Publications:

Journal article, first author

1. Hoppe A, Vlaic S, Braun S, Müller S, D'Alessandro L, U Klingmüller, Guthke R, Holzhütter HG, Börries M, Busch H. Evaluating the transcriptional signature of the cross-talk between HGF and IL-6 revealed new roles for Cxcl10 and Socs3 in hepatocyte proliferation control. In preparation.
2. Abshagen K*, Hoppe A* , Thomas M, Müller I, Ebert M, Weng H, Holzhütter HG, Zanger U, Bode J, Vollmar B, Dooley S. Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice. Submitted. * contributed equally
3. 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].
4. Hoppe A. (2012) What mRNA abundances can tell us about metabolism. Metabolites, 2012; 2(3):614-631. [doi, pdf, PubMed].
5. 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]
6. 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]
7. 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]
8. 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
9. 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.
10. 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]

Journal article, contribution

1. 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. 31:419-425. [pdf, doi, PubMed]
2. 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]
3. Gille C, Hübner K, Hoppe A, Holzhütter HG. Metannogen: annotation of biological reaction networks. Bioinformatics, 2011;27(19):2763-4. [pdf, doi, PubMed]
4. Huthmacher C, Hoppe A, Bulik S, Holzhütter HG. (2010) Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC Syst Biol., 4(1):120. [PubMed]
5. 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]
6. 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]
7. 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]
8. Günther S, May P, Hoppe A, Frömmel 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]
9. 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]
10. 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

1. 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.
2. 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.

Theses

1. Effiziente Algorithmen zur Berechnung von Elementarteilern ganzzahliger Matrizen - Implementation in GAP. Diplomarbeit im Lehrstuhl D für Mathematik \\ an der RWTH Aachen. Download pdf.
2. 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.