Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows. - Yishai Shimoni; Marc Y. Fink; Soon-gang Choi; Stuart C. Sealfon (PLoS Comput. Biol., 2010)

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling. - Erhan Bilal; Janusz Dutkowski; Justin Guinney; In Sock Jang; Benjamin A. Logsdon; Gaurav Pandey 002; Benjamin A. Sauerwine; Yishai Shimoni; Hans Kristian Moen Vollan; Brigham H. Mecham; Oscar M. Rueda; Jorg Tost; et al. (PLoS Comput. Biol., 2013)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

Benchmarking Framework for Performance-Evaluation of Causal Inference Analysis. - Yishai Shimoni; Chen Yanover; Ehud Karavani; Yaara Goldschmidt (CoRR, 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 Comput. Biol., 2018)

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 (CoRR, 2019)

A discriminative approach for finding and characterizing positivity violations using decision trees. - Ehud Karavani; Peter Bak; Yishai Shimoni (CoRR, 2019)

Towards effect estimation of COVID-19 Non-pharmaceutical Interventions. - Vesna Resende Barros; Victor Akinwande; Itay Manes; Osnat Bar-Shira; Celia Cintas; Yishai Shimoni; Michal Rosen-Zvi (AMIA, 2021)

Does your model understand genes? A benchmark of gene properties for biological and text models. - Yoav Kan-Tor; Michael Morris Danziger; Eden Zohar; Matan Ninio; Yishai Shimoni (CoRR, 2024)

Hierarchical Bias-Driven Stratification for Interpretable Causal Effect Estimation. - Lucile Ter-Minassian; Liran Szlak; Ehud Karavani; Christopher C. Holmes; Yishai Shimoni (AISTATS, 2025)

BMFM-RNA: An Open Framework for Building and Evaluating Transcriptomic Foundation Models. - Bharath Dandala; Michael M. Danziger; Ella Barkan; Tanwi Biswas; Viatcheslav Gurev; Jianying Hu; Matthew Madgwick; Akira Koseki; Tal Kozlovski; Michal Rosen-Zvi; Yishai Shimoni; Ching-Huei Tsou (CoRR, 2025)