Publications

Conference Papers: Refereed

2011

Identifying Similarities in TMBL Programs with Alignment to Quicken their Compilation for GPUs
Tony E Lewis, George D Magoulas
GECCO 2011, Dublin, Ireland
Proceedings of the 13th Annual Conference Companion on Genetic and Evolutionary Computation, 978-1-4503-0690-4, Pages 447–454

TMBL Kernels for CUDA GPUs Compile Faster Using PTX
Tony E Lewis, George D Magoulas
GECCO 2011, Dublin, Ireland
Proceedings of the 13th Annual Conference Companion on Genetic and Evolutionary Computation, 978-1-4503-0690-4, Pages 455–462

2010

Tweaking a Tower of Blocks Leads to a TMBL: Pursuing Long Term Fitness Growth in Program Evolution
[pdf]
Tony E Lewis, George D Magoulas
CEC 2010, Barcelona, Spain (poster and paper in conference proceedings)
Proceedings of the IEEE Congress on Evolutionary Computation (CEC) 2010, 978-1-4244-6910-9, Pages 4465–4472

2009

Strategies to Minimise the Total Run Time of Cyclic Graph-Based Genetic Programming with GPUs
Best Paper Award
Tony E Lewis, George D Magoulas
GECCO 2009, Montreal, Québec, Canada
Proceedings of the 11th Annual Conference on Genetic and Evolutionary Computation, 978-1-60558-325-9, Pages 1379–1386

2008

TREAD: A New Genetic Programming Representation Aimed at Research of Long Term Complexity Growth
Tony E Lewis, George D Magoulas
GECCO 2008, Atlanta, Georgia, USA (short paper and poster presentation)
Proceedings of the 10th Annual Conference on Genetic and Evolutionary Computation, 978-1-60558-130-9, Pages 1339–1340

Journal Papers: Refereed

2016

CATH: an expanded resource to predict protein function through structure and sequence
Natalie L Dawson, Tony E Lewis, Sayoni Das, Jonathan G Lees, David Lee, Paul Ashford, Christine A Orengo and Ian Sillitoe
Nucleic Acids Research, first published online November 28, 2016 doi:10.1093/nar/gkw1098

2015

Genome3D: exploiting structure to help users understand their sequences
Tony E Lewis, Ian Sillitoe [joint first author], Antonina Andreeva, Tom L Blundell, Daniel W.A Buchan, Cyrus Chothia, Domenico Cozzetto, José M Dana, Ioannis Filippis, Julian Gough, David T Jones, Lawrence A Kelley, Gerard J Kleywegt, Federico Minneci, Jaina Mistry, Alexey G Murzin, Bernardo Ochoa-Montaño, Matt E Oates, Marco Punta, Owen J L Rackham, Jonathan Stahlhacke, Michael J.E Sternberg, Sameer Velankar, and Christine Orengo
Nucleic Acids Research, Volume 43, D382-386, Oxford University Press

CATH: comprehensive structural and functional annotations for genome sequences
Ian Sillitoe, Tony E Lewis [joint first author], Alison Cuff, Sayoni Das, Paul Ashford, Natalie L Dawson, Nicholas Furnham, Roman A Laskowski, David Lee, Jonathan G Lees, Sonja Lehtinen, Romain A Studer, Janet Thornton, and Christine A Orengo
Nucleic Acids Research, Volume 43, D376-381, Oxford University Press

Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins
Ian Sillitoe, Tony Lewis and Christine Orengo
Current Protocols in Bioinformatics. 2015 Jun 19;50:1.28.1-21. doi: 10.1002/0471250953.bi0128s50. PubMed PMID: 26087950.

2013

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
Tony E Lewis, Ian Sillitoe, Antonina Andreeva, Tom L Blundell, Daniel Buchan, Cyrus W A Chothia, Alison Cuff, Jose M Dana, Ioannis Filippis, Julian Gough, Sarah Hunter, David T Jones, Lawrence A Kelley, Gerard J Kleywegt, Federico Minneci, Alex Mitchell, Alexey G Murzin, Bernardo Ochoa-Montaño, Owen J L Rackham, James Smith, Michael J E Sternberg, Sameer Velankar, Corin Yeats, Christine Orengo
Nucleic Acids Research, Volume 41, D499–507, Oxford University Press

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures
Ian Sillitoe, Alison L Cuff, Benoit H Dessailly, Natalie L Dawson, Nicholas Furnham, David Lee, Jonathan G Lees, Tony E Lewis, Romain A Studer, Robert Rentzsch, Corin Yeats, Janet M Thornton, Christine A Orengo
Nucleic Acids Research, Volume 41, D490–498, Oxford University Press

2011

Extending CATH: Increasing Coverage of the Protein Structure Universe and Linking Structure with Function
Alison L Cuff, Ian Sillitoe, Tony Lewis, Andrew B Clegg, Robert Rentzsch, Nicholas Furnham, Marialuisa Pellegrini-Calace, David Jones, Janet Thornton, Christine A Orengo
Nucleic Acids Research, Volume 39, Issue suppl 1, Pages D420–426, Oxford University Press

2009

The CATH Hierarchy Revisited–Structural Divergence in Domain Superfamilies and the Continuity of Fold Space
Alison Cuff, Oliver C Redfern, Lesley Greene, Ian Sillitoe, Tony Lewis, Mark Dibley, Adam Reid, Frances Pearl, Tim Dallman, Annabel Todd, Richard Garratt, Janet Thornton, Christine Orengo
Structure, Volume 17, Issue 8, Pages 1051–1062, Cell Press

The CATH Classification Revisited—Architectures Reviewed and New Ways to Characterize Structural Divergence in Superfamilies
Alison L Cuff, Ian Sillitoe, Tony Lewis, Oliver C Redfern, Richard Garratt, Janet Thornton, Christine A Orengo
Nucleic Acids Research, Volume 37, Issue suppl 1, Pages D310–D314, Oxford University Press

2007

Towards a Comprehensive Structural Coverage of Completed Genomes: A Structural Genomics Viewpoint
Russell Marsden, Tony Lewis, Christine Orengo
BMC Bioinformatics, Volume 8, Issue 1, BioMed Central Ltd

The CATH Domain Structure Database: New Protocols and Classification Levels Give a More Comprehensive Resource for Exploring Evolution
Lesley H Greene, Tony E Lewis [joint first author], Sarah Addou, Alison Cuff, Tim Dallman, Mark Dibley, Oliver Redfern, Frances Pearl, Rekha Nambudiry, Adam Reid, Ian Sillitoe, Corin Yeats, Janet M Thornton, Christine A Orengo
Nucleic Acids Research, Volume 35, Issue suppl 1, Pages D291–D297, Oxford University Press

2005

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
Frances Pearl, Annabel Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony Lewis, Christopher Bennett, Russell Marsden, Alistair Grant, David Lee, Adrian Akpor, Michael Maibaum, Andrew Harrison, Timothy Dallman, Gabrielle Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline Johnston, Antonio Sillero, Janet Thornton, Christine Orengo
Nucleic Acids Research, Volume 33, Issue suppl 1, Pages D247–D251, Oxford University Press

PhD Thesis

“Accelerating Genetic Programming Using Graphics Processing Units” [PDF]
Birkbeck, University of London
Examined by Professor Yaochu Jin and Professor Qingfu Zhang
Submission: 29th September 2011; viva: 16th December 2011; final revision after minor corrections: 11th March 2012; final submission: 16th March 2012; award: 31st March 2012

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