Publications

Journal and Conference Papers

  1. 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.

  2. 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).

  3. 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

  4. 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.

  5. 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.

  6. 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]
  7. E. Holtzapple, C. A. Telmer, N. Miskov-Zivanov. "FLUTE: Fast and reliable knowledge retrieval from biomedical literature," in Database, August 2020.
  8. 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.
  9. 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.
  10. 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.
  11. 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).
  12. 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.
  13. 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. 
  14. 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.
  15. 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.
  16. 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. 
  17. N. Miskov-Zivanov, “Automation of biological model learning, design and analysis.” In Proc. of Great Lakes Symposium on VLSI (GLSVLSI), May 2015.
  18. 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.
  19. 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. 
  20. 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.
  21. 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). 
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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. 
  28. 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).
  29. 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).
  30. 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. 
  31. 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.
  32. 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).
  33. 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).
  34. 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).
  35. 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. 
  36. 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.
  37. N. Miskov-Zivanov and D. Marculescu, “Circuit Reliability Analysis Using Symbolic Techniques.” In Proc. of International Workshop on Logic and Synthesis (IWLS), June 2005.
  38. 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

  1. K. Sayed and N. Miskov-Zivanov, “Automation of Delay Modeling for Cell Signaling Networks,” Cold Spring Harbor Laboratory Computational Cell Biology Meeting, April 2017.
  2. A. Butchy and N. Miskov-Zivanov, "Discrete modeling of macrophage differentiation," The Journal of Immunology, May 1, 2017, 198 (1 Supplement) 67.13.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.