CV  |  Publications  |  Teaching  |  Research  |  CNRS  |  Past activities  

Welcome to the homepage of

Karsten Suhre

 

Position until March 2011

    Professor for Bioinformatics (LMU)
    Institute of Bioinformatics and Systems Biology
    Helmholtz Zentrum München (formerly GSF)
    German Research Center for Environmental Health (GmbH)
    Ingolstaedter Landstrasse 1
    D-85764 Neuherberg

    Secr.:+49 89 3187 3581
    Fax: +49 89 3187 3538
    Homepage: http://www.suhre.fr

New location after March 2011

    Weill Cornell Medical College in Qatar
    Qatar Foundation - Education City
    PO Box 24144
    Doha, Qatar
    Mobile:+974 3354 1843
    E-mail:
    Homepage: http://qatar-weill.cornell.edu


Curriculum Vitae

09/2006 - 03/2011 Professor for Bioinformatics at the Ludwig-Maximilians-University (Faculty of Biology) in association with the Institute for Bioinformatics and Systems Biology (MIPS) at Helmholtz Zentrum München, Munich, Germany
(metabolomics)
10/2005 - 08/2006 Senior Scientist CNRS ("Directeur de Recherche") at Information Genomique & Structurale, Marseille, France
(bioinformatics and structural biology)
02/2002 - 09/2005 Scientist CNRS ("Charge de Recherche") at Information Genomique & Structurale, Marseille, France
(bioinformatics and structural biology)
26/10/2004 Habilitation bioinformatics and structural biology Université Aix-Marseille II, France [HDR thesis].
01/2000 - 01/2002 Project Engineer at Wilhelm Karmann GmbH, Osnabruck, Germany
(project management in the automobile industry, R&D department)
10/1994 - 12/1999 Scientist CNRS ("Charge de Recherche") CNRS at Laboratoire d'Aerologie, Toulouse, France
(atmospheric chemistry and meteorology modelling)
10/1993 - 09/1994 Postdoc at Laboratoire d'Aerologie (Marie-Curie fellowship)
(atmospheric chemistry and meteorology modelling)
01/1992 - 04/1994 Ph.D. Thesis at University of Toulouse, France 
(atmospheric chemistry and meteorology modelling)
10/1984 - 09/1991 Diplom Physik at University of Osnabruck, Germany 
(speciality of diploma thesis: quantum field theory) 

Vordiplom Mathematik at University of Osnabruck, Germany

10/1986 - 09/1988,
04/1989 - 09/1991
Student Assistent (46h/month) at the Computer Center of the University of Osnabruck
10/1988 - 04/1989 Exchange student at the Department of Applied Mathematics, University of Hull, England 
(fluid dynamics and partial differential equations, B.Sc. level)


Publications

2011

  • Suhre K., Wallaschofski H., RafflerJ., Friedrich N., Haring R., Michael K., Wasner C., Krebs A., Kronenberg F., Chang D., Meisinger C., Wichmann H.-E., Hoffmann W., Völzke H., Völker U., Teumer A., Biffar R., Kocher T., Felix S.B., Illig T., Kroemer H.K., GiegerC., Römisch-Margl W., Nauck M., A genome-wide association study of metabolic traits in human urine Nature Genetics, forthcoming.
  • Römisch-Margl W.,Prehn C., Bogumil R., Röhring C., Suhre K., Adamski J., A procedure for tissue sample preparation and metabolite extraction for high-throughput targeted metabolomics, Metabolomics, forthcoming.
  • Suhre K., Römisch-Margl W., Hrabé de Angelis M., Adamski J., Luippold G., Augustin R., Identification of a potential biomarker for FABP4 inhibition: the power of lipidomics in pre-clinical drug testing, Journal of Biomolecular Screening, forthcoming.
  • Krumsiek J., Suhre K., Illig T., Adamski J., Theis F.J., Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data, BMC Systems Biology, 5:21, 2011.
  • Mewes H.W., Ruepp A., Theis F., Rattei T., Walter M., Frishman D., Suhre K., Spannagl M., Mayer K.F., Stümpflen V., Antonov A.. MIPS: curated databases and comprehensive secondary data resources in 2010, Nucleic Acids Res., 39(Database issue):D220-224, 2011.
  • Kastenmüller G., Römisch-Margl W., Wägele B., Altmaier E., Suhre K., metaP-Server: a web-based metabolomics data analysis tool, J. Biomedicine & Biotechnology, pii:839862, 2011.

2010

2009

2008

2007

2006

2005

2004

2003

2002

  • Tulet P, Suhre K, Mari C, Solmon F, Rosset R. Mixing of boundary layer and upper tropospheric ozone during a deep convective event over Western Europe. Atmospheric Environment 2002. Vol. 36 pp. 4491-4501.

1994 - 2000


Theses


Patent Applications


Teaching

Bioinformatik München
  • Bachelor and Masters courses in Bioinformatics
EESlmu Master program
  • A new Masters course in Ecology, Evolution and Systematics
RECESS
  • DFG funded International Research Training School (IRTG) Regulation and Evolution of Cellular Systems
European School of Genetic Medicine
  • 9th Course in Bioinformatics & Systems Biology for Molecular Biologists, March 22th-26th 2009, Bertinoro di Romagna, ITALY: flyer, program, website of the course venue
  • 8th course in Bioinformatics & Systems Biology for Molecular Biologists, 16th - 20th March 2008, Bertinoro di Romagna, ITALY (programme 2008)

Winter Semester 2009/10
  • Metabolomics
  • Evolutionsbiologie 2
    Bachelor Biology, block course 08-26 February 2010
    (together with John Parsch)

Summer Semester 2009

Winter Semester 2008/09

Summer Semester 2008

Winter Semester 2007/08

Summer Semester 2007


Research


Metabolomics research
  • My present personal interest is in genetically determined human metabotypes and their link to complex disease. Metabolomics studies in animal models, such as mice and bovine are used in complement to studies in a human population. As a bioinformatician, I combine data from different sources, many of them from local HelmholtzMuenchen instruments, such as targeted quantitative metabolomics from a API Q TRAP 4000, non-targeted metabolomics from a Bruker 12 Tesla APEX FT-ICR, and genotyping information using Affymetrix 500k and 6.0 GeneChip arrays on the KORA population.
  • I am presently setting up a new group in metabolic research, with partners from the Helmholtz Zentrum München institutes GAC (J. Adamski), EPI (T. Illig), and IOEC (P. Schmitt-Kopplin). Our group is providing different bioinformatics ressources, which are available through this metabolomics web server. On that site, a Wiki for the metabolic initiative MetaP is available for registered users.
  • We are organizing the conference Metabolomics & More : The Impact of Metabolomics on the Life Sciences, which will be held on March 10-12, 2010 in Freising-Weihenstephan, Germany. Register now at this site
  • MassTRIX: Mass TRanslator into Pathways is a web server for the annotation of high precision mass spectrometry data. It is available at www.masstrix.org.
  • REF1: Gieger et al., PLoS Genetics, 2008.
  • REF2: Altmaier et al.,Endocrinology, 2008 [PDF].
  • REF3: Suhre and Schmitt-Kopplin, Nucleic Acids Research, 2008.
  • REF4: Wang-Sattler et al., PLoS One, 2008.
  • REF5: Altmaier et al., Molecular Nutrition & Food Research, 2009.
  • REF6: Suhre and Gieger, BioSpektrum, 2009.
  • REF7: Illig, Gieger et al., Nature Genetics, 2009.

Conference



metaP ressources



MassTRIX.org







German Centre for Diabetes Research - DZD e.V.
  • The "Deutsches Zentrum fuer Diabetesforschung e.V." (DZD) is an intertdisciplinary cooperation of the Helmholtz Association and the Leibniz Association with strong contributions from the University of Tuebingen and the University Clinic Dresden. The managing office is at the Helmholtz Centre Munich.

Gani_Med
  • Greifswald Approach to Individualized Medicine (BMBF-research project). The objective of Gani_Med is to use state-of-the-art diagnostics and novel therapeutic interventions that take into account the specific requirements and characteristics of the individual patient in order to increase the effectiveness of treatments, avoid unwanted adverse reactions and significantly reduce health care costs.

SysMBo
  • Systems Biology of Metabotypes (BMBF-research project). SysMBo is an interdisciplinary research consortium aiming to unravel the complex relations between genetic predisposition, environmental stimuli and disease. With the help of high-throughput metabolite profiling and powerful modelling tools, the researchers take a system based approach in order to understand the complex interplay between numerous factors leading to a pathophenotype.

Genome Analysis Centre (GAC)
  • The Metabolomic Platform (metaP) is a scientific interdisciplinary cooperation of Institutes of the Helmholtz Zentrum München. The activities include both profiling (analyses of all measurable analytes to identify differences) and targeted analyses (quantification of a chosen set of analytes). These activities are possible by the unique contributions of participating Helmholtz Zentrum München institutes in the GAC.

What are genetically determined metabotypes?

Common genetic polymorphisms induce major differentiations in the metabolic make-up of the human population. We conducted a genome-wide association study with metabolomics, identifying genetic variants in genes involved in the breakdown of fats (Gieger et al., PLoS Genetics, 2008). The resulting differences in metabolic capacity can affect individuals' susceptibility to complex diseases such as diabetes and hyperactivity. In the rapidly evolving field of metabolomics, scientists aim to measure all endogenous metabolites in a cell or body fluid. These measurements provide a functional readout of the physiological state of the human body. Investigation into these so-called "genetically determined metabotypes" in their biochemical context may help determine the pathogenesis of common diseases and gene-environment interactions. We identified four single nucleotide polymorphisms (SNPs) located in genes coding for well-characterized enzymes of the lipid metabolism. Individuals with different genotypes in these genes have significantly different metabolic capacities with respect to the synthesis of some polyunsaturated fatty acids, the beta-oxidation of short- and medium-chain fatty acids and the breakdown of triglycerides. By simultaneous measurements of both SNPs and serum concentrations of endogenous metabolites, the researchers determined the metabolome of several hundred healthy individuals and compared it to their genetic inheritance. The results suggest that most individuals carry one or more risk alleles in their genetic inheritance that may determine a certain medical phenotype, the response to a given drug treatment, or the reaction to a nutritional intervention or environmental challenge. These findings may lead to more targeted approaches to health care based on a combination of genotyping and metabolic characterization. To achieve this goal, it will be necessary to identify the major genetically determined metabotypes and their association to complex diseases.

A new and much larger study has just been published in Nature Genetics (Illig, Gieger et al., 2009). This study identifies a number of new genetically determined metabotypes.


Projects formerly developped at IGS-CNRS


Normal mode analysis
The Elastic Network Model

Docking - In Silico screening

GFscore
Mimivirus genome analysis




Repeat Protein Analysis
  • CaMBOT probing led to the isolation of a novel calmodulin binding protein cmbB in the social amoeba Dictyostelium discoideum. Structural and bioinformatic analyses reveal that the cmbB protein is almost entirely comprised of tandem repeats of an IP22 motif, which is a more precise representation of the previously identified FNIP repeat. cmbB also appears to share structural homology to YopM, from the plague bacterium Yersenia pestis, and its closest homologues are found in Mimivirus.
  • Collaboration with Prof. Danton O'Day.
  • REF: O'Day et al., BBRC, 2006.


PhydBac - phylogenomic display of bacterial genes





CaspR: Automated molecular replacement using homology modelling
  • CaspR is a web-server for automated molecular replacement by screening a large number of homology models for a potential solution.
  • The method that is implemented in CaspR was first used to solve the crystal structure of the E. coli protein YecD (PDB-id 1J2R).
  • The implementation of this method as a web-based server is part of the PhD research work of Jean-Baptiste Claude
  • REF: Claude et al., NAR, 2004.

3D-Coffee: multiple sequence-structure alignments with T-Coffee

Microarray data analysis

Structural biology

FusionDB - a database of prokaryotic gene fusion events

Genomic correlates of hyperthermostability
  • Statistical (principal component) analysis of the amino acid composition of most sequenced bacterial genomes. We show that the CHA-POL criteria (replacement of polar by charges residues in thermophilic organisms) is an optimal criteria to discriminate meso-philic from thermophilic proteins.
  • REF: Suhre and Claverie, J. Biol. Chem., 2003

Bacterial genome sequencing and annotation

     

Past activities

A209: The new Mercedes CLK convertible
the new Mercedes CLK convertible
ACE
Aerosol Characterization Experiments 1, 2, Asia.
  • Coupled physico-chemical modelling of ACE-1 and ACE-2 Lagrangian experiments
  • Co-ordinator of the modelling activities in ACE-2 (IntegModel)
  • Principal investigator in the ACE-2 EU project CloudyColumn
  • Preparatory studies for Lagrangian experiments in ACE-Asia
MOZAIC
Measurement of Ozone, Water Vapor, Carbon Monoxide and Nitrogen Oxides by Airbus-In-Service Aircraft.
  • Troposphere-stratosphere exchange in the tropics
  • Feasability studies of an aerosol measurement device for MOZAIC
MesoNH
The non-hydrostatic mesoscale atmospheric model of the French atmospheric research community.
  • Responsible of the atmospheric chemistry module MesoNH-chemistry (MNHC)
  • 3-D mesoscale and large eddy simulations of ACE-2 situations
Quantum field theory (diploma work)
Das Feld am Punkt im auesseren elektromagnetischen Feld
  • The Fermifield in an external electro-magnetic field will be defined as a sesquilinear form at one point without using test functions. It will be shown to satisfy the Dirac-equation and to be local in an appropriate sense. Moreover, based on the field at one point von-Neuman algebrae will be defined that are identical to the smeared field. This fact is not a straight forward deduction as the field is not translationally invariant. The twisted duality R(O) = R(O')t' will be proven in this work.

last update: 18 March 2011