My research interests are in modeling and analyzing complex systems (including biological systems and reactive software) using formal reasoning and synthesis methods. I am also interested in the application of visual languages to model the behavior of reactive systems. I work on development of new computational methods and tools towards enabling a deeper understanding of biological computation.

For Students and Postdocs:

מתענינים בחישוב ביולוגי, כלים מתקדמים לניתוח תוכנה, אימות של מערכות מורכבות או פתרון חידות מתמטיות? צרו קשר לבדוק אפשרות להשתלב במחקר לתארים מתקדמים או בפרויקט בתואר ראשון

I am currently looking for talented and highly motivated students and postdocs, if you are interested please email me with a CV to hillelk at

Selected Publications:

M. Aluf-Medina, T. Korten, A. Raviv, D.V. Nicolau Jr. and H. Kugler. Formal Semantics and Verification of Network-Based Biocomputation Circuits. To appear, VMCAI'21, 2021.

H. Kugler, S-J. Dunn, and B. Yordanov. Formal Analysis of Network Motifs. CMSB'18, 2018.

B. Yordanov, S-J. Dunn, H. Kugler, A. Smith, G. Martello and S. Emmott. A Method to Identify and Analyze Biological Programs through Automated Reasoning, in npj Systems Biology and Applications, Nature Publishing Group, 2016

K. Atwell, Z. Qin, D. Gavaghan, H. Kugler, E.J.A. Hubbard, and J.M. Osborne  Mechano-logical model of C. elegans germ line suggests feedback on the cell cycle, in Development, Advanced Onlne Article, October 2015.

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

N. Paoletti, B. Yordanov, Y. Hamadi, C.M. Wintersteiger, and H. Kugler, Analyzing and Synthesizing Genomic Logic Functions, in CAV'14, Springer,  2014.

B. Yordanov, C.M.  Wintersteiger, Y. Hamadi, and H.Kugler, SMT-based Analysis of Biological Computation, in NASA Formal Methods Symposium 2013, Springer Verlag, 2013.

B.  Yordanov, C.M. Wintersteiger, Y. Hamadi, A. Phillips, and H. Kugler, Functional Analysis of Large-scale DNA Strand Displacement Circuits, in International Conference on DNA Computing and Molecular Programming, vol. 8141, pp. 189-203, Springer, 2013

Y. Setty, D.Dalfó, D.Z. Korta, EJA. Hubbard, and H. Kugler, A model of stem cell population dynamics: in-silico analysis and in-vivo validation, in Development, vol. 139,  2012.

H. Kugler, C. Plock, and A. Roberts, Synthesizing Biological Theories, in Computer Aided Verification (CAV'11), Springer Verlag, July 2011.

H. Kugler, C. Plock, and A. Pnueli, Controller Synthesis from LSC Requirements, in Fundamental Approaches to Software Engineering (FASE'09), Springer Verlag, March 2009.

Kam N, Kugler H, Marelly R, Appleby L, Fisher J, 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 , in Developmental Biology, vol. 323, no. 1, Elsevier ,  2008.