Anil Wipat

58 papers B 2C 9Journal 41Unranked 6
YearRankTypeTitle / Venue / Authors
2024 J jnl
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem.
Biosyst.
Christian Atallah, Katherine James, Zhen Ou, James Skelton, David Markham, Matt S. Burridge, James Finnigan, Simon Charnock, Anil Wipat
2024 — conf
NeDRex-Web: An Interactive Web Tool for Drug Repurposing by Exploring Heterogeneous Molecular Networks.
BIBM
Andreas Maier, 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, Sepideh Sadegh, Jan Baumbach
2023 J jnl
Synthetic biology open language (SBOL) version 3.1.0.
J. Integr. Bioinform.
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, Vishwesh Kulkarni, James Alastair McLaughlin, Göksel Misirli, Ernst Oberortner, Anil Wipat, Chris J. Myers
2022 C conf
Automatic Diverse Subset Selection From Enzyme Families by Solving the Maximum Diversity Problem.
CIBCB
Christian Atallah, Katherine James, Zhen Ou, James Skelton, David Markham, James Finnigan, Simon Charnock, Anil Wipat
2022 J jnl
Computational intelligence and machine learning in bioinformatics and computational biology.
Biosyst.
Madhu Chetty, Jennifer Hallinan, Gonzalo A. Ruz, Anil Wipat
2022 J jnl
Integration of probabilistic functional networks without an external Gold Standard.
BMC Bioinform.
Katherine James, Aoesha Alsobhe, Simon J. Cockell, Anil Wipat, Matthew R. Pocock
2022 J jnl
Modelling the fitness landscapes of a SCRaMbLEd yeast genome.
Biosyst.
Bill Yang, Goksel Misirli, Anil Wipat, Jennifer Hallinan
2021 J jnl
Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis.
Sensors
Yiming Huang, Wendy Smith, Colin Harwood, Anil Wipat, Jaume Bacardit
2021 C conf
Modelling The Fitness Landscapes of a SCRaMbLEd Yeast Genome.
CIBCB
Bill Yang, Goksel Misirli, Anil Wipat, Jennifer Hallinan
2021 J jnl
Synthetic biology open language visual (SBOL Visual) version 2.3.
J. Integr. Bioinform.
Hasan Baig, Pedro Fontanarosa, Vishwesh Kulkarni, James Alastair McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Shyam Bhakta, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Robert Sidney Cox III, Ángel Goñi-Moreno, Thomas E. Gorochowski, Raik Grünberg, Jihwan Lee, Augustin Luna, Curtis Madsen, Goksel Misirli, Tramy Nguyen, Nicolas Le Novère, Zachary Palchick, Matthew R. Pocock, Nicholas Roehner, Herbert M. Sauro, James Scott-Brown, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Logan Terry, Marta Vazquez Vilar, Christopher A. Voigt, Anil Wipat, David Zong, Zach Zundel, Jacob Beal, Chris J. Myers
2020 J jnl
Synthetic biology open language (SBOL) version 3.0.0.
J. Integr. Bioinform.
Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James Alastair McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Jacob Beal, Matthew Crowther, Thomas E. Gorochowski, Raik Grünberg, Goksel Misirli, James Scott-Brown, Ernst Oberortner, Anil Wipat, Chris J. Myers
2020 J jnl
Synthetic biology open language visual (SBOL visual) version 2.2.
J. Integr. Bioinform.
Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James Alastair McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Swapnil Bhatia, Shyam Bhakta, Michael Bissell, Kevin Clancy, Robert Sidney Cox III, Ángel Goñi-Moreno, Thomas E. Gorochowski, Raik Grünberg, Augustin Luna, Curtis Madsen, Goksel Misirli, Tramy Nguyen, Nicolas Le Novère, Zachary Palchick, Matthew R. Pocock, Nicholas Roehner, Herbert M. Sauro, James Scott-Brown, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Marta Vazquez Vilar, Christopher A. Voigt, Anil Wipat, David Zong, Zach Zundel, Jacob Beal, Chris J. Myers
2019 J jnl
Harmonizing semantic annotations for computational models in biology.
Briefings Bioinform.
Maxwell Lewis Neal, Matthias König, 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, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
2019 J jnl
Synthetic Biology Open Language (SBOL) Version 2.3.
J. Integr. Bioinform.
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, James Alastair McLaughlin, Xianwei Meng, Tramy Nguyen, Matthew R. Pocock, Meher Samineni, James Scott-Brown, Ysis Tarter, Michael Zhang, Zhen Zhang, Zach Zundel, Jacob Beal, Michael Bissell, Kevin Clancy, John H. Gennari, Goksel Misirli, Chris J. Myers, Ernst Oberortner, Herbert M. Sauro, Anil Wipat
2019 J jnl
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1.
J. Integr. Bioinform.
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, Raik Grünberg, Augustin Luna, James Alastair McLaughlin, Tramy Nguyen, Nicolas Le Novère, Matthew R. Pocock, Herbert M. Sauro, James Scott-Brown, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Christopher A. Voigt, Zach Zundel, Chris J. Myers, Jacob Beal, Anil Wipat
2018 J jnl
Compiling Combinatorial Genetic Circuits with Semantic Inference.
CoRR
William Waites, Goksel Misirli, Matteo Cavaliere, Vincent Danos, Anil Wipat
2018 J jnl
Synthetic Biology Open Language (SBOL) Version 2.2.0.
J. Integr. Bioinform.
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, Goksel Misirli, Ernst Oberortner, Matthew R. Pocock, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris J. Myers, Herbert M. Sauro, Anil Wipat
2018 J jnl
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.
J. Integr. Bioinform.
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, Nicolas Le Novère, Matthew R. Pocock, Herbert M. Sauro, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Christopher A. Voigt, Zach Zundel, Chris J. Myers, Jacob Beal, Anil Wipat
2016 J jnl
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.
Bioinform.
Goksel Misirli, Matteo Cavaliere, William Waites, Matthew R. Pocock, Curtis Madsen, Owen Gilfellon, Ricardo Honorato-Zimmer, Paolo Zuliani, Vincent Danos, Anil Wipat
2016 C conf
Computational intelligence for metabolic pathway design: Application to the pentose phosphate pathway.
CIBCB
James Skelton, Jennifer Hallinan, S. Park, Anil Wipat
2016 C conf
Engineering bacterial populations for pattern formation.
CIBCB
Daniel Sutantyo, Christopher Walker, Nicholas deBono, Jarryd Vargas, Anil Wipat, Jennifer S. Hallinan
2016 J jnl
Synthetic Biology Open Language (SBOL) Version 2.1.0.
J. Integr. Bioinform.
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, Ernst Oberortner, Matthew R. Pocock, Nicholas Roehner, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris J. Myers, Herbert M. Sauro, Anil Wipat
2015 J jnl
Synthetic Biology Open Language (SBOL) Version 2.0.0.
J. Integr. Bioinform.
Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Nicholas Roehner, Ernst Oberortner, Matthew R. Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Zhen Zhang, John H. Gennari, Chris J. Myers, Anil Wipat, Herbert M. Sauro
2014 J jnl
A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci.
J. Integr. Bioinform.
Keith Flanagan, Simon J. Cockell, Colin Harwood, Jennifer Hallinan, Sirintra Nakjang, Beth Lawry, Anil Wipat
2014 J jnl
BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species.
J. Integr. Bioinform.
Goksel Misirli, Jennifer Hallinan, Richard Röttger, Jan Baumbach, Anil Wipat
2014 J jnl
Composable Modular Models for Synthetic Biology.
ACM J. Emerg. Technol. Comput. Syst.
Goksel Misirli, Jennifer Hallinan, Anil Wipat
2014 J jnl
Introduction to the Special Issue on Computational Synthetic Biology.
ACM J. Emerg. Technol. Comput. Syst.
Chris J. Myers, Herbert M. Sauro, Anil Wipat
2014 J jnl
Probabilistic Latent Semantic Analysis Applied to Whole Bacterial Genomes Identifies Common Genomic Features.
J. Integr. Bioinform.
Julija Rusakovica, Jennifer Hallinan, Anil Wipat, Paolo Zuliani
2014 C conf
Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts.
CIBCB
Jennifer Hallinan, Owen Gilfellon, Goksel Misirli, Anil Wipat
2013 J jnl
BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology.
J. Integr. Bioinform.
Goksel Misirli, Anil Wipat, Joseph Mullen, Katherine James, Matthew R. Pocock, Wendy Smith, Nick Allenby, Jennifer Hallinan
2012 J jnl
Bayesian integration of networks without gold standards.
Bioinform.
Jochen Weile, Katherine James, Jennifer Hallinan, Simon J. Cockell, Phillip W. Lord, Anil Wipat, Darren J. Wilkinson
2012 — conf
Bridging the Gap between Design and Reality - A Dual Evolutionary Strategy for the Design of Synthetic Genetic Circuits.
BIOINFORMATICS
Jennifer Hallinan, S. Park, Anil Wipat
2012 J jnl
Data mining the human gut microbiota for therapeutic targets.
Briefings Bioinform.
Matthew Collison, Robert P. Hirt, Anil Wipat, Sirintra Nakjang, Philippe Sanseau, James R. Brown
2012 J jnl
Microbase2.0: A Generic Framework for Computationally Intensive Bioinformatics Workflows in the Cloud.
J. Integr. Bioinform.
Keith Flanagan, Sirintra Nakjang, Jennifer Hallinan, Colin Harwood, Robert P. Hirt, Matthew R. Pocock, Anil Wipat
2011 J jnl
Automatic extraction of microorganisms and their habitats from free text using text mining workflows.
J. Integr. Bioinform.
BalaKrishna Kolluru, Sirintra Nakjang, Robert P. Hirt, Anil Wipat, Sophia Ananiadou
2011 J jnl
Customizable views on semantically integrated networks for systems biology.
Bioinform.
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
2011 J jnl
KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data.
Internet Math.
Nicolas Alcaraz, Hande Kücük, Jochen Weile, Anil Wipat, Jan Baumbach
2011 J jnl
Model annotation for synthetic biology: automating model to nucleotide sequence conversion.
Bioinform.
Goksel Misirli, Jennifer Hallinan, Tommy Yu, James R. Lawson, Sarala M. Wimalaratne, Mike T. Cooling, Anil Wipat
2010 J jnl
An integrated dataset for in silico drug discovery.
J. Integr. Bioinform.
Simon J. Cockell, Jochen Weile, Phillip W. Lord, Claire Wipat, Dmytro Andriychenko, Matthew R. Pocock, Darren J. Wilkinson, Malcolm Young, Anil Wipat
2010 J jnl
Annotation of SBML models through rule-based semantic integration.
J. Biomed. Semant.
Allyson L. Lister, Phillip W. Lord, Matthew R. Pocock, Anil Wipat
2010 J jnl
Standard virtual biological parts: a repository of modular modeling components for synthetic biology.
Bioinform.
Mike T. Cooling, V. Rouilly, Goksel Misirli, James R. Lawson, Tommy Yu, Jennifer Hallinan, Anil Wipat
2009 C conf
Clustering incorporating shortest paths identifies relevant modules in functional interaction networks.
CIBCB
Jennifer Hallinan, Matthew R. Pocock, Stephen G. Addinall, David A. Lydall, Anil Wipat
2009 — conf
Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes.
DILS
Katherine James, Anil Wipat, Jennifer Hallinan
2009 J jnl
Saint: a lightweight integration environment for model annotation.
Bioinform.
Allyson L. Lister, Matthew R. Pocock, Morgan L. Taschuk, Anil Wipat
2008 C conf
Network motifs in context: An exploration of the evolution of oscillatory dynamics in transcriptional networks.
CIBCB
Jennifer Hallinan, Anil Wipat
2007 J jnl
Exploring Microbial Genome Sequences to Identify Protein Families on the Grid.
IEEE Trans. Inf. Technol. Biomed.
Yudong Sun, Anil Wipat, Matthew R. Pocock, P. A. Lee, Keith Flanagan, J. T. Worthington
2007 J jnl
Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models.
J. Integr. Bioinform.
Allyson L. Lister, Matthew R. Pocock, Anil Wipat
2007 C conf
Motifs and Modules in Fractured Functional Yeast Networks.
CIBCB
Jennifer Hallinan, Anil Wipat
2007 J jnl
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach.
Bioinform.
L. Jason Steggles, Richard Banks, Oliver Shaw, Anil Wipat
2006 C conf
Clustering and Cross-talk in a Yeast Functional Interaction Network.
CIBCB
Jennifer Hallinan, Anil Wipat
2006 — conf
Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets.
CMSB
L. Jason Steggles, Richard Banks, Anil Wipat
2006 J jnl
Taverna: lessons in creating a workflow environment for the life sciences.
Concurr. Comput. Pract. Exp.
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, Matthew R. Pocock, Martin Senger, Robert Stevens, Anil Wipat, Chris Wroe
2005 B conf
A grid-based system for microbial genome comparison and analysis.
CCGRID
Yudong Sun, Anil Wipat, Matthew R. Pocock, Pete A. Lee, Paul Watson, Keith Flanagan, James T. Worthington
2005 — conf
Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks.
PASM@FM
Oliver Shaw, L. Jason Steggles, Anil Wipat
2004 — conf
Delivering web service coordination capability to users.
WWW (Alternate Track Papers & Posters)
Thomas M. Oinn, Matthew Addis, Justin Ferris, Darren Marvin, Robert Mark Greenwood, Carole A. Goble, Anil Wipat, Peter Li, Tim Carver
2004 J jnl
SARGE: a tool for creation of putative genetic networks.
Bioinform.
O. J. Shaw, Colin Harwood, L. Jason Steggles, Anil Wipat
2004 J jnl
Taverna: a tool for the composition and enactment of bioinformatics workflows.
Bioinform.
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
2003 B conf
On the Use of Agents in BioInformatics Grid.
CCGRID
Luc Moreau, 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, Chris Greenhalgh, Peter Li, Xiaojian Liu, Phillip W. Lord, Michael Luck, Darren Marvin, Thomas M. Oinn, Norman W. Paton, Steve Pettifer, Milena V. Radenkovic, Angus Roberts, Alan J. Robinson, Tom Rodden, Martin Senger, Nick Sharman, Robert Stevens, Brian Warboys, Anil Wipat, Chris Wroe