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ORCIDDouglas B. Kell
Person information
- affiliation: University of Manchester, School of Chemistry, UK
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Journal Articles
- 2020
[j43]Yash Khemchandani, Stephen O'Hagan, Soumitra Samanta, Neil Swainston, Timothy J. Roberts, Danushka Bollegala
, Douglas B. Kell:
DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach. J. Cheminformatics 12(1): 53 (2020)- 2018
- [j42]Pablo Carbonell, Jerry Wong, Neil Swainston, Eriko Takano, Nicholas J. Turner, Nigel S. Scrutton, Douglas B. Kell, Rainer Breitling, Jean-Loup Faulon:
Selenzyme: enzyme selection tool for pathway design. Bioinform. 34(12): 2153-2154 (2018) - [j41]Neil Swainston, Mark Dunstan, Adrian J. Jervis, Christopher J. Robinson, Pablo Carbonell, Alan R. Williams, Jean-Loup Faulon, Nigel S. Scrutton, Douglas B. Kell:
PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts. Bioinform. 34(13): 2327-2329 (2018) - 2017
- [j40]Douglas B. Kell:
Evolutionary algorithms and synthetic biology for directed evolution: commentary on "on the mapping of genotype to phenotype in evolutionary algorithms" by Peter A. Whigham, Grant Dick, and James Maclaurin. Genet. Program. Evolvable Mach. 18(3): 373-378 (2017) - [j39]Steve O'Hagan, Douglas B. Kell:
Analysis of drug-endogenous human metabolite similarities in terms of their maximum common substructures. J. Cheminformatics 9(1): 18:1-18:17 (2017) - [j38]Neil Swainston, Andrew Currin, Lucy Green, Rainer Breitling, Philip J. Day, Douglas B. Kell:
CodonGenie: optimised ambiguous codon design tools. PeerJ Comput. Sci. 3: e120 (2017) - 2015
- [j37]Steve O'Hagan, Douglas B. Kell:
Software review: the KNIME workflow environment and its applications in genetic programming and machine learning. Genet. Program. Evolvable Mach. 16(3): 387-391 (2015) - 2014
- [j36]Neil Swainston, Andrew Currin, Philip J. Day, Douglas B. Kell:
GeneGenie: optimized oligomer design for directed evolution. Nucleic Acids Res. 42(Webserver-Issue): 395-400 (2014) - 2013
- [j35]Makoto Miwa, Tomoko Ohta, Rafal Rak, Andrew Rowley, Douglas B. Kell, Sampo Pyysalo, Sophia Ananiadou:
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. Bioinform. 29(13): 44-52 (2013) - [j34]Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn P. van Iersel, Sarah M. Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère:
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 7: 116 (2013) - 2012
- [j33]Marie Brown, David C. Wedge, Royston Goodacre, Douglas B. Kell, Philip N. Baker, Louise C. Kenny, Mamas A. Mamas, Ludwig Neyses, Warwick B. Dunn:
Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. Bioinform. 28(1): 149 (2012) - [j32]Makoto Miwa, Paul Thompson, John McNaught, Douglas B. Kell, Sophia Ananiadou:
Extracting semantically enriched events from biomedical literature. BMC Bioinform. 13: 108 (2012) - [j31]Pinar Pir, Alex Gutteridge, Jian Wu, Bharat Rash, Douglas B. Kell, Nianshu Zhang, Stephen G. Oliver:
The genetic control of growth rate: a systems biology study in yeast. BMC Syst. Biol. 6: 4 (2012) - [j30]Dave Lee, Kieran Smallbone, Warwick B. Dunn, Ettore Murabito, Catherine Winder, Douglas B. Kell, Pedro Mendes, Neil Swainston:
Improving metabolic flux predictions using absolute gene expression data. BMC Syst. Biol. 6: 73 (2012) - 2011
- [j29]Marie Brown, David C. Wedge, Royston Goodacre, Douglas B. Kell, Philip N. Baker, Louise C. Kenny, Mamas A. Mamas, Ludwig Neyses, Warwick B. Dunn:
Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. Bioinform. 27(8): 1108-1112 (2011) - [j28]Yunjiao Wang, Pawel Paszek, Caroline A. Horton, Douglas B. Kell, Michael R. H. White, David S. Broomhead, Mark R. Muldoon:
Interactions among oscillatory pathways in NF-kappa B signaling. BMC Syst. Biol. 5: 23 (2011) - [j27]Yogendra Patel, Catherine A. Heyward, Michael R. H. White, Douglas B. Kell:
Predicting the points of interaction of small molecules in the NF-κB pathway. BMC Syst. Biol. 5: 32 (2011) - [j26]Neil Swainston, Kieran Smallbone, Pedro Mendes, Douglas B. Kell, Norman W. Paton:
The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. J. Integr. Bioinform. 8(2) (2011) - 2010
- [j25]Alice Villéger, Stephen Pettifer, Douglas B. Kell:
Arcadia: a visualization tool for metabolic pathways. Bioinform. 26(11): 1470-1471 (2010) - [j24]William Rowe, David C. Wedge, Mark Platt, Douglas B. Kell, Joshua D. Knowles:
Predictive models for population performance on real biological fitness landscapes. Bioinform. 26(17): 2145-2152 (2010) - [j23]Terri K. Attwood, Douglas B. Kell, Philip McDermott, James Marsh, Stephen Pettifer, David Thorne:
Utopia documents: linking scholarly literature with research data. Bioinform. 26(18) (2010) - [j22]Peter Li, Joseph O. Dada, Daniel Jameson, Irena Spasic, Neil Swainston, Kathleen Carroll, Warwick B. Dunn, Farid Khan, Naglis Malys, Hanan L. Messiha, Evangelos Simeonidis, Dieter Weichart, Catherine Winder, Jill Wishart, David S. Broomhead, Carole A. Goble, Simon J. Gaskell, Douglas B. Kell, Hans V. Westerhoff, Pedro Mendes, Norman W. Paton:
Systematic integration of experimental data and models in systems biology. BMC Bioinform. 11: 582 (2010) - [j21]Paul D. Dobson, Kieran Smallbone, Daniel Jameson, Evangelos Simeonidis, Karin Lanthaler, Pinar Pir, Chuan Lu, Neil Swainston, Warwick B. Dunn, Paul Fisher, Duncan Hull, Marie Brown, Olusegun Oshota, Natalie J. Stanford, Douglas B. Kell, Ross D. King, Stephen G. Oliver, Robert D. Stevens, Pedro Mendes:
Further developments towards a genome-scale metabolic model of yeast. BMC Syst. Biol. 4: 145 (2010) - 2009
- [j20]Irena Spasic, Evangelos Simeonidis, Hanan L. Messiha, Norman W. Paton, Douglas B. Kell:
KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways. Bioinform. 25(11): 1404-1411 (2009) - [j19]Daniel Jameson, David A. Turner, John Ankers, Stephnie Kennedy, Sheila Ryan, Neil Swainston, Tony Griffiths, David G. Spiller, Stephen G. Oliver, Michael R. H. White, Douglas B. Kell, Norman W. Paton:
Information management for high content live cell imaging. BMC Bioinform. 10 (2009) - [j18]Steve Pettifer, David Thorne, Philip McDermott, James Marsh, Alice Villéger, Douglas B. Kell, Teresa K. Attwood:
Visualising biological data: a semantic approach to tool and database integration. BMC Bioinform. 10(S-6) (2009) - [j17]Thomas Williamson, Jean-Marc Schwartz, Douglas B. Kell, Lubomira Stateva:
Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae. BMC Syst. Biol. 3: 70 (2009) - 2008
- [j16]Yisu Jin, Joshua D. Knowles, Hongmei Lu, Yizeng Liang, Douglas B. Kell:
The landscape adaptive particle swarm optimizer. Appl. Soft Comput. 8(1): 295-304 (2008) - [j15]Peter Li, Tom Oinn, Stian Soiland, Douglas B. Kell:
Automated manipulation of systems biology models using libSBML within Taverna workflows. Bioinform. 24(2): 287-289 (2008) - [j14]Bayu Jayawardhana, Douglas B. Kell, Magnus Rattray:
Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo. Bioinform. 24(9): 1191-1197 (2008) - [j13]Peter Li, Juan I. Castrillo, Giles Velarde, Ingo Wassink, Stian Soiland-Reyes, Stuart Owen, David Withers, Tom Oinn, Matthew R. Pocock, Carole A. Goble, Stephen G. Oliver, Douglas B. Kell:
Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data. BMC Bioinform. 9 (2008) - [j12]Irena Spasic, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B. Kell, Norman W. Paton:
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. BMC Bioinform. 9(S-5) (2008) - [j11]Duncan Hull, Steve Pettifer, Douglas B. Kell:
Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web. PLoS Comput. Biol. 4(10) (2008) - 2007
- [j10]Thomas Williamson, Frank Bruggemann, Douglas B. Kell, Lubomira Stateva:
Towards a mathematical model of the cAMP pathway in S. cerevisiae. BMC Syst. Biol. 1(S-1): P18 (2007) - [j9]Julia Handl, Douglas B. Kell, Joshua D. Knowles:
Multiobjective Optimization in Bioinformatics and Computational Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 4(2): 279-292 (2007) - 2006
- [j8]Irena Spasic, Warwick B. Dunn, Giles Velarde, Andy Tseng, Helen Jenkins, Nigel Hardy, Stephen G. Oliver, Douglas B. Kell:
MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics. BMC Bioinform. 7: 281 (2006) - 2005
- [j7]Julia Handl, Joshua D. Knowles, Douglas B. Kell:
Computational cluster validation in post-genomic data analysis. Bioinform. 21(15): 3201-3212 (2005) - [j6]David Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, A. Joseph Wood, Karim Nashar, Douglas B. Kell, Andy Brass:
maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination. BMC Bioinform. 6: 264 (2005) - 2001
- [j5]Pedro Mendes, Douglas B. Kell:
MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. Bioinform. 17(3): 288-289 (2001) - [j4]Christopher H. Bryant, Stephen H. Muggleton, Stephen G. Oliver, Douglas B. Kell, Philip G. K. Reiser, Ross D. King:
Combining Inductive Logic Programming, Active Learning and Robotics to Discover the Function of Genes. Electron. Trans. Artif. Intell. 5(B): 1-36 (2001) - [j3]Philip G. K. Reiser, Ross D. King, Douglas B. Kell, Stephen H. Muggleton, Christopher H. Bryant, Stephen G. Oliver:
Developing a Logical Model of Yeast Metabolism. Electron. Trans. Artif. Intell. 5(B): 223-244 (2001) - 2000
- [j2]Helen E. Johnson, Richard J. Gilbert, Michael K. Winson, Royston Goodacre, Aileen R. Smith, Jem J. Rowland, Michael A. Hall, Douglas B. Kell:
Explanatory Analysis of the Metabolome Using Genetic Programming of Simple, Interpretable Rules. Genet. Program. Evolvable Mach. 1(3): 243-258 (2000) - 1998
- [j1]Pedro Mendes, Douglas B. Kell:
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinform. 14(10): 869-883 (1998)
Conference and Workshop Papers
- 2008
- [c11]Caroline Farrelly, Douglas B. Kell, Joshua D. Knowles:
Molecular Structure Elucidation Using Ant Colony Optimization: A Preliminary Study. ANTS Conference 2008: 120-131 - [c10]David C. Wedge, Douglas B. Kell:
Rapid prediction of optimum population size in genetic programming using a novel genotype -: fitness correlation. GECCO 2008: 1315-1322 - 2007
- [c9]Yisu Jin, Hong Yue, Martin Brown, Yizeng Liang, Douglas B. Kell:
Improving Data Fitting of a Signal Transduction Model by Global Sensitivity Analysis. ACC 2007: 2708-2713 - [c8]David C. Wedge, Simon J. Gaskell, Simon J. Hubbard, Douglas B. Kell, King Wai Lau, Claire Eyers:
Peptide detectability following ESI mass spectrometry: prediction using genetic programming. GECCO 2007: 2219-2225 - 2003
- [c7]David Corne, Martin J. Oates, Douglas B. Kell:
Landscape State Machines: Tools for Evolutionary Algorithm Performance Analyses and Landscape/Algorithm Mapping. EvoWorkshops 2003: 187-198 - 2002
- [c6]David W. Corne, Martin J. Oates, Douglas B. Kell:
Fitness Gains and Mutation Patterns: Deriving Mutation Rates by Exploiting Landscape Data. FOGA 2002: 347-364 - [c5]David Corne, Martin J. Oates, Douglas B. Kell:
On Fitness Distributions and Expected Fitness Gain of Mutation Rates in Parallel Evolutionary Algorithms. PPSN 2002: 132-141 - [c4]Martin J. Oates, David Corne, Douglas B. Kell:
Observed dynamics of Large Scale Parallel Evolutionary Algorithms with Implications for protein Engineering. SEAL 2002: 208-229 - 2001
- [c3]Janet Taylor, Jem J. Rowland, Douglas B. Kell:
Spectral analysis via supervised genetic search with application-specific mutations. CEC 2001: 481-486 - [c2]Wei Liu, Andy Woodward, Douglas B. Kell:
Compression of proteome gel images using complex wavelet transform. German Conference on Bioinformatics 2001: 207 - 2000
- [c1]Richard J. Gilbert, Jem J. Rowland, Douglas B. Kell:
Genomic computing: explanatory modelling for functional genomics. GECCO 2000: 551-557
Parts in Books or Collections
- 2007
- [p1]Tom Oinn, Peter Li, Douglas B. Kell, Carole A. Goble, Antoon Goderis, Robert Mark Greenwood, Duncan Hull, Robert Stevens, Daniele Turi, Jun Zhao:
Taverna/myGrid: Aligning a Workflow System with the Life Sciences Community. Workflows for e-Science, Scientific Workflows for Grids 2007: 300-319
Informal and Other Publications
- 2017
- [i3]Andreas Holzinger, Chris Biemann, Constantinos S. Pattichis, Douglas B. Kell:
What do we need to build explainable AI systems for the medical domain? CoRR abs/1712.09923 (2017) - [i2]Neil Swainston, Andrew Currin, Lucy Green, Rainer Breitling, Philip J. Day, Douglas B. Kell:
CodonGenie: optimised ambiguous codon design tools. PeerJ Prepr. 5: e2797 (2017) - 2016
- [i1]Andrew Currin, Konstantin Korovin, Maria Ababi, Katherine Roper, Douglas B. Kell, Philip J. Day, Ross D. King:
Computing exponentially faster: Implementing a nondeterministic universal Turing machine using DNA. CoRR abs/1607.08078 (2016)
Coauthor Index
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