{"id":18,"date":"2015-08-06T20:40:30","date_gmt":"2015-08-06T17:40:30","guid":{"rendered":"http:\/\/www.eng.biu.ac.il\/hillelk\/?page_id=18"},"modified":"2026-06-11T11:21:37","modified_gmt":"2026-06-11T08:21:37","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.eng.biu.ac.il\/hillelk\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
Publications<\/h5>\n

Avraham Raviv,\u00a0 Yizhak Y. Elboher,\u00a0Omri Isac, Michelle Aluf-Medina, Ben Hagag, Golan Shmueli, Guy Katz and Hillel Kugler. Towards Formal Verification of Deep Neural Networks for Object Detection. NFM26<\/a>\u00a0, 2026.<\/p>\n

Y. Gerber, et al.\u00a0 Reasoning about monotonic regulation conditions<\/a> BIBM'25<\/p>\n

E. Tannenbaum, D. Markiewitz, T. Kalisky and H. Kugler. Characterizing Gene Regulatory Network Ensembles in Kidney Injury and Repair \u00a0<\/a>ACM-BCB'25, Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2025.<\/p>\n

A. Raviv, Y. Gerber, L. Benzinou, M. Aluf-Medina and Hillel Kugler. Prediction and Control of Stochastic Agents Using Formal Methods. FoMLAS23, 2023.<\/em><\/p>\n

A. Raviv, M. Aluf-Medina, E. Bronshtein, O. Reginiano, and H. Kugler.\u00a0 Learning Through Imitation by Using Formal Verification.\u00a0 SOFSEM'23<\/em>, 2023.<\/p>\n

B. Yordanov, S-J Dunn, C. Gravill, H. Kugler and C.M. Wintersteiger.\u00a0 An SMT-based Framework for Reasoning about Discrete Biological Models<\/a>. ISBRA'22<\/em>, 2022. (Appendix<\/a>)<\/p>\n

A. <\/span>Amar, <\/span><\/span><\/a>E. Jane Albert <\/span>Hubbard and <\/span><\/span><\/span>H. <\/span>Kugler. <\/span><\/span><\/span>Modeling the\u00a0C<\/em>.\u00a0elegans<\/em>\u00a0Germline Stem Cell Genetic Network using Automated Reasoning<\/a>.\u00a0 Biosystems<\/em>, 2022.<\/p>\n

F. van Delft<\/span>,\u00a0A. M\u00e5nsson<\/span>,\u00a0H. Kugler<\/span>,\u00a0T. Korten<\/span>,\u00a0C. Reuther<\/span>,\u00a0J. Zhu<\/span>,\u00a0R. Lyttleton<\/span>,\u00a0T. Blaudeck<\/span>,\u00a0C. R. Meinecke<\/span>,\u00a0D. Reuter<\/span>,\u00a0S. Diez<\/span>\u00a0and\u00a0H. Linke. Roadmap for network-based biocomputation<\/a>.\u00a0 Nano Futures<\/em>\u00a06<\/b> 032002, 2022.<\/span><\/span><\/span><\/p>\n

J. Zhu, A. Salhotra, C.R. Meinecke, P. Surendiran, R. Lyttleton, D. Reuter, H. Kugler, S. Diez, A. M\u00e5nsson, H. Linke, T. Korten. Solving the 3\u2010Satisfiability Problem Using Network\u2010Based Biocomputation.<\/a> Advanced Intelligent Systems<\/em>, 2022.<\/p>\n

P. Surendiran,<\/em> C.R Meinecke, A. Salhotra, G. Heldt, J. Zhu, A. M\u00e5nsson, S. Diez, D. Reuter, H. Kugler, H. Linke, T. Korten. Solving Exact Cover Instances with Molecular-Motor-Powered Network-Based Biocomputation<\/a>. ACS Nanoscience Au<\/em>, 2022.<\/p>\n

J. Zhu, T. Korten, H. Kugler, F. Van Delft, A. M\u00e5nsson, D. Reuter, S. Diez, H. Linke.\u00a0 Physical requirements for scaling up network-based biocomputation<\/a> New J. Phys.<\/em>\u00a023<\/b> 105004, 2021.<\/p>\n

T Korten, S Diez, H Linke, DV Nicolau, H and Kugler. Design of network-based biocomputation circuits for the exact cover problem<\/a>. New J.\u00a0 Physics<\/em> 23 (8), 085004, 2021.<\/p>\n

M. Aluf-Medina, T. Korten, A. Raviv, D.V. Nicolau Jr. and H. Kugler. Formal Semantics and Verification of Network-Based Biocomputation Circuits<\/a>.\u00a0 VMCAI'21<\/em>, 2021.<\/p>\n

A. Occhipinti, Y. Hamadi, H. Kugler, C.M. Wintersteiger, B. Yordanov and C. Angione. Discovering Essential Multiple Gene Effects through Large Scale Optimization: an Application to Human Cancer Metabolism<\/a>. IEEE TCBB<\/em>, 2020.<\/p>\n

\u00a0S-J. Dunn, H. Kugler and B. Yordanov. <\/span>Formal Analysis of Network Motifs Links Structure to Function in Biological Programs.<\/a> IEEE TCBB<\/em>, 2021.\u00a0<\/span><\/p>\n

J.\u00a0Goldfeder and H. Kugler. <\/span>BRE:IN - A Backend for Reasoning About Interaction Networks with Temporal Logic. CMSB<\/em>'19,\u00a0 2019.<\/span><\/p>\n

T. Munk, H. Kugler, O. Maori and A. Teman. TEMPO: Thermal-efficient Management of Power in High-Throughput Network Switches. VLSI-DAT'19, 2019.<\/p>\n

J.\u00a0Goldfeder and H. Kugler. Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks.\u00a0 MLCSB<\/em>'18, 2018.<\/p>\n

D. Fisman and H. Kugler.\u00a0 Temporal Reasoning on Incomplete Paths<\/a>. ISOLA<\/em>'18, 2018.\u00a0 (pdf)<\/a><\/p>\n

H. Kugler, S-J. Dunn, and B. Yordanov. Formal Analysis of Network Motifs<\/a>. CMSB<\/em>'18,\u00a0 2018. (PDF)<\/a><\/p>\n

H. Kugler. Explainable Verification-Based Approaches in Systems Biology.\u00a0FEVER'17, 2017.<\/em><\/p>\n

K. Atwell, S-J. Dunn, J.M. Osborne, H. Kugler and E.J.A. Hubbard. How computational models contribute to our understanding of the grem line<\/a>, in Molecular Reproduction and<\/em>\u00a0Development<\/span><\/i>, September 2016.<\/p>\n

B. Yordanov, S-J. Dunn, H. Kugler, A. Smith, G. Martello and S.\u00a0Emmott.\u00a0A Method to Identify and Analyze Biological Programs through\u00a0Automated Reasoning<\/a>,\u00a0in npj\u00a0Systems Biology and Applications, <\/em>Nature Publishing Group, 2016. <\/em>(PDF)<\/a><\/p>\n

Y. Shavit, B. Yordanov, S-J. Dunn, C.M. Wintersteiger, T. Otani, Y. Hamadi, F.J. Livesey \u00a0and H. Kugler. Automated Synthesis and Analysis of Switching Gene Regulatory Network<\/a>s, in BioSystems, 2016.<\/p>\n

K. Atwell, Z. Qin, D. Gavaghan, H. Kugler, E.J.A. Hubbard and J.M. Osborne \u00a0Mechano-logical model of C. elegans germ line suggests feedback on the cell cycle<\/a>, in Development<\/span><\/i>, 142: 3902-3911, October 2015. (PDF)<\/a><\/p>\n

Y. Shavit, B. Yordanov, S-J. Dunn, C.M. Wintersteiger, Y. Hamadi and H. Kugler, Switching Gene Regulatory Networks<\/a>, in 10th International Conference on Information Processing in Cells and Tissues (IPCAT 2015)<\/i>, Springer, September 2015. (PDF)<\/a><\/p>\n

N. Paoletti, B. Yordanov, Y. Hamadi, C.M. Wintersteiger and Hillel Kugler, Analyzing and Synthesizing Genomic Logic Functions<\/a>, in 26th International Conference<\/span> on Computer Aided Verification<\/span> (CAV'14),<\/em> Springer, July 2014. (PDF)<\/a><\/p>\n

M.N. Rabe, C.M. Wintersteiger, H. Kugler<\/span>, B. Yordanov and Y. Hamadi. Symbolic Approximation of the Bounded Reachability Probability in Large Markov Chains<\/a>, in Quantitative Evaluation of Systems (QEST'14),<\/em> LNCS vol. 8657, pp<\/span>\u00a0388-403, 2014. (PDF)<\/a><\/p>\n

B. Yordanov, C.M. Wintersteiger, Y. Hamadi, A. Phillips and H. Kugler, <\/span>Functional Analysis of Large-scale DNA Strand Displacement Circuits<\/span><\/u><\/a>, in <\/span>International Conference on DNA Computing and Molecular Programming<\/i>, LNCS vol. 8141, pp. 189-203, Springer, September 2013. (PDF)<\/a><\/span><\/p>\n

B. Yordanov, C.M. Wintersteiger, Y. Hamadi and H. Kugler, SMT-based Analysis of Biological Computation<\/a>, in NASA Formal Methods Symposium (NFM'13)<\/i>, Springer Verlag, May 2013.<\/p>\n

H. Kugler, <\/span>Biocharts: Unifying Biological Hypotheses with Models and Experiments, in 9th IEEE International Conference on eScience<\/em>, pp<\/span>\u00a0317-325, 2013.<\/p>\n

H. Kugler,\u00a0 <\/span>Runtime Verification and Refutation for Biological Systems, in\u00a04th International Conference on Runtime Verification (RV'13), <\/em>LNCS vol. 8174, Springer, 2013.<\/span><\/p>\n

Y. Setty, D. Dalf\u00f3, D.Z. Korta, E.J.A. Hubbard and H. Kugler, A model of stem cell population dynamics: in-silico analysis and in-vivo validation<\/a>, in Development<\/i>, 139: 47-56, January 2012.<\/p>\n

H. Kugler, C. Plock, and A. Roberts, Synthesizing Biological Theories<\/a>, in Computer Aided Verification (CAV'11)<\/i>, Springer Verlag, July 2011.<\/p>\n

A. Milicevic, H. Kugler, <\/span>Model Checking Using SMT and Theory of Lists, in 3rd International symposium on NASA Formal Methods (NFM'11), <\/em>LNCS vol. 6617, <\/em>pp<\/span>\u00a0282-297, Springer, 2011.<\/p>\n

H. Kugler, C. Plock, and A. Pnueli, Controller Synthesis from LSC Requirements<\/a>, in Fundamental Approaches to Software Engineering (FASE'09)<\/i>, Springer Verlag, March 2009.<\/p>\n

N. Kam, H. Kugler, R. Marelly, L. Appleby, J. Fisher, A. Pnueli, D. Harel, M.J. Stern, and E.J.A. Hubbard, A scenario-based approach to modeling development: A prototype model of C. elegans vulval fate specification <\/a>, in Developmental Biology<\/i>, vol. 323, no. 1, pp. 1-5, Elsevier , August 2008.<\/p>\n

<\/div>\n","protected":false},"excerpt":{"rendered":"

Publications Avraham Raviv,\u00a0 Yizhak Y. Elboher,\u00a0Omri Isac, Michelle Aluf-Medina, Ben Hagag, Golan Shmueli, Guy Katz and Hillel Kugler. Towards Formal Verification of Deep Neural Networks for Object Detection. NFM26\u00a0, 2026. Y. Gerber, et al.\u00a0 Reasoning about monotonic regulation conditions BIBM’25 E. Tannenbaum, D. Markiewitz, T. Kalisky and H. Kugler. Characterizing Gene Regulatory Network Ensembles in … Continue reading Publications<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":60,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-18","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.eng.biu.ac.il\/hillelk\/wp-json\/wp\/v2\/pages\/18"}],"collection":[{"href":"https:\/\/www.eng.biu.ac.il\/hillelk\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.eng.biu.ac.il\/hillelk\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.eng.biu.ac.il\/hillelk\/wp-json\/wp\/v2\/users\/60"}],"replies":[{"embeddable":true,"href":"https:\/\/www.eng.biu.ac.il\/hillelk\/wp-json\/wp\/v2\/comments?post=18"}],"version-history":[{"count":71,"href":"https:\/\/www.eng.biu.ac.il\/hillelk\/wp-json\/wp\/v2\/pages\/18\/revisions"}],"predecessor-version":[{"id":303,"href":"https:\/\/www.eng.biu.ac.il\/hillelk\/wp-json\/wp\/v2\/pages\/18\/revisions\/303"}],"wp:attachment":[{"href":"https:\/\/www.eng.biu.ac.il\/hillelk\/wp-json\/wp\/v2\/media?parent=18"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}