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CORDIS - EU research results
CORDIS

Contextualizing biomolecular circuit models for synthetic biology

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Data Management Plan (opens in new window)

We will provide a plan for dissemination the data and models generated and used within CONSYN

Publications

Forward-Backward Latent State Inference for Hidden Continuous-Time semi-Markov Chains

Author(s): Engelmann, Nicolai; Koeppl, Heinz
Published in: Proceedings of the 36th Conference on Neural Information Processing Systems (NeurIPS 2022), 2022
Publisher: NeurIPS 2022

POMDPs in Continuous Time and Discrete Spaces

Author(s): Alt, Bastian; Schultheis, Matthias; Koeppl, Heinz
Published in: Advances in Neural Information Processing Systems, Issue 1, 2020, Page(s) 13151--13162
Publisher: Curran Associates, Inc

Genetic Circuit Design Automation involving Structural Variants and Parameter Statistics

Author(s): Tobias Schladt, Erik Kubaczka, Nicolai Engelmann, Christian Hochburger, Heinz Koeppl
Published in: Proceedings of the 12th International Workshop on Bio-Design Automation, 2020
Publisher: IWBDA

Multiclass Yeast Segmentation in Microstructured Environments with Deep Learning

Author(s): Tim Prangemeier, Christian Wildner, André O. Françani, Christoph Reich, Heinz Koeppl
Published in: International Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2020
Publisher: IEEE

Variational Inference for Continuous-Time Switching Dynamical Systems

Author(s): Koehs, Lukas; Alt, Bastian; Koeppl, Heinz
Published in: Proceedings of the 35th Conference on Neural Information Processing Systems (NeurIPS 2021), 2021, Page(s) 20545-20557
Publisher: Conference Proceedings of NeurIPS

Attention-Based Transformers for Instance Segmentation of Cells in Microstructures (opens in new window)

Author(s): Tim Prangemeier, Christoph Reich, Heinz Koeppl
Published in: 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2020, Page(s) 700-707, ISBN 978-1-7281-6215-7
Publisher: IEEE
DOI: 10.1109/bibm49941.2020.9313305

Moment-Based Variational Inference for Stochastic Differential Equations

Author(s): Wildner, Christian; Koeppl, Heinz
Published in: Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, Issue 130, 2021, Page(s) 1918--1926
Publisher: PMLR

Moment-Based Variational Inference for Markov Jump Processes

Author(s): Christian Wildner, Heinz Koeppl
Published in: Proceedings of the 36th International Conference on Machine Learning, 2019
Publisher: ICML 2019

Scalable Structure Learning of Continuous-Time Bayesian Networks from Incomplete Data

Author(s): Dominik Lindner, Michael Schmidt, Heinz Koeppl
Published in: 2019
Publisher: NeurIPS 2019

Maximizing information gain for the characterization of biomolecular circuits (opens in new window)

Author(s): Tim Prangemeier, Christian Wildner, Maleen Hanst, Heinz Koeppl
Published in: Proceedings of the 5th ACM International Conference on Nanoscale Computing and Communication - NANOCOM '18, 2018, Page(s) 1-6, ISBN 9781-450357111
Publisher: ACM Press
DOI: 10.1145/3233188.3233217

Markov Chain Monte Carlo for Continuous-Time Switching Dynamical Systems

Author(s): Koehs, Lukas; Koeppl, Heinz
Published in: Proceedings of the 39th International Conference on Machine Learning, Issue PMLR 162, 2022, Page(s) 11430-11454
Publisher: JMLR

Continuous-Time Bayesian Networks with Clocks

Author(s): Nicolai Engelmann, Dominik Linzner, Heinz Koeppl
Published in: International Conference on Machine Learning 2020, 2020
Publisher: International Conference on Machine Learning 2020

Poisson channel with binary Markov input and average sojourn time constraint (opens in new window)

Author(s): Mark Sinzger, Maximilian Gehri, Heinz Koeppl
Published in: 2020 IEEE International Symposium on Information Theory (ISIT), 2020, Page(s) 2873-2878, ISBN 978-1-7281-6432-8
Publisher: IEEE
DOI: 10.1109/isit44484.2020.9174360

A Finite Volume Method for Continuum Limit Equations of Nonlocally Interacting Active Chiral Particles (opens in new window)

Author(s): Nikita Kruk, José A. Carillo, Heinz Koeppl
Published in: Journal of Computational Physics, 2020, ISSN 0021-9991
Publisher: Academic Press
DOI: 10.1016/j.jcp.2021.110275

A Variational Perturbative Approach to Planning in Graph-Based Markov Decision Processes (opens in new window)

Author(s): Dominik Linzner, Heinz Koeppl
Published in: Proceedings of the AAAI Conference on Artificial Intelligence, Issue 34/05, 2020, Page(s) 7203-7210, ISSN 2374-3468
Publisher: AAAI
DOI: 10.1609/aaai.v34i05.6210

Yeast cell segmentation in microstructured environments with deep learning. (opens in new window)

Author(s): Tim Prangemeier; Christian Wildner; André O. Françani; Christoph Reich; Heinz Koeppl
Published in: Biosystems, Issue 3, 2022, ISSN 0303-2647
Publisher: Elsevier BV
DOI: 10.1016/j.biosystems.2021.104557

Microfluidic platforms for the dynamic characterisation of synthetic circuitry (opens in new window)

Author(s): Tim Prangemeier, François-Xavier Lehr, Rogier M Schoeman, Heinz Koeppl
Published in: Current Opinion in Biotechnology, Issue 63, 2020, Page(s) 167-176, ISSN 0958-1669
Publisher: Elsevier BV
DOI: 10.1016/j.copbio.2020.02.002

Solitary states in the mean-field limit (opens in new window)

Author(s): N. Kruk, Y. Maistrenko, H. Koeppl
Published in: Chaos: An Interdisciplinary Journal of Nonlinear Science, Issue 30/11, 2020, Page(s) 111104, ISSN 1054-1500
Publisher: American Institute of Physics
DOI: 10.1063/5.0029585

Functionalizing Cell-Free Systems with CRISPR-Associated Proteins: Application to RNA-Based Circuit Engineering. (opens in new window)

Author(s): François-Xavier Lehr; Alina Kuzembayeva; Megan E Bailey; Werner Kleindienst; Johannes Kabisch; Heinz Koeppl
Published in: ACS Synthetic Biology, Issue 2, 2021, Page(s) 2138-2150, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00386

Cell-Free Prototyping of AND-Logic Gates Based on Heterogeneous RNA Activators (opens in new window)

Author(s): François-Xavier Lehr, Maleen Hanst, Marc Vogel, Jennifer Kremer, H. Ulrich Göringer, Beatrix Suess, Heinz Koeppl
Published in: ACS Synthetic Biology, Issue 8/9, 2019, Page(s) 2163-2173, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.9b00238

Context in synthetic biology: Memory effects of environments with mono-molecular reactions (opens in new window)

Author(s): Johannes Falk, Leo Bronstein, Maleen Hanst, Barbara Drossel, Heinz Koeppl
Published in: The Journal of Chemical Physics, Issue 150/2, 2019, Page(s) 024106, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5053816

Hybrid master equation for jump-diffusion approximation of biomolecular reaction networks

Author(s): Derya Altıntan, Heinz Koeppl
Published in: BIT Numerical Mathematics, 2019, ISSN 1572-9125
Publisher: Springer Netherlands

Nonparametric Bayesian inference for meta-stable conformational dynamics (opens in new window)

Author(s): Koehs, Lukas; Kukovetz, Kerri; Rauh, Oliver; Koepp,Heinz
Published in: Physical Biology, Issue Aug 30;19(5), 2022, Page(s) 056006, ISSN 1478-3975
Publisher: IOP Publishing
DOI: 10.1088/1478-3975/ac885e

Automated Design of Robust Genetic Circuits: Structural Variants and Parameter Uncertainty (opens in new window)

Author(s): Tobias Schladt, Nicolai Engelmann, Erik Kubaczka, Christian Hochberger, and Heinz Koeppl
Published in: ACS Synthetic Biology, Issue 21615063, 2021, Page(s) 3316–3329, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.1c00193

Context-Aware Technology Mapping in Genetic Design Automation (opens in new window)

Author(s): Nicolai Engelmann, Tobias Schwarz, Erik Kubaczka, Christian Hochberger, Heinz Koeppl
Published in: ACS Synthetic Biology, 2023, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.2c00361

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