The relationship between domain-domain interaction orientation and sequence similarity. - Emily R. Jefferson; Geoffrey J. Barton (BMC Syst. Biol., 2007)

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. - Emily R. Jefferson; Thomas P. Walsh; Timothy J. Roberts; Geoffrey J. Barton (Nucleic Acids Res., 2007)

The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. - Jonathan R. Manning; Emily R. Jefferson; Geoffrey J. Barton (BMC Bioinform., 2008)

Standardizing Biochemistry Dataset for Medical Research. - Wilfred Bonney; Alexander S. Doney; Emily R. Jefferson (HEALTHINF, 2014)

Mapping Local Codes to Read Codes. - Wilfred Bonney; James Galloway; Christopher Hall; Mikhail Ghattas; Leandro Tramma; Thomas Nind; Louise Donnelly; Emily R. Jefferson; Alexander S. Doney (ITCH, 2017)

Knowledge Driven Phenotyping. - Honghan Wu; Minhong Wang 002; Qianyi Zeng; Wenjun Chen; Thomas Nind; Emily R. Jefferson; Marion Bennie; Corri Black; Jeff Z. Pan; Cathie Sudlow; Dave Robertson 001 (MIE, 2020)

Machine Learning Models Disclosure from Trusted Research Environments (TRE), Challenges and Opportunities. - Esma Mansouri-Benssassi; Simon Rogers; Jim Smith; Felix Ritchie; Emily R. Jefferson (CoRR, 2021)

GRAIMATTER Green Paper: Recommendations for disclosure control of trained Machine Learning (ML) models from Trusted Research Environments (TREs). - Emily R. Jefferson; James Liley; Maeve Malone; Smarti Reel; Alba Crespi-Boixader; Xaroula Kerasidou; Francesco Tava; Andrew McCarthy; Richard Preen; Alberto Blanco-Justicia; Esma Mansouri-Benssassi; Josep Domingo-Ferrer; et al. (CoRR, 2022)

Navigating the development challenges in creating complex data systems. - Sören Dittmer; Michael Roberts; Julian D. Gilbey; Ander Biguri; Ian Selby; Anna Breger; Matthew Thorpe; Jonathan R. Weir-McCall; Effrossyni Gkrania-Klotsas; Anna Korhonen; Emily R. Jefferson; Georg Langs; et al. (Nat. Mac. Intell., 2023)

A pipeline for harmonising NHS Scotland laboratory data to enable national-level analyses. - Chuang Gao; Shahzad Mumtaz; Sophie McCall; Katherine O'sullivan; Mark M. McGilchrist; Daniel R. Morales; Christopher Hall; Katie Wilde; Charlie Mayor; Pamela Linksted; Kathy Harrison; Christian Cole; et al. (J. Biomed. Informatics, 2025)