Comparative Genomics

Prof. Dr. Martijn Huynen  
CMBI
Tel. +31 24 3619543
E-mail: M.Huynen@cmbi.ru.nl

Introduction

The sequencing of complete genomes raises the question: how do we show that a genome is more than the sum of its genes ?, or, how do the proteins encoded in these genomes interact with each other to produce cells and phenotypes ? The core research focus of the Huynen group is to predict such functional interactions between proteins as there exist e.g. in metabolic pathways, signalling pathways or protein complexes.

On the one hand we develop computational genomics techniques that exploit the information in sequenced genomes and functional genomics data, like mRNA expression and protein-protein interactions, to make such predictions. Techniques that are used for this are sequence analysis tools for the prediction of homology and orthology, in combination with tools that combine the data for various sequenced genomes and functional genomics datasets with each other to make predictions about specific pathways. In this we collaborate with the computational biology department at the EMBL (Bork group).

On the other hand we make specific, testable predictions about pathways and the functions of proteins therein. For the latter we are directing our attention to systems that are relevant to the research at the RU/UMC, thus exploiting the possibilities there are for experimental testing of our predictions. As part of this we are presently using computational genomics to predict pathways and protein functions in the mitochondria. A specific example is a study on the likely interaction partners of frataxin. Frataxin is a well-known disease gene (Friedreich's ataxia) whose function has remained elusive despite more than six years of intensive experimental research. Using computational genomics we have shown that frataxin is likely involved in iron-sulfur cluster assembly in conjunction with the co-chaperone HscB/JAC1. We have also identified the complete eukaryotic protein set that has been derived from the alpha-proteobacteria, and that are mainly functioning in the mitochondria to predict pathways among these. Other examples include the prediction of a new protein interaction with Complex I (B17.2l), which was subsequently experimentally corroborated.

 We are also very much interested i n the evolution of the eukaryotic cell and in the origin and evolution of organelles like the mitochondria and the peroxisomes. The latter have often been hypothesized to be of "endosymbiotic" origin. However, based on our analyses they can be shown not to have an independent origin, but to have arisen fro the Endplasmic Reticulum.

Student projects

Biology, Molecular Life Sciences, Chemistry, Natural Sciences and Informatics students can do a research project at the CMBI. Some examples within the Computational Genomics group are described below.
Proteomics of mitochondria.
Prediction of protein interaction from genome data.

Team members

Martijn A. Huynen, group leader

Bas E. Dutilh, Postdoc

Daniel Garza, Postdoc

Wynand Alkema, Postdoc

Anneke Sijbers, Postdoc 

Selma van Esveld, PhD student

Lisette Meerstein-van Kessel; PhD student

Carolien Ruesen; PhD student

Felipe Coutinho, visiting PhD student

Edwin Ardiansyah, student

Emma Vos, student 

Joeri van Strien, student

Kai Francke, student 

 



Former team members

Staff 

Edwin Lasonder

Postdocs

Robin van der Lee 

John van Dam

Richard Notebaart

Radek Szklarczyk

Shivakumar Keerthikumar

Thijs Ettema

Juan Antonio Gabaldon Estevan

René van der Heijden

Rasa Jurgelenaite

Urszula Kudla

Martin Oti

Ludo Pagie

Joanna Parmley

Sergio Rossell

Berend Snel

PhD students

Robin van der Lee 

Dei Martinez Elurbe 

Xiaowen Lu

Rob ter Horst

Wout Megchelenbrink 

Isabel Duarte

Tim Hulsen

Philip Kensche

Fiona Nielsen

Isiah Sama

Vera van Noort

Jeroen van Reeuwijk

Guénola Ricard

Students

Ronald Duim, 2017 

Veerle van Winden, 2017 

Sebastian Muraru, 2017

Ilja van Hoek, 2016 

Cenna van Manen, 2016 

Stephanie Cornelis, 2016 

Mark Schuurman, 2015

Sarah Stolle

Emily Cadot

Bas van Gestel

Gonny Velemans

Clive Michelo

Jakob Goldman

Jonas Falck 

Lucas Brouwers, 2009

Luiz Canalle, 2003

Qian Cheng, 2010

Thomas Cuijpers, 2009

Evy van Damme, 2006

Ana Freitas, 2009

Ying He, 2007

Walter Hoolwerf, 2003 

Leo Jacobs,  2006

Mark Jans, 2003 

Gera Jellema

Maarten Kooyman, 2008

Sjoerd Paans, 2006

Daphne Rainey, 2003

Andreia Reis, 2009

Edouard Severing

Frank van Zimmeren, 2003