. E. Dutilh;BE Dutilh;Dutilh, BE;Dutilh, BasE;DUTILH, BAS E;Dutilh, B. E;DUTILH, B. E. (Bas E. Dutilh)

Endereço


Endereço Profissional
Universidade Federal do Rio de Janeiro.
CCS - Centro de Ciências da Saúde
Cidade Universitária
21941902 - Rio de Janeiro, RJ - Brasil
Telefone: (21) 25626567


Formação acadêmica/titulação


2002 - 2007
Doutorado em Medical Sciences.
Radboud University Nijmegen, RUN, Holanda.
Título: Extracting the evolutionary signal from genomes, Ano de obtenção: 2007.
Orientador: Prof. dr. Martijn A. Huynen.
1994 - 1999
Mestrado em Theoretical Biology and Bioinformatics.
Utrecht University, UU, Holanda.
Título: Gene networks from microarray data,Ano de Obtenção: 1999.
Orientador: Paulien Hogeweg.
Palavras-chave: microarray; gene network; network reconstruction.





Membro de corpo editorial


2014 - Atual
Periódico: Frontiers in Microbiology (Online)
2011 - Atual
Periódico: Plos One


Áreas de atuação


1.
Grande área: Ciências Biológicas / Área: Biologia Geral / Subárea: Bioinformatica.


Idiomas


Holandês
Compreende Bem, Fala Bem, Lê Bem, Escreve Bem.
Inglês
Compreende Bem, Fala Bem, Lê Bem, Escreve Bem.
Português
Compreende Pouco, Fala Pouco, Lê Pouco, Escreve Pouco.
Francês
Compreende Pouco, Fala Pouco, Lê Pouco, Escreve Pouco.
Alemão
Compreende Pouco, Fala Pouco, Lê Pouco, Escreve Pouco.
Espanhol
Compreende Pouco, Fala Pouco, Lê Pouco, Escreve Pouco.


Prêmios e títulos


2010
Veni award, Dutch Foundation for Scientific Research NWO.


Produções



Produção bibliográfica
Artigos completos publicados em periódicos

1.
MOKILI, JOHN L.2013MOKILI, JOHN L. ; Dutilh, Bas E. ; LIM, YAN WEI ; SCHNEIDER, BRADLEY S. ; TAYLOR, TRAVIS ; HAYNES, MATTHEW R. ; METZGAR, DAVID ; MYERS, CHRISTOPHER A. ; BLAIR, PATRICK J. ; NOSRAT, BAHADOR ; WOLFE, NATHAN D. ; ROHWER, FOREST . Identification of a Novel Human Papillomavirus by Metagenomic Analysis of Samples from Patients with Febrile Respiratory Illness. Plos One, v. 8, p. e58404, 2013.

2.
Dutilh, Bas E.2013Dutilh, Bas E.; BACKUS, LENNART ; VAN HIJUM, SACHA A.F.T. ; TJALSMA, HAROLD . Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer. Baillière's Best Practice & Research. Clinical Gastroenterology, v. 27, p. 85-99, 2013.

3.
DUTILH, B. E.2013DUTILH, B. E.; BACKUS, L. ; EDWARDS, R. A. ; WELS, M. ; BAYJANOV, J. R. ; VAN HIJUM, S. A. F. T. . Explaining microbial phenotypes on a genomic scale: GWAS for microbes. BRIEF FUNCT GENOMICS, v. 12, p. 366-380, 2013.

4.
SILVA, GENIVALDO GZ2013SILVA, GENIVALDO GZ ; DUTILH, BAS E ; MATTHEWS, T ; ELKINS, KERI ; SCHMIEDER, ROBERT ; DINSDALE, ELIZABETH A ; EDWARDS, ROBERT A . Combining de novo and reference-guided assembly with scaffold_builder. Source Code for Biology and Medicine, v. 8, p. 23, 2013.

5.
MOKILI, JOHN L2012MOKILI, JOHN L ; ROHWER, FOREST ; DUTILH, BAS E . Metagenomics and future perspectives in virus discovery. Current Opinion in Virology, v. 2, p. 63-77, 2012.

6.
LUCKWU DE LUCENA, B. T.2012LUCKWU DE LUCENA, B. T. ; SILVA, G. G. Z. ; MANOEL DOS SANTOS, B. ; DIAS, G. M. ; AMARAL, G. R. S. ; MOREIRA, A. P. B. ; DE MORAIS JUNIOR, M. A. ; DUTILH, B. E. ; EDWARDS, R. A. ; BALBINO, V. ; THOMPSON, C. C. ; THOMPSON, F. L. . Genome Sequences of the Ethanol-Tolerant Lactobacillus vini Strains LMG 23202T and JP7.8.9. Journal of Bacteriology (Print), v. 194, p. 3018-3018, 2012.

7.
GARZA, DANIEL RIOS2012GARZA, DANIEL RIOS ; THOMPSON, CRISTIANE C. ; LOUREIRO, EDVALDO CARLOS BRITO ; Dutilh, Bas E. ; INADA, DAVI TOSHIO ; JUNIOR, EDIVALDO COSTA SOUSA ; CARDOSO, JEDSON FERREIRA ; NUNES, MÁRCIO ROBERTO T. ; DE LIMA, CLAYTON PEREIRA SILVA ; SILVESTRE, RODRIGO VELLASCO DUARTE ; NUNES, KELEY NASCIMENTO BARBOSA ; SANTOS, ELISABETH C. O. ; EDWARDS, ROBERT A. ; VICENTE, ANA CAROLINA P. ; DE SÁ MORAIS, LENA LILLIAN CANTO . Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic. Plos One, v. 7, p. e37283, 2012.

8.
BOLEIJ, A.2012BOLEIJ, A. ; DUTILH, B. E. ; KORTMAN, G. A. M. ; ROELOFS, R. ; LAARAKKERS, C. M. ; ENGELKE, U. F. ; TJALSMA, H. . Bacterial Responses to a Simulated Colon Tumor Microenvironment. Molecular & Cellular Proteomics (Online), v. 11, p. 851-862, 2012.

9.
TJALSMA, HAROLD2012 TJALSMA, HAROLD ; BOLEIJ, ANNEMARIE ; MARCHESI, JULIAN R. ; Dutilh, Bas E. . A bacterial driver passenger model for colorectal cancer: beyond the usual suspects. Nature Review, Microbiology (Print), v. 10, p. 575-582, 2012.

10.
TRINDADE-SILVA, AMARO E.2012TRINDADE-SILVA, AMARO E. ; RUA, CINTIA ; SILVA, GENIVALDO G. Z. ; Dutilh, Bas E. ; MOREIRA, ANA PAULA B. ; EDWARDS, ROBERT A. ; HAJDU, EDUARDO ; LOBO-HAJDU, GISELE ; VASCONCELOS, ANA TEREZA ; BERLINCK, ROBERTO G. S. ; THOMPSON, FABIANO L. . Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis. Plos One, v. 7, p. e39905, 2012.

11.
CASSMAN, NORIKO2012CASSMAN, NORIKO ; PRIETO-DAVÓ, ALEJANDRA ; WALSH, KEVIN ; SILVA, GENIVALDO G. Z. ; ANGLY, FLORENT ; AKHTER, SAJIA ; BAROTT, KATIE ; BUSCH, JULIA ; MCDOLE, TRACEY ; HAGGERTY, J. MATTHEW ; WILLNER, DANA ; ALARCÓN, GADIEL ; ULLOA, OSVALDO ; DELONG, EDWARD F. ; Dutilh, Bas E. ; ROHWER, FOREST ; DINSDALE, ELIZABETH A. . Oxygen minimum zones harbour novel viral communities with low diversity. Environmental Microbiology (Print), v. 14, p. 3043-3065, 2012.

12.
DUTILH, B. E.2012DUTILH, B. E.; SCHMIEDER, R. ; NULTON, J. ; FELTS, B. ; SALAMON, P. ; EDWARDS, R. A. ; MOKILI, J. L. . Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics (Oxford. Print), v. 28, p. 3225-3231, 2012.

13.
CAMPS, SIMONE M. T.2012CAMPS, SIMONE M. T. ; Dutilh, Bas E. ; ARENDRUP, MAIKEN C. ; RIJS, ANTONIUS J. M. M. ; SNELDERS, EVELINE ; HUYNEN, MARTIJN A. ; VERWEIJ, PAUL E. ; MELCHERS, WILLEM J. G. . Discovery of a hapE Mutation That Causes Azole Resistance in Aspergillus fumigatus through Whole Genome Sequencing and Sexual Crossing. Plos One, v. 7, p. e50034, 2012.

14.
KIP, NARDY2011KIP, NARDY ; Dutilh, Bas E. ; PAN, YAO ; BODROSSY, LEVENTE ; NEVELING, KORNELIA ; KWINT, MICHAEL P. ; JETTEN, MIKE S. M. ; OP DEN CAMP, HUUB J. M. . Ultra-deep pyrosequencing of pmoA amplicons confirms the prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog. Environmental Microbiology Reports, v. 3, p. 667-673, 2011.

15.
EMONS, J.2011EMONS, J. ; DUTILH, B. E. ; DECKER, E. ; PIRZER, H. ; STICHT, C. ; GRETZ, N. ; RAPPOLD, G. ; CAMERON, E. R. ; NEIL, J. C. ; STEIN, G. S. ; VAN WIJNEN, A. J. ; WIT, J. M. ; POST, J. N. ; KARPERIEN, M. . Genome-wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation. Journal of Endocrinology, v. 209, p. 245-254, 2011.

16.
DE GRAAF, R. M.2011DE GRAAF, R. M. ; RICARD, G. ; VAN ALEN, T. A. ; DUARTE, I. ; DUTILH, B. E. ; BURGTORF, C. ; KUIPER, J. W. P. ; VAN DER STAAY, G. W. M. ; TIELENS, A. G. M. ; HUYNEN, M. A. ; HACKSTEIN, J. H. P. . The Organellar Genome and Metabolic Potential of the Hydrogen-Producing Mitochondrion of Nyctotherus ovalis. Molecular Biology and Evolution, v. 28, p. 2379-2391, 2011.

17.
TJALSMA, HAROLD2011TJALSMA, HAROLD ; LAARAKKERS, COBY M. M. ; VAN SWELM, RACHEL P. L. ; THEURL, MILAN ; THEURL, IGOR ; KEMNA, ERWIN H. ; VAN DER BURGT, YURI E. M. ; VENSELAAR, HANKA ; Dutilh, Bas E. ; RUSSEL, FRANS G. M. ; WEISS, GÜNTER ; MASEREEUW, ROSALINDE ; FLEMING, ROBERT E. ; SWINKELS, DORINE W. . Mass Spectrometry Analysis of Hepcidin Peptides in Experimental Mouse Models. Plos One, v. 6, p. e16762, 2011.

18.
MARCHESI, JULIAN R.2011MARCHESI, JULIAN R. ; Dutilh, Bas E. ; HALL, NEIL ; PETERS, WILBERT H. M. ; ROELOFS, RIAN ; BOLEIJ, ANNEMARIE ; TJALSMA, HAROLD . Towards the Human Colorectal Cancer Microbiome. Plos One, v. 6, p. e20447, 2011.

19.
DUTILH, B. E.2011DUTILH, B. E.; JURGELENAITE, R. ; SZKLARCZYK, R. ; VAN HIJUM, S. A. F. T. ; HARHANGI, H. R. ; SCHMID, M. ; DE WILD, B. ; FRANCOIJS, K.-J. ; STUNNENBERG, H. G. ; STROUS, M. ; JETTEN, M. S. M. ; OP DEN CAMP, H. J. M. ; HUYNEN, M. A. . FACIL: Fast and Accurate Genetic Code Inference and Logo. Bioinformatics (Oxford. Print), v. 27, p. 1929-1933, 2011.

20.
THOMPSON, C. C.2011THOMPSON, C. C. ; MARÍN, M. F. A. ; DIAS, G. M. ; DUTILH, B. E. ; EDWARDS, R. A. ; IIDA, T. ; THOMPSON, F. L. ; VICENTE, A. C. P. . Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia. Journal of Bacteriology (Print), v. 193, p. 5877-5878, 2011.

21.
VAN KESSEL, MAARTJE AHJ2011VAN KESSEL, MAARTJE AHJ ; DUTILH, BAS E ; NEVELING, KORNELIA ; KWINT, MICHAEL P ; VELTMAN, JORIS A ; FLIK, GERT ; JETTEN, MIKE SM ; KLAREN, PETER HM ; OP DEN CAMP, HUUB JM . Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.). AMB Express, v. 1, p. 41, 2011.

22.
ETTWIG, KATHARINA F.2010 ETTWIG, KATHARINA F. ; BUTLER, MARGARET K. ; LE PASLIER, DENIS ; PELLETIER, ERIC ; MANGENOT, SOPHIE ; KUYPERS, MARCEL M. M. ; SCHREIBER, FRANK ; Dutilh, Bas E. ; ZEDELIUS, JOHANNES ; DE BEER, DIRK ; GLOERICH, JOLEIN ; WESSELS, HANS J. C. T. ; VAN ALEN, THEO ; LUESKEN, FRANCISCA ; WU, MING L. ; VAN DE PAS-SCHOONEN, KATINKA T. ; OP DEN CAMP, HUUB J. M. ; JANSSEN-MEGENS, EVA M. ; FRANCOIJS, KEES-JAN ; STUNNENBERG, HENK ; WEISSENBACH, JEAN ; JETTEN, MIKE S. M. ; STROUS, MARC . Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature (London), v. 464, p. 543-548, 2010.

23.
KOUWENHOVEN, EVELYN N.2010KOUWENHOVEN, EVELYN N. ; VAN HEERINGEN, SIMON J. ; TENA, JUAN J. ; OTI, MARTIN ; Dutilh, Bas E. ; ALONSO, M. EVA ; DE LA CALLE-MUSTIENES, ELISA ; SMEENK, LEONIE ; RINNE, TUULA ; PARSAULIAN, LILIAN ; BOLAT, EMINE ; JURGELENAITE, RASA ; HUYNEN, MARTIJN A. ; HOISCHEN, ALEXANDER ; VELTMAN, JORIS A. ; BRUNNER, HAN G. ; ROSCIOLI, TONY ; OATES, EMILY ; WILSON, MEREDITH ; MANZANARES, MIGUEL ; GÓMEZ-SKARMETA, JOSÉ LUIS ; STUNNENBERG, HENDRIK G. ; LOHRUM, MARION ; VAN BOKHOVEN, HANS ; ZHOU, HUIQING . 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 (Online), v. 6, p. e1001065, 2010.

24.
NOTEBAART, RICHARD A2009NOTEBAART, RICHARD A ; KENSCHE, PHILIP R ; HUYNEN, MARTIJN A ; DUTILH, BAS E . Asymmetric relationships between proteins shape genome evolution. GenomeBiology.com (London. Print), v. 10, p. R19, 2009.

25.
DUTILH, B. E.2009DUTILH, B. E.; HUYNEN, M. A. ; STROUS, M. . Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics (Oxford. Print), v. 25, p. 2878-2881, 2009.

26.
DE GRAAF, ROB M2009DE GRAAF, ROB M ; VAN ALEN, THEO A ; DUTILH, BAS E ; KUIPER, JAN WP ; VAN ZOGGEL, HANNEKE JAA ; HUYNH, MINH ; GÖRTZ, HANS-DIETER ; HUYNEN, MARTIJN A ; HACKSTEIN, JOHANNES HP . The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus. BMC Genomics, v. 10, p. 514, 2009.

27.
KENSCHE, P. R2008KENSCHE, P. R ; VAN NOORT, V. ; Dutilh, B. E ; HUYNEN, M. A . Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. Journal of the Royal Society Interface (Print), v. 5, p. 151-170, 2008.

28.
KENSCHE, PHILIP R.2008KENSCHE, PHILIP R. ; OTI, MARTIN ; Dutilh, Bas E. ; HUYNEN, MARTIJN A. . Conservation of divergent transcription in fungi. Trends in Genetics (Regular ed.), v. 24, p. 207-211, 2008.

29.
DUTILH, B. E.2008DUTILH, B. E.; HE, Y. ; HEKKELMAN, M. L. ; HUYNEN, M. A. . Signature, a web server for taxonomic characterization of sequence samples using signature genes. Nucleic Acids Research (Online), v. 36, p. W470-W474, 2008.

30.
DUTILH, B. E.2008DUTILH, B. E.; SNEL, B. ; ETTEMA, T. J. G. ; HUYNEN, M. A. . Signature Genes as a Phylogenomic Tool. Molecular Biology and Evolution, v. 25, p. 1659-1667, 2008.

31.
RICARD, GUÉNOLA2008RICARD, GUÉNOLA ; DE GRAAF, ROB M ; DUTILH, BAS E ; DUARTE, I ; VAN ALEN, THEO A ; VAN HOEK, ANGELA HAM ; BOXMA, BRIGITTE ; VAN DER STAAY, GEORG WM ; MOON-VAN DER STAAY, SEUNG ; CHANG, WEI-JEN ; LANDWEBER, LAURA F ; HACKSTEIN, JOHANNES HP ; HUYNEN, MARTIJN A . Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns. BMC Genomics, v. 9, p. 587, 2008.

32.
DUTILH, B. E.2007DUTILH, B. E.; VAN NOORT, V. ; VAN DER HEIJDEN, R. T. J. M. ; BOEKHOUT, T. ; SNEL, B. ; HUYNEN, M. A. . Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics (Oxford. Print), v. 23, p. 815-824, 2007.

33.
DATSON, NICOLE A2007DATSON, NICOLE A ; MORSINK, MAARTEN C ; ATANASOVA, SREBRENA ; ARMSTRONG, VICTOR W ; ZISCHLER, HANS ; SCHLUMBOHM, CHRISTINA ; DUTILH, BAS E ; HUYNEN, MARTIJN A ; WAEGELE, BRIGITTE ; RUEPP, ANDREAS ; DE KLOET, E RONALD ; FUCHS, EBERHARD . 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, v. 8, p. 190, 2007.

34.
Dutilh, BasE2006Dutilh, BasE; HUYNEN, MARTIJNA ; SNEL, BEREND . A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. BMC Genomics, v. 7, p. 10, 2006.

35.
RICARD, GUÉNOLA2006RICARD, GUÉNOLA ; MCEWAN, NEILR ; Dutilh, BasE ; JOUANY, JEAN-PIERRE ; MACHEBOEUF, DIDIER ; MITSUMORI, MAKOTO ; MCINTOSH, FREDAM ; MICHALOWSKI, TADEUSZ ; NAGAMINE, TAKAFUMI ; NELSON, NANCY ; NEWBOLD, CHARLESJ ; NSABIMANA, ELI ; TAKENAKA, AKIO ; THOMAS, NADINEA ; USHIDA, KAZUNARI ; HACKSTEIN, JOHANNESHP ; HUYNEN, MARTIJNA . Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics, v. 7, p. 22, 2006.

36.
STROUS, MARC2006 STROUS, MARC PELLETIER, ERIC MANGENOT, SOPHIE RATTEI, THOMAS LEHNER, ANGELIKA TAYLOR, MICHAEL W. HORN, MATTHIAS DAIMS, HOLGER BARTOL-MAVEL, DELPHINE WINCKER, PATRICK BARBE, VALÉRIE FONKNECHTEN, NURIA VALLENET, DAVID SEGURENS, BÉATRICE SCHENOWITZ-TRUONG, CHANTAL MÉDIGUE, CLAUDINE COLLINGRO, ASTRID SNEL, BEREND Dutilh, Bas E. OP DEN CAMP, HUUB J. M. VAN DER DRIFT, CHRIS CIRPUS, IRINA VAN DE PAS-SCHOONEN, KATINKA T. HARHANGI, HARRY R. VAN NIFTRIK, LAURA , et al.SCHMID, MARKUS KELTJENS, JAN VAN DE VOSSENBERG, JACK KARTAL, BORAN MEIER, HARALD FRISHMAN, DMITRIJ HUYNEN, MARTIJN A. MEWES, HANS-WERNER WEISSENBACH, JEAN JETTEN, MIKE S. M. WAGNER, MICHAEL LE PASLIER, DENIS ; Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (London), v. 440, p. 790-794, 2006.

37.
SNEL, BEREND2005 SNEL, BEREND ; HUYNEN, MARTIJN A. ; Dutilh, Bas E. . GENOME TREES AND THE NATURE OF GENOME EVOLUTION. Annual Review of Microbiology (Print), v. 59, p. 191-209, 2005.

38.
Dutilh, Bas E.2004 Dutilh, Bas E.; HUYNEN, MARTIJN A. ; BRUNO, WILLIAM J. ; SNEL, BEREND . The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise. Journal of Molecular Evolution, v. 58, p. 527-539, 2004.

39.
Dutilh, Bas E.2003Dutilh, Bas E.. Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells. Journal of Theoretical Biology, v. 224, p. 351-358, 2003.

Livros publicados/organizados ou edições
1.
Bas E. Dutilh. Extracting the evolutionary signal from genomes. 1. ed. Nijmegen: Bas E. Dutilh, 2007. v. 1. 96p .

Capítulos de livros publicados
1.
DUTILH, BAS E; AZIZ, R. K. . Genomes, metagenomes, and microbiomes: a new biology for a new millennium. In: Bibliotheca Alexandrina. (Org.). New Life Sciences: Linking Science to Society, BioVisionAlexandria 2012 Proceedings. 1ed.: , 2013, v. , p. 105-116.

2.
MARCHESI, J. R. ; TJALSMA, H. ; DUTILH, BAS E ; BOLEIJ, A. . Colorectal Cancer Associated Microbiota. In: Sarah Highlander and Karen E. Nelson. (Org.). Encyclopedia of Metagenomics III: Human Metagenomics. 1ed.: , 2013, v. , p. 1-.

3.
Bas E. Dutilh; HUYNEN, M. A. ; Jolein Gloerich ; Marc Strous . 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. 1ed.: , 2011, v. 1, p. 379-.



Educação e Popularização de C & T



Artigos
Artigos completos publicados em periódicos
1.
Dutilh, Bas E.2003Dutilh, Bas E.. Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells. Journal of Theoretical Biology, v. 224, p. 351-358, 2003.

2.
Dutilh, Bas E.2004 Dutilh, Bas E.; HUYNEN, MARTIJN A. ; BRUNO, WILLIAM J. ; SNEL, BEREND . The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise. Journal of Molecular Evolution, v. 58, p. 527-539, 2004.

3.
SNEL, BEREND2005 SNEL, BEREND ; HUYNEN, MARTIJN A. ; Dutilh, Bas E. . GENOME TREES AND THE NATURE OF GENOME EVOLUTION. Annual Review of Microbiology (Print), v. 59, p. 191-209, 2005.

4.
Dutilh, BasE2006Dutilh, BasE; HUYNEN, MARTIJNA ; SNEL, BEREND . A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. BMC Genomics, v. 7, p. 10, 2006.

5.
RICARD, GUÉNOLA2006RICARD, GUÉNOLA ; MCEWAN, NEILR ; Dutilh, BasE ; JOUANY, JEAN-PIERRE ; MACHEBOEUF, DIDIER ; MITSUMORI, MAKOTO ; MCINTOSH, FREDAM ; MICHALOWSKI, TADEUSZ ; NAGAMINE, TAKAFUMI ; NELSON, NANCY ; NEWBOLD, CHARLESJ ; NSABIMANA, ELI ; TAKENAKA, AKIO ; THOMAS, NADINEA ; USHIDA, KAZUNARI ; HACKSTEIN, JOHANNESHP ; HUYNEN, MARTIJNA . Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics, v. 7, p. 22, 2006.

6.
STROUS, MARC2006 STROUS, MARC PELLETIER, ERIC MANGENOT, SOPHIE RATTEI, THOMAS LEHNER, ANGELIKA TAYLOR, MICHAEL W. HORN, MATTHIAS DAIMS, HOLGER BARTOL-MAVEL, DELPHINE WINCKER, PATRICK BARBE, VALÉRIE FONKNECHTEN, NURIA VALLENET, DAVID SEGURENS, BÉATRICE SCHENOWITZ-TRUONG, CHANTAL MÉDIGUE, CLAUDINE COLLINGRO, ASTRID SNEL, BEREND Dutilh, Bas E. OP DEN CAMP, HUUB J. M. VAN DER DRIFT, CHRIS CIRPUS, IRINA VAN DE PAS-SCHOONEN, KATINKA T. HARHANGI, HARRY R. VAN NIFTRIK, LAURA , et al.SCHMID, MARKUS KELTJENS, JAN VAN DE VOSSENBERG, JACK KARTAL, BORAN MEIER, HARALD FRISHMAN, DMITRIJ HUYNEN, MARTIJN A. MEWES, HANS-WERNER WEISSENBACH, JEAN JETTEN, MIKE S. M. WAGNER, MICHAEL LE PASLIER, DENIS ; Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (London), v. 440, p. 790-794, 2006.

7.
DUTILH, B. E.2007DUTILH, B. E.; VAN NOORT, V. ; VAN DER HEIJDEN, R. T. J. M. ; BOEKHOUT, T. ; SNEL, B. ; HUYNEN, M. A. . Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics (Oxford. Print), v. 23, p. 815-824, 2007.

8.
DATSON, NICOLE A2007DATSON, NICOLE A ; MORSINK, MAARTEN C ; ATANASOVA, SREBRENA ; ARMSTRONG, VICTOR W ; ZISCHLER, HANS ; SCHLUMBOHM, CHRISTINA ; DUTILH, BAS E ; HUYNEN, MARTIJN A ; WAEGELE, BRIGITTE ; RUEPP, ANDREAS ; DE KLOET, E RONALD ; FUCHS, EBERHARD . 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, v. 8, p. 190, 2007.

9.
KENSCHE, P. R2008KENSCHE, P. R ; VAN NOORT, V. ; Dutilh, B. E ; HUYNEN, M. A . Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. Journal of the Royal Society Interface (Print), v. 5, p. 151-170, 2008.

10.
KENSCHE, PHILIP R.2008KENSCHE, PHILIP R. ; OTI, MARTIN ; Dutilh, Bas E. ; HUYNEN, MARTIJN A. . Conservation of divergent transcription in fungi. Trends in Genetics (Regular ed.), v. 24, p. 207-211, 2008.

11.
DUTILH, B. E.2008DUTILH, B. E.; HE, Y. ; HEKKELMAN, M. L. ; HUYNEN, M. A. . Signature, a web server for taxonomic characterization of sequence samples using signature genes. Nucleic Acids Research (Online), v. 36, p. W470-W474, 2008.

12.
DUTILH, B. E.2008DUTILH, B. E.; SNEL, B. ; ETTEMA, T. J. G. ; HUYNEN, M. A. . Signature Genes as a Phylogenomic Tool. Molecular Biology and Evolution, v. 25, p. 1659-1667, 2008.

13.
RICARD, GUÉNOLA2008RICARD, GUÉNOLA ; DE GRAAF, ROB M ; DUTILH, BAS E ; DUARTE, I ; VAN ALEN, THEO A ; VAN HOEK, ANGELA HAM ; BOXMA, BRIGITTE ; VAN DER STAAY, GEORG WM ; MOON-VAN DER STAAY, SEUNG ; CHANG, WEI-JEN ; LANDWEBER, LAURA F ; HACKSTEIN, JOHANNES HP ; HUYNEN, MARTIJN A . Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns. BMC Genomics, v. 9, p. 587, 2008.

14.
NOTEBAART, RICHARD A2009NOTEBAART, RICHARD A ; KENSCHE, PHILIP R ; HUYNEN, MARTIJN A ; DUTILH, BAS E . Asymmetric relationships between proteins shape genome evolution. GenomeBiology.com (London. Print), v. 10, p. R19, 2009.

15.
DUTILH, B. E.2009DUTILH, B. E.; HUYNEN, M. A. ; STROUS, M. . Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics (Oxford. Print), v. 25, p. 2878-2881, 2009.

16.
DE GRAAF, ROB M2009DE GRAAF, ROB M ; VAN ALEN, THEO A ; DUTILH, BAS E ; KUIPER, JAN WP ; VAN ZOGGEL, HANNEKE JAA ; HUYNH, MINH ; GÖRTZ, HANS-DIETER ; HUYNEN, MARTIJN A ; HACKSTEIN, JOHANNES HP . The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus. BMC Genomics, v. 10, p. 514, 2009.

17.
ETTWIG, KATHARINA F.2010 ETTWIG, KATHARINA F. ; BUTLER, MARGARET K. ; LE PASLIER, DENIS ; PELLETIER, ERIC ; MANGENOT, SOPHIE ; KUYPERS, MARCEL M. M. ; SCHREIBER, FRANK ; Dutilh, Bas E. ; ZEDELIUS, JOHANNES ; DE BEER, DIRK ; GLOERICH, JOLEIN ; WESSELS, HANS J. C. T. ; VAN ALEN, THEO ; LUESKEN, FRANCISCA ; WU, MING L. ; VAN DE PAS-SCHOONEN, KATINKA T. ; OP DEN CAMP, HUUB J. M. ; JANSSEN-MEGENS, EVA M. ; FRANCOIJS, KEES-JAN ; STUNNENBERG, HENK ; WEISSENBACH, JEAN ; JETTEN, MIKE S. M. ; STROUS, MARC . Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature (London), v. 464, p. 543-548, 2010.

18.
KOUWENHOVEN, EVELYN N.2010KOUWENHOVEN, EVELYN N. ; VAN HEERINGEN, SIMON J. ; TENA, JUAN J. ; OTI, MARTIN ; Dutilh, Bas E. ; ALONSO, M. EVA ; DE LA CALLE-MUSTIENES, ELISA ; SMEENK, LEONIE ; RINNE, TUULA ; PARSAULIAN, LILIAN ; BOLAT, EMINE ; JURGELENAITE, RASA ; HUYNEN, MARTIJN A. ; HOISCHEN, ALEXANDER ; VELTMAN, JORIS A. ; BRUNNER, HAN G. ; ROSCIOLI, TONY ; OATES, EMILY ; WILSON, MEREDITH ; MANZANARES, MIGUEL ; GÓMEZ-SKARMETA, JOSÉ LUIS ; STUNNENBERG, HENDRIK G. ; LOHRUM, MARION ; VAN BOKHOVEN, HANS ; ZHOU, HUIQING . 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 (Online), v. 6, p. e1001065, 2010.

19.
KIP, NARDY2011KIP, NARDY ; Dutilh, Bas E. ; PAN, YAO ; BODROSSY, LEVENTE ; NEVELING, KORNELIA ; KWINT, MICHAEL P. ; JETTEN, MIKE S. M. ; OP DEN CAMP, HUUB J. M. . Ultra-deep pyrosequencing of pmoA amplicons confirms the prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog. Environmental Microbiology Reports, v. 3, p. 667-673, 2011.

20.
EMONS, J.2011EMONS, J. ; DUTILH, B. E. ; DECKER, E. ; PIRZER, H. ; STICHT, C. ; GRETZ, N. ; RAPPOLD, G. ; CAMERON, E. R. ; NEIL, J. C. ; STEIN, G. S. ; VAN WIJNEN, A. J. ; WIT, J. M. ; POST, J. N. ; KARPERIEN, M. . Genome-wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation. Journal of Endocrinology, v. 209, p. 245-254, 2011.

21.
DE GRAAF, R. M.2011DE GRAAF, R. M. ; RICARD, G. ; VAN ALEN, T. A. ; DUARTE, I. ; DUTILH, B. E. ; BURGTORF, C. ; KUIPER, J. W. P. ; VAN DER STAAY, G. W. M. ; TIELENS, A. G. M. ; HUYNEN, M. A. ; HACKSTEIN, J. H. P. . The Organellar Genome and Metabolic Potential of the Hydrogen-Producing Mitochondrion of Nyctotherus ovalis. Molecular Biology and Evolution, v. 28, p. 2379-2391, 2011.

22.
TJALSMA, HAROLD2011TJALSMA, HAROLD ; LAARAKKERS, COBY M. M. ; VAN SWELM, RACHEL P. L. ; THEURL, MILAN ; THEURL, IGOR ; KEMNA, ERWIN H. ; VAN DER BURGT, YURI E. M. ; VENSELAAR, HANKA ; Dutilh, Bas E. ; RUSSEL, FRANS G. M. ; WEISS, GÜNTER ; MASEREEUW, ROSALINDE ; FLEMING, ROBERT E. ; SWINKELS, DORINE W. . Mass Spectrometry Analysis of Hepcidin Peptides in Experimental Mouse Models. Plos One, v. 6, p. e16762, 2011.

23.
MARCHESI, JULIAN R.2011MARCHESI, JULIAN R. ; Dutilh, Bas E. ; HALL, NEIL ; PETERS, WILBERT H. M. ; ROELOFS, RIAN ; BOLEIJ, ANNEMARIE ; TJALSMA, HAROLD . Towards the Human Colorectal Cancer Microbiome. Plos One, v. 6, p. e20447, 2011.

24.
DUTILH, B. E.2011DUTILH, B. E.; JURGELENAITE, R. ; SZKLARCZYK, R. ; VAN HIJUM, S. A. F. T. ; HARHANGI, H. R. ; SCHMID, M. ; DE WILD, B. ; FRANCOIJS, K.-J. ; STUNNENBERG, H. G. ; STROUS, M. ; JETTEN, M. S. M. ; OP DEN CAMP, H. J. M. ; HUYNEN, M. A. . FACIL: Fast and Accurate Genetic Code Inference and Logo. Bioinformatics (Oxford. Print), v. 27, p. 1929-1933, 2011.

25.
THOMPSON, C. C.2011THOMPSON, C. C. ; MARÍN, M. F. A. ; DIAS, G. M. ; DUTILH, B. E. ; EDWARDS, R. A. ; IIDA, T. ; THOMPSON, F. L. ; VICENTE, A. C. P. . Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia. Journal of Bacteriology (Print), v. 193, p. 5877-5878, 2011.

26.
VAN KESSEL, MAARTJE AHJ2011VAN KESSEL, MAARTJE AHJ ; DUTILH, BAS E ; NEVELING, KORNELIA ; KWINT, MICHAEL P ; VELTMAN, JORIS A ; FLIK, GERT ; JETTEN, MIKE SM ; KLAREN, PETER HM ; OP DEN CAMP, HUUB JM . Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.). AMB Express, v. 1, p. 41, 2011.

27.
MOKILI, JOHN L2012MOKILI, JOHN L ; ROHWER, FOREST ; DUTILH, BAS E . Metagenomics and future perspectives in virus discovery. Current Opinion in Virology, v. 2, p. 63-77, 2012.

28.
LUCKWU DE LUCENA, B. T.2012LUCKWU DE LUCENA, B. T. ; SILVA, G. G. Z. ; MANOEL DOS SANTOS, B. ; DIAS, G. M. ; AMARAL, G. R. S. ; MOREIRA, A. P. B. ; DE MORAIS JUNIOR, M. A. ; DUTILH, B. E. ; EDWARDS, R. A. ; BALBINO, V. ; THOMPSON, C. C. ; THOMPSON, F. L. . Genome Sequences of the Ethanol-Tolerant Lactobacillus vini Strains LMG 23202T and JP7.8.9. Journal of Bacteriology (Print), v. 194, p. 3018-3018, 2012.

29.
GARZA, DANIEL RIOS2012GARZA, DANIEL RIOS ; THOMPSON, CRISTIANE C. ; LOUREIRO, EDVALDO CARLOS BRITO ; Dutilh, Bas E. ; INADA, DAVI TOSHIO ; JUNIOR, EDIVALDO COSTA SOUSA ; CARDOSO, JEDSON FERREIRA ; NUNES, MÁRCIO ROBERTO T. ; DE LIMA, CLAYTON PEREIRA SILVA ; SILVESTRE, RODRIGO VELLASCO DUARTE ; NUNES, KELEY NASCIMENTO BARBOSA ; SANTOS, ELISABETH C. O. ; EDWARDS, ROBERT A. ; VICENTE, ANA CAROLINA P. ; DE SÁ MORAIS, LENA LILLIAN CANTO . Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic. Plos One, v. 7, p. e37283, 2012.

30.
BOLEIJ, A.2012BOLEIJ, A. ; DUTILH, B. E. ; KORTMAN, G. A. M. ; ROELOFS, R. ; LAARAKKERS, C. M. ; ENGELKE, U. F. ; TJALSMA, H. . Bacterial Responses to a Simulated Colon Tumor Microenvironment. Molecular & Cellular Proteomics (Online), v. 11, p. 851-862, 2012.

31.
TJALSMA, HAROLD2012 TJALSMA, HAROLD ; BOLEIJ, ANNEMARIE ; MARCHESI, JULIAN R. ; Dutilh, Bas E. . A bacterial driver passenger model for colorectal cancer: beyond the usual suspects. Nature Review, Microbiology (Print), v. 10, p. 575-582, 2012.

32.
TRINDADE-SILVA, AMARO E.2012TRINDADE-SILVA, AMARO E. ; RUA, CINTIA ; SILVA, GENIVALDO G. Z. ; Dutilh, Bas E. ; MOREIRA, ANA PAULA B. ; EDWARDS, ROBERT A. ; HAJDU, EDUARDO ; LOBO-HAJDU, GISELE ; VASCONCELOS, ANA TEREZA ; BERLINCK, ROBERTO G. S. ; THOMPSON, FABIANO L. . Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis. Plos One, v. 7, p. e39905, 2012.

33.
CASSMAN, NORIKO2012CASSMAN, NORIKO ; PRIETO-DAVÓ, ALEJANDRA ; WALSH, KEVIN ; SILVA, GENIVALDO G. Z. ; ANGLY, FLORENT ; AKHTER, SAJIA ; BAROTT, KATIE ; BUSCH, JULIA ; MCDOLE, TRACEY ; HAGGERTY, J. MATTHEW ; WILLNER, DANA ; ALARCÓN, GADIEL ; ULLOA, OSVALDO ; DELONG, EDWARD F. ; Dutilh, Bas E. ; ROHWER, FOREST ; DINSDALE, ELIZABETH A. . Oxygen minimum zones harbour novel viral communities with low diversity. Environmental Microbiology (Print), v. 14, p. 3043-3065, 2012.

34.
DUTILH, B. E.2012DUTILH, B. E.; SCHMIEDER, R. ; NULTON, J. ; FELTS, B. ; SALAMON, P. ; EDWARDS, R. A. ; MOKILI, J. L. . Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics (Oxford. Print), v. 28, p. 3225-3231, 2012.

35.
CAMPS, SIMONE M. T.2012CAMPS, SIMONE M. T. ; Dutilh, Bas E. ; ARENDRUP, MAIKEN C. ; RIJS, ANTONIUS J. M. M. ; SNELDERS, EVELINE ; HUYNEN, MARTIJN A. ; VERWEIJ, PAUL E. ; MELCHERS, WILLEM J. G. . Discovery of a hapE Mutation That Causes Azole Resistance in Aspergillus fumigatus through Whole Genome Sequencing and Sexual Crossing. Plos One, v. 7, p. e50034, 2012.


Livros e capítulos
1.
DUTILH, BAS E; AZIZ, R. K. . Genomes, metagenomes, and microbiomes: a new biology for a new millennium. In: Bibliotheca Alexandrina. (Org.). New Life Sciences: Linking Science to Society, BioVisionAlexandria 2012 Proceedings. 1ed.: , 2013, v. , p. 105-116.




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