Anil Wipat

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Synthetic biology open language (SBOL) version 3.0.0

Jacob Beal, Hasan Baig, Pedro Fontanarrosa, 2020, J. Integr. Bioinform..

Taverna: lessons in creating a workflow environment for the life sciences: Research Articles

Mark Greenwood, Carole Goble, Matthew R. Pocock, 2006 .

Synthetic Biology Open Language (SBOL) Version 2.2.0

Zhen Zhang, Chris J. Myers, Jacob Beal, 2018, J. Integr. Bioinform..

A Computational Workflow for the Automated Generation of Models of Genetic Designs.

James Alastair McLaughlin, Prashant Vaidyanathan, Anil Wipat, 2019, ACS synthetic biology.

Microbial synthetic biology

Anil Wipat, Colin R. Harwood, 2013 .

Bioinformatics in aging research: a workshop report.

Anil Wipat, Günter Lepperdinger, Georg Fuellen, 2010, Rejuvenation research.

Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes

Anil Wipat, Katherine James, Jennifer Hallinan, 2009, DILS.

sboljs: Bringing the Synthetic Biology Open Language to the Web Browser.

James Alastair McLaughlin, Anil Wipat, Chris J Myers, 2019, ACS synthetic biology.

Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks

Anil Wipat, L. Jason Steggles, Oliver Shaw, 2006, PASM@FM.

A synthetic biology workflow using SBOL

Chris J. Myers, James Alastair McLaughlin, Goksel Misirli, 2017 .

BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species

Goksel Misirli, Anil Wipat, Jennifer Hallinan, 2014, J. Integr. Bioinform..

Semantic subgraph searching in integrated biological graphs: an approach for mining drug repositioning networks

Joseph Mullen, Anil Wipat, Jennifer Hallinan, 2014 .

Proceedings of 8th International Workshop on Bio-Design Automation IWBDA 2016

Paolo Zuliani, Goksel Misirli, Anil Wipat, 2016 .

A grid-based system for microbial genome comparison and analysis

Matthew R. Pocock, Yudong Sun, Anil Wipat, 2005, CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005..

Saint: a lightweight integration environment for model annotation

Morgan Taschuk, Matthew R. Pocock, Allyson L. Lister, 2009, Bioinform..

Customizable views on semantically integrated networks for systems biology

Matthew R. Pocock, Darren J. Wilkinson, Phillip W. Lord, 2011, Bioinform..

Exploring Microbial Genome Sequences to Identify Protein Families on the Grid

Matthew R. Pocock, Yudong Sun, Anil Wipat, 2007, IEEE Transactions on Information Technology in Biomedicine.

An integrated dataset for in silico drug discovery

Matthew R. Pocock, Darren J. Wilkinson, Phillip W. Lord, 2010, J. Integr. Bioinform..

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

Matthew R. Pocock, James Alastair McLaughlin, Anil Wipat, 2016, ACS synthetic biology.

Data mining the human gut microbiota for therapeutic targets

Anil Wipat, James R. Brown, Philippe Sanseau, 2012, Briefings Bioinform..

Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models

Matthew R. Pocock, Allyson L. Lister, Anil Wipat, 2007, J. Integr. Bioinform..

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach

Richard Banks, Anil Wipat, L. Jason Steggles, 2007, Bioinform..

Detecting Infectious Organisms: A Concerted Approach using Genomics, Molecular Engineering and Nano-enabled bio-MEMS Technologies

Anil Wipat, Colin R. Harwood, Keith Flanagan, 2011 .

The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.

Matthew R. Pocock, James Alastair McLaughlin, Anil Wipat, 2016, ACS synthetic biology.

Heterogeneity in Pure Microbial Systems: Experimental Measurements and Modeling

Anil Wipat, Rebeca González-Cabaleiro, Anca M. Mitchell, 2017, Front. Microbiol..

Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud.

Matthew R. Pocock, Anil Wipat, Jennifer Hallinan, 2012, Journal of integrative bioinformatics.

Engineering bacterial populations for pattern formation

Anil Wipat, Daniel Sutantyo, Christopher Walker, 2016, 2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).

Synthetic Biology Open Language (SBOL) Version 2.0.0.

Zhen Zhang, Chris J. Myers, Jacob Beal, 2015, Journal of integrative bioinformatics.

Clustering and Cross-talk in a Yeast Functional Interaction Network

Anil Wipat, Jennifer Hallinan, J. Hallinan, 2006, 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL).

Jacob Beal, James Alastair McLaughlin, Bryan Bartley, 2020, ACS synthetic biology.

libSBOLj 2.0: A Java Library to Support SBOL 2.0

Zhen Zhang, Chris J. Myers, Jacob Beal, 2015, IEEE Life Sciences Letters.

The development and application of molecular detection and recovery systems for genetically-engineered streptomycetes in soil.

Anil Wipat, 1992 .

University of Newcastle upon Tyne Computing Science Geli: a Data Model for the Representation of a Gel Electrophoresis Experiment a Data Model for the Representation of a Gel Electrophoresis Experiment

Matthew R. Pocock, Anil Wipat, Matthew Pocock, 2022 .

Data Integration and Mining for Synthetic Biology Design.

Matthew R. Pocock, Phillip Lord, James Alastair McLaughlin, 2016, ACS synthetic biology.

KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data

Jan Baumbach, Anil Wipat, Nicolas Alcaraz, 2011, Internet Math..

Synthetic Biology Open Language (SBOL) Version 2.1.0

Zhen Zhang, Chris J. Myers, Jacob Beal, 2016, J. Integr. Bioinform..

Harmonizing semantic annotations for computational models in biology

Chris J. Myers, Olaf Wolkenhauer, Jacky L. Snoep, 2018, bioRxiv.

Synthetic Biology Open Language (SBOL) Version 2.0.0

Zhen Zhang, Jacob Beal, Matthew R. Pocock, 2015, J. Integr. Bioinform..

Microbase2.0: A Generic Framework for Computationally Intensive Bioinformatics Workflows in the Cloud

Anil Wipat, Jennifer Hallinan, Keith Flanagan, 2012, J. Integr. Bioinform..

Future‐proofing synthetic biology: educating the next generation

Anil Wipat, Richard I. Kitney, Kenneth Taylor, 2019, Engineering Biology.

Clustering incorporating shortest paths identifies relevant modules in functional interaction networks

Matthew R. Pocock, Anil Wipat, Jennifer Hallinan, 2009, 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0

Jacob Beal, Robert Sidney Cox, James McLaughlin, 2018, J. Integr. Bioinform..

Implementing the FuGE Object Model: a Systems Biology Data Portal and Integrator

Allyson L. Lister, Andrew R. Jones, Anil Wipat, 2007 .

Delivering web service coordination capability to users

Carole A. Goble, Anil Wipat, Peter Li, 2004, WWW Alt. '04.

Modeling and managing experimental data using FuGE.

Martin Eisenacher, Andrew R Jones, Anil Wipat, 2009, Omics : a journal of integrative biology.

SBOL-OWL: An ontological approach for formal and semantic representation of synthetic genetic circuits

Chris J. Myers, Phillip Lord, John H. Gennari, 2018 .

Bayesian integration of networks without gold standards

Darren J. Wilkinson, Phillip W. Lord, Anil Wipat, 2012, Bioinform..

Title: Synthetic Biology Open Language (SBOL) Version 1.0.0

Allan Kuchinsky, Chris J. Myers, Jacob Beal, 2011 .

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1

Robert Sidney Cox, James McLaughlin, Bryan Bartley, 2019, J. Integr. Bioinform..

SBOL Visual 2 Ontology

Thomas E. Gorochowski, Anil Wipat, Guy-Bart Stan, 2020 .

ShortBOL: A language for scripting designs for engineered biological systems using SyntheticBiology Open Language (SBOL).

Jacob Beal, Bryan Bartley, Matthew Crowther, 2020, ACS synthetic biology.

Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts

Goksel Misirli, Anil Wipat, Jennifer Hallinan, 2014, 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology.

A Multi-scale evolutionary algorithm for engineering bacterial populations

Anil Wipat, Jennifer Hallinan, 2015, IEEE CIBCB 2015.

{myGrid} and the drug discovery process

Robert Stevens, Mark Greenwood, Carole Goble, 2004 .

Applying Petri Nets to Systems Biology using XML Technologies

Anil Wipat, Albert Koelmans, Jason Steggles, 2004 .

Drug repurposing prediction for COVID-19 using probabilistic networks and crowdsourced curation

Matthew R. Pocock, James Alastair McLaughlin, Anil Wipat, 2020, 2005.11088.

Synthetic Biological Construction: Beyond 'bio-inspired' in the design of new materials and fabrication systems

Anil Wipat, Martyn Dade-Robertson, Helen Mitrani, 2017 .

SBOL Visual 2 Ontology.

Jacob Beal, Thomas E Gorochowski, Goksel Misirli, 2020, ACS synthetic biology.

Guidelines for reporting the use of gel electrophoresis in proteomics

Chris F. Taylor, Joachim Klose, Gyorgy Babnigg, 2008, Nature Biotechnology.

BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology

Matthew R. Pocock, Joseph Mullen, Goksel Misirli, 2013, J. Integr. Bioinform..

Automatic extraction of microorganisms and their habitats from free text using text mining workflows

Sophia Ananiadou, Anil Wipat, BalaKrishna Kolluru, 2011, J. Integr. Bioinform..

Systems biology of bacteria

Anil Wipat, Colin R. Harwood, 2012 .

Motifs and Modules in Fractured Functional Yeast Networks

Anil Wipat, Jennifer Hallinan, J. Hallinan, 2007, 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.

Modular Composition of Synthetic Biology Designs using Rule-Based Models

Vincent Danos, Paolo Zuliani, Goksel Misirli, 2016 .

Mining integrated semantic networks for drug repositioning opportunities

Joseph Mullen, Anil Wipat, Hannah Tipney, 2016, PeerJ.

Communicating Structure and Function in Synthetic Biology Diagrams.

Jacob Beal, James Alastair McLaughlin, Bryan Bartley, 2019, ACS synthetic biology.

Bridging the Gap between Design and Reality - A Dual Evolutionary Strategy for the Design of Synthetic Genetic Circuits

S. Park, Anil Wipat, Jennifer Hallinan, 2012, BIOINFORMATICS.

Performing \emph{In Silico} Experiments on the Grid: A Users' Perspective

Chris Greenhalgh, Anil Wipat, Robert Stevens, 2003 .

A standard-enabled workflow for synthetic biology.

Jacob Beal, James Alastair McLaughlin, Thomas E Gorochowski, 2017, Biochemical Society transactions.

On the use of agents in a BioInformatics grid

Michael Luck, Tom Rodden, Carole A. Goble, 2003, CCGrid 2003. 3rd IEEE/ACM International Symposium on Cluster Computing and the Grid, 2003. Proceedings..

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

Allan Kuchinsky, Jacob Beal, Drew Endy, 2014, Nature Biotechnology.

Thinking Soils: a synthetic biology approach to material-based design computation

Meng Zhang, Anil Wipat, Luis Hernan, 2016 .

Functional Analysis of Enzyme Families Using Residue-Residue Coevolution Similarity Networks

Anil Wipat, Christian Atallah, David James Skelton, 2019, bioRxiv.

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering

Thomas E. Gorochowski, Chris J. Myers, Jacob Beal, 2020, Frontiers in Bioengineering and Biotechnology.

Proposed data model for the next version of the synthetic biology open language.

Jacob Beal, Matthew R. Pocock, Goksel Misirli, 2015, ACS synthetic biology.

Synthetic Biology Open Language (SBOL) Version 2.1.0

Zhen Zhang, Jacob Beal, Matthew R. Pocock, 2012, Journal of integrative bioinformatics.

Codon optimisation for maximising gene expression in multiple species and microbial consortia

Anil Wipat, Michael A. White, Russell J. Davenport, 2020, bioRxiv.

A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference

Vincent Danos, Goksel Misirli, Anil Wipat, 2018, ACS synthetic biology.

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology.

James Alastair McLaughlin, Anil Wipat, Chris J Myers, 2018, ACS synthetic biology.

Model annotation for synthetic biology: automating model to nucleotide sequence conversion

Goksel Misirli, Anil Wipat, James R. Lawson, 2011, Bioinform..

Experiences with e-Science workflow specification and enactment in bioinformatics

Anil Wipat, Peter Li, Tom Oinn, 2003 .

SARGE: a tool for creation of putative genetic networks

Anil Wipat, L. Jason Steggles, Colin Harwood, 2004, Bioinform..

A RESTful API for Supporting Automated BioBrick Model Assembly

Anil Wipat, Matthew Pocock, J Hallinan, 2010 .

Annotation of SBML Models Through Rule-Based Semantic Integration

Phillip Lord, Allyson L. Lister, Anil Wipat, 2009 .

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization

Vincent Danos, Matthew R. Pocock, Paolo Zuliani, 2015, Bioinform..

A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci

Anil Wipat, Jennifer Hallinan, Keith Flanagan, 2014, J. Integr. Bioinform..

Sharing Structure and Function in Biological Design with SBOL 2.0.

Zhen Zhang, Jacob Beal, Matthew R. Pocock, 2016, ACS synthetic biology.

Network motifs in context: An exploration of the evolution of oscillatory dynamics in transcriptional networks

Anil Wipat, Jennifer Hallinan, J. Hallinan, 2008, 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE Concurrency Computat.: Pract. Exper. 2000; 00:1–7 Prepared using cpeauth.cls [Version: 2002/09/19 v2.02] Taverna: Lessons in creating

Edward A. Lee, Carole A. Goble, Robert Stevens, 2022 .

Standard virtual biological parts: a repository of modular modeling components for synthetic biology

Goksel Misirli, Anil Wipat, James R. Lawson, 2010, Bioinform..

Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL)

Jacob Beal, James Alastair McLaughlin, Goksel Misirli, 2018 .

Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets

Richard Banks, Anil Wipat, L. Jason Steggles, 2006, CMSB.

Computational intelligence for metabolic pathway design: Application to the pentose phosphate pathway

S. Park, Anil Wipat, Jennifer Hallinan, 2016, 2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).

The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative

Henning Hermjakob, Gyorgy Babnigg, Andrew R Jones, 2010, Proteomics.

SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design.

James Alastair McLaughlin, Anil Wipat, Chris J Myers, 2017, ACS synthetic biology.

Taverna: a tool for the composition and enactment of bioinformatics workflows

Matthew R. Pocock, Anil Wipat, Peter Li, 2004, Bioinform..

Annotation of SBML models through rule-based semantic integration

Matthew R. Pocock, Allyson L. Lister, Phillip W. Lord, 2009, J. Biomed. Semant..

Introduction to the Special Issue on Computational Synthetic Biology

Chris J. Myers, Anil Wipat, Herbert M. Sauro, 2014, ACM J. Emerg. Technol. Comput. Syst..

Compiling Combinatorial Genetic Circuits with Semantic Inference pdf

Vincent Danos, Goksel Misirli, Anil Wipat, 2018, ArXiv.

SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information.

Phillip Lord, James Alastair McLaughlin, Anil Wipat, 2019, ACS synthetic biology.

A Visual Language for Protein Design.

Jacob Beal, Robert Sidney Cox, James Alastair McLaughlin, 2017, ACS synthetic biology.

Composable Modular Models for Synthetic Biology

Goksel Misirli, Anil Wipat, Jennifer Hallinan, 2014, ACM J. Emerg. Technol. Comput. Syst..

Synthetic Biology Open Language (SBOL) Version 2.3

Matthew R. Pocock, John H. Gennari, Robert Sidney Cox, 2019, J. Integr. Bioinform..

The manual of industrial microbiology and biotechnology

Anil Wipat, Colin R. Harwood, Sierd Bron, 1999 .

Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis

Jaume Bacardit, Anil Wipat, Wendy Smith, 2021, Sensors.

Modelling The Fitness Landscapes of a SCRaMbLEd Yeast Genome

Goksel Misirli, Anil Wipat, Jennifer Hallinan, 2021, 2021 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).

Synthetic biology open language visual (SBOL Visual) version 2.3

Jacob Beal, Matthew R. Pocock, Robert Sidney Cox, 2021, J. Integr. Bioinform..

Ontology for Genome Comparison and Genomic Rearrangements

Robert Stevens, Anil Wipat, Matthew Pocock, 2004, Comparative and functional genomics.

Microfluidics for bacterial imaging

Anil Wipat, Lucy E. Eland, A. Wipat, 2016 .

Association of variations in I kappa B-epsilon with Graves’ disease using classical and myGrid methodologies

Robert Stevens, Anil Wipat, C Jennings, 2004 .

e-science tools for the genomic scale characterisation of bacterial secreted proteins

Phillip Lord, Anil Wipat, Colin R. Harwood, 2006 .

A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome

Anil Wipat, Ian Giles, Jennifer Hallinan, 2015, PloS one.