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
Ahmed, Y., Telmer, C.A., Zhou, G., & Miskov-Zivanov, N. (2024). Context-aware knowledge selection and reliable model recommendation with ACCORDION. FRONTIERS IN SYSTEMS BIOLOGY, 4, 1308292.Frontiers. doi: 10.3389/fsysb.2024.1308292.
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 Synth Biol, 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.). Bioinform Adv, 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 (Oxford), 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 Immunol Res, 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. Annu Int Conf IEEE Eng Med Biol Soc, 2018, 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. J Immunol, 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. J Pharmacokinet Pharmacodyn, 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 Synth Biol, 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. Sci Signal, 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., Kashinkunti, P., Marculescu, D., & Faeder, J.R. (2011). Regulatory network analysis acceleration with reconfigurable hardware. Annu Int Conf IEEE Eng Med Biol Soc, 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., & Miskov-Zivanov, N. (2021). Guided assembly of cellular network models from knowledge in literature. In Annu Int Conf IEEE Eng Med Biol Soc, 2021, (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 Annu Int Conf IEEE Eng Med Biol Soc, 2019, (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.