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

by Hrovat, Katarina, Dutilh, Bas, Medema, Marnix, Melkonian, Chrats

OGRE: Overlap Graph-based metagenomic Read clustEring

by Balvert, Marleen, Luo, Xiao, Hauptfeld, Ernestina, Schönhuth, Alexander, Dutilh, Bas E.

Improving genome-scale metabolic models of incomplete genomes with deep learning

by Boer, Meine D., Melkonian, Chrats, Zafeiropoulos, Haris, Haas, Andreas F., Garza, Daniel R., Dutilh, Bas E.

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

by Roux, Simon, Camargo, Antonio Pedro, Coutinho, Felipe Hernandes, Dabdoub, Shareef M., Dutilh, Bas E., Nayfach, Stephen, Tritt, Andrew
Published 2023-04

Lifestyle of sponge symbiont phages by host prediction and correlative microscopy

by Jahn, Martin T., Lachnit, Tim, Markert, Sebastian M., Stigloher, Christian, Pita, Lucía, Ribes, Marta, Dutilh, Bas E., Hentschel, Ute
Published 2021-01

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

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

Metagenomic sequencing of groundwater for drinking water production in the Netherlands

by Hauptfeld, Ernestina, Pappas, Nikolaos, van Iwaarden, Sandra, Snoek, Basten L., Aldas-Vargas, Andrea, Dutilh, Bas E., von Meijenfeldt, Bastiaan

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

by Hauptfeld, Ernestina, Pappas, Nikolaos, van Iwaarden, Sandra, Snoek, Basten L., Aldas-Vargas, Andrea, Dutilh, Bas E., von Meijenfeldt, Bastiaan

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters

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

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

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

A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion

by Jahn, Martin T., Arkhipova, Ksenia, Markert, Sebastian M., Stigloher, Christian, Lachnit, Tim, Pita, Lucía, Kupczok, Anne, Ribes, Marta, Stengel, Stephanie T., Rosenstiel, Philip C., Dutilh, Bas E., Hentschel, Ute
Published 2019-10

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

by Gregory, Ann C., Zayed, Ahmed A., Conceição-Neto, Nadia, Temperton, Ben, Alberti, Adriana, Ardyna, Mathieu, Arkhipova, Ksenia, Carmichael, Margaux, Cruaud, Corinne, Dimier, Céline, Domínguez-Huerta, Guillermo, Ferland, Joannie, Kandels‐Lewis, Stefanie, Liu, Yunxiao, Marec, Claudie, Pesant, Stéphane, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tremblay, J. E., Vik, Dean, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, Vargas, Colomban de, Follows, M.J., Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels‐Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulton, N.J., Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Wincker, Patrick, Culley, Alexander I., Dutilh, Bas E., Roux, Simon, Sullivan, Matthew B.
Published 2019-05

Eleven grand challenges in single-cell data science

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