Bas E Dutilh

Affiliations

Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands. bedutilh@gmail.com.
Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands. bedutilh@gmail.com.

Publications (75)

Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT.

Genome biology

Avec: F A Bastiaan von Meijenfeldt , Ksenia Arkhipova , Diego D Cambuy , Felipe H Coutinho , Bas E Dutilh

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Nature microbiology

Avec: Robert A Edwards , Alejandro A Vega , Holly M Norman , Maria Ohaeri , Kyle Levi , Elizabeth A Dinsdale , Ondrej Cinek , Ramy K Aziz , Katelyn McNair , Jeremy J Barr , Kyle Bibby , Stan J J Brouns , Adrian Cazares , Patrick A de Jonge , Christelle Desnues , Samuel L Díaz Muñoz , Peter C Fineran , Alexander Kurilshikov , Rob Lavigne , Karla Mazankova , David T McCarthy , Franklin L Nobrega , Alejandro Reyes Muñoz , German Tapia , Nicole Trefault , Alexander V Tyakht , Pablo Vinuesa , Jeroen Wagemans , Alexandra Zhernakova , Frank M Aarestrup , Gunduz Ahmadov , Abeer Alassaf , Josefa Anton , Abigail Asangba , Emma K Billings , Vito Adrian Cantu , Jane M Carlton , Daniel Cazares , Gyu-Sung Cho , Tess Condeff , Pilar Cortés , Mike Cranfield , Daniel A Cuevas , Rodrigo De la Iglesia , Przemyslaw Decewicz , Michael P Doane , Nathaniel J Dominy , Lukasz Dziewit , Bashir Mukhtar Elwasila , A Murat Eren , Charles Franz , Jingyuan Fu , Cristina Garcia-Aljaro , Elodie Ghedin , Kristen M Gulino , John M Haggerty , Steven R Head , Rene S Hendriksen , Colin Hill , Heikki Hyöty , Elena N Ilina , Mitchell T Irwin , Thomas C Jeffries , Juan Jofre , Randall E Junge , Scott T Kelley , Mohammadali Khan Mirzaei , Martin Kowalewski , Deepak Kumaresan , Steven R Leigh , David Lipson , Eugenia S Lisitsyna , Montserrat Llagostera , Julia M Maritz , Linsey C Marr , Angela McCann , Shahar Molshanski-Mor , Silvia Monteiro , Benjamin Moreira-Grez , Megan Morris , Lawrence Mugisha , Maite Muniesa , Horst Neve , Nam-Phuong Nguyen , Olivia D Nigro , Anders S Nilsson , Taylor O'Connell , Rasha Odeh , Andrew Oliver , Mariana Piuri , Aaron J Prussin Ii , Udi Qimron , Zhe-Xue Quan , Petra Rainetova , Adán Ramírez-Rojas , Raul Raya , Kim Reasor , Gillian A O Rice , Alessandro Rossi , Ricardo Santos , John Shimashita , Elyse N Stachler , Lars C Stene , Ronan Strain , Rebecca Stumpf , Pedro J Torres , Alan Twaddle , MaryAnn Ugochi Ibekwe , Nicolás Villagra , Stephen Wandro , Bryan White , Andy Whiteley , Katrine L Whiteson , Cisca Wijmenga , Maria M Zambrano , Henrike Zschach , Bas E Dutilh

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages.

Systematic biology

Avec: Jakub Barylski , François Enault , Bas E Dutilh , Margo Bp Schuller , Robert A Edwards , Annika Gillis , Jochen Klumpp , Petar Knezevic , Mart Krupovic , Jens H Kuhn , Rob Lavigne , Hanna M Oksanen , Matthew B Sullivan , Ho Bin Jang , Peter Simmonds , Pakorn Aiewsakun , Johannes Wittmann , Igor Tolstoy , J Rodney Brister , Andrew M Kropinski , Evelien M Adriaenssens

Prophages are associated with extensive CRISPR-Cas auto-immunity.

Nucleic acids research

Avec: Franklin L Nobrega , Hielke Walinga , Bas E Dutilh , Stan J J Brouns

Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes.

BMC ecology and evolution

Avec: Daniel R Garza , F A Bastiaan von Meijenfeldt , Bram van Dijk , Annemarie Boleij , Martijn A Huynen , Bas E Dutilh

Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022).

Archives of virology

Avec: Peter J Walker , Stuart G Siddell , Elliot J Lefkowitz , Arcady R Mushegian , Evelien M Adriaenssens , Poliane Alfenas-Zerbini , Donald M Dempsey , Bas E Dutilh , María Laura García , R Curtis Hendrickson , Sandra Junglen , Mart Krupovic , Jens H Kuhn , Amy J Lambert , Małgorzata Łobocka , Hanna M Oksanen , Richard J Orton , David L Robertson , Luisa Rubino , Sead Sabanadzovic , Peter Simmonds , Donald B Smith , Nobuhiro Suzuki , Koenraad Van Doorslaer , Anne-Mieke Vandamme , Arvind Varsani , Francisco Murilo Zerbini

Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome.

ISME communications

Avec: Bram van Dijk , Pauline Buffard , Andrew D Farr , Franz Giersdorf , Jeroen Meijer , Bas E Dutilh , Paul B Rainey

Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes.

Genome biology

Avec: Ling-Yi Wu , Yasas Wijesekara , Gonçalo J Piedade , Nikolaos Pappas , Corina P D Brussaard , Bas E Dutilh

Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome.

The Science of the total environment

Avec: F H Coutinho , F A B von Meijenfeldt , J M Walter , J M Haro-Moreno , M Lopéz-Pérez , M C van Verk , C C Thompson , C A N Cosenza , L Appolinario , R Paranhos , A Cabral , B E Dutilh , F L Thompson

Molecular and Evolutionary Determinants of Bacteriophage Host Range.

Trends in microbiology

Avec: Patrick A de Jonge , Franklin L Nobrega , Stan J J Brouns , Bas E Dutilh

Integrating Computational Methods to Investigate the Macroecology of Microbiomes.

Frontiers in genetics

Avec: Rilquer Mascarenhas , Flávia M Ruziska , Eduardo Freitas Moreira , Amanda B Campos , Miguel Loiola , Kaike Reis , Amaro E Trindade-Silva , Felipe A S Barbosa , Lucas Salles , Rafael Menezes , Rafael Veiga , Felipe H Coutinho , Bas E Dutilh , Paulo R Guimarães , Ana Paula A Assis , Anderson Ara , José G V Miranda , Roberto F S Andrade , Bruno Vilela , Pedro Milet Meirelles

Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering.

PloS one

Avec: Joël Klein , Manon Neilen , Marcel van Verk , Bas E Dutilh , Guido Van den Ackerveken

Finding functional associations between prokaryotic virus orthologous groups: a proof of concept.

BMC bioinformatics

Avec: Nikolaos Pappas , Bas E Dutilh

Quantifying the Impact of Human Leukocyte Antigen on the Human Gut Microbiota.

mSphere

Avec: Stijn P Andeweg , Can Keşmir , Bas E Dutilh

Novel high-resolution targeted sequencing of the cervicovaginal microbiome.

BMC biology

Avec: Karolina M Andralojc , Mariano A Molina , Mengjie Qiu , Bram Spruijtenburg , Menno Rasing , Bernard Pater , Martijn A Huynen , Bas E Dutilh , Thomas H A Ederveen , Duaa Elmelik , Albert G Siebers , Diede Loopik , Ruud L M Bekkers , William P J Leenders , Willem J G Melchers

Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.

Nature communications

Avec: Ernestina Hauptfeld , Nikolaos Pappas , Sandra van Iwaarden , Basten L Snoek , Andrea Aldas-Vargas , Bas E Dutilh , F A Bastiaan von Meijenfeldt

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria.

PLoS biology

Avec: Simon Roux , Antonio Pedro Camargo , Felipe H Coutinho , Shareef M Dabdoub , Bas E Dutilh , Stephen Nayfach , Andrew Tritt

Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023).

Archives of virology

Avec: Francisco Murilo Zerbini , Stuart G Siddell , Elliot J Lefkowitz , Arcady R Mushegian , Evelien M Adriaenssens , Poliane Alfenas-Zerbini , Donald M Dempsey , Bas E Dutilh , María Laura García , R Curtis Hendrickson , Sandra Junglen , Mart Krupovic , Jens H Kuhn , Amy J Lambert , Małgorzata Łobocka , Hanna M Oksanen , David L Robertson , Luisa Rubino , Sead Sabanadzovic , Peter Simmonds , Donald B Smith , Nobuhiro Suzuki , Koenraad Van Doorslaer , Anne-Mieke Vandamme , Arvind Varsani

A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists.

Cell reports

Avec: Daniel Loos , Ailton Pereira da Costa Filho , Bas E Dutilh , Amelia E Barber , Gianni Panagiotou

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria.

ISME communications

Avec: Katarina Hrovat , Bas E Dutilh , Marnix H Medema , Chrats Melkonian

Examining the healthy human microbiome concept.

Nature reviews. Microbiology

Avec: Raphaela Joos , Katy Boucher , Aonghus Lavelle , Manimozhiyan Arumugam , Martin J Blaser , Marcus J Claesson , Gerard Clarke , Paul D Cotter , Luisa De Sordi , Maria G Dominguez-Bello , Bas E Dutilh , Stanislav D Ehrlich , Tarini Shankar Ghosh , Colin Hill , Christophe Junot , Leo Lahti , Trevor D Lawley , Tine R Licht , Emmanuelle Maguin , Thulani P Makhalanyane , Julian R Marchesi , Jelle Matthijnssens , Jeroen Raes , Jacques Ravel , Anne Salonen , Pauline D Scanlan , Andrey Shkoporov , Catherine Stanton , Ines Thiele , Igor Tolstoy , Jens Walter , Bo Yang , Natalia Yutin , Alexandra Zhernakova , Hub Zwart , Auteur inconnu , Joël Doré , R Paul Ross

Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape.

Nature communications

Avec: Gonçalo J Piedade , Max E Schön , Cédric Lood , Mikhail V Fofanov , Ella M Wesdorp , Tristan E G Biggs , Lingyi Wu , Henk Bolhuis , Matthias G Fischer , Natalya Yutin , Bas E Dutilh , Corina P D Brussaard

Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020).

Archives of virology

Avec: Peter J Walker , Stuart G Siddell , Elliot J Lefkowitz , Arcady R Mushegian , Evelien M Adriaenssens , Donald M Dempsey , Bas E Dutilh , Balázs Harrach , Robert L Harrison , R Curtis Hendrickson , Sandra Junglen , Nick J Knowles , Andrew M Kropinski , Mart Krupovic , Jens H Kuhn , Max Nibert , Richard J Orton , Luisa Rubino , Sead Sabanadzovic , Peter Simmonds , Donald B Smith , Arvind Varsani , Francisco Murilo Zerbini , Andrew J Davison

Correction to: Binomial nomenclature for virus species: a consultation.

Archives of virology

Avec: Stuart G Siddell , Peter J Walker , Elliot J Lefkowitz , Arcady R Mushegian , Bas E Dutilh , Balázs Harrach , Robert L Harrison , Sandra Junglen , Nick J Knowles , Andrew M Kropinski , Mart Krupovic , Jens H Kuhn , Max L Nibert , Luisa Rubino , Sead Sabanadzovic , Peter Simmonds , Arvind Varsani , Francisco Murilo Zerbini , Andrew J Davison

Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity.

BMC genomics

Avec: Amber C A Hendriks , Frans A G Reubsaet , A M D Mirjam Kooistra-Smid , John W A Rossen , Bas E Dutilh , Aldert L Zomer , Maaike J C van den Beld , Auteur inconnu

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.

Archives of virology

Avec: Evelien M Adriaenssens , Matthew B Sullivan , Petar Knezevic , Leonardo J van Zyl , B L Sarkar , Bas E Dutilh , Poliane Alfenas-Zerbini , Małgorzata Łobocka , Yigang Tong , James Rodney Brister , Andrea I Moreno Switt , Jochen Klumpp , Ramy Karam Aziz , Jakub Barylski , Jumpei Uchiyama , Rob A Edwards , Andrew M Kropinski , Nicola K Petty , Martha R J Clokie , Alla I Kushkina , Vera V Morozova , Siobain Duffy , Annika Gillis , Janis Rumnieks , İpek Kurtböke , Nina Chanishvili , Lawrence Goodridge , Johannes Wittmann , Rob Lavigne , Ho Bin Jang , David Prangishvili , Francois Enault , Dann Turner , Minna M Poranen , Hanna M Oksanen , Mart Krupovic

Binomial nomenclature for virus species: a consultation.

Archives of virology

Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype.

Bioinformatics (Oxford, England)

Avec: Bojian Yin , Marleen Balvert , Rick A A van der Spek , Bas E Dutilh , Sander Bohté , Jan Veldink , Alexander Schönhuth

Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019).

Archives of virology

Avec: Peter J Walker , Stuart G Siddell , Elliot J Lefkowitz , Arcady R Mushegian , Donald M Dempsey , Bas E Dutilh , Balázs Harrach , Robert L Harrison , R Curtis Hendrickson , Sandra Junglen , Nick J Knowles , Andrew M Kropinski , Mart Krupovic , Jens H Kuhn , Max Nibert , Luisa Rubino , Sead Sabanadzovic , Peter Simmonds , Arvind Varsani , Francisco Murilo Zerbini , Andrew J Davison

Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018).

Archives of virology

Avec: Stuart G Siddell , Peter J Walker , Elliot J Lefkowitz , Arcady R Mushegian , Michael J Adams , Bas E Dutilh , Alexander E Gorbalenya , Balázs Harrach , Robert L Harrison , Sandra Junglen , Nick J Knowles , Andrew M Kropinski , Mart Krupovic , Jens H Kuhn , Max Nibert , Luisa Rubino , Sead Sabanadzovic , Hélène Sanfaçon , Peter Simmonds , Arvind Varsani , Francisco Murilo Zerbini , Andrew J Davison

Differentiating between viruses and virus species by writing their names correctly.

Archives of virology

Avec: Francisco Murilo Zerbini , Stuart G Siddell , Arcady R Mushegian , Peter J Walker , Elliot J Lefkowitz , Evelien M Adriaenssens , Poliane Alfenas-Zerbini , Bas E Dutilh , María Laura García , Sandra Junglen , Mart Krupovic , Jens H Kuhn , Amy J Lambert , Małgorzata Łobocka , Hanna M Oksanen , David L Robertson , Luisa Rubino , Sead Sabanadzovic , Peter Simmonds , Nobuhiro Suzuki , Koenraad Van Doorslaer , Anne-Mieke Vandamme , Arvind Varsani

Lifestyle of sponge symbiont phages by host prediction and correlative microscopy.

The ISME journal

Avec: M T Jahn , T Lachnit , S M Markert , C Stigloher , L Pita , M Ribes , B E Dutilh , U Hentschel

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters.

Environmental microbiology

Avec: Daan M van Vliet , F A Bastiaan von Meijenfeldt , Bas E Dutilh , Laura Villanueva , Jaap S Sinninghe Damsté , Alfons J M Stams , Irene Sánchez-Andrea

Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks.

Water research

Avec: I Douterelo , B E Dutilh , C Calero , E Rosales , K Martin , S Husband

Evolutionary Study of the Crassphage Virus at Gene Level.

Viruses

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

The human gut microbiome and health inequities.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Katherine R Amato , Marie-Claire Arrieta , Meghan B Azad , Michael T Bailey , Josiane L Broussard , Carlijn E Bruggeling , Erika C Claud , Elizabeth K Costello , Emily R Davenport , Bas E Dutilh , Holly A Swain Ewald , Paul Ewald , Erin C Hanlon , Wrenetha Julion , Ali Keshavarzian , Corinne F Maurice , Gregory E Miller , Geoffrey A Preidis , Laure Segurel , Burton Singer , Sathish Subramanian , Liping Zhao , Christopher W Kuzawa

Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021.

Archives of virology

Avec: Mart Krupovic , Dann Turner , Vera Morozova , Mike Dyall-Smith , Hanna M Oksanen , Rob Edwards , Bas E Dutilh , Susan M Lehman , Alejandro Reyes , Diana P Baquero , Matthew B Sullivan , Jumpei Uchiyama , Jesca Nakavuma , Jakub Barylski , Mark J Young , Shishen Du , Poliane Alfenas-Zerbini , Alla Kushkina , Andrew M Kropinski , Ipek Kurtböke , J Rodney Brister , Cédric Lood , B L Sarkar , Tong Yigang , Ying Liu , Li Huang , Johannes Wittmann , Nina Chanishvili , Leonardo J van Zyl , Janis Rumnieks , Tomohiro Mochizuki , Matti Jalasvuori , Ramy K Aziz , Małgorzata Łobocka , Kenneth M Stedman , Andrey N Shkoporov , Annika Gillis , Xu Peng , François Enault , Petar Knezevic , Rob Lavigne , Sung-Keun Rhee , Virginija Cvirkaite-Krupovic , Cristina Moraru , Andrea I Moreno Switt , Minna M Poranen , Andrew Millard , David Prangishvili , Evelien M Adriaenssens

Growth rate is a dominant factor predicting the rhizosphere effect.

The ISME journal

Avec: José L López , Arista Fourie , Sanne W M Poppeliers , Nikolaos Pappas , Juan J Sánchez-Gil , Ronnie de Jonge , Bas E Dutilh

Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis.

Journal of Crohn's & colitis

Avec: Carlijn E Bruggeling , Maarten Te Groen , Daniel R Garza , Famke van Heeckeren Tot Overlaer , Joyce P M Krekels , Basma-Chick Sulaiman , Davy Karel , Athreyu Rulof , Anne R Schaaphok , Daniel L A H Hornikx , Iris D Nagtegaal , Bas E Dutilh , Frank Hoentjen , Annemarie Boleij

Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV).

The Journal of general virology

Avec: Stuart G Siddell , Donald B Smith , Evelien Adriaenssens , Poliane Alfenas-Zerbini , Bas E Dutilh , Maria Laura Garcia , Sandra Junglen , Mart Krupovic , Jens H Kuhn , Amy J Lambert , Elliot J Lefkowitz , Małgorzata Łobocka , Arcady R Mushegian , Hanna M Oksanen , David L Robertson , Luisa Rubino , Sead Sabanadzovic , Peter Simmonds , Nobuhiro Suzuki , Koenraad Van Doorslaer , Anne-Mieke Vandamme , Arvind Varsani , F Murilo Zerbini

Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee.

Archives of virology

Avec: Dann Turner , Andrey N Shkoporov , Cédric Lood , Andrew D Millard , Bas E Dutilh , Poliane Alfenas-Zerbini , Leonardo J van Zyl , Ramy K Aziz , Hanna M Oksanen , Minna M Poranen , Andrew M Kropinski , Jakub Barylski , J Rodney Brister , Nina Chanisvili , Rob A Edwards , François Enault , Annika Gillis , Petar Knezevic , Mart Krupovic , Ipek Kurtböke , Alla Kushkina , Rob Lavigne , Susan Lehman , Malgorzata Lobocka , Cristina Moraru , Andrea Moreno Switt , Vera Morozova , Jesca Nakavuma , Alejandro Reyes Muñoz , Jānis Rūmnieks , B L Sarkar , Matthew B Sullivan , Jumpei Uchiyama , Johannes Wittmann , Tong Yigang , Evelien M Adriaenssens

Graphite: painting genomes using a colored de Bruijn graph.

NAR genomics and bioinformatics

Avec: Rick Beeloo , Aldert L Zomer , Sebastian Deorowicz , Bas E Dutilh

OGRE: Overlap Graph-based metagenomic Read clustEring.

Bioinformatics (Oxford, England)

Avec: Marleen Balvert , Xiao Luo , Ernestina Hauptfeld , Alexander Schönhuth , Bas E Dutilh

Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts.

iScience

Avec: Patrick A de Jonge , F A Bastiaan von Meijenfeldt , Ana Rita Costa , Franklin L Nobrega , Stan J J Brouns , Bas E Dutilh

Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia.

Microbial ecology

Avec: Juline M Walter , Felipe H Coutinho , Luciana Leomil , Paulo I Hargreaves , Mariana E Campeão , Verônica V Vieira , Beatriz S Silva , Giovana O Fistarol , Paulo S Salomon , Tomoo Sawabe , Sayaka Mino , Masashi Hosokawa , Hideaki Miyashita , Fumito Maruyama , Marcel C van Verk , Bas E Dutilh , Cristiane C Thompson , Fabiano L Thompson

Microsatellite instability screening in colorectal adenomas to detect Lynch syndrome patients? A systematic review and meta-analysis.

European journal of human genetics : EJHG

Avec: Parag D Dabir , Carlijn E Bruggeling , Rachel S van der Post , Bas E Dutilh , Nicoline Hoogerbrugge , Marjolijn J L Ligtenberg , Annemarie Boleij , Iris D Nagtegaal

The Third Annual Meeting of the European Virus Bioinformatics Center.

Viruses

Avec: Franziska Hufsky , Bashar Ibrahim , Sejal Modha , Martha R J Clokie , Stefanie Deinhardt-Emmer , Bas E Dutilh , Samantha Lycett , Peter Simmonds , Volker Thiel , Aare Abroi , Evelien M Adriaenssens , Marina Escalera-Zamudio , Jenna Nicole Kelly , Kevin Lamkiewicz , Lu Lu , Julian Susat , Thomas Sicheritz , David L Robertson , Manja Marz

Marine DNA Viral Macro- and Microdiversity from Pole to Pole.

Cell

Avec: Ann C Gregory , Ahmed A Zayed , Nádia Conceição-Neto , Ben Temperton , Ben Bolduc , Adriana Alberti , Mathieu Ardyna , Ksenia Arkhipova , Margaux Carmichael , Corinne Cruaud , Céline Dimier , Guillermo Domínguez-Huerta , Joannie Ferland , Stefanie Kandels , Yunxiao Liu , Claudie Marec , Stéphane Pesant , Marc Picheral , Sergey Pisarev , Julie Poulain , Jean-Éric Tremblay , Dean Vik , Auteur inconnu , Marcel Babin , Chris Bowler , Alexander I Culley , Colomban de Vargas , Bas E Dutilh , Daniele Iudicone , Lee Karp-Boss , Simon Roux , Shinichi Sunagawa , Patrick Wincker , Matthew B Sullivan

ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics.

Viruses

Avec: Winfried Goettsch , Niko Beerenwinkel , Li Deng , Lars Dölken , Bas E Dutilh , Florian Erhard , Lars Kaderali , Max von Kleist , Roland Marquet , Jelle Matthijnssens , Shawna McCallin , Dino McMahon , Thomas Rattei , Ronald P Van Rij , David L Robertson , Martin Schwemmle , Noam Stern-Ginossar , Manja Marz

Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids.

The ISME journal

Avec: Laura Villanueva , F A Bastiaan von Meijenfeldt , Alexander B Westbye , Subhash Yadav , Ellen C Hopmans , Bas E Dutilh , Jaap S Sinninghe Damsté

Growth rate alterations of human colorectal cancer cells by 157 gut bacteria.

Gut microbes

Avec: Rahwa Taddese , Daniel R Garza , Lilian N Ruiter , Marien I de Jonge , Clara Belzer , Steven Aalvink , Iris D Nagtegaal , Bas E Dutilh , Annemarie Boleij

High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems.

Current biology : CB

Avec: Sean Meaden , Ambarish Biswas , Ksenia Arkhipova , Sergio E Morales , Bas E Dutilh , Edze R Westra , Peter C Fineran

Perspective on taxonomic classification of uncultivated viruses.

Current opinion in virology

Avec: Bas E Dutilh , Arvind Varsani , Yigang Tong , Peter Simmonds , Sead Sabanadzovic , Luisa Rubino , Simon Roux , Alejandro Reyes Muñoz , Cédric Lood , Elliot J Lefkowitz , Jens H Kuhn , Mart Krupovic , Robert A Edwards , J Rodney Brister , Evelien M Adriaenssens , Matthew B Sullivan

RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.

Patterns (New York, N.Y.)

Avec: Felipe Hernandes Coutinho , Asier Zaragoza-Solas , Mario López-Pérez , Jakub Barylski , Andrzej Zielezinski , Bas E Dutilh , Robert Edwards , Francisco Rodriguez-Valera

Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons.

Viruses

Avec: Liliane S Oliveira , Alejandro Reyes , Bas E Dutilh , Arthur Gruber

A social niche breadth score reveals niche range strategies of generalists and specialists.

Nature ecology & evolution

Avec: F A Bastiaan von Meijenfeldt , Paulien Hogeweg , Bas E Dutilh

Guidance for creating individual and batch latinized binomial virus species names.

The Journal of general virology

Avec: Thomas S Postler , Luisa Rubino , Evelien M Adriaenssens , Bas E Dutilh , Balázs Harrach , Sandra Junglen , Andrew M Kropinski , Mart Krupovic , Jiro Wada , Anya Crane , Jens H Kuhn , Arcady Mushegian , Jānis Rūmnieks , Sead Sabanadzovic , Peter Simmonds , Arvind Varsani , F Murilo Zerbini , Julie Callanan , Lorraine A Draper , Colin Hill , Stephen R Stockdale

Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Aldert Zomer , Colin J Ingham , F A Bastiaan von Meijenfeldt , Álvaro Escobar Doncel , Gea T van de Kerkhof , Raditijo Hamidjaja , Sanne Schouten , Lukas Schertel , Karin H Müller , Laura Catón , Richard L Hahnke , Henk Bolhuis , Silvia Vignolini , Bas E Dutilh

Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages.

Viruses

Avec: Patrick A de Jonge , F A Bastiaan von Meijenfeldt , Laura E van Rooijen , Stan J J Brouns , Bas E Dutilh

Modelling the influence of environmental parameters over marine planktonic microbial communities using artificial neural networks.

The Science of the total environment

Avec: F H Coutinho , C C Thompson , A S Cabral , R Paranhos , B E Dutilh , F L Thompson

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Nature biotechnology

Avec: Simon Roux , Evelien M Adriaenssens , Bas E Dutilh , Eugene V Koonin , Andrew M Kropinski , Mart Krupovic , Jens H Kuhn , Rob Lavigne , J Rodney Brister , Arvind Varsani , Clara Amid , Ramy K Aziz , Seth R Bordenstein , Peer Bork , Mya Breitbart , Guy R Cochrane , Rebecca A Daly , Christelle Desnues , Melissa B Duhaime , Joanne B Emerson , François Enault , Jed A Fuhrman , Pascal Hingamp , Philip Hugenholtz , Bonnie L Hurwitz , Natalia N Ivanova , Jessica M Labonté , Kyung-Bum Lee , Rex R Malmstrom , Manuel Martinez-Garcia , Ilene Karsch Mizrachi , Hiroyuki Ogata , David Páez-Espino , Marie-Agnès Petit , Catherine Putonti , Thomas Rattei , Alejandro Reyes , Francisco Rodriguez-Valera , Karyna Rosario , Lynn Schriml , Frederik Schulz , Grieg F Steward , Matthew B Sullivan , Shinichi Sunagawa , Curtis A Suttle , Ben Temperton , Susannah G Tringe , Rebecca Vega Thurber , Nicole S Webster , Katrine L Whiteson , Steven W Wilhelm , K Eric Wommack , Tanja Woyke , Kelly C Wrighton , Pelin Yilmaz , Takashi Yoshida , Mark J Young , Natalya Yutin , Lisa Zeigler Allen , Nikos C Kyrpides , Emiley A Eloe-Fadrosh

Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia.

Journal of global antimicrobial resistance

Avec: Lidya Chaidir , Carolien Ruesen , Bas E Dutilh , Ahmad R Ganiem , Anggriani Andryani , Lika Apriani , Martijn A Huynen , Rovina Ruslami , Philip C Hill , Reinout van Crevel , Bachti Alisjahbana

A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion.

Cell host & microbe

Avec: Martin T Jahn , Ksenia Arkhipova , Sebastian M Markert , Christian Stigloher , Tim Lachnit , Lucia Pita , Anne Kupczok , Marta Ribes , Stephanie T Stengel , Philip Rosenstiel , Bas E Dutilh , Ute Hentschel

Microbial diversity, ecological networks and functional traits associated to materials used in drinking water distribution systems.

Water research

Avec: I Douterelo , B E Dutilh , K Arkhipova , C Calero , S Husband

Eleven grand challenges in single-cell data science.

Genome biology

Avec: David Lähnemann , Johannes Köster , Ewa Szczurek , Davis J McCarthy , Stephanie C Hicks , Mark D Robinson , Catalina A Vallejos , Kieran R Campbell , Niko Beerenwinkel , Ahmed Mahfouz , Luca Pinello , Pavel Skums , Alexandros Stamatakis , Camille Stephan-Otto Attolini , Samuel Aparicio , Jasmijn Baaijens , Marleen Balvert , Buys de Barbanson , Antonio Cappuccio , Giacomo Corleone , Bas E Dutilh , Maria Florescu , Victor Guryev , Rens Holmer , Katharina Jahn , Thamar Jessurun Lobo , Emma M Keizer , Indu Khatri , Szymon M Kielbasa , Jan O Korbel , Alexey M Kozlov , Tzu-Hao Kuo , Boudewijn P F Lelieveldt , Ion I Mandoiu , John C Marioni , Tobias Marschall , Felix Mölder , Amir Niknejad , Alicja Rączkowska , Marcel Reinders , Jeroen de Ridder , Antoine-Emmanuel Saliba , Antonios Somarakis , Oliver Stegle , Fabian J Theis , Huan Yang , Alex Zelikovsky , Alice C McHardy , Benjamin J Raphael , Sohrab P Shah , Alexander Schönhuth

Metabolic models predict bacterial passengers in colorectal cancer.

Cancer & metabolism

Avec: Daniel R Garza , Rahwa Taddese , Jakob Wirbel , Georg Zeller , Annemarie Boleij , Martijn A Huynen , Bas E Dutilh

Production of inactivated gram-positive and gram-negative species with preserved cellular morphology and integrity.

Journal of microbiological methods

Avec: Rahwa Taddese , Clara Belzer , Steven Aalvink , Marien I de Jonge , Iris D Nagtegaal , Bas E Dutilh , Annemarie Boleij

Stability of the human gut virome and effect of gluten-free diet.

Cell reports

Avec: Sanzhima Garmaeva , Anastasia Gulyaeva , Trishla Sinha , Andrey N Shkoporov , Adam G Clooney , Stephen R Stockdale , Johanne E Spreckels , Thomas D S Sutton , Lorraine A Draper , Bas E Dutilh , Cisca Wijmenga , Alexander Kurilshikov , Jingyuan Fu , Colin Hill , Alexandra Zhernakova

Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions.

Journal of virology

Avec: Patrick A de Jonge , Dieuwke J C Smit Sibinga , Oliver A Boright , Ana Rita Costa , Franklin L Nobrega , Stan J J Brouns , Bas E Dutilh

Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain.

eLife

Avec: Michael Sheinman , Ksenia Arkhipova , Peter F Arndt , Bas E Dutilh , Rutger Hermsen , Florian Massip

Optimized bacterial DNA isolation method for microbiome analysis of human tissues.

MicrobiologyOpen

Avec: Carlijn E Bruggeling , Daniel R Garza , Soumia Achouiti , Wouter Mes , Bas E Dutilh , Annemarie Boleij

Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021).

Archives of virology

Avec: Peter J Walker , Stuart G Siddell , Elliot J Lefkowitz , Arcady R Mushegian , Evelien M Adriaenssens , Poliane Alfenas-Zerbini , Andrew J Davison , Donald M Dempsey , Bas E Dutilh , María Laura García , Balázs Harrach , Robert L Harrison , R Curtis Hendrickson , Sandra Junglen , Nick J Knowles , Mart Krupovic , Jens H Kuhn , Amy J Lambert , Małgorzata Łobocka , Max L Nibert , Hanna M Oksanen , Richard J Orton , David L Robertson , Luisa Rubino , Sead Sabanadzovic , Peter Simmonds , Donald B Smith , Nobuhiro Suzuki , Koenraad Van Dooerslaer , Anne-Mieke Vandamme , Arvind Varsani , Francisco Murilo Zerbini

Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces.

Nature communications

Avec: Piotr Rozwalak , Jakub Barylski , Yasas Wijesekara , Bas E Dutilh , Andrzej Zielezinski

A metagenomic portrait of the microbial community responsible for two decades of bioremediation of poly-contaminated groundwater.

Water research

Avec: Ernestina Hauptfeld , Jordi Pelkmans , Terry T Huisman , Armin Anocic , Basten L Snoek , F A Bastiaan von Meijenfeldt , Jan Gerritse , Johan van Leeuwen , Gert Leurink , Arie van Lit , Ruud van Uffelen , Margot C Koster , Bas E Dutilh

Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome.

Nature communications

Avec: Patrick A de Jonge , Koen Wortelboer , Torsten P M Scheithauer , Bert-Jan H van den Born , Aeilko H Zwinderman , Franklin L Nobrega , Bas E Dutilh , Max Nieuwdorp , Hilde Herrema

Réseau de co-auteurs

Mart Krupovic 17 collaborations

Jens H Kuhn 14 collaborations

Peter Simmonds 14 collaborations

Evelien M Adriaenssens 13 collaborations

Arvind Varsani 13 collaborations

Luisa Rubino 12 collaborations

Sead Sabanadzovic 12 collaborations

Andrew M Kropinski 11 collaborations

Elliot J Lefkowitz 11 collaborations

Sandra Junglen 11 collaborations

F A Bastiaan von Meijenfeldt 10 collaborations

Stuart G Siddell 10 collaborations

Arcady R Mushegian 10 collaborations

Hanna M Oksanen 9 collaborations

Francisco Murilo Zerbini 9 collaborations

Peter J Walker 8 collaborations

Poliane Alfenas-Zerbini 8 collaborations

Matthew B Sullivan 7 collaborations

Annemarie Boleij 7 collaborations

Małgorzata Łobocka 7 collaborations

David L Robertson 7 collaborations

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Stan J J Brouns 6 collaborations

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Rob Lavigne 6 collaborations

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Ksenia Arkhipova 5 collaborations

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Donald M Dempsey 5 collaborations

R Curtis Hendrickson 5 collaborations

Amy J Lambert 5 collaborations

Donald B Smith 5 collaborations

Nobuhiro Suzuki 5 collaborations

Anne-Mieke Vandamme 5 collaborations

B E Dutilh 5 collaborations

Felipe H Coutinho 4 collaborations

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None None 3 collaborations

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