A software tool for the analysis of mass spectrometric disulfide mapping experiments. - David Fenyö (Comput. Appl. Biosci., 1997)

The Biopolymer Markup Language. - David Fenyö (Bioinform., 1999)

The GPMDB REST interface. - David Fenyö; Ronald C. Beavis (Bioinform., 2015)

A First Step towards a Clinical Decision Support System for Post-traumatic Stress Disorders. - Sisi Ma; Isaac R. Galatzer-Levy; Xuya Wang; David Fenyö; Arieh Shalev (AMIA, 2016)

TranspoScope: interactive visualization of retrotransposon insertions. - Mark Grivainis; Zuojian Tang; David Fenyö (Bioinform., 2020)

L1EM: a tool for accurate locus specific LINE-1 RNA quantification. - Wilson H. McKerrow; David Fenyö (Bioinform., 2020)

Classification of breast cancer subtypes: A study based on representative genes. - Rayol Mendonca-Neto; João Reis; Leandro Y. S. Okimoto; David Fenyö; Cláudio T. Silva; Fabíola G. Nakamura; Eduardo Freire Nakamura (J. Braz. Comput. Soc., 2022)

A Gene Selection Method Based on Outliers for Breast Cancer Subtype Classification. - Rayol Mendonca-Neto; Zhi Li; David Fenyö; Cláudio T. Silva; Fabíola G. Nakamura; Eduardo Freire Nakamura (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification. - Leandro Y. S. Okimoto; Rayol Mendonca-Neto; Fabíola G. Nakamura; Eduardo Freire Nakamura; David Fenyö; Cláudio Teixeira Silva (BMC Bioinform., 2024)

BDIViz: An Interactive Visualization System for Biomedical Schema Matching with LLM-Powered Validation. - Eden Wu; Dishita G. Turakhia; Guande Wu; Christos Koutras; Sarah Keegan; Wenke Liu; Beata Szeitz; David Fenyö; Cláudio T. Silva; Juliana Freire (CoRR, 2025)