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Computational Systems Biochemistry Group Charité - Universitätsmedizin Berlin Institut für Biochemie Seestr. 73 13347 Berlin Germany phone: (+49-30) 450 528 176 |
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Research interests:
- Understanding metabolic functions through expression profiles
- Modelling zonation of hepatocytes along the liver lobulus
- Flux-balance analysis,
- Mode decomposition.
- Influence of enzyme costs on fluxes in metabolic networks.
- Molecular geometry for protein structure theory and drug design.
- Software engineering, development and implementation of efficient algorithms.
Software
FASIMU: FBA simulation software for metabolomicsNeedleHaystack: A program for the rapid recognition of local structures in large sets of atomic coordinates
Curriculum vitae:
Born 1970, married, four children.
Degrees:
- 1994
- Diploma in Mathematics at the Humboldt University Berlin
- 1998
- Dr. rer. nat. in Mathematics (Normal forms in Dedekind domains) in Computational Number Theory (Michael E. Pohst) at the Technical University Berlin
Scientific career:
- 1999-2005
- Post-Doc in Protein Structure Theory (Cornelius Frömmel) at Charité Berlin
- 2005-now
- Post-Doc in Computational Systems Biochemistry (Hermann-Georg Holzhütter) at Charité Berlin
Publications:
Journal article, first author
- Hoppe A, Richter C, Holzhütter HG. (2011) Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes. BioSystems. [doi]
- Hoppe A, Hoffmann S, Gerasch A, Gille C, Holzhütter HG. (2011) FASIMU: flexible software for flux-balance computation series in large metabolic networks. BMC Bioinformatics., 12(1):28. [PubMed]
- Gille C*, Bölling C*, Hoppe A*, Bulik S, Hoffmann S, Hübner K, Karlstädt A, Ganeshan R, König M, Rother K, Weidlich M, Behre J, Holzhütter HG. HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol Syst Biol., (2010) 6:411. [PubMed] * contributed equally
- Hoppe A, Hoffmann S, and Holzhütter HG. Including metabolite concentrations into flux-balance analysis: Thermodynamic realizability as a constraint on flux distributions in metabolic networks BMC Syst. Biol., (2007) 1(1): 23. [pdf, journal, PubMed] 30 citations as of 1.11.10.
- Andreas Hoppe and Cornelius Frömmel. NeedleHaystack: A program for the rapid recognition of local structures in large sets of atomic coordinates. J. Appl. Cryst. (2003). 36, 1090-1097. [pdf, ps]
Journal article, contribution
- Huthmacher C, Hoppe A, Bulik S, Holzhutter HG. (2010) Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC Syst Biol., 4(1):120. [Epub ahead of print] [PubMed]
- Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhütter HG. (2010) IGERS: Inferring Gibbs energy changes of biochemical reactions from reaction similarities. Biophys J., 98(11):2478-86. [PubMed]
- Bauer RA, Bourne PE, Formella A, Frömmel C, Gille C, Goede A, Guerler A, Hoppe A, Knapp EW, Pöschel T, Wittig B, Ziegler V, Preissner R. Superimpose: a 3D structural superposition server Nucleic Acids Res., (2008) 36(W47-W54). [pdf, journal, PubMed]
- Gille C, Hoppe A, Holzhütter HG. (2008) Web-Links as a Means to Document Annotated Sequence and 3D-Structure Alignments in Systems Biology. Genome Inform.; 20:277-84. [PubMed]
- Günther S, May P, Hoppe A, Froemmel C, Preissner R. Docking without docking: ISEARCH-prediction of interactions using known interfaces. Proteins. CAPRI, Special Issue. Sep 5;69(4):839-844 (2007) [pdf, journal, PubMed]
- Hoffmann S, Hoppe A and Holzhütter HG. Pruning genome-scale metabolic models to consistent ad functionem networks. Genome Informatics, (2007) 18(1), 308-19. [pdf]
- Hoffmann S, Hoppe A and Holzhütter HG. Composition of Metabolic Flux Distributions by Functionally Interpretable Minimal Flux Modes (MinModes). Genome Informatics (2006) 17(1), 195-207. [pdf, PubMed]
Article in book
- Andreas Hoppe and Cornelius Frömmel. Total surface comparison - Glimpse into the morphogenesis of Proteins. In: QSAR and Molecular Modelling in Rational Design of Bioactive Molecules. Editors: Esin Aki Sener and Ismail Yalcin. Computer-aided drug design & development society in Turkey, 2006. ISBN 975-00782-0-9.
- Andreas Hoppe and Cornelius Frömmel. The molecular mimicry hypothesis: Foundation and limits of rational drug design. In: Designing Drugs and Crop Protectants: processes, problems and solutions. Editors: Martyn Ford, David Livingston, John Dearden, Han Van de Waaterbeemd. Blackwell Publishings 2003. ISBN 1-4051-2516-0.
Selected conference talks
- Integrating metabolome and expression data into optimization-based network analysis. Three approaches developed in the Holzhütter group. at IOMPA 2010, a workshop at ICSB 2010, Edinburgh.
- HepatoNet - Stoichiometric model of the human hepatocyte. Curation and applications.at Brasil Deutschland Systems Biology meeting in Ouro Preto.
- The molecular mimicry hypothesis: Foundation and limits of rational drug design. at .
Selected posters
- Hoppe A, Richter C, Holzhütter HG. Are enzyme costs minimized in evolution? Enzyme size, efficiency and turnover as a mean for better flux predictions in FBA. Poster P02.284 at ICSB 2010, Edinburgh. Download.
- Hoppe A, Hoffmann S, Gerasch A, König M, Gille C, Holzhütter HG. FASIMU: A flexible software for flux-balance computation series in large metabolic networks Poster M007 at SBMC 2010, Freiburg. Download.
- Hoppe A, Gerasch A, Hoffmann S. How visualization of flux modes helps to generate biochemical hypotheses Poster M007 at VizBi 2010, Freiburg. Download.
- Hoppe A, Hoffmann S, Holzhütter HG. Constrained optimization sheds light in the metabolic functioning of higher cells. Poster DS2-2-134 at ICSB 2008, Gothenborg. Download.
- Hoppe A and Frömmel C. . Poster at Euro-QSAR 2004, "QSAR and Molecular Modelling in Rational Design of Bioactive Molecules." Istanbul. Download.
- Hoppe A and Frömmel C. Looking for the Needle in the Haystack: An Algorithm for the Rapid Recognition of Local Structures in Proteins. Poster at Euro-QSAR 2000, "Rational Approaches to Drug Design" Düsseldorf. Download.