Publications
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23. Naturally occurring combinations of receptors from single cell transcriptomics in endothelial cells. S. Domanskyi, A. Hakansson, M. Meng, J. S. Graff Zivin, C. Piermarocchi, G. Paternostro, N. Ferrara, in review (2021). GitHub DECNEO
22. Visibility Graph Based Community Detection for Biological Time Series. M. Zheng, S. Domanskyi, C. Piermarocchi, G. I. Mias, Scientific Reports, 11, 5623 (2021).
21. Digital Cell Sorter (DCS): a cell type identification, anomaly detection, and Hopfield landscapes toolkit for single-cell transcriptomics. S. Domanskyi, A. Hakansson, T. Bertus, G. Paternostro, C. Piermarocchi, PeerJ, 9:e10670 (2021). GitHub DCS
20. Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study. G. I. Mias, V. V. Singh, L. R. K. Rogers, S. Xue, M. Zheng, S. Domanskyi, M. Kanada, C. Piermarocchi, J. He, Scientific Reports, 11, 710 (2021).
19. Modeling drug combination sensitivity with Hopfield networks and transcriptomics data. C. Piermarocchi, S. Domanskyi, A. Hakansson, G. Paternostro, CANCER RESEARCH 80 (11), 41-41 (2020).
18. PyIOmica: Longitudinal Omics Analysis and Classification, S. Domanskyi, C. Piermarocchi, G. I. Mias, Bioinformatics 36 (7), 2306-2307 (2020). GitHub PyIOmica
17. Modeling disease progression in Multiple Myeloma with Hopfield networks and single-cell RNA-seq, S. Domanskyi, A. Hakansson, G. Paternostro, C. Piermarocchi, IEEE International Conference on Bioinformatics and Biomedicine, 2129-2136 (2019).
16. Polled Digital Cell Sorter (p-DCS): Automatic identification of hematological cell types from single cell RNA-sequencing clusters, S. Domanskyi, A. Szedlak, N. T. Hawkins, J. Wang, G. Paternostro, C. Piermarocchi, BMC Bioinformatics 20, Article number: 369 (2019).
15. Predictive Design of Polymer Molecular Weight Distributions from Living Anionic Polymerization with Controlled Temporal Supply of Initiator, S. Domanskyi, D. T. Gentekos, V. Privman, B. P. Fors, Polym. Chem., 11, 326-336 (2019).
14. Biomolecular Release from Alginate Triggered by Chemical Inputs Processed Through a Biocatalytic Cascade – Integration of Biomolecular Computing and Actuation, A. V. Okhokhonin, S. Domanskyi, Y. Filipov, M. Gamella, A. N. Kozitsina, V. Privman, E. Katz, Electroanalysis 30 (3), 426-435 (2018).
13. Experimental Realization of High Quality Biochemical XOR Gate, Y. Filipov, S. Domanskyi, M. L. Wood, M. Gamella, V. Privman, E. Katz, ChemPhysChem 18 (20), 2908–2915 (2017).
12. SIRT6 Knockout Cells Resist Apoptosis Initiation but not Progression after Nutrient Stress, S. Domanskyi, J. Nicholatos, J. Schilling, V. Privman, S. Libert, Apoptosis 22 (11), 1336–1343 (2017).
11. Glucose-triggered Insulin Release from Fe3+-cross-linked Alginate Hydrogel: Experimental Study and Theoretical Modeling, S. Scheja, S. Domanskyi, M. Gamella, K. L. Wormwood, C. C. Darie, A. Poghossian, M. J. Schöning, A. Melman, V. Privman, and E. Katz, ChemPhysChem 18 (12), 1541-1551 (2017).
10. Design of High Quality Chemical XOR Gates with Noise Reduction, M. L. Wood, S. Domanskyi, and V. Privman, ChemPhysChem 18 (13), 1773-1781 (2017).
9. Rate-Equation Modelling and Ensemble Approach to Extraction of Parameters for Viral Infection-Induced Cell Apoptosis and Necrosis, S. Domanskyi, J. E. Schilling, V. Gorshkov, S. Libert, and V. Privman, J. Chem. Phys. 145 (9), Article 094103, 8 pages (2016).
8. Invited Review: Modeling and modifying response of biochemical processes for biocomputing and biosensing signal processing, S. Domanskyi, and V. Privman, Ch. 3 in Advances in Unconventional Computing, Vol. 2: Prototypes, Models and Algorithms, pages 61-83, edited by A. Adamatzky, Vol. 23 of Emergence, Complexity and Computation (Springer Nature, Basel, Switzerland, 2017).
7. Diffusion of oligonucleotides from within iron-crosslinked polyelectrolyte-modified alginate beads: a model system for drug release, V. Privman, S. Domanskyi, R. A. S. Luz, N. Guz, M. L. Glasser, and E. Katz, ChemPhysChem 17, 976-984 (2016).
Journal Issue Cover: Results of this work have been highlighted by the Editors of ChemPhysChem, by using a compilation of images for a cover of Issue 7 of the Volume in which it will be printed.
6. Refereed Conference Proceeding Article: Challenges in modeling delayed erosion due to degradation of novel polyanhydride biomaterials, V. Privman, S. Domanskyi, K. L. Poetz, and D. A. Shipp, in: Proc. Conf. ICQNM 2015 (ThinkMind Digital Publishing: thinkmind.org, Wilmington, DE, 2015), pages 10-15.
5. Reaction-Diffusion Degradation Model for Delayed Erosion of Cross-Linked Polyanhydride Biomaterials, S. Domanskyi, K. L. Poetz, D. A. Shipp and V. Privman, Phys. Chem. Chem. Phys. 17 (20), 13215-13222 (2015).
Journal Issue Cover: Results of this work have been highlighted by the Editors of Phys. Chem. Chem. Phys., by using a compilation of images for a cover of Issue 20 of Volume 17.
4. Kinetic Model for a Threshold Filter in an Enzymatic System for Bioanalytical and Biocomputing Applications, V. Privman, S. Domanskyi, S. Mailloux, Y. Holade and E. Katz, J. Phys. Chem. B 118 (43), 12435-12443 (2014).
Journal Issue Cover: Results of this work have been highlighted by the Editors of J. Phys. Chem. B, by using a compilation of images for a cover of Issue 43 of Volume B 118.
3. Percolation Modeling of Self-Damaging of Composite Materials, S. Domanskyi and V. Privman, Physica A 405, 1-9 (2014).
2. Conference Proceeding Editing: Proceedings of The Seventh International Conference on Quantum, Nano and Micro Technologies (ICQNM 2013), edited by V. Privman and V. Ovchinnikov (ThinkMind Digital Publishing: thinkmind.org, Wilmington, DE, 2013); Proceedings of The Sixth International Conference on Advances in Circuits, Electronics and Microelectronics (CENICS 2013), edited by V. Privman (ThinkMind Digital Publishing: thinkmind.org, Wilmington, DE, 2013). Article: Design of Biosensors with Extended Linear Response and Binary-Type Sigmoid Output Using Multiple Enzymes, O. Zavalov, S. Domanskyi, V. Privman and A. Simonian, in: Proc. Conf. ICQNM 2013 (ThinkMind Digital Publishing: thinkmind.org, Wilmington, DE, 2013), pages 54-59.
1. Design of Digital Response in Enzyme-Based Bioanalytical Systems for Information Processing Applications, S. Domanskyi and V. Privman, J. Phys. Chem. B 116 (46), 13690-13695 (2012).