Publications by authors named "Tim Breitenbach"

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Mathematical strategies for predicting resistant subpopulations from scRNAseq data of a PANC-1 3D tissue model: Insight into gemcitabine resistance and TGFB1-induced invasion and EMT.
Aylin Caliskan, Samantha A W Crouch, Jesús Guillermo Nieves Pereira, Thomas Dandekar, Gudrun Dandekar, Tim Breitenbach

Comput Struct Biotechnol J· November 2025

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gSELECT: A novel pre-analysis machine-learning library enabling early hypothesis testing and predictive gene selection in single-cell data.
Deniz Caliskan, Aylin Caliskan, Thomas Dandekar, Tim Breitenbach

Comput Struct Biotechnol J· September 2025

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Adaptive sampling methods facilitate the determination of reliable dataset sizes for evidence-based modeling.
Tim Breitenbach, Thomas Dandekar

Front Bioinform· September 2025

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Transcriptome and protein network analyses of 3D-tissue lung cancer models reveal combinatorial targets for KRAS-mutation.
Samantha A W Crouch, Matthias Peindl, Elena Bencúrová, Aylin Caliskan, Thomas Dandekar, Tim Breitenbach

Lung Cancer· August 2025

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DataXflow: Synergizing data-driven modeling with best parameter fit and optimal control - An efficient data analysis for cancer research.
Samantha A W Crouch, Jan Krause, Thomas Dandekar, Tim Breitenbach

Comput Struct Biotechnol J· December 2024

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An orchestra of machine learning methods reveals landmarks in single-cell data exemplified with aging fibroblasts.
Lauritz Rasbach, Aylin Caliskan, Fatemeh Saderi, Thomas Dandekar, Tim Breitenbach

PLoS One· April 2024

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Optimized cell type signatures revealed from single-cell data by combining principal feature analysis, mutual information, and machine learning.
Aylin Caliskan, Deniz Caliskan, Lauritz Rasbach, Weimeng Yu, Thomas Dandekar, Tim Breitenbach

Comput Struct Biotechnol J· June 2023

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Software JimenaE allows efficient dynamic simulations of Boolean networks, centrality and system state analysis.
Martin Kaltdorf, Tim Breitenbach, Stefan Karl, Maximilian Fuchs, David Komla Kessie

Sci Rep· February 2023

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A modular systems biological modelling framework studies cyclic nucleotide signaling in platelets.
Tim Breitenbach, Nils Englert, Özge Osmanoglu, Natalia Rukoyatkina, Gaby Wangorsch

J Theor Biol· October 2022

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Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing.
Tim Breitenbach, Matthias Jürgen Schmitt, Thomas Dandekar

Bioinformatics· September 2022

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An effective model of endogenous clocks and external stimuli determining circadian rhythms.
Tim Breitenbach, Charlotte Helfrich-Förster, Thomas Dandekar

Sci Rep· August 2021

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Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks.
Tim Breitenbach, Chunguang Liang, Niklas Beyersdorf, Thomas Dandekar

PLoS Comput Biol· July 2019

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How to Steer and Control ERK and the ERK Signaling Cascade Exemplified by Looking at Cardiac Insufficiency.
Tim Breitenbach, Kristina Lorenz, Thomas Dandekar

Int J Mol Sci· May 2019

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