Contextualizing biomolecular circuit models for synthetic biology

Resultado final

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

Publicaciones

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

Autores: Engelmann, Nicolai; Koeppl, Heinz
Publicado en: Proceedings of the 36th Conference on Neural Information Processing Systems (NeurIPS 2022), 2022
Editor: NeurIPS 2022

POMDPs in Continuous Time and Discrete Spaces

Autores: Alt, Bastian; Schultheis, Matthias; Koeppl, Heinz
Publicado en: Advances in Neural Information Processing Systems, Edición 1, 2020, Página(s) 13151--13162
Editor: Curran Associates, Inc

Genetic Circuit Design Automation involving Structural Variants and Parameter Statistics

Autores: Tobias Schladt, Erik Kubaczka, Nicolai Engelmann, Christian Hochburger, Heinz Koeppl
Publicado en: Proceedings of the 12th International Workshop on Bio-Design Automation, 2020
Editor: IWBDA

Multiclass Yeast Segmentation in Microstructured Environments with Deep Learning

Autores: Tim Prangemeier, Christian Wildner, André O. Françani, Christoph Reich, Heinz Koeppl
Publicado en: International Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2020
Editor: IEEE

Variational Inference for Continuous-Time Switching Dynamical Systems

Autores: Koehs, Lukas; Alt, Bastian; Koeppl, Heinz
Publicado en: Proceedings of the 35th Conference on Neural Information Processing Systems (NeurIPS 2021), 2021, Página(s) 20545-20557
Editor: Conference Proceedings of NeurIPS

Attention-Based Transformers for Instance Segmentation of Cells in Microstructures

Autores: Tim Prangemeier, Christoph Reich, Heinz Koeppl
Publicado en: 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2020, Página(s) 700-707, ISBN 978-1-7281-6215-7
Editor: IEEE
DOI: 10.1109/bibm49941.2020.9313305

Moment-Based Variational Inference for Stochastic Differential Equations

Autores: Wildner, Christian; Koeppl, Heinz
Publicado en: Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, Edición 130, 2021, Página(s) 1918--1926
Editor: PMLR

Moment-Based Variational Inference for Markov Jump Processes

Autores: Christian Wildner, Heinz Koeppl
Publicado en: Proceedings of the 36th International Conference on Machine Learning, 2019
Editor: ICML 2019

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

Autores: Dominik Lindner, Michael Schmidt, Heinz Koeppl
Publicado en: 2019
Editor: NeurIPS 2019

Maximizing information gain for the characterization of biomolecular circuits

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

Markov Chain Monte Carlo for Continuous-Time Switching Dynamical Systems

Autores: Koehs, Lukas; Koeppl, Heinz
Publicado en: Proceedings of the 39th International Conference on Machine Learning, Edición PMLR 162, 2022, Página(s) 11430-11454
Editor: JMLR

Continuous-Time Bayesian Networks with Clocks

Autores: Nicolai Engelmann, Dominik Linzner, Heinz Koeppl
Publicado en: International Conference on Machine Learning 2020, 2020
Editor: International Conference on Machine Learning 2020

Poisson channel with binary Markov input and average sojourn time constraint

Autores: Mark Sinzger, Maximilian Gehri, Heinz Koeppl
Publicado en: 2020 IEEE International Symposium on Information Theory (ISIT), 2020, Página(s) 2873-2878, ISBN 978-1-7281-6432-8
Editor: IEEE
DOI: 10.1109/isit44484.2020.9174360

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

Autores: Nikita Kruk, José A. Carillo, Heinz Koeppl
Publicado en: Journal of Computational Physics, Edición 00219991, 2020, ISSN 0021-9991
Editor: Academic Press
DOI: 10.1016/j.jcp.2021.110275

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

Autores: Dominik Linzner, Heinz Koeppl
Publicado en: Proceedings of the AAAI Conference on Artificial Intelligence, Edición 34/05, 2020, Página(s) 7203-7210, ISSN 2374-3468
Editor: AAAI
DOI: 10.1609/aaai.v34i05.6210

Yeast cell segmentation in microstructured environments with deep learning.

Autores: Tim Prangemeier; Christian Wildner; André O. Françani; Christoph Reich; Heinz Koeppl
Publicado en: Biosystems, Edición 03032647, 2022, ISSN 0303-2647
Editor: Elsevier BV
DOI: 10.1016/j.biosystems.2021.104557

Microfluidic platforms for the dynamic characterisation of synthetic circuitry

Autores: Tim Prangemeier, François-Xavier Lehr, Rogier M Schoeman, Heinz Koeppl
Publicado en: Current Opinion in Biotechnology, Edición 63, 2020, Página(s) 167-176, ISSN 0958-1669
Editor: Elsevier BV
DOI: 10.1016/j.copbio.2020.02.002

Solitary states in the mean-field limit

Autores: N. Kruk, Y. Maistrenko, H. Koeppl
Publicado en: Chaos: An Interdisciplinary Journal of Nonlinear Science, Edición 30/11, 2020, Página(s) 111104, ISSN 1054-1500
Editor: American Institute of Physics
DOI: 10.1063/5.0029585

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

Autores: François-Xavier Lehr; Alina Kuzembayeva; Megan E Bailey; Werner Kleindienst; Johannes Kabisch; Heinz Koeppl
Publicado en: ACS Synthetic Biology, Edición 2, 2021, Página(s) 2138-2150, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.0c00386

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

Autores: François-Xavier Lehr, Maleen Hanst, Marc Vogel, Jennifer Kremer, H. Ulrich Göringer, Beatrix Suess, Heinz Koeppl
Publicado en: ACS Synthetic Biology, Edición 8/9, 2019, Página(s) 2163-2173, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.9b00238

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

Autores: Johannes Falk, Leo Bronstein, Maleen Hanst, Barbara Drossel, Heinz Koeppl
Publicado en: The Journal of Chemical Physics, Edición 150/2, 2019, Página(s) 024106, ISSN 0021-9606
Editor: American Institute of Physics
DOI: 10.1063/1.5053816

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

Autores: Derya Altıntan, Heinz Koeppl
Publicado en: BIT Numerical Mathematics, 2019, ISSN 1572-9125
Editor: Springer Netherlands

Nonparametric Bayesian inference for meta-stable conformational dynamics

Autores: Koehs, Lukas; Kukovetz, Kerri; Rauh, Oliver; Koepp,Heinz
Publicado en: Physical Biology, Edición Aug 30;19(5), 2022, Página(s) 056006, ISSN 1478-3975
Editor: IOP Publishing
DOI: 10.1088/1478-3975/ac885e

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

Autores: Tobias Schladt, Nicolai Engelmann, Erik Kubaczka, Christian Hochberger, and Heinz Koeppl
Publicado en: ACS Synthetic Biology, Edición 21615063, 2021, Página(s) 3316–3329, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.1c00193

Context-Aware Technology Mapping in Genetic Design Automation

Autores: Nicolai Engelmann, Tobias Schwarz, Erik Kubaczka, Christian Hochberger, Heinz Koeppl
Publicado en: ACS Synthetic Biology, 2023, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.2c00361

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