SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. - Bernd W. Brandt; Jaap Heringa; Jack A. M. Leunissen (Nucleic Acids Res., 2008)

Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data. - Alexander E. Ivliev; Peter A. C. 't Hoen; Michel P. Villerius; Johan T. den Dunnen; Bernd W. Brandt (Nucleic Acids Res., 2008)

webPRC: the Profile Comparer for alignment-based searching of public domain databases. - Bernd W. Brandt; Jaap Heringa (Nucleic Acids Res., 2009)

PhyloPars: estimation of missing parameter values using phylogeny. - Jorn Bruggeman; Jaap Heringa; Bernd W. Brandt (Nucleic Acids Res., 2009)

Multi-Harmony: detecting functional specificity from sequence alignment. - Bernd W. Brandt; K. Anton Feenstra; Jaap Heringa (Nucleic Acids Res., 2010)

Protein analysis tools and services at IBIVU. - Bernd W. Brandt; Jaap Heringa (J. Integr. Bioinform., 2011)

Comparing clustering and pre-processing in taxonomy analysis. - Marc J. Bonder; Sanne Abeln; Egija Zaura; Bernd W. Brandt (Bioinform., 2012)

TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage. - Bernd W. Brandt; Marc J. Bonder; Susan M. Huse; Egija Zaura (Nucleic Acids Res., 2012)

Towards a database for genotype-phenotype association research: mining data from encyclopaedia. - Vesna Pajic; Gordana Pavlovic-Lazetic; Milos V. Beljanski; Bernd W. Brandt; Milos Pajic (Int. J. Data Min. Bioinform., 2013)

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. - Ali May; Sanne Abeln; Wim Crielaard; Jaap Heringa; Bernd W. Brandt (Bioinform., 2014)

A web server for protein-protein interaction network querying. - Mohammed El-Kebir; Bernd W. Brandt; Jaap Heringa; Gunnar W. Klau (BMC Syst. Biol., 2014)

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL. - Ali May; Sanne Abeln; Mark J. Buijs; Jaap Heringa; Wim Crielaard; Bernd W. Brandt (Nucleic Acids Res., 2015)

metaModules identifies key functional subnetworks in microbiome-related disease. - Ali May; Bernd W. Brandt; Mohammed El-Kebir; Gunnar W. Klau; Egija Zaura; Wim Crielaard; Jaap Heringa; Sanne Abeln (Bioinform., 2016)

A new approach to describe the taxonomic structure of microbiome and its application to assess the relationship between microbial niches. - Vincent Y. Pappalardo; Leyla Azarang; Egija Zaura; Bernd W. Brandt; Renée X. de Menezes (BMC Bioinform., 2024)