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1

Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)

King, Andrew M. Q., Lefkowitz, Elliot J., Mushegian, Arcady R., Adams, Michael J., Dutilh, Bas E., Gorbalenya, Alexander E., Harrach, Balázs, Harrison, Robert L., Junglen, Sandra, Knowles, Nick J., Kr

Journal:

Archives of Virology

Year:

2018

Language:

english

File:

PDF, 1.21 MB

english, 2018

2

GENOME TREES AND THE NATURE OF GENOME EVOLUTION

Snel, Berend, Huynen, Martijn A., Dutilh, Bas E.

Journal:

Annual Review of Microbiology

Year:

2005

Language:

english

File:

PDF, 385 KB

english, 2005

3

Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses

Maat, Douwe, Biggs, Tristan, Evans, Claire, van Bleijswijk, Judith, van der Wel, Nicole, Dutilh, Bas, Brussaard, Corina

Journal:

Year:

2017

Language:

english

File:

PDF, 4.14 MB

english, 2017

4

Targeting mechanisms of tailed bacteriophages

Nobrega, Franklin L., Vlot, Marnix, de Jonge, Patrick A., Dreesens, Lisa L., Beaumont, Hubertus J. E., Lavigne, Rob, Dutilh, Bas E., Brouns, Stan J. J.

Journal:

Nature Reviews Microbiology

Year:

2018

Language:

english

File:

PDF, 25.42 MB

english, 2018

5

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

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

Journal:

Year:

2010

Language:

english

File:

PDF, 468 KB

english, 2010

6

Pharmacomicrobiomics: The Impact of Human Microbiome Variations on Systems Pharmacology and Personalized Therapeutics

ElRakaiby, Marwa, Dutilh, Bas E., Rizkallah, Mariam R., Boleij, Annemarie, Cole, Jason N., Aziz, Ramy K.

Journal:

Omics A Journal of Integrative Biology

Year:

2014

Language:

english

File:

PDF, 562 KB

english, 2014

7

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

Thompson, Cristiane C., Amaral, Gilda R., Campeão, Mariana, Edwards, Robert A., Polz, Martin F., Dutilh, Bas E., Ussery, David W., Sawabe, Tomoo, Swings, Jean, Thompson, Fabiano L.

Journal:

Archives of Microbiology

Year:

2015

Language:

english

File:

PDF, 589 KB

english, 2015

8

Water Regime Influences Bulk Soil and Rhizosphere of Cereus jamacaru Bacterial Communities in the Brazilian Caatinga Biome

Nessner Kavamura, Vanessa, Taketani, Rodrigo Gouvêa, Lançoni, Milena Duarte, Andreote, Fernando Dini, Mendes, Rodrigo, Soares de Melo, Itamar, Dutilh, Bas E.

Journal:

Year:

2013

Language:

english

File:

PDF, 2.02 MB

english, 2013

9

Effect of Abandonment on Diversity and Abundance of Free-Living Nitrogen-Fixing Bacteria and Total Bacteria in the Cropland Soils of Hulun Buir, Inner Mongolia

Huhe,, Borjigin, Shinchilelt, Cheng, Yunxiang, Nomura, Nobukiko, Nakajima, Toshiaki, Nakamura, Toru, Uchiyama, Hiroo, Dutilh, Bas E.

Journal:

Year:

2014

Language:

english

File:

PDF, 344 KB

english, 2014

10

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

Gambelli, Lavinia, Cremers, Geert, Mesman, Rob, Guerrero, Simon, Dutilh, Bas E., Jetten, Mike S. M., Op den Camp, Huub J. M., van Niftrik, Laura

Journal:

Frontiers in Microbiology

Year:

2016

Language:

english

File:

PDF, 4.60 MB

english, 2016

11

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

Motlagh, Amir Mohaghegh, Bhattacharjee, Ananda S., Coutinho, Felipe H., Dutilh, Bas E., Casjens, Sherwood R., Goel, Ramesh K.

Journal:

Frontiers in Microbiology

Year:

2017

Language:

english

File:

PDF, 9.10 MB

english, 2017

12

Ecogenomics and Taxonomy of Cyanobacteria Phylum

Walter, Juline M., Coutinho, Felipe H., Dutilh, Bas E., Swings, Jean, Thompson, Fabiano L., Thompson, Cristiane C.

Journal:

Frontiers in Microbiology

Year:

2017

Language:

english

File:

PDF, 7.29 MB

english, 2017

13

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, B

Journal:

Nature Biotechnology

Year:

2018

Language:

english

File:

PDF, 1.15 MB

english, 2018

14

Evolutionary Study of the Crassphage Virus at Gene Level

Rossi, Alessandro, Treu, Laura, Toppo, Stefano, Zschach, Henrike, Campanaro, Stefano, Dutilh, Bas E.

Journal:

Year:

2020

File:

PDF, 1.52 MB

2020

15

Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpioL.)

Maartje AHJ van Kessel, Bas E Dutilh, Kornelia Neveling, Michael P Kwint, Joris A Veltman, Gert Flik, Mike SM Jetten, Peter HM Klaren, Huub JM Op den Camp

Journal:

Year:

2011

Language:

english

File:

PDF, 595 KB

english, 2011

16

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

Bas E. Dutilh, Rob J. de Boer

Journal:

Journal of Theoretical Biology

Year:

2003

Language:

english

File:

PDF, 175 KB

english, 2003

17

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

Tjalsma, Harold, Boleij, Annemarie, Marchesi, Julian R., Dutilh, Bas E.

Journal:

Nature Reviews Microbiology

Year:

2012

Language:

english

File:

PDF, 632 KB

english, 2012

18

Conservation of divergent transcription in fungi

Philip R. Kensche, Martin Oti, Bas E. Dutilh, Martijn A. Huynen

Journal:

Trends in Genetics

Year:

2008

Language:

english

File:

PDF, 338 KB

english, 2008

19

The mitochondrial genomes of the ciliatesEuplotes minutaandEuplotes crassus

Rob M de Graaf, Theo A van Alen, Bas E Dutilh, Jan WP Kuiper, Hanneke JAA van Zoggel, Minh Bao Huynh, Hans-Dieter Görtz, Martijn A Huynen, Johannes HP Hackstein

Journal:

Year:

2009

Language:

english

File:

PDF, 2.27 MB

english, 2009

20

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

Bas E Dutilh, Martijn A Huynen, Berend Snel

Journal:

Year:

2006

Language:

english

File:

PDF, 861 KB

english, 2006

21

Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment

Guénola 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 Nsa

Journal:

Year:

2006

Language:

english

File:

PDF, 1.21 MB

english, 2006

22

Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate

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, Ebe

Journal:

Year:

2007

Language:

english

File:

PDF, 353 KB

english, 2007

23

Macronuclear genome structure of the ciliateNyctotherus ovalis: Single-gene chromosomes and tiny introns

Guénola Ricard, Rob M de Graaf, Bas E Dutilh, I Duarte, Theo A van Alen, Angela HAM van Hoek, Brigitte Boxma, Georg WM van der Staay, Seung Yeo Moon-van der Staay, Wei-Jen Chang, Laura F Landweber, Jo

Journal:

Year:

2008

Language:

english

File:

PDF, 1.44 MB

english, 2008

24

The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium

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,

Journal:

Environmental Microbiology

Year:

2012

Language:

english

File:

PDF, 784 KB

english, 2012

25

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

Nardy Kip, Bas E. Dutilh, Yao Pan, Levente Bodrossy, Kornelia Neveling, Michael P. Kwint, Mike S. M. Jetten, Huub J. M. Op den Camp

Journal:

Environmental Microbiology Reports

Year:

2011

Language:

english

File:

PDF, 433 KB

english, 2011

26

Metagenomics and future perspectives in virus discovery

John L Mokili, Forest Rohwer, Bas E Dutilh

Journal:

Current Opinion in Virology

Year:

2012

Language:

english

File:

PDF, 690 KB

english, 2012

27

Asymmetric relationships between proteins shape genome evolution

Richard A Notebaart, Philip R Kensche, Martijn A Huynen, Bas E Dutilh

Journal:

Year:

2009

Language:

english

File:

PDF, 287 KB

english, 2009

28

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

Dutilh, Bas E., Backus, Lennart, van Hijum, Sacha A.F.T., Tjalsma, Harold

Journal:

Best Practice & Research Clinical Gastroenterology

Year:

2013

Language:

english

File:

PDF, 937 KB

english, 2013

29

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

Dutilh, Bas E., Cassman, Noriko, McNair, Katelyn, Sanchez, Savannah E., Silva, Genivaldo G. Z., Boling, Lance, Barr, Jeremy J., Speth, Daan R., Seguritan, Victor, Aziz, Ramy K., Felts, Ben, Dinsdale,

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 1.25 MB

english, 2014

30

Comparative genomics of 274Vibrio choleraegenomes reveals mobile functions structuring three niche dimensions

Bas E Dutilh,Cristiane C Thompson,Ana CP Vicente,Michel A Marin…

Journal:

Year:

2014

Language:

english

File:

PDF, 2.99 MB

english, 2014

31

Combining de novo and reference-guided assembly with scaffold_builder

Genivaldo GZ Silva,Bas E Dutilh,T David Matthews…

Journal:

Source Code for Biology and Medicine

Year:

2013

Language:

english

File:

PDF, 217 KB

english, 2013

32

Modifications de la paroi au cours de la maturation des conidies chez Pseudallescheria boydii

Ghamrawi, S., Gilles, R., Saulnier, P., Cuenot, S., Zykwinska, A., Dutilh Bas, E., Thornton, C., Faure, S., Bouchara, J.-P.

Journal:

Journal de Mycologie Médicale / Journal of Medical Mycology

Year:

2014

File:

PDF, 159 KB

2014

33

Microbial community diversity and physical–chemical features of the Southwestern Atlantic Ocean

Alves Junior, Nelson, Meirelles, Pedro Milet, de Oliveira Santos, Eidy, Dutilh, Bas, Silva, Genivaldo G. Z., Paranhos, Rodolfo, Cabral, Anderson S., Rezende, Carlos, Iida, Tetsuya, de Moura, Rodrigo L

Journal:

Archives of Microbiology

Year:

2015

Language:

english

File:

PDF, 1.87 MB

english, 2015

34

Draft Genome Sequence of Anammox Bacterium “Candidatus Scalindua brodae,” Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor Enrichments

Speth, Daan R., Russ, Lina, Kartal, Boran, op den Camp, Huub J. M., Dutilh, Bas E., Jetten, Mike S. M.

Journal:

Genome Announcements

Year:

2015

Language:

english

File:

PDF, 155 KB

english, 2015

35

Cloning, Expression and Characteristics of a Novel Alkalistable and Thermostable Xylanase Encoding Gene (Mxyl) Retrieved from Compost-Soil Metagenome

Verma, Digvijay, Kawarabayasi, Yutaka, Miyazaki, Kentaro, Satyanarayana, Tulasi, Dutilh, Bas E.

Journal:

Year:

2013

Language:

english

File:

PDF, 527 KB

english, 2013

36

Copper tolerance and distribution of epibiotic bacteria associated with giant kelpMacrocystis pyriferain southern California

Busch, Julia, Nascimento, Juliana Ribeiro, Magalhães, Ana Carolina Rubem, Dutilh, Bas E., Dinsdale, Elizabeth

Journal:

Year:

2015

Language:

english

File:

PDF, 902 KB

english, 2015

37

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

Hall, Richard J., Draper, Jenny L., Nielsen, Fiona G. G., Dutilh, Bas E.

Journal:

Frontiers in Microbiology

Year:

2015

Language:

english

File:

PDF, 245 KB

english, 2015

38

Genome-Wide Profiling of p63 DNA–Binding Sites Identifies an Element that Regulates Gene Expression during Limb Development in the 7q21 SHFM1 Locus

Kouwenhoven, 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, Emin

Journal:

Year:

2010

Language:

english

File:

PDF, 2.72 MB

english, 2010

39

Metagenomic ventures into outer sequence space

Journal:

Year:

2014

Language:

english

File:

PDF, 66 KB

english, 2014

40

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

Garza, Daniel R., Dutilh, Bas E.

Journal:

Cellular and Molecular Life Sciences

Year:

2015

Language:

english

File:

PDF, 2.26 MB

english, 2015

41

Immunoglobulin rearrangement analysis from multiple lesions in the same patient using next-generation sequencing

Appenzeller, Silke, Gilissen, Christian, Rijntjes, Jos, Tops, Bastiaan B J, Kastner-van Raaij, Annemiek, Hebeda, Konnie M, Nissen, Loes, Dutilh, Bas E, van Krieken, J Han J M, Groenen, Patricia J T A

Journal:

Year:

2015

File:

PDF, 1.07 MB

2015

42

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

Silva, Genivaldo Gueiros Z., Green, Kevin T., Dutilh, Bas E., Edwards, Robert A.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.29 MB

english, 2015

43

Immunoglobulin rearrangement analysis from multiple lesions in the same patient using next-generation sequencing

Appenzeller, Silke, Gilissen, Christian, Rijntjes, Jos, Tops, Bastiaan B J, Kastner-van Raaij, Annemiek, Hebeda, Konnie M, Nissen, Loes, Dutilh, Bas E, van Krieken, J Han J M, Groenen, Patricia J T A

Journal:

Year:

2015

Language:

english

File:

PDF, 1.07 MB

english, 2015

44

Computational approaches to predict bacteriophage–host relationships

Edwards, Robert A., McNair, Katelyn, Faust, Karoline, Raes, Jeroen, Dutilh, Bas E., Smith, Maggie

Journal:

FEMS Microbiology Reviews

Year:

2015

Language:

english

File:

PDF, 1.11 MB

english, 2015

45

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

Krupovic, Mart, Dutilh, Bas E., Adriaenssens, Evelien M., Wittmann, Johannes, Vogensen, Finn K., Sullivan, Mathew B., Rumnieks, Janis, Prangishvili, David, Lavigne, Rob, Kropinski, Andrew M., Klumpp,

Journal:

Archives of Virology

Year:

2016

Language:

english

File:

PDF, 400 KB

english, 2016

46

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

Barr, Jeremy J., Dutilh, Bas E., Skennerton, Connor T., Fukushima, Toshikazu, Hastie, Marcus L., Gorman, Jeffrey J., Tyson, Gene W., Bond, Philip L.

Journal:

Environmental Microbiology

Year:

2016

Language:

english

File:

PDF, 2.20 MB

english, 2016

47

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

Hou, Qingzhen, Dutilh, Bas E., Huynen, Martijn A., Heringa, Jaap, Feenstra, K. Anton

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 2.19 MB

english, 2015

48

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

Speth, Daan R., in ’t Zandt, Michiel H., Guerrero-Cruz, Simon, Dutilh, Bas E., Jetten, Mike S. M.

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 593 KB

english, 2016

49

Draft Genome ofScalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

Speth, Daan R., Lagkouvardos, Ilias, Wang, Yong, Qian, Pei-Yuan, Dutilh, Bas E., Jetten, Mike S. M.

Journal:

Microbial Ecology

Year:

2017

Language:

english

File:

PDF, 387 KB

english, 2017

50

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

Coutinho, Felipe H., Silveira, Cynthia B., Gregoracci, Gustavo B., Thompson, Cristiane C., Edwards, Robert A., Brussaard, Corina P. D., Dutilh, Bas E., Thompson, Fabiano L.

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 1.81 MB

english, 2017