MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. - Chittibabu Guda; Eoin Fahy; Shankar Subramaniam (Bioinform., 2004)

MitoProteome: mitochondrial protein sequence database and annotation system. - Dawn Cotter; Purnima Guda; Eoin Fahy; Shankar Subramaniam (Nucleic Acids Res., 2004)

MITOPRED: a web server for the prediction of mitochondrial proteins. - Chittibabu Guda; Purnima Guda; Eoin Fahy; Shankar Subramaniam (Nucleic Acids Res., 2004)

LIPID MAPS online tools for lipid research. - Eoin Fahy; Manish Sud; Dawn Cotter; Shankar Subramaniam (Nucleic Acids Res., 2007)

LMSD: LIPID MAPS structure database. - Manish Sud; Eoin Fahy; Dawn Cotter; Alex Brown; Edward A. Dennis; Christopher K. Glass; Alfred H. Merrill Jr.; Robert C. Murphy; Christian R. H. Raetz; David W. Russell; Shankar Subramaniam (Nucleic Acids Res., 2007)

Template-based combinatorial enumeration of virtual compound libraries for lipids. - Manish Sud; Eoin Fahy; Shankar Subramaniam (J. Cheminformatics, 2012)

A combined omics study on activated macrophages - enhanced role of STATs in apoptosis, immunity and lipid metabolism. - Ashok Reddy Dinasarapu; Shakti Gupta; Mano Ram Maurya; Eoin Fahy; Jun Min; Manish Sud; Merril J. Gersten; Christopher K. Glass; Shankar Subramaniam (Bioinform., 2013)

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. - Yannick Djoumbou; Roman Eisner; Craig Knox; Leonid L. Chepelev; Janna Hastings; Gareth I. Owen; Eoin Fahy; Christoph Steinbeck; Shankar Subramanian; Evan Bolton; Russell Greiner; David S. Wishart (J. Cheminformatics, 2016)

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. - Manish Sud; Eoin Fahy; Dawn Cotter; Kenan Azam; Ilango Vadivelu; Charles F. Burant; Arthur Edison; Oliver Fiehn; Richard M. Higashi; K. Sreekumaran Nair; Susan Sumner; Shankar Subramaniam (Nucleic Acids Res., 2016)

LipidFinder on LIPID MAPS: peak filtering, MS searching and statistical analysis for lipidomics. - Eoin Fahy; Jorge Álvarez-Jarreta; Christopher J. Brasher; An Nguyen; Jade I Hawksworth; Patricia Rodrigues; Sven Meckelmann; Stuart M. Allen; Valerie B. O'Donnell (Bioinform., 2019)

LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications. - Jorge Álvarez-Jarreta; Patricia Rodrigues; Eoin Fahy; Anne O'connor; Anna Price; Caroline Gaud; Simon Andrews; H. Paul Benton; Gary Siuzdak; Jade I Hawksworth; Maria Valdivia-Garcia; Stuart M. Allen; et al. (Bioinform., 2021)

Playbook workflow builder: Interactive construction of bioinformatics workflows. - Daniel J. B. Clarke; John Erol Evangelista; Zhuorui Xie; Giacomo B. Marino; Anna I. Byrd; Mano Ram Maurya; Sumana Srinivasan; Keyang Yu; Varduhi Petrosyan; Matthew E. Roth; Miroslav Milinkov; Charles Hadley King; et al. (PLoS Comput. Biol., 2025)