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Contextualizing biomolecular circuit models for synthetic biology

Deliverables

Data Management Plan

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

Publications

POMDPs in Continuous Time and Discrete Spaces

Author(s): Alt, Bastian; Schultheis, Matthias; Koeppl, Heinz
Published in: Advances in Neural Information Processing Systems, 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

Attention-Based Transformers for Instance Segmentation of Cells in Microstructures

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, 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

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

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

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

Author(s): Nikita Kruk, José A. Carillo, Heinz Koeppl
Published in: submitted to: Journal of Computational Physics, 2020
Publisher: Academic Press

A Variational Perturbative Approach to Planning in Graph-Based Markov Decision Processes

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

Microfluidic platforms for the dynamic characterisation of synthetic circuitry

Author(s): Tim Prangemeier, François-Xavier Lehr, Rogier M Schoeman, Heinz Koeppl
Published in: Current Opinion in Biotechnology, 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

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

Cell-Free Prototyping of AND-Logic Gates Based on Heterogeneous RNA Activators

Author(s): François-Xavier Lehr, Maleen Hanst, Marc Vogel, Jennifer Kremer, H. Ulrich Göringer, Beatrix Suess, Heinz Koeppl
Published in: ACS Synthetic Biology, 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

Author(s): Johannes Falk, Leo Bronstein, Maleen Hanst, Barbara Drossel, Heinz Koeppl
Published in: The Journal of Chemical Physics, 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