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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
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Posts
Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
publications
Bipartite subgraphs and the signless Laplacian matrix
Published in , 2011
Abstract
Recommended citation: Kirkland, S. and Paul, D., 2011. Bipartite subgraphs and the signless Laplacian matrix. Applicable Analysis and Discrete Mathematics 5(1), pp.1-13.
A volumetric method for representing and comparing regions of electrostatic focusing in molecular structure
Published in , 2012
Recommended citation: Chen, B.Y. and Paul, D., 2012. A volumetric method for representing and comparing regions of electrostatic focusing in molecular structure. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine pp.242-249.
Robustness and filtering properties of ubiquitous signaling network motifs
Published in , 2016
Abstract
Recommended citation: Paul, D. and Radde, N., 2016. Robustness and filtering properties of ubiquitous signaling network motifs. IFAC-PapersOnLine 49(26), pp.120-127.
Structural Design with Biological Methods: Optimality, Multi-functionality and Robustness
Published in , 2016
Abstract
Recommended citation: Paul, D., Dehkordi, L.K.F.,von Scheven, M.,Bischoff, M. and Radde, N., 2016. Structral Design With Biological Methods:Optimality, Multi-functionality and Robustness. In Biomimetic Research for Architecture and Building Construction (pp. 341-360). Springer, Cham.'
The role of stochastic sequestration dynamics for intrinsic noise filtering in signaling network motifs
Published in , 2018
Abstract
Recommended citation: Paul, D. and Radde, N., 2018.The role of stochastic sequestration dynamics for intrinsic noise filtering in signaling network motifs. Journal of Theoretical Biology 455, pp.86-96.
Eigenvector-based identification of bipartite subgraphs
Published in , 2019
Abstract
Recommended citation: Paul, D. and Stevanović, D., 2019. Eigenvector-based identification of bipartite subgraphs. Discrete Applied Mathematics 269, pp.146-158.
An in silico -in vitro pipeline identifying an HLA-A*02:01+ KRAS G12V+ spliced epitope candidate for a broad tumor-immune response in cancer patients
Published in , 1900
Recommended citation: Mishto, M.,Mansurkhodzhaev, A.,Ying, G.,Bitra, A.,Cordfunke, A R.,Henze, S., Paul, D.,Sidney, J.,Urlaub, H.,Neefjes, J., Sette, A.,Dirk, Z.,Liepe, J., 2019. An in silico-in vitro pipeline identifying an HLA-A*02:01+ KRAS G12V+spliced epitope candidate for a broad tumor-immune response in cancer patients. Frontiers in Immunology. Accepted for publication.
talks
Comparison between combinatorial and spectral approaches in identifying the largest bipartite subgraphs of a graph
Published:
Abstract
In this work, we compare the performances between a combinatorial approach by Erdös [1] and approaches based on the non-zero entries of eigenvectors corresponding to the extremal eigenvalues of four different matrices: adjacency, Laplacian, normalized Laplacian and signless Laplacian matrix, in identifying the largest bipartite subgraphs of a simple connected graph. We employ these approaches to one scale-free and three random graph models, which cover a wide range of real-world networks. It is observed that the normalized Laplacian and the adjacency matrix based approaches yield slightly better but comparable results to that of the combinatorial approach. Using these two matrices, we subsequently formulate a new index, analogous to the edge bipartivity index of Estrada and Rodríguez-Velázquez [2]. Our results indicate that the application of this new index not only significantly outperforms combinatorial approach but also performs better than the edge bipartivity index in identifying the largest bipartite subgraphs.
Stochastic sequestration dynamics can act as intrinsic noise filter in signaling network motifs
Published:
Abstract
The relation between design principles of signaling network motifs and their robustness against intrinsic noise still remains illusive. In this talk, I will summarize our recent investigation on the role of cascading for coping with intrinsic noise due to stochasticity in molecular reactions. We use stochastic modeling approaches to quantify fluctuations in the terminal kinase of phosphorylation-dephosphorylation cascade motifs and demonstrate that cascading highly affects these fluctuations. We show that this purely stochastic effect can be explained by time-varying sequestration of upstream kinase molecules. In particular, we discuss conditions on time scales and parameter regimes which lead to a reduction of output fluctuations. Our results are put into biological context by adapting rate parameters of our modeling approach to biologically feasible ranges for general binding-unbinding and phosphorylation-dephosphorylation mechanisms. Overall, this study reveals a novel role of stochastic sequestration for dynamic noise filtering in ubiquitous signaling motifs.
teaching
Systems theory in Systems biology
graduate course, University of Stuttgart, Institute for Systems Theory and Automatic Control, 2016
Role: course assistant
Statische Lernverfahren und stochastiche Regelungen
graduate course, University of Stuttgart, Institute for Systems Theory and Automatic Control, 2017