Ecological genomics is a new scientific discipline, which studies ecological complexity, nutrient cycles, life-history patterns and responses of organisms to environmental stress at the genomic level. Analysis of environmental genomes will improve our understanding of ecosystem functions and biodiversity and may help to define and measure environmental quality. This course is intended for those just embarking on genomics within an ecological setting and teaches the fundamentals of the discipline, while concentrating on ecological questions. The course will focus on four topics, each of which is treated by introductory lectures, assignments, case studies and student presentations.

This course is organised by Prof Dr. Nico M. van Straalen.

Monday, February 18th
09.00 – 09:30 Arrival, coffee
09.30 – 10:00 Welcome, introduction Nico van Straalen, Hauke Smidt
10.00 – 10:45 The purpose and approach of ecological genomics Nico van Straalen
Session on comparative genomics and phylogeny
Chair: N.M. van Straalen
11.00 – 12.45 Comparative genomics and phylogenomics Bas Dutilh (CMBI, Nijmegen)
13.00 – 14.00 Lunch
14.00 – 15.45 Phylogenetics and speciation Martijn Timmermans (Imperial College, London)
15.45 – 16.00 Tea
16.00 – 17.00 Discussion All

18.00 – 19.00 Dinner
19.30 – 20.30 Porky genomics and the ecology of pigs Martien Groenen (Wageningen University)

Tuesday, February 19th
Session on metagenomics and microbial ecology
Chair: Hauke Smidt
09.00 – 10.45 Systems biology of microbial communities Bas Teusink (VU, Amsterdam)
10.45 – 11.15 Coffee
11.15 – 13.00 Microbial communities analyzed by genomics methods George Kowalchuk (NIOO)
13.00 – 14.00 Lunch
14.00 – 15.45 Genomics and biogeochemical cycles Christa Schleper (University of Vienna)
15.45 – 16.00 Tea
16.00 – 17.00 Discussion All

18.00 – 19.00 Dinner
19.30 – 20.30 Genomics and human identity Hub Zwart (Radboud University)

Wednesday, February 20th
09.00 – 12.30 Computer exercises; analyses of microarray data Mark van Passel, Hauke Smidt, Nico van Straalen
13.00 – 14.00 Lunch
14.00 – 15.30 Computer exercises; analyses of microarray data All
15.40 – 16.00 Tea
16.00 – 18.00 Presentations by participants All

18.00 – 19.00 Dinner
19.30 – 22.00 Presentations by participants All

Thursday, February 21th
Session on genomics of life-histories and population biology
Chair: Jan Kammenga
09.00 – 10.45 Functional genomics of phenotypic plasticity Jan Kammenga (Wageningen UR)
10.45 – 11.15 Coffee
11.15 – 13.00 Genomics basis for evolution and speciation in birds John Stinchcombe (Toronto University)
13.00 – 14.00 Lunch
14.00 – 14.45 Genomics analysis of species interactions Bregje Wertheim (Groningen University)
15.45 – 16.00 Tea
16.00 – 17.00 Discussion All

18.00 – 19.00 Dinner
19.30 – 20.30 Prospects for the validation of ecogenomic tools Bram Brouwer (BDS)

Friday, February 22nd
Session on genomics of stress responses and toxicogenomic risk assessment
Chair: Dick Roelofs
09.00 – 10.45 Toxicogenomics in the zebrafish Jessica Legradi (VU, Amsterdam)
10.45 – 11.15 Coffee
11.15 – 13.00 Stress responses and systems toxicology Peter Kille (University of Cardiff, UK)
13.00 – 14.00 Lunch
14.00 – 15.00 Discussion All
15.00 – 15.30 Summary, goodbye Nico van Straalen, Hauke Smidt

- Prof.dr. Nico M. van Straalen, Department of Ecological Science, VU University Amsterdam
- Prof.dr.ir. Hauke Smidt, Department of Microbiology, Wageningen University
- Dr. Bas Dutilh, Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen
- Prof.dr. Bas Teusink, Department of Integrative Bioinformatics, VU University Amsterdam
- Dr.ir. Martijn Timmermans, Division of Ecology and Evolution, Imperial College, London
- Prof.dr. Martien A.M. Groenen, Animal Breeding and Genomics Centre, Wageningen University
- Prof.dr. George Kowalchuk, Department of Microbiology, Netherlands Institute of Ecology, Wageningen
- Prof.dr. Christa Schleper, Department of Genetics in Ecology, University of Vienna
- Prof.dr. Hub Zwart, Centre for Society and the Life Sciences, Radboud University Nijmegen
- Dr. ir. Jan Kammenga, Department of Nematology, Wageningen University
- Dr. John Stinchcombe, Department of Ecology and Evolutionary Biology, Toronto University
- Dr. Bregje Wertheim, Department of Evolutionary Genetics, University of Groningen
- Prof.dr. Bram Brouwer, Biodetection Systems, Amsterdam
- Dr.ir. Dick Roelofs, Department of Ecological Science, VU University Amsterdam
- Dr.ir. Jessica Legradi, Institute for Environmental Studies, VU University Amsterdam
- Dr. Peter Kille, School of Biosciences, Cardiff University

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