Publications

spectral graph theory, complex networks

Eigenvector-based identification of bipartite subgraphs
Paul, D. and Stevanović, D., 2019. Eigenvector-based identification of bipartite subgraphs. Discrete Applied Mathematics 269, pp.146-158.

Bipartite subgraphs and the signless Laplacian matrix
Kirkland, S. and Paul, D., 2011. Bipartite subgraphs and the signless Laplacian matrix. Applicable Analysis and Discrete Mathematics 5(1), pp.1-13.

Mathematical modeling, systems biology, systems theory, stochastic simulation, biomimetics

The role of stochastic sequestration dynamics for intrinsic noise filtering in signaling network motifs
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.

Robustness and filtering properties of ubiquitous signaling network motifs
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
Paul, D., Dehkordi, L.K.F., von Scheven, M., Bischoff, M. and Radde, N., 2016. Structural Design with Biological Methods: Optimality, Multi-functionality and Robustness. In Biomimetic Research for Architecture and Building Construction pp. 341-360. Springer, Cham.

structural bioinformatics, computational geometry

A volumetric method for representing and comparing regions of electrostatic focusing in molecular structure
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 (Acceptance rate: 20.7%).

immunopeptidomics, Bayesian inference, MCMC

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
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 Immunology. Accepted for publication.