T Korten, S Diez, H Linke, DV Nicolau, H and Kugler. Design of network-based biocomputation circuits for the exact cover problem. New Journal of Physics 23 (8), 085004, 2021.

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

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. IEEE TCBB, 2020.

 S-J. Dunn, H. Kugler and B. Yordanov. Formal Analysis of Network Motifs Links Structure to Function in Biological Programs. IEEE TCBB, 2021. 

J. Goldfeder and H. Kugler. BRE:IN - A Backend for Reasoning About Interaction Networks with Temporal Logic. CMSB'19,  2019.

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

J. Goldfeder and H. Kugler. Temporal Logic Based Synthesis of Experimentally Constrained Interaction Networks.  MLCSB'18, 2018.

D. Fisman and H. Kugler.  Temporal Reasoning on Incomplete Paths. ISOLA'18, 2018.  (pdf)

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

H. Kugler. Explainable Verification-Based Approaches in Systems Biology. FEVER'17, 2017.

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, in Molecular Reproduction and , September 2016.

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. (PDF)

Y. Shavit, B. Yordanov, S-J. Dunn, C.M. Wintersteiger, T. Otani, Y. Hamadi, F.J. Livesey  and H. Kugler. Automated Synthesis and Analysis of Switching Gene Regulatory Networks, in BioSystems, 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 , 142: 3902-3911, October 2015. (PDF)

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. (PDF)

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

M.N. Rabe, C.M. Wintersteiger, H. Kugler, B. Yordanov and Y. Hamadi. Symbolic Approximation of the Bounded Reachability Probability in Large Markov Chains, in Quantitative Evaluation of Systems (QEST'14), LNCS vol. 8657, pp 388-403, 2014. (PDF)

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, LNCS vol. 8141, pp. 189-203, Springer, September 2013. (PDF)

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

H. Kugler, Biocharts: Unifying Biological Hypotheses with Models and Experiments, in 9th IEEE International Conference on eScience, pp 317-325, 2013.

H. Kugler,  Runtime Verification and Refutation for Biological Systems, in 4th International Conference on Runtime Verification (RV'13), LNCS vol. 8174, Springer, 2013.

Y. Setty, D. Dalfó, D.Z. Korta, E.J.A. Hubbard,and H. Kugler, A model of stem cell population dynamics: in-silico analysis and in-vivo validation, in Development, 139: 47-56, January 2012.

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

A. Milicevic, H. Kugler, Model Checking Using SMT and Theory of Lists, in 3rd International symposium on NASA Formal Methods (NFM'11), LNCS vol. 6617, pp 282-297, Springer, 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.

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 , in Developmental Biology, vol. 323, no. 1, pp. 1-5, Elsevier , August 2008.