2024

Schladt, Tobias ; Engelmann, Nicolai ; Kubaczka, Erik ; Hochberger, Christian ; Koeppl, Heinz (2024)
Automated Design of Robust Genetic Circuits: Structural Variants and Parameter Uncertainty.
In: ACS Synthetic Biology, 2021, 10 (12)
doi: 10.26083/tuprints-00026627
Article, Secondary publication, Publisher's Version

Sporns, Olaf ; Hafner, Marc ; Koeppl, Heinz ; Gonze, Didier (2024)
Effect of Network Architecture on Synchronization and Entrainment Properties of the Circadian Oscillations in the Suprachiasmatic Nucleus.
In: PLoS Computational Biology, 2012, 8 (3)
doi: 10.26083/tuprints-00026934
Article, Secondary publication, Publisher's Version

Papin, Jason A. ; Hafner, Marc ; Koeppl, Heinz ; Hasler, Martin ; Wagner, Andreas (2024)
‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators.
In: PLoS Computational Biology, 2009, 5 (10)
doi: 10.26083/tuprints-00026926
Article, Secondary publication, Publisher's Version

Altıntan, Derya ; Koeppl, Heinz (2024)
Hybrid master equation for jump-diffusion approximation of biomolecular reaction networks.
In: BIT Numerical Mathematics, 2020, 60 (2)
doi: 10.26083/tuprints-00027079
Article, Secondary publication, Publisher's Version

Johannes, Ludger ; Klann, Michael ; Koeppl, Heinz ; Reuss, Matthias (2024)
Spatial Modeling of Vesicle Transport and the Cytoskeleton: The Challenge of Hitting the Right Road.
In: PLoS ONE, 2012, 7 (1)
doi: 10.26083/tuprints-00026930
Article, Secondary publication, Publisher's Version

Kramat, Janice ; Kraus, Leon ; Gunawan, Vincent J. ; Smyej, Elias ; Froehlich, Philipp ; Weber, Tim E. ; Spiehl, Dieter ; Koeppl, Heinz ; Blaeser, Andreas ; Suess, Beatrix (2024)
Sensing Levofloxacin with an RNA Aptamer as a Bioreceptor.
In: Biosensors, 2024, 14 (1)
doi: 10.26083/tuprints-00027255
Article, Secondary publication, Publisher's Version

Camporesi, Ferdinanda ; Feret, Jérôme ; Koeppl, Heinz ; Petrov, Tatjana (2024)
Combining Model Reductions.
In: Electronic Notes in Theoretical Computer Science, 2010, 265
doi: 10.26083/tuprints-00026719
Article, Secondary publication, Publisher's Version

Benenson, Yaakov ; Dalchau, Neil ; Koeppl, Heinz ; Maler, Oded (2024)
Formal Methods for the Synthesis of Biomolecular Circuits.
In: Dagstuhl Reports, 2018, 8 (2)
doi: 10.26083/tuprints-00026921
Article, Secondary publication, Publisher's Version

Hiroi, Noriko ; Klann, Michael ; Iba, Keisuke ; Heras Ciechomski, Pablo de ; Yamashita, Shuji ; Tabira, Akito ; Okuhara, Takahiro ; Kubojima, Takeshi ; Okada, Yasunori ; Oka, Kotaro ; Mange, Robin ; Unger, Michael ; Funahashi, Akira ; Koeppl, Heinz (2024)
From microscopy data to in silico environments for in vivo-oriented simulations.
In: EURASIP Journal on Bioinformatics and Systems Biology, 2012, 1 (7)
doi: 10.26083/tuprints-00026938
Article, Secondary publication, Publisher's Version

Sulaimanov, Nurgazy ; Koeppl, Heinz (2024)
Graph reconstruction using covariance-based methods.
In: EURASIP Journal on Bioinformatics and Systems Biology, 2016
doi: 10.26083/tuprints-00026979
Article, Secondary publication, Publisher's Version

Cui, Kai ; KhudaBukhsh, Wasiur R. ; Koeppl, Heinz (2024)
Hypergraphon mean field games.
In: Chaos: An Interdisciplinary Journal of Nonlinear Science, 2022, 32 (11)
doi: 10.26083/tuprints-00026621
Article, Secondary publication, Publisher's Version

Šošić, Adrian ; Rueckert, Elmar ; Peters, Jan ; Zoubir, Abdelhak M. ; Koeppl, Heinz (2024)
Inverse Reinforcement Learning via Nonparametric Spatio-Temporal Subgoal Modeling.
In: Journal of Machine Learning Research, 2018, 19 (69)
doi: 10.26083/tuprints-00026700
Article, Secondary publication, Publisher's Version

Koeppl, Heinz ; Hafner, Marc ; Lu, James (2024)
Mapping behavioral specifications to model parameters in synthetic biology.
In: BMC Bioinformatics, 2013, 14 (S10)
doi: 10.26083/tuprints-00026717
Article, Secondary publication, Publisher's Version

Petrov, Tatjana ; Ganguly, Arnab ; Koeppl, Heinz (2024)
Model Decomposition and Stochastic Fragments.
In: Electronic Notes in Theoretical Computer Science, 2012, 284
doi: 10.26083/tuprints-00026720
Article, Secondary publication, Publisher's Version

Danos, Vincent ; Koeppl, Heinz (2024)
Self-assembly and Self-organization in Computer Science and Biology.
In: Dagstuhl Reports, 2016, 5 (9)
doi: 10.26083/tuprints-00026922
Article, Secondary publication, Publisher's Version

Klann, Michael ; Koeppl, Heinz (2024)
Spatial Simulations in Systems Biology: From Molecules to Cells.
In: International Journal of Molecular Sciences, 2012, 13 (6)
doi: 10.26083/tuprints-00026923
Article, Secondary publication, Publisher's Version

Koeppl, Heinz ; Petrov, Tatjana (2024)
Stochastic Semantics of Signaling as a Composition of Agent-view Automata.
In: Electronic Notes in Theoretical Computer Science, 2011, 272
doi: 10.26083/tuprints-00026721
Article, Secondary publication, Publisher's Version

Ion, Ion Gabriel ; Wildner, Christian ; Loukrezis, Dimitrios ; Koeppl, Heinz ; De Gersem, Herbert (2024)
Tensor-train approximation of the chemical master equation and its application for parameter inference.
In: The Journal of Chemical Physics, 2021, 155 (3)
doi: 10.26083/tuprints-00026628
Article, Secondary publication, Publisher's Version

Hill, Steven M. ; Heiser, Laura M. ; Cokelaer, Thomas ; Unger, Michael ; Nesser, Nicole K. ; Carlin, Daniel E. ; Zhang, Yang ; Sokolov, Artem ; Paull, Evan O. ; Wong, Chris K. ; Graim, Kiley ; Bivol, Adrian ; Wang, Haizhou ; Zhu, Fan ; Afsari, Bahman ; Danilova, Ludmila V. ; Favorov, Alexander V. ; Lee, Wai Shing ; Taylor, Dane ; Hu, Chenyue W. ; Long, Byron L. ; Noren, David P. ; Bisberg, Alexander J. ; Mills, Gordon B. ; Gray, Joe W. ; Kellen, Michael ; Norman, Thea ; Friend, Stephen ; Qutub, Amina A. ; Fertig, Elana J. ; Guan, Yuanfang ; Song, Mingzhou ; Stuart, Joshua M. ; Spellman, Paul T. ; Koeppl, Heinz ; Stolovitzky, Gustavo ; Saez-Rodriguez, Julio ; Mukherjee, Sach (2024)
Inferring causal molecular networks: empirical assessment through a community-based effort.
In: Nature Methods, 2016, 13 (4)
doi: 10.26083/tuprints-00027016
Article, Secondary publication, Publisher's Version

Nandy, Preetam ; Unger, Michael ; Zechner, Christoph ; Dey, Kushal K. ; Koeppl, Heinz (2024)
Learning diagnostic signatures from microarray data using L1-regularized logistic regression.
In: Systems Biomedicine, 2013, 1 (4)
doi: 10.26083/tuprints-00027017
Article, Secondary publication, Publisher's Version

Alkhalili, Yassin ; Weil, Jannis ; Tahir, Anam ; Meuser, Tobias ; Koldehofe, Boris ; Mauthe, Andreas ; Koeppl, Heinz ; Steinmetz, Ralf (2024)
Towards QoE-Driven Optimization of Multi-Dimensional Content Streaming.
In: Electronic Communications of the EASST, 2021, 80
doi: 10.26083/tuprints-00027018
Article, Secondary publication, Publisher's Version

Kuebert, Thomas ; Puder, Henning ; Koeppl, Heinz (2024)
Daily Routine Recognition for Hearing Aid Personalization.
In: SN Computer Science, 2021, 2 (3)
doi: 10.26083/tuprints-00023594
Article, Secondary publication, Publisher's Version

Tahir, Anam ; Cui, Kai ; Koeppl, Heinz (2024)
Learning Mean-Field Control for Delayed Information Load Balancing in Large Queuing Systems.
51st International Conference on Parallel Processing (ICPP ’22). Bordeaux, France (29.08. - 01.09.2022)
doi: 10.26083/tuprints-00026518
Conference or Workshop Item, Secondary publication, Publisher's Version

2023

Linzner, Dominik ; Koeppl, Heinz (2023)
Active Learning of Continuous-time Bayesian Networks through Interventions.
Thirty-eighth International Conference on Machine Learning. Virtual (18.-24.07.2021)
doi: 10.26083/tuprints-00023308
Conference or Workshop Item, Secondary publication, Publisher's Version

Alt, Bastian ; Schultheis, Matthias ; Koeppl, Heinz (2023)
POMDPs in Continuous Time and Discrete Spaces.
34th Conference on Neural Information Processing Systems. virtual (06.-12.12.2020)
doi: 10.26083/tuprints-00023309
Conference or Workshop Item, Secondary publication, Publisher's Version

2022

Köhs, Lukas ; Kukovetz, Kerri ; Rauh, Oliver ; Koeppl, Heinz (2022)
Nonparametric Bayesian inference for meta-stable conformational dynamics.
In: Physical Biology, 2022, 19 (5)
doi: 10.26083/tuprints-00022096
Article, Secondary publication, Publisher's Version

Sinzger, Mark ; Gehri, Maximilian ; Koeppl, Heinz (2022)
Poisson channel with binary Markov input and average sojourn time constraint.
ISIT'20 - International Symposium on Information Theory. Online (21.-26.06.2020)
doi: 10.26083/tuprints-00021525
Conference or Workshop Item, Secondary publication, Postprint

Cui, Kai ; Koeppl, Heinz (2022)
Approximately Solving Mean Field Games via Entropy-Regularized Deep Reinforcement Learning.
24th International Conference on Artificial Intelligence and Statistics (AISTATS) 2021. Virtual (13.-15.04.2021)
doi: 10.26083/tuprints-00021511
Conference or Workshop Item, Secondary publication, Publisher's Version

Prangemeier, Tim ; Reich, Christoph ; Koeppl, Heinz (2022)
Attention-Based Transformers for Instance Segmentation of Cells in Microstructures.
IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2020). virtual Conference (16.-19.12.2020)
doi: 10.26083/tuprints-00021666
Conference or Workshop Item, Secondary publication, Postprint

Engelmann, Nicolai ; Linzner, Dominik ; Koeppl, Heinz (2022)
Continuous Time Bayesian Networks with Clocks.
37th International Conference on Machine Learning. Online (12.-18.07.2020)
doi: 10.26083/tuprints-00021516
Conference or Workshop Item, Secondary publication, Publisher's Version

Khuda Bukhsh, Wasiur R. ; Kar, Sounak ; Alt, Bastian ; Rizk, Amr ; Koeppl, Heinz (2022)
Generalized Cost-Based Job Scheduling in Very Large Heterogeneous Cluster Systems.
In: IEEE Transactions on Parallel and Distributed Systems, 2020, 31 (11)
doi: 10.26083/tuprints-00021667
Article, Secondary publication, Postprint

Yang, Sikun ; Koeppl, Heinz (2022)
The Hawkes Edge Partition Model for Continuous-time Event-based Temporal Networks.
Conference on Uncertainty in Artificial Intelligence (UAI). Online (03.-06.08.2020)
doi: 10.26083/tuprints-00021515
Conference or Workshop Item, Secondary publication, Publisher's Version

Wildner, Christian ; Koeppl, Heinz (2022)
Moment-Based Variational Inference for Stochastic Differential Equations.
24th International Conference on Artificial Intelligence and Statistics (AISTATS) 2021. Virtual (13.-15.04.2021)
doi: 10.26083/tuprints-00021512
Conference or Workshop Item, Secondary publication, Publisher's Version

Prangemeier, Tim ; Wildner, Christian ; Françani, André O. ; Reich, Christoph ; Koeppl, Heinz (2022)
Multiclass Yeast Segmentation in Microstructured Environments with Deep Learning.
IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB). Online (27.-29.10.2020)
doi: 10.26083/tuprints-00021524
Conference or Workshop Item, Secondary publication, Postprint

Kar, Sounak ; Rehrmann, Robin ; Mukhopadhyay, Arpan ; Alt, Bastian ; Ciucu, Florin ; Koeppl, Heinz ; Binnig, Carsten ; Rizk, Amr (2022)
On the Throughput Optimization in Large-scale Batch-processing Systems.
In: Performance Evaluation, 2020, 144
doi: 10.26083/tuprints-00021522
Article, Secondary publication, Postprint

Kruk, Nikita ; Maistrenko, Yuriy ; Koeppl, Heinz (2022)
Solitary states in the mean-field limit.
In: Chaos: An Interdisciplinary Journal of Nonlinear Science, 2020, 30 (11)
doi: 10.26083/tuprints-00021568
Article, Secondary publication, Publisher's Version

Kumar, Sunil ; Lun, Xiao-Kang ; Bodenmiller, Bernd ; Rodríguez Martínez, María ; Koeppl, Heinz (2022)
Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data.
In: Scientific Reports, 2020, (1)
doi: 10.26083/tuprints-00021513
Article, Secondary publication, Publisher's Version

Kruk, Nikita ; Carrillo, José A. ; Koeppl, Heinz (2022)
Traveling bands, clouds, and vortices of chiral active matter.
In: Physical Review E, 2020, 102 (2)
doi: 10.26083/tuprints-00021567
Article, Secondary publication, Publisher's Version

2019

Hofmann, Anja ; Falk, Johannes ; Prangemeier, Tim ; Happel, Dominic ; Köber, Adrian ; Christmann, Andreas ; Koeppl, Heinz ; Kolmar, Harald (2019)
A tightly regulated and adjustable CRISPR-dCas9 based AND gate in yeast.
In: Nucleic Acids Research, 2018, 47 (1)
Article, Secondary publication, Publisher's Version