Dr. Andreas Hoppe
Computational Systems Biochemistry Group

Charité - Universitätsmedizin Berlin
Institut für Biochemie
Charitéplatz 1 (Virchowweg 6)
10117 Berlin
Germany

phone: (+49-30) 450 528 176
fax: (+49-30) 450 528 937
e-mail: andreas.hoppe@charite.de
Curriculum vitae

Research interests:

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:

For citation numbers, see my site on Google Scholar.

Journal article, first author

2012
  • 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, PubMed].
  • Hoppe A. (2012) What mRNA abundances can tell us about metabolism. Metabolites, 2012; 2(3):614-631. [doi, pdf, PubMed].
  • 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]
2011
  • 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]
before
  • 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

2013
  • Thiele I, Swainston N, Fleming RM, 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 Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO. (2013) A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 Mar 3. doi: 10.1038/nbt.2488. [Epub ahead of print]
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]
2011
  • Gille C, Hübner K, Hoppe A, Holzhütter HG. Metannogen: annotation of biological reaction networks. Bioinformatics, 2011;27(19):2763-4. [pdf, doi, PubMed]
2010
  • 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]
before
  • 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

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.

Diploma and PhD thesis

  • Effiziente Algorithmen zur Berechnung von Elementarteilern ganzzahliger Matrizen - Implementation in GAP. Diplomarbeit im Lehrstuhl D für Mathematik \\ an der RWTH Aachen. Download pdf.
  • Normal forms over Dedekind domains, efficient implementation in the computer algebra system KANT. Accepted thesis of the department 3, Mathematics, of the Technical University of Berlin for the award of the academical degree Doctor of the natural sciences. Download pdf.

Links to associated institutions: