Anil Wipat

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 21

Top Topics

Computational Models

Semantic Annotation

Learning From Positive Data

Top Venues

J. Integr. Bioinform.

ACM J. Emerg. Technol. Comput. Syst.

Publications

Christian Atallah, Katherine James, Zhen Ou, James Skelton, David Markham, Matt S. Burridge, James Finnigan, Simon Charnock, Anil Wipat
A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem. Biosyst. 236 (2024)
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 V. Kulkarni, James Alastair McLaughlin, Göksel Misirli, Ernst Oberortner, Anil Wipat, Chris J. Myers
Synthetic biology open language (SBOL) version 3.1.0. J. Integr. Bioinform. 20 (1) (2023)
Bill Yang, Goksel Misirli, Anil Wipat, Jennifer Hallinan
Modelling the fitness landscapes of a SCRaMbLEd yeast genome. Biosyst. 219 (2022)
Christian Atallah, Katherine James, Zhen Ou, James Skelton, David Markham, James Finnigan, Simon Charnock, Anil Wipat
Automatic Diverse Subset Selection From Enzyme Families by Solving the Maximum Diversity Problem. CIBCB (2022)
Madhu Chetty, Jennifer Hallinan, Gonzalo A. Ruz, Anil Wipat
Computational intelligence and machine learning in bioinformatics and computational biology. Biosyst. 222 (2022)
Katherine James, Aoesha Alsobhe, Simon J. Cockell, Anil Wipat, Matthew R. Pocock
Integration of probabilistic functional networks without an external Gold Standard. BMC Bioinform. 23 (1) (2022)
Hasan Baig, Pedro Fontanarossa, Vishwesh V. 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
Synthetic biology open language visual (SBOL Visual) version 2.3. J. Integr. Bioinform. 18 (3) (2021)
Yiming Huang, Wendy Smith, Colin Harwood, Anil Wipat, Jaume Bacardit
Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis. Sensors 21 (7) (2021)
Bill Yang, Goksel Misirli, Anil Wipat, Jennifer Hallinan
Modelling The Fitness Landscapes of a SCRaMbLEd Yeast Genome. CIBCB (2021)
Hasan Baig, Pedro Fontanarrosa, Vishwesh V. 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 Gambardella, 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
Synthetic biology open language visual (SBOL visual) version 2.2. J. Integr. Bioinform. 17 (2-3) (2020)
Hasan Baig, Pedro Fontanarrosa, Vishwesh V. 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
Synthetic biology open language (SBOL) version 3.0.0. J. Integr. Bioinform. 17 (2-3) (2020)
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
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20 (2) (2019)
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
Synthetic Biology Open Language (SBOL) Version 2.3. J. Integr. Bioinform. 16 (2) (2019)
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
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. J. Integr. Bioinform. 16 (2) (2019)
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
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. J. Integr. Bioinform. 15 (1) (2018)
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
Synthetic Biology Open Language (SBOL) Version 2.2.0. J. Integr. Bioinform. 15 (1) (2018)
William Waites, Goksel Misirli, Matteo Cavaliere, Vincent Danos, Anil Wipat
Compiling Combinatorial Genetic Circuits with Semantic Inference. CoRR (2018)
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
Synthetic Biology Open Language (SBOL) Version 2.1.0. J. Integr. Bioinform. 13 (3) (2016)
D. J. Skelton, Jennifer Hallinan, S. Park, Anil Wipat
Computational intelligence for metabolic pathway design: Application to the pentose phosphate pathway. CIBCB (2016)
Daniel Sutantyo, Christopher Walker, Nicholas deBono, Jarryd Vargas, Anil Wipat, Jennifer S. Hallinan
Engineering bacterial populations for pattern formation. CIBCB (2016)
Goksel Misirli, Matteo Cavaliere, William Waites, Matthew R. Pocock, Curtis Madsen, Owen Gilfellon, Ricardo Honorato-Zimmer, Paolo Zuliani, Vincent Danos, Anil Wipat
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. Bioinform. 32 (6) (2016)
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
Synthetic Biology Open Language (SBOL) Version 2.0.0. J. Integr. Bioinform. 12 (2) (2015)
Goksel Misirli, Jennifer Hallinan, Anil Wipat
Composable Modular Models for Synthetic Biology. ACM J. Emerg. Technol. Comput. Syst. 11 (3) (2014)
Goksel Misirli, Jennifer Hallinan, Richard Röttger, Jan Baumbach, Anil Wipat
BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species. J. Integr. Bioinform. 11 (2) (2014)
Chris J. Myers, Herbert M. Sauro, Anil Wipat
Introduction to the Special Issue on Computational Synthetic Biology. ACM J. Emerg. Technol. Comput. Syst. 11 (3) (2014)
Julija Rusakovica, Jennifer Hallinan, Anil Wipat, Paolo Zuliani
Probabilistic Latent Semantic Analysis Applied to Whole Bacterial Genomes Identifies Common Genomic Features. J. Integr. Bioinform. 11 (2) (2014)
Jennifer Hallinan, Owen Gilfellon, Goksel Misirli, Anil Wipat
Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts. CIBCB (2014)
Keith Flanagan, Simon J. Cockell, Colin Harwood, Jennifer Hallinan, Sirintra Nakjang, Beth Lawry, Anil Wipat
A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci. J. Integr. Bioinform. 11 (2) (2014)
Goksel Misirli, Anil Wipat, Joseph Mullen, Katherine James, Matthew R. Pocock, Wendy Smith, Nick Allenby, Jennifer Hallinan
BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. J. Integr. Bioinform. 10 (2) (2013)
Jochen Weile, Katherine James, Jennifer Hallinan, Simon J. Cockell, Phillip W. Lord, Anil Wipat, Darren J. Wilkinson
Bayesian integration of networks without gold standards. Bioinform. 28 (11) (2012)
Matthew Collison, Robert P. Hirt, Anil Wipat, Sirintra Nakjang, Philippe Sanseau, James R. Brown
Data mining the human gut microbiota for therapeutic targets. Briefings Bioinform. 13 (6) (2012)
Jennifer Hallinan, S. Park, Anil Wipat
Bridging the Gap between Design and Reality - A Dual Evolutionary Strategy for the Design of Synthetic Genetic Circuits. BIOINFORMATICS (2012)
Keith Flanagan, Sirintra Nakjang, Jennifer Hallinan, Colin Harwood, Robert P. Hirt, Matthew R. Pocock, Anil Wipat
Microbase2.0: A Generic Framework for Computationally Intensive Bioinformatics Workflows in the Cloud. J. Integr. Bioinform. 9 (2) (2012)
BalaKrishna Kolluru, Sirintra Nakjang, Robert P. Hirt, Anil Wipat, Sophia Ananiadou
Automatic extraction of microorganisms and their habitats from free text using text mining workflows. J. Integr. Bioinform. 8 (2) (2011)
Goksel Misirli, Jennifer Hallinan, Tommy Yu, James R. Lawson, Sarala M. Wimalaratne, Mike T. Cooling, Anil Wipat
Model annotation for synthetic biology: automating model to nucleotide sequence conversion. Bioinform. 27 (7) (2011)
Nicolas Alcaraz, Hande Kücük, Jochen Weile, Anil Wipat, Jan Baumbach
KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data. Internet Math. 7 (4) (2011)
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
Customizable views on semantically integrated networks for systems biology. Bioinform. 27 (9) (2011)
Mike T. Cooling, V. Rouilly, Goksel Misirli, James R. Lawson, Tommy Yu, Jennifer Hallinan, Anil Wipat
Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinform. 26 (7) (2010)
Allyson L. Lister, Phillip W. Lord, Matthew R. Pocock, Anil Wipat
Annotation of SBML models through rule-based semantic integration. J. Biomed. Semant. 1 (S-1) (2010)
Simon J. Cockell, Jochen Weile, Phillip W. Lord, Claire Wipat, Dmytro Andriychenko, Matthew R. Pocock, Darren J. Wilkinson, Malcolm Young, Anil Wipat
An integrated dataset for in silico drug discovery. J. Integr. Bioinform. 7 (3) (2010)
Katherine James, Anil Wipat, Jennifer Hallinan
Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes. DILS (2009)
Allyson L. Lister, Matthew R. Pocock, Morgan L. Taschuk, Anil Wipat
Saint: a lightweight integration environment for model annotation. Bioinform. 25 (22) (2009)
Jennifer Hallinan, Matthew R. Pocock, Stephen G. Addinall, David A. Lydall, Anil Wipat
Clustering incorporating shortest paths identifies relevant modules in functional interaction networks. CIBCB (2009)
Jennifer Hallinan, Anil Wipat
Network motifs in context: An exploration of the evolution of oscillatory dynamics in transcriptional networks. CIBCB (2008)
Yudong Sun, Anil Wipat, Matthew R. Pocock, P. A. Lee, Keith Flanagan, J. T. Worthington
Exploring Microbial Genome Sequences to Identify Protein Families on the Grid. IEEE Trans. Inf. Technol. Biomed. 11 (4) (2007)
L. Jason Steggles, Richard Banks, Oliver Shaw, Anil Wipat
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach. Bioinform. 23 (3) (2007)
Jennifer Hallinan, Anil Wipat
Motifs and Modules in Fractured Functional Yeast Networks. CIBCB (2007)
Allyson L. Lister, Matthew R. Pocock, Anil Wipat
Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models. J. Integr. Bioinform. 4 (3) (2007)
L. Jason Steggles, Richard Banks, Anil Wipat
Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets. CMSB (2006)
Jennifer Hallinan, Anil Wipat
Clustering and Cross-talk in a Yeast Functional Interaction Network. CIBCB (2006)
Oliver Shaw, L. Jason Steggles, Anil Wipat
Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks. Electron. Notes Theor. Comput. Sci. 151 (3) (2006)
Thomas M. Oinn, Robert Mark Greenwood, Matthew Addis, M. 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
Taverna: lessons in creating a workflow environment for the life sciences. Concurr. Comput. Pract. Exp. 18 (10) (2006)
Yudong Sun, Anil Wipat, Matthew R. Pocock, P. A. Lee, P. Watson, Keith Flanagan, J. T. Worthington
A grid-based system for microbial genome comparison and analysis. CCGRID (2005)
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
Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinform. 20 (17) (2004)
Thomas M. Oinn, Matthew Addis, Justin Ferris, Darren Marvin, Robert Mark Greenwood, Carole A. Goble, Anil Wipat, Peter Li, Tim Carver
Delivering web service coordination capability to users. WWW (Alternate Track Papers & Posters) (2004)
O. J. Shaw, Colin Harwood, L. Jason Steggles, Anil Wipat
SARGE: a tool for creation of putative genetic networks. Bioinform. 20 (18) (2004)
Luc Moreau, Simon Miles, Carole A. Goble, Robert Mark Greenwood, Vijay Dialani, Matthew Addis, M. 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
On the Use of Agents in BioInformatics Grid. CCGRID (2003)