Assessment of phylogenomic and orthology approaches for phylogenetic inference. - Bas E. Dutilh; Vera van Noort; René T. J. M. van der Heijden; T. Boekhout; Berend Snel; Martijn A. Huynen (Bioinform., 2007)

Signature, a web server for taxonomic characterization of sequence samples using signature genes. - Bas E. Dutilh; Ying He; Maarten L. Hekkelman; Martijn A. Huynen (Nucleic Acids Res., 2008)

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. - Bas E. Dutilh; Martijn A. Huynen; Marc Strous (Bioinform., 2009)

FACIL: Fast and Accurate Genetic Code Inference and Logo. - Bas E. Dutilh; Rasa Jurgelenaite; Radek Szklarczyk; Sacha A. F. T. van Hijum; Harry R. Harhangi; Markus Schmid 002; Bart de Wild; Kees-Jan Françoijs; Henk Stunnenberg; Marc Strous; Mike S. M. Jetten; Huub J. M. Op den Camp; et al. (Bioinform., 2011)

Reference-independent comparative metagenomics using cross-assembly: crAss. - Bas E. Dutilh; Robert Schmieder; James Nulton; Ben Felts; Peter Salamon; Robert A. Edwards; John Mokili (Bioinform., 2012)

Combining de novo and reference-guided assembly with scaffold_builder. - Genivaldo Gueiros Z. Silva; Bas E. Dutilh; T. David Matthews; Keri Elkins; Robert Schmieder; Elizabeth A. Dinsdale; Robert A. Edwards (Source Code Biol. Medicine, 2013)

Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. - Qingzhen Hou; Bas E. Dutilh; Martijn A. Huynen; Jaap Heringa; K. Anton Feenstra (BMC Bioinform., 2015)

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. - Genivaldo Gueiros Z. Silva; Kevin T. Green; Bas E. Dutilh; Robert A. Edwards (Bioinform., 2016)

Metagenomic read clustering based on overlap graphs. - Marleen Balvert; Alexander Schönhuth; Bas E. Dutilh (ICCABS, 2018)

Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype. - Bojian Yin; Marleen Balvert; Rick A. A. van der Spek; Bas E. Dutilh; Sander M. Bohté; Jan Veldink; Alexander Schönhuth (Bioinform., 2019)

A Drug Recommendation System (Dr.S) for cancer cell lines. - Marleen Balvert; Georgios Patoulidis; Andrew Patti; Timo M. Deist; Christine Eyler; Bas E. Dutilh; Alexander Schönhuth; David Craft (CoRR, 2019)

12 Grand Challenges in Single-Cell Data Science. - David Laehnemann; Johannes Köster; Ewa Szczurek; Davis J. McCarthy; Stephanie C. Hicks; Mark D. Robinson; Catalina A. Vallejos; Niko Beerenwinkel; Kieran R. Campbell; Ahmed Mahfouz; Luca Pinello; Pavel Skums; et al. (PeerJ Prepr., 2019)

OGRE: Overlap Graph-based metagenomic Read clustEring. - Marleen Balvert; Xiao Luo; Ernestina Hauptfeld; Alexander Schönhuth; Bas E. Dutilh (Bioinform., 2021)

Finding functional associations between prokaryotic virus orthologous groups: a proof of concept. - Nikolaos Pappas 003; Bas E. Dutilh (BMC Bioinform., 2021)

RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content. - Felipe Hernandes Coutinho; Asier Zaragoza-Solas; Mario López-Pérez; Jakub Barylski; Andrzej Zielezinski; Bas E. Dutilh; Robert A. Edwards; Francisco Rodríguez-Valera (Patterns, 2021)

Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data. - Pilleriin Peets; Aristeidis Litos; Kai Dührkop; Daniel R. Garza; Justin J. J. van der Hooft; Sebastian Böcker; Bas E. Dutilh (J. Cheminformatics, 2025)