Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. - Andrew Ernest Torda; James B. Procter; Thomas Huber (Nucleic Acids Res., 2004)

Jalview: Visualization and Analysis of Molecular Sequences, Alignments, and Structures. - Andrew M. Waterhouse; James B. Procter; David M. A. Martin; Geoffrey J. Barton (BMC Bioinform., 2005)

MACSIMS : multiple alignment of complete sequences information management system. - Julie Dawn Thompson; Arnaud Muller; Andrew M. Waterhouse; James B. Procter; Geoffrey J. Barton; Frédéric Plewniak; Olivier Poch (BMC Bioinform., 2006)

Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. - Andrew M. Waterhouse; James B. Procter; David M. A. Martin; Michele E. Clamp; Geoffrey J. Barton (Bioinform., 2009)

Java bioinformatics analysis web services for multiple sequence alignment - JABAWS: MSA. - Peter V. Troshin; James B. Procter; Geoffrey J. Barton (Bioinform., 2011)

Ten Simple Rules for the Open Development of Scientific Software. - Andreas Prlic; James B. Procter (PLoS Comput. Biol., 2012)

JPred4: a protein secondary structure prediction server. - Alexey Drozdetskiy; Christian Cole; James B. Procter; Geoffrey J. Barton (Nucleic Acids Res., 2015)

MSAViewer: interactive JavaScript visualization of multiple sequence alignments. - Guy Yachdav; Sebastian Wilzbach; Benedikt Rauscher; Robert Sheridan; Ian Sillitoe; James B. Procter; Suzanna E. Lewis; Burkhard Rost; Tatyana Goldberg (Bioinform., 2016)

JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure. - Peter V. Troshin; James B. Procter; Alexander Sherstnev; Daniel L. Barton; Fábio Madeira; Geoffrey J. Barton (Bioinform., 2018)

Foreword to the special section on visual computing for biology and medicine (VCBM 2023). - Renata G. Raidou; James B. Procter; Christian Hansen; Thomas Höllt; Daniel Jönsson (Comput. Graph., 2025)