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Computational Systems Biochemistry Group Charité - Universitätsmedizin Berlin Institut für Biochemie Charitéplatz 1 (Virchowweg 6) 10117 Berlin Germany phone: (+49-30) 450 528 176 |
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Research interests:
- Metabolic consequences of TGFβ stimulation in cultured primary mouse hepatocytes
- Metabolic consequences of the cytokines HGFα and IL6 stimulation in cultured primary mouse hepatocytes
- Metabolic consequences of the treatment with intoxication analoga on primary human hepatocyte cultures
- Metabolic consequences of statin treatment on primary human hepatocyte cultures
- Understanding metabolic functions through expression profiles
- Prediction of flux changes with high-thruput data
- 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
ModeScore: infer metabolic activity changes from expression data (RNA,protein)FASIMU: FBA simulation software for metabolomics
NeedleHaystack: 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, Ilkavets I, Dooley S, Holzhütter HG. (2012) Metabolic consequences of the cultivation of primary mouse hepatocytes and the effect of TGFβ stimulation screened from transcript data. Metabolites, 2012; 2(4): 983-1003. [doi, pdf].
- Hoppe A. (2012) What mRNA abundances can tell us about metabolism. Metabolites, 2012; 2(3):614-631. [doi, pdf].
- Hoppe A, Holzhütter HG. (2012) ModeScore: A method to infer changed activity of metabolic function from transcript profiles. OpenAccess Series in Informatics (OASIcs), 26:1-11. [pdf, doi]
- 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, 105(2):122–129. [doi, PubMed]
- 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. [pdf, doi, 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. [doi, pdf, 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, doi, PubMed] 53 citations as of 4.9.12.
- Hoppe A and Frömmel C. 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
- Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov Sr. E, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JHGM, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ. A community-driven global reconstruction of human metabolism, Nat. Biotech., Accepted (2012).
- Bazzani S, Hoppe A, Holzhütter HG. (2012) Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism. BMC Syst Biol. 6(1):118. [pdf, doi, PubMed]
- Gille C, Hübner K, Hoppe A, Holzhütter HG. Metannogen: annotation of biological reaction networks. Bioinformatics, 2011;27(19):2763-4. [pdf, doi, PubMed]
- 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. [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
- ModeScore A method to infer changed activity of metabolic functions from transcript profiles. At: German Conference of Bioinformatics, Jena, 2012. Download.
- 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 Euro-QSAR 2002.
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.
Links to associated institutions:
- Computational Systems Biochemistry Group
- Institute for Biochemistry
- Charité - Universitätsmedizin Berlin