On the Use of Agents in BioInformatics Grid. - Luc Moreau 001; Simon Miles; Carole A. Goble; Robert Mark Greenwood; Vijay Dialani; Matthew Addis; Mahmut Nedim Alpdemir; Rich Cawley; David De Roure; Justin Ferris; Robert J. Gaizauskas; Kevin Glover; et al. (CCGRID, 2003)

Delivering web service coordination capability to users. - Thomas M. Oinn; Matthew Addis; Justin Ferris; Darren Marvin; Robert Mark Greenwood; Carole A. Goble; Anil Wipat; Peter Li; Tim Carver (WWW (Alternate Track Papers & Posters), 2004)

Taverna: a tool for the composition and enactment of bioinformatics workflows. - Thomas M. Oinn; Matthew Addis; Justin Ferris; Darren Marvin; Martin Senger; Robert Mark Greenwood; Tim Carver; Kevin Glover; Matthew R. Pocock; Anil Wipat; Peter Li (Bioinform., 2004)

SARGE: a tool for creation of putative genetic networks. - O. J. Shaw; Colin Harwood; L. Jason Steggles; Anil Wipat (Bioinform., 2004)

A grid-based system for microbial genome comparison and analysis. - Yudong Sun; Anil Wipat; Matthew R. Pocock; Pete A. Lee; Paul Watson 001; Keith Flanagan; James T. Worthington (CCGRID, 2005)

Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks. - Oliver Shaw; L. Jason Steggles; Anil Wipat (PASM@FM, 2005)

Clustering and Cross-talk in a Yeast Functional Interaction Network. - Jennifer Hallinan; Anil Wipat (CIBCB, 2006)

Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets. - L. Jason Steggles; Richard Banks; Anil Wipat (CMSB, 2006)

Taverna: lessons in creating a workflow environment for the life sciences. - Thomas M. Oinn; Robert Mark Greenwood; Matthew Addis; Mahmut Nedim Alpdemir; Justin Ferris; Kevin Glover; Carole A. Goble; Antoon Goderis; Duncan Hull; Darren Marvin; Peter Li; Phillip W. Lord; et al. (Concurr. Comput. Pract. Exp., 2006)

Motifs and Modules in Fractured Functional Yeast Networks. - Jennifer Hallinan; Anil Wipat (CIBCB, 2007)

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach. - L. Jason Steggles; Richard Banks; Oliver Shaw; Anil Wipat (Bioinform., 2007)

Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models. - Allyson L. Lister; Matthew R. Pocock; Anil Wipat (J. Integr. Bioinform., 2007)

Exploring Microbial Genome Sequences to Identify Protein Families on the Grid. - Yudong Sun; Anil Wipat; Matthew R. Pocock; P. A. Lee; Keith Flanagan; J. T. Worthington (IEEE Trans. Inf. Technol. Biomed., 2007)

Network motifs in context: An exploration of the evolution of oscillatory dynamics in transcriptional networks. - Jennifer Hallinan; Anil Wipat (CIBCB, 2008)

Clustering incorporating shortest paths identifies relevant modules in functional interaction networks. - Jennifer Hallinan; Matthew R. Pocock; Stephen G. Addinall; David A. Lydall; Anil Wipat (CIBCB, 2009)

Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes. - Katherine James; Anil Wipat; Jennifer Hallinan (DILS, 2009)

Saint: a lightweight integration environment for model annotation. - Allyson L. Lister; Matthew R. Pocock; Morgan L. Taschuk; Anil Wipat (Bioinform., 2009)

Standard virtual biological parts: a repository of modular modeling components for synthetic biology. - Mike T. Cooling; V. Rouilly; Goksel Misirli; James R. Lawson; Tommy Yu; Jennifer Hallinan; Anil Wipat (Bioinform., 2010)

Annotation of SBML models through rule-based semantic integration. - Allyson L. Lister; Phillip W. Lord; Matthew R. Pocock; Anil Wipat (J. Biomed. Semant., 2010)

An integrated dataset for in silico drug discovery. - Simon J. Cockell; Jochen Weile; Phillip W. Lord; Claire Wipat; Dmytro Andriychenko; Matthew R. Pocock; Darren J. Wilkinson; Malcolm Young; Anil Wipat (J. Integr. Bioinform., 2010)

Model annotation for synthetic biology: automating model to nucleotide sequence conversion. - Goksel Misirli; Jennifer Hallinan; Tommy Yu; James R. Lawson; Sarala M. Wimalaratne; Mike T. Cooling; Anil Wipat (Bioinform., 2011)

Customizable views on semantically integrated networks for systems biology. - Jochen Weile; Matthew R. Pocock; Simon J. Cockell; Phillip W. Lord; James M. Dewar; Eva-Maria Holstein; Darren J. Wilkinson; David A. Lydall; Jennifer Hallinan; Anil Wipat (Bioinform., 2011)

KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data. - Nicolas Alcaraz; Hande Kücük; Jochen Weile; Anil Wipat; Jan Baumbach (Internet Math., 2011)

Automatic extraction of microorganisms and their habitats from free text using text mining workflows. - BalaKrishna Kolluru; Sirintra Nakjang; Robert P. Hirt; Anil Wipat; Sophia Ananiadou (J. Integr. Bioinform., 2011)

Bridging the Gap between Design and Reality - A Dual Evolutionary Strategy for the Design of Synthetic Genetic Circuits. - Jennifer Hallinan; S. Park; Anil Wipat (BIOINFORMATICS, 2012)

Data mining the human gut microbiota for therapeutic targets. - Matthew Collison; Robert P. Hirt; Anil Wipat; Sirintra Nakjang; Philippe Sanseau; James R. Brown (Briefings Bioinform., 2012)

Bayesian integration of networks without gold standards. - Jochen Weile; Katherine James; Jennifer Hallinan; Simon J. Cockell; Phillip W. Lord; Anil Wipat; Darren J. Wilkinson (Bioinform., 2012)

Microbase2.0: A Generic Framework for Computationally Intensive Bioinformatics Workflows in the Cloud. - Keith Flanagan; Sirintra Nakjang; Jennifer Hallinan; Colin Harwood; Robert P. Hirt; Matthew R. Pocock; Anil Wipat (J. Integr. Bioinform., 2012)

BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. - Goksel Misirli; Anil Wipat; Joseph Mullen; Katherine James; Matthew R. Pocock; Wendy Smith; Nick Allenby; Jennifer Hallinan (J. Integr. Bioinform., 2013)

Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts. - Jennifer Hallinan; Owen Gilfellon; Goksel Misirli; Anil Wipat (CIBCB, 2014)

Composable Modular Models for Synthetic Biology. - Goksel Misirli; Jennifer Hallinan; Anil Wipat (ACM J. Emerg. Technol. Comput. Syst., 2014)

Introduction to the Special Issue on Computational Synthetic Biology. - Chris J. Myers; Herbert M. Sauro; Anil Wipat (ACM J. Emerg. Technol. Comput. Syst., 2014)

A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci. - Keith Flanagan; Simon J. Cockell; Colin Harwood; Jennifer Hallinan; Sirintra Nakjang; Beth Lawry; Anil Wipat (J. Integr. Bioinform., 2014)

BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species. - Goksel Misirli; Jennifer Hallinan; Richard Röttger; Jan Baumbach; Anil Wipat (J. Integr. Bioinform., 2014)

Probabilistic Latent Semantic Analysis Applied to Whole Bacterial Genomes Identifies Common Genomic Features. - Julija Rusakovica; Jennifer Hallinan; Anil Wipat; Paolo Zuliani (J. Integr. Bioinform., 2014)

Synthetic Biology Open Language (SBOL) Version 2.0.0. - Bryan Bartley; Jacob Beal; Kevin Clancy; Goksel Misirli; Nicholas Roehner; Ernst Oberortner; Matthew R. Pocock; Michael Bissell; Curtis Madsen; Tramy Nguyen; Zhen Zhang 006; John H. Gennari; et al. (J. Integr. Bioinform., 2015)

Computational intelligence for metabolic pathway design: Application to the pentose phosphate pathway. - James Skelton; Jennifer Hallinan; S. Park; Anil Wipat (CIBCB, 2016)

Engineering bacterial populations for pattern formation. - Daniel Sutantyo; Christopher Walker; Nicholas deBono; Jarryd Vargas; Anil Wipat; Jennifer S. Hallinan (CIBCB, 2016)

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. - Goksel Misirli; Matteo Cavaliere; William Waites; Matthew R. Pocock; Curtis Madsen; Owen Gilfellon; Ricardo Honorato-Zimmer; Paolo Zuliani; Vincent Danos; Anil Wipat (Bioinform., 2016)

Synthetic Biology Open Language (SBOL) Version 2.1.0. - Jacob Beal; Robert Sidney Cox III; Raik Grünberg; James Alastair McLaughlin; Tramy Nguyen; Bryan Bartley; Michael Bissell; Kiri Choi; Kevin Clancy; Chris Macklin; Curtis Madsen; Goksel Misirli; et al. (J. Integr. Bioinform., 2016)

Compiling Combinatorial Genetic Circuits with Semantic Inference. - William Waites; Goksel Misirli; Matteo Cavaliere; Vincent Danos; Anil Wipat (CoRR, 2018)

Synthetic Biology Open Language (SBOL) Version 2.2.0. - Robert Sidney Cox III; Curtis Madsen; James Alastair McLaughlin; Tramy Nguyen; Nicholas Roehner; Bryan Bartley; Jacob Beal; Michael Bissell; Kiri Choi; Kevin Clancy; Raik Grünberg; Chris Macklin; et al. (J. Integr. Bioinform., 2018)

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. - Robert Sidney Cox III; Curtis Madsen; James Alastair McLaughlin; Tramy Nguyen; Nicholas Roehner; Bryan Bartley; Swapnil Bhatia; Mike Bissell; Kevin Clancy; Thomas E. Gorochowski; Raik Grünberg; Augustin Luna; et al. (J. Integr. Bioinform., 2018)

Harmonizing semantic annotations for computational models in biology. - Maxwell Lewis Neal; Matthias König 003; David P. Nickerson; Goksel Misirli; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T. Cooling; Daniel L. Cook; Sharon M. Crook; Miguel de Alba; et al. (Briefings Bioinform., 2019)

Synthetic Biology Open Language (SBOL) Version 2.3. - Curtis Madsen; Ángel Goñi-Moreno; Umesh P; Zachary Palchick; Nicholas Roehner; Christian Atallah; Bryan Bartley; Kiri Choi; Robert Sidney Cox III; Thomas E. Gorochowski; Raik Grünberg; Chris Macklin; et al. (J. Integr. Bioinform., 2019)

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. - Curtis Madsen; Ángel Goñi-Moreno; Zachary Palchick; Umesh P; Nicholas Roehner; Bryan Bartley; Swapnil Bhatia; Shyam Bhakta; Mike Bissell; Kevin Clancy; Robert Sidney Cox III; Thomas E. Gorochowski; et al. (J. Integr. Bioinform., 2019)

Synthetic biology open language visual (SBOL visual) version 2.2. - Hasan Baig; Pedro Fontanarrosa; Vishwesh Kulkarni 002; James Alastair McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Swapnil Bhatia; Shyam Bhakta; Michael Bissell; Kevin Clancy; Robert Sidney Cox III; Ángel Goñi-Moreno; et al. (J. Integr. Bioinform., 2020)

Synthetic biology open language (SBOL) version 3.0.0. - Hasan Baig; Pedro Fontanarrosa; Vishwesh Kulkarni 002; James Alastair McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Jacob Beal; Matthew Crowther; Thomas E. Gorochowski; Raik Grünberg; Goksel Misirli; James Scott-Brown; et al. (J. Integr. Bioinform., 2020)

Synthetic biology open language visual (SBOL Visual) version 2.3. - Hasan Baig; Pedro Fontanarossa; Vishwesh Kulkarni 002; James Alastair McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Shyam Bhakta; Swapnil Bhatia; Mike Bissell; Kevin Clancy; Robert Sidney Cox III; Ángel Goñi-Moreno; et al. (J. Integr. Bioinform., 2021)

Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis. - Yiming Huang; Wendy Smith; Colin Harwood; Anil Wipat; Jaume Bacardit (Sensors, 2021)

Automatic Diverse Subset Selection From Enzyme Families by Solving the Maximum Diversity Problem. - Christian Atallah; Katherine James; Zhen Ou; James Skelton; David Markham; James Finnigan; Simon Charnock; Anil Wipat (CIBCB, 2022)

Computational intelligence and machine learning in bioinformatics and computational biology. - Madhu Chetty; Jennifer Hallinan; Gonzalo A. Ruz; Anil Wipat (Biosyst., 2022)

Modelling the fitness landscapes of a SCRaMbLEd yeast genome. - Bill Yang; Goksel Misirli; Anil Wipat; Jennifer Hallinan (Biosyst., 2022)

Integration of probabilistic functional networks without an external Gold Standard. - Katherine James; Aoesha Alsobhe; Simon J. Cockell; Anil Wipat; Matthew R. Pocock (BMC Bioinform., 2022)

Synthetic biology open language (SBOL) version 3.1.0. - Lukas Buecherl; Thomas Mitchell; James Scott-Brown; Prashant Vaidyanathan; Gonzalo Vidal; Hasan Baig; Bryan Bartley; Jacob Beal; Matthew Crowther; Pedro Fontanarrosa; Thomas E. Gorochowski; Raik Grünberg; et al. (J. Integr. Bioinform., 2023)

NeDRex-Web: An Interactive Web Tool for Drug Repurposing by Exploring Heterogeneous Molecular Networks. - Andreas Maier 009; Mahdie Rafiei; Elisa Anastasi; Olga I. Zolotareva; James Skelton; Maria L. Elkjaer; Ana I. Casas; Cristian Nogales; Harald H. H. W. Schmidt; Tim Kacprowski; David B. Blumenthal; Anil Wipat; et al. (BIBM, 2024)

A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem. - Christian Atallah; Katherine James; Zhen Ou; James Skelton; David Markham; Matt S. Burridge; James Finnigan; Simon Charnock; Anil Wipat (Biosyst., 2024)