PhD students
Bastiaan von Meijenfeldt 2015-201? Ecological modeling
Patrick de jonge 2015-201? Phage-host interactions
Rahwa Taddese 2015-201? Colorectal cancer microbiology
Diego Cambuy 2014-201? Metagenomic virus discovery
Daniel Garza 2014-201? Reverse engineering of bacterial phenotypes
Daan Speth 2013-201? Metagenomics of anammox wastewater treatment plant
Felipe Coutinho 2013-201? Marine metagenomics
Juline Walter 2012-201? Marine metagenomics
Pedro Meirelles 2012-201? Marine metagenomics
Genivaldo G.Z. Silva 2014-201? FOCUS
 Genivaldo G.Z. Silva, Daniel A. Cuevas, Bas E. Dutilh and Robert A. Edwards (2014)
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares
PeerJ 2: e425.
Carolien Ruesen 2014 Comparative genomics of Mycobacterium tuberculosis
Adriana Fróes 2013-2014 Marine metagenomics
Silke Appenzeller 2013 Euroclonality
Master and Bachelor students
Please contact me if you want to do a student project: .
Jard de Vries 2014 Functional analysis of metagenomes
Genivaldo G.Z. Silva 2011-2013 Scaffold builder
 Genivaldo G.Z. Silva, Bas E. Dutilh, T. David Matthews, Keri Elkins, Robert Schmieder, Elizabeth A. Dinsdale and Robert A. Edwards (2013)
Combining de novo and reference-guided assembly with Scaffold_builder
Source Code for Biology and Medicine 8: 23.
Mark Schuurman 2013-2014 Coreographer
Nathalie de Wagenaar 2013 Plasmodium falciparum genome phylogeny
Haydee Garrido 2012 Virus-host prediction
Michiyo Wellington-Oguri 2011-2012 Virus-host prediction, SDSU Computer Science Class of 2012 Outstanding Graduate
Amanda C. Trindade da Silva 2011 Copper in San Diego Bay
Alexey Gritsenko 2010-2011 Scaffolding next-generation sequencing assemblies
 Alexey A. Gritsenko, Jurgen F. Nijkamp, Marcel J.T. Reinders and Dick de Ridder (2012)
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies
Bioinformatics 28: 1429-1437.
Qian Cheng 2010 Origin of mitochondrial targeting signal
Anne van der Ham 2009 Debating genomics and ancestry
Ana A. Freitas 2009 Analysis of Aspergillus fumigatus Solexa sequencing data
Lucas Brouwers 2009 Pathway signatures
Ana A. Freitas 2007-2008 Evolution of functions in the p53 family - Alignment analysis
Ying He 2007 Signature genes search tool
 Bas E. Dutilh, Ying He, Maarten L. Hekkelman and Martijn A. Huynen (2008)
Signature, a web server for taxonomic characterization of sequence samples using signature genes
Nucleic Acids Research 36 (Web Server issue): W470-W474.
Sjoerd Paans 2006-2007 A web application to identify signature genes