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2020 – today
- 2024
[j40]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: 105105 (2024)- 2023
- [j39]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:
Synthetic biology open language (SBOL) version 3.1.0. J. Integr. Bioinform. 20(1) (2023) - 2022
- [j38]Bill Yang, Goksel Misirli, Anil Wipat, Jennifer Hallinan:
Modelling the fitness landscapes of a SCRaMbLEd yeast genome. Biosyst. 219: 104730 (2022) - [j37]Madhu Chetty, Jennifer Hallinan, Gonzalo A. Ruz, Anil Wipat:
Computational intelligence and machine learning in bioinformatics and computational biology. Biosyst. 222: 104792 (2022) - [j36]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): 302 (2022) - [c16]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: 1-9 - 2021
- [j35]Hasan Baig, Pedro Fontanarossa, 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:
Synthetic biology open language visual (SBOL Visual) version 2.3. J. Integr. Bioinform. 18(3) (2021) - [j34]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): 2436 (2021) - [c15]Bill Yang, Goksel Misirli, Anil Wipat, Jennifer Hallinan:
Modelling The Fitness Landscapes of a SCRaMbLEd Yeast Genome. CIBCB 2021: 1-9 - 2020
- [j33]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:
Synthetic biology open language visual (SBOL visual) version 2.2. J. Integr. Bioinform. 17(2-3) (2020) - [j32]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:
Synthetic biology open language (SBOL) version 3.0.0. J. Integr. Bioinform. 17(2-3) (2020)
2010 – 2019
- 2019
- [j31]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): 540-550 (2019) - [j30]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) - [j29]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) - 2018
- [j28]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) - [j27]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) - [i1]William Waites, Goksel Misirli, Matteo Cavaliere, Vincent Danos, Anil Wipat:
Compiling Combinatorial Genetic Circuits with Semantic Inference. CoRR abs/1811.01793 (2018) - 2016
- [j26]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): 908-917 (2016) - [j25]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) - [c14]James Skelton, Jennifer Hallinan, S. Park, Anil Wipat:
Computational intelligence for metabolic pathway design: Application to the pentose phosphate pathway. CIBCB 2016: 1-6 - [c13]Daniel Sutantyo, Christopher Walker, Nicholas deBono, Jarryd Vargas, Anil Wipat, Jennifer S. Hallinan:
Engineering bacterial populations for pattern formation. CIBCB 2016: 1-6 - 2015
- [j24]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) - 2014
- [j23]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): 20:1-20:5 (2014) - [j22]Goksel Misirli, Jennifer Hallinan, Anil Wipat:
Composable Modular Models for Synthetic Biology. ACM J. Emerg. Technol. Comput. Syst. 11(3): 22:1-22:19 (2014) - [j21]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) - [j20]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) - [j19]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) - [c12]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: 1-8 - 2013
- [j18]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) - 2012
- [j17]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): 751-768 (2012) - [j16]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): 1495-1500 (2012) - [j15]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) - [c11]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: 263-268 - 2011
- [j14]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): 973-979 (2011) - [j13]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): 1299-1306 (2011) - [j12]Nicolas Alcaraz, Hande Kücük, Jochen Weile, Anil Wipat, Jan Baumbach:
KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data. Internet Math. 7(4): 299-313 (2011) - [j11]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) - 2010
- [j10]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): 925-931 (2010) - [j9]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): S3 (2010) - [j8]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)
2000 – 2009
- 2009
- [j7]Allyson L. Lister, Matthew R. Pocock, Morgan L. Taschuk, Anil Wipat:
Saint: a lightweight integration environment for model annotation. Bioinform. 25(22): 3026-3027 (2009) - [c10]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: 228-236 - [c9]Katherine James, Anil Wipat, Jennifer Hallinan:
Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes. DILS 2009: 31-46 - 2008
- [c8]Jennifer Hallinan, Anil Wipat:
Network motifs in context: An exploration of the evolution of oscillatory dynamics in transcriptional networks. CIBCB 2008: 83-89 - 2007
- [j6]L. Jason Steggles, Richard Banks, Oliver Shaw, Anil Wipat:
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach. Bioinform. 23(3): 336-343 (2007) - [j5]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) - [j4]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): 435-442 (2007) - [c7]Jennifer Hallinan, Anil Wipat:
Motifs and Modules in Fractured Functional Yeast Networks. CIBCB 2007: 189-196 - 2006
- [j3]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:
Taverna: lessons in creating a workflow environment for the life sciences. Concurr. Comput. Pract. Exp. 18(10): 1067-1100 (2006) - [c6]Jennifer Hallinan, Anil Wipat:
Clustering and Cross-talk in a Yeast Functional Interaction Network. CIBCB 2006: 1-8 - [c5]L. Jason Steggles, Richard Banks, Anil Wipat:
Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets. CMSB 2006: 127-141 - 2005
- [c4]Yudong Sun, Anil Wipat, Matthew R. Pocock, Pete A. Lee, Paul Watson, Keith Flanagan, James T. Worthington:
A grid-based system for microbial genome comparison and analysis. CCGRID 2005: 977-984 - [c3]Oliver Shaw, L. Jason Steggles, Anil Wipat:
Automatic Parameterisation of Stochastic Petri Net Models of Biological Networks. PASM@FM 2005: 111-129 - 2004
- [j2]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): 3045-3054 (2004) - [j1]O. J. Shaw, Colin Harwood, L. Jason Steggles, Anil Wipat:
SARGE: a tool for creation of putative genetic networks. Bioinform. 20(18): 3638-3640 (2004) - [c2]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: 438-439 - 2003
- [c1]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:
On the Use of Agents in BioInformatics Grid. CCGRID 2003: 653-660
Coauthor Index
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