Contextualizing biomolecular circuit models for synthetic biology

Rezultaty

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

Publikacje

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

Autorzy: Engelmann, Nicolai; Koeppl, Heinz
Opublikowane w: Proceedings of the 36th Conference on Neural Information Processing Systems (NeurIPS 2022), 2022
Wydawca: NeurIPS 2022

POMDPs in Continuous Time and Discrete Spaces

Autorzy: Alt, Bastian; Schultheis, Matthias; Koeppl, Heinz
Opublikowane w: Advances in Neural Information Processing Systems, Numer 1, 2020, Strona(/y) 13151--13162
Wydawca: Curran Associates, Inc

Genetic Circuit Design Automation involving Structural Variants and Parameter Statistics

Autorzy: Tobias Schladt, Erik Kubaczka, Nicolai Engelmann, Christian Hochburger, Heinz Koeppl
Opublikowane w: Proceedings of the 12th International Workshop on Bio-Design Automation, 2020
Wydawca: IWBDA

Multiclass Yeast Segmentation in Microstructured Environments with Deep Learning

Autorzy: Tim Prangemeier, Christian Wildner, André O. Françani, Christoph Reich, Heinz Koeppl
Opublikowane w: International Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2020
Wydawca: IEEE

Variational Inference for Continuous-Time Switching Dynamical Systems

Autorzy: Koehs, Lukas; Alt, Bastian; Koeppl, Heinz
Opublikowane w: Proceedings of the 35th Conference on Neural Information Processing Systems (NeurIPS 2021), 2021, Strona(/y) 20545-20557
Wydawca: Conference Proceedings of NeurIPS

Attention-Based Transformers for Instance Segmentation of Cells in Microstructures

Autorzy: Tim Prangemeier, Christoph Reich, Heinz Koeppl
Opublikowane w: 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2020, Strona(/y) 700-707, ISBN 978-1-7281-6215-7
Wydawca: IEEE
DOI: 10.1109/bibm49941.2020.9313305

Moment-Based Variational Inference for Stochastic Differential Equations

Autorzy: Wildner, Christian; Koeppl, Heinz
Opublikowane w: Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, Numer 130, 2021, Strona(/y) 1918--1926
Wydawca: PMLR

Moment-Based Variational Inference for Markov Jump Processes

Autorzy: Christian Wildner, Heinz Koeppl
Opublikowane w: Proceedings of the 36th International Conference on Machine Learning, 2019
Wydawca: ICML 2019

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

Autorzy: Dominik Lindner, Michael Schmidt, Heinz Koeppl
Opublikowane w: 2019
Wydawca: NeurIPS 2019

Maximizing information gain for the characterization of biomolecular circuits

Autorzy: Tim Prangemeier, Christian Wildner, Maleen Hanst, Heinz Koeppl
Opublikowane w: Proceedings of the 5th ACM International Conference on Nanoscale Computing and Communication - NANOCOM '18, 2018, Strona(/y) 1-6, ISBN 9781-450357111
Wydawca: ACM Press
DOI: 10.1145/3233188.3233217

Markov Chain Monte Carlo for Continuous-Time Switching Dynamical Systems

Autorzy: Koehs, Lukas; Koeppl, Heinz
Opublikowane w: Proceedings of the 39th International Conference on Machine Learning, Numer PMLR 162, 2022, Strona(/y) 11430-11454
Wydawca: JMLR

Continuous-Time Bayesian Networks with Clocks

Autorzy: Nicolai Engelmann, Dominik Linzner, Heinz Koeppl
Opublikowane w: International Conference on Machine Learning 2020, 2020
Wydawca: International Conference on Machine Learning 2020

Poisson channel with binary Markov input and average sojourn time constraint

Autorzy: Mark Sinzger, Maximilian Gehri, Heinz Koeppl
Opublikowane w: 2020 IEEE International Symposium on Information Theory (ISIT), 2020, Strona(/y) 2873-2878, ISBN 978-1-7281-6432-8
Wydawca: IEEE
DOI: 10.1109/isit44484.2020.9174360

A Finite Volume Method for Continuum Limit Equations of Nonlocally Interacting Active Chiral Particles

Autorzy: Nikita Kruk, José A. Carillo, Heinz Koeppl
Opublikowane w: Journal of Computational Physics, Numer 00219991, 2020, ISSN 0021-9991
Wydawca: Academic Press
DOI: 10.1016/j.jcp.2021.110275

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

Autorzy: Dominik Linzner, Heinz Koeppl
Opublikowane w: Proceedings of the AAAI Conference on Artificial Intelligence, Numer 34/05, 2020, Strona(/y) 7203-7210, ISSN 2374-3468
Wydawca: AAAI
DOI: 10.1609/aaai.v34i05.6210

Yeast cell segmentation in microstructured environments with deep learning.

Autorzy: Tim Prangemeier; Christian Wildner; André O. Françani; Christoph Reich; Heinz Koeppl
Opublikowane w: Biosystems, Numer 03032647, 2022, ISSN 0303-2647
Wydawca: Elsevier BV
DOI: 10.1016/j.biosystems.2021.104557

Microfluidic platforms for the dynamic characterisation of synthetic circuitry

Autorzy: Tim Prangemeier, François-Xavier Lehr, Rogier M Schoeman, Heinz Koeppl
Opublikowane w: Current Opinion in Biotechnology, Numer 63, 2020, Strona(/y) 167-176, ISSN 0958-1669
Wydawca: Elsevier BV
DOI: 10.1016/j.copbio.2020.02.002

Solitary states in the mean-field limit

Autorzy: N. Kruk, Y. Maistrenko, H. Koeppl
Opublikowane w: Chaos: An Interdisciplinary Journal of Nonlinear Science, Numer 30/11, 2020, Strona(/y) 111104, ISSN 1054-1500
Wydawca: American Institute of Physics
DOI: 10.1063/5.0029585

Functionalizing Cell-Free Systems with CRISPR-Associated Proteins: Application to RNA-Based Circuit Engineering.

Autorzy: François-Xavier Lehr; Alina Kuzembayeva; Megan E Bailey; Werner Kleindienst; Johannes Kabisch; Heinz Koeppl
Opublikowane w: ACS Synthetic Biology, Numer 2, 2021, Strona(/y) 2138-2150, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.0c00386

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

Autorzy: François-Xavier Lehr, Maleen Hanst, Marc Vogel, Jennifer Kremer, H. Ulrich Göringer, Beatrix Suess, Heinz Koeppl
Opublikowane w: ACS Synthetic Biology, Numer 8/9, 2019, Strona(/y) 2163-2173, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.9b00238

Context in synthetic biology: Memory effects of environments with mono-molecular reactions

Autorzy: Johannes Falk, Leo Bronstein, Maleen Hanst, Barbara Drossel, Heinz Koeppl
Opublikowane w: The Journal of Chemical Physics, Numer 150/2, 2019, Strona(/y) 024106, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.5053816

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

Autorzy: Derya Altıntan, Heinz Koeppl
Opublikowane w: BIT Numerical Mathematics, 2019, ISSN 1572-9125
Wydawca: Springer Netherlands

Nonparametric Bayesian inference for meta-stable conformational dynamics

Autorzy: Koehs, Lukas; Kukovetz, Kerri; Rauh, Oliver; Koepp,Heinz
Opublikowane w: Physical Biology, Numer Aug 30;19(5), 2022, Strona(/y) 056006, ISSN 1478-3975
Wydawca: IOP Publishing
DOI: 10.1088/1478-3975/ac885e

Automated Design of Robust Genetic Circuits: Structural Variants and Parameter Uncertainty

Autorzy: Tobias Schladt, Nicolai Engelmann, Erik Kubaczka, Christian Hochberger, and Heinz Koeppl
Opublikowane w: ACS Synthetic Biology, Numer 21615063, 2021, Strona(/y) 3316–3329, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.1c00193

Context-Aware Technology Mapping in Genetic Design Automation

Autorzy: Nicolai Engelmann, Tobias Schwarz, Erik Kubaczka, Christian Hochberger, Heinz Koeppl
Opublikowane w: ACS Synthetic Biology, 2023, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.2c00361

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