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Publications

MeLoDy Lab Publications

Journal Papers
 

  1. Butchy, A.A., Arazkhani, N., Telmer, C.A., and Miskov-Zivanov, N., "Automating Knowledge-Driven Model Recommendation: Methodology, Evaluation, and Key Challenges," accepted at IEEE/ACM Transactions on Computational Biology and Bioinformatics. 
  2. Holtzapple, E., Zhou, G., Luo, H., Tang, D., Arazkhani, N., Hansen, C., Telmer, C., Miskov-Zivanov, N., “The BioRECIPE Knowledge Representation Format,” ACS Synthetic Biology, 2024, 13(8), pp. 2621-2624.
  3. Ahmed, Y., Telmer, C.A., Zhou, G., Miskov-Zivanov, N., “Context-aware information selection and model recommendation with ACCORDION,” Frontiers in Systems Biology, 2024, Vol. 4, pp. 1308292(13 pages), doi: 10.3389/fsysb.2024.1308292, (also on bioRxiv).
  4. Ruffo, E., Butchy, A.A., Tivon, Y., So, V., Kvorjak, M., Parikh, A. B., Adams, E. L., Miskov-Zivanov, N., Finn O. J., Deiters, A., Lohmueller, J., “Post-translational covalent assembly of CAR and synNotch receptors for programmable antigen targeting,” Nature Communications, 2023, 14 (1), pp. 2463(16 pages), doi: 10.1038/s41467-023-37863-5.
  5. Ahmed, Y., Telmer, C.A., Miskov-Zivanov, N., “CLARINET: Efficient learning of dynamic network models from literature,” Bioinformatics Advances, 2021, 1(1), pp. vbab006(9 pages), doi: 10.1093/bioadv/vbab006.
  6. Holtzapple, E., Telmer, C.A., Miskov-Zivanov, N., “FLUTE – A FiLter for Understanding True Events: Fast and reliable knowledge retrieval from biomedical literature,” Database, 2020, Vol. 2020, pp. baaa056(17 pages), doi: 10.1093/database/baaa056.
  7. 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., “Increased expression of ST6GALNAC1 and MUC1-sTn in ulcerative colitis and colitis associated cancer results from the cross-talk between colon cells and macrophages,” Cancer Immunology Research, 2020, 8(2), pp. 167-178, (featured on the issue cover: https://cancerimmunolres.aacrjournals.org/content/8/2.cover-expansion).

Conference Paper

  1. Arazkhani, N.,  Zhang, H., Luo, H., Tang, D., Cochran, B., and Miskov-Zivanov, N., “The role of NLP and LLMs in automating expert-driven model refinement: a GBM case study,” in Proceedings of the 16th International Workshop on Bio-Design Automation (IWBDA)
  2. Luo, H., Tang, D., Zivanov, A., and Miskov-Zivanov, N., “Knowledge retrieval and information reuse: a receptor design study,” in Proceedings of the 16th International Workshop on Bio-Design Automation (IWBDA)
  3. Tang, D., Tam, T., and Miskov-Zivanov, N., “Open-Set Biomedical Context Extraction via Multi-Task and Semi-Supervised Learning,” in Proceedings of the 16th International Workshop on Bio-Design Automation (IWBDA).
  4. Holtzapple, E., Verma, T.4, and Miskov-Zivanov, N., “Automated model curation using LLMs: Integration of ChatGPT with the DySE framework,” Proc. of the 15th International Workshop on Bio-Design Automation (IWBDA), September 2023, pp. 79-81. 
  5. Luo, H., Zivanov, A., and Miskov-Zivanov, N., “Encoding Process Markers with Neural Networks to Simplify the Complexity of Engineering CAR T cells,” Proc. of the 15th International Workshop on Bio-Design Automation (IWBDA), September 2023, pp. 85-88.
  6. Zhou, G. and Miskov-Zivanov, N., “Knowledge-Based Pathway Extraction and Verification,” Proc. of the 15th International Workshop on Bio-Design Automation (IWBDA), September 2023, pp. 82-84.
  7. Zhou, G. and Miskov-Zivanov, N., “Dynamic Behavior Alters Influences and Sensitivities in Biological Networks,“ Proc. of the 14th International Workshop on Bio-Design Automation (IWBDA), October 2022, pp. 103-105.
  8. Tang, D., Zhou, G., and Miskov-Zivanov, N., “Exploring Advantages and Limitations of Discrete Modeling of Biological Network Motifs,“ Proc. of the 14th International Workshop on Bio-Design Automation (IWBDA), October 2022, pp. 97-99.
  9. Andjelkovic, S. and Miskov-Zivanov, N., “DiSH-trend: Intervention Modeling Simulator That Accounts for Trend Influences,” Proc. of the IEEE Winter Simulation Conference (WSC), December 2021, pp. 1-12.
  10. Ahmed, Y. and Miskov-Zivanov, N., “Guided assembly of cellular network models from knowledge in literature,” in Proc. of the 43rd IEEE Engineering in Medicine and Biology Society (EMBC), November 2021, pp. 4458-4464.
  11. Li, E.4, Holtzapple, E., Sundaram, N., and Miskov-Zivanov, N., “Automated translation of logical models to SystemVerilog enables simulation speedup,” Proc. of the 13th International Workshop on Bio-Design Automation (IWBDA), September 2021, pp. 36-39.
  12. Ahmed, Y., Butchy, A. A., Sayed, K., Telmer, C.A., and Miskov-Zivanov, N., “New advances in the automation of context-aware information selection and guided model assembly,” Proc. of the 13th International Workshop on Bio-Design Automation (IWBDA), September 2021, pp. 52-55, (also on arXiv).
  13. Hansen, C.E., Kisslinger, J., Krishna, N., Holtzapple, E., Ahmed, Y., and Miskov-Zivanov, N., “Classifying Literature Extracted Events for Automated Model Extension,” Proc. of the 13th International Workshop on Bio-Design Automation (IWBDA), September 2021 pp. 49-51, (also on bioRxiv).
  14. Holtzapple, E., Cochran, B., and Miskov-Zivanov, N., "Context-aware query design combines knowledge and data for efficient reading and reasoning," Proc. of the 20th ACL Workshop on Biomedical Language Processing (BioNLP), June 2021, pp. 238-246.
  15. Telmer, C.A., Sayed, K., Butchy, A. A., Bocan, K., Kaltenmeier, C., Lotze, M.T., and Miskov-Zivanov, N., “Computational modeling of cell signaling and mutations in pancreatic cancer,” Proc. of the AAAI Fall Symposium: Artificial Intelligence for Synthetic Biology (AI4SynBio), November 2019, pp. 1-7, (also on bioRxiv).
  16. Becker, E.W., Bocan, K.N., and Miskov-Zivanov, N., "Nested Event Representation for Automated Assembly of Cell Signaling Network Models," Proc. of the International Symposium on Formal Methods (FM 2019), Workshop on Static Analysis for Systems Biology (SASB), October 2019, pp. 480-499. 
  17. Gilboy, K., Sayed, K., Sundaram, N., Bocan, K.N., and Miskov-Zivanov, N., “A Faster DiSH: Hardware Implementation of a Discrete Cell Signaling Simulator,” Proc. of the 41st IEEE Engineering in Medicine and Biology Society (EMBC), 2895-2899, July 2019, pp. 2895-2899, (also on arXiv).
  18. Telmer, C.A., Sayed, K., Butchy, A.A., Bocan, K.N., Holtzapple, E., Hansen, C.E., Zhou, G., Ahmed, Y., and Miskov-Zivanov, N., “Dynamic System Explanation, DySE - a framework that evolves to reason about complex systems,” Proc. of the Conference on Artificial Intelligence for Data Discovery and Reuse (AIDR), May 2019, pp. 1-10.
  19. Zhou, G., Liang, K.-W., and Miskov-Zivanov, N., “Sensitivity Analysis of Discrete Models and Application in Biological Networks,” Proc. of the 9th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), August 2018, pp. 605-606.
  20. Sayed, K., Bocan, K.N., and Miskov-Zivanov, N., “Automated Extension of Cell Signaling Models with Genetic Algorithm,” Proc. of the 40th IEEE Engineering in Medicine and Biology Society (EMBC), July 2018, pp. 5030-5033.
  21. Sayed, K., Telmer, C.A., Butchy, A.A., and Miskov-Zivanov, N., “Recipes for Translating Big Data Machine Reading to Executable Cellular Signaling Models,” Proc. of Machine Learning, Optimization, and Big Data: Third International Conference (MOD) September 2017, pp. 1-15, (Best Paper Award).
  22. Liang, K.-W., Wang, Q., Ravichandran, D., Spirtes, P., Telmer, C.A., and Miskov-Zivanov, N., “Methods to Expand Cell Signaling Models using Automated Reading and Model Checking,” Proc. of the 15th International Conference on Computational Methods in Systems Biology (CMSB), September 2017, pp. 145-159.
  23. Sayed, K., Kuo, Y.-H., Kulkarni., and Miskov-Zivanov, N., “DiSH-Simulator: Capturing Dynamics of Cellular Signaling with Heterogeneous Knowledge,” Proc. of the IEEE Winter Simulation Conference (WSC), December 2017, pp. 896-907.
  24. Sayed, K., Telmer, C.A., and Miskov-Zivanov, N., “From Machine Reading to Discrete Models of Cellular Signaling,” Proc. of the 9th International Workshop on Bio-Design Automation (IWBDA), August 2017, pp. 52-53.
  25. Holtzapple, E., Telmer, C.A., and Miskov-Zivanov, N., “Automated creation of temporal properties from protein interaction data,” Proc. of the 9th International Workshop on Bio-Design Automation (IWBDA), August 2017, pp. 62-63.
  26. Butchy, A. A., Terrier, A., Telmer, C.A., Faeder, J.R., and Miskov-Zivanov, N., “Discrete Modeling of the JAK2/STAT5 Signaling pathway to Determine Important Negative Feedback Mechanisms,” Proc. of the 9th International Workshop on Bio-Design Automation (IWBDA), August 2017, pp. 68-69.
  27. Sayed, K., Telmer, C.A., and Miskov-Zivanov, N., “Motif modeling for cell signaling networks,” Proc. of the 8th IEEE Cairo International Biomedical Engineering Conference (CIBEC), December 2016, pp. 114-117, (Third Best Paper Award). 
  28. Miskov-Zivanov, N., Zuliani, P., Clarke, E.M., and Faeder, J.R., “High-level modeling and verification of cellular signaling,” Proc. of the IEEE International High-Level Design Validation and Test Workshop (HLDVT), October 2016, pp. 162-169.
  29. Wang, Q., Miskov-Zivanov, N., Liu, B., Faeder, J.R., Lotze, M.T., and Clarke, E.M., “Formal Modeling and Analysis of Pancreatic Cancer Microenvironment,” Proc. of the 14th International Conference on Computational Methods in Systems Biology (CMSB), September 2016, pp. 289-305.

Abstracts

  1. Zhou, G. and Miskov-Zivanov, N., “BioRECIPE (Biological system Representation for Evaluation, Curation, Interoperability, Preserving, and Execution),” ISCB 32nd Conference on Intelligent Systems for Molecular Biology (ISMB), SysMod COSI (poster), July 2024.
  2. Zhou, G., Tang, D., Luo, H., Arazkhani, N., and Miskov-Zivanov, N., “BioRECIPE: Biological knowledge Representation for Evaluation, Curation, Interoperability, Preserving, and Execution,” ISCB 16th Great Lakes Bioinformatics Conference (GLBIO) (poster), May 2024.
  3. Zhou, G. and Miskov-Zivanov, N., “A Novel Node Influence Metric for Complex Networks with Semantic Knowledge,” 22nd International Conference on Systems Biology (ICSB) (long talk), October 2023.
  4. Ahmed, Y., Telmer, C.A., Zhou, G., and Miskov-Zivanov, N., “ACCORDION: An expert system for knowledge selection and model recommendation,” 22nd International Conference on Systems Biology (ICSB), (long talk), October 2023.
  5. Zhou, G. and Miskov-Zivanov, N., “Unraveling the Dynamics of Complex Systems through Element-Based Approaches,” 22nd International Conference on Systems Biology (ICSB) (long talk), October 2023.
  6. Tang, D. and Miskov-Zivanov, N., “A method for automatic network assembly from biological event annotations,” 22nd International Conference on Systems Biology (ICSB) (poster), October 2023.
  7. Holtzapple, E., Verma, T., and Miskov-Zivanov, N., “Automated model curation using LLMs: Integration of ChatGPT with the DySE framework,” 22nd International Conference on Systems Biology (ICSB) (long talk), October 2023.
  8. Zhou, G. and Miskov-Zivanov, N., “Knowledge-Based Pathway Extraction and Validation in Cell Signaling Networks,” Computational Modeling in Biology Network (COMBINE) (long talk), October 2023.
  9. Zhou, G., Tang, D., and Miskov-Zivanov, N., “Introducing the BioRECIPE Format: A Human-Centric Representation For Computational Modeling in Systems Biology,” Computational Modeling in Biology Network (COMBINE) (tutorial) October 2023.
  10. Butchy, A.A., Gottschalk, R.A., Miskov-Zivanov, N., “Large-scale discrete executable modeling of alveolar macrophages,” Cold Spring Harbor Laboratory (CSHL) Meeting: Systems Immunology (poster), April 2023.
  11. Ahmed, Y. and N. Miskov-Zivanov, “Rapid assembly and extension of network models in cancer from the information in literature,“ ACSB Biennial Meeting on Systems Approaches to Cancer Biology (SACB) (long talk), October 2022.
  12. Zhou, G., Tang, D., and Miskov-Zivanov, N., “DySE: Dynamic System Explanation framework,” 14th International Workshop on Bio-Design Automation (IWBDA) (tutorial), October 2022; abstract in Journal of Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation, 14(6), pp. 1713.
  13. Miskov-Zivanov, N. and Andjelkovic, S., “Natural language processing to aggregate knowledge of biological networks,” 4th International Brain Stimulation Conference (long talk), December 2021. 
  14. Miskov-Zivanov, N., “Automated and systematic verification and validation increases quality and long-term reuse of models,” ISCB 18th Rocky Mountain Bioinformatics Conference (ROCKY) (talk), December 2021.
  15. Holtzapple, E., Miskov-Zivanov, N., and Cochran, B., “A dynamic causal model of glioblastoma stem cell signaling predicts effects of kinase inhibitors,” SNO 26th Annual Scientific Meeting and Education Day (poster), November 2021; abstract in Journal of Neuro-oncology, 23(Suppl 6), pp. vi35.
  16. Holtzapple, E., Miskov-Zivanov, N., and Cochran, B., “Use of multi-omics data to initialize and validate a causal model of glioblastoma stem cell signaling,” SNO Conference on Basic and Translational Omics of Brain Tumors and Their Microenvironment (poster), July 2021; abstract in Journal of Neuro-oncology Advances, 3(Suppl 2), pp. ii5.
  17. Holtzapple, E., Cochran, B., and Miskov-Zivanov, N., “A data-driven Glioblastoma stem cell model provides insight into cell line differences in treatment resistance,” ISCB 29th Conference on Intelligent Systems for Molecular Biology Conference (ISMB), SysMod COSI (long talk), July 2021.
  18. Ahmed, Y., Telmer, C.A., and Miskov-Zivanov, N., “CLARINET: Efficient learning of dynamic network models from literature,” ISCB 29th Conference on Intelligent Systems for Molecular Biology Conference (ISMB), Text Mining COSI (long talk), July 2021.
  19. Ahmed, Y., Telmer, C.A., and Miskov-Zivanov, N., “Automated curation and selection of relevant data to guide network extension and query-answering,” ISCB 14th Great Lakes Bioinformatics Conference (GLBIO) (poster), May 2021.
  20. Zhou, G. and Miskov-Zivanov, N., “Comparison of Common Element-based Modeling Approaches in Biology,” ISCB 14th Great Lakes Bioinformatics Conference (GLBIO) (poster), May 2021.
  21. Zhou, G. and Miskov-Zivanov, N., “Intervention Pathway Discovery in Complex Systems via Scenario-Dependent Sensitivity Analysis,” 47th Northeast Bioengineering Conference (NEBEC) (poster), March 2021.
  22. Hansen, C., Rispoli, E., and Miskov-Zivanov, N., “Optimizing Automatic Classification for Biological Literature for Model Extension,” 47th Northeast Bioengineering Conference (NEBEC) (poster), March 2021.
  23. Holtzapple, E., Cochran, B., and Miskov-Zivanov, N., “Model Initialization Methodology Determines Cell State Outcomes in a Discrete Glioblastoma Stem Cell Model,” 47th Northeast Bioengineering Conference (NEBEC) (poster), March 2021.
  24. Butchy, A.A., Telmer C.A., and Miskov-Zivanov, N., “Discrete model of macrophage simulates six clinically relevant activation states,” ISCB 28th Conference on Intelligent Systems for Molecular Biology Conference (ISMB), SysMod COSI (poster and short talk), July 2020.
  25. Ahmed, Y., Telmer, C.A., and Miskov-Zivanov, N., “ACCORDION: Clustering and Selecting Relevant Data for Guided Network Extension and Query Answering,” ISCB 28th Conference on Intelligent Systems for Molecular Biology Conference (ISMB), SysMod COSI (poster and short talk), July 2020.
  26. Miskov-Zivanov, N., “Filtering, classification, and selection of new knowledge for model assembly and extension,” 17th ISCB Rocky Mountain Bioinformatics Conference (ROCKY) (poster and talk), December 2019.
  27. Hansen, C., Spirtes, P., Telmer, C.A., Bocan, K.N., Holtzapple, E., Ahmed, Y., Butchy, A.A., Sayed, K., and Miskov-Zivanov, N., “Interaction Classifier Improves Accuracy of Fully Automated Model Expansion,” q-bio Conference on Cellular Information Processing (poster), July 2019.
  28. Ahmed, Y., Liang, K.-W., Bocan, K.N., Telmer, C.A., and Miskov-Zivanov, N., “Automated extension of executable intra-cellular network models,” q-bio Conference on Cellular Information Processing (poster and poster spotlight), July 2019.
  29. Ahmed, Y., Bocan, K.N., Telmer, C.A., and Miskov-Zivanov, N., “Automated assembly of models: Applications in biology and world systems,” Modeling the World’s Systems Conference (MWS) (poster and poster spotlight), May 2019.
  30. Sayed, K., Bocan, K.N., Telmer, C.A., and Miskov-Zivanov, N., “Stochastic Simulations of Hybrid Models with DiSH,” Modeling the World’s Systems Conference (MWS) (poster and poster spotlight), May 2019.
  31. Cascio, S., Kvorjak, M., Ahmed, Y., Miller, M., Al Hashash, J., Hartman, D., Miskov-Zivanov, N., Telmer, C.A., and Finn, O. J., “The cross-talk between infiltrating macrophages and inflamed or malignant colonic epithelium promotes overexpression of ST6GALNAC1 and epithelial MUC1 tumor form MUC1-sTn,” Annual Meeting of the American Association of Immunologists (AAI) (poster and talk), May 2019; abstract in Journal of Immunology 202(1_Supplement), pp. 135.5.
  32. Lomueller, J., Butchy, A.A., Tivon, Y., Kvorjak, M., Miskov-Zivanov, N., Deiters, A., and Finn, O. J., “Covalent adaptor synNotch and chimeric antigen receptors (CARs) for programmable antigen targeting,” Annual Meeting of the American Association of Immunologists (AAI) (poster and talk), May 2019; abstract in Journal of Immunology 202(1_Supplement), pp. 71.18. 
  33. Holtzapple, E., Cochran, B., and Miskov-Zivanov, N., “Modeling of glioblastoma stem cell kinase signaling—Toward personalized therapy,” Cold Spring Harbor Laboratory (CSHL) Meeting: Cellular Dynamics & Models (poster), April 2019.
  34. Hansen, C., Spirtes, P., Telmer, C.A., Bocan, K.N., Holtzapple, E., Ahmed, Y., Butchy, A.A., Sayed, K., and Miskov-Zivanov, N., “Interaction Classifier improves accuracy of fully automated model expansion,” Cold Spring Harbor (CSHL) Meeting: Cellular Dynamics & Models (poster), April 2019.
  35. Holtzapple, E., Miskov-Zivanov, N., Jahan, K., Zhang, Y., Young, S., and Cochran, B., “Computational modeling of glioblastoma stem cell signaling networks,” 23rd SNO Annual Neuro-Oncology Meeting (poster), November 2018; abstract in Journal of Neuro-oncology, 20(suppl_6), pp. vi45.
  36. Miskov-Zivanov, N., “DySE – Dynamic System Explanation Framework: Application in Cancer”, ISCB Rocky Mountain Bioinformatics Conference (ROCKY) (poster and short talk), December 2017.
  37. Butchy, A.A., Telmer, C.A., and Miskov-Zivanov, N., “Preliminary Validation of a Discrete Macrophage Model using Published Experimental Results,” BMES Annual Meeting (poster), October 2017.
  38. Holtzapple, E. and Miskov-Zivanov, N., “Automated identification of system properties from data,” q-bio Conference on Cellular Information Processing (poster), July 2017.
  39. Butchy, A.A., Telmer, C.A., and Miskov-Zivanov, N., Determining Bias in Macrophage Activation: How Strongly is the M2 Phenotype Favored?,” q-bio Conference on Cellular Information Processing (poster), July 2017.
  40. Sayed, K., Kuo. Y-S., and Miskov-Zivanov, N., DiSH simulator: Capturing dynamics of cellular signaling with heterogeneous knowledge,” q-bio Conference on Cellular Information Processing (poster), July 2017.
  41. Butchy, A.A. and Miskov-Zivanov, N., “Discrete modeling of macrophage differentiation,” Annual Meeting of the American Association of Immunologists (AAI) (poster), May 2017; abstract in Journal of Immunology, 198(1_Supplement), pp. 67.13.
  42. Sayed, K. and Miskov-Zivanov, N., “Automation of Delay Modeling for Cell Signaling Networks,” Cold Spring Harbor Laboratory (CSHL) Meeting: Cellular Dynamics & Models, (poster), April 2017. 
  43. Butchy, A.A. and Miskov-Zivanov, N., “Discrete model of macrophage differentiation and simulation of dynamic macrophage plasticity,” Cold Spring Harbor Laboratory (CSHL) Meeting: Cellular Dynamics & Models, (poster), April 2017.
  44. Butchy, A.A., Sayed, K., Liang, K.-W., Aidukaitis, B., Telmer, C.A., and Miskov-Zivanov, N., “Explaining the Cancer Microenvironment via Automated Literature Exploration,” Cold Spring Harbor Laboratory (CSHL) Meeting: Biological Data Science (poster), October 2016. 
  45. Lemmon-Kishi, M., Peddada, V., Chu, C., Perdoncin, M., Ni Chochlain, A., Antoszewski, L., Lohmueller, J., Miskov-Zivanov, N., Telmer, C.A., Shroff, S., and Deiters, A., “Thallium Detection Using Paper-Based Cell-Free Sensor Circuitry,” BMES Annual Meeting (poster), October 2016.

Other Publications

  1. Holtzapple, E., Zhou, G., Telmer, C.A., Hansen, C., Tang, D., Luo, H., and Miskov-Zivanov, N., “The BioRECIPE Representation Format,” Technical Report, University of Pittsburgh, D-Scholarship@Pitt, 2024.
Preprints
  1. Luo, H., Hansen, C.E., Telmer, C.A., Tang, D., Arazkhani, N., Zhou, G., Spirtes, P., and Miskov-Zivanov, N., “Context-driven interaction retrieval and classification for modeling, curation, and reuse,” bioRxiv, 2024. 
  2. Tang, D., Tam, T.Y.C., and Miskov-Zivanov, N., “An Open-Set Semi-Supervised Multi-Task Learning Framework for Context Classification in Biomedical Texts,” bioRxiv, 2024.
  3. Bocan, K.N. and Miskov-Zivanov, N., "Mixed-resolution hybrid modeling in an element-based framework," arXiv, 2024.
  4. Wittenberg, G. F., Fang, X., Roy, S., Lee, B., Miskov-Zivanov, N., Hochheiser, H.,  Banihashemi, L.,  Vesia, M.,  and Ramsey, J., “Representation and Retrieval of Brain Connectivity Information derived from TMS Experiments,” bioRxiv, 2023.
  5. Holtzapple, E., Cochran, B., and Miskov-Zivanov, N., “Automated verification, assembly, and extension of GBM stem cell network model with knowledge from literature and data,” bioRxiv, 2021.
  6. Butchy, A.A., Telmer C.A., and Miskov-Zivanov, N., “FIDDLE: Efficient Assembly of Networks That Satisfy Desired Behavior,” ResearchSquare, 2021.
  7. Ahmed, Y., Telmer C.A., and Miskov-Zivanov, N., “ACCORDION: clustering and selecting relevant data for guided network extension and query answering,” arXiv, 2020.
  8. Zhou, G., Liang, K.-W., and Miskov-Zivanov, N.,  “Intervention Pathway Discovery via Context-Dependent Dynamic Sensitivity Analysis,” arXiv, 2019.
Before 2016

Journal Papers
 

  1. Hawse, W.F., Sheehan, R.P., Miskov-Zivanov, N., Kane, L.P., Faeder, J.R., Morel, P.A., “Differential regulation of PTEN by TCR, Akt and FoxO1 controls CD4+ T cell fate decisions,” Journal of Immunology, 2015, 194(10), pp. 4615-4619.
  2. Morel, P.A., Faeder, J.R., Hawse, W.F., Miskov-Zivanov, N., “Modeling the T cell immune response: a fascinating challenge,” Journal of Pharmacokinetics and Pharmacodynamics, 2014, 41(5), pp. 401-413.
  3. Miskov-Zivanov, N., Turner, M.S., Kane, L.P., Morel, P.A., Faeder, J.R., “The duration of T cell stimulation is a critical determinant of cell fate and plasticity,” Science Signaling, 2013, 6(300), pp. ra97(16 pages), (podcast featuring publication: http://stke.sciencemag.org/cgi/content/full/sigtrans;6/300/pc29/DC1).
  4. Miskov-Zivanov, N. and Marculescu, D., “Multiple Transient Faults in Combinational and Sequential Circuits: A Systematic Approach,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2010, 29(10), pp. 1614-1627.
  5. Miskov-Zivanov, N. and Marculescu, D., “Modeling and Optimization for Soft-Error Reliability of Sequential Circuits,” 2008, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 27(5), pp. 803-816.
  6. Miskov-Zivanov, N. and Marculescu, D., “Circuit Reliability Analysis Using Symbolic Techniques,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2006, 25(12), pp. 2638-2649.

Conference Paper

  1. Kulkarni, A., Telmer, C.A., and Miskov-Zivanov, N., “Big Mechanism Design and Analysis Automation,” Proc. of the 7th International Workshop on Bio-Design Automation (IWBDA), August 2015, pp. 56-57.
  2. Miskov-Zivanov, N., “Automation of biological model learning, design and analysis,” Proc. of the 25th Great Lakes Symposium on VLSI (GLSVLSI), May 2015, pp. 327-329.
  3. Wang, Q., Miskov-Zivanov, N., Telmer, C.A., and Clarke, E.M., “Formal analysis provides parameters for guiding hyperoxidation in bacteria using phototoxic proteins,” Proc. of the 25th Great Lakes Symposium on VLSI (GLSVLSI), May 2015, pp. 315-320.
  4. Miskov-Zivanov, N., Wei, P.4, Loh, C.S.C.4, “THiMED: Time in Hierarchical Model Extraction and Design,” Proc. of the 12th International Conference on Computational Methods in Systems Biology (CMSB), November 2014, pp. 260-263.
  5. Miskov-Zivanov, N., Loh, C.S.C.4, Wei, P.4, and Faeder, J.R., “Delay modeling in cell signaling and gene regulatory networks,” Proc. of the 7th International Workshop on Bio-Design Automation (IWBDA), June 2014, pp. 28-29.
  6. Miskov-Zivanov, N., Zuliani, P., Clarke, E.M., and Faeder, J.R., "Studies of biological networks with statistical model checking: application to immune system cells," Proc. of the 4th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), September 2013, pp. 728-729.
  7. Miskov-Zivanov, N., Marculescu, D., and Faeder, J.R., "Dynamic behavior of cell signaling networks: model design and analysis automation." Proc. of the 50th Design Automation Conference (DAC), June 2013, pp. 1-6.
  8. Miskov-Zivanov, N., Faeder, J. R., Myers, C. J., and Sauro, H. M., "Modeling and design automation of biological circuits and systems," Proc. of the International Conference of Computer-Aided Design (ICCAD), November 2012, pp. 291-293.
  9. Zuliani, P., Miskov-Zivanov, N., Morel, P., Faeder, J. R., and Clarke, E.M., “Model checking for studying timing of events in T cell differentiation,” Proc. of the 4th International Workshop on Bio-Design Automation (IWBDA), June 2012, pp. 29-30.
  10. Miskov-Zivanov, N., Bresticker, A., Krishnaswamy, D., Venkatakrishnan, S., Kashinkunti, P., Marculescu, D., and Faeder, J.R., "Regulatory Network Analysis Acceleration with Reconfigurable Hardware," Proc. of the 33rd IEEE Engineering in Medicine and Biology Society (EMBC), September 2011, pp. 149-152.
  11. Miskov-Zivanov, N., Bresticker, A., Krishnaswamy, D., Venkatakrishnan, S., Marculescu, D., and Faeder, J.R., "Emulation of Biological Networks in Reconfigurable Hardware," Proc. of the 2nd ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), August 2011, pp. 536-540.
  12. Miskov-Zivanov, N., Bresticker, A., Krishnaswamy, D., Venkatakrishnan, S., Marculescu, D., and Faeder, J.R., “Biological Network Emulation in FPGA,” Proc. of the 3rd International Workshop on Bio-Design Automation (IWBDA), June 2011, pp. 34-35.
  13. Miskov-Zivanov, N., and Marculescu, D., “Formal Modeling and Reasoning for Reliability Analysis,” in Proc. of the 47th Design Automation Conference (DAC), June 2010, pp. 531-536 (invited paper).
  14. Miskov-Zivanov, N., Sekar, J., Turner, M., Kane, L., Morel, P., and Faeder, J.R., “Logical Modeling of Peripheral T Cell Differentiation,” Proc. of the 2nd International Workshop on Bio-Design Automation (IWBDA), June 2010, pp. 73-74.
  15. Miskov-Zivanov, N., and Marculescu, D., “Modeling and Analysis of SER in Combinational Circuits,” Proc. of the IEEE Workshop on Silicon Errors in Logic – System Effects (SELSE), March 2010, 6 pages, (invited paper).
  16. Miskov-Zivanov, N. and Marculescu, D., “A Systematic Approach to Modeling and Analysis of Transient Faults in Logic Circuits,” Proc. of the 10th IEEE International Symposium on Quality Electronic Design (ISQED), 2009, pp. 408-413, (accepted in 2008, published in 2009, due to publisher error).
  17. Miskov-Zivanov, N., Wu, K.-C., and Marculescu, D., “Process Variability-Aware Transient Fault Modeling  and Analysis,” Proc. of the IEEE/ACM International Conference on Computer-Aided Design (ICCAD), November 2008, pp. 685-690.
  18. Miskov-Zivanov, N. and Marculescu, D., “Soft Error Rate Analysis for Sequential Circuits,” Proc. of Design, Automation and Test in Europe (DATE), April 2007, pp. 1436-1441, (listed in ten years of DATE under honors).
  19. Miskov-Zivanov, N. and Marculescu, D., “MARS-S: Modeling and Reduction of Soft Errors in Sequential Circuits,” Proc. of the 8th IEEE International Symposium on Quality Electronic Design (ISQED), March 2007, pp. 893-898, (Best Paper Award nomination).
  20. Miskov-Zivanov, N. and Marculescu, D., “MARS-C: Modeling and Reduction of Soft Errors in Combinational Circuits,” Proc. of the 43rd Design Automation Conference (DAC), July 2006, pp. 767-772.
  21. Miskov-Zivanov, N. and Marculescu, D., “Circuit Reliability Analysis Using Symbolic Techniques,” Proc. of the International Workshop on Logic and Synthesis (IWLS), June 2005.
  22. Jelicic, Z.D., Miskov, N., and Petrovacki, D., “Extended LQR control for first-order plus time-delay system,” Proc. of the International Symposium on Interdisciplinary Regional Research (Hungary, Romania, Serbia), Novi Sad, Serbia, 2002.

Abstracts

  1. Miskov-Zivanov, N., Lukchart, S., Vodovotz, Y., and Faeder, J. R., “Computational model of immune crosstalk in malaria suggests key mechanisms of parasite killing in mosquitoes,” Systems Biology of Infectious Disease, 2014.
  2. Miskov-Zivanov, N., Hawse, W., Kane, L.P., Morel, P.A., and Faeder, J.R., “Signal Processing Modulation via Duration of Cell Receptor Contact: Application to the Control of T Cell Differentiation,” BMES Annual Meeting (poster accepted, withdrawn), 2014.
  3. Miskov-Zivanov, N., Hawse, W., Morel, P.A., and Faeder, J.R., “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) (poster), May 2014; abstract in Journal of Immunology, 192(1_Supplement), pp. 63.1.
  4. Hawse, W., Miskov-Zivanov, N., Morel, P.A., and Faeder, J.R., “PTEN Regulates CD4+ T cell differentiation,” Annual Meeting of the American Association of Immunologists (AAI) (poster), May 2014; abstract in Journal of Immunology, 192(1_Supplement), pp. 63.8.
  5. Miskov-Zivanov, N., Turner, M.S., Kane, L. P., Morel, P.A., and Faeder, J.R. “Model predicts timing of T cell stimulation is critical for T cell fate,” Cold Spring Harbor Laboratory (CSHL) Meeting: Computational Cell Biology (poster), March 2013.
  6. Miskov-Zivanov, N., Luckhart, S., Vodovotz, Y., Marculescu, D., and Faeder, J.R., “Circuit design techniques for automated construction of mosquito immune response model in malaria infection,” Cold Spring Harbor Laboratory (CSHL) Meeting: Computational Cell Biology (poster), March 2013.
  7. Miskov-Zivanov, N., Zuliani, P., Morel, P.A., Clarke, E., and Faeder, J.R., “Model checking for studying temporal behavior in cell differentiation,” q-bio Conference on Cellular Information Processing (poster), August 2012.
  8. Miskov-Zivanov, N., Marculescu, D., Morel, P., and Faeder, J.R., “Automating the construction of discrete models of biological systems,” q-bio Conference on Cellular Information Processing (poster), August 2011.
  9. Miskov-Zivanov, N., Bresticker, A., Krishnaswamy, D., Venkatakrishnan, S., Marculescu, D., and Faeder, J.R., “Emulation of Biological Networks in Reconfigurable Hardware,” Cold Spring Harbor Laboratory (CSHL) Meeting: Computational Cell Biology (poster), March 2011.
  10. Miskov-Zivanov, N., Turner, M.S., Morel, P.A. and Faeder, J. R. “T cell differentiation modeling and analysis through circuit design,” Cold Spring Harbor Laboratory (CSHL) Meeting: Computational Cell Biology (talk), March 2011.
  11. Miskov-Zivanov, N., Turner, M.S., Morel, P.A. and Faeder, J.R. “Peripheral T Cell Differentiation Modeling,” 14th Annual Meeting of the Translational Research Cancer Centers Consortium (TRC3), February 2011.
  12. Miskov-Zivanov, N., Sekar, J., Turner, M., Kane, L., Morel, P.A., and Faeder, J.R., “Modeling of Peripheral T Cell Differentiation,” q-bio Conference on Cellular Information Processing (talk), August 2010.
  13. Miskov-Zivanov, N., Sekar, J., Turner, M., Morel, P.A., and Faeder, J.R., “Logical model of the differentiation of naïve T cells into regulatory and effector cells,” SIAM Conference on the Life Sciences (LS), July 2010.
  14. Sekar, J., Miskov-Zivanov, N., Morel, P.A., Turner, M., and Faeder, J.R., “Modeling of the peripheral naïve T-cell differentiation,” Annual Meeting of the American Association of Immunologists (AAI) (poster), May 2010; abstract in Journal of Immunology, 184(1_Supplement), 36.52.

Other Publications

  1. Bleris, L., Miskov-Zivanov, N. and Myers, C.J., “IWBDA 2012 Special Issue,” ACS Synthetic Biology, 2(5), May 2013, pp. 203, Editorial (podcast: http://pubs.acs.org/page/asbcd6/audio/index.html).
  2. Fey, G., Fujita, M., Miskov-Zivanov, N., Roy, K., Sonza Reorda, M., “Verifying Reliability,” Dagstuhl Seminar Reports, 2(8), August 2012, pp. 57-73.
  3. Miskov-Zivanov, N., “Design automation tools for biological systems and biologically-inspired computing,” What is? Column in ACM SIGDA E-Newsletter, Invited Article, December 2011.