COPASI's Use In Research

2017
Agrawal R, Kalmady SV, Venkatasubramanian G (2017) In Silico Model-driven Assessment of the Effects of Brain-derived Neurotrophic Factor Deficiency on Glutamate and Gamma-Aminobutyric Acid: Implications for Understanding Schizophrenia Pathophysiology. Clinical Psychopharmacology and Neuroscience 15:115 Physiology Signaling Link
Baumgart L, Mather W, Hasty J (2017) Synchronized DNA cycling across a bacterial population. Nature Genetics, 49:1282–128 Synthetic Biology Microbiology Link
Beuke K, Schildberg FA, Pinna F, Albrecht U, Liebe R, Bissinger M, Schirmacher P, Dooley S, Bode JG, Knolle PA, Kummer U, Breuhahn K, Sahle S (2017) Quantitative and integrative analysis of paracrine hepatocyte activation by non-parenchymal cells upon lipopolysaccharide induction. The FEBS Journal 284:796–813 Immunology Link
Brezny AC, Landis CR (2017) Unexpected CO Dependencies, Catalyst Speciation, and Single-Turnover Hydrogenolysis Studies of Hydroformylation via High Pressure NMR Spectroscopy. Journal of the American Chemical Society 139:2778–2785 Chemistry Link
Chelushkin MA, Panteleev MA, Sveshnikova AN (2017) Activation of the contact pathway of blood coagulation on the circulating microparticles may explain blood plasma coagulation induced by dilution. Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology 11:130–143 Biophysics Link
Dalle Pezze P, Le Novère N (2017) SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology, 11:46 Computational Method Software Link
Fortuny AF (2017) Chemometric Approaches for Systems Biology. PhD Thesis, Universitat Politècnica de València. Computational Method Link
Haanstra JR, Gerding A, Dolga AM, Sorgdrager FJ, Buist-Homan M, du Toit F, Faber KN, Holzhütter H-G, Szöör B, Matthews KR, Snoep JL, Westerhoff HV, Bakker BM (2017) Targeting pathogen metabolism without collateral damage to the host. Scientific Reports 7:40406 Microbiology Parasitology Metabolism Link
Haffez H, Chisholm DR, Valentine R, Pohl E, Redfern C, Whiting A (2017) The molecular basis of the interactions between synthetic retinoic acid analogues and the retinoic acid receptors. MedChemComm 8:578 Biochemistry Pharmacology Link
Hagen SJ, Son M (2017) Origins of heterogeneity in Streptococcus mutans competence: interpreting an environment-sensitive signaling pathway. Physical Biology 14:015001 Signaling Microbiology Link
Haurat MF, Figueiredo AS, Hoffmann L, Li L, Herr K, J Wilson A, Beeby M, Schaber J, Albers S-V (2017) ArnS, a kinase involved in starvation-induced archaellum expression. Molecular Microbiology 103:181–194 Microbiology Signaling Link
Kagan VE, Mao G, Qu F, Angeli JPF, Doll S, Croix CS, Dar HH, Liu B, Tyurin VA, Ritov VB, Kapralov AA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli RK, Stockwell BR, Tyurina YY, Conrad M, Bayır H (2017) Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis. Nature Chemical Biology 13:81–90 Signaling Cell Biology Link
Kaushik AC, Kumar A, Dwivedi VD, Bharadwaj S, Kumar S, Bharti K, Kumar P, Chaudhary RK, Mishra SK (2017) Deciphering the Biochemical Pathway and Pharmacokinetic Study of Amyloid βeta-42 with Superparamagnetic Iron Oxide Nanoparticles (SPIONs) Using Systems Biology Approach. Molecular Neurobiology Biochemistry Pharmacology Laboratory Method Link
Komasilovs V, Pentjuss A, Elsts A, Stalidzans E (2017) Total enzyme activity constraint and homeostatic constraint impact on the optimization potential of a kinetic model. Biosystems 162:128-134 Computational Method Biotechnology Link
Stalidzans E, Mozga I, Sulins J, Zikmanis P (2017) Search for a Minimal Set of Parameters by Assessing the Total Optimization Potential for a Dynamic Model of a Biochemical Network. IEEE/ACM transactions on computational biology and bioinformatics 14:978–985 Computational Method Biotechnology Link
Stasiw DE, Mandal M, Neisen BD, Mitchell LA, Cramer CJ, Tolman WB (2017) Why So Slow? Mechanistic Insights from Studies of a Poor Catalyst for Polymerization of ε-Caprolactone. Inorganic Chemistry 56:725–728 Chemistry Link
Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT (2017) A proteomic approach to analyse the aspirin-mediated lysine acetylome. Molecular & Cellular Proteomics 16:310–326 Pharmacology Biochemistry Laboratory Method Link
Tolleter D, Chochois V, Poiré R, Price GD, Badger MR (2017) Measuring CO2 and HCO3- permeabilities of isolated chloroplasts using a MIMS-18O approach. Journal of Experimental Botany. doi:10.1093/jxb/erx188 Laboratory Method Physiology Link
Winter F, Bludszuweit-Philipp C, Wolkenhauer O (2017) Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer’s disease. Journal of Cerebral Blood Flow & Metabolism 0271678X17693024 Metabolism Biophysics Link
Zaccarin M, Bosello-Travain V, Di Paolo ML, Falda M, Maiorino M, Miotto G, Piccolo S, Roveri A, Ursini F, Venerando R, Toppo S (2017) Redox status in a model of cancer stem cells. Archives of Biochemistry and Biophysics 617:120–128 Biochemistry Cell Biology Link
Zimmer C, Yaesoubi R, Cohen T (2017) A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models. PLOS Computational Biology 13:e1005257 Computational Method Link

21 publications
2016
Andrews SS, Peria WJ, Richard CY, Colman-Lerner A, Brent R (2016) Push-pull and feedback mechanisms can align signaling system outputs with inputs. Cell Systems 3:444–455 Signaling Link
Barbon A, Bortolus M, Isse AA, Reznikov VA, Weiner L (2016) Electron transfer in pH-sensitive nitroxide radicals. Chemical Physics Letters 665:137–140 Chemistry Link
Behinaein B, Rudie K, Sangrar W (2016) Petri net siphon analysis and graph theoretic measures for identifying combination therapies in cancer. IEEE/ACM Transactions on Computational Biology and Bioinformatics doi:10.1109/TCBB.2016.2614301 Computational Method Link
Bergmann FT, Sahle S, Zimmer C (2016) Piecewise parameter estimation for stochastic models in COPASI. Bioinformatics 32:1586–1588 Computational Method Link
Beuke K (2016) TNF-induced NF-κB Signal Transduction in the Liver. PhD Thesis, Heidelberg University. Immunology Signaling Link
Boross G, Papp B (2016) No evidence that protein noise-induced epigenetic epistasis constrains gene expression evolution. Molecular Biology and Evolution 34:380–390 Metabolism Genetics Link
Burés J (2016) A Simple Graphical Method to Determine the Order in Catalyst. Angew. Chem. Int. Ed. Engl. 55:2028-31 Chemistry Link
Bush A, Vasen G, Constantinou A, Dunayevich P, Patop IL, Blaustein M, Colman-Lerner A (2016) Yeast GPCR signaling reflects the fraction of occupied receptors, not the number. Molecular Systems Biology 12:898 Signaling Link
Claudino M, Zhang X, Alim MD, Podgórski M, Bowman CN (2016) Mechanistic Kinetic Modeling of Thiol–Michael Addition Photopolymerizations via Photocaged “Superbase” Generators: An Analytical Approach. Macromolecules 49:8061–8074 Chemistry Link
Coakley S, Richmond P, Gheorghe M, Chin S, Worth D, Holcombe M, Greenough C (2016) Large-Scale Simulations with FLAME. In Intelligent Agents in Data-intensive Computing (Kolodziej J, Correia L, Molina JM eds.), Springer pp.123-142 Software Link
Compel WS (2016) The use of coordinating solvents in gold cluster synthesis. PhD Thesis, Colorado State University. Chemistry Link
Costa RS, Vinga S (2016) Control analysis of the impact of allosteric regulation mechanism in a Escherichia coli kinetic model: Application to serine production. Biochemical Engineering Journal 110:59–70 Metabolism Link
Dalle Pezze P, Ruf S, Sonntag AG, Langelaar-Makkinje M, Hall P, Heberle AM, Navas PR, Van Eunen K, Tölle RC, Schwarz JJ, Wiese H, Warscheid B, Deitersen J, Stork B, Fäßler E, Schäuble S, Horvatovich P, Shanley DP, Thedieck K (2016) A systems study reveals concurrent activation of AMPK and mTOR by amino acids. Nature Communications 7:13254 Signaling Link
del Pozo J, Salas G, Álvarez R, Casares JA, Espinet P (2016) The Negishi Catalysis: Full Study of the Complications in the Transmetalation Step and Consequences for the Coupling Products. Organometallics 35:3604–3611 Chemistry Link
Di Camillo B, Carlon A, Eduati F, Toffolo GM (2016) A rule-based model of insulin signalling pathway. BMC Systems Biology 10:38 Signaling Link
Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T (2016) Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science advances 2:e1600823 Biochemistry Signaling Link
Dunn AL, Landis CR (2016) Progress toward reaction monitoring at variable temperatures: a new stopped-flow NMR probe design. Magnetic Resonance in Chemistry 55:329–336 Laboratory Method Link
Froese RD, Whiteker GT, Peterson TH, Arriola DJ, Renga JM, Shearer JW (2016) Computational and Experimental Studies of Regioselective SNAr Halide Exchange (Halex) Reactions of Pentachloropyridine. The Journal of Organic Chemistry 81:10672–10682 Chemistry Link
Furrow SD, Cervellati R, Greco E (2016) Study of the transition to higher iodide in the malonic acid Briggs–Rauscher oscillator. Reaction Kinetics, Mechanisms and Catalysis 118:59–71 Chemistry Link
Ganesan N, Li J, Sharma V, Jiang H, Compagnoni A (2016) Process Simulation of Complex Biological Pathways in Physical Reactive Space and Reformulated for Massively Parallel Computing Platforms. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13:365–379 Computational Method Link
Gerber S, Fröhlich M, Lichtenberg-Fraté H, Shabala S, Shabala L, Klipp E (2016) A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae. PLOS Computational Biology 12:e1004703 Metabolism Physiology Link
Haffez HRS (2016) Design, synthesis and biological evaluation of small molecules for controlling cellular development. PhD Thesis, Durham University, UK. Biochemistry Pharmacology Link
Hamgini BB (2016) Petri net siphon analysis and network centrality measures for identifying combination therapies in signaling pathways. PhD Thesis, Queen’s University, Kingston, Ontario, Canada Computational Method Link
Hendrickx DM, Souza T, Jennen DG, Kleinjans JC (2016) DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. Archives of Toxicology 1–10 Toxicology Link
Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D (2016) Notions of similarity for systems biology models. Briefings in Bioinformatics bbw090 Computational Method Link
Ihekwaba AE, Mura I, Walshaw J, Peck MW, Barker GC (2016) An Integrative Approach to Computational Modelling of the Gene Regulatory Network Controlling Clostridium botulinum Type A1 Toxin Production. PLoS Computational Biology 12:e1005205 Microbiology Link
Julien-Laferrière A (2016) Models and algorithms applied to metabolism: From revealing the responses to perturbations towards the design of microbial consortia. PhD Thesis, Université Lyon 1-Claude Bernard Computational Method Metabolism Microbiology Link
Jung J, Czabany T, Wilding B, Klempier N, Nidetzky B (2016) Kinetic analysis and probing with substrate analogues of the reaction pathway of the nitrile reductase QueF from Escherichia coli. Journal of Biological Chemistry 291:25411–25426 Enzymology Link
Jungmann R, Avendaño MS, Dai M, Woehrstein JB, Agasti SS, Feiger Z, Rodal A, Yin P (2016) Quantitative super-resolution imaging with qPAINT. Nature Methods 13:439–442 Laboratory Method Macromolecular Biochemistry Link
Kagan VE, Mao G, Qu F, Angeli JPF, Doll S, St Croix C, Dar HH, Liu B, Tyurin VA, Ritov VB, Kapralov AA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli RK, Stockwell BR, Tyurina YY, Conrad M, Bayır H (2017) Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis. Nature Chemical Biology 13:81–90 Metabolism Cell Biology Link
Kilner J, Corfe BM, McAuley MT, Wilkinson SJ (2016) A deterministic oscillatory model of microtubule growth and shrinkage for differential actions of short chain fatty acids. Mol. BioSystems 12:93-101 Cell Biology Link
Kollarovic G, Studencka M, Ivanova L, Lauenstein C, Heinze K, Lapytsko A, Talemi SR, Figueiredo AS, Schaber J (2016) To senesce or not to senesce: how primary human fibroblasts decide their cell fate after DNA damage. Aging 8:158 Cell Biology Link
Laviska DA, Zhou T, Kumar A, Emge TJ, Krogh-Jespersen K, Goldman AS (2016) Single and Double C–H Activation of Biphenyl or Phenanthrene. An Example of C–H Addition to Ir(III) More Facile than Addition to Ir(I). Organometallics 35:1613–1623 Chemistry Link
Leber A, Abedi V, Hontecillas R, Viladomiu M, Hoops S, Ciupe S, Caughman J, Andrew T, Bassaganya-Riera J (2016) Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection. Journal of Theoretical Biology 398:74–84 Immunology Link
Leber A, Bassaganya-Riera J, Tubau-Juni N, Zoccoli-Rodriguez V, Viladomiu M, Abedi V, Lu P, Hontecillas R (2016) Modeling the Role of Lanthionine Synthetase C-Like 2 (LANCL2) in the Modulation of Immune Responses to Helicobacter pylori Infection. PloS One 11:e0167440 Immunology Link
Ledwitch KV, Barnes RW, Roberts AG (2016) Unravelling the complex drug–drug interactions of the cardiovascular drugs, verapamil and digoxin, with P-glycoprotein. Bioscience Reports 36:e00309 Pharmacology Biochemistry Link
Ledwitch KV, Gibbs ME, Barnes RW, Roberts AG (2016) Cooperativity between verapamil and ATP bound to the efflux transporter P-glycoprotein. Biochemical Pharmacology 118:96–108 Pharmacology Biochemistry Link
Levenhagen MA, Ferreira GA, Pereira GM, Santos AR (2016) A computer simulation model for Strongyloides infection. PeerJ Preprints 4:e2399v1 Immunology Parasitology Link
Levin MD, Kaphan DM, Hong CM, Bergman RG, Raymond KN, Toste FD (2016) Scope and Mechanism of Cooperativity at the Intersection of Organometallic and Supramolecular Catalysis. Journal of the American Chemical Society 138:9682–9693 Enzymology Chemistry Link
Lima AP, Baixinho V, Machado D, Rocha I (2016) A Comparative Analysis of Dynamic Models of the Central Carbon Metabolism of Escherichia coli. IFAC-PapersOnLine 49:270–276 Metabolism Link
Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen W-H, Bork P, Glass JI, Serrano L, Lluch-Senar M (2016) Bacterial antisense RNAs are mainly the product of transcriptional noise. Science Advances 2:e1501363 Microbiology Genetics Link
Marín-Hernández Á, Rodríguez-Zavala JS, Del Mazo-Monsalvo I, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2016) Inhibition of Non-flux-Controlling Enzymes Deters Cancer Glycolysis by Accumulation of Regulatory Metabolites of Controlling Steps. Frontiers in Physiology 7:412 Metabolism Link
McClary WD (2016) Interactions of Cytochrome P450 3A4 with Phospholipid Bilayer Nanodiscs. PhD Thesis, Seattle, University of Washington. Biochemistry Macromolecular Biochemistry Link
Meng X, Firczuk H, Pietroni P, Westbrook R, Dacheux E, Mendes P, McCarthy JE (2016) Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis. Nucleic Acids Research 45:1015–1025 Biochemistry Macromolecular Biochemistry Link
Mizeranschi AE, Swain MT, Scona R, Fazilleau Q, Bosak B, Piontek T, Kopta P, Thompson P, Dubitzky W (2016) MultiGrain/MAPPER: A distributed multiscale computing approach to modeling and simulating gene regulation networks. Future Generation Computer Systems 63:1–14 Computational Method Link
Monti M, Matos MR, Choi J-M, Ferry MS, Borek B (2016) A modified galactose network model with implications for growth. arXiv preprint arXiv:1601.03235 Link
Morgan AE, Mooney KM, Wilkinson SJ, Pickles NA, Mc Auley MT (2016) Mathematically modelling the dynamics of cholesterol metabolism and ageing. Biosystems 145:19–32 Metabolism Link
Orlenko A, Hermansen RA, Liberles DA (2016) Flux control in glycolysis varies across the tree of life. Journal of Molecular Evolution 82:146–161 Metabolism Link
Orlenko A, Teufel AI, Chi PB, Liberles DA (2016) Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable. Biology Direct 11:31 Genetics Metabolism Link
Ouzounoglou E, Dionysiou D, Stamatakos GS (2016) Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway. BMC Systems Biology 10:23 Cell Biology Link
Özkar S, Finke RG (2016) Palladium(0) Nanoparticle Formation, Stabilization, and Mechanistic Studies: Pd(acac) 2 as a Preferred Precursor, [Bu 4 N] 2 HPO 4 Stabilizer, plus the Stoichiometry, Kinetics, and Minimal, Four-Step Mechanism of the Palladium Nanoparticle Formation and Subsequent Agglomeration Reactions. Langmuir 32:3699–3716 Chemistry Link
Palai T, Kumar A, Bhattacharya PK (2016) Enzyme immobilization/bioconjugation in producing galactio-oligosaccharidies from lactose: developments of kinetic models and bio-reactors. Materials Today: Proceedings 3:3568–3586 Biotechnology Link
Panchal C, Azimi S, Petre I (2016) Generating the Logicome of a Biological Network. International Conference on Algorithms for Computational Biology. Springer, 38–49 Computational Method Signaling Link
Pappalardo F, Russo G, Candido S, Pennisi M, Cavalieri S, Motta S, McCubrey JA, Nicoletti F, Libra M (2016) Computational Modeling of PI3K/AKT and MAPK Signaling Pathways in Melanoma Cancer. PLOS ONE 11:e0152104 Signaling Link
Pires JC, Conant GC (2016) Robust yet fragile: expression noise, protein misfolding, and gene dosage in the evolution of genomes. Annual Review of Genetics 50:113–131 Genetics Genomics Link
Pletneva NV, Pletnev S, Pakhomov AA, Chertkova RV, Martynov VI, Muslinkina L, Dauter Z, Pletnev VZ (2016) Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms. Acta Crystallographica Section D: Structural Biology D72:922-932 Biophysics Link
Proctor CJ, Gartland A (2016) Simulated interventions to ameliorate age-related bone loss indicate the importance of timing. Frontiers in Endocrinology 7:61 Physiology Signaling Link
Rantasalo A, Czeizler E, Virtanen R, Rousu J, Lähdesmäki H, Penttilä M, Jäntti J, Mojzita D (2016) Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae. PLOS ONE 11:e0148320 Genetics Microbiology Synthetic Biology Link
Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G (2016) Cellular Growth Arrest and Persistence from Enzyme Saturation. PLOS Computational Biology 12:e1004825 Microbiology Metabolism Link
Reichard EL, Chirico GG, Dewey WJ, Nassif ND, Bard KE, Millas NE, Kraut DA (2016) Substrate Ubiquitination Controls the Unfolding Ability of the Proteasome. Journal of Biological Chemistry 291:18547–18561 Biochemistry Macromolecular Biochemistry Link
Rentergent J, Driscoll MD, Hay S (2016) Time course analysis of enzyme-catalyzed DNA polymerization. Biochemistry 55:5622–5634 Biochemistry Enzymology Macromolecular Biochemistry Link
Salcedo-Sora JE, Mc Auley MT (2016) A mathematical model of microbial folate biosynthesis and utilisation: implications for antifolate development. Molecular BioSystems 12:923–933 Microbiology Metabolism Biotechnology Link
Sano T, Kawata K, Ohno S, Yugi K, Kakuda H, Kubota H, Uda S, Fujii M, Kunida K, Hoshino D, Hatano, Atsushi, Matsuoka Y, Sato M, Suzuki Y, Kuroda S (2016) Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin. Science Signaling 9:ra112–ra112 Signaling Physiology Link
Scharm M, Waltemath D (2016) A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research 5:2421 Computational Method Link
Semenov SN, Kraft LJ, Ainla A, Zhao M, Baghbanzadeh M, Campbell VE, Kang K, Fox JM, Whitesides GM (2016) Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions. Nature 537:656–660 Chemistry Biochemistry Link
Seo D, Soeta T, Sakurai H, Sétif P, Sakurai T (2016) Pre-steady-state kinetic studies of redox reactions catalysed by Bacillus subtilis ferredoxin-NADP+ oxidoreductase with NADP+/NADPH and ferredoxin. Biochimica et Biophysica Acta 1857:678–687 Microbiology Enzymology Link
Shepelyuk TO, Panteleev MA, Sveshnikova AN (2016) Computational modeling of quiescent platelet energy metabolism in the context of whole-body glucose turnover. Mathematical Modelling of Natural Phenomena 11:91–101 Metabolism Physiology Link
Shi Q, Mower MP, Blackmond DG, Rebek J (2016) Water-soluble cavitands promote hydrolyses of long-chain diesters. Proceedings of the National Academy of Sciences 113:9199–9203 Chemistry Link
Sluka JP, Fu X, Swat M, Belmonte JM, Cosmanescu A, Clendenon SG, Wambaugh JF, Glazier JA (2016) A Liver-Centric Multiscale Modeling Framework for Xenobiotics. PloS One 11:e0162428 Physiology Pharmacology Link
Stalidzans E, Mozga I, Sulins J, Zikmanis P (2016) Search for a minimal set of parameters by assessing the total optimisation potential for a dynamic model of a biochemical network. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14:978–985 Computational Method Link
Stanger FV, Burmann BM, Harms A, Aragão H, Mazur A, Sharpe T, Dehio C, Hiller S, Schirmer T (2016) Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification. Proceedings of the National Academy of Sciences 113:E529–E537 Enzymology Link
Sung S, Sale D, Braddock DC, Armstrong A, Brennan C, Davies RP (2016) Mechanistic Studies on the Copper-Catalyzed N-Arylation of Alkylamines Promoted by Organic Soluble Ionic Bases. ACS Catalysis 6:3965–74 Chemistry Link
Sveshnikova AN, Balatskiy AV, Demianova AS, Shepelyuk TO, Shakhidzhanov SS, Balatskaya MN, Pichugin AV, Ataullakhanov FI, Panteleev MA (2016) Systems biology insights into the meaning of the platelet’s dual-receptor thrombin signaling. Journal of Thrombosis and Haemostasis 14:2045–2057 Physiology Signaling Link
Thiaville JJ, Frelin O, García-Salinas C, Harrison K, Hasnain G, Horenstein NA, de la Garza RID, Henry CS, Hanson AD, de Crécy-Lagard V (2016) Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB). Frontiers in Microbiology 7:431 Metabolism Link
Tomalin LE, Day AM, Underwood ZE, Smith GR, Dalle Pezze P, Rallis C, Patel W, Dickinson BC, Bähler J, Brewer TF, Chang CJ-L, Shanley DP, Veal EA (2016) Increasing extracellular H2O2 produces a bi-phasic response in intracellular H2O2, with peroxiredoxin hyperoxidation only triggered once the cellular H2O2-buffering capacity is overwhelmed. Free Radical Biology and Medicine 95:333–348 Metabolism Link
Tootoonchi MH, Sharma G, Calles J, Prabhakar R, Kaifer AE (2016) Cooperative Self-Assembly of a Quaternary Complex Formed by Two Cucurbit [7] uril Hosts, Cyclobis (paraquat-p-phenylene), and a “Designer” Guest. Angewandte Chemie 128:11679–83 Chemistry Link
Troják M, Šafránek D, Hrabec J, Šalagovič J, Romanovská F, Červenỳ J (2016) E-Cyanobacterium. org: A Web-Based Platform for Systems Biology of Cyanobacteria. International Conference on Computational Methods in Systems Biology. Springer, 316–322. Software Link
Tyc KM, Herwald SE, Hogan JA, Pierce JV, Klipp E, Kumamoto CA (2016) The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression. BMC Systems Biology 10:20 Microbiology Immunology Signaling Link
Valero E, Macià H, Ildefonso M, Hernández J-A, González-Sánchez M-I, García-Carmona F (2016) Modeling the ascorbate-glutathione cycle in chloroplasts under light/dark conditions. BMC Systems Biology 10:11 Metabolism Physiology Link
van Eunen K, Volker-Touw CM, Gerding A, Bleeker A, Wolters JC, van Rijt WJ, Martines A-CM, Niezen-Koning KE, Heiner RM, Permentier H, Groen AK, Reijngoud D-J, Derks TGJ, Bakker BM (2016) Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders. BMC Biology 14:107 Metabolism Link
Vinciotti V, Augugliaro L, Abbruzzo A, Wit EC (2016) Model selection for factorial Gaussian graphical models with an application to dynamic regulatory networks. Statistical Applications in Genetics and Molecular Biology 15:193–212 Computational Method Link
Vranish JN, Das D, Barondeau DP (2016) Real-Time Kinetic Probes Support Monothiol Glutaredoxins As Intermediate Carriers in Fe–S Cluster Biosynthetic Pathways. ACS Chemical Biology 11:3114–3121 Enzymology Biochemistry Link
Walker MA, Madduri R, Rodriguez A, Greenstein JL, Winslow RL (2016) Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models. Biophysical Journal 110:1038–1043 Computational Method Link
Wei D, Roisnel T, Darcel C, Clot E, Sortais J-B (2016) Hydrogenation of Carbonyl Derivatives with a Well-Defined Rhenium Precatalyst. ChemCatChem 9:80–83 Chemistry Link
Woller A, Duez H, Staels B, Lefranc M (2016) A mathematical model of the liver circadian clock linking feeding and fasting cycles to clock function. Cell Reports 17:1087–1097 Metabolism Physiology Signaling Link
Xie Y (2016) Multi-scale modelling of the cellular and molecular mechanisms of hyperpolarisation mediated synaptic plasticity in the vestibular nuclei. MSc Thesis, The University of Edinburgh Signaling Physiology Link
Xu H, Diccianni JB, Katigbak J, Hu C, Zhang Y, Diao T (2016) Bimetallic C–C Bond-Forming Reductive Elimination from Nickel. Journal of the American Chemical Society 138:4779–4786 Chemistry Link
Zaccarin M, Bosello-Travain V, Di Paolo ML, Falda M, Maiorino M, Miotto G, Piccolo S, Roveri A, Ursini F, Venerando R, Toppo, Stefano (2016) Redox status in a model of cancer stem cells. Archives of Biochemistry and Biophysics 617:120–128 Metabolism Biochemistry Link
Zimmer C, Bergmann FT, Sahle S (2016) Reducing local minima in fitness landscapes of parameter estimation by using piecewise evaluation and state estimation. arXiv preprint arXiv:1601.04458 Computational Method Link
Zimmer C, Sahle S (2016) Comparison of approaches for parameter estimation on stochastic models: Generic least squares versus specialized approaches. Computational Biology and Chemistry 61:75–85 Computational Method Link

90 publications
2015
Amemiya T, Honma M, Kariya Y, Ghosh S, Kitano H, Kurachi Y, Fujita K, Sasaki Y, Homma Y, Abernethy DR, Kume H, Suzuki H (2015) Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology. npj Systems Biology and Applications 1:15005 Toxicology Signaling Link
Aullón G, Crespo M, Font-Bardia M, Jover J, Martínez M, Pike J (2015) A combined kinetico-mechanistic and computational study on the competitive formation of seven- versus five-membered platinacycles; the relevance of spectator halide ligands. Dalton Trans. 44:17968-79 Chemistry Link
Azimi S, Czeizler E, Gratie C, Gratie D, Iancu B, Ibssa N, Petre I, Rogojin V, Shadbahr T, Shokri F (2015) An Excursion Through Quantitative Model Refinement. Lecture Notes in Computer Science 9504:25-47 Computational Method Software Link
Bodei C, Bortolussi L, Chiarugi D, Guerriero ML, Policriti A, Romanel A (2015) On the impact of discreteness and abstractions on modelling noise in gene regulatory networks. Comput. Biol Chem. 56:98-1089 Computational Method Link
Castello MA (2015) Lipid Regulation as a Critical Factor in the Development of Alzheimer’s Disease. PhD Thesis, Loma Linda University, Loma Linda, California, USA. Metabolism Link
Compel WS, Wong OA, Chen X, Yi C, Geiss R, Häkkinen H, Knappenberger KL Jr, Ackerson CJ (2015) Dynamic Diglyme-Mediated Self-Assembly of Gold Nanoclusters. ACS Nano. 9:11690-8. Chemistry Link
Czabany T; Schmölzer K, Luley-Goedl C, Ribitsch D, Nidetzky B (2015) All-in-one assay for beta-D-galactoside sialyltransferases: quantification of productive turnover, error hydrolysis and site selectivity. Anal. Biochem. 483:47-53 Laboratory Method Enzymology Link
D'Aguanno E, Altamura E, Mavelli F, Fahr A, Stano P, Luisi PL (2015) Physical Routes to Primitive Cells: An Experimental Model Based on the Spontaneous Entrapment of Enzymes inside Micrometer-Sized Liposomes. Life 5:969-96 Synthetic Biology Link
Dacheux E, Firczuk H, McCarthy JEG (2015) Rate control in yeast protein synthesis at the population and single-cell levels. Bioch. Soc. Trans. 43:1266-70 Macromolecular Biochemistry Link
Daneshjou N, Sieracki N, van Nieuw Amerongen GP, Schwartz MA, Komarova YA, Malik AB, Conway DE (2015) Rac1 functions as a reversible tension modulator to stabilize VE-cadherin trans-interaction. J. Cell Biol. 208:23-32 Macromolecular Biochemistry Cell Biology Link
della Sala F, Kay ER (2015) Reversible Control of Nanoparticle Functionalization and Physicochemical Properties by Dynamic Covalent Exchange. Angew. Chem. 127:4261-5 Chemistry Link
Donovan S, Eaton CD, Gower ST, Jenkins KP, LaMar MD, Poli DB, Sheehy R, Wojdak JM (2015) QUBES: a community focused on supporting teaching and learning in quantitative biology, Lett. Biomath. 2:46-55 Education Link
Dornseifer S, Willkomm S, Far RK, Liebschwager J, Beltsiou F, Frank K, Laufer SD, Martinetz T, Sczakiel G, Claussen JC, Restle T (2015) RNAi revised - target mRNA-dependent enhancement of gene silencing. Nucl. Acids Res. 43:10623-32. Macromolecular Biochemistry Genetics Link
Dromms RA, Styczynski MP (2015) Improved metabolite profile smoothing for flux estimation. Molecular BioSystems 11:2394-2405 Computational Method Laboratory Method Link
Dutta-Roy R, Rosenmund C, Edelstein SJ, Le Novère N (2015) Ligand-Dependent Opening of the Multiple AMPA Receptor Conductance States: A Concerted Model. PLoS ONE 10:e0116616 Physiology Macromolecular Biochemistry Link
Emiola A, George J, Andrews SS (2015) A Complete Pathway Model for Lipid A Biosynthesis in Escherichia coli. PLoS ONE 10:e0121216 Metabolism Microbiology Link
Everetts NJ (2015) Computational Analysis of the Control of Cell Cycle Entry. Bachelor's Thesis, Department of Molecular and Cellular Biology, University of Arizona Cell Biology Signaling Link
Gladkovskaya O, Greaney P, Gun'ko YK, O'Connor GM, Meere M, Rochev Y (2015) An experimental and theoretical assessment of quantum dot cytotoxicity. Toxicol. Res. 4:1409-15 Toxicology Link
Hamacher-Brady A, Brady NR (2015) Bax/Bak-Dependent, Drp1-Independent Targeting of XIAP into Inner-Mitochondrial Compartments Counteracts Smac-Dependent Effector Caspase Activation. J. Biol. Chem. 290:22005-18. Signaling Link
Hinze T, Kirkici K, Sauer P, Sauer P, Behre J (2015) Membrane Computing Meets Temperature: A Thermoreceptor Model as Molecular Slide Rule with Evolutionary Potential. Lecture Notes Comp. Sci. 9504:215-235 Computational Method Link
Hristova-Neeley D, Neshchadin D, Gescheidt G (2015) Time-Resolved EPR as a Tool to Investigate Oxygen Quenching in Photoinitiated Radical Polymerizations. J. Phys. Chem. B, 119:13883-7 Chemistry Link
Hudson DA, Gannon SA, Thorpe C, (2015) Oxidative protein folding: From thiol-disulfide exchange reactions to the redox poise of the endoplasmic reticulum. Free Radicals Biol. Med. 80:171-182 Macromolecular Biochemistry Link
Intosalmi J, Ahlfors H, Rautio S, Mannerstöm H, Chen ZJ, Lahesmaa R, Stockinger B, Lähdesmäki H. (2015) Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data. BMC Systems Biol. 9:81. Immunology Cell Biology Signaling Link
Jeong H, John JM, Schrock RR, Hoveyda AH (2015) Synthesis of Alternating trans-AB Copolymers through Ring-Opening Metathesis Polymerization Initiated by Molybdenum Alkylidenes. J. Am. Chem. Soc. 137:2239-42 Chemistry Link
Ji Y, Benkovics T, Beutner GL, Sfouggatakis C, Eastgate MD, Blackmond DG (2015) Mechanistic Insights into the Vanadium-Catalyzed Achmatowicz Rearrangement of Furfurol. J. Organic Chem. 80:1696-1702 Chemistry Link
Jones AR, Rentergent J, Scrutton NS, Hay S (2015) Probing reversible chemistry in coenzyme B12-dependent ethanolamine amonnia lyase with kinetic isotope effects. Chem. Eur. J. 21:8826-31 Enzymology Link
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V (2015) BioModels: Content, Features, Functionality, and Use. CPT:Pharmacometrics & Systems Pharmacology 4:1-14 Software Link
Karapetyan S, Buchler NE (2015) Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators. Phys. Rev. E 92:062712 Macromolecular Biochemistry Theory Link
Kashyap R, Palai T, Bhattacharya PK (2015) Kinetics and model development for enzymatic synthesis of fructo-oligosaccharides using fructosyltransferase. Bioprocess Biosystems Eng. 38:2417-26 Biotechnology Metabolism Link
Kesten D, Kummer U, Sahle S, Hübner K (2015) A new model for the aerobic metabolism of yeast allows the detailed analysis of the metabolic regulation during glucose pulse. Biophys. Chem. 206:40-57. Metabolism Link
Koutsouradis E, Provelengios G, Kouskoumvekakis E, Manolakos ES (2015) Scalable FPGA Accelerator of the NRM Algorithm for Efficient Stochastic Simulation of Large-Scale Biochemical Reaction Networks. in 2015 Euromicro Conference on Digital System Design (DSD) pp.583-590 Computational Method Link
Laurell Nash A, Hertzberg R, Wen YQ, Dahlgren B, Brinck T, Moberg C (2015) Dual Lewis Acid-Lewis Base Catalyzed Acylcyanation of Aldehydes: A Mechanistic Study. Chemistry doi:10.1002/chem.201503782 Chemistry Link
Leber A, Viladomiu M, Hontecillas R, Abedi V, Philipson C, Hoops S, Howard B, Bassaganya-Riera J (2015) Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection. PLoS ONE 10:e0134849 Immunology Link
Lee TW, Yang AS-P, Brittain T, Birch NP (2015) An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: Application to neuroserpin reveals regions that differentially regulate inhibitory activity. Proteins Struct. Funct. Bioinformatics 83:135-52 Macromolecular Biochemistry Link
Li L, Gervasi N, Girault J-A (2015) Dendritic geometry shapes neuronal cAMP signalling to the nucleus. Nature Comm. 6:6319 Cell Biology Signaling Link
Lu P, Abedi V, Mei Y, Hontecillas R, Hoops S, Carbo A, Bassaganya-Riera J (2015) Supervised learning methods in modeling of CD4+ T cell heterogeneity. BioData Mining 8:1-21 Computational Method Immunology Link
Luna A, McFadden GB, Aladjem MI, Kohn KW (2015) Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response. PLoS Comput Biol 11:e1004144 Cell Biology Link
Luo J, Theron R, Sewell LJ, Hooper TN, Weller AS, Oliver AG, McIndoe JS (2015) Rhodium-Catalyzed Selective Partial Hydrogenation of Alkynes. Organometallics 34:3021-8 Chemistry Link
Madsen C, Shmarov F, Zuliani P (2015) BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models. Proceedings 13th International Conference, CMSB 2015 (Roux O, Bourdon J, Eds.), Springer pp182-94 Computational Method Link
Mandlik V, Gurav M, Singh S (2015) Regulatory dynamics of network architecture and function in tristable genetic circuit of Leishmania: a mathematical biology approach. J Biomol. Struct. Dyn. 33:2554-62 Synthetic Biology Genetics Metabolism Link
Marwaha S (2015) A Genomics and Mathematical Modeling Approach for the study of Helicobacter pylori associated Gastritis and Gastric Cancer. PhD Thesis, University of Cincinnati Immunology Signaling Link
Mei Y, Abedi V, Carbo A, Zhang X, Lu P, Philipson C, Hontecillas R, Hoops S, Liles N, Bassaganya-Riera J. (2015) Multiscale modeling of mucosal immune responses. BMC Bioinformatics. 16 Suppl 12:S2 Immunology Link
Mei Y, Carbo A, Hoops S, Hontecillas R, Bassaganya-Riera J (2015) ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes. IEEE/ACM Trans. Comput. Biol. Bioinformatics 12:289-97 Software Link
Mendes P, Oliver SG, Kell DB (2015) Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly. Trends Pharmacological Sciences 36:710-23 Physiology Pharmacology Link
Montes MR, Ferreira-Gomes MS, Centeno M, Rossi RC (2015) The E2P-like state induced by magnesium fluoride complexes in the Na, K-ATPase. Kinetics of formation and interaction with Rb+. Biochim. Biophys Acta 1848:1514-23 Enzymology Link
Müller JM, Risse JM, Friehs K, Flaschel E (2015) Model-based development of an assay for the rapid detection of biotin-blocked binding sites of streptavidin. Eng. Life Sci. 15:627-639 Laboratory Method Link
Nelsen ER, Brezny AC, Landis CR (2015) Interception and Characterization of Catalyst Species in Rhodium Bis(diazaphospholane)-Catalyzed Hydroformylation of Octene, Vinyl Acetate, Allyl Cyanide, and 1-Phenyl-1,3-butadiene. J. Am. Chem. Soc., 2015, 137:14208-219 Chemistry Link
Palaia T, Kumarb A, Bhattacharyaa PK (2015) Kinetic studies and model development for the formation of galacto-oligosaccharides from lactose using synthesized thermo-responsive bioconjugate. Enzyme Microbial Technol. 70:42-49 Biotechnology Enzymology Link
Palmisano A, Hoops S, Watson LT, Jones TC Jr, Tyson JJ, Shaffer CA (2015) JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. BMC Systems Biol. 9:95 Software Link
Patschinski P (2015) Chemoselective Silylation of Alcohols Through Lewis Base-catalyzed Reactions. Experimental and Theoretical Studies. PhD Thesis, Ludwig-Maximilians University of Munich Chemistry Link
Paul D, Dasgupta A, De RK (2015) Exploring the Altered Dynamics of Mammalian Central Carbon Metabolic Pathway in Cancer Cells: A Classical Control Theoretic Approach. PLoS ONE 10:e0137728. Theory Link
Penkler G, du Toit F, Adams W, Rautenbach M, Palm DC, van Niekerk DD, Snoep JL (2015) Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum. FEBS J. 282:1481-511 Metabolism Link
Peñarrubia L, Romero P, Carrió-Seguí A, Andrés-Bordería A, Moreno J and Sanz A (2015) Temporal aspects of copper homeostasis and its crosstalk with hormones. Front. Plant Sci. 6:255. Physiology Link
Phelix CF, Feltus FA (2015) Plant stress biomarkers from biosimulations: the Transcriptome-To-Metabolome(TTM) technology-effects of drought stress on rice. Plant Biol. 17:63-73 Computational Method Link
Philipson CW, Bassaganya-Riera J, Viladomiu M, Kronsteiner B, Abedi V, Hoops S, Michalak P, Kang L, Girardin SE, Hontecillas R (2015) Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection. PLoS ONE 10(9):e0137839 Immunology Link
Pineda E, Encalada R, Vázquez C, González Z, Moreno-Sánchez R, Saavedra E (2015) Glucose Metabolism and Its Controlling Mechanisms in Entamoeba histolytica. In Amebiasis. Part IV Biology and Pathogenesis of Entamoeba (Nozaki T, Bhattacharya A eds.) Springer pp.351-372 Metabolism Microbiology Link
Raganatia F, Procentese A, Olivieri G, Götzc P, Salatino P, Marzocchella A (2015) Kinetic study of butanol production from various sugars by Clostridium acetobutylicum using a dynamic model. Biochem. Eng. J. 99:156-66. Biotechnology Metabolism Microbiology Link
Rastgou Talemi S, Kollarovic G, Lapytsko A, Schaber J (2015) Development of a robust DNA damage model including persistent telomere-associated damage with application to secondary cancer risk assessment. Sci. Rep. 5:13540 Genetics Macromolecular Biochemistry Link
Rezgui A, Madec M, Lallement C, Haiech J (2015) Integration of SBML models for the description of biological system in a lab-on-chip. Proceedings of the 22nd International Conference Mixed Design of Integrated Circuits & Systems 165-70 Computational Method Laboratory Method Link
Rosenthal RG, Vögeli B, Quade N, Capitani G, Kiefer P, Vorholt JA, Ebert MO, Erb TJ (2015) The use of ene adducts to study and engineer enoyl-thioester reductases. Nature Chem. Biol. 11:398-400. Enzymology Link
Roy RD, Stefan MI (2015) Cooperative Binding Mitigates the High-Dose Hook Effect. BioArchive doi:10.1101/021717 Theory Macromolecular Biochemistry Link
Samal SS, Grigoriev D, Fröhlich H, Weber A, Radulescu O (2015) A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions. Bull. Math. Biol. 77:2180-211. Computational Method Theory Link
Sengupta A, Grover M, Chakraborty A, Saxena S (2015) HEPNet: A Knowledge Base Model of Human Energy Pool Network for Predicting the Energy Availability Status of an Individual. PLoS ONE 10(6):e0127918 Metabolism Link
Sier JH (2015) Investigation of the impact of MRP3 and MRP4 on the disposition of drugs and conjugates in rat and human. Doctoral thesis, University of Surrey Physiology Link
Subburaj Y, Ros U, Hermann E, Tong R, García-Sáez AJ (2015) Toxicity of an alpha-Pore-forming Toxin Depends on the Assembly Mechanism on the Target Membrane as Revealed by Single Molecule Imaging. J. Biol. Chem. 290:4856-4865 Macromolecular Biochemistry Link
Subramanian A, Sarkar RR (2015) Dynamics Of GLI Regulation And A Strategy To Control Cancerous Situation: Hedgehog Signaling Pathway Revisited. J. Biol. Systems 23:681-719 Signaling Link
Subramanian A, Singh V, Sarkar RR (2015) Understanding Visceral Leishmaniasis Disease Transmission and its Control - A Study Based on Mathematical Modeling. Mathematics 3:913-944 Epidemiology Link
Suwanmajo T, Krishnan J (2015) Mixed mechanisms of multi-site phosphorylation. J. Royal Soc. Interface 12:20141405 Signaling Link
Sveshnikova AN, Ataullakhanov FL, Panteleev MA (2015) Compartmentalized calcium signaling triggers subpopulation formation upon platelet activation through PAR1. Molecular BioSystems 11:1052-60 Signaling Link
Talawar B (2015) A Crossbar Interconnection Network in DNA. Proceedings of 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, pp. 342-5 Synthetic Biology Link
Torbensen K, Rossi F, Pantani OL, Ristori S, Abou-Hassan A (2015) Interaction of the Belousov-Zhabotinsky Reaction with Phospholipid Engineered Membranes. J. Phys. Chem. B 119:10224-30 Chemistry Link
Trausinger G, Gruber C, Krahulec S, Magnes C, Nidetzky B, Klimacek M (2015) Identification of novel metabolic interactions controlling carbon flux from xylose to ethanol in natural and recombinant yeasts. Biotechnol. Biofuels 8:157 Biotechnology Metabolism Link
Tummler K, Kühn C, Klipp E (2015) Dynamic metabolic models in context: biomass backtracking. Integr. Biol.7:940-51 Computational Method Link
Twycross J, Bennett M, Krasnogor N (2015) A High-Performance Multicompartment Stochastic Simulator for Executable Biology. Link
Tóth A, Brózik A, Szakács G, Sarkadi B, Hegedüs T (2015) A Novel Mathematical Model Describing Adaptive Cellular Drug Metabolism and Toxicity in the Chemoimmune System. PLoS ONE 10:e0115533 Toxicology Link
Villaverde AF, Henriques D, Smallbone K; Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR (2015) BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biol. 9:8 Computational Method Link
Wang, H-Y, Huang Y-X, Zheng L-H, Bao Y-L, Sun L-G, Wu Y, Yu C-L, Song Z-B, Sun Y, Wang G-N, Ma Z-Q, Li Y-X Li (2015) Modelling Coupled Oscillations in the Notch, Wnt, and FGF Signaling Pathways during Somitogenesis: A Comprehensive Mathematical Model. Comput. Intelligence Neurosci. 2015:387409 Signaling Link
Willems PH, Pahle J, Stalpers XL, Mugahid D, Nikolaew A, Koopman WJ, Kummer U (2015) PKC-mediated inhibitory feedback of the cholecystokinin 1 receptor controls the shape of oscillatory Ca2+ signals. FEBS J. 282:2187-201 Signaling Link
Zhou J, Aponte-Santamaría C, Sturm S, Bullerjahn JT, Bronowska A, Gräter F (2015) Mechanism of Focal Adhesion Kinase Mechanosensing. PLoS Comput. Biol. 11:e1004593 Macromolecular Biochemistry Cell Biology Link
Zimmer C (2015) Reconstructing the hidden states in time course data of stochastic models. Math. Biosci. 269:117-29 Computational Method Link
Zimmer C, Sahle S. (2015) A termination criterion for parameter estimation in stochastic models in systems biology. Biosystems 9:181-92 Computational Method Link

81 publications
2014
Antunes G, Sebastião AM, de Souza FMS (2014) Mechanisms of regulation of olfactory transduction and adaptation in the olfactory cilium. PLoS One 9:e105531 Signaling Pharmacology Link
Aubert N, Mosca C, Fujii T, Hagiya M, Rondelez Y (2014) Computer-assisted design for scaling up systems based on DNA reaction networks J. Royal Soc. Interface 11:20131167 Software Link
Beauvoit BP, Colombié S, Monier A, Andrieu M-H, Biais B, Bénard C, Chéniclet C, Dieuaide-Noubhani M, Nazaret C, Mazat J-P, Gibon Y (2014) Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion. Plant Cell 26:3224-42 Metabolism Link
Bellini M, Besozzi D, Cazzaniga P, Mauri G, Nobile MS (2014) Simulation and analysis of the blood coagulation cascade accelerated on GPU. 2014 22nd Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), IEEE, 590–593 Computational Method Link
Benfeitas R, Selvaggio G, Antunes F, Coelho PMBM, Salvador A (2014) Hydrogen peroxide metabolism and sensing in human erythrocytes: a validated kinetic model and reappraisal of the role of peroxiredoxin II. Free Radical Biology and Medicine 74:35-49 Metabolism Link
Bhosle A, Chandra N (2014) Different cancer cell lines resistant to the same drug exhibit differences in folate pathway dynamics. Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 209-213 Metabolism Link
Boba P, Gries S, Hamacher K (2014) R as an Integration Tool in High Performance Computing - Lessons Learned. GI-Jahrestagung. Lecture Notes in Informatics 232:138–148 Computational Method Software Link
Carbo A, Olivares-Villagómez D, Hontecillas R, Bassaganya-Riera J, Chaturvedi R, Piazuelo MB, Delgado A, Washington MK, Wilson KT, Algood HMS (2014) Systems modeling of the role of IL-21 in the maintenance of effector CD4+ T cell responses during chronic Helicobacter pylori infection. mBio 5:e01243-14 Immunology Link
Carrasco D, Pérez-Temprano MH, Casares JA, Espinet P (2014) Cross Alkyl-Aryl versus Homo Aryl-Aryl Coupling in Palladium-Catalyzed Coupling of Alkyl-Gold (I) and Aryl-Halide. Organometallics 33:3540-3545 Chemistry Link
Castaldi DF (2014) Network Based Simulation on HPC for Translational Medicine: an Application to Anticoagulation. PhD Thesis, University of Milano-Bicocca, Milan, Italy. Computational Method Link
Cazzaniga P, Nobile MS, Besozzi D, Bellini M, Mauri G (2014) Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. BioMed Res. Int. 2014:863298 Computational Method Link
Claudino M, Jonsson M, Johansson M (2014) Utilizing thiol-ene coupling kinetics in the design of renewable thermoset resins based on D-limonene and polyfunctional thiols. Royal Soc. Chem. Advances 4:10317-10329 Chemistry Link
Clough JM, Sijbesma RP (2014) Dioxetane scission products unchanged by mechanical force. ChemPhysChem 15:3565–3571 Chemistry Link
Costa RS, Hartmann A, Gaspar P, Neves AR, Vinga S (2014) An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production. Mol. BioSystems 10:628-639 Microbiology Metabolism Link
Dalle Pezze P, Nelson G, Otten EG, Korolchuk VI, Kirkwood TBL, von Zglinicki T, Shanley DP (2014) Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions. PLoS Comput. Biol. 10:e1003728. Signaling Link
Drees B, Reiger M, Jung K, Bischofs IB (2014) A modular view of the diversity of cell-density-encoding schemes in bacterial quorum-sensing systems. Biophys. J. 107:266-277 Microbiology Link
Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews K, Clayton C (2014) Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels. Mol. Microbiol. 94:307-326 Microbiology Genomics Link
Gautam VK, Czeizler E, Haddow PC, Kuiper M (2014) Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles. In: Dediu AH, Lozano M, Martín-Vide C (eds) Theory and Practice of Natural Computing. TPNC 2014. Lecture Notes in Computer Science, 8890:119-133 Synthetic Biology Link
Godfrey L, Yamada-Fowler N, Smith J, Thornalley PJ, Rabbani N (2014) Arginine-directed glycation and decreased HDL plasma concentration and functionality. Nutrition & Diabetes 4:e134 Physiology Link
Graybill C, Prehoda KE (2014) Ordered multisite phosphorylation of lethal giant larvae by atypical protein kinase C. Biochemistry 53:4931-7 Signaling Link
Guillaud F, Dröse S, Kowald A, Brandt U, Klipp E (2014) Superoxide production by cytochrome bc 1 complex: A mathematical model. Biochimica et Biophysica Acta 1837:1643–1652 Enzymology Link
Hallinan JS, Gilfellon O, Misirli G, Wipat A (2014) Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts. Proceedings of the 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 1-8 Synthetic Biology Link
Helgeson L (2014) Mechanisms of Branched Actin Network Formation through Coordinate Activation of Arp2/3 Complex. PhD Thesis, University of Oregon. Cell Biology Link
Hui W, Young DA, Rowan AD, Xu X, Cawston TE, Proctor CJ (2014) Oxidative changes and signalling pathways are pivotal in initiating age-related changes in articular cartilage. Annals of the Rheumatic Diseases 75:449–458 Signaling Immunology Link
Ihekwaba AEC, Mura I, Barker GC (2014) Computational modelling and analysis of the molecular network regulating sporulation initiation in Bacillus subtilis. BMC Systems Biology 8:119 Microbiology Link
Irving JA, Haq I, Dickens JA, Faull SV, Lomas DA (2014) Altered native stability is the dominant basis for susceptibility of α1-antitrypsin mutants to polymerization. Biochemical Journal 460:103–119 Macromolecular Biochemistry Link
Ivan ANY (2014) Assisted Design of DNA Computing Systems: the DNA Toolbox and Beyond. PhD Thesis, University of Tokyo. Synthetic Biology Computational Method Link
Jakubík J, Zimčík P, Randáková A, Fuksová K, El-Fakahany EE, Doležal V (2014) Molecular mechanisms of methoctramine binding and selectivity at muscarinic acetylcholine receptors. Molecular pharmacology 86:180–192 Pharmacology Link
James AI, Imran HAQ, Jennifer AD, Sarah VF, David AL (2014) Altered native stability is the dominant basis for susceptibility of alpha1-antitrypsin mutants to polymerization. Biochem. J. 460:103-115 Macromolecular Biochemistry Link
Jarrah AS, Castiglione F, Evans NP, Grange RW, Laubenbacher R (2014) A Mathematical Model of Skeletal Muscle Disease and Immune Response in the mdx Mouse. BioMed Research International 2014:871810 Immunology Link
Jones A (2014) Mechanistic studies of enantioselective alkene bromolactonisation reactions. PhD Thesis, Imperial College London. Chemistry Link
Karonen M, Mattila H, Huang P, Mamedov F, Styring S, Tyystjärvi E (2014) A tandem mass spectrometric method for singlet oxygen measurement. Photochem. Photobiol. 90:965-971 Laboratory Method Link
Kefalidis CE, Davi M, Holstein PM, Clot E, Baudoin O (2014) Mechanistic Study of the Selectivity of Olefin versus Cyclobutene Formation by Palladium (0)-Catalyzed Intramolecular C (sp3)-H Activation. J. Organic Chem. 79:11903-11910 Chemistry Link
Kent PD, Mondloch JE, Finke RG (2014) A Four-Step Mechanism for the Formation of Supported-Nanoparticle Heterogenous Catalysts in Contact with Solution: The Conversion of Ir (1, 5-COD) Cl/gamma-Al2O3 to Ir (0) 170/gamma-Al2O3. J Am. Chem. Soc. 136:1930-41 Chemistry Link
Khandekar DC, Palai T, Agarwal A, Bhattacharya PK (2014) Kinetics of sucrose conversion to fructo-oligosaccharides using enzyme (invertase) under free condition. Bioprocess and Biosystems Engineering 37:2529–2537 Enzymology Biotechnology Link
Kleppe R, Ghorbani S, Martinez A, Haavik J (2014) Modelling cellular signal communication mediated by phosphorylation dependent interaction with 14-3-3 proteins. FEBS Letters 588:92–98 Signaling Link
Lakin MR, Minnich A, Lane T, Stefanovic D (2014) Design of a biochemical circuit motif for learning linear functions. J. Royal Soc. Interface 11:20140902 Synthetic Biology Link
Le Muzic M, Parulek J, Stavrum A-K, Viola I (2014) Illustrative visualization of molecular reactions using omniscient intelligence and passive agents. Computer Graphics Forum 33:141-150 Software Link
Leal Denis MF (2014) Homeostasis de ATP extracelular en eritrocitos: interregulación y consecuencias funcionales. PhD Thesis, Universidad de Buenos Aires, Buenos Aires, Argentina. Physiology Link
Liao C, Cai Y (2014) Towards Modeling Automation for Synthetic Biology. In: Kulkarni V., Stan GB., Raman K. (eds) A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems. Springer, Dordrecht, 201–217 Synthetic Biology Computational Method Link
Ligon TS, Leonhardt C, Rädler JO (2014) Multi-level kinetic model of mRNA delivery via transfection of lipoplexes. PLoS One 9:e107148 Cell Biology Genomics Link
Luo J (2014) Mechanistic investigation of catalytic organometallic reactions using ESI MS. PhD Thesis, University of Victoria, British Columbia, Canada. Chemistry Link
Lutz A, Sanwald J, Thomas M, Feuer R, Sawodny O, Ederer M, Borner C, Humar M, Merfort I (2014) Interleukin-1beta Enhances FasL-Induced Caspase-3/-7 Activity without Increasing Apoptosis in Primary Mouse Hepatocytes. PLoS ONE 9:e115603. Immunology Link
Machado D, Rodrigues LR, Rocha I (2014) A kinetic model for curcumin production in Escherichia coli. BioSystems 125:16-21 Synthetic Biology Metabolism Link
Marwaha S, Schumacher MA, Zavros Y, Eghbalnia HR (2014) Crosstalks between Cytokines and Sonic Hedgehog in Helicobacter pylori Infection: A Mathematical Model. PLoS ONE 9:e111338. Immunology Signaling Link
Marín-Hernández A, López-Ramírez SY, Del Mazo-Monsalvo I, Gallardo-Pérez JC, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2014) Modeling cancer glycolysis under hypoglycemia, and the role played by the differential expression of glycolytic isoforms. FEBS Journal 281:3325–3345 Metabolism Link
Marín-Hernández A, López-Ramírez SY, Gallardo-Pérez JC, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2014) Systems biology approaches to cancer energy metabolism. in M.A. Aon et al. (eds.), Systems Biology of Metabolic and Signaling Networks, Springer-Verlag pp.213-239 Metabolism Link
Matsuoka Y, Funahashi A, Ghosh S, Kitano H (2014) Modeling and simulation using CellDesigner. Methods Mol. Biol. 1164:121-145 Software Link
Mei Y, Carbo A, Hontecillas R, Hoops S, Liles N, Lu P, Philipson C, Bassaganya-Riera J (2014) ENISI MSM: A novel multi-scale modeling platform for computational immunology. 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, 391–396 Software Link
McAuley MT, Khalil R, Stockton DJ, Schilstra MJ (2014) Modelling the flagellar motor assembly process to help improve industrial operations systems design. Signaling Link
Mei Y, Carbo A, Hontecillas R, Hoops S, Liles N, Lu P, Philipson C, Bassaganya-Riera J (2014) ENISI MSM: A novel multi-scale modeling platform for computational immunology. Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 391-396 Software Link
Miller AJM, Kaminsky W, Goldberg KI (2014) Arene Activation at Iridium Facilitates C-O Bond Cleavage of Aryl Ethers. Organometallics 33:1245-1252 Chemistry Link
Mozga I, Stalidzans E (2014) Reduction of Combinatorial Space of Adjustable Kinetic Parameters of Biochemical Network Models in Optimisation Task. Baltic Journal of Modern Computing 150:150–159 Computational Method Link
Nobile MS, Cazzaniga P, Besozzi D, Mauri G (2014) GPU-accelerated simulations of mass-action kinetics models with cupSODA. J. Supercomputing 69:17-24 Computational Method Link
Nobile MS, Cazzaniga P, Besozzi D, Pescini D, Mauri G (2014) cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems. PLoS ONE 9:e91963. Computational Method Link
Ouzounoglou E, Kalamatianos D, Emmanouilidou E, Xilouri M, Stefanis L, Vekrellis K, Manolakos ES (2014) In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis. BMC Systems Biology 8:54 Physiology Cell Biology Link
Palai T, Singh AK, Bhattacharya PK (2014) Enzyme, beta-galactosidase immobilized on membrane surface for galacto-oligosaccharides formation from lactose: kinetic study with feed flow under recirculation loop. Biochem. Eng. J. 88:68-76 Biotechnology Enzymology Link
Palmisano A, Hoops S, Watson LT, Jones Jr TC, Tyson JJ, Shaffer CA (2014) Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. BMC Systems Biology 8:42 Software Computational Method Link
Pandey V (2014) Metabolic modeling of different degrees of steatohepatitis in mice. PhD Thesis, Department of Mathematics and Computer Science, Free University of Berlin. Metabolism Link
Pandey V, Sultan M, Kashofer K, Ralser M, Amstislavskiy V, Starmann J, Osprian I, Grimm C, Hache H, Yaspo M-L, Sültmann H, Trauner M, Denk M, Zatloukal K, Lehrach H, Wierling C (2014) Comparative Analysis and Modeling of the Severity of Steatohepatitis in DDC-Treated Mouse Strains. PLoS ONE 9:e111006. Metabolism Link
Peterson JR, Labhsetwar P, Ellermeier JR, Kohler PR, Jain A, Ha T, Metcalf WW, Luthey-Schulten Z (2014) Towards a computational model of a methane producing archaeum. Archaea 2014:898453 Whole-Cell Models Microbiology Link
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Phelix CF, Villareal G, LeBaron RG, Perry G, Roberson DJ (2014) Precision medicine using individualized biosimulations of drug dosing: Alzheimer’s disease. Healthcare Innovation Conference (HIC), IEEE, 292–295 Pharmacology Link
Proctor CJ, Macdonald C, Milner JM, Rowan AD, Cawston TE (2014) A Computer Simulation Approach to Assessing Therapeutic Intervention Points for the Prevention of Cytokine-Induced Cartilage Breakdown. Arthritis & Rheumatology 66:979-989 Immunology Link
Rabbani N, Xue M, Thornalley PJ (2014) Activity, regulation, copy number and function in the glyoxalase system. Biochemical Society Transactions 42:419–424 Metabolism Link
Raganati F (2014) Butanol production by fermentation of renewable feedstocks. PhD Thesis, Università di Napoli Federico II, Naples, Italy Biotechnology Link
Rao S, van der Schaft A, van Eunen K, Bakker BM, Jayawardhana B (2014) A model reduction method for biochemical reaction networks. BMC systems biology 8:52 Computational Method Link
Rossi F, Ristori S, Marchettini N, Pantani OL (2014) Functionalized clay microparticles as catalysts for chemical oscillators. The Journal of Physical Chemistry C 118:24389–24396 Chemistry Link
Sakkalis V, Sfakianakis S, Tzamali E, Marias K, Stamatakos G, Misichroni F, Ouzounoglou E, Kolokotroni E, Dionysiou D, Johnson D, McKeever S, Graf N (2014) Web-based workflow planning platform supporting the design and execution of complex multiscale cancer models. IEEE J. Biomededical Health Informatics 18:824-31 Software Link
Sapra A, Ramadan D, Thorpe C (2014) Multivalency in the inhibition of oxidative protein folding by arsenic (III) species. Biochemistry 54:612–621 Biochemistry Link
Saller S, Kunz L, Berg D, Berg U, Lara H, Urra J, Hecht S, Pavlik R, Thaler CJ, Mayerhofer A (2014) Dopamine in human follicular fluid is associated with cellular uptake and metabolism-dependent generation of reactive oxygen species in granulosa cells: implications for physiology and pathology. Human Reproduction 29:555-67 Physiology Metabolism Link
Schaber J, Lapytsko A, Flockerzi D (2014) Nested autoinhibitory feedbacks alter the resistance of homeostatic adaptive biochemical networks. J. Royal Soc. Interface 11:20130971 Signaling Link
Schleicher J, Guthke R, Dahmen U, Dirsch O, Holzhuetter HG, Schuster S (2014) A theoretical study of lipid accumulation in the liver—Implications for nonalcoholic fatty liver disease. Biochimica et Biophysica Acta 1841:62–69 Metabolism Link
Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta SK (2014) Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic Acids Res. 42:7539-7552 Computational Method Link
Shinde S, Mol M, Singh S (2014) Regulatory networks, genes and glycerophospholipid biosynthesis pathway in schistosomiasis: A systems biology view for pharmacological intervention. Gene 550:214-22. Pharmacology Genomics Link
Smallbone K, M Corfe B (2014) A mathematical model of the colon crypt capturing compositional dynamic interactions between cell types. International Journal of Experimental Pathology 95:1–7 Physiology Link
Sosa CM, Pavarotti MA, Zanetti MN, Zoppino FCM, De Blas GA, Mayorga LS (2014) Kinetics of human sperm acrosomal exocytosis. MHR: Basic science of reproductive medicine 21:244–254 Cell Biology Link
Spiaggi AJ (2014) Caracterización de los pasos involucrados en el transporte de K+ por la Na+/K+-ATPasa. PhD Thesis, Universidad de Buenos Aires, Argentina. Enzymology Link
Talemi SR, Jacobson T, Garla V, Navarrete C, Wagner A, Tamás MJ, Schaber J (2014) Mathematical modelling of arsenic transport, distribution and detoxification processes in yeast. Molecular microbiology 92:1343–1356 Toxicology Metabolism Link
Tunnicliffe RB, Hautbergue GM, Wilson SA, Kalra P, Golovanov AP (2014) Competitive and Cooperative Interactions Mediate RNA Transfer from Herpesvirus Saimiri ORF57 to the Mammalian Export Adaptor ALYREF. PLoS Pathog 10(2): e1003907. Macromolecular Biochemistry Link
Valero G, Ribó JM, Moyano A (2014) A closer look at spontaneous mirror symmetry breaking in aldol reactions. Chemistry-A European Journal 20:17395–17408 Chemistry Link
Valero González G (2014) Estudis mecanístics i metodològics de processos d'autocatàlisi i organocatàlisi asimètriques. Ph.D. Thesis, Department of Organic Chemistry, University of Barcelona Chemistry Link
Ventura AC, Bush A, Vasen G, Goldín MA, Burkinshaw B, Bhattacharjee N, Folch A, Brent R, Chernomoretz A, Colman-Lerner A (2014) Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range. Proceedings of the National Academy of Sciences 111:E3860–E3869 Signaling Link
Vickers JW, Sumliner JM, Lv H, Morris M, Geletii YV, Hill CL (2014) Collecting meaningful early-time kinetic data in homogeneous catalytic water oxidation with a sacrificial oxidant. Phys. Chem. Chemical Physics 16:11942-11949 Chemistry Link
Wang CCN, Chang P-C, Ng K-L, Chang C-M, Sheu PCY, Tsai JJP (2014) A model comparison study of the flowering time regulatory network in Arabidopsis. BMC Systems Biology 8:15 Signaling Link
Yang X, Zhang Y, Zheng Y, Ma H (2014) Development and analysis of a kinetic model for Escherichia coli threonine biosynthesis. Chinese J. Biotechnol. 30:18-29. Metabolism Microbiology Link
Zimmer C, Sahle S, Pahle J (2014) Exploiting intrinsic fluctuations to identify model parameters. IET Systems Biology 9:64-73 Computational Method Link

87 publications
2013
Berestovsky N, Nakhleh L (2013) An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data. PLoS ONE 8:e66031 Computational Method Link
Bulipopa N, Sulins J (2013) Automatic termination of parallel optimization runs of global stochastic optimization methods by upper limit criterion. Biosystems and Information Technol. 2:15-18 Computational Method Link
Carbo A, Bassaganya-Riera J, Pedragosa M, Viladomiu M, Marathe M, Eubank S, Wendelsdorf K, Bisset K, Hoops S, Deng X, Alam M, Kronsteiner B, Mei Y, Hontecillas R (2013) Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection. PLoS ONE 8(9): e73365 Immunology Link
Chelliah V, Laibe C, Le Novere N (2013) BioModels database: a repository of mathematical models of biological processes. Methods in Molecular Biology 1021:189–199 Software Link
Claudino M (2013) Macromolecular design: UV-curable thiol-ene networks based on renewable resources. PhD Thesis, KTH Royal Institute of Technology, Stockholm, Sweden Chemistry Link
Claudino M, Jonsson M, Johansson M (2013) Thiol–ene coupling kinetics of d-limonene: a versatile ‘non-click’free-radical reaction involving a natural terpene. RSC Advances 3:11021–11034 Chemistry Link
Cornish-Bowden A, Piedrafita G, Morán F, Cárdenas ML, Montero F (2013) Simulating a model of metabolic closure. Biological Theory 8:383-390 Theory Link
Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G (2013) An online model composition tool for system biology models. BMC Systems Biol. 7:88 Computational Method Link
Diao T, Pun D, Stahl SS (2013) Aerobic Dehydrogenation of Cyclohexanone to Cyclohexenone Catalyzed by Pd(DMSO)2(TFA)2: Evidence for Ligand-Controlled Chemoselectivity. J. Am. Chem. Soc. 135:8205-8212 Chemistry Link
Emiola A, Falcarin P, Tocher J, George J (2013) A model for the proteolytic regulation of LpxC in the lipopolysaccharide pathway of Escherichia coli. Computational Biology and Chemistry 47:1–7 Biochemistry Microbiology Link
Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff H, Mendes P, McCarthy JEG (2013) An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology 9:635 Macromolecular Biochemistry Cell Biology Link
Fröhlich M (2013) Computational and experimental investigation of the mechanisms involved in cellular water transport and (cat)ion homeostasis. Ph.D. Thesis, Department of Mathematics and Computer Science, Free University of Berlin Physiology Link
Galazka M, Hay JO (2013) In silico metabolic control analysis of Brassica napus seeds based on dynamic kinetic modeling. A Compilation of Internship Reports. Brookhaven National Laboratory, Office of Educational Programs. pp. 75–80 Metabolism Link
Geenen S, du Preez FB, Snoep JL, Foster AJ, Sarda S, Kenna JG, Wilson ID, Westerhoff HV (2013) Glutathione metabolism modeling: a mechanism for liver drug-robustness and a new biomarker strategy. Biochim. Biophys. Acta 1830:4943- 59 Toxicology Metabolism Link
Gow C-H (2013) Novel mechanisms of transcriptional regulation by leukemia fusion proteins. PhD Thesis, University of Cincinnati, Cincinnati, OH. Signaling Link
Haq I, Irving JA, Faull SV, Dickens JA, Ordonez A, Belorgey D, Gooptu B, Lomas, DA (2013) Reactive centre loop mutants of alpha-1-antitrypsin reveal position-specific effects on intermediate formation along the polymerization pathway. Biosci. Rep. 33:499-511 Macromolecular Biochemistry Link
Helgeson LA, Nolen BJ (2013) Mechanism of synergistic activation of Arp2/3 complex by cortactin and N-WASP. eLife 2:e00884 Macromolecular Biochemistry Signaling Link
Incicco JJ, Gebhard LG, González-Lebrero RM, Gamarnik AV, Kaufman SB (2013) Steady-State NTPase Activity of Dengue Virus NS3: Number of Catalytic Sites, Nucleotide Specificity and Activation by ssRNA. PLoS ONE 8:e58508 Macromolecular Biochemistry Link
Jensen MV, Hay JO (2013) Systems Biology Markup Language formulation of a dynamic kinetic model and its uses in quantitative and computational metabolic modeling. A Compilation of Internship Reports. Brookhaven National Laboratory, Office of Educational Programs. pp. 108–112 Computational Method Link
Kennedy N, Mizeranschi A, Thompson P, Zheng H, Dubitzky W (2013) Reverse engineering of gene regulation models from multi-condition experiments. Proceedings of the 2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), pp.112-119 Computational Method Link
Kent E, Neumann S, Kummer U, Mendes P (2013) What Can We Learn from Global Sensitivity Analysis of Biochemical Systems? PLoS ONE 8:e79244 Computational Method Link
Kerkhoven EJ, Achcar F, Alibu VP, Burchmore RJ, Gilbert IH, Trybilo M, Driessen NN, Gilbert D, Breitling R, Bakker BM, Barrett MP (2013) Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei. PLoS Comput. Biol. 9:e1003371. Metabolism Link
Khan HA (2013) Asymmetric Synthesis of Lactones and Lactams: Rhodium Catalysis in the Hydroacylation of Ketones and the Hydrogenation of Cyclic Dehydropeptides. Ph.D. Thesis, Department of Chemistry, University of Toronto Chemistry Link
Klement M, Safránek D, Ded T, Pejznoch A, Nedbal L, Steuer R, Cerveny J, Müller S (2013) A comprehensive web-based platform for domain-specific biological models. Electronic Notes in Theoretical Computer Science 299:61-67 Software Link
Kolodkin A, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, Plant N (2013) Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature Communications 4:1792 Signaling Link
Kourdis PD, Goussis DA (2013) Glycolysis in Saccharomyces cerevisiae: Algorithmic exploration of robustness and origin of oscillations. Math. Biosci. 243:190-214 Theory Link
Kraut DA (2013) Slippery substrates impair ATP-dependent protease function by slowing unfolding. J. Biol. Chem. 288:34729-34735 Enzymology Link
Leroux AE, Haanstra JR, Bakker BM, Krauth-Siegel RL (2013) Dissecting the catalytic mechanism of Trypanosoma brucei trypanothione synthetase by kinetic analysis and computational modeling. J. Biol. Chem. 288:23751-23764 Metabolism Link
Levering, J, Kummer U, Becker K, Sahle S (2013) Glycolytic oscillations in a model of a lactic acid bacterium metabolism. Biophys. Chem. 172:53-60 Metabolism Link
Lv H, Rudd JA, Zhuk PF, Lee JY, Constable EC, Housecroft CE, Hill CL, Musaev DG, Geletii YV (2013) Bis (4'-(4-pyridyl)-2,2':6',2''-terpyridine)ruthenium (ii) complexes and their N-alkylated derivatives in catalytic light-driven water oxidation. Royal Soc. Chem. Advances 3:20647-20654 Chemistry Link
Maccari G, Mori M, Rodríguez-Salarichs J, Fang W, Díaz JF, Botta M (2013) Free Energy Profile and Kinetics Studies of Paclitaxel Internalization from the Outer to the Inner Wall of Microtubules. Journal of Chemical Theory and Computation 9:698-706 Cell Biology Macromolecular Biochemistry Pharmacology Link
Mednis M, Vigants A (2013) Automatic comparison of metabolites names: impact of criteria thresholds. Biosystems and Information Technol. 2:1-5 Computational Method Link
Mei Y, Carbo A, Hontecillas R, Bassaganya-Riera J (2013) ENISI SDE: a novel web-based stochastic modeling tool for computational biology. 2013 Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 392-397 Computational Method Software Link
Mei Y, Hontecillas R, Zhang X; Carbo A, Bassaganya-Riera J (2013) Neural network models for classifying immune cell subsets. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 18-21 Dec. 2013, pp.5-11 Computational Method Link
Mensonides FIC, Bakker BM, Cremazy F, Messiha HL , Mendes P, Boogerd FC, Westerhoff HV (2013) A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides illustrated for the glycolytic enzymes of Saccharomyces cerevisiae. FEBS Lett. 587:2860-7 Metabolism Link
Miah F, Koliwer-Brandl H, Rejzek M, Field RA, Kalscheuer R, Bornemann S (2013) Flux through trehalose synthase flows from trehalose to the alpha anomer of maltose in mycobacteria. Chem. Biol. 20:487-493 Metabolism Link
Mitchell S, Mendes P (2013) A Computational Model of Liver Iron Metabolism. PLoS Comput. Biol. 9:e1003299 Metabolism Link
Mozga I (2013) Determinition of best set of adjustable parameters with full search and limited search methods. Biosystems and Information Technology 2:11–14 Computational Method Link
Nobile MS , Besozzi D, Cazzaniga P, Mauri G, Pescini D (2013) cupSODA: a CUDA-powered simulator of mass-action kinetics. Parallel Computing Technologies Proceedings of the 12th International Conference, PaCT 2013, St. Petersburg, pp.344-357 Computational Method Link
Nägele T, Weckwerth W (2013) A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana. Frontiers Plant Sci. 4:541 Metabolism Link
Palai T, Bhattacharya PK (2013) Kinetics of lactose conversion to galacto-oligosaccharides by beta-galactosidase immobilized on PVDF membrane. J. Biosci. Bioeng. 115:668-673 Enzymology Link
Palaniappan SK (2013) Probabilistic verification and analysis of biopathway dynamics. Ph.D. Thesis School of Computing, National University of Singapore Computational Method Link
Penkler GP (2013) A kinetic model of glucose catabolism in Plasmodium falciparum. Ph.D. Thesis, Faculty of Science, University of Stellenbosch, South Africa Metabolism Link
Philipson CW, Bassaganya-Riera J, Hontecillas R (2013) Animal models of enteroaggregative Escherichia coli infection. Gut Microbes 4:281-291 Immunology Link
Proctor CJ, Boche D, Gray DA, Nicoll JAR (2013) Investigating Interventions in Alzheimer's Disease with Computer Simulation Models. PLoS ONE 8:e73631 Macromolecular Biochemistry Link
Pun D, Diao T, Stahl SS (2013) Aerobic dehydrogenation of cyclohexanone to phenol catalyzed by Pd (TFA) 2/2-dimethylaminopyridine: Evidence for the role of Pd nanoparticles. Journal of the American Chemical Society 135:8213–8221 Chemistry Link
Ravichandran S, Rao KVS, Jain S (2013) Bistability in a model of early B cell receptor activation and its role in tonic signaling and system tunability. Molecular BioSystems 9:2498-2511 Signaling Link
Reeves BD, Hilmer JK, Mellmann L, Hartzheim M, Poffenberger K, Johnson K, Joshi N, Singel DJ, Grieco PA (2013) Selective trapping of SNO-BSA and GSNO by benzenesulfinic acid sodium salt: mechanistic study of thiosulfonate formation and feasibility as a protein S-nitrosothiol detection strategy. Tetrahedron Lett. 54:5707-10 Chemistry Link
Roberts E, Stone JE, Luthey-Schulten Z (2013) Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. J. Comput. Chem. 34:245-255 Computational Method Link
Rutkis R, Kalnenieks U, Stalidzans E, Fell DA (2013) Kinetic modeling of Zymomonas mobilis Entner-Doudoroff pathway: insights into control and functionality. Microbiol. 159:2674-2689 Metabolism Microbiology Link
Sahaboglu A, Paquet-Durand O, Dietter J, Dengler K, Bernhard-Kurz S, Ekström PAR, Hitzmann B, Ueffing M, Paquet-Durand F (2013) Retinitis pigmentosa: rapid neurodegeneration is governed by slow cell death mechanisms. Cell Death & Disease 4:e488 Cell Biology Signaling Link
Sarma U, Gade PM, Saha B (2013) A mathematical model for dynamics of CD40 clustering. Systems and Synthetic Biol. 7:197-208 Macromolecular Biochemistry Link
Scheller S, Goenrich M, Thauer RK, Jaun B (2013) Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on label exchange and ethane formation with the homologous substrate ethyl-coenzyme M. J. Am. Chem. Soc 135:14985-14995 Chemistry Enzymology Link
Schäuble S, Stavrum AK, Puntervoll P, Schuster S, Heiland I (2013) Effect of substrate competition in kinetic models of metabolic networks. FEBS Lett. 587:2818-2824 Metabolism Link
Sharma V, Compagnoni A (2013) Computational and mathematical models of the JAK-STAT signal transduction pathway. Proceedings of the 2013 Summer Computer Simulation Conference 15 Computational Method Signaling Link
Sharp GC (2013) Comprehensive data analysis to study parturition. PhD Thesis, University of Edinburgh. Signaling Link
Sharp GC, Ma H, Saunders PTK, Norman JE (2013) A Computational Model of Lipopolysaccharide-Induced Nuclear Factor Kappa B Activation: A Key Signalling Pathway in Infection-Induced Preterm Labour. PLoS ONE 8:e70180 Signaling Link
Shemirani MI (2013) Construction of metabolic pathway of catecholamine from tyrosine in human fibroblast cell. Degree Project in Medicine, School of Medicine and Health Science, Orerbo University, Sweden Metabolism Link
Sheng X (2013) Evolutionary and Functional Aspects of Two-Component Signalling Systems. PhD Thesis, Imperial College London. Microbiology Link
Singh VK, Ghosh I (2013) Methylerythritol phosphate pathway to isoprenoids: kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum. FEBS Lett. 587:2806-2817 Metabolism Link
Skvortsov A, Gray P (2013) A simple model for assessment of anti-toxin antibodies. BioMed Res. Int. 2013:230906 Laboratory Method Link
Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasic I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P (2013) A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes. FEBS Letters 587:2832-41 Metabolism Link
Smith GR, Shanley, DP (2013) Computational modelling of the regulation of Insulin signalling by oxidative stress. BMC Systems Biol. 7:41 Signaling Link
Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W (2013) Systematic construction of kinetic models from genome-scale metabolic networks. PloS One 8:e79195 Computational Method Whole-Cell Models Link
Stavrum A-K, Heiland I, Schuster S, Puntervoll P, Ziegler M (2013) Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data. J. Biol. Chem. 288:34555-34566 Metabolism Link
Sundin S, Dahlgren B, Roth O, Jonsson M (2013) H2O2 and radiation induced dissolution of UO2 and SIMFUEL in deficient aqueous solution. J. Nuclear Materials 443:291-297 Chemistry Link
Sütterlin T, Kolb C, Dickhaus H, Jäger D, Grabe N (2013) Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI. Bioinformatics 29:223-9 Software Link
Tapinos A, Mendes P (2013) A Method for Comparing Multivariate Time Series with Different Dimensions. PLoS ONE 8:e54201 Computational Method Theory Link
Toney MD (2013) Common enzymological experiments allow free energy profile determination. Biochemistry 52:5952-5965 Enzymology Link
van't Erve TJ (2013) Discoveries on the storage of red blood cells and the exposure of cells in culture to xenobiotics. D.Phil. Thesis, The University of Iowa Toxicology Link
Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC (2013) Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria. PLoS Comput. Biol. 9:e1003159 Metabolism Microbiology Link
Viladomiu M, Hontecillas R, Yuan L, Lu P, Bassaganya-Riera J (2013) Nutritional protective mechanisms against gut inflammation. J. Nutritional Biochem. 24:929-939 Immunology Link

72 publications
2012
Achcar F, Kerkhoven EJ, The SilicoTryp Consortium, Bakker BM, Barrett MP, Breitling R (2012) Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism. PLoS Computational Biology 8:e1002352 Metabolism Link
Adamczyk M, Westerhoff HV (2012) Engineering of self-sustaining systems: Substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system in a Lactococcus lactis network in silico. Biotechnology Journal 7:877-883 Metabolism Microbiology Link
Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ (2012) The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. Journal of Biological Rhythms 27:328–332 Computational Method Link
Adiamah DA, Schwartz J-M (2012) Construction of a Genome-Scale Kinetic Model of Mycobacterium Tuberculosis Using Generic Rate Equations. Metabolites 2:382-397 Metabolism Whole-Cell Models Link
Betney R, de Silva E, Mertens C, Knox Y, Krishnan J, Stansfield I (2012) Regulation of release factor expression using a translational negative feedback loop: A systems analysis. RNA 18:2320-2334 Signaling Link
Biswas S, Huang Z, Choliy Y, Wang DY, Brookhart M, Krogh-Jespersen K, Goldman AS (2012) Olefin Isomerization by Iridium Pincer Catalysts. Experimental Evidence for an η 3 -Allyl Pathway and an Unconventional Mechanism Predicted by DFT Calculations. Journal of the American Chemical Society 134:13276-13295 Chemistry Link
Bodenstein C, Heiland I, Schuster S (2012) Temperature compensation and entrainment in circadian rhythms. Physical Biology 9:036011 Theory Link
Bortolussi L, Policriti A (2012) Studying cancer-cell populations by programmable models of networks. Network Modeling Analysis in Health Informatics and Bioinformatics 1:117-133 Cell Biology Link
Burés J, Armstrong A, Blackmond DG (2012) Curtin-Hammett Paradigm for Stereocontrol in Organocatalysis by Diarylprolinol Ether Catalysts. Journal of the American Chemical Society 134:6741-6750 Chemistry Link
Challenger JD, McKane AJ, Pahle J (2012) Multi-compartment linear noise approximation. Journal of Statistical Mechanics: Theory and Experiment 2012:P11010 Computational Method Link
Chang J-Y, Chantrathammachart P, Monroe DM, Key NS (2012) Studies on the mechanism of action of the aptamer BAX499, an Inhibitor of tissue factor pathway inhibitor. Thrombosis Research 130:e151-e157 Macromolecular Biochemistry Link
Chua HE, Bhowmick SS, Tucker-Kellogg L, Forbes Dewey, Jr C (2012) STEROID: in silico heuristic target combination identification for disease-related signaling networks. Proceedings of the 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine BCB'12 pp. 4-11 Computational Method Link
Criquet J, Allard S, Salhi E, Joll CA, Heitz A, von Gunten U (2012) Iodate and Iodo-Trihalomethane Formation during Chlorination of Iodide-Containing Waters: Role of Bromide. Environmental Science & Technology 46:7350-7357 Chemistry Link
Cristovao M, Sisamakis E, Hingorani MM, Marx AD, Jung CP, Rothwell PJ, Seidel CAM, Friedhoff P (2012) Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA. Nucleic Acids Research 40:5448-5464 Genomics Link
Czeizler E, Mizera A, Czeizler E, Back R-J, Eriksson JE, Petre I (2012) Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentin. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9:885-898 Cell Biology Link
Dada JO, Mendes P (2012) ManyCell: A Multiscale Simulator for Cellular Systems. (Gilbert D and Heiner M eds) Computational Methods in Systems Biology. Berlin, Heidelberg: Springer Berlin Heidelberg, 366-369. Software Link
Dalle Pezze P, Sonntag AG, Thien A, Prentzell MT, Godel M, Fischer S, Neumann-Haefelin E, Huber TB, Baumeister R, Shanley DP, Thedieck K (2012) A Dynamic Network Model of mTOR Signaling Reveals TSC-Independent mTORC2 Regulation. Science Signaling 5:ra25-ra25 Signaling Link
Davies O, Mendes P, Smallbone K, Malys N (2012) Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism. BMB reports 45:259-264 Enzymology Metabolism Link
Ding K, Miranda MO, Moscato-Goodpaster B, Ajellal N, Breyfogle LE, Hermes ED, Schaller CP, Roe SE, Cramer CJ, Hillmyer MA, Tolman WB (2012) Roles of Monomer Binding and Alkoxide Nucleophilicity in Aluminum-Catalyzed Polymerization of ε - Caprolactone. Macromolecules 45:5387-5396 Chemistry Link
Friedrich LC, Mendes MA, Silva VO, Zanta CLPS, Machulek Jr. A, Quina FH (2012) Mechanistic implications of zinc(II) ions on the degradation of phenol by the fenton reaction. Journal of the Brazilian Chemical Society 23:1372-1377 Chemistry Link
Gatti DL (2012) Biapenem Inactivation by B2 Metallo β-Lactamases: Energy Landscape of the Post-Hydrolysis Reactions. PLoS ONE 7:e30079 Enzymology Link
Gebhard LG, Kaufman SB, Gamarnik AV (2012) Novel ATP-Independent RNA Annealing Activity of the Dengue Virus NS3 Helicase. PLoS ONE 7:e36244 Enzymology Link
Georgoulas A, Clark A, Ocone A, Gilmore S, Sanguinetti G (2012) A subsystems approach for parameter estimation of ODE models of hybrid systems. Electronic Proceedings in Theoretical Computer Science 92:30-41 Computational Method Link
Guo C, Gow C-H, Li Y, Gardner A, Khan S, Zhang J (2012) Regulated Clearance of Histone Deacetylase 3 Protects Independent Formation of Nuclear Receptor Corepressor Complexes. Journal of Biological Chemistry 287:12111-12120 Enzymology Link
Hamberg A, Maurer S, Hult K (2012) Rational engineering of Candida antarctica lipase B for selective monoacylation of diols. Chemical Communications 48:10013 Biochemistry Link
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Holcombe M, Adra S, Bicak M, Chin S, Coakley S, I. Graham A, Green J, Greenough C, Jackson D, Kiran M, MacNeil S, Maleki-Dizaji A, McMinn P, Pogson M, Poole R, Qwarnstrom E, Ratnieks F, D. Rolfe M, Smallwood R, Sun T, Worth D (2012) Modelling complex biological systems using an agent-based approach. Integrative Biology 4:53–64 Computational Method Link
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Kent E, Hoops S, Mendes P (2012) Condor-COPASI: high-throughput computing for biochemical networks. BMC Systems Biology 6:91 Software Link
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Kowald A, Hamann A, Zintel S, Ullrich S, Klipp E, Osiewacz HD (2012) A systems biological analysis links ROS metabolism to mitochondrial protein quality control. Mechanisms of Ageing and Development 133:331-337 Cell Biology Link
Kraut DA, Israeli E, Schrader EK, Patil A, Nakai K, Nanavati D, Inobe T, Matouschek A (2012) Sequence- and Species-Dependence of Proteasomal Processivity. ACS Chemical Biology 7:1444–1453 Biochemistry Macromolecular Biochemistry Link
Leach MD, Tyc KM, Brown AJP, Klipp E (2012) Modelling the Regulation of Thermal Adaptation in Candida albicans, a Major Fungal Pathogen of Humans. PLoS ONE 7:e32467 Signaling Link
Levering J, Musters MWJM, Bekker M, Bellomo D, Fiedler T, de Vos WM, Hugenholtz J, Kreikemeyer B, Kummer U, Teusink B (2012) Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach: Modelling glycolysis of lactic acid bacteria. FEBS Journal 279:1274-1290 Metabolism Link
Li Y, Wang M, Carra C, Cucinotta FA (2012) Modularized Smad-regulated TGFβ signaling pathway. Mathematical Biosciences 240:187-200 Signaling Link
Lindner C (2012) Phosphane in der Organokatalyse: experimentelle und theoretische Studien. PhD Thesis, Ludwig-Maximilians University Munich. Chemistry Link
Maiwald, Tim (2012) Computational Analysis of The Interferon Alpha Signalling Using a Systems Biology Modelling Approach Pathway. PhD Thesis, Heidelberg University. Signaling Link
Mayorga LS, Lopez MJ, Becker WM (2012) Molecular Thermodynamics for Cell Biology as Taught with Boxes. Cell Biology Education 11:31-38 Cell Biology Education Link
Mazemondet O, John M, Leye S, Rolfs A, Uhrmacher AM (2012) Elucidating the Sources of β-Catenin Dynamics in Human Neural Progenitor Cells. PLoS ONE 7:e42792 Signaling Link
Mc Auley MT, Wilkinson DJ, Jones JJ, Kirkwood TB (2012) A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. BMC Systems Biology 6:130 Metabolism Physiology Link
Micheau J-C, Coudret C, Cruz J-M, Buhse T (2012) Amplification of enantiomeric excess, mirror-image symmetry breaking and kinetic proofreading in Soai reaction models with different oligomeric orders. Physical Chemistry Chemical Physics 14:13239 Chemistry Link
Monge ME, Rosenorn T, Favez O, Muller M, Adler G, Abo Riziq A, Rudich Y, Herrmann H, George C, D’Anna B (2012) Alternative pathway for atmospheric particles growth. Proceedings of the National Academy of Sciences 109:6840-6844 Chemistry Link
Moscato BM, Zhu B, Landis CR (2012) Mechanistic Investigations into the Behavior of a Labeled Zirconocene Polymerization Catalyst. Organometallics 31:2097-2107 Chemistry Link
Muntean N, Thuy LB, Kály-Kullai K, Wittmann M, Noszticzius Z, Onel L, Furrow SD (2012) Measurement of Hypoiodous Acid Concentration by a Novel Type Iodide Selective Electrode and a New Method To Prepare HOI. Monitoring HOI Levels in the Briggs-Rauscher Oscillatory Reaction. The Journal of Physical Chemistry A 116:6630-6642 Chemistry Link
Olin-Sandoval V, González-Chávez Z, Berzunza-Cruz M, Martínez I, Jasso-Chávez R, Becker I, Espinoza B, Moreno-Sánchez R, Saavedra E (2012) Drug target validation of the trypanothione pathway enzymes through metabolic modelling: Kinetic modelling of trypanothione metabolism. FEBS Journal 279:1811-1833 Metabolism Link
Pahle J, Challenger JD, Mendes P, McKane AJ (2012) Biochemical fluctuations, optimisation and the linear noise approximation. BMC Systems Biology 6:86 Computational Method Software Link
Palai T, Mitra S, Bhattacharya PK (2012) Kinetics and design relation for enzymatic conversion of lactose into galacto-oligosaccharides using commercial grade β-galactosidase. Journal of Bioscience and Bioengineering 114:418-423 Metabolism Link
Pinna F, Sahle S, Beuke K, Bissinger M, Tuncay S, D’Alessandro LA, Gauges R, Raue A, Timmer J, Klingmüller U, Schirmacher P, Kummer U, Breuhahn K (2012) A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes. Frontiers in Physiology 3:466 Signaling Link
Piras V, Hayashi K, Tomita M, Selvarajoo K (2012) Investigation of stochasticity in TRAIL signaling cancer model. IEEE, 609-614. Signaling Link
Ray JCJ, Igoshin OA (2012) Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization. PLoS Comput. Biol. 8:e1002672 Microbiology Genetics Link
Reyes-Palomares A, Montañez R, Sánchez-Jiménez F, Medina MÁ (2012) A combined model of hepatic polyamine and sulfur amino acid metabolism to analyze S-adenosyl methionine availability. Amino acids 42:597–610 Metabolism Link
Salvado B, Vilaprinyo E, Karathia H, Sorribas A, Alves R (2012) Two Component Systems: Physiological Effect of a Third Component. PLoS ONE 7:e31095 Signaling Link
Sarma U, Ghosh I (2012) Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade. BMC Systems Biology 6:82 Signaling Link
Sarma U, Ghosh I (2012) Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops. BMC Research Notes 5:287 Signaling Link
Sarma U, Sareen A, Maiti M, Kamat V, Sudan R, Pahari S, Srivastava N, Roy S, Sinha S, Ghosh I, Chande AG, Mukhopadhyaya R, Saha B (2012) Modeling and Experimental Analyses Reveals Signaling Plasticity in a Bi-Modular Assembly of CD40 Receptor Activated Kinases. PLoS ONE 7:e39898 Signaling Link
Schaber J (2012) Easy parameter identifiability analysis with COPASI. Biosystems 110:183-185 Computational Method Link
Schimek C, Vlaic S, Wöstemeyer J, Werner S, Schuster S, Schroeter A (2012) Model of the synthesis of trisporic acid in Mucorales showing bistability. IET Systems Biology 6:207-214 Signaling Link
Singh VK, Das K, Seshadri K (2012) Kinetic Modelling of GlmU Reactions - Prioritization of Reaction for Therapeutic Application. PLoS ONE 7:e43969 Metabolism Link
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Stefan MI, Marshall DP, Le Novère N (2012) Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII. PLoS ONE 7:e29406 Enzymology Link
Steinacher A, Leyser O, H. Clayton R (2012) A computational model of auxin and pH dynamics in a single plant cell. Journal of Theoretical Biology 296:84-94 Cell Biology Link
Sulins J, Mednis M (2012) Automatic termination of parallel optimization runs of stochastic global optimization methods in consensus or stagnation cases. Biosystems and Information technology 1:1-5 Software Computational Method Link
Surovtsova I, Simus N, Hübner K, Sahle S, Kummer U (2012) Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics. BMC Systems Biology 6:14 Software Computational Method Link
Tagore S, De RK (2012) SAGPAR: Structural Grammar-based automated pathway reconstruction. Interdisciplinary Sciences: Computational Life Sciences 4:116-127 Software Computational Method Link
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Warren PB, Allen RJ (2012) Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting. The Journal of Chemical Physics 136:104106 Computational Method Link
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74 publications
2011
Baez M, Wilson CA, Babul J (2011) Folding kinetic pathway of phosphofructokinase-2 from Escherichia coli: a homodimeric enzyme with a complex domain organization. FEBS Letters 585:2158–2164 Macromolecular Biochemistry Link
Bairy S, Wong CF (2011) Influence of kinetics of drug binding on EGFR signaling: A comparative study of three EGFR signaling pathway models. Proteins: Structure, Function, and Bioinformatics 79:2491–2504 Signaling Link
Bandaru P, Bansal M, Nemenman I (2011) Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data. J. Comput. Biol. 18:147-154 Laboratory Method Computational Method Link
Berestovsky N (2011) On the modeling of signaling networks with petri nets. MS Thesis, Rice University, Houston, Texas, USA. Computational Method Link
Casas A, Ramos MJ, Pérez Á (2011) Kinetics of chemical interesterification of sunflower oil with methyl acetate for biodiesel and triacetin production. Chemical Engineering Journal 171:1324–1332 Biotechnology Chemistry Link
Chandran D (2011) TinkerCell: Computer-Aided Design for Synthetic Biology. PhD Thesis, University of Washington, Seattle. Software Synthetic Biology Link
Checkley S (2011) Engineering Tuneable Gene Circuits in Yeast. PhD Thesis, University of Manchester. Synthetic Biology Link
Chen X (2011) Glutathione suppresses the autoxidation of 2’,5’-dihydroxy-4-chlorobiphenyl. MS Thesis, University of Iowa. Toxicology Link
Danis J, Turányi T (2011) Sensitivity analysis of bacterial chemotaxis models. Procedia Computer Science 7:233–234 Signaling Microbiology Link
DasGupta B, Vera-Licona P, Sontag E (2011) Reverse engineering of molecular networks from a common combinatorial approach. In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, M. Elloumi and A. Zomaya (editors). John Wiley & Sons, Inc. Computational Method Link
Diao T, Stahl SS (2011) Synthesis of Cyclic Enones via Direct Palladium-Catalyzed Aerobic Dehydrogenation of Ketones. Journal of the American Chemical Society , 133:14566–9 Chemistry Link
Fedosov SN, Xu X (2011) Enzymatic synthesis of biodiesel from fatty acids. Kinetics of the reaction measured by fluorescent response of Nile Red. Biochemical engineering journal 56:172–183 Biotechnology Link
Gauges R (2011) Standards and Tools for Model Exchange and Analysis in Systems Biology. PhD Thesis, Heidelberg University Software Computational Method Link
Genc S, Kurnaz IA, Ozilgen M (2011) Astrocyte-neuron lactate shuttle may boost more ATP supply to the neuron under hypoxic conditions-in silico study supported by in vitro expression data. BMC Systems Biology 5:162 Cell Biology Metabolism Link
Gerber S (2011) In silico modeling of cation homeostasis in Saccharomyces cerevisiae. PhD Thesis, Humboldt-University of Berlin. Physiology Link
Hein JE, Armstrong A, Blackmond DG (2011) Kinetic profiling of prolinate-catalyzed α-amination of aldehydes. Organic Letters 13:4300–4303 Chemistry Link
Hill MP, Freer LH, Vang MC, Carroll EC, Larsen DS (2011) Multiphoton Manipulations of Enzymatic Photoactivity in Aspartate Aminotransferase. The Journal of Physical Chemistry B 115:4474–4483 Enzymology Link
Hinze T, Schumann M, Bodenstein C, Heiland I, Schuster S (2011) Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In Silico Study of Modules for Circadian Clock Systems. Computational Intelligence and Neuroscience 2011:1–9 Theory Link
Hoffman-Sommer M, Supady A, Klipp E (2011) Cell-to-Cell Communication Circuits: Quantitative Analysis of Synthetic Logic Gates. Frontiers in Physiology 3:287–287 Synthetic Biology Link
Iwasaki H, Takeuchi O, Teraguchi S, Matsushita K, Uehata T, Kuniyoshi K, Satoh T, Saitoh T, Matsushita M, Standley DM, Akira S (2011) The IkB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1. Nature Immunology 12:1167-75 Immunology Signaling Link
Izawa Y, Pun D, Stahl SS (2011) Palladium-Catalyzed Aerobic Dehydrogenation of Substituted Cyclohexanones to Phenols. Science 333:209-213 Chemistry Link
Kleppe R, Martinez A, Døskeland SO, Haavik J (2011) The 14-3-3 proteins in regulation of cellular metabolism. Seminars in Cell & Developmental Biology. 22:713–719 Signaling Metabolism Link
Johnson KRD, Hayes PG (2011) Kinetic and Mechanistic Investigation of Metallacycle Ring Opening in an Ortho-Metalated Lutetium Aryl Complex. Organometallics 30:58–67 Chemistry Link
Keitz BK, Grubbs RH (2011) Probing the origin of degenerate metathesis selectivity via characterization and dynamics of ruthenacyclobutanes containing variable NHCs. Journal of the American Chemical Society 133:16277-16284 Chemistry Link
Klotz C, Ziegler T, Figueiredo AS, Rausch S, Hepworth MR, Obsivac N, Sers C, Lang R, Hammerstein P, Lucius R, Hartmann S (2011) A Helminth Immunomodulator Exploits Host Signaling Events to Regulate Cytokine Production in Macrophages. PLoS Pathogogens 7:e1001248 Immunology Link
Kolodkin AN (2011) Emergence of design. PhD Thesis, Vrije Universiteit Amsterdam, The Netherlands. Theory Metabolism Link
Lauro FM, DeMaere MZ, Yau S, Brown MV, Ng C, Wilkins D, Raftery MJ, Gibson JAE, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Thomas T, Cavicchioli R (2011) An integrative study of a meromictic lake ecosystem in Antarctica. ISME J. 5:879-95 Ecology Link
Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP (2011) A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Molecular Systems Biology 7:514 Genomics Link
Marchisio MA, Stelling J (2011) Automatic Design of Digital Synthetic Gene Circuits. PLoS Comput. Biol. 7:e1001083 Synthetic Biology Link
Mauch S, Stalzer M (2011) Efficient formulations for exact stochastic simulation of chemical systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8:27-35 Computational Method Link
Qian L, Winfree E (2011) A simple DNA gate motif for synthesizing large-scale circuits. J. Royal Soc. Interface 8:1281-97 Synthetic Biology Link
Qian L, Winfree E (2011) Scaling up digital circuit computation with DNA strand displacement cascades. Science 332:1196–1201 Synthetic Biology Link
Rodriguez F, Bustos MA, Zanetti MN, Ruete MC, Mayorga LS, Tomes CN (2011) alpha-SNAP prevents docking of the acrosome during sperm exocytosis because it sequesters monomeric syntaxin. PLoS ONE 6:e21925 Cell Biology Macromolecular Biochemistry Link
Schweizer N (2011) Calcium signaling in fish cells. PhD Thesis, University of Heidelberg Signaling Link
Shivanandan A (2011) Stochastic modelling and identification of arabinose uptake network in Escherichia coli (PDF Download Available). MS Thesis, Université Joseph Fourier, Grenoble, France. Metabolism Microbiology Link
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Novère NL (2011) Minimum Information About a Simulation Experiment (MIASE). PLOS Computational Biology 7:e1001122 Computational Method Link
Wendelsdorf KV (2011) Models of the Mucosal Inflammatory and Regulatory Immune Pathways: The Role of Host Response in Microbial Persistence and Pathogenesis. PhD Thesis, Virginia Tech, Blacksburg, Virginia, USA. Immunology Link
Yang J (2011) Midazolam as a Probe Drug to Study Cytochrome P450 3A Allosterism. PhD Thesis, University of Washington, Seattle, USA. Enzymology Pharmacology Link
Yao G, Tan C, West M, Nevins JR, You L (2011) Origin of bistability underlying mammalian cell cycle entry. Mol. Systems Biol. 7:485 Cell Biology Link

39 publications
2010
Adra S, Sun T, MacNeil S, Holcombe M, Smallwood R (2010) Development of a Three Dimensional Multiscale Computational Model of the Human Epidermis. PLoS ONE 5:e8511. Physiology Link
Andreani A, Burnelli S, Granaiola M, Leoni A, Locatelli A, Morigi R, Rambaldi M, Varoli L, Cremonini MA, Placucci G (2010) New isatin derivatives with antioxidant activity. European Journal of Medicinal Chemistry 45:1374–1378 Chemistry Link
Baker, S.M., Schallau, K., Junker, B.H. (2010). Comparison of different algorithms for simultaneous estimation of multiple parameters in kinetic metabolic models. Journal of Integrative Bioinformatics 7(3):519-520 Computational Method Link
Brasen JC, Barington T, Olsen LF (2010) On the mechanism of oscillations in neutrophils. Biophysical Chemistry 148:82-92 Cell Biology Link
Chi CN, Bach A, Gottschalk M, Kristensen AS, Stromgaard K, Jemth P (2010) Deciphering the Kinetic Binding Mechanism of Dimeric Ligands Using a Potent Plasma-stable Dimeric Inhibitor of Postsynaptic Density Protein-95 as an Example. Journal of Biological Chemistry 285:28252–28260 Macromolecular Biochemistry Link
Colby DA, Bergman RG, Ellman JA (2010) Rhodium-Catalyzed C−C Bond Formation via Heteroatom-Directed C−H Bond Activation. Chemical Reviews 110:624–655 Link
Dada JO, Spasic I, Paton NW, Mendes P (2010) SBRML: a markup language for associating systems biology data with models. Bioinformatics 26:932–938 Computational Method Link
Dimitrova ES, Vera Licona MP, McGee J, Laubenbacher R. (2010) Discretization of Time Series Data. J. Comput. Biol. J17:853-68. Computational Method Link
Escuela G, Hinze T, Dittrich P, Schuster S, Moreno-Alvarez M (2010) Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems. BIOSIGNALS, 306–311 Computational Method Biotechnology Link
Fujita KA, Toyoshima Y, Uda S, Ozaki Y, Kubota H, Kuroda S (2010) Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics. Science Signaling 3:ra56-ra56 Signaling Link
Furrow SD, Aurentz DJ (2010) Reactions of Iodomalonic Acid, Diiodomalonic Acid, and Other Organics in the Briggs−Rauscher Oscillating System. The Journal of Physical Chemistry A 114:2526–2533 Chemistry Link
Hallinan JS, Misirli G, Wipat A (2010) Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. IEEE, 768–774 Synthetic Biology Link
Hill MP, Carroll EC, Vang MC, Addington TA, Toney MD, Larsen DS (2010) Light-Enhanced Catalysis by Pyridoxal Phosphate-Dependent Aspartate Aminotransferase. Journal of the American Chemical Society 132:16953–16961 Enzymology Link
Huang R, Grabarek Z, Wang C-LA (2010) Differential effects of caldesmon on the intermediate conformational states of polymerizing actin. J. Biol. Chem. 285:71-79 Macromolecular Biochemistry Link
Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW (2010) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics 11:582 Computational Method Metabolism Link
Liu J, Mehdi S, Topping J, Tarkowski P, Lindsey K (2010) Modelling and experimental analysis of hormonal crosstalk in Arabidopsis. Molecular Systems Biology 6 Signaling Link
Maiwald T, Schneider A, Busch H, Sahle S, Gretz N, Weiss TS, Kummer U, Klingmüller U (2010) Combining theoretical analysis and experimental data generation reveals IRF9 as a crucial factor for accelerating interferon α-induced early antiviral signalling: IRF9 accelerates IFNα signal transduction. FEBS Journal 277:4741-4754 Signaling Link
Morrissey ER, Juarez MA, Denby KJ, Burroughs NJ (2010) On reverse engineering of gene interaction networks using time course data with repeated measurements. Bioinformatics 26:2305–2312 Computational Method Link
Nakano T, Doi T, Yoshimoto J, Doya K (2010) A Kinetic Model of Dopamine- and Calcium-Dependent Striatal Synaptic Plasticity. PLoS Comput Biol 6(2): e1000670. Physiology Link
Orrillo AG, Furlan RLE (2010) Supramolecular Interactions between Library Members Modulate the Behavior of Dynamic Combinatorial Libraries. The Journal of Organic Chemistry 75:211–214 Chemistry Link
Pezzola S, Antonini G, Geroni C, Beria I, Colombo M, Broggini M, Mongelli N, Leboffe L, MacArthur R, Mozzi AF, Federici G, Caccuri AM (2010) Role of Glutathione Transferases in the Mechanism of Brostallicin Activation. Biochemistry 49:226–235 Enzymology Link
Samorodnitsky E, Pugh BF (2010) Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data. PLoS Comput. Biol. 6:e1000733 Macromolecular Biochemistry Genomics Link
Smallbone, K, Simeonidis, E, Swainston, N, Mendes, P (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Sys. Biol. 4:6 Genomics Whole-Cell Models Metabolism Link
Swainston N, Jameson D, Li P, Spasic I, Mendes P, Paton N (2010) Integrative information management for systems biology. Data Integration in the Life Sciences, DILS2010 (Lambrix P, Kemp G, eds.), Lecture Notes in Computer Science, 6254:164–178 Computational Method Link
Tiwari A, Balázsi G, Gennaro ML, Igoshin OA (2010) The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response. Physical Biology 7:36005 Microbiology Genetics Link
Watkins AL, Landis CR (2010) Origin of Pressure Effects on Regioselectivity and Enantioselectivity in the Rhodium-Catalyzed Hydroformylation of Styrene with ( S , S , S )-BisDiazaphos. Journal of the American Chemical Society 132:10306–10317 Chemistry Link
Wendelsdorf K, Bassaganya-Riera J, Hontecillas R, Eubank S (2010) Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease. J. Theoret. Biol. 264:1225-1239 Immunology Link
Yao G, Tan C, West M, Nevins JR, You L (2010) A Minimal Gene Circuit Underlying the Bistable Cell Cycle Entry. Synthetic Biology Link
Zhang R, Monsma F (2010) Binding kinetics and mechanism of action: toward the discovery and development of better and best in class drugs. Expert opinion on drug discovery 5:1023–1029 Enzymology Pharmacology Link
Zhang Y, Song D, Lanni LM, Shimizu KD (2010) Importance of Functional Monomer Dimerization in the Molecular Imprinting Process. Macromolecules 43:6284–6294 Chemistry Link

30 publications
2009
Baralla A, Mentzen WI, De La Fuente A (2009) Inferring Gene Networks: Dream or Nightmare?: Part 1: Challenges 1 and 3. Annals of the New York Academy of Sciences 1158:246-256 Computational Method Link
Bauer-Mehren A, Furlong LI, Rautschka M, Sanz F (2009) From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways. BMC Bioinformatics 10:S6 Signaling Link
Blaquiere N, Shore DG, Rousseaux S, Fagnou K (2009) Decarboxylative Ketone Aldol Reactions: Development and Mechanistic Evaluation under Metal-Free Conditions. The Journal of Organic Chemistry 74:6190–6198 Chemistry Link
Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars. PLoS Computational Biology 5:e1000529 Synthetic Biology Computational Method Laboratory Method Link
Cimetiere N, Dossier-Berne F, De Laat J (2009) Monochloramination of Resorcinol: Mechanism and Kinetic Modeling. Environmental Science & Technology 43:9380–9385 Chemistry Link
Curien G, Bastien O, Robert-Genthon M, Cornish-Bowden A, Cárdenas ML, Dumas R (2009) Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters. Mol. Sys. Biol. 5:271 Metabolism Link
Figueiredo AS, Höfer T, Klotz C, Sers C, Hartmann S, Lucius R, Hammerstein P (2009) Modelling and simulating interleukin-10 production and regulation by macrophages after stimulation with an immunomodulator of parasitic nematodes: Modelling interleukin-10 production and regulation. FEBS Journal 276:3454-3469 Signaling Link
Friedrich A, Ghosh R, Kolb R, Herdtweck E, Schneider S (2009) Iridium Olefin Complexes Bearing Dialkylamino/amido PNP Pincer Ligands: Synthesis, Reactivity, and Solution Dynamics †. Organometallics 28:708-718 Biochemistry Link
Gallagher SS, Sable JE, Sheetz MP, Cornish VW (2009) An In Vivo Covalent TMP-Tag Based on Proximity-Induced Reactivity. ACS Chem. Biol. 4:547-56 Laboratory Method Link
Goyal M, Rizzo M, Schumacher F, Wong CF (2009) Beyond thermodynamics: drug binding kinetics could influence epidermal growth factor signaling. J. Medicinal Chem. 52:5582-5585 Signaling Link
Hower V, Mendes P, Torti FM, Laubenbacher R, Akman S, Shulaev V, Torti SV (2009) A general map of iron metabolism and tissue-specific subnetworks. Molecular BioSystems 5:422 Metabolism Link
Ibrahim B, Schmitt E, Dittrich P, Diekmann S (2009) In silico study of kinetochore control, amplification, and inhibition effects in MCC assembly. Biosystems 95:35-50 Signaling Link
Katzberg, M., Wechler, K., Müller, M., Dünkelmann, P., Stohrer, J., Hummel, W., & Bertau, M. (2009). Biocatalytical production of (5S)-hydroxy-2-hexanone. Org. Biomol. Chem. 7(2):304-314 Biochemistry Link
Knoke B, Textor S, Gershenzon J, Schuster S (2009) Mathematical modelling of aliphatic glucosinolate chain length distribution in Arabidopsis thaliana leaves. Phytochemistry Reviews 8:39-51 Metabolism Link
Kona F, Tao P, Martin P, Xu X, Gatti DL (2009) Electronic Structure of the Metal Center in the Cd 2+ , Zn 2+ , and Cu 2+ Substituted Forms of KDO8P Synthase: Implications for Catalysis. Biochemistry 48:3610–3630 Enzymology Biochemistry Link
Kovács K, Hurst LD, Papp B (2009) Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli. PLoS Biology 7:e1000115 Genetics Link
Liu J, Brazier-Hicks M, Edwards R (2009) A kinetic model for the metabolism of the herbicide safener fenclorim in Arabidopsis thaliana. Biophysical Chemistry 143:85–94 Metabolism Link
Magarkar A, Banerji A, Kolhi S (2009) Quantification of Biological Robustness at the Systemic Level. arXiv preprint arXiv:0903.4844 Theory Link
Mellmann LJ (2009) Exogenous ligand effects on S-nitrosohemoglobin formation in reactions of methemoglobin with nitric oxide. PhD Thesis Montana State University-Bozeman Chemistry Link
Mendes P, Messiha H, Malys N, Hoops S (2009) Enzyme Kinetics and Computational Modeling for Systems Biology. Methods in Enzymology 467:583–599 Enzymology Computational Method Link
Menolascina F, Bellomo D, Maiwald T, Bevilacqua V, Ciminelli C, Paradiso A, Tommasi S (2009) Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering. BMC Bioinformatics 10:S4 Laboratory Method Signaling Link
Modre-Osprian R, Osprian I, Tilg B, Schreier G, Weinberger KM, Graber A (2009) Dynamic simulations on the mitochondrial fatty acid Beta-oxidation network. BMC Systems Biology 3:2 Metabolism Link
Orton RJ, Adriaens ME, Gormand A, Sturm OE, Kolch W, Gilbert DR (2009) Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. BMC Systems Biology 3:100 Signaling Link
Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, Mones L, Fuxreiter M, Pingoud A (2009) On the Divalent Metal Ion Dependence of DNA Cleavage by Restriction Endonucleases of the EcoRI Family. J. Mol. Biol. 393:140-60 Macromolecular Biochemistry Link
Pokrzywa RM (2009) Systems Biology in an Imperfect World: Modeling Biological Systems with Incomplete Information. PhD Thesis, Virginia Tech Computational Method Link
Ricagno S, Caccia S, Sorrentino G, Antonini G, Bolognesi M (2009) Human Neuroserpin: Structure and Time-Dependent Inhibition. Journal of Molecular Biology 388:109–121 Enzymology Macromolecular Biochemistry Link
Schulz M, Bakker BM, Klipp E (2009) TIde: a software for the systematic scanning of drug targets in kinetic network models. BMC Bioinformatics 10:344 Software Link
Shen Z, Dornan PK, Khan HA, WooTK, Dong VM (2009) Mechanistic Insights into the Rhodium-Catalyzed Intramolecular Ketone Hydroacylation (2009) J. Am. Chem. Soc. 131:1077-91 Chemistry Link
Shi Y, Varghese SM, Huang S, White J, Pervaiz S, Tucker-Kellogg L (2009) Computational modeling of pathway dynamics for detecting drug effects: paradoxical effects of LYS303511 on TRAIL-induced apoptosis. Proc LSS Comput Syst Bioinform Conf, 213–224 Toxicology Link
Sun T, Adra S, Smallwood R, Holcombe M, MacNeil S (2009) Exploring Hypotheses of the Actions of TGF-β1 in Epidermal Wound Healing Using a 3D Computational Multiscale Model of the Human Epidermis. PLoS ONE 4:e8515 Immunology Computational Method Software Link
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Troncoso-Ponce MA, Kruger NJ, Ratcliffe G, Garcés R, Martínez-Force E (2009) Characterization of glycolytic initial metabolites and enzyme activities in developing sunflower (Helianthus annuus L.) seeds. Phytochemistry 70:1117–1122 Metabolism Link

32 publications
2008
Chao-Fang Chu (2009) Computational characterization of the role of antioxidant potential in the tonifying mechanism of Yang-invigorating Chinese tonifying herbs. Link
Ciocchetta F, Hillston J, Kos M, Tollervey D (2008) Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA. Theoretical Computer Science 408:41–54 Macromolecular Biochemistry Link
Colby DA, Bergman RG, Ellman JA (2008) Synthesis of dihydropyridines and pyridines from imines and alkynes via C- H activation. Journal of the American Chemical Society 130:3645–3651 Chemistry Link
Colvin RA, Bush AI, Volitakis I, Fontaine CP, Thomas D, Kikuchi K, Holmes WR (2008) Insights into Zn2+ homeostasis in neurons from experimental and modeling studies. America Journal of Physiology 294:C726-C742 Physiology Link
Del Conte-Zerial P, Brusch L, Rink JC, Collinet C, Kalaidzidis Y, Zerial M, Deutsch A (2008) Membrane identity and GTPase cascades regulated by toggle and cut-out switches. Mol. Sys. Biol. 4:206 Signaling Link
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kırdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology 26:1155–1160 Microbiology Computational Method Link
Jordão L, Bleck CKE, Mayorga L, Griffiths G, Anes E (2008) On the killing of mycobacteria by macrophages. Cell. Microbiol. 10:529-48 Immunology Link
Jungmann R, Renner S, Simmel FC (2008) From DNA nanotechnology to synthetic biology. HFSP Journal 2:99-109 Synthetic Biology Link
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Kühnel M, Mayorga LS, Dandekar T, Thakar J, Schwarz R, Anes E, Griffiths G, Reich J (2008) Modelling phagosomal lipid networks that regulate actin assembly. BMC Systems Biology 2:107 Metabolism Macromolecular Biochemistry Link
Long J, Roth M (2008) Synthetic microarray data generation with RANGE and NEMO. Bioinformatics 24:132–134 Computational Method Genomics Link
Marchisio MA (2008) How to design synthetic gene circuits with composable parts and pools in the ProMoT framework. Synthetic Biology Link
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Schmierer B, Tournier AL, Bates PA, Hill CS (2008) Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. PNAS 105:6608-13 Cell Biology Signaling Link
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18 publications
2007
Camacho, D, Vera-Licona P, Mendes P, Laubenbacher R (2007) Comparison of reverse-engineering methods using an in silico network. Ann. N.Y. Acad. Sci. 1115:73-89. Computational Method Link
Ellman JA, Colby D, Bergman R (2007) Synthesis of Dihydropyridines and Pyridines from Imines and Alkynes via CH Activation. Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US) Link
Kelly MP, Isiegas C, Cheung YF, Tokarczyk J, Yang X, Esposito MF, Rapoport DA, Fabian SA, Siegel SJ, Wand G, Houslay MD, Kanes SJ, Abel T (2007) Constitutive activation of Galphas within forebrain neurons causes deficits in sensorimotor gating because of PKA-dependent decreases in cAMP. Neuropsychopharmacology 32:577-88 Pharmacology Signaling Link
Klipp E, Liebermeister W, Helbig A, Kowald A, Schaber J (2007) Standards in computational systems biology. Link
Kummer U, Zobeley J, Brasen JC, Fahmy R, Kindzelskii AL, Petty AR, Clark AJ, Petty HR (2007) Elevated Glucose Concentrations Promote Receptor-Independent Activation of Adherent Human Neutrophils: An Experimental and Computational Approach. Biophys. J. 92:2597-2607 Immunology Link
Rippe K, Schrader A, Riede P, Strohner R, Lehmann E,Längst G (2007) DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. PNAS 104:15635-40 Macromolecular Biochemistry Cell Biology Link
Uys L, Botha FC, Hofmeyr J-HS, Rohwer JM (2007) Kinetic model of sucrose accumulation in maturing sugarcane culm tissue. Phytochemistry 68:2375-92 Metabolism Link
Xie Z (2007) Modelling genetic regulatory networks: A new model for circadian rhythms in Drosophila and investigation of genetic noise in a viral infection process. PhD Thesis. Lincoln University, New Zealand Cell Biology Link

8 publications
2006
Frein D (2006) Signaling and Redox Regulation by Nitric Oxide, Superoxide and Carbon Monoxide. Signaling Link

1 publication