Robust Perron Cluster Analysis for Various Applications in Computational Life Science. - Marcus Weber; Susanna Kube (CompLife, 2005)

An Indicator for the Number of Clusters: Using a Linear Map to Simplex Structure. - Marcus Weber; Wasinee Rungsarityotin; Alexander Schliep (GfKl, 2005)

Stable Computation of Probability Densities for Metastable Dynamical Systems. - Marcus Weber; Susanna Kube; Lionel Walter; Peter Deuflhard (Multiscale Model. Simul., 2007)

Selection and flexible optimization of binding modes from conformation ensembles. - Aysam Gürler; Sebastian Moll; Marcus Weber; Holger Meyer 002; Frank Cordes (Biosyst., 2008)

Efficient Simulation of ligand-receptor Binding Processes Using the Conformation Dynamics Approach. - Alexander Bujotzek; Marcus Weber (J. Bioinform. Comput. Biol., 2009)

Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics. - Susanna Kube; Caroline Lasser; Marcus Weber (J. Comput. Phys., 2009)

Towards a rational spacer design for bivalent inhibition of estrogen receptor. - Alexander Bujotzek; Min Shan; Rainer Haag; Marcus Weber (J. Comput. Aided Mol. Des., 2011)

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification. - Susanna Röblitz; Marcus Weber (Adv. Data Anal. Classif., 2013)

Hands-off Linear Interaction Energy Approach to Binding Mode and Affinity Estimation of Estrogens. - Vedat Durmaz; Sebastian Schmidt; Peggy Sabri; Christian Piechotta; Marcus Weber (J. Chem. Inf. Model., 2013)

A Square Root Approximation of Transition Rates for a Markov State Model. - Han Cheng Lie; Konstantin Fackeldey; Marcus Weber (SIAM J. Matrix Anal. Appl., 2013)

Adaptive Spectral Clustering in Molecular Simulation. - Marcus Weber (Classification and Data Mining, 2013)

Investigation of the Ergopeptide Epimerization Process. - Karsten Andrae; Stefan Merkel; Vedat Durmaz; Konstantin Fackeldey; Robert Köppen; Marcus Weber; Matthias Koch (Comput., 2014)

Computing the Minimal Rebinding Effect Included in a Given Kinetics. - Marcus Weber; Konstantin Fackeldey (Multiscale Model. Simul., 2014)

Applications of the Cross-Entropy Method to Importance Sampling and Optimal Control of Diffusions. - Wei Zhang 065; Han Wang; Carsten Hartmann; Marcus Weber; Christof Schütte (SIAM J. Sci. Comput., 2014)

Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes. - Isabel Beckenbach; Leon Eifler; Konstantin Fackeldey; Ambros M. Gleixner; Andreas Grever; Marcus Weber; Jakob Witzig (CoRR, 2016)

Finding Dominant Structures of Nonreversible Markov Processes. - Natasa Djurdjevac Conrad; Marcus Weber; Christof Schütte (Multiscale Model. Simul., 2016)

Implications of PCCA+ in Molecular Simulation. - Marcus Weber (Comput., 2018)

Mixed-Integer Programming for Cycle Detection in Nonreversible Markov Processes. - Jakob Witzig; Isabel Beckenbach; Leon Eifler; Konstantin Fackeldey; Ambros M. Gleixner; Andreas Grever; Marcus Weber (Multiscale Model. Simul., 2018)

Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC. - Franziska Erlekam; Sinaida Igde; Susanna Röblitz; Laura Hartmann; Marcus Weber (Comput., 2019)

Analyzing Raman Spectral Data without Separability Assumption. - Konstantin Fackeldey; Jonas Röhm; Amir Niknejad; Surahit Chewle; Marcus Weber (CoRR, 2020)

Computing the minimal rebinding effect for non-reversible processes. - Susanne Röhl; Marcus Weber; Konstantin Fackeldey (CoRR, 2020)

The Complexity of Comparative Text Analysis - "The Gardener is always the Murderer" says the Fourth Machine. - Marcus Weber; Konstantin Fackeldey (CoRR, 2020)

Computing the Minimal Rebinding Effect for NonReversible Processes. - Susanne Röhl; Marcus Weber; Konstantin Fackeldey (Multiscale Model. Simul., 2021)

Estimation of the Koopman Generator by Newton's Extrapolation. - Renata Sechi; Alexander Sikorski; Marcus Weber (Multiscale Model. Simul., 2021)

SepFree NMF: A Toolbox for Analyzing the Kinetics of Sequential Spectroscopic Data. - Renata Sechi; Konstantin Fackeldey; Surahit Chewle; Marcus Weber (Algorithms, 2022)

The Mathematics of Comparing Objects. - Marcus Weber; Konstantin Fackeldey (CoRR, 2022)

MaRDMO Plugin Document and Retrieve Workflows Using the MaRDI Portal. - Marco Reidelbach; Eloi Ferrer; Marcus Weber (CoRDI, 2023)

Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists. - Christopher Secker; Konstantin Fackeldey; Marcus Weber; Sourav Ray; Christoph Gorgulla; Christof Schütte (J. Cheminformatics, 2023)

Towards a FAIR Documentation of Workflows and Models in Applied Mathematics. - Marco Reidelbach; Björn Schembera; Marcus Weber (ICMS, 2024)

A case study of the use of logical data analysis in the Workmen's Village in Tell el-Amarna, Egypt. - Sarah M. Klasse; Marcus Weber (it Inf. Technol., 2024)

Exploring Metastable Dynamics of Gene Regulatory Networks with ISOKANN. - Maryam Yousefian; Luca Donati; Alexander Sikorski; Marcus Weber; Susanna Röblitz (CMSB, 2025)

Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition. - Maryam Yousefian; Anna-Simone Frank; Marcus Weber; Susanna Röblitz (BMC Bioinform., 2025)