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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

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Publications

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

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

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

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

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
DOI: 10.1109/isit44484.2020.9174360

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, Issue 34/05, 2020, Page(s) 7203-7210, ISSN 2374-3468
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, Issue 63, 2020, Page(s) 167-176, ISSN 0958-1669
DOI: 10.1016/j.copbio.2020.02.002

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, Issue 8/9, 2019, Page(s) 2163-2173, ISSN 2161-5063
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, Issue 150/2, 2019, Page(s) 024106, ISSN 0021-9606
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