PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations. - Nadav Rappoport; Menachem Fromer; Regev Schweiger; Michal Linial (Nucleic Acids Res., 2010)

ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. - Nadav Rappoport; Solange Karsenty; Amos Stern; Nathan Linial; Michal Linial (Nucleic Acids Res., 2012)

Viral Proteins Acquired from a Host Converge to Simplified Domain Architectures. - Nadav Rappoport; Michal Linial (PLoS Comput. Biol., 2012)

Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. - Nadav Rappoport; Michal Linial (BMC Bioinform., 2013)

Entropy-driven partitioning of the hierarchical protein space. - Nadav Rappoport; Amos Stern; Nathan Linial; Michal Linial (Bioinform., 2014)

NeuroPID: a classifier of neuropeptide precursors. - Solange Karsenty; Nadav Rappoport; Dan Ofer; Adva Zair; Michal Linial (Nucleic Acids Res., 2014)

ProtoBug: functional families from the complete proteomes of insects. - Nadav Rappoport; Michal Linial (Database J. Biol. Databases Curation, 2015)

Gaining functional and quantitative knowledge on genes and molecular machines using a computational approach (שער נוסף בעברית: הפקת ידע תיפקודי וכמותי על גנים ומכונות מולקולריות בעזרת גישות חישוביות.). - Nadav Rappoport (2015)

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. - Benjamin S. Glicksberg; Boris Oskotsky; Phyllis M. Thangaraj; Nicholas Giangreco; Marcus A. Badgeley; Kipp W. Johnson; Debajyoti Datta; Vivek A. Rudrapatna; Nadav Rappoport; Mark M. Shervey; Riccardo Miotto; Theodore C. Goldstein; et al. (Bioinform., 2019)

Improving Prediction Models' Propriety in Intensive-Care Unit, by Enforcing an Advance Notice Period. - Tomer Hermelin; Pierre Singer; Nadav Rappoport (AIME, 2022)

Comparison of Classification with Reject Option Approaches on MIMIC-IV Dataset. - Gerta Salillari; Nadav Rappoport (AIME, 2022)

Multi-Dimensional Laboratory Test Score as a Proxy for Health. - Bar H. Ezra; Shreyas Havaldar; Benjamin S. Glicksberg; Nadav Rappoport (MIE, 2022)

Deviation of Physiological from Chronological Age Is Associated with Health. - Lin Peretz; Nadav Rappoport (MIE, 2022)

Optimizing Operation Room Utilization - A Prediction Model. - Benyamine Abbou; Orna Tal; Gil Frenkel; Robyn Rubin; Nadav Rappoport (Big Data Cogn. Comput., 2022)

ProteinBERT: a universal deep-learning model of protein sequence and function. - Nadav Brandes; Dan Ofer; Yam Peleg; Nadav Rappoport; Michal Linial (Bioinform., 2022)

Federated Learning of Medical Concepts Embedding using BEHRT. - Ofir Ben Shoham; Nadav Rappoport (CoRR, 2023)

Ensemble Synthetic EHR Generation for Increasing Subpopulation Model's Performance. - Oriel Perets; Nadav Rappoport (CoRR, 2023)

CPLLM: Clinical Prediction with Large Language Models. - Ofir Ben Shoham; Nadav Rappoport (CoRR, 2023)

Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study. - Anna Ostropolets; Yasser Albogami; Mitchell Conover; Juan M. Banda; William A. Baumgartner Jr.; Clair Blacketer; Priyamvada Desai; Scott L. DuVall; Stephen P. Fortin; James P. Gilbert; Asieh Golozar; Joshua Ide; et al. (J. Am. Medical Informatics Assoc., 2023)

DSF-GAN: Downstream Feedback Generative Adversarial Network. - Oriel Perets; Nadav Rappoport (Tiny Papers @ ICLR, 2024)

MedConceptsQA: Open source medical concepts QA benchmark. - Ofir Ben Shoham; Nadav Rappoport (Comput. Biol. Medicine, 2024)

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup. - Nephi A. Walton; Radhakrishnan Nagarajan; Chen Wang 001; Murat Sincan; Robert R. Freimuth; David B. Everman; Derek C. Walton; Scott P. McGrath; Dominick J. Lemas; Panayiotis V. Benos; Alexander V. Alekseyenko; Qianqian Song; et al. (J. Am. Medical Informatics Assoc., 2024)

Surgery Duration Prediction Using Multi-Task Feature Selection. - David Azriel; Yosef Rinott; Orna Tal; Benyamine Abbou; Nadav Rappoport (IEEE J. Biomed. Health Informatics, 2024)

CUPCase: Clinically Uncommon Patient Cases and Diagnoses Dataset. - Oriel Perets; Ofir Ben Shoham; Nir Grinberg; Nadav Rappoport (AAAI, 2025)

Reducing Total Fertilization Failure in In-Vitro Fertilization: A Prescriptive Analytics Framework for Controlled Ovarian Stimulation Protocol Recommendations. - Shira Sadot Shaharabani; Tal Shavit; Nadav Rappoport (AIME (2), 2025)