##### Publications

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.