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Contextualizing biomolecular circuit models for synthetic biology

Risultati finali

Data Management Plan

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

Pubblicazioni

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

Autori: Engelmann, Nicolai; Koeppl, Heinz
Pubblicato in: Proceedings of the 36th Conference on Neural Information Processing Systems (NeurIPS 2022), 2022
Editore: NeurIPS 2022

POMDPs in Continuous Time and Discrete Spaces

Autori: Alt, Bastian; Schultheis, Matthias; Koeppl, Heinz
Pubblicato in: Advances in Neural Information Processing Systems, Numero 1, 2020, Pagina/e 13151--13162
Editore: Curran Associates, Inc

Genetic Circuit Design Automation involving Structural Variants and Parameter Statistics

Autori: Tobias Schladt, Erik Kubaczka, Nicolai Engelmann, Christian Hochburger, Heinz Koeppl
Pubblicato in: Proceedings of the 12th International Workshop on Bio-Design Automation, 2020
Editore: IWBDA

Multiclass Yeast Segmentation in Microstructured Environments with Deep Learning

Autori: Tim Prangemeier, Christian Wildner, André O. Françani, Christoph Reich, Heinz Koeppl
Pubblicato in: International Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2020
Editore: IEEE

Variational Inference for Continuous-Time Switching Dynamical Systems

Autori: Koehs, Lukas; Alt, Bastian; Koeppl, Heinz
Pubblicato in: Proceedings of the 35th Conference on Neural Information Processing Systems (NeurIPS 2021), 2021, Pagina/e 20545-20557
Editore: Conference Proceedings of NeurIPS

Attention-Based Transformers for Instance Segmentation of Cells in Microstructures

Autori: Tim Prangemeier, Christoph Reich, Heinz Koeppl
Pubblicato in: 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2020, Pagina/e 700-707, ISBN 978-1-7281-6215-7
Editore: IEEE
DOI: 10.1109/bibm49941.2020.9313305

Moment-Based Variational Inference for Stochastic Differential Equations

Autori: Wildner, Christian; Koeppl, Heinz
Pubblicato in: Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, Numero 130, 2021, Pagina/e 1918--1926
Editore: PMLR

Moment-Based Variational Inference for Markov Jump Processes

Autori: Christian Wildner, Heinz Koeppl
Pubblicato in: Proceedings of the 36th International Conference on Machine Learning, 2019
Editore: ICML 2019

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

Autori: Dominik Lindner, Michael Schmidt, Heinz Koeppl
Pubblicato in: 2019
Editore: NeurIPS 2019

Maximizing information gain for the characterization of biomolecular circuits

Autori: Tim Prangemeier, Christian Wildner, Maleen Hanst, Heinz Koeppl
Pubblicato in: Proceedings of the 5th ACM International Conference on Nanoscale Computing and Communication - NANOCOM '18, 2018, Pagina/e 1-6, ISBN 9781-450357111
Editore: ACM Press
DOI: 10.1145/3233188.3233217

Markov Chain Monte Carlo for Continuous-Time Switching Dynamical Systems

Autori: Koehs, Lukas; Koeppl, Heinz
Pubblicato in: Proceedings of the 39th International Conference on Machine Learning, Numero PMLR 162, 2022, Pagina/e 11430-11454
Editore: JMLR

Continuous-Time Bayesian Networks with Clocks

Autori: Nicolai Engelmann, Dominik Linzner, Heinz Koeppl
Pubblicato in: International Conference on Machine Learning 2020, 2020
Editore: International Conference on Machine Learning 2020

Poisson channel with binary Markov input and average sojourn time constraint

Autori: Mark Sinzger, Maximilian Gehri, Heinz Koeppl
Pubblicato in: 2020 IEEE International Symposium on Information Theory (ISIT), 2020, Pagina/e 2873-2878, ISBN 978-1-7281-6432-8
Editore: IEEE
DOI: 10.1109/isit44484.2020.9174360

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

Autori: Nikita Kruk, José A. Carillo, Heinz Koeppl
Pubblicato in: Journal of Computational Physics, Numero 00219991, 2020, ISSN 0021-9991
Editore: Academic Press
DOI: 10.1016/j.jcp.2021.110275

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

Autori: Dominik Linzner, Heinz Koeppl
Pubblicato in: Proceedings of the AAAI Conference on Artificial Intelligence, Numero 34/05, 2020, Pagina/e 7203-7210, ISSN 2374-3468
Editore: AAAI
DOI: 10.1609/aaai.v34i05.6210

Yeast cell segmentation in microstructured environments with deep learning.

Autori: Tim Prangemeier; Christian Wildner; André O. Françani; Christoph Reich; Heinz Koeppl
Pubblicato in: Biosystems, Numero 03032647, 2022, ISSN 0303-2647
Editore: Elsevier BV
DOI: 10.1016/j.biosystems.2021.104557

Microfluidic platforms for the dynamic characterisation of synthetic circuitry

Autori: Tim Prangemeier, François-Xavier Lehr, Rogier M Schoeman, Heinz Koeppl
Pubblicato in: Current Opinion in Biotechnology, Numero 63, 2020, Pagina/e 167-176, ISSN 0958-1669
Editore: Elsevier BV
DOI: 10.1016/j.copbio.2020.02.002

Solitary states in the mean-field limit

Autori: N. Kruk, Y. Maistrenko, H. Koeppl
Pubblicato in: Chaos: An Interdisciplinary Journal of Nonlinear Science, Numero 30/11, 2020, Pagina/e 111104, ISSN 1054-1500
Editore: American Institute of Physics
DOI: 10.1063/5.0029585

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

Autori: François-Xavier Lehr; Alina Kuzembayeva; Megan E Bailey; Werner Kleindienst; Johannes Kabisch; Heinz Koeppl
Pubblicato in: ACS Synthetic Biology, Numero 2, 2021, Pagina/e 2138-2150, ISSN 2161-5063
Editore: American Chemical Society
DOI: 10.1021/acssynbio.0c00386

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

Autori: François-Xavier Lehr, Maleen Hanst, Marc Vogel, Jennifer Kremer, H. Ulrich Göringer, Beatrix Suess, Heinz Koeppl
Pubblicato in: ACS Synthetic Biology, Numero 8/9, 2019, Pagina/e 2163-2173, ISSN 2161-5063
Editore: American Chemical Society
DOI: 10.1021/acssynbio.9b00238

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

Autori: Johannes Falk, Leo Bronstein, Maleen Hanst, Barbara Drossel, Heinz Koeppl
Pubblicato in: The Journal of Chemical Physics, Numero 150/2, 2019, Pagina/e 024106, ISSN 0021-9606
Editore: American Institute of Physics
DOI: 10.1063/1.5053816

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

Autori: Derya Altıntan, Heinz Koeppl
Pubblicato in: BIT Numerical Mathematics, 2019, ISSN 1572-9125
Editore: Springer Netherlands

Nonparametric Bayesian inference for meta-stable conformational dynamics

Autori: Koehs, Lukas; Kukovetz, Kerri; Rauh, Oliver; Koepp,Heinz
Pubblicato in: Physical Biology, Numero Aug 30;19(5), 2022, Pagina/e 056006, ISSN 1478-3975
Editore: IOP Publishing
DOI: 10.1088/1478-3975/ac885e

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

Autori: Tobias Schladt, Nicolai Engelmann, Erik Kubaczka, Christian Hochberger, and Heinz Koeppl
Pubblicato in: ACS Synthetic Biology, Numero 21615063, 2021, Pagina/e 3316–3329, ISSN 2161-5063
Editore: American Chemical Society
DOI: 10.1021/acssynbio.1c00193

Context-Aware Technology Mapping in Genetic Design Automation

Autori: Nicolai Engelmann, Tobias Schwarz, Erik Kubaczka, Christian Hochberger, Heinz Koeppl
Pubblicato in: ACS Synthetic Biology, 2023, ISSN 2161-5063
Editore: American Chemical Society
DOI: 10.1021/acssynbio.2c00361

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