Journal and Conference Papers
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Y. Ahmed and N. Miskov-Zivanov, "Guided assembly of cellular network models from knowledge in literature," 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2021, pp. 4458-4464, doi: 10.1109/EMBC46164.2021.9630181.
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M. Kvorjak, Y. Ahmed, M. Miller, R. Sriram, C. Coronnello, J. Hashash, D. Hartman, C. Telmer, N. Miskov-Zivanov, O. J. Finn, and S. Cascio, \Increased expression of ST6GALNAC1 and MUC1-sTn in ulcerative colitis and colitis associated cancer results from the cross-talk between colon cells and macrophages," in Cancer Immunology Research, February, 2020 Volume 8, Issue 2, pp. 167-178; doi 10.1158/2326-6066.CIR-19-0514 (featured on the issue cover).
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Y. Ahmed, C. Telmer, N. Miskov-Zivanov, "CLARINET: Efficient learning of dynamic network models from literature," Bioinformatics Advances, 2021;, vbab006, https://doi.org/10.1093/bioadv/vbab006
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E. Holtzapple, B. Cochran, and N. Miskov-Zivanov, “Context-aware query design combines knowledge and data for efficient reading and reasoning,” in Proceedings of the 20th Workshop on Biomedical Language Processing, Online, 2021, pp. 238–246. doi: 10.18653/v1/2021.bionlp-1.26.
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E. Holtzapple, B. Cochran, and N. Miskov-Zivanov, “Automated verification, assembly, and extension of GBM stem cell network model with knowledge from literature and data,” Systems Biology, preprint, Jul. 2021. doi: 10.1101/2021.07.04.451062.
- A. A. Butchy, C. A. Telmer, N. Miskov-Zivanov et al. "FIDDLE: Efficient Assembly of Networks That Satisfy Desired Behavior," 02 June 2021, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-562692/v1]
- E. Holtzapple, C. A. Telmer, N. Miskov-Zivanov. "FLUTE: Fast and reliable knowledge retrieval from biomedical literature," in Database, August 2020.
- C. A. Telmer, K. Sayed, A. Butchy, K. N. Bocan, E. Holtzapple, C. E. Hansen, G. Zhou, Y. Ahmed, N. Miskov-Zivanov. "Dynamic system explanation: DySE, a framework that evolves to reason about complex systems - lessons learned," in AIDR '19: Proceedings of the Conference on Artificial Intelligence for Data Discovery and Reuse, pp. 1-10, May 2019.
- K. Sayed, K. N. Bocan, N. Miskov-Zivanov. "Automated Extension of Cell Signaling Models with Genetic Algorithm," In 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), July 2018.
- K. Sayed, Y.-H. Kuo, A. Kulkarni, and N. Miskov-Zivanov. "DiSH Simulator: Capturing Dynamics of Cellular Signaling with Heterogeneous Knowledge." In The Winter Simulation Conference (WSC), December 2017.
- K. Sayed, C. A. Telmer, A. A. Butchy, and N. Miskov-Zivanov. "Recipes for Translating Big Data Machine Reading to Executable Cellular Signaling Models." In The Third International Conference on Machine learning, Optimization and big Data (MOD), September 2017 (Best Paper Award).
- K.-W. Liang, Q. Wang, D. Ravichandran, P. Spirtes, C. A. Telmer, and N. Miskov-Zivanov. "Methods to Expand Cell Signaling Models Using Automated Reading and Model Checking." In International Conference on Computational Methods in Systems Biology, pp. 145-159. Springer, Cham, September 2017.
- K. Sayed, C. A. Telmer, and N. Miskov-Zivanov. "Motif modeling for cell signaling networks." In Proc. of 8th Cairo International Biomedical Engineering Conference (CIBEC), pp. 114-117. IEEE, 2016.
- N. Miskov-Zivanov, P. Zuliani, E.M. Clarke, J.R. Faeder, “High-level modeling and verification of cellular signaling.” In Proc. of International High-Level Design Validation and Test Workshop (HLDVT), pp. 162-169, 2016.
- Q. Wang, N. Miskov-Zivanov, B. Liu, J.R. Faeder, M.T. Lotze, E.M. Clarke, “Formal Modeling and Analysis of Pancreatic Cancer Microenvironment.” In Proc. of Computational Methods in Systems Biology (CMSB), pp. 289-305, 2016.
- W. F. Hawse, R. P. Sheehan, N. Miskov-Zivanov, L. P. Kane, J. R. Faeder, and P. A. Morel, “Differential regulation of PTEN by TCR, Akt and FoxO1 controls CD4+ T cell fate decisions.” The Journal of Immunology, Vol. 194, Issue 10, pp. 4615- 4619, 2015.
- N. Miskov-Zivanov, “Automation of biological model learning, design and analysis.” In Proc. of Great Lakes Symposium on VLSI (GLSVLSI), May 2015.
- Q. Wang, N. Miskov-Zivanov, C. Telmer, E. M. Clarke, “Formal analysis provides parameters for guiding hyperoxidation in bacteria using phototoxic proteins.” In Proc. of Great Lakes Symposium on VLSI (GLSVLSI), May 2015.
- P. A Morel, J. R Faeder, W. F Hawse, and N. Miskov-Zivanov, “Modeling the T cell immune response: a fascinating challenge.” Journal of Pharmacokinetics and Pharmacodynamics, Vol. 41, Issue 5, pp. 401-413, October 2014.
- N. Miskov-Zivanov, P. Wei, C.S.C. Loh, “THiMED: Time in Hierarchical Model Extraction and Design.” In Proc. of Computational Methods in Systems Biology (CMSB), pp. 260-263, November 2014.
- N. Miskov-Zivanov, M. S. Turner, L. P. Kane, P. A. Morel, and J. R. Faeder, "The duration of T cell stimulation is a critical determinant of cell fate and plasticity." Science Signaling, 6, ra97, November 2013 (link to podcast featuring publication).
- N. Miskov-Zivanov, P. Zuliani, E. M. Clarke, and J. R. Faeder, "Studies of biological networks with statistical model checking: application to immune system cells." In Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), September 2013, pp. 728.
- N. Miskov-Zivanov, D. Marculescu, and J. R. Faeder, "Dynamic behavior of cell signaling networks: model design and analysis automation." In Proc. of Design Automation Conference (DAC), Article 8, 6 p., June 2013.
- N. Miskov-Zivanov, J. R. Faeder, C. J. Myers, and H. M. Sauro. "Modeling and design automation of biological circuits and systems." In Proc. of International Conference of Computer-Aided Design (ICCAD), pp. 291-293, November 2012.
- N. Miskov-Zivanov, A. Bresticker, S. Venkatakrishnan, P. Kashinkunti, D. Krishnaswamy, D. Marculescu and J. R. Faeder, "Regulatory Network Analysis Acceleration with Reconfigurable Hardware." In Proc. of International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp. 149-152, September 2011.
- N. Miskov-Zivanov, A. Bresticker, D. Krishnaswamy, S. Venkatakrishnan, D. Marculescu and J. R. Faeder, "Emulation of Biological Networks in Reconfigurable Hardware." In Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), pp. 536-540, August 2011.
- N. Miskov-Zivanov and D. Marculescu, “Multiple Transient Faults in Combinational and Sequential Circuits: A Systematic Approach.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), Vol. 29, No. 10, pp. 1614-1627, October 2010.
- N. Miskov-Zivanov and D. Marculescu, “Formal Modeling and Reasoning for Reliability Analysis.” In Proc. of Design Automation Conference (DAC), pp. 531-536, June 2010 (invited paper).
- N. Miskov-Zivanov and D. Marculescu, “Modeling and Analysis of SER in Combinational Circuits.” In Proc. of IEEE Workshop on Silicon Errors in Logic – System Effects (SELSE), March 2010 (invited paper).
- N. Miskov-Zivanov and D. Marculescu, “Modeling and Optimization for Soft-Error Reliability of Sequential Circuits.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), Vol. 27, No. 5, pp. 803-816, May 2008.
- N. Miskov-Zivanov, K.-C. Wu and D. Marculescu, “Process Variability-Aware Transient Fault Modeling and Analysis.” In Proc. of IEEE/ACM International Conference on Computer-Aided Design (ICCAD), pp. 685-690, November 2008.
- N. Miskov-Zivanov and D. Marculescu, “A Systematic Approach to Modeling and Analysis of Transient Faults in Logic Circuits.” In Proc. of IEEE International Symposium on Quality Electronic Design (ISQED), pp. 408-413, 2009 (accepted in 2008, published in 2009, due to publisher error).
- N. Miskov-Zivanov and D. Marculescu, “Soft Error Rate Analysis for Sequential Circuits.” In Proc. of Design, Automation and Test in Europe (DATE), pp. 1436-1441, April 2007 (short-listed for ten years of DATE under honors).
- N. Miskov-Zivanov and D. Marculescu, “MARS-S: Modeling and Reduction of Soft Errors in Sequential Circuits.” In Proc. of IEEE International Symposium on Quality Electronic Design (ISQED), pp. 893-898, March 2007 (Best Paper Award nomination).
- N. Miskov-Zivanov and D. Marculescu, “Circuit Reliability Analysis Using Symbolic Techniques.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), Vol. 25, No. 12, pp. 2638-2649, December 2006.
- N. Miskov-Zivanov and D. Marculescu, “MARS-C: Modeling and Reduction of Soft Errors in Combinational Circuits.” In Proc. of Design Automation Conference (DAC), pp. 767-772, July 2006.
- N. Miskov-Zivanov and D. Marculescu, “Circuit Reliability Analysis Using Symbolic Techniques.” In Proc. of International Workshop on Logic and Synthesis (IWLS), June 2005.
- Z. D. Jelicic, N. Miskov, and D. Petrovacki, “Extended LQR control for first-order plus time-delay system.” In Proc. of International Symposium on Interdisciplinary Regional Research (Hungary, Romania, Yugoslavia), Novi Sad, Yugoslavia, 2002.
Conference Abstracts
- K. Sayed and N. Miskov-Zivanov, “Automation of Delay Modeling for Cell Signaling Networks,” Cold Spring Harbor Laboratory Computational Cell Biology Meeting, April 2017.
- A. Butchy and N. Miskov-Zivanov, "Discrete modeling of macrophage differentiation," The Journal of Immunology, May 1, 2017, 198 (1 Supplement) 67.13.
- A. Butchy, K. Sayed, K.-W. Liang, B. Aidukaitis, C. A. Telmer, and N. Miskov-Zivanov, “Explaining the Cancer Microenvironment via Automated Literature Exploration,” Cold Spring Harbor Laboratory Computational Cell Biology Meeting on Biological Data Science (CSHL), October 2016.
- M. Lemmon-Kishi, V. Peddada, C. Chu, M. Perdoncin, A. Ni Chochlain, L. Antoszewski, J. Lohmueller, N. Miskov-Zivanov, C. Telmer, S. Shroff, A. Deiters, “Thallium Detection Using Paper-Based Cell-Free Sensor Circuitry,” Biomedical Engineering Society (BMES) Annual Meeting, October 2016.
- A. Kulkarni, C. Telmer, N. Miskov-Zivanov, “Big Mechanism Design and Analysis Automation,” in Proc. of International Workshop on Bio-Design Automation (IWBDA), August 2015.
- N. Miskov-Zivanov, S. Lukchart, Y. Vodovotz, and J. R. Faeder, “Computational model of immune crosstalk in malaria suggests key mechanisms of parasite killing in mosquitoes,” Systems Biology of Infectious Disease, 2014.
- N. Miskov-Zivanov, C. S. Loh, P. Wei, and J. R. Faeder, “Delay modeling in cell signaling and gene regulatory networks,” International Workshop on Bio-Design Automation (IWBDA), 2014.
- N. Miskov-Zivanov, W. Hawse, L. P. Kane, P. A. Morel, and J. R. Faeder, “Signal Processing Modulation via Duration of Cell Receptor Contact: Application to the Control of T Cell Differentiation,” accepted/withdrawn Annual Meeting of the Biomedical Engineering Society (BMES), 2014.
- N. Miskov-Zivanov, W. Hawse, P. A. Morel, and J. R. Faeder, “Interplay of phosphorylation kinetics and methylation dynamics leads to complex behavior of Foxp3 and PTEN in computational model of T cell differentiation,” Annual Meeting of the American Association of Immunologists (AAI), May 2014.
- W. Hawse, N. Miskov-Zivanov, P. A. Morel, and J. R. Faeder, “PTEN Regulates CD4+ T cell differentiation,” Annual Meeting of the American Association of Immunologists (AAI), May 2014.
- N. Miskov-Zivanov, M. S. Turner, L. P. Kane, P. A. Morel, and J. R. Faeder, "Model predicts timing of T cell stimulation is critical for T cell fate," Cold Spring Harbor Laboratory Computational Cell Biology Meeting, March 2013.
- N. Miskov-Zivanov, S. Luckhart, Y. Vodovotz, D. Marculescu, J. R. Faeder, "Circuit design techniques for automated construction of mosquito immune response model in malaria infection," Cold Spring Harbor Laboratory Computational Cell Biology Meeting, March 2013.
- N. Miskov-Zivanov, P. Zuliani, P. Morel, E. Clarke and J. Faeder, "Model checking for studying temporal behavior in cell differentiation," in Proc. of q-bio Conference on Cellular Information Processing, August 2012.
- N. Miskov-Zivanov, P. Zuliani, P. Morel, E. Clarke and J. Faeder, "Model checking for studying timing of events in T cell differentiation," in Proc. of International Workshop on Bio-Design Automation (IWBDA), June 2012.
- N. Miskov-Zivanov, D. Marculescu, P. Morel and J. Faeder, "Automating the construction of discrete models of biological systems," in Proc. of q-bio Conference on Cellular Information Processing, August 2011.
- N. Miskov-Zivanov, A. Bresticker, D. Krishnaswamy, S. Venkatakrishnan, D. Marculescu and J. R. Faeder, "Emulation of Biological Networks in FPGA," in Proc. of International Workshop on Bio-Design Automation (IWBDA), June 2011.
- N. Miskov-Zivanov, A. Bresticker, D. Krishnaswamy, S. Venkatakrishnan, D. Marculescu and J. R. Faeder, "Emulation of Biological Networks in Reconfigurable Hardware," Cold Spring Harbor Laboratory Computational Cell Biology Meeting, March 2011.
- N. Miskov-Zivanov, M. S. Turner, P. A. Morel and J. R. Faeder, "T cell differentiation modeling and analysis through circuit design," Cold Spring Harbor Laboratory Computational Cell Biology Meeting, March 2011.
- N. Miskov-Zivanov, M. S. Turner, P. A. Morel and J. R. Faeder, "Peripheral T Cell Differentiation Modeling," 14th Annual Meeting of the Translational Research Cancer Centers Consortium (TRC3), February 2011.
- N. Miskov-Zivanov, J. Sekar, M. Turner, L. Kane, P. Morel and J. Faeder, “Modeling of Peripheral T Cell Differentiation,” in Proc. of q-bio Conference on Cellular Information Processing, August 2010.
- N. Miskov-Zivanov, J. Sekar, M. Turner, P. Morel and J. Faeder, “Logical model of the differentiation of naïve T cells into regulatory and effector cells,” in Society for Industrial and Applied Mathematics (SIAM) Conference on the Life Sciences (LS), July 2010.
- N. Miskov-Zivanov, J. Sekar, M. Turner, L. Kane, P. Morel and J. Faeder, “Logical Modeling of Peripheral T Cell Differentiation,” in Proc. of International Workshop on Bio-Design Automation (IWBDA), June 2010.
- J. Sekar, N. Miskov-Zivanov, P. Morel, M. Turner and J. Faeder, “Modeling of the peripheral naïve T-cell differentiation,” in Proc. of Annual Meeting of the American Association of Immunologists (AAI), May 2010.