Sunkara, Dr. Vikram

Position:

Head of Research Group

Room:

4024

Division:

Mathematics of Complex Systems

Department:

Visual and Data-Centric Computing

Research group:

Explainable AI for Biology

Mail:

sunkara

zib.de

Phone:

+49 30 841 85 - 432

Fax:

+49 30 841 85 - 107

Projects

Head

Math-Powered Drug Design

Publications

2023 2022 2021 2020 2019

2023
Arne Thies, Vikram Sunkara, Sourav Ray, Hanna Wulkow, M. Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann	Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design	Scientific Reports, 13(607), 2023	BibTeX DOI
Mustafa Chaukair, Christof Schütte, Vikram Sunkara	On the Activation Space of ReLU Equipped Deep Neural Networks	Procedia Computer Science, pp. 624-635, Vol.222, 2023	BibTeX DOI
2022
Vikram Sunkara, Angus Lewis, Giang T. Nguyen, Malgorzata M. O'Reilly, Nigel Bean	A discontinuous Galerkin method for approximating the stationary distribution of stochastic fluid-fluid processes	Methodology and Computing in Applied Probability, 2022	BibTeX DOI
Kenrick Schulze, Felix Peppert, Christof Schütte, Vikram Sunkara	Chimeric U-Net–Modifying the standard U-Net towards Explainability	bioRxiv, 2022 (under review)	BibTeX DOI
Felix Peppert, Max von Kleist, Christof Schütte, Vikram Sunkara	On the Sufficient Condition for Solving the Gap-Filling Problem Using Deep Convolutional Neural Networks	IEEE Transactions on Neural Networks and Learning Systems, 33(11), pp. 6194-6205, 2022	BibTeX DOI
Annemarie Lang, Antja Vester, M. Ferreira-Gomes, G.M. Guerra, Fredrich R. Heinrich, C.C. Götzke, Sebastian Kurmies, Vikram Sunkara, Pawel Durek, Joel D. Boerckel, Mir-Farzin Mashreghi	PIPELINE FOR SINGLE CELL SEQUENCING OF HUMAN CHONDROCYTE PELLET CULTURES TO DELINEATE IL-1β MODULATED CHANGES IN CELL HETEROGENEITY	Osteoarthritis and Cartilage, 30(Supplement 1), p. S90, 2022	BibTeX DOI
Margarita Kostré, Vikram Sunkara, Christof Schütte, Natasa Djurdjevac Conrad	Understanding the Romanization Spreading on Historical Interregional Networks in Northern Tunisia	Applied Network Science, Vol.7, 2022 (preprint available as ZIB-Report 22-10)	PDF (ZIB-Report) BibTeX DOI
Noushin Hajarolasvadi, Vikram Sunkara, Sagar Khavnekar, Florian Beck, Robert Brandt, Daniel Baum	Volumetric macromolecule identification in cryo-electron tomograms using capsule networks	BMC Bioinformatics, 23(360), 2022	BibTeX DOI
2021
Vikram Sunkara, Gitta A. Heinz, Frederik F. Heinrich, Pawel Durek, Ali Mobasheri, Mir-Farzin Mashreghi, Annemarie Lang	Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint	Osteoarthritis and Cartilage, 29(6), pp. 905-914, 2021	BibTeX DOI
Niklas Wulkow, Péter Koltai, Vikram Sunkara, Christof Schütte	Data-driven modelling of nonlinear dynamics by barycentric coordinates and memory	J. Stat. Phys., 2021 (under review)	BibTeX arXiv
Margarita Kostre, Vikram Sunkara, Natasa Djurdjevac Conrad	Inference of historical influence networks	International Conference on Complex Networks & Their Applications Proceedings, pp. 110-113, 2021	BibTeX DOI
Ralph Birk, N. Alexia Raharinirina, Konstantin Fackeldey, Tonio Sebastian Richter, Marcus Weber	Inferring cultural and social processes based on patterns of statistical relationships between Synodal texts	2021 (in progress)	BibTeX
Alexia N. Raharinirina, Felix Peppert, Max von Kleist, Christof Schütte, Vikram Sunkara	Inferring gene regulatory networks from single-cell RNA-seq temporal snapshot data requires higher-order moments	Patterns, 2(9), 2021 (preprint available as ZIB-Report 20-25)	PDF (ZIB-Report) BibTeX DOI
Sourav Ray, Arne Thies, Vikram Sunkara, Hanna Wulkow, Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann	Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design	ZIB-Report 21-19	PDF BibTeX URN
2020
Vikram Sunkara, Gitta A. Heinz, Frederik F. Heinrich, Pawel Durek, Ali Mobasheri, Mir-Farzin Mashreghi, Annemarie Lang	Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint	bioarxiv (Accepted in Osteoarthr. Cartil.), 2020	BibTeX DOI
Annemarie Lang, Sarah Helfmeier, Jonathan Stefanowski, Aditi Kuppe, Vikram Sunkara, Moritz Pfeiffenberger, Angelique Wolter, Alexandra Damerau, Shabnam Hemmati-Sadeghi, Jochen Ringe, Rainer Haag, Anja E. Hauser, Max Löhning, Carsten Perka, Georg N. Duda, Paula Hoff, Katharina Schmidt-Bleek, Timo Gaber, Frank Buttgereit	HIF-stabilization prevents delayed fracture healing	bioarxiv, 2020 (under review)	BibTeX DOI
Sourav Ray, Vikram Sunkara, Christof Schütte, Marcus Weber	How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs	Molecular Simulation, 46(18), pp. 1443-1452, 2020 (preprint available as ZIB-Report 20-18)	PDF (ZIB-Report) BibTeX DOI
Jan Möller, Ali Isbilir, Titiwat Sungkaworn, Brenda Osberg, Christos Karathanasis, Vikram Sunkara, Eugene O Grushevsky, Andreas Bock, Paolo Annibale, Mike Heilemann, Christof Schütte, Martin J. Lohse	Single molecule mu-opioid receptor membrane-dynamics reveal agonist-specific dimer formation with super-resolved precision	Nature Chemical Biology, Vol.16, pp. 946-954, 2020	BibTeX DOI
Daniel J. Laydon, Vikram Sunkara, Lies Boelen, Charles R. M. Bangham, Becca Asquith	The relative contributions of infectious and mitotic spread to HTLV-1 persistence	PLOS Computational Biology, 2020	BibTeX DOI
2019
Vikram Sunkara	Algebraic Expressions of Conditional Expectations in Gene Regulatory Networks	Journal of Mathematical Biology, pp. 1779-1829, 2019	PDF BibTeX URN DOI
Tobias Haase, Vikram Sunkara, Benjamin Kohl, Carola Meier, Patricia Bußmann, Jessica Becker, Michal Jagielski, Max von Kleist, Wolfgang Ertel	Discerning the spatio-temporal disease patterns of surgically induced OA mouse models	PLOS One, 14(4), 2019	BibTeX DOI
Vikram Sunkara	On the Properties of the Reaction Counts Chemical Master Equation	Entropy, 21(6), p. 607, 2019	BibTeX DOI
Julia Temp, Dominika Labuz, Roger Negrete, Vikram Sunkara, Halina Machelska	Pain and knee damage in male and female mice in the medial meniscal transection-induced osteoarthritis	Osteoarthritis and Cartilage, 2019	BibTeX DOI
Anika Rettig, Tobias Haase, Alexandr Pletnyov, Benjamin Kohl, Wolfgang Ertel, Max von Kleist, Vikram Sunkara	SLCV – A Supervised Learning - Computer Vision combined strategy for automated muscle fibre detection in cross sectional images	PeerJ, 2019	PDF BibTeX URN DOI