Probabilities for having a new fold on the basis of a map of all protein sequences. - Elon Portugaly; Michal Linial (RECOMB, 2000)

Selecting targets for structural determination by navigating in a graph of protein families. - Elon Portugaly; Ilona Kifer; Michal Linial (Bioinform., 2002)

ProtoNet: hierarchical classification of the protein space. - Ori Sasson; Avishay Vaaknin; Hillel Fleischer; Elon Portugaly; Yonatan Bilu; Nathan Linial; Michal Linial (Nucleic Acids Res., 2003)

Noise and the two-thirds power Law. - Uri Maoz; Elon Portugaly; Tamar Flash; Yair Weiss (NIPS, 2005)

ProtoNet 4.0: A hierarchical classification of one million protein sequences. - Noam Kaplan; Ori Sasson; Uri Inbar; Moriah Friedlich; Menachem Fromer; Hillel Fleischer; Elon Portugaly; Nathan Linial; Michal Linial (Nucleic Acids Res., 2005)

EVEREST: automatic identification and classification of protein domains in all protein sequences. - Elon Portugaly; Amir Harel; Nathan Linial; Michal Linial (BMC Bioinform., 2006)

EVEREST: a collection of evolutionary conserved protein domains. - Elon Portugaly; Nathan Linial; Michal Linial (Nucleic Acids Res., 2007)

Identifying and classifying recurrent evolutionary conserved units in proteins (נוספו שער, תקציר ותכן בעברית: זיהוי וסיווג יחידות שמורות אבולוציונית החוזרות בחלבונים.). - Elon Portugaly (2007)

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. - Yaniv Loewenstein; Elon Portugaly; Menachem Fromer; Michal Linial (ISMB, 2008)

Hidden Markov model speed heuristic and iterative HMM search procedure. - L. Steven Johnson; Sean R. Eddy; Elon Portugaly (BMC Bioinform., 2010)

Counterfactual Reasoning and Learning Systems - Léon Bottou; Jonas Peters; Joaquin Quiñonero Candela; Denis Xavier Charles; Max Chickering; Elon Portugaly; Dipankar Ray; Patrice Y. Simard; Ed Snelson (CoRR, 2012)

Counterfactual reasoning and learning systems: the example of computational advertising. - Léon Bottou; Jonas Peters; Joaquin Quiñonero Candela; Denis Xavier Charles; Max Chickering; Elon Portugaly; Dipankar Ray; Patrice Y. Simard; Ed Snelson (J. Mach. Learn. Res., 2013)

Unbiased Estimation of the Value of an Optimized Policy. - Elon Portugaly; Joseph J. Pfeiffer III (CoRR, 2018)

Scalable Universal T-Cell Receptor Embeddings from Adaptive Immune Repertoires. - Paidamoyo Chapfuwa; Ilker Demirel; Lorenzo Pisani; Javier Zazo; Elon Portugaly; H. Jabran Zahid; Julia Greissl (ICLR, 2025)