Yishai Shimoni : publications

Computational Biology

1. Highly conserved ceRNA regulatory interactions cooperate with genomic variability to modulate drivers of tumorigenesis
   H. Chiu, X. Yang, M. R. Martinez, et al.
   Nature Biotechnology, in review
2. Elucidating Compound Mechanism of Action by Network Dysregulation Analysis in Perturbed Cells
   J. H. Woo^*, Y. Shimoni^*, W. S. Yang^*, et al.
   Cell 162(2), p441-451. doi:10.1016/j.cell.2015.05.056 (2015)
3. Stochastic Analysis of Bistability in Coherent Mixed Feedback Loops Combining Transcriptional and Post-Transcriptional Regulations
   M. Nitzan^*, Y. Shimoni^*, O. Rosolio, H. Margalit, and O. Biham
   Phys. Rev. E 91, 052706. doi:10.1103/PhysRevE.91.052706 (2015)  [  arXiv:1412.0986 [q-bio.MN]  ]
4. A promoter-level mammalian expression atlas
   The FANTOM Consortium and the RIKEN PMI and CLST (DGT)
   Nature 507, 462.470 doi:10.1038/nature13182 (2014)
5. Improving Breast Cancer Survival Analysis through Competition-based Multidimensional Modeling
   E. Bilal^*, J. Dutkowski^*, J. Guinney^*, I. S. Jang^*, B. A. Logsdon^*, G. Pandey^*, B. Sauerwine^*, Y. Shimoni^*, et al.
   PLoS Comput Biol 9(5): e1003047. doi:10.1371/journal.pcbi.1003047 (2013)
6. Multi-scale stochastic simulation of diffusion-coupled agents and its application to cell culture simulation
   Y. Shimoni^*, G. Nudelman^*, F. Hayot, and S. C. Sealfon
   PLoS ONE 6(12): e29298. doi:10.1371/journal.pone.0029298 (2011)
7. Role of Cell-to-Cell Variability in Activating a Positive Feedback Antiviral Response in Human Dendritic Cells.
   J. Hu, G. Nudelman, Y. Shimoni, C. B. López, M. Kumar, Y. Ding, F. Hayot, J. G. Wetmur, and S. C. Sealfon
   PLoS ONE 6(2): e16614. doi:10.1371/journal.pone.0016614 (2011)
8. Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows
   Y. Shimoni^*, M. Y. Fink^*, Soon-Gang Choi, and S. C. Sealfon
   PLoS Comput Biol 6(6): e1000828. doi:10.1371/journal.pcbi.1000828 (2010)
9. Stochastic Analysis of the SOS Response in Escherichia coli
   Y. Shimoni, S. Altuvia, H. Margalit, and O. Biham
   PLoS ONE 4(5): e5363 doi:10.1371/journal.pone.0005363 (2009)
10. Regulation of gene expression by small non-coding RNAs: A quantitative view
    Y. Shimoni, G. Friedlander, G. Hetzroni, G. Niv, S. Altuvia, O. Biham, and H. Margalit
    Molecular Systems Biology 3:138 (2007)

Quantum Computation

1. Entanglement of periodic states, the quantum Fourier transform and Shor's factoring algorithm
   Y. Most, Y. Shimoni, and O. Biham
   Phys. Rev. A 81, 052306 (2010)  [  arXiv:1001.3145v1[quant-ph]  ]
2. Formation of multipartite entanglement using random quantum gates
   Y. Most, Y. Shimoni, and O. Biham
   Phys. Rev. A 76, 022328 (2007)  [  arXiv:0708.3481[quant-ph]  ]
   The paper also appeared in the Virutal Journal of Quantum Information 7(9), 2009.
3. Groverian entanglement measure of pure quantum states with arbitrary partitions 
   Y. Shimoni and O. Biham
   Phys. Rev. A 75, 022308 (2007)  [  arXiv:quant-ph/0702179  ]
   The paper also appeared in the Virutal Journal of Quantum Information 7(2), 2009.
4. Groverian measure of entanglement for mixed states
   D. Shapira, Y. Shimoni and O. Biham
   Phys. Rev A. 73, 044301 (2006)  [   arXiv:quant-ph/0508108 ]
5. Entangled quantum states generated by Shor's factoring algorithm
   Y. Shimoni and O. Biham
   Phys Rev A. 72, 062308 (2005)  [   arXiv:quant-ph/0510042  ]
6. Algebraic analysis of quantum search with pure and mixed states
   D. Shapira, Y. Shimoni and O. Biham
   Phys. Rev. A 71, 042320 (2005)  [   arXiv:quant-ph/0504149  ]
7. Characterization of pure quantum states of multiple qubits using the Groverian entanglement measure
   Y. Shimoni, D. Shapira, and O. Biham
   Phys. Rev. A 69, 062303 (2004)  [   arXiv:quant-ph/0309062  ]
8. Analysis of Grover's quantum search algorithm as a dynamical system
   O. Biham, D. Shapira, and Y. Shimoni
   Phys. Rev. A 68, 022326 (2003)  [   arXiv:quant-ph/0307141  ]