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1. Full Text Computational methods in systems biology: 15th international conference, CMSB 2017 Darmstadt, Germany, september 27–29, 2017 proceedings
by Feret, Jérôme and Koeppl, Heinz
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), ISSN 0302-9743, 2017, Volume 10545, pp. III - IV
Life Sciences | Quantitative Methods
Conference Proceeding
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2. Full Text A variational approach to moment-closure approximations for the kinetics of biomolecular reaction networks
by Bronstein, Leo and Koeppl, Heinz
The Journal of chemical physics, ISSN 0021-9606, 01/2018, Volume 148, Issue 1, pp. 014105 - 014105
Physical Sciences | Chemistry | Physics, Atomic, Molecular & Chemical | Chemistry, Physical | Physics | Science & Technology | Organic chemistry | Approximation | Mathematical analysis | Failure modes | Reaction kinetics | Markov processes | Fokker-Planck equation | Poisson distributions
Journal Article
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3. Full Text Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings
by Zechner, Christoph and Unger, Michael and Pelet, Serge and Peter, Matthias and Koeppl, Heinz
Nature methods, ISSN 1548-7091, 02/2014, Volume 11, Issue 2, pp. 197 - 202
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Signal Transduction | Saccharomyces cerevisiae - genetics | Cell Physiological Phenomena | Galactokinase - genetics | Saccharomyces cerevisiae Proteins - genetics | Saccharomyces cerevisiae - metabolism | Algorithms | Galactokinase - metabolism | Image Processing, Computer-Assisted | Stochastic Processes | Models, Biological | Computer Simulation | Bayes Theorem | Saccharomyces cerevisiae Proteins - metabolism | Kinetics | Monte Carlo Method | Microscopy, Fluorescence | Luminescent Proteins - metabolism | Biological research | Models | Research | Chemical reaction, Rate of | Cellular control mechanisms | Biology, Experimental | Statistical inference | Gene expression | Bayesian analysis | Cells | Reaction kinetics | Index Medicus
Journal Article
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4. Full Text Sensitivity estimation for stochastic models of biochemical reaction networks in the presence of extrinsic variability
by Ruess, Jakob and Koeppl, Heinz and Zechner, Christoph
The Journal of chemical physics, ISSN 0021-9606, 03/2017, Volume 146, Issue 12, pp. 124122 - 124122
Physical Sciences | Chemistry | Physics, Atomic, Molecular & Chemical | Chemistry, Physical | Physics | Science & Technology | Networks | Sensitivity analysis | Computer simulation | Construction methods | Likelihood ratio | Nutrients | Robustness | Parameter sensitivity | Life Sciences | Mathematics | Quantitative Methods | Statistics
Journal Article
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5. Full Text Spatial simulations in systems biology: from molecules to cells
by Klann, Michael and Koeppl, Heinz
International journal of molecular sciences, ISSN 1661-6596, 2012, Volume 13, Issue 6, pp. 7798 - 7827
nonlinear diffusion | diffusion-controlled reactions | Brownian dynamics | agent-based modeling | fractal kinetics | spatial-temporal dynamics | Biochemistry & Molecular Biology | Physical Sciences | Chemistry | Life Sciences & Biomedicine | Chemistry, Multidisciplinary | Science & Technology | Index Medicus | Review
Journal Article
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6. Full Text Quasi-Steady-State Approximations Derived from the Stochastic Model of Enzyme Kinetics
by Kang, Hye-Won and KhudaBukhsh, Wasiur R and Koeppl, Heinz and Rempała, Grzegorz A
Bulletin of mathematical biology, ISSN 0092-8240, 5/2019, Volume 81, Issue 5, pp. 1303 - 1336
Mathematical and Computational Biology | Michaelis–Menten kinetics | Mathematics | Cell Biology | Stochastic reaction network | 34E15 | Multiscale approximation | 92C45 | 92C42 | Life Sciences, general | QSSA | 92B25 | 60J28 | 60J27 | Biology | Life Sciences & Biomedicine - Other Topics | Life Sciences & Biomedicine | Science & Technology | Mathematical & Computational Biology | Biocatalysis | Enzyme Inhibitors - metabolism | Metabolic Networks and Pathways | Stochastic Processes | Models, Biological | Mathematical Concepts | Substrate Specificity | Kinetics | Enzymes - metabolism | Electrical engineering | Enzymes | Models | Enzyme kinetics | Chemical speciation | Organic chemistry | Differential equations | Reaction kinetics | Ordinary differential equations | Substrate inhibition | Stochasticity | Stochastic models | Steady state | Index Medicus
Journal Article
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7. Full Text Context in synthetic biology: Memory effects of environments with mono-molecular reactions
by Falk, Johannes and Bronstein, Leo and Hanst, Maleen and Drossel, Barbara and Koeppl, Heinz
The Journal of chemical physics, ISSN 0021-9606, 01/2019, Volume 150, Issue 2, pp. 024106 - 024106
Physical Sciences | Chemistry | Physics, Atomic, Molecular & Chemical | Chemistry, Physical | Physics | Science & Technology | Probability | Synthetic Biology | Gene Regulatory Networks | Models, Biological | Coupling (molecular) | Biological effects | Modular design | Circuit design | Chain dynamics | Mathematical analysis | Dynamics | Random walk | Mapping | Synthetic biology | Biology | Molecular chains | Index Medicus
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8. Full Text Dynamical properties of Discrete Reaction Networks
by Paulevé, Loïc and Paulevé, Loïc and Craciun, Gheorghe and Craciun, Gheorghe and Koeppl, Heinz and Koeppl, Heinz
Journal of mathematical biology, ISSN 0303-6812, 7/2014, Volume 69, Issue 1, pp. 55 - 72
92C45 | 92C42 | 92D25 | Mathematical and Computational Biology | 37N25 | Mathematics | Applications of Mathematics | 80A30 | Biology | Life Sciences & Biomedicine - Other Topics | Life Sciences & Biomedicine | Science & Technology | Mathematical & Computational Biology | Circadian Clocks | Phosphorylation | Kinetics | Models, Chemical | Stochastic Processes | Models, Biological | Dynamical systems | Species | Research | Index Medicus | Combinatorics
Journal Article
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9. Full Text A variational approach to path estimation and parameter inference of hidden diffusion processes
by Sutter, Tobias and Ganguly, Arnab and Koeppl, Heinz
Journal of machine learning research, ISSN 1532-4435, 09/2016, Volume 17
Hidden Markov model | Stochastic differential equations | Variational inference | Diffusion processes | Optimal control | Automation & Control Systems | Computer Science, Artificial Intelligence | Technology | Computer Science | Science & Technology
Journal Article
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10. Full Text Marginal process framework: A model reduction tool for Markov jump processes
by Bronstein, Leo and Koeppl, Heinz
Physical review. E, ISSN 2470-0045, 06/2018, Volume 97, Issue 6
Physical Sciences | Physics, Fluids & Plasmas | Physics | Physics, Mathematical | Science & Technology
Journal Article
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11. Full Text Jump-diffusion approximation of stochastic reaction dynamics: Error bounds and algorithms
by Ganguly, Arnab and Altintan, Derya and Koeppl, Heinz
Multiscale modeling & simulation, ISSN 1540-3459, 2015, Volume 13, Issue 4, pp. 1390 - 1419
Biochemical reaction networks | Diffusion approximation | Markov chains | Multiscale networks | Jump diffusion processes | Mathematics, Interdisciplinary Applications | Physical Sciences | Mathematics | Physics | Physics, Mathematical | Science & Technology
Journal Article
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12. Full Text Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data
by Kumar, Sunil and Lun, Xiao-Kang and Bodenmiller, Bernd and Rodríguez Martínez, María and Koeppl, Heinz
Scientific reports, ISSN 2045-2322, 01/2020, Volume 10, Issue 1, pp. 1233 - 1233
Cytometry | γ-Interferon | 1-Phosphatidylinositol 3-kinase | Index Medicus
Journal Article
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13. Full Text Approximate lumpability for Markovian agent-based models using local symmetries
by KhudaBukhsh, Wasiur R and Auddy, Arnab and Disser, Yann and Koeppl, Heinz
Journal of applied probability, ISSN 0021-9002, 09/2019, Volume 56, Issue 3, pp. 647 - 671
Research Papers | Statistics & Probability | Physical Sciences | Mathematics | Science & Technology | Divergence | Lumping | Approximation | Probability | Markov chains | Markov analysis | Automorphisms | Apexes | Mathematical analysis | Ordinary differential equations | Graphs | Model reduction | Symmetry
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