Making CASE Work. - John Parkinson (CAiSE, 1990)

A model for the study and design of teaching situations with ICT. - Steve Kennewell; Howard Tanner; John Parkinson (Communications and Networking in Education, 1999)

Making sense of EST sequences by CLOBBing them. - John Parkinson; David B. Guiliano; Mark L. Blaxter (BMC Bioinform., 2002)

SimiTri-visualizing similarity relationships for groups of sequences. - John Parkinson; Mark L. Blaxter (Bioinform., 2003)

PartiGene-constructing partial genomes. - John Parkinson; Alasdair Anthony; James Wasmuth; Ralf Schmid; Ann Hedley; Mark L. Blaxter (Bioinform., 2004)

Mediating Science Learning Through Information and Communications Technology: Holliman, Richard and Scanlon, Eileen (Eds.) (2004) London: RoutledgeFalmer, 211pp, ISBN 0-415-32832-2. - John Parkinson (Comput. Educ., 2004)

NEMBASE: a resource for parasitic nematode ESTs. - John Parkinson; Claire Whitton; Ralf Schmid; Marian Thomson; Mark L. Blaxter (Nucleic Acids Res., 2004)

Exploring Parasite Gene Space. - James Wasmuth; Ralf Schmid; Alasdair Anthony; John Parkinson; Mark L. Blaxter (BMC Bioinform., 2005)

PartiGeneDB - collating partial genomes. - José M. Peregrín-Alvarez; Andrew Yam; Gaya Sivakumar; John Parkinson (Nucleic Acids Res., 2005)

Cell++ - simulating biochemical pathways. - Christopher Sanford; Matthew L. K. Yip; Carl White; John Parkinson (Bioinform., 2006)

SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences. - David He; John Parkinson (Bioinform., 2008)

Pupils' attitudes towards school science as they transfer from an ICT-rich primary school to a secondary school with fewer ICT resources: Does ICT matter? - Gary Beauchamp; John Parkinson (Educ. Inf. Technol., 2008)

Bacteriome.org - an integrated protein interaction database for E. coli. - Chong Su; José M. Peregrín-Alvarez; Gareth Butland; Sadhna Phanse; Vincent Fong; Andrew Emili; John Parkinson (Nucleic Acids Res., 2008)

The Modular Organization of Protein Interactions in Escherichia coli. - José M. Peregrín-Alvarez; Xuejian Xiong; Chong Su; John Parkinson (PLoS Comput. Biol., 2009)

DETECT - a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum. - Stacy S. Hung; James Wasmuth; Christopher Sanford; John Parkinson (Bioinform., 2010)

PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya. - Xuejian Xiong; Hongyan Song; Tuan On; Lucas Lochovsky; Nicholas J. Provart; John Parkinson (Bioinform., 2011)

DAnCER: Disease-Annotated Chromatin Epigenetics Resource. - Andrei L. Turinsky; Brian Turner; Rosanne C. Borja; James A. Gleeson; Michael Heath; Shuye Pu; Thomas Switzer; Dong Dong; Yunchen Gong; Tuan On; Xuejian Xiong; Andrew Emili; et al. (Nucleic Acids Res., 2011)

Modelling the Self-Assembly of Elastomeric Proteins Provides Insights into the Evolution of Their Domain Architectures. - Hongyan Song; John Parkinson (PLoS Comput. Biol., 2012)

IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology. - Henry C. M. Leung; Siu-Ming Yiu; John Parkinson; Francis Y. L. Chin (J. Comput. Biol., 2013)

Identification of a Functional Connectome for Long-Term Fear Memory in Mice. - Anne L. Wheeler; Cátia M. Teixeira; Afra H. Wang; Xuejian Xiong; Natasa Kovacevic; Jason P. Lerch; Anthony Randal McIntosh; John Parkinson; Paul W. Frankland (PLoS Comput. Biol., 2013)

Hyperscape: visualization for complex biological networks. - Graham L. Cromar; Anthony Zhao; Alex Yang; John Parkinson (Bioinform., 2015)

PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. - Graham L. Cromar; Anthony Zhao; Xuejian Xiong; Lakshmipuram S. Swapna; Noeleen Loughran; Hongyan Song; John Parkinson (Database J. Biol. Databases Curation, 2016)

Improved enzyme annotation with EC-specific cutoffs using DETECT v2. - Nirvana Nursimulu; Leon L. Xu; James D. Wasmuth; Ivan Krukov; John Parkinson (Bioinform., 2018)

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries. - Cedoljub Bundalovic-Torma; Gregory B. Whitfield; Lindsey S. Marmont; P. Lynne Howell; John Parkinson (PLoS Comput. Biol., 2020)

Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation. - Nirvana Nursimulu; Alan M. Moses; John Parkinson (PLoS Comput. Biol., 2022)

ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii. - Lakshmipuram S. Swapna; Grant C. Stevens; Aline Sardinha-Silva; Lucas Zhongming Hu; Verena Brand; Daniel D. Fusca; Cuihong Wan; Xuejian Xiong; Jon P. Boyle; Michael E. Grigg; Andrew Emili; John Parkinson (PLoS Comput. Biol., 2024)

Cell4D: a general purpose spatial stochastic simulator for cellular pathways. - Donny Chan; Graham L. Cromar; Billy Taj; John Parkinson (BMC Bioinform., 2024)