PhD, Electrical and Computer Engineering, Carnegie Mellon University, 2009
MS, Electrical and Computer Engineering, Carnegie Mellon University, 2005
BS, Electrical Engineering and Computer Science, University of Novi Sad, 2003
Bocan, K., & Miskov-Zivanov, N. (2024). Mixed-resolution hybrid modeling in an element-based framework.
Holtzapple, E., Luo, H., Tang, D., Zhou, G., Arazkhani, N., Hansen, C., Telmer, C.A., & Miskov-Zivanov, N. (2024). The BioRECIPE Knowledge Representation Format. 2024.02.12.579694.Cold Spring Harbor Laboratory. doi: 10.1101/2024.02.12.579694.
Holtzapple, E., Zhou, G., Luo, H., Tang, D., Arazkhani, N., Hansen, C., Telmer, C.A., & Miskov-Zivanov, N. (2024). The BioRECIPE Knowledge Representation Format. ACS SYNTHETIC BIOLOGY, 13(8), 2621-2624.American Chemical Society (ACS). doi: 10.1021/acssynbio.4c00096.
Tang, D., Tam, T.Y.C., & Miskov-Zivanov, N. (2024). An Open-Set Semi-Supervised Multi-Task Learning Framework for Context Classification in Biomedical Texts. 2024.07.22.604491.Cold Spring Harbor Laboratory. doi: 10.1101/2024.07.22.604491.
Ahmed, Y., Telmer, C.A., Zhou, G., & Miskov-Zivanov, N. (2022). Context-aware knowledge selection and reliable model recommendation with ACCORDION. 2022.01.22.477231.Cold Spring Harbor Laboratory. doi: 10.1101/2022.01.22.477231.
Ahmed, Y., Telmer, C.A., & Miskov-Zivanov, N. (2021). CLARINET: efficient learning of dynamic network models from literature. In Kuijjer, M.L. (Ed.). BIOINFORMATICS ADVANCES, 1(1), vbab006.Oxford University Press (OUP). doi: 10.1093/bioadv/vbab006.
Telmer, C.A., Sayed, K., Butchy, A.A., Bocan, K., Kaltenmeier, C., Lotze, M., & Miskov-Zivanov, N. (2021). Computational modeling of cell signaling and mutations in pancreatic cancer. 2021.06.08.447557.Cold Spring Harbor Laboratory. doi: 10.1101/2021.06.08.447557.
Holtzapple, E., Telmer, C.A., & Miskov-Zivanov, N. (2020). FLUTE: Fast and reliable knowledge retrieval from biomedical literature. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2020, baaa056.Oxford University Press (OUP). doi: 10.1093/database/baaa056.
Kvorjak, M., Ahmed, Y., Miller, M.L., Sriram, R., Coronnello, C., Hashash, J.G., Hartman, D.J., Telmer, C.A., Miskov-Zivanov, N., Finn, O.J., & Cascio, S. (2020). Cross-talk between Colon Cells and Macrophages Increases ST6GALNAC1 and MUC1-sTn Expression in Ulcerative Colitis and Colitis-Associated Colon Cancer. CANCER IMMUNOLOGY RESEARCH, 8(2), 167-178.American Association for Cancer Research (AACR). doi: 10.1158/2326-6066.CIR-19-0514.
Sayed, K., Bocan, K.N., & Miskov-Zivanov, N. (2018). Automated Extension of Cell Signaling Models with Genetic Algorithm. Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 00, 5030-5033.Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/embc.2018.8513431.
Hawse, W.F., Sheehan, R.P., Miskov-Zivanov, N., Menk, A.V., Kane, L.P., Faeder, J.R., & Morel, P.A. (2015). Cutting Edge: Differential Regulation of PTEN by TCR, Akt, and FoxO1 Controls CD4+ T Cell Fate Decisions. JOURNAL OF IMMUNOLOGY, 194(10), 4615-4619.The American Association of Immunologists. doi: 10.4049/jimmunol.1402554.
Morel, P.A., Faeder, J.R., Hawse, W.F., & Miskov-Zivanov, N. (2014). Modeling the T cell immune response: a fascinating challenge. JOURNAL OF PHARMACOKINETICS AND PHARMACODYNAMICS, 41(5), 401-413.Springer Nature. doi: 10.1007/s10928-014-9376-y.
Bleris, L., Miskov-Zivanov, N., & Myers, C.J. (2013). IWBDA 2012 Special Issue. ACS SYNTHETIC BIOLOGY, 2(5), 203.American Chemical Society (ACS). doi: 10.1021/sb400042a.
Miskov-Zivanov, N., Turner, M.S., Kane, L.P., Morel, P.A., & Faeder, J.R. (2013). The Duration of T Cell Stimulation Is a Critical Determinant of Cell Fate and Plasticity. SCIENCE SIGNALING, 6(300), ra97.American Association for the Advancement of Science (AAAS). doi: 10.1126/scisignal.2004217.
Vodovotz, Y., Azhar, N., Miskov-Zivanov, N., Buliga, M., Zamora, R., Ermentrout, B., Constantine, G.M., Faeder, J.R., Pakpour, N., & Luckhart, S. (2013). Modeling Host–Vector–Pathogen Immuno-inflammatory Interactions in Malaria. In Complex Systems and Computational Biology Approaches to Acute Inflammation. 9781461480082, (pp. 265-279).Springer Nature. doi: 10.1007/978-1-4614-8008-2_14.
Miskov-Zivanov, N., Bresticker, A., Krishnaswamy, D., Venkatakrishnan, S., Kashinkunt, P., Marculescu, D., & Faeder, J.R. (2011). Regulatory Network Analysis Acceleration with Reconfigurable Hardware. Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2011, 149-152.Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/iembs.2011.6089916.
Miskov-Zivanov, N., & Marculescu, D. (2010). Multiple Transient Faults in Combinational and Sequential Circuits: A Systematic Approach. IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS, 29(10), 1614-1627.Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/TCAD.2010.2061131.
Miskov-Zivanov, N., & Marculescu, D. (2008). Modeling and optimization for soft-error reliability of sequential circuits. IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS, 27(5), 803-816.Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/TCAD.2008.917591.
Miskov-Zivanov, N., & Marculescu, D. (2006). Circuit Reliability Analysis Using Symbolic Techniques. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, 25(12), 2638-2649.Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/tcad.2006.882592.
Miskov-Zivanov, N., & Marculescu, D. (2006). Circuit reliability analysis using symbolic techniques. IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS, 25(12), 2638-2649. doi: 10.1109/TCAD.2006.882592.
Ahmed, Y., Telmer, C.A., Zhou, G., & Miskov-Zivanov, N. Context-aware knowledge selection and reliable model recommendation with ACCORDION. Frontiers in Systems Biology, 4, 1308292.Frontiers. doi: 10.3389/fsysb.2024.1308292.
Ahmed, Y., & Miskov-Zivanov, N. (2021). Guided assembly of cellular network models from knowledge in literature. In Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 00, (pp. 4458-4464).Institute of Electrical and Electronics Engineers (IEEE).United States. doi: 10.1109/embc46164.2021.9630181.
Andjelkovic, S., & Miskov-Zivanov, N. (2021). Dish-Trend: Intervention Modeling Simulator That Accounts for Trend Influences. In 2021 Winter Simulation Conference (WSC), 00, (pp. 1-12).Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/wsc52266.2021.9715401.
Holtzapple, E., Cochran, B., & Miskov-Zivanov, N. (2021). Context-aware query design combines knowledge and data for efficient reading and reasoning. In Proceedings of the 20th Workshop on Biomedical Language Processing, (pp. 238-246).Association for Computational Linguistics (ACL). doi: 10.18653/v1/2021.bionlp-1.26.
Holzapple, E., Miskov-Zivanov, N., & Cochran, B. (2021). A DYNAMIC CAUSAL MODEL OF GLIOBLASTOMA STEM CELL SIGNALING PREDICTS EFFECTS OF KINASE INHIBITORS. In NEURO-ONCOLOGY, 23, (pp. 35-36).
Becker, E.W., Bocan, K.N., & Miskov-Zivanov, N. (2020). Nested Event Representation for Automated Assembly of Cell Signaling Network Models. In Lecture Notes in Computer Science, 12233, (pp. 480-499).Springer Nature. doi: 10.1007/978-3-030-54997-8_30.
Cascio, S., Kvorjak, M., Ahmed, Y., Miller, M., Al Hashash, J., Hartman, D., Miskov-Zivanov, N., Telmer, C., & Finn, O.J. (2019). The cross-talk between infiltrating macrophages and inflamed or malignant colonic epithelium promotes overexpression of ST6GALNAC1 and epithelial MUC1 tumor form MUC1-sTn. In JOURNAL OF IMMUNOLOGY, 202(1).
Gilboy, K., Sayed, K., Sundaram, N., Bocan, K.N., & Miskov-Zivanov, N. (2019). A Faster DiSH: Hardware Implementation of a Discrete Cell Signaling Simulator. In Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 00, (pp. 2895-2899).Institute of Electrical and Electronics Engineers (IEEE).United States. doi: 10.1109/embc.2019.8857495.
Telmer, C.A., Sayed, K., Butchy, A., Bocan, K.N., Holtzapple, E., Hansen, C.E., Zhou, G., Ahmed, Y., & Miskov-Zivanov, N. (2019). Dynamic system explanation. In Proceedings of the Conference on Artificial Intelligence for Data Discovery and Reuse, (pp. 1-10).Association for Computing Machinery (ACM). doi: 10.1145/3359115.3359123.
Holtzapple, E., Miskov-Zivanov, N., Jahan, K., Zhang, Y., Young, S., & Cochran, B. (2018). COMPUTATIONAL MODELING OF GLIOBLASTOMA STEM CELL SIGNALING NETWORKS. In NEURO-ONCOLOGY, 20, (p. 45).
Sayed, K., Telmer, C.A., Butchy, A.A., & Miskov-Zivanov, N. (2018). Recipes for Translating Big Data Machine Reading to Executable Cellular Signaling Models. In Lecture Notes in Computer Science, 10710, (pp. 1-15).Springer Nature. doi: 10.1007/978-3-319-72926-8_1.
Zhou, G., Liang, K.W., & Miskov-Zivanov, N. (2018). Sensitivity Analysis of Discrete Models and Application in Biological Networks. In Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, (pp. 605-606).Association for Computing Machinery (ACM). doi: 10.1145/3233547.3233694.
Butchy, A.A., & Miskov-Zivanov, N. (2017). Discrete modeling of macrophage differentiation. In JOURNAL OF IMMUNOLOGY, 198(1).
Liang, K.W., Wang, Q., Telmer, C., Ravichandran, D., Spirtes, P., & Miskov-Zivanov, N. (2017). Methods to Expand Cell Signaling Models Using Automated Reading and Model Checking. In Lecture Notes in Computer Science, 10545, (pp. 145-159).Springer Nature. doi: 10.1007/978-3-319-67471-1_9.
Sayed, K., Kuo, Y.H., Kulkarni, A., & Miskov-Zivanov, N. (2017). Dish Simulator: Capturing Dynamics of Cellular Signaling with Heterogeneous Knowledge. In 2017 Winter Simulation Conference (WSC), (pp. 896-907).Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/wsc.2017.8247841.
Miskov-Zivanov, N., Zuliani, P., Wang, Q., Clarke, E.M., & Faeder, J.R. (2016). High-Level Modeling and Verification of Cellular Signaling. In 2016 IEEE International High Level Design Validation and Test Workshop (HLDVT), (pp. 162-169).Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/hldvt.2016.7748271.
Sayed, K., Telmer, C.A., & Miskov-Zivanov, N. (2016). Motif Modeling for Cell Signaling Networks. In 2016 8th Cairo International Biomedical Engineering Conference (CIBEC), (pp. 114-117).Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/cibec.2016.7836133.
Wang, Q., Miskov-Zivanov, N., Liu, B., Faeder, J.R., Lotze, M., & Clarke, E.M. (2016). Formal Modeling and Analysis of Pancreatic Cancer Microenvironment. In Lecture Notes in Computer Science, 9859, (pp. 289-305).Springer Nature. doi: 10.1007/978-3-319-45177-0_18.
Miskov-Zivanov, N. (2015). Automation of Biological Model Learning, Design and Analysis. In Proceedings of the 25th edition on Great Lakes Symposium on VLSI, 20-22-May-2015, (pp. 327-329).Association for Computing Machinery (ACM). doi: 10.1145/2742060.2743765.
Wang, Q., Miskov-Zivanov, N., Telmer, C., & Clarke, E.M. (2015). Formal Analysis Provides Parameters for Guiding Hyperoxidation in Bacteria using Phototoxic Proteins. In Proceedings of the 25th edition on Great Lakes Symposium on VLSI, 20-22-May-2015, (pp. 315-320).Association for Computing Machinery (ACM). doi: 10.1145/2742060.2743762.
Hawse, W., Miskov-Zivanov, N., Faeder, J., & Morel, P. (2014). PTEN regulates CD4+T cell differentiation. In JOURNAL OF IMMUNOLOGY, 192.
Miskov-Zivanov, N., Hawse, W., Morel, P., & Faeder, J. (2014). Interplay of phosphorylation kinetics and methylation dynamics leads to complex behavior of Foxp3 and PTEN in computational model of T cell differentiation. In JOURNAL OF IMMUNOLOGY, 192.
Miskov-Zivanov, N., Wei, P., & Loh, C.S.C. (2014). THiMED: Time in Hierarchical Model Extraction and Design. In Lecture Notes in Computer Science, 8859, (pp. 260-263).Springer Nature. doi: 10.1007/978-3-319-12982-2_22.
Miskov-Zivanov, N., Marculescu, D., & Faeder, J.R. (2013). Dynamic behavior of cell signaling networks. In Proceedings of the 50th Annual Design Automation Conference, (pp. 1-6).Association for Computing Machinery (ACM). doi: 10.1145/2463209.2488743.
Miskov-Zivanov, N., Zuliani, P., Clarke, E.M., & Faeder, J.R. (2013). Studies of biological networks with statistical model checking. In Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, (pp. 728-729).Association for Computing Machinery (ACM). doi: 10.1145/2506583.2512390.
Miskov-Zivanov, N., Faeder, J.R., Myers, C.J., & Sauro, H.M. (2012). Modeling and design automation of biological circuits and systems. In Proceedings of the International Conference on Computer-Aided Design, (pp. 291-293).Association for Computing Machinery (ACM). doi: 10.1145/2429384.2429444.
Miskov-Zivanov, N., Bresticker, A., Krishnaswamy, D., Venkatakrishnan, S., Marculescu, D., & Faeder, J.R. (2011). Emulation of biological networks in reconfigurable hardware. In Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, (pp. 536-540).Association for Computing Machinery (ACM). doi: 10.1145/2147805.2147893.
Miskov-Zivanov, N., & Marculescu, D. (2010). Formal modeling and reasoning for reliability analysis. In Proceedings of the 47th Design Automation Conference, (pp. 531-536).Association for Computing Machinery (ACM). doi: 10.1145/1837274.1837406.
Sekar, J., Miskov-Zivanov, N., Turner, M., Morel, P., & Faeder, J. (2010). Modeling the Role of Antigen Stimulation in Treg vs. Teff Fate Selection. In JOURNAL OF IMMUNOLOGY, 184.
Miskov-Zivanov, N., & Marculescu, D. (2009). A Systematic Approach to Modeling and Analysis of Transient Faults in Logic Circuits. In 2009 10th International Symposium on Quality of Electronic Design, 1, (pp. 408-413).Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/isqed.2009.4810329.
Miskov-Zivanov, N., Wu, K.C., & Marculescu, D. (2008). Process variability-aware transient fault modeling and analysis. In Proceedings of the 2006 IEEE/ACM international conference on Computer-aided design - ICCAD '06, (pp. 685-690).Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/iccad.2008.4681651.
Miskov-Zivanov, N., & Marculescu, D. (2007). MARS-S: Modeling and Reduction of Soft Errors in Sequential Circuits. In 9th International Symposium on Quality Electronic Design (isqed 2008), (pp. 893-898).Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/isqed.2007.100.
Miskov-Zivanov, N., & Marculescu, D. (2007). Soft Error Rate Analysis for Sequential Circuits *. In 2007 Design, Automation & Test in Europe Conference & Exhibition, (pp. 1436-1441).Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/date.2007.364500.
Miskov-Zivanov, N., & Marculescu, D. (2006). MARS-C. In Proceedings of the 43rd annual conference on Design automation - DAC '06, (pp. 767-772).Association for Computing Machinery (ACM). doi: 10.1145/1146909.1147104.