| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/bioinformatics/HoopsSGLPSSXMK06 |
| P356 | DOI | 10.1093/BIOINFORMATICS/BTL485 |
| P3181 | OpenCitations bibliographic resource ID | 131936 |
| P698 | PubMed publication ID | 17032683 |
| P5875 | ResearchGate publication ID | 6761935 |
| P50 | author | Jürgen Pahle | Q57574724 |
| Pedro Mendes | Q7159862 | ||
| P2093 | author name string | Liang Xu | |
| Mudita Singhal | |||
| Christine Lee | |||
| Stefan Hoops | |||
| Ursula Kummer | |||
| Sven Sahle | |||
| Ralph Gauges | |||
| Natalia Simus | |||
| P2860 | cites work | The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models | Q28212902 |
| P433 | issue | 24 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | computational mathematics | Q1122491 |
| P304 | page(s) | 3067-3074 | |
| P577 | publication date | 2006-10-10 | |
| P1433 | published in | Bioinformatics | Q4914910 |
| P1476 | title | COPASI--a COmplex PAthway SImulator | |
| P478 | volume | 22 |
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| Q54360333 | Folding kinetic pathway of phosphofructokinase-2 from Escherichia coli: a homodimeric enzyme with a complex domain organization. |
| Q34273084 | Foundations for the design and implementation of synthetic genetic circuits |
| Q24650577 | From DNA nanotechnology to synthetic biology |
| Q33503931 | From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways |
| Q47596954 | From word models to executable models of signaling networks using automated assembly. |
| Q92774155 | Gamma-glutamylcysteine synthetase and tryparedoxin 1 exert high control on the antioxidant system in Trypanosoma cruzi contributing to drug resistance and infectivity |
| Q28473490 | Genome-wide modeling of transcription preinitiation complex disassembly mechanisms using ChIP-chip data |
| Q47555105 | Genomic, Biochemical, and Modeling Analyses of Asparagine Synthetases from Wheat. |
| Q61797119 | Global Implications of Local Unfolding Phenomena, Probed by Cysteine Reactivity in Human Frataxin |
| Q38806208 | Graphical Modeling Meets Systems Pharmacology. |
| Q38893459 | Graphics processing units in bioinformatics, computational biology and systems biology. |
| Q28548020 | HEPNet: A Knowledge Base Model of Human Energy Pool Network for Predicting the Energy Availability Status of an Individual |
| Q42698038 | Halide Abstraction Competes with Oxidative Addition in the Reactions of Aryl Halides with [Ni(PMen Ph(3-n) )4 ]. |
| Q28536028 | Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei |
| Q93270171 | Harmonizing semantic annotations for computational models in biology |
| Q64936477 | High-resolution computational modeling of immune responses in the gut. |
| Q89940975 | Highly selective hydrogenation of amides catalysed by a molybdenum pincer complex: scope and mechanism |
| Q41458532 | Homocoupling versus reduction of radicals: an experimental and theoretical study of Ti(III)-mediated deoxygenation of activated alcohols. |
| Q37486247 | Human augmenter of liver regeneration: probing the catalytic mechanism of a flavin-dependent sulfhydryl oxidase |
| Q44031214 | Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics |
| Q92188785 | Hypoxia Inducible Factor 1α Inhibits the Expression of Immunosuppressive Tryptophan-2,3-Dioxygenase in Glioblastoma |
| Q92153132 | Identification of evolutionary and kinetic drivers of NAD-dependent signaling |
| Q98303095 | Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches |
| Q30402420 | Identification of novel metabolic interactions controlling carbon flux from xylose to ethanol in natural and recombinant yeasts |
| Q47898972 | Impact of binding mechanism on selective inhibition of histone deacetylase isoforms. |
| Q42116249 | Important amino acid residues of hexachlorocyclohexane dehydrochlorinases (LinA) for enantioselective transformation of hexachlorocyclohexane isomers |
| Q34447440 | Improved inhibitor screening experiments by comparative analysis of simulated enzyme progress curves |
| Q38985000 | Improved metabolite profile smoothing for flux estimation |
| Q34652065 | Improving collaboration by standardization efforts in systems biology. |
| Q33662831 | In SilicoModel-driven Assessment of the Effects of Brain-derived Neurotrophic Factor Deficiency on Glutamate and Gamma-Aminobutyric Acid: Implications for Understanding Schizophrenia Pathophysiology. |
| Q90640172 | In silico Metabolic Pathway Analysis Identifying Target Against Leishmaniasis - A Kinetic Modeling Approach |
| Q33772734 | In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis. |
| Q36962711 | Increasing extracellular H2O2 produces a bi-phasic response in intracellular H2O2, with peroxiredoxin hyperoxidation only triggered once the cellular H2O2-buffering capacity is overwhelmed |
| Q38905586 | Inferring Mechanistic Parameters from Amyloid Formation Kinetics by Approximate Bayesian Computation |
| Q54585320 | Influence of kinetics of drug binding on EGFR signaling: a comparative study of three EGFR signaling pathway models. |
| Q37277390 | Inhibition of Non-flux-Controlling Enzymes Deters Cancer Glycolysis by Accumulation of Regulatory Metabolites of Controlling Steps |
| Q46815661 | Insights into Zn2+ homeostasis in neurons from experimental and modeling studies |
| Q30480219 | Integrated network reconstruction, visualization and analysis using YANAsquare. |
| Q38119873 | Integrating pathways of Parkinson's disease in a molecular interaction map. |
| Q28740525 | Integrating systems biology models and biomedical ontologies |
| Q28534507 | Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum |
| Q91712018 | Integrative Computational Framework for Understanding Metabolic Modulation in Leishmania |
| Q35536427 | Interleukin-1β enhances FasL-induced caspase-3/-7 activity without increasing apoptosis in primary mouse hepatocytes |
| Q90567475 | Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity |
| Q36563109 | Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification |
| Q46130452 | Introduction of a new platform for parameter estimation of kinetically complex environmental systems |
| Q41886452 | Invariants and other structural properties of biochemical models as a constraint satisfaction problem. |
| Q35009820 | Investigating interventions in Alzheimer's disease with computer simulation models |
| Q91864503 | JigCell Model Connector: building large molecular network models from components |
| Q35878537 | JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations |
| Q90337547 | K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data |
| Q28651992 | KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems |
| Q39277115 | Kinetic Analysis and Probing with Substrate Analogues of the Reaction Pathway of the Nitrile Reductase QueF from Escherichia coli. |
| Q58693980 | Kinetic mechanism of coupled binding in sodium-aspartate symporter GltPh |
| Q65000956 | Kinetic modeling of Stickland reactions-coupled methanogenesis for a methanogenic culture. |
| Q33881486 | Kinetic modeling of biological systems |
| Q28482687 | Kinetic modelling of GlmU reactions - prioritization of reaction for therapeutic application |
| Q38205653 | Kinetic models in industrial biotechnology - Improving cell factory performance |
| Q51697204 | Kinetics and model development for enzymatic synthesis of fructo-oligosaccharides using fructosyltransferase. |
| Q37723601 | Kinetics of extracellular ATP in mastoparan 7-activated human erythrocytes |
| Q43995167 | Kinetics of sucrose conversion to fructo-oligosaccharides using enzyme (invertase) under free condition |
| Q29994733 | LASSIE: simulating large-scale models of biochemical systems on GPUs. |
| Q89980566 | LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism |
| Q56913847 | Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli |
| Q30544055 | Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation |
| Q31061814 | Learning stochastic process-based models of dynamical systems from knowledge and data |
| Q64233922 | Length-independent telomere damage drives post-mitotic cardiomyocyte senescence |
| Q42181605 | Leveraging modeling approaches: reaction networks and rules |
| Q28539118 | Leveraging systems biology approaches in clinical pharmacology |
| Q34420422 | LibKiSAO: a Java library for Querying KiSAO. |
| Q35550638 | Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model |
| Q34496057 | Light-enhanced catalysis by pyridoxal phosphate-dependent aspartate aminotransferase |
| Q47114235 | Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology |
| Q36215331 | Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders. |
| Q34484814 | Logic modeling and the ridiculome under the rug. |
| Q47305365 | MAMMOTh: A new database for curated mathematical models of biomolecular systems |
| Q108126729 | MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics |
| Q92837425 | MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework |
| Q33806474 | MEMOSys: Bioinformatics platform for genome-scale metabolic models |
| Q38671211 | MUFINS: multi-formalism interaction network simulator. |
| Q26801210 | Macroscopic modeling of mammalian cell growth and metabolism |
| Q33818583 | Mass conservation and inference of metabolic networks from high-throughput mass spectrometry data |
| Q42213727 | Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization |
| Q49804607 | Mathematical Modelling of Nitric Oxide/Cyclic GMP/Cyclic AMP Signalling in Platelets. |
| Q38809377 | Mathematical Models for Immunology: Current State of the Art and Future Research Directions |
| Q38921582 | Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer's disease |
| Q28082151 | Mathematical and computational modeling in biology at multiple scales |
| Q35161056 | Mathematical descriptions of biochemical networks: stability, stochasticity, evolution |
| Q36638792 | Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system |
| Q34531633 | Mathematical modeling of sustainable synaptogenesis by repetitive stimuli suggests signaling mechanisms in vivo |
| Q51089841 | Mathematical modelling of arsenic transport, distribution and detoxification processes in yeast. |
| Q38448975 | Mathematical modelling of metabolic regulation in aging |
| Q36828180 | Mathematical models for the Notch and Wnt signaling pathways and the crosstalk between them during somitogenesis |
| Q34776635 | Mathematical models in biology: from molecules to life |
| Q46346574 | Measuring CO2 and HCO3- permeabilities of isolated chloroplasts using a MIMS-18O approach |
| Q91663379 | Mechanism of Catalytic O2 Reduction by Iron Tetraphenylporphyrin |
| Q28550745 | Mechanism of Focal Adhesion Kinase Mechanosensing |
| Q37145133 | Mechanism of synergistic activation of Arp2/3 complex by cortactin and N-WASP |
| Q42157338 | Mechanisms of regulation of olfactory transduction and adaptation in the olfactory cilium. |
| Q42275459 | Mechanistic Kinetic Modeling of Thiol-Michael Addition Photopolymerizations via Photocaged "Superbase" Generators: An Analytical Approach |
| Q38769967 | Mechanosensing of shear by Pseudomonas aeruginosa leads to increased levels of the cyclic-di-GMP signal initiating biofilm development |
| Q90678591 | Membrane Tension Orchestrates Rear Retraction in Matrix-Directed Cell Migration |
| Q30483077 | Membrane identity and GTPase cascades regulated by toggle and cut-out switches |
| Q39970633 | MetaCrop 2.0: managing and exploring information about crop plant metabolism. |
| Q42082854 | MetaCrop: a detailed database of crop plant metabolism. |
| Q36276893 | Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. |
| Q42925318 | Metabolica: a statistical research tool for analyzing metabolic networks |
| Q56974486 | Metabolomic biomarkers: search, discovery and validation |
| Q27144251 | Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery |
| Q38665803 | Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends. |
| Q43956692 | Methylerythritol phosphate pathway to isoprenoids: kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum |
| Q33830181 | Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus |
| Q42320855 | Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis |
| Q41511168 | Mixed mechanisms of multi-site phosphorylation |
| Q37426285 | ModeLang: a new approach for experts-friendly viral infections modeling |
| Q34587158 | Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways |
| Q40820351 | Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease |
| Q30678210 | Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data |
| Q46850321 | Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion |
| Q38892442 | Modeling Intercellular Communication as a Survival Strategy of Cancer Cells: An In Silico Approach on a Flexible Bioinformatics Framework |
| Q34344753 | Modeling and experimental analyses reveals signaling plasticity in a bi-modular assembly of CD40 receptor activated kinases |
| Q41281433 | Modeling and simulation of biological systems using SPICE language |
| Q33280162 | Modeling biochemical transformation processes and information processing with Narrator |
| Q51080469 | Modeling cancer glycolysis under hypoglycemia, and the role played by the differential expression of glycolytic isoforms. |
| Q58751607 | Modeling clock-related metabolic syndrome due to conflicting light and food cues |
| Q64269457 | Modeling genotypes in their microenvironment to predict single- and multi-cellular behavior |
| Q24651812 | Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies |
| Q46249708 | Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica |
| Q21145352 | Modeling structure-function relationships in synthetic DNA sequences using attribute grammars |
| Q41861941 | Modeling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii |
| Q34066290 | Modeling the Calvin-Benson cycle |
| Q34494038 | Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection |
| Q36217991 | Modeling the Role of Lanthionine Synthetase C-Like 2 (LANCL2) in the Modulation of Immune Responses to Helicobacter pylori Infection |
| Q35900690 | Modeling the ascorbate-glutathione cycle in chloroplasts under light/dark conditions |
| Q36375897 | Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient |
| Q30424551 | Modeling the role of peroxisome proliferator-activated receptor γ and microRNA-146 in mucosal immune responses to Clostridium difficile |
| Q26766623 | Modeling-Enabled Systems Nutritional Immunology |
| Q42249980 | Modelling and experimental analysis of hormonal crosstalk in Arabidopsis |
| Q37952605 | Modelling complex biological systems using an agent-based approach |
| Q35238701 | Modelling coupled oscillations in the Notch, Wnt, and FGF signaling pathways during somitogenesis: a comprehensive mathematical model |
| Q33390476 | Modelling phagosomal lipid networks that regulate actin assembly |
| Q42431432 | Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast |
| Q40292403 | Modelling the regulation of thermal adaptation in Candida albicans, a major fungal pathogen of humans |
| Q33612153 | Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways |
| Q33968220 | Modelling the role of the Hsp70/Hsp90 system in the maintenance of protein homeostasis |
| Q36678678 | Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models. |
| Q34346565 | Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits |
| Q64256132 | Molecular crypsis by pathogenic fungi using human factor H. A numerical model |
| Q30513833 | Molecular thermodynamics for cell biology as taught with boxes |
| Q34657714 | MonaLisa--visualization and analysis of functional modules in biochemical networks |
| Q37419056 | Monitoring of multiple sclerosis immunotherapy: from single candidates to biomarker networks. |
| Q35264385 | Multi-level kinetic model of mRNA delivery via transfection of lipoplexes |
| Q37826628 | Multi-scale modelling and simulation in systems biology |
| Q58417407 | Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease |
| Q18145441 | Multi-state modeling of biomolecules |
| Q104064550 | Multiplicity of carotene patterns derives from competition between phytoene desaturase diversification and biological environments |
| Q92824558 | Multiscale Process Modelling in Translational Systems Biology of Leishmania major: A Holistic view |
| Q28752388 | Multiscale modeling for biologists |
| Q35761666 | Multiscale modeling of mucosal immune responses |
| Q44731939 | Multiscale modelling approach combining a kinetic model of glutathione metabolism with PBPK models of paracetamol and the potential glutathione-depletion biomarkers ophthalmic acid and 5-oxoproline in humans and rats |
| Q90103694 | Multisite rate control analysis identifies ribosomal scanning as the sole high-capacity/low-flux-control step in mRNA translation |
| Q28652052 | Multistate Model Builder (MSMB): a flexible editor for compact biochemical models |
| Q35001166 | Multivalency in the inhibition of oxidative protein folding by arsenic(III) species |
| Q96303813 | NMR and MS-based Stable Isotope-Resolved Metabolomics and Applications in Cancer Metabolism |
| Q37406084 | Nested autoinhibitory feedbacks alter the resistance of homeostatic adaptive biochemical networks. |
| Q34198065 | Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis |
| Q91941572 | Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer |
| Q89678898 | Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies |
| Q26823013 | New types of experimental data shape the use of enzyme kinetics for dynamic network modeling |
| Q39063396 | No Evidence That Protein Noise-Induced Epigenetic Epistasis Constrains Gene Expression Evolution |
| Q34505131 | Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways |
| Q35836933 | Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics |
| Q38811523 | Notions of similarity for systems biology models |
| Q34257351 | Novel ATP-independent RNA annealing activity of the dengue virus NS3 helicase |
| Q57981903 | Numerical Simulation of ODE Models |
| Q27028202 | Nutritional protective mechanisms against gut inflammation |
| Q57981907 | ODE Models for Systems Biological Networks |
| Q47798116 | ODE-Based Modeling of Complex Regulatory Circuits |
| Q51342628 | Observation conflict resolution in steady-state metabolic network dynamics analysis. |
| Q33575122 | Odefy--from discrete to continuous models. |
| Q30639272 | On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data. |
| Q33635208 | On reverse engineering of gene interaction networks using time course data with repeated measurements |
| Q43985483 | On the killing of mycobacteria by macrophages |
| Q28661919 | On the need for mechanistic models in computational genomics and metagenomics |
| Q35765830 | On the translocation of bacteria and their lipopolysaccharides between blood and peripheral locations in chronic, inflammatory diseases: the central roles of LPS and LPS-induced cell death |
| Q58052287 | Optimization in Biology Parameter Estimation and the Associated Optimization Problem |
| Q28397689 | Optimization of stress response through the nuclear receptor-mediated cortisol signalling network |
| Q28535193 | Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria |
| Q33883302 | Origin of bistability underlying mammalian cell cycle entry |
| Q51165855 | Origins of heterogeneity in Streptococcus mutans competence: interpreting an environment-sensitive signaling pathway. |
| Q34303057 | Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops |
| Q38406442 | Oxidative changes and signalling pathways are pivotal in initiating age-related changes in articular cartilage. |
| Q38236912 | Oxidative protein folding: from thiol-disulfide exchange reactions to the redox poise of the endoplasmic reticulum |
| Q33897013 | Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis |
| Q50947147 | PKC-mediated inhibitory feedback of the cholecystokinin 1 receptor controls the shape of oscillatory Ca²⁺ signals. |
| Q47100426 | PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K. |
| Q38468279 | Palladium-catalyzed aerobic dehydrogenation of substituted cyclohexanones to phenols |
| Q57981911 | Parameter Identification in ODE Models |
| Q39045810 | Parameter estimation for dynamical systems with discrete events and logical operations |
| Q28751984 | Pathway databases and tools for their exploitation: benefits, current limitations and challenges |
| Q38626560 | Performance of objective functions and optimisation procedures for parameter estimation in system biology models |
| Q33849372 | Perspectives for computer modeling in the study of T cell activation |
| Q60323404 | Photo-Induced Depletion of Binding Sites in DNA-PAINT Microscopy. |
| Q52688323 | PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems. |
| Q39429444 | Physical Routes to Primitive Cells: An Experimental Model Based on the Spontaneous Entrapment of Enzymes inside Micrometer-Sized Liposomes. |
| Q40085573 | Piecewise parameter estimation for stochastic models in COPASI. |
| Q26852422 | Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering |
| Q35199634 | Plant stress biomarkers from biosimulations: the Transcriptome-To-Metabolome (TTM) technology - effects of drought stress on rice. |
| Q38199642 | Plant systems biology: insights, advances and challenges. |
| Q60213945 | Polarized displacement by transcription activator-like effectors for regulatory circuits |
| Q58608601 | Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse |
| Q41331576 | Postsynaptic signal transduction models for long-term potentiation and depression |
| Q36351777 | Predictive Modeling of Drug Treatment in the Area of Personalized Medicine |
| Q34988965 | Predictive computational modeling of the mucosal immune responses during Helicobacter pylori infection |
| Q50028742 | Probing biological activity through structural modelling of ligand-receptor interactions of 2,4-disubstituted thiazole retinoids. |
| Q40965673 | Probing reversible chemistry in coenzyme B12 -dependent ethanolamine ammonia lyase with kinetic isotope effects |
| Q38731492 | Probing the origin of degenerate metathesis selectivity via characterization and dynamics of ruthenacyclobutanes containing variable NHCs |
| Q34328597 | Programming biological models in Python using PySB |
| Q48313939 | Progress toward reaction monitoring at variable temperatures: a new stopped-flow NMR probe design |
| Q99346653 | Promiscuous phosphoketolase and metabolic rewiring enables novel non-oxidative glycolysis in yeast for high-yield production of acetyl-CoA derived products |
| Q35420913 | Proteasomal degradation from internal sites favors partial proteolysis via remote domain stabilization |
| Q83229489 | Proteostasis collapse, a hallmark of aging, hinders the chaperone-Start network and arrests cells in G1 |
| Q51898580 | Proximate parameter tuning for biochemical networks with uncertain kinetic parameters. |
| Q44610032 | Push-Pull and Feedback Mechanisms Can Align Signaling System Outputs with Inputs |
| Q90110751 | PyBioNetFit and the Biological Property Specification Language |
| Q61982458 | PyCoTools: a Python toolbox for COPASI |
| Q28727231 | Qualitative translation of relations from BioPAX to SBML qual |
| Q42318220 | Quantifying Fenton reaction pathways driven by self-generated H2O2 on pyrite surfaces. |
| Q92422904 | Quantitative Analyses of the Yeast Oxidative Protein Folding Pathway In Vitro and In Vivo |
| Q48050591 | Quantitative DFT modeling of product concentration in organometallic reactions: Cu-mediated pentafluoroethylation of benzoic acid chlorides as a case study |
| Q34205663 | Quantitative analysis of cellular metabolic dissipative, self-organized structures |
| Q39008508 | Quantitative and integrative analysis of paracrine hepatocyte activation by nonparenchymal cells upon lipopolysaccharide induction |
| Q28083248 | Quantitative and logic modelling of molecular and gene networks |
| Q38680217 | Quantitative computational models of molecular self-assembly in systems biology |
| Q64106754 | Quantitative dynamics of reversible platelet aggregation: mathematical modelling and experiments |
| Q41009828 | Quantitative interactome of a membrane Bcl-2 network identifies a hierarchy of complexes for apoptosis regulation. |
| Q27313334 | Quantitative super-resolution imaging with qPAINT. |
| Q64240805 | Quantitative systems pharmacology of interferon alpha administration: A multi-scale approach |
| Q43976166 | Querying metabolism under different physiological constraints |
| Q33285703 | RMBNToolbox: random models for biochemical networks |
| Q40310761 | RNAi revised--target mRNA-dependent enhancement of gene silencing |
| Q33361469 | Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle |
| Q42028214 | Rate and extent of protein localization is controlled by peptide-binding domain association kinetics and morphology |
| Q56927576 | Rational engineering of Candida antarctica lipase B for selective monoacylation of diols |
| Q90448390 | Rational selection of co-catalysts for the deaminative hydrogenation of amides |
| Q43116515 | Reactive centre loop mutants of α-1-antitrypsin reveal position-specific effects on intermediate formation along the polymerization pathway |
| Q28608563 | Reactome pathway analysis to enrich biological discovery in proteomics data sets |
| Q28082443 | Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery |
| Q47819372 | Recent Advances in the Systems Biology of Aging |
| Q38525312 | Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies. |
| Q38700387 | Reciprocal regulation of ARPP-16 by PKA and MAST3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition |
| Q31126762 | Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data |
| Q30465511 | Reduction of dynamical biochemical reactions networks in computational biology |
| Q35874448 | Regulated clearance of histone deacetylase 3 protects independent formation of nuclear receptor corepressor complexes. |
| Q41752115 | Regulation of release factor expression using a translational negative feedback loop: a systems analysis |
| Q41058068 | Regulatory dynamics of network architecture and function in tristable genetic circuit of Leishmania: a mathematical biology approach |
| Q92619960 | Repository of proposed pathways and protein-protein interaction networks in age-related macular degeneration |
| Q56988947 | Reproducible Research Using Biomodels |
| Q21202776 | Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language |
| Q57014509 | Reproducible model development in the cardiac electrophysiology Web Lab |
| Q41370456 | Retinitis pigmentosa: rapid neurodegeneration is governed by slow cell death mechanisms |
| Q34840961 | Revealing neuronal function through microelectrode array recordings |
| Q55192761 | Reversible Control of Nanoparticle Functionalization and Physicochemical Properties by Dynamic Covalent Exchange. |
| Q39958002 | Reversible control of nanoparticle functionalization and physicochemical properties by dynamic covalent exchange. |
| Q33793614 | Revision history aware repositories of computational models of biological systems. |
| Q33645846 | Rhodium-catalyzed C-C bond formation via heteroatom-directed C-H bond activation |
| Q28538077 | Robustness analysis of stochastic biochemical systems |
| Q46085877 | Rods progressively escape saturation to drive visual responses in daylight conditions. |
| Q38762692 | Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators. |
| Q34488992 | Role of a GAG hinge in the nucleotide-induced conformational change governing nucleotide specificity by T7 DNA polymerase |
| Q34253620 | Role of phosphate in the central metabolism of two lactic acid bacteria--a comparative systems biology approach |
| Q93069869 | Room Temperature Acceptorless Alkane Dehydrogenation from Molecular σ-Alkane Complexes |
| Q37626541 | Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. |
| Q57038543 | Rule-based modelling of iron homeostasis in tuberculosis |
| Q43447225 | SAGPAR: structural grammar-based automated pathway reconstruction |
| Q38534028 | SBML and CellML translation in antimony and JSim. |
| Q51604954 | SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models. |
| Q33360434 | SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool |
| Q90641625 | SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology |
| Q38430285 | SBMLmod: a Python-based web application and web service for efficient data integration and model simulation |
| Q35802135 | SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks |
| Q27499005 | SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks |
| Q113227862 | SBMLtoODEpy: A software program for converting SBML models into ODE models in Python |
| Q36342436 | SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks |
| Q52765469 | SED-ML web tools: generate, modify and export standard-compliant simulation studies. |
| Q47313302 | SELANSI: a toolbox for Simulation of Stochastic Gene Regulatory Networks |
| Q42669808 | SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations. |
| Q34762128 | SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments |
| Q28818540 | Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks |
| Q41841882 | Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable |
| Q50544066 | Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin. |
| Q37265068 | Selective trapping of SNO-BSA and GSNO by benzenesulfinic acid sodium salt: mechanistic study of thiosulphonate formation and feasibility as a protein S-nitrosothiol detection strategy |
| Q41691396 | Self-organization of signal transduction |
| Q42911961 | SensA: web-based sensitivity analysis of SBML models |
| Q33412397 | Signaling logic of activity-triggered dendritic protein synthesis: an mTOR gate but not a feedback switch |
| Q34184822 | Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics |
| Q36995768 | Simulated Interventions to Ameliorate Age-Related Bone Loss Indicate the Importance of Timing |
| Q36791279 | Simulated de novo assembly of golgi compartments by selective cargo capture during vesicle budding and targeted vesicle fusion |
| Q82715439 | Simulating plant metabolic pathways with enzyme-kinetic models |
| Q64096181 | Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art |
| Q41884304 | Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA |
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