Yishai Shimoni

Yishai Shimoni


Research Scientist, IBM

Yishai Shimoni is an associate research scientist in the Califano Lab whose research focuses on gene regulatory networks and how they control phenotypes in several contexts. In one project he has helped to develop methods for comparing cellular phenotypes before and after treatment by a compound, enabling the identification of the compound's mechanism of action. In another context he has compared phenotypes in cancer (for example relapse vs. long survival) in order to identify genes that can control the difference in phenotype.

Yishai received training in physics and computer science at the Hebrew University in Israel, where he did his PhD in quantum computation, performing detailed simulations of quantum systems and quantum computers. He moved into the field of computational biology in 2007, performing stochastic simulations of small regulatory networks that provided one of the first quantitative analyses of regulation by small non-coding RNAs. In postdoctoral studies at Mount Sinai School of Medicine he extended his stochastic simulations to include a population of immune cells when infected by a virus, showing how the variability in response within a population of cells leads to a robust and controlled response.

Education History

PhD, The Hebrew University, Israel

MSc, The Hebrew University, Israel

BSc, The Hebrew University, Israel
Physics and Computer Science


Woo JH, Shimoni Y, Yang WS, Subramaniam P, Iyer A, Nicoletti P, Rodríguez Martínez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A. Elucidating compound mechanism of action by network perturbation analysis. Cell. 2015 Jul 16;162(2):441-51. 

The FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70.

Bilal E*, Dutkowski J*, Guinney J*, Jang IS*, Logsdon BA*, Pandey G*, Sauerwine BA*, Shimoni Y*, et al. Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol. 2013;9(5):e1003047. 

Shimoni Y*, Nudelman G*, Hayot F, Sealfon SC. Multi-scale stochastic simulation of diffusion-coupled agents and its application to cell culture simulation. PLoS One. 2011;6(12):e29298. 

Hu J, Nudelman G, Shimoni Y, Kumar M, Ding Y, López C, Hayot F, Wetmur JG, Sealfon SC. Role of cell-to-cell variability in activating a positive feedback antiviral response in human dendritic cells. PLoS One. 2011 Feb 8;6(2):e16614.

Shimoni Y*, Fink MY*, Choi SG, Sealfon SC. Plato's cave algorithm: inferring functional signaling networks from early gene expression shadowsPLoS Comput Biol. 2010 Jun 24;6(6):e1000828. 

Shimoni Y, Altuvia S, Margalit H, Biham O. Stochastic analysis of the SOS response in Escherichia coli. PPLoS One. 2009;4(5):e5363. 

Shimoni Y, Friedlander G, Hetzroni G, Niv G, Altuvia S, Biham O, Margalit H. Regulation of gene expression by small non-coding RNAs: A quantitative view. Mol Syst Biol. 2007;3:138. 

Publications on quantum computation

Most Y, Shimoni Y, Biham O. Entanglement of periodic states, the quantum Fourier transform and Shor's factoring algorithm. Phys Rev A. 2010;81(5):052306.

Most Y, Shimoni Y, Biham O. Formation of multipartite entanglement using random quantum gates. Phys Rev A. 2007;76(2):022328.

Shimoni Y, Biham O. Groverian entanglement measure of pure quantum states with arbitrary partitions. Phys Rev A. 2007;75(2):022308.

Shapira D,  Shimoni Y, Biham O. Groverian measure of entanglement for mixed states. Phys Rev A. 2006;73(4):044301.

Shimoni Y, Biham O. Entangled quantum states generated by Shor's factoring algorithm. Phys Rev A. 2005;72(6):062308.

Shapira D,  Shimoni Y, Biham O. Algebraic analysis of quantum search with pure and mixed states. Phys Rev A. 2005;71(4):042320.

Shimoni Y, Shapira D,  Biham O. Characterization of pure quantum states of multiple qubits using the Groverian entanglement measure. Phys Rev A. 2004;69(6):062303.

Biham O, Shapira D,  Shimoni Y. Analysis of Grover's quantum search algorithm as a dynamical system. Phys Rev A. 2003;68(2):022326.