The immune system and other cognitive systems. - Uri Hershberg; Sol Efroni (Complex., 2001)

Reactive Animation. - David Harel; Sol Efroni; Irun R. Cohen (FMCO, 2002)

Reactive Animation: Realistic Modeling of Complex Dynamic Systems. - Sol Efroni; David Harel; Irun R. Cohen (Computer, 2005)

Concurrency in Biological Modeling: Behavior, Execution and Visualization. - David Harel; Yaki Setty; Sol Efroni; Naamah Swerdlin; Irun R. Cohen (FBTC@CONCUR, 2007)

Emergent Dynamics of Thymocyte Development and Lineage Determination. - Sol Efroni; David Harel; Irun R. Cohen (PLoS Comput. Biol., 2007)

The PathOlogist: An Automated Tool for Pathway-Centric Analysis. - Sharon I. Greenblum; Sol Efroni; Carl F. Schaefer 002; Kenneth H. Buetow (BMC Bioinform., 2011)

The whole-organism heavy chain B cell repertoire from Zebrafish self-organizes into distinct network features. - Rotem Ben-Hamo; Sol Efroni (BMC Syst. Biol., 2011)

Biomarker robustness reveals the PDGF network as driving disease outcome in ovarian cancer patients in multiple studies. - Rotem Ben-Hamo; Sol Efroni (BMC Syst. Biol., 2012)

MicroRNA-Gene Association As a Prognostic Biomarker in Cancer Exposes Disease Mechanisms. - Rotem Ben-Hamo; Sol Efroni (PLoS Comput. Biol., 2013)

PhenoNet: identification of key networks associated with disease phenotype. - Rotem Ben-Hamo; Moriah Gidoni; Sol Efroni (Bioinform., 2014)

Spatial regulation dominates gene function in the ganglia chain. - Dror Hibsh; Hadas Schori; Sol Efroni; Orit Shefi (Bioinform., 2014)

Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans. - Miri Gordin; Hagit Philip; Alona Zilberberg; Moriah Gidoni; Raanan Margalit; Christopher Clouser; Kristofor Adams; Francois Vigneault; Irun R. Cohen; Gur Yaari; Sol Efroni (PLoS Comput. Biol., 2021)

PathWeigh - Quantifying the Behavior of Biochemical Pathway Cascades. - Dani Livne; Sol Efroni (IWBBIO (2), 2022)

A Language Model identifies population-level features of the T cell Receptor via self-supervised learning. - Romi Goldner Kabeli; Sol Efroni (TransAI, 2022)

GENTLE: a novel bioinformatics tool for generating features and building classifiers from T cell repertoire cancer data. - Dhiego Souto Andrade; Patrick Terrematte; César Rennó-Costa; Alona Zilberberg; Sol Efroni (BMC Bioinform., 2023)

Ovarian cancer is detectable from peripheral blood using machine learning over T-cell receptor repertoires. - Miriam Zuckerbrot-Schuldenfrei; Sarit Aviel-Ronen; Alona Zilberberg; Sol Efroni (Briefings Bioinform., 2024)

Pathway metrics accurately stratify T cells to their cells states. - Dani Livne; Sol Efroni (BioData Min., 2024)