Yishai Shimoni  Yishai Shimoni photo         

contact information

Manager, Machine Learning for Healthcare and Life Sciences
Haifa Research Lab, Haifa, Israel



A discriminative approach for finding and characterizing positivity violations using decision trees
Ehud Karavani, Peter Bak, Yishai Shimoni
arXiv preprint arXiv:1907.08127, 2019

Y Shimoni, S Ravid, P Bak, E Karavani, S Hensley Alford, D Meade, Y Goldschmidt
Value in Health22, S389, Elsevier, 2019

An Evaluation Toolkit to Guide Model Selection and Cohort Definition in Causal Inference
Yishai Shimoni, Ehud Karavani, Sivan Ravid, Peter Bak, Tan Hung Ng, Sharon Hensley Alford, Denise Meade, Yaara Goldschmidt
arXiv preprint arXiv:1906.00442, 2019

Comment: Causal Inference Competitions: Where Should We Aim?
Ehud Karavani, Tal El-Hay, Yishai Shimoni, Chen Yanover, others
Statistical Science 34(1), 86--89, Institute of Mathematical Statistics, 2019


Benchmarking framework for performance-evaluation of causal inference analysis
Yishai Shimoni, Chen Yanover, Ehud Karavani, Yaara Goldschmnidt
arXiv preprint arXiv:1802.05046, 2018

Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification
Yishai Shimoni
PLoS computational biology 14(2), e1006026, Public Library of Science, 2018


Using DeMAND, a package for Interrogating Drug Mechanism of Action using Network Dysregulation analysis
Jung Hoon Woo, Yishai Shimoni, Mukesh Bansal, Andrea Califano

Elucidating compound mechanism of action by network perturbation analysis
Jung Hoon Woo, Yishai Shimoni, Wan Seok Yang, Prem Subramaniam, Archana Iyer, Paola Nicoletti, María Rodríguez-Martínez, Gonzalo López, Michela Mattioli, Ronald Realubit, Charles Karan, Brent R. Stockwell, Mukesh Bansal and And
Cell 162(2), 441-451, 2015

Stochastic analysis of bistability in coherent mixed feedback loops combining transcriptional and posttranscriptional regulations
Mor Nitzan, Yishai Shimoni, Oded Rosolio, Hanah Margalit, Ofer Biham
PHYSICAL REVIEW E 91(5), 052706, APS physics, 2015


An atlas of active enhancers across human cell types and tissues
Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki, others
Nature 507(7493), 455--461, Nature Publishing Group, 2014

A promoter-level mammalian expression atlas
The FANTOM Consortium, others
Nature 507(7493), 462--470, Nature Publishing Group, 2014


Improving breast cancer survival analysis through competition-based multidimensional modeling
Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Sock Jang, Benjamin A Logsdon, Gaurav Pandey, Benjamin A Sauerwine, Yishai Shimoni, Hans Kristian Moen Vollan, Brigham H Mecham, others


Multi-scale stochastic simulation of diffusion-coupled agents and its application to cell culture simulation
Yishai Shimoni, German Nudelman, Fernand Hayot, Stuart C Sealfon
PloS one 6(12), Public Library of Science, 2011

Role of cell-to-cell variability in activating a positive feedback antiviral response in human dendritic cells
Jianzhong Hu, German Nudelman, Yishai Shimoni, Madhu Kumar, Yaomei Ding, Carolina L\'opez, Fernand Hayot, James G Wetmur, Stuart C Sealfon
PLoS One 6(2), e16614, Public Library of Science, 2011


Plato's cave algorithm: inferring functional signaling networks from early gene expression shadows
Yishai Shimoni, Marc Y Fink, Soon-gang Choi, Stuart C Sealfon

Entanglement of periodic states, the quantum Fourier transform, and Shor’s factoring algorithm
Yonatan Most, Yishai Shimoni, Ofer Biham
Physical Review A 81(5), 052306, APS, 2010


Stochastic analysis of the SOS response in Escherichia coli
Yishai Shimoni, Shoshy Altuvia, Hanah Margalit, Ofer Biham
PLoS One 4(5), e5363, Public Library of Science, 2009


Multipartite Entanglement and Its Role in Quantum Algorithms
Yishai Shimoni
Ph.D. Thesis, 2007

Groverian entanglement measure of pure quantum states with arbitrary partitions
Yishai Shimoni, Ofer Biham
Physical Review A 75(2), 022308, APS, 2007

Formation of multipartite entanglement using random quantum gates
Yonatan Most, Yishai Shimoni, Ofer Biham
Physical Review A 76(2), 022328, APS, 2007

Regulation of gene expression by small non-coding RNAs: a quantitative view
Yishai Shimoni, Gilgi Friedlander, Guy Hetzroni, Gali Niv, Shoshy Altuvia, Ofer Biham, Hanah Margalit
Molecular Systems Biology 3(1), 138, EMBO Press, 2007


Groverian measure of entanglement for mixed states
Daniel Shapira, Yishai Shimoni, Ofer Biham
Physical Review A 73(4), 044301, APS, 2006


Algebraic analysis of quantum search with pure and mixed states
Daniel Shapira, Yishai Shimoni, Ofer Biham
Physical Review A 71(4), 042320, APS, 2005

Entangled quantum states generated by Shor’s factoring algorithm
Yishai Shimoni, Daniel Shapira, Ofer Biham
Physical Review A 72(6), 062308, APS, 2005


Characterization of pure quantum states of multiple qubits using the Groverian entanglement measure
Yishai Shimoni, Daniel Shapira, Ofer Biham
Physical Review A 69(6), 062303, APS, 2004


Analysis of Grover’s quantum search algorithm as a dynamical system
Ofer Biham, Daniel Shapira, Yishai Shimoni
Physical Review A 68(2), 022326, APS, 2003

Year Unknown

GWAS next generation: identifying mechanisms of action in association studies.
Mar\'\ia Rodr\'\iguez Mart\'\inez, Paola Nicoletti, Gonzalo L\'opez, Mukesh Bansal, Yishai Shimoni, Andrea Califano
Regulatory Genomics Special Interest Group (RegGen SIG) Program July 20, 2013