Berndt N*, Hudert CA*, Eckstein J, Loddenkemper C, Henning S, Bufler P, Meierhofer D, Sack I, Wiegand S, Wallach I, Holzhütter HG.
Alterations of Central Liver Metabolism of Pediatric Patients with Non-Alcoholic Fatty Liver Disease.
Int J Mol Sci. 2022 Sep 21;23(19):11072.

Maechler M, Rösner J, Wallach I, Geiger JRP, Spies C, Liotta A*, Berndt N*.
Sevoflurane Effects on Neuronal Energy Metabolism Correlate with Activity States while Mitochondrial Function Remains Intact.
Int J Mol Sci. 2022 Mar 11;23(6):3037.

*shared first or last authorship

Berndt N, Eckstein J, Heucke N, Wuensch T, Gajowski R, Stockmann M, Meierhofer D, Holzhütter HG.
Metabolic heterogeneity of human hepatocellular carcinoma: implications for personalized pharmacological treatment.
FEBS J. 2021 Apr;288(7):2332-2346.

Berndt N, Eckstein J, Wallach I, Nordmeyer S, Kelm M, Kirchner M, Goubergrits L, Schafstedde M, Hennemuth A, Kraus M, Grune T, Mertins P, Kuehne T, Holzhütter HG.
CARDIOKIN1: Computational Assessment of Myocardial Metabolic Capability in Healthy Controls and Patients With Valve Diseases.
Circulation. 2021 Dec 14;144(24):1926-1939. Supplemental Material

Berndt N*, Kolbe E*, Gajowski R, Eckstein J, Ott F, Meierhofer D, Holzhütter HG*, Matz-Soja M*.
Functional consequences of metabolic zonation in murine livers: New insights for an old story.
Hepatology. 2021 Feb;73(2):795-810.

Berndt N, Kovács R, Schoknecht K, Rösner J, Reiffurth C, Maechler M, Holzhütter HG, Dreier JP, Spies C, Liotta A.
Low neuronal metabolism during isoflurane-induced burst suppression is related to synaptic inhibition while neurovascular coupling and mitochondrial function remain intact.
J Cereb Blood Flow Metab. 2021 Oct;41(10):2640-2655.

Garczynska K, Tzschätzsch H, Assili S, Kühl AA, Häckel A, Schellenberger E, Berndt N, Holzhütter HG, Braun J, Sack I, Guo J.
Effect of Post-mortem Interval and Perfusion on the Biophysical Properties of ex vivo Liver Tissue Investigated Longitudinally by MRE and DWI.
Front. Physiol. 2021 Aug 3;12:696304.

Holzhütter HG, Berndt N.
Computational Hypothesis: How Intra-Hepatic Functional Heterogeneity May Influence the Cascading Progression of Free Fatty Acid-Induced Non-Alcoholic Fatty Liver Disease (NAFLD).
Cells. 2021 Mar 5;10(3):578.

Hudert CA, Tzschätzsch H, Rudolph B, Loddenkemper C, Holzhütter HG, Kalveram L, Wiegand S, Braun J, Sack I, Guo J.
How histopathologic changes in pediatric nonalcoholic fatty liver disease influence in vivo liver stiffness.
Acta Biomater. 2021 Mar 15;123:178-186.

Kalveram L, Schunck WH, Rothe M, Rudolph B, Loddenkemper C, Holzhütter HG, Henning S, Bufler P, Schulz M, Meierhofer D, Zhang IW, Weylandt KH, Wiegand S, Hudert CA.
Regulation of the cytochrome P450 epoxyeicosanoid pathway is associated with distinct histologic features in pediatric non-alcoholic fatty liver disease.
Prostaglandins Leukot Essent Fatty Acids. 2021 Jan;164:102229.

Schreyer S, Berndt N, Eckstein J, Mülleder M, Hemmati-Sadeghi S, Klein C, Abuelnor B, Panzel A, Meierhofer D, Spranger J, Steiner B, Brachs S.
Dietary-challenged mice with Alzheimer-like pathology show increased energy expenditure and reduced adipocyte hypertrophy and steatosis.
Aging (Albany NY). 2021 Apr 16;13(8):10891-10919.

Willimsky G, Beier C, Immisch L, Papafotiou G, Scheuplein V, Goede A, Holzhütter HG, Blankenstein T, Kloetzel PM.
In vitro proteasome processing of neo-splicetopes does not predict their presentation in vivo.
Elife. 2021 Apr 20;10:e62019.

*shared first or last authorship

Berndt N.
Modeling of liver metabolism.
Habilitation, Charité – Universitätsmedizin Berlin, 2020-05-25

Berndt N*, Egners A*, Mastrobuoni G*, Vvedenskaya O, Fragoulis A, Dugourd A, Bulik S, Pietzke M, Bielow C, van Gassel R, Damink SWO, Erdem M, Saez-Rodriguez J, Holzhütter HG*, Kempa S*, Cramer T*.
Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer.
Br J Cancer. 2020 Jan;122(2):233-244.

Berndt N, Kovács R, Rösner J, Wallach I, Dreier JP, Liotta A.
Flavin Adenine Dinucleotide Fluorescence as an Early Marker of Mitochondrial Impairment During Brain Hypoxia.
Int J Mol Sci. 2020 Jun 1;21(11):3977.

Garczyńska K, Tzschätzsch H, Kühl AA, Morr AS, Lilaj L, Häckel A, Schellenberger E, Berndt N, Holzhütter HG, Braun J, Sack I, Guo J.
Changes in Liver Mechanical Properties and Water Diffusivity During Normal Pregnancy Are Driven by Cellular Hypertrophy.
Front Physiol. 2020 Nov 23;11:605205.

Holzhütter HG, Wuensch T, Gajowski R, Berndt N, Bulik S, Meierhofer D, Stockmann M.
A novel variant of the ¹³C-methacetin liver function breath test that eliminates the confounding effect of individual differences in systemic CO₂ kinetics.
Arch Toxicol. 2020 Feb;94(2):401-415.

Kespohl M, Bredow C, Klingel K, Voß M, Paeschke A, Zickler M, Poller W, Kaya Z, Eckstein J, Fechner H, Spranger J, Fähling M, Wirth EK, Radoshevich L, Thery F, Impens F, Berndt N, Knobeloch K-P, Beling A.
Protein modification with ISG15 blocks coxsackievirus pathology by antiviral and metabolic reprogramming.
Science Advances. 2020 Mar 11;6(11):eaay1109.

*shared first or last authorship

Berndt N, Eckstein J, Heucke N, Gajowski R, Stockmann M, Meierhofer D, Holzhütter HG. 
Characterization of Lipid and Lipid Droplet Metabolism in Human HCC.
Cells. 2019 May 27;8(5):512.

Berndt N, Patzak A, Holzhütter HG.
Metabolic Modeling of Kidney Diseases: Lessons learned from the Liver.
Acta Physiol (Oxf). 2019 Oct;227(2):e13350.

Brosig A, Fuchs J, Ipek F, Kroon C, Schrötter S, Vadhvani M, Polyzou A, Ledderose J, van Diepen M, Holzhütter HG, Trimbuch T, Gimber N, Schmoranzer J, Lieberam I, Rosenmund C, Spahn C, Scheerer P, Szczepek M, Leondaritis G, Eickholt BJ.
The Axonal Membrane Protein PRG2 Inhibits PTEN and Directs Growth to Branches.
Cell Rep. 2019 Nov 12;29(7):2028-2040.e8.

Hudert CA, Selinski S, Rudolph B, Bläker H, Loddenkemper C, Thielhorn R, Berndt N, Golka K, Cadenas C, Reinders J, Henning S, Bufler P, Jansen PLM, Holzhütter HG, Meierhofer D, Hengstler JG, Wiegand S.
Genetic determinants of steatosis and fibrosis progression in pediatric non-alcoholic fatty liver disease.
Liver Int. 2019 Mar;39(3):540-556.

Hudert CA, Tzschätzsch H, Rudolph B, Bläker H, Loddenkemper C, Müller HP, Henning S, Bufler P, Hamm B, Braun J, Holzhütter HG, Wiegand S, Sack I, Guo J.
Tomoelastography for the Evaluation of Pediatric Nonalcoholic Fatty Liver Disease.
Invest Radiol. 2019 Apr;54(4):198-203.

Schneider J*, Berndt N*, Papageorgiou IE, Maurer J, Bulik S, Both M, Draguhn A, Holzhütter HG, Kann O.
Local oxygen homeostasis during various neuronal network activity states in the mouse hippocampus.
J Cereb Blood Flow Metab. 2019 May;39(5):859-873.

*shared first or last authorship

Berndt N, Bulik S, Holzhütter HG.
Corrigendum to "Kinetic Modeling of the Mitochondrial Energy Metabolism of Neuronal Cells: The Impact of Reduced alpha-Ketoglutarate Dehydrogenase Activities on ATP Production and Generation of Reactive Oxygen Species."
Int J Cell Biol. 2018 Sep 9;2018:6139262.

Berndt N, Bulik S, Wallach I, Wünsch T, König M, Stockmann M, Meierhofer D, Holzhütter HG.
HEPATOKIN1 is a biochemistry-based model of liver metabolism for applications in medicine and pharmacology.
Nat Commun. 2018 Jun 19;9(1):2386.

Berndt N, Holzhütter HG.
Dynamic Metabolic Zonation of the Hepatic Glucose Metabolism Is Accomplished by Sinusoidal Plasma Gradients of Nutrients and Hormones.
Front Physiol. 2018 Dec 12;9:1786.

Berndt N, Horger MS, Bulik S, Holzhütter HG.
A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism.
PLoS Comput Biol. 2018 Feb 15;14(2):e1006005.

Berndt N, Rösner J, Haq RU, Kann O, Kovács R, Holzhütter HG, Spies C, Liotta A.
Possible neurotoxicity of the anesthetic propofol: evidence for the inhibition of complex II of the respiratory chain in area CA3 of rat hippocampal slices.
Arch Toxicol. 2018 Oct;92(10):3191-3205.

Borchert A, Kalms J, Roth SR, Rademacher M, Schmidt A, Holzhutter HG, Kuhn H, Scheerer P.
Crystal structure and functional characterization of selenocysteine-containing glutathione peroxidase 4 suggests an alternative mechanism of peroxide reduction.
Biochim Biophys Acta Mol Cell Biol Lipids. 2018 Sep;1863(9):1095-1107.  

Eckstein J, Holzhütter HG*, Berndt N*.
Correction: The importance of membrane microdomains for bile salt-dependent biliary lipid secretion.
J Cell Sci. 2018 Mar 19;131(6):jcs217414.

Eckstein J, Holzhütter HG*, Berndt N*.
The importance of membrane microdomains for bile salt-dependent biliary lipid secretion.
J Cell Sci. 2018 Mar 1;131(5):jcs211524.

Hudert CA, Tzschätzsch H, Guo J, Rudolph B, Bläker H, Loddenkemper C, Luck W, Müller HP, Baumgart DC, Hamm B, Braun J, Holzhütter HG, Wiegand S, Sack I.
US Time-Harmonic Elastography: Detection of Liver Fibrosis in Adolescents with Extreme Obesity with Nonalcoholic Fatty Liver Disease.
Radiology. 2018 Jul;288(1):99-106.

Kovács R, Gerevich Z, Friedman A, Otáhal J, Prager O, Gabriel S, Berndt N.
Bioenergetic Mechanisms of Seizure Control.
Front Cell Neurosci. 2018 Oct 8;12:335.

*shared first or last authorship

Haanstra JR, Gerding A, Dolga AM, Sorgdrager FJH, Buist-Homan M, du Toit F, Faber KN, Holzhütter HG, Szöör B, Matthews KR, Snoep JL, Westerhoff HV, Bakker BM.
Targeting pathogen metabolism without collateral damage to the host.
Sci Rep. 2017 Jan 13;7:40406.

Kalms J, Banthiya S, Galemou Yoga E, Hamberg M, Holzhutter HG, Kuhn H, Scheerer P.
The crystal structure of Pseudomonas aeruginosa lipoxygenase Ala420Gly mutant explains the improved oxygen affinity and the altered reaction specificity.
Biochim Biophys Acta Mol Cell Biol Lipids. 2017 May;1862(5):463-473.

Kürschner G, Zhang Q, Clima R, Xiao Y, Busch JF, Kilic E, Jung K, Berndt N, Bulik S, Holzhütter HG, Gasparre G, Attimonelli M, Babu M, Meierhofer D.
Renal oncocytoma characterized by the defective complex I of the respiratory chain boosts the synthesis of the ROS scavenger glutathione.
Oncotarget, 2017. 8(62): p. 105882-105904.

Schoknecht K*, Berndt N*, Rösner J, Heinemann U, Dreier JP, Kovács R, Friedman A, Liotta A.
Event-Associated Oxygen Consumption Rate Increases ca. Five-Fold When Interictal Activity Transforms into Seizure-Like Events In Vitro.
Int J Mol Sci. 2017 Sep 7;18(9):1925.

Wallstab C, Eleftheriadou D, Schulz T, Damm G, Seehofer D, Borlak J, Holzhütter HG, Berndt N.
A unifying mathematical model of lipid droplet metabolism reveals key molecular players in the development of hepatic steatosis.
FEBS J. 2017 Oct;284(19):3245-3261.

*shared first or last authorship

Berndt N, Holzhütter HG.
Mathematical Modeling of Cellular Metabolism.
Recent Results Cancer Res, 2016. 207: p. 221-32. 

Bulik S, Holzhütter HG, Berndt N.
The relative importance of kinetic mechanisms and variable enzyme abundances for the regulation of hepatic glucose metabolism - insights from mathematical modeling.
BMC Biol. 2016 Mar 2;14:15.

Taegtmeyer H, Young ME, Lopaschuk GD, Abel ED, Brunengraber H, Darley-Usmar V, Des Rosiers C, Gerszten R, Glatz JF, Griffin JL, Gropler RJ, Holzhuetter HG, Kizer JR, Lewandowski ED, Malloy CR, Neubauer S, Peterson LR, Portman MA, Recchia FA, Van Eyk JE, Wang TJ; American Heart Association Council on Basic Cardiovascular Sciences.
Assessing Cardiac Metabolism: A Scientific Statement From the American Heart Association.
Circ Res. 2016 May 13;118(10):1659-701.

Abshagen K, König M, Hoppe A, Müller I, Ebert M, Weng H, Holzhütter HG, Zanger UM, Bode J, Vollmar B, Thomas M, Dooley S.
Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice.
BMC Syst Biol. 2015 Nov 20;9:83.

Berndt N, Kann O, Holzhütter HG.
Physiology-based kinetic modeling of neuronal energy metabolism unravels the molecular basis of temporal NAD(P)H fluorescence profiles.
J Cereb Blood Flow Metab. 2015 Sep;35(9):1494-506.

Eckstein J, Berndt N*, Holzhütter HG*.
Computer simulations suggest a key role of membranous nanodomains in biliary lipid secretion.
PLoS Comput Biol, 2015. 11(2): p. e1004033.

Knüppel S, Meidtner K, Arregui M, Holzhütter HG, Boeing H.
Joint Effect of Unlinked Genotypes: Application to Type 2 Diabetes in the EPIC-Potsdam Case-Cohort Study.
Ann Hum Genet. 2015 Jul;79(4):253-63. doi: 10.1111/ahg.12115. Epub 2015 Apr 23. PMID: 25907404

Liepe J, Holzhütter HG, Bellavista E, Kloetzel PM, Stumpf MP, Mishto M.
Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes.
Elife. 2015 Sep 22;4:e07545.

Palinkas A, Bulik S, Bockmayr A, Holzhütter HG.
Sequential metabolic phases as a means to optimize cellular output in a constant environment.
PLoS One. 2015 Mar 18;10(3):e0118347. doi: 10.1371/journal.pone.0118347. eCollection 2015. PMID: 25786979

Ricken T, Werner D, Holzhütter HG, König M, Dahmen U, Dirsch O.
Modeling function-perfusion behavior in liver lobules including tissue, blood, glucose, lactate and glycogen by use of a coupled two-scale PDE-ODE approach.
Biomech Model Mechanobiol. 2015 Jun;14(3):515-36. doi: 10.1007/s10237-014-0619-z. Epub 2014 Sep 19.

Zeigerer A, Bogorad RL, Gilleron J, Sharma K, Seifert S, Sales S, Berndt N, Bulik S, D'Souza RCJ, Marsico G, Lakshmanaperumal N, Meganathan K, Natarajan K, Sachinidis A, Dahl A, Shevchenko A, Mann M, Holzhütter HG, Koteliansky V, Zerial M.
Regulation of liver metabolism by the endosomal GTPase Rab5.
Cell Rep, 2015. 11(6): p. 884-92.

*shared first or last authorship

Bölling C, Weidlich M, Holzhütter HG.
SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques.
Journal of Biomedical Semantics 2014, 5(Suppl 1):S1

Drasdo D, Bode J, Dahmen U, Dirsch O, Dooley S, Gebhardt R, Ghallab A, Godoy P, Häussinger D, Hammad S, Hoehme S, Holzhütter HG, Klingmüller U, Kuepfer L, Timmer J, Zerial M, Hengstler JG.
The virtual liver: state of the art and future perspectives.
Arch Toxicol. 2014 Dec;88(12):2071-5.

Liepe J, Holzhütter HG, Kloetzel PM, Stumpf MP, Mishto M.
Modelling proteasome and proteasome regulator activities. Biomolecules.
2014 Jun 20;4(2):585-99.

Schleicher J, Guthke R, Dahmen U, Dirsch O, Holzhuetter HG, Schuster S.
A theoretical study of lipid accumulation in the liver-implications for nonalcoholic fatty liver disease.
Biochim Biophys Acta. 2014 Jan;1841(1):62-9.

Berndt N, Holzhütter HG.
The High Energy Demand of Neuronal Cells Caused by Passive Leak Currents is Not a Waste of Energy.
Cell Biochem Biophys. 2013 Nov;67(2):527-35.

Berndt N, Holzhütter HG, Bulik S.
Implications of enzyme deficiencies on mitochondrial energy metabolism and reactive oxygen species formation of neurons involved in rotenone-induced Parkinson's disease: a model-based analysis.
FEBS J. 2013 Oct;280(20):5080-93.

Godoy P, Hewitt NJ, Albrecht U, Andersen ME, Ansari N, Bhattacharya S, Bode JG, Bolleyn J, Borner C, Böttger J, Braeuning A, Budinsky RA, Burkhardt B, Cameron NR, Camussi G, Cho CS, Choi YJ, Craig Rowlands J, Dahmen U, Damm G, Dirsch O, Donato MT, Dong J, Dooley S, Drasdo D, Eakins R, Ferreira KS, Fonsato V, Fraczek J, Gebhardt R, Gibson A, Glanemann M, Goldring CE, Gómez-Lechón MJ, Groothuis GM, Gustavsson L, Guyot C, Hallifax D, Hammad S, Hayward A, Häussinger D, Hellerbrand C, Hewitt P, Hoehme S, Holzhütter HG, Houston JB, Hrach J, Ito K, Jaeschke H, Keitel V, Kelm JM, Kevin Park B, Kordes C, Kullak-Ublick GA, Lecluyse EL, Lu P, Luebke-Wheeler J, Lutz A, Maltman DJ, Matz-Soja M, McMullen P, Merfort I, Messner S, Meyer C, Mwinyi J, Naisbitt DJ, Nussler AK, Olinga P, Pampaloni F, Pi J, Pluta L, Przyborski SA, Ramachandran A, Rogiers V, Rowe C, Schelcher C, Schmich K, Schwarz M, Singh B, Stelzer EH, Stieger B, Stöber R, Sugiyama Y, Tetta C, Thasler WE, Vanhaecke T, Vinken M, Weiss TS, Widera A, Woods CG, Xu JJ, Yarborough KM, Hengstler JG.
Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME.
Arch Toxicol. 2013 Aug;87(8):1315-530. Epub 2013 Aug 23.

Holzhütter HG, Lock JF, Taheri P, Bulik S, Goede A, Stockmann M.
Assessment of hepatic detoxification activity: proposal of an improved variant of the (13)c-methacetin breath test.
PLoS One. 2013 Aug 15;8(8):e70780.

Hovestädt M, Kuckelkorn U, Niewienda A, Keller C, Goede A, Ay B, Günther S, Janek K, Volkmer R, Holzhütter HG.
Rapid degradation of solid-phase bound peptides by the 20S proteasome.
J Pept Sci. 2013 Sep;19(9):588-97. Epub 2013 Jul 28. 

Huchzermeyer C*, Berndt N*, Holzhütter HG*, Kann O*.
Oxygen consumption rates during three different neuronal activity states in the hippocampal CA3 network.
J Cereb Blood Flow Metab. 2013 Feb;33(2):263-71.

Jacobasch G, Holzhütter HG, M. Kruschewski M, Pforte H, Dongowski G.
Dickdarmentzündungen hemmen die Butyratresorption im Kolonepithel – Schutzeffekte durch resistente Stärke Typ 3 (RS3) und RS3/Rutin.
Ernährung/Nutrition, 37, 365-382

Knüppel S, Rohde K, Meidtner K, Drogan D, Holzhütter HG, Boeing H, Fisher E.
Evaluation of 41 Candidate Gene Variants for Obesity in the EPIC-Potsdam Cohort by Multi-Locus Stepwise Regression.
PLoS One. 2013 Jul 12;8(7):e68941.

König M., Holzhütter HG., Berndt N.
Metabolic Gradients as Key Regulators in Zonation of Tumor Energy Metabolism: A Tissue-scale Model Based Study.
Biotechnol J. 2013 Sep;8(9):1058-69.

*shared first or last authorship

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. 2012 Aug 31;6:118.

Berndt N.
Theoretische Untersuchungen zur Kopplung von neuronaler Erregung und neuronalem Energiestoffwechsel.
Dissertation, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012-11-07

Berndt N, Bulik S, Holzhütter HG.
Kinetic Modeling of the Mitochondrial Energy Metabolism of Neuronal Cells: The Impact of Reduced Α-Ketoglutarate Dehydrogenase Activities on ATP Production and Generation of Reactive Oxygen Species.
Int J Cell Biol. 2012;2012:757594.

Binder B, Holzhütter HG. (2012)
A Hypothetical Model of Cargo-Selective Rab Recruitment During Organelle Maturation.
Cell Biochem Biophys. 2012 May;63(1):59-71.

Bölling C, Dumontier M, Weidlich M, Holzhütter HG. (2012)
Role-based representation and inference of biochemical processes.
ICBO 2012: 3rd International Conference on Biomedical Ontology

Holzhütter HG, Drasdo D, Preusser T, Lippert J, Henney AM. (2012)
The virtual liver: a multidisciplinary, multilevel challenge for systems biology.
Wiley Interdiscip Rev Syst Biol Med. 2012 May-Jun;4(3):221-35.

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.

Hoppe A, Ilkavets I, Dooley S, Holzhütter HG. (2012)
Metabolic Consequences of TGFb Stimulation in Cultured Primary Mouse Hepatocytes Screened from Transcript Data with ModeScore.
Metabolites 2012, 2(4), 983-1003.

Karlstaedt A, Fliegner D, Kararigas G, Ruderisch HS, Regitz-Zagrosek V, Holzhütter HG. (2012)
CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism.
BMC Syst Biol. 2012 Aug 29;6(1):114.

Knüppel S, Esparza-Gordillo J, Marenholz I, Holzhütter HG, Bauerfeind A, Ruether A, Weidinger S, Lee YA, Rohde K. (2012)
Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis.
BMC Med Genet. 2012 Jan 27;13:8.

König M., Bulik S. and Holzhütter HG. (2012) Quantifying the Contribution of the Liver to the Homeostasis of Plasma Glucose: A Detailed Kinetic Model of Hepatic Glucose Metabolism. PLoS Comput Biol. 2012;8(6):e1002577.

König M., Dräger A. and Holzhütter HG. (2012)
CySBML: a Cytoscape plugin for SBML.
Bioinformatics. 2012 Sep 15;28(18):2402-3.

König M. and Holzhütter HG. (2012)
Kinetic Modeling of Human Hepatic Glucose Metabolism in T2DM Predicts Higher Risk of Hypoglycemic Events in Rigorous Insulin Therapy.

Berndt N, Hoffmann S, Benda J, Holzhütter HG.
The influence of the chloride currents on action potential firing and volume regulation of excitable cells studied by a kinetic model.
J Theor Biol. 2011 May 7;276(1):42-9.

Gille C, Hübner K, Hoppe A, Holzhütter HG.
Metannogen: annotation of biological reaction networks.
Bioinformatics. 2011 Oct 1;27(19):2763-4.

Herling A, König M, Bulik S, Holzhütter HG.
Enzymatic Features of the Glucose Metabolism in Tumor Cells.
FEBS J. 2011 Jul;278(14):2436-59.

Hoppe A, Hoffmann S, Gerasch A, Gille C, Holzhütter HG.
FASIMU: flexible software for flux-balance computation series in large metabolic networks.
BMC Bioinformatics. 2011 Jan 22;12:28.

Hoppe A, Richter C, Holzhütter HG.
Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes.
Biosystems. 2011 Aug;105(2):122-9.

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 Sep 7;6:411.

Huthmacher C, Hoppe A, Bulik S, Holzhütter HG.
Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis.
BMC Syst Biol. 2010 Aug 31;4:120.

König M and Holzhütter HG.
FluxViz - Cytoscape Plug-in for Vizualisation of Flux Distributions in Networks.
Genome Inform. 2010;24:96-103.

Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhütter HG.
IGERS: Inferring Gibbs energy changes of biochemical reactions from reaction similarities.
Biophys J. 2010 Jun 2;98(11):2478-86.

Sun G, Rosu DM, Zhang X, Hovestädt M, Pop S, Schade U, Aulich D, Gensch M, Ay B, Holzhütter HG, Zahn DRT, Esser N, Volkmer R, Rappich J and Hinrichs K.
Synchrotron infrared spectroscopic ellipsometry (IRSE) for characterization of biofunctional surfaces.
physica status solidi (b) 247(8):1925-1931 · August 2010

Bech-Otschir D, Helfrich A, Enenkel C, Consiglieri G, Seeger M, Holzhütter HG, Dahlmann B, Kloetzel PM.
Polyubiquitin substrates allosterically activate their own degradation by the 26S proteasome.
Nat Struct Mol Biol. 2009 Feb;16(2):219-25.

Binder B, Goede A, Berndt N, Holzhütter HG.
A conceptual mathematical model of the dynamic self-organisation of dinstinct cellular organelles.
PLoS One. 2009 Dec 30;4(12):e8295.

Bulik S, Grimbs S, Huthmacher C, Selbig J, Holzhütter HG.
Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws - a promising method for speeding up the kinetic modelling of complex metabolic networks.
FEBS J. 2009 Jan;276(2):410-24.

Hoffmann S, Holzhütter HG.
Uncovering metabolic objectives pursued by changes of enzyme levels.
Ann N Y Acad Sci. 2009 Mar;1158:57-70.

Lock JF, Taheri P, Bauer S, Holzhütter HG, Malinowski M, Neuhaus P, Stockmann M.
Interpretation of Non-Invasive Breath Tests Using 13C-labeled Substrates - A Preliminary Report With superset13 C-Methacetin.
Eur J Med Res. 2009;14(12):547-50.

Schlüter H, Apweiler R, Holzhütter HG, Jungblut PR.
Finding one's way in proteomics: a protein species nomenclature.
Chem Cent J. 2009 Sep 9;3:11.

2008

Berndt N, Rendall AD.
Isotropization in the approach to big rip singularities for Cardassian models.
Classical and Quantum Gravity, 2008. 25(14).

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. 2008;20:277-84.

Hübner K, Schwager T, Winkler K, Reich JG, Holzhütter HG. (2008)
Computational lipidology: predicting lipoprotein density profiles in human blood plasma.
PLoS Comput Biol. 2008 May 23;4(5):e1000079.

Huthmacher C, Gille C, Holzhütter HG. (2008)
A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling.
J Theor Biol. 2008 Jun 7;252(3):456-64.

Jungblut PR, Holzhütter HG, Apweiler R, Schlüter H. (2008)
The speciation of the proteome.
Chem Cent J. 2008 Jul 18;2:16.

Menküc BS, Gille C, Holzhütter HG. (2008)
Computer aided optimization of carbon atom labeling for tracer experiments.
Genome Inform. 20, 270-276

Mishto M, Luciani F, Holzhütter HG, Bellavista E, Santoro A, Textoris-Taube K, Franceschi C, Kloetzel PM, Zaikin A. (2008)
Modeling the in vitro 20S proteasome activity: The effect of PA28 - and of the sequence and length of polypeptides on the degradation kinetics.
J Mol Biol. 2008 Apr 11;377(5):1607-17

Schatz MM, Peters B, Akkad N, Ullrich N, Martinez AN, Carroll O, Bulik S, Rammensee HG, van Endert P, Holzhütter HG, Tenzer S, Schild H. (2008) 
Characterizing the N-terminal processing motif of MHC class I ligands.
J Immunol. 2008 Mar 1;180(5):3210-7.

2007

Gille C, Hoffmann S, Holzhütter HG. (2007)
METANNOGEN: compiling features of bio¬che¬mi¬cal reactions needed for the reconstruction of metabolic networks.
BMC Syst Biol. 2007 Jan 9;1:5.

Grimbs S, Selbig J, Bulik S, Holzhütter HG, Steuer R. (2007)
The stability and robustness of metabolic networks.
Mol Syst Biol. 2007;3:146.

Hoffmann S, Hoppe A, Holzhütter HG. (2007)
Pruning genome-scale metabolic models to consistent ad functionen networks.
Genome Inform. 2007;18:308-19.

Hoppe A, Hoffmann S, Holzhütter HG. (2007)
Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distri¬bu¬tions in metabolic networks.
BMC Syst Biol. 2007 Jun 1;1:23.

Huthmacher C, Gille C, Holzhütter HG. (2007)
Computational analysis of protein-protein interactions in metabolic networks of Escherichia coli and yeast.
Genome Inform. 2007;18:162-72.

Saam J, Ivanov I, Walther M, Holzhütter HG, Kuhn H. (2007)
Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels.
Proc Natl Acad Sci U S A. 2007 Aug 14;104(33):13319-24.

2006

Hoffmann S, Hoppe A, Holzhütter HG. (2006)
Composition of metabolic flux distributions by functonally interpretable minimal flux modes (MinModes).
Genome Inform. 2006;17(1):195-207.

Holzhütter HG. (2006)
The generalized flux-minimization method and ist application to metabolic networks affected by enzyme deficiencies.
Biosystems. 2006 Feb-Mar;83(2-3):98-107.

2005

Bulik S, Peters B, Holzhütter HG. (2005)
Quantifying the contribution of defective ribosomal products to antigen production: a model-based computational analysis.
J Immunol., 175(12):7957-64.

Gille C, Hoffmann S, Holzhütter HG. (2005)
Combining bioinformatics resources for the struc¬tu¬ral modelling of eukaryotic metabolic networks.
Genome Inform. 2005;16(1):223-32.

Ivanov I, Saam J, Kuhn H, Holzhütter HG. (2005)
Dual role of oxygen during lipoxygenase reactions.
FEBS J. 2005 May;272(10):2523-35.

Kühn H, Saam J, Eibach S, Holzhütter HG, Ivanov I, Walther M. (2005)
Structural biology of mammalian lipoxygenases: enzymatic consequences of targeted alterations of the protein structure.
Biochem Biophys Res Commun. 2005 Dec 9;338(1):93-101.

Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild H, Holzhütter HG. (2005)
Modeling the MHC class I binding.
Cell Mol Life Sci. 2005 May;62(9):1025-37.

2004

Bulik, S., Peters, B., Ebeling, C. and Holzhütter, H. (2004)
Cytosolic processing of proteasomal cleavage products can enhance the presentation effiiency of MHC-1 epitopes.
Genome Inform. 2004;15(1):24-34.

Epple G, Langfeld K, Baier M, Holzhütter HG, Schleuning WD, Köttgen E, Gessner R, Praus M. (2004)
Both lysine-clusters of the NH(2)-terminal prion-protein fragment PrP23 are essential for t-PA mediated plasminogen activation.
Thromb Haemost. 2004 Mar;91(3):465-72.

Holzhütter HG. (2004)
Mathematische Zellmodelle - Fiktion oder greifbare Wirklichkeit?
Bioforum.

Holzhütter HG. (2004)
Studying enzyme kinetics by means of progress-curve analysis.
In: Proc. of the 1st International Beilstein Workshop on Exp. Standard Conditions of Enzyme Characterizations, 5.-8.Oct. 2003. Logos Verlag Berlin, pp. 99-113

Holzhütter HG. (2004)
The principle of flux minimization and ist application to estimate stationary fluxes in metabolic networks.
Eur J Biochem. 2004 Jul;271(14):2905-22.

Holzhütter S, Holzhütter HG. (2004)
Computational design of reduced metabolic networks.
Chembiochem. 2004 Oct 4;5(10):1401-22.

Ivanov I, Romanov S, Ozdoba C, Holzhütter HG, Myagkova G, Kühn H. (2004)
Enantioselective substrate specificity of 15-lipoxygenase 1.
Biochemistry. 2004 Dec 21;43(50):15720-8.

2003

Hakenberg J, Nussbaum AK, Schild H, Rammensee HG, Kuttler C, Holzhütter HG, Kloetzel PM, Kaufmann SH, Mollenkopf HJ. (2003)
MAPPP: MHC class I antigenic peptide processing prediction.
Appl Bioinformatics. 2003;2(3):155-8.

Holzhütter HG, Genschow E, Diener W, Schlede E. (2003)
Dermal and inhalaton acute toxic class methods: test procedures and biometric avaluations for the Globally Harmonized Classification System.
Arch Toxicol. 2003 May;77(5):243-54.

Peters B, Bulik S, Tampe R, Van Endert PM, Holzhütter HG. (2003)
Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors.
J Immunol. 2003 Aug 15;171(4):1741-9.

Praus M, Kettelgerdes G, Baier M, Holzhütter HG, Jungblut PR, Maissen M, Epple G, Schleuning WD, Köttgen E, Aguzzi A, Gessner R. (2003)
Stimulation of plasminogen activaton by recombinant cellular prion protein is conserved in the NH2-terminal fragment PrP23-10.
Thromb Haemost. 2003 May;89(5):812-9.

Stohwasser R, Holzhütter HG, Lehmann U, Henklein P, Kloetzel PM. (2003)
Hepatitis B virus HBx peptide 116-138 and proteasome activator PA28 compete for binding to the proteasome alpha4/MC6 subunit. 
Biol Chem. 2003 Jan;384(1):39-49.

2002

Klipp E, Heinrich R, Holzhütter HG. (2002)
Prediction of temporal gene expression. Metabolic optimization by re-distribution of enzyme acitivities.
Eur J Biochem. 2002 Nov;269(22):5406-13.

Peters B, Holzhütter HG. (2002)
In vitro phototoxicity testing: development and validation of a new concentration response analysis software and biostatistical analsyses related to the use of various prediction models.
Altern Lab Anim. 2002 Jul-Aug;30(4):415-32.

Peters B, Janek K, Kuckelkorn U, Holzhütter HG. (2002)
Assessment of proteasomal cleavage probabilities from kinetic analysis of time-dependent product formation.
J Mol Biol. 2002 May 3;318(3):847-62.

2001

Kuon W, Holzhütter HG, Appel H, Grolms M, Kollnberger S, Traeder A, Henklein P, Weiss E, Thiel A, Lauster R, Bowness P, Radbruch A, Kloetzel PM, Sieper J. (2001)
Identification of HLA-B27-restricted peptides from the Chlamydia tra¬cho¬matis proteome with possible relevance to HLA-B27-associated diseases.
J Immunol. 2001 Oct 15;167(8):4738-46.

Pospisil H, Holzhütter HG. (2001)
A compartment model to calculate time-dependent con¬cen¬tra¬tion profiles to topically applied chemical compounds in the anterior com¬part¬ments of the rabbit eye. Altern Lab Anim. 2001 May-Jun;29(3):347-65.
Schreiber S, Ludwig K, Herrmann A, Holzhütter HG. (2001) Stochastic simulation of hemag¬glu¬tinin-medited fusion pore formation. Biophys J. 2001 Sep;81(3):1360-72.
Velders MP, Macedo MF, Provenzano M, Elmishad AG, Holzhütter HG, Carbone M, Kast WM. (2001) Human T cell response to endogenously presented HLA-A*0201 restric peptides of simian virus 40 large T antigen. J Cell Biochem. 2001 Apr 2-27;82(1):155-62.

2000

Belkner J, Stender H, Holzhütter HG, Holm C, Kühn H. (2000)
Macrophage cholesteryl ester hydrolases and hormone-sensitive lipase prefer specifically oxidized chol¬esteryl esters as substrates over their non-oxidized counterparts.
Biochem J. 2000 Nov 15;352 Pt 1:125-33.

Holzhütter HG, Kloetzel PM. (2000)
A kinetic model of vertebrate 20S proteasome accounting for the generation of major proteolytic fragments from oligomeric peptide substrates.
Biophys J. 2000 Sep;79(3):1196-205.

Liebsch M, Traue D, Barrabas C, Spielmann H, Uphill P, Wilkins S, McPherson JP, Wiemann C, Kaufmann T, Remmele M, Holzhütter HG. (2000)
The ECVAM prevalidation study on the use of EpiDerm for skin corrosivity testing.
Altern Lab Anim. 2000 May-Jun;28(3):371-401.

Marx U, Lassmann G, Holzhütter HG, Wüstner D, Müller P, Höhlig A, Kubelt J, Herrmann A. (2000)
Rapid flip-flop of phospholipids in endoplasmatic reticulum mem¬branes studied by a stopped-flow approach.
Biophys J. 2000 May;78(5):2628-40.

Schmidtke G, Emch S, Groettrup M, Holzhütter HG. (2000)
Evidence for the existence of a non-catalytic modifier site of peptide hydrolysis by the 20S proteasome.
J Biol Chem. 2000 Jul 21;275(29):22056-63.

Stohwasser R, Salzmann U, Giesebrecht J, Kloetzel PM, Holzhütter HG. (2000)
Kinetic evidences for facilitation of peptide channeling by the protesomal activator PA28.
Eur. Eur J Biochem. 2000 Oct;267(20):6221-30.

1999

Holzhütter HG, Frömmel C, Kloetzel PM. (1999)
A theoretical approach towards the identificatiion of cleavage-determining amino acid motifs of the 20 S proteasome.
J Mol Biol. 1999 Mar 5;286(4):1251-65.

Kuon, W., Lauster, R., Holzhütter, H.G., Braun, J., Sieper, J. (1999)
Screening of the whole chlamydia trachomatis genome for peptides presented by HLA-B27.
Arthritis & Rheumatism 42(9)Suppl., S375 (abstract)

Schmidtke G, Holzhütter HG, Bogyo M, Kairies N, Groll M, de Giuli R, Emch S, Groettrup M. (1999)
How an inhibitor of the HIV-1 protease modulates proteasome activity.
J Biol Chem. 1999 Dec 10;274(50):35734-40.

Walther M, Holzhütter HG, Kuban RJ, Wiesner R, Rathmann J, Kühn H. (1999)
The Inhibition of Mammalian 15-Lipoxygenases by the Anti-Inflammatory Drug Ebselen: Dual-Type Mechanism Involving Covalent Linkage and Alteration of the Iron Ligand Sphere.
Mol Pharmacol. 1999 Jul;56(1):196-203.

Zaiss DM, Standera S, Holzhütter H, Kloetzel P, Sijts AJ. (1999)
The proteasome inhibitor PI31 competes with PA28 for binding to 20S proteasomes.
FEBS Lett. 1999 Sep 3;457(3):333-8.

1998

Fentem JH, Archer GE, Balls M, Botham PA, Curren RD, Earl LK, Esdaile DJ, Holzhütter HG, Liebsch M. (1998)
The ECVAM international validation study on in vitro tests for skin corrosivity. 2. Results and evaluation by the management team.
Toxicol In Vitro. 1998 Aug;12(4):483-524.

Ivanov I, Schwarz K, Holzhütter HG, Myagkova G, Kühn H. (1998)
Omega-oxidation impairs oxidizability of polyenoic fatty acids by 15-lipoxygenases: consequences for substrate orientation at the active site.
Biochem J. 1998 Dec 1;336 ( Pt 2):345-52.

Spielmann H, Balls M, Dupuis J, Pape WJ, de Silva O, Holzhütter HG, Gerberick F, Liebsch M, Lovell WW, Pfannenbecker U. (1998)
A Study on UV-Filter Chemicals from annex VII of European Union Directive 76/768/EEC in the in vitro 3T3 NRU phototoxicity test.
Altern Lab Anim. 1998 Sep-Oct;26(5):679-708.

Spielmann H, Balls M, Dupuis J, Pape WJ, Pechovitch G, de Silva O, Holzhütter HG, Clothier R, Desolle P, Gerberick F, Liebsch M, Lovell WW, Maurer T, Pfannenbecker U, Potthast JM, Csato M, Sladowski D, Steiling W, Brantom P. (1998)
The International EU/COLIOPA in vitro phototoxicity validation study: results of phase II (Blind Trial). Part 1: The 3T3 NRU phototoxicity.
Toxicol In Vitro. 1998 Jun 1;12(3):305-27.

1997

Archer G, Balls M, Bruner LH, Curren RD, Fentem JH, Holzhütter HG, Liebsch M, Lovell DP, Southee JA. (1997)
The validation of toxicological prediction models.

Feder P, Carr G, Holzhütter HG, Lovell D, Springer J. (1997)
Statistical planning and analysis considerations in the evaluation of in vitro alternatives to whole animal use for eye irritation testing.
Food Chem Toxicol. 1997 Jan;35(1):167-74.

Holzhütter HG. (1997)
A general measure of in vitro phototoxicity derived from pairs of dose-response curves and its use for predicting the in vivo phototoxicity of chemicals.
ATLA 25: 445-462

Holzhütter HG, Wiesner R, Rathmann J, Stösser R, Kühn H. (1997)
A kinetic model for the in¬ter¬action of nitric oxide with a mammalian lipoxygenase.
Eur J Biochem. 1997 May 1;245(3):608-16

Schwendel A, Grune T, Holzhütter HG, Siems WG. (1997)
Models for the regulation of purine metabolism in rat hepatocytes: evaluation of tracer experiments.
Am J Physiol. 1997 Jul;273(1 Pt 1):G239-46.

Spielmann H, Balls M, Pechovitch G, Dupuis J, deSilva O, Pape W, Holzhütter HG. (1997)
A validaton study of in vitro photoirritation test in a joint EU/COLIPA project: preliminary report.
In: Proc. of the World Congress on Animal Alternatives Welfare and Ethics (L.F.M. von Zutphen and M. Balls, eds.) pp 1135-1143.

Spielmann H, Liebsch M, Döring B, Moldenhauer F, Holzhütter HG. et al. (1997)
Possibilities to check in vitro/in vivo correlations when validating in vitro methods in toxicology. In: Correlations between in vitro and in vivo investigation in inhalation toxicology.
ILSI Monographs, ILSI Press Washington, DC (Eds. Mohr, U. et al.) pp. 94-111

Spielmann H, Liebsch M, Moldenhauer F, Holzhütter HG, Bagley DM, Lipman JM, Pape WJ, Miltenburger H, de Silva O, Hofer H, Steiling W. (1997)
IRAG working group 2. CAM-based assays. Interagency Regulatory Alternatives Group.
Food Chem Toxicol. 1997 Jan;35(1):39-66.

1996

Holzhütter HG, Archer G, Dami N, Lovell DP, Saltelli A, Sjönstrom M. (1996)
Recommendations for the application of biostatistical methods during the development and validation of alternative toxicological methods.
ATLA 24: 511-530

Holzhütter HG, Spielmann H. (1996)
The use of prediction models in validation studies: What should they predict?
ATLA 24: 881-884

Spielmann H, Liebsch M, Kalweit S, Moldenhauer F, Wirnsberger T, Holzhütter HG, SCHNEIDER B, GLASER S, GERNER I, PAPE WJW, KREILING R, KRAUSER K, MILTENBURGER HG, STEILING W,  LUEPKE NP,  MÜLLER N, KREUZER H, MÜRMANN P, SPENGLER J, BERTRAM-NEIS E, SIEGEMUND B, WIEBEL FJ. (1996)
Results of a validation study in Germany on two in vitro alternatives to the draize eye irritation test, the HET-CAM test and the 3T3 NRU cytotoxicity test.
ATLA. 1996, 24(5): 741-858

Wiesner R, Rathmann J, Holzhütter HG, Stösser R, Mäder K, Nolting H, Kühn H. (1996)
Nitric oxide oxidises a ferrous mammalian lipoxygenase to a pre-activated ferric species.
FEBS Lett. 1996 Jul 8;389(3):229-32.

1985 - 1995

Spielmann H, Liebsch M, Moldenhauer F, Holzhütter HG, de Silva O. (1995)
Modern biostatistical methods for assessing in vitro/in vivo correlation of severely eye irritating chemicals in a validation study of in vitro alternatives to the Draize eye test.
Toxicol In Vitro. 1995 Aug;9(4):549-56.

Hausdorf G, Krüger K, Küttner G, Holzhütter HG, Frömmel C, Höhne WE. (1988)
Oxydation of a methionine residue in subtilisin-type proteinases by the hydrogenperoxide-borate system - an active site directed reaction.
Biochim Biophys Acta. 1988 Jan 4;952(1):20-6.

Frömmel C, Holzhütter HG. (1985)
An estimate on the effect of point mutation and natural selection on the rate of amino acid replacement in proteins.
J Mol Evol. 1984-1985;21(3):233-57.

Holzhütter HG, Henke W, Dubiel W, Gerber G. (1985)
A mathematical model to study the short-term regulation of mitochondrial energy transduction.
Biochim Biophys Acta. 1985 Nov 27;810(2):252-68.

Küttner GA, Holzhütter HG, Frömmel C. (1985)
The use of progress curves for the estimation of inactivation rate constants of enzymes.
Biomed Biochim Acta. 1985;44(7-8):1025-34.