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Simon Hubbard

Research Profile

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Chemicals & Drugs

Genes & Molecular Sequences

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Physiology

Protein Folding

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Publications

TOP 3
Philip Brownridge; Christopher M Grant; Victoria M Harman; Stephen W Holman; Karin Lanthaler; Craig Lawless; Aishwarya B Payapilly; Robert J Beynon; Simon Hubbard
Quantitative analysis of chaperone network throughput in budding yeast.
Paul Blakeley; Ian M Overton; Simon Hubbard
Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies.
Craig Lawless; Simon Hubbard
Prediction of missed proteolytic cleavages for the selection of surrogate peptides for quantitative proteomics.

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All Publications

2013: Philip Brownridge; Christopher M Grant; Victoria M Harman; Stephen W Holman; Karin Lanthaler; Craig Lawless; Aishwarya B Payapilly; Robert J Beynon; Simon Hubbard
Quantitative analysis of chaperone network throughput in budding yeast.
Proteomics 2013;13(8):1276-91.
2012: Paul Blakeley; Ian M Overton; Simon Hubbard
Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies.
Journal of proteome research 2012;11(11):5221-34.
2012: Craig Lawless; Simon Hubbard
Prediction of missed proteolytic cleavages for the selection of surrogate peptides for quantitative proteomics.
Omics : a journal of integrative biology 2012;16(9):449-56.
2012: Faviel F Gonzalez-Galarza; Henning Hermjakob; Simon Hubbard; Conrad Bessant; Jun Fan; Craig Lawless; Andrew R Jones
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.
Omics : a journal of integrative biology 2012;16(9):431-42.
2012: Andrew R Jones; Randall Julian; Oliver Kohlbacher; Gerhard Mayer; Angel Pizarro; Florian Reisinger; Brian C Searle; Julian N Selley; Sean L Seymour; James Shofstahl; Jennifer Siepen; Juan Antonio Vizcaino; Eric Deutsch; Martin Eisenacher; Johannes Griss; Henning Hermjakob; Simon Hubbard; Pierre-Alain Binz; Matthew Chambers; David Creasy
The mzIdentML data standard for mass spectrometry-based proteomics results.
Molecular & cellular proteomics : MCP 2012;11(7):M111.014381.
2011: Claire E Eyers; Simon J Gaskell; King Wai Lau; Craig Lawless; David C Wedge; Simon Hubbard
CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches.
Molecular & cellular proteomics : MCP 2011;10(11):M110.003384.
2011: Philip Brownridge; Simon J Gaskell; Christopher M Grant; Victoria M Harman; Stephen W Holman; Simon Hubbard; Karin Lanthaler; Craig Lawless; Ronan O'Cualain; Paul Sims; Rachel Watkins; Robert J Beynon
Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy.
Proteomics 2011;11(15):2957-70.
2011: David C Wedge; Ritesh Krishna; Paul Blackhurst; Jennifer A Siepen; Andrew R Jones; Simon Hubbard
FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines.
Journal of proteome research 2011;10(4):2088-94.
2011: Sarah Hart; King Wai Lau; Simon J Gaskell; Simon Hubbard
Distributions of ion series in ETD and CID spectra: making a comparison.
Methods in molecular biology (Clifton, N.J.) 2011;696():327-37.
2010: Paul Blakeley; Jennifer A Siepen; Craig Lawless; Simon Hubbard
Investigating protein isoforms via proteomics: a feasibility study.
Proteomics 2010;10(6):1127-40.
2010: J C Wright; Robert Beynon; Simon Hubbard
Cross species proteomics.
Methods in molecular biology (Clifton, N.J.) 2010;604():123-35.
2010: Simon Hubbard
Computational approaches to peptide identification via tandem MS.
Methods in molecular biology (Clifton, N.J.) 2010;604():23-42.
2010: Andrew R Jones; Simon Hubbard
An introduction to proteome bioinformatics.
Methods in molecular biology (Clifton, N.J.) 2010;604():1-5.
2009: King Wai Lau; Sarah Hart; Jennifer A Lynch; Stephen C C Wong; Simon Hubbard; Simon J Gaskell
Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides.
Rapid communications in mass spectrometry : RCM 2009;23(10):1508-14.
2009: Andrew R Jones; Jennifer A Siepen; Simon Hubbard; Norman W Paton
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines.
Proteomics 2009;9(5):1220-9.
2009: James C Wright; Simon Hubbard
Recent developments in proteome informatics for mass spectrometry analysis.
Combinatorial chemistry & high throughput screening 2009;12(2):194-202.
2009: Sarah Baxendale; Chao-Kung Chen; Haizhou Tang; Claire Davison; Lisa Van Hateren; Mike D R Croning; Sean J Humphray; Simon Hubbard; Philip Ingham
Expression screening and annotation of a zebrafish myoblast cDNA library.
Gene expression patterns : GEP 2009;9(2):73-82.
2009: Sarah Hart; King Wai Lau; Zhiqi Hao; Richard Broadhead; Neil Portman; Andreas Hühmer; Keith Gull; Paul G McKean; Simon Hubbard; Simon J Gaskell
Analysis of the trypanosome flagellar proteome using a combined electron transfer/collisionally activated dissociation strategy.
Journal of the American Society for Mass Spectrometry 2009;20(2):167-75.
2009: James C Wright; Deana Sugden; Sue Francis-McIntyre; Isabel Riba; Simon J Gaskell; Igor V Grigoriev; Scott E Baker; Robert Beynon; Simon Hubbard
Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger.
BMC genomics 2009;10():61.
2009: Craig Lawless; Richard D Pearson; Julian N Selley; Julia B Smirnova; Chris M Grant; Mark Ashe; Graham D Pavitt; Simon Hubbard
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast.
BMC genomics 2009;10():7.
2008: Jennifer A Siepen; Khalid Belhajjame; Julian N Selley; Suzanne M Embury; Norman W Paton; Carole Goble; Stephen G Oliver; Robert Stevens; Lucas Zamboulis; Nigel Martin; Alexandra Poulovassillis; Philip Jones; Richard Côté; Henning Hermjakob; Melissa M Pentony; David T Jones; Christine A Orengo; Simon Hubbard
ISPIDER Central: an integrated database web-server for proteomics.
Nucleic acids research 2008;36(Web Server issue):W485-90.
2008: Jennifer A Siepen; Julian N Selley; Simon Hubbard
PepSeeker: mining information from proteomic data.
Methods in molecular biology (Clifton, N.J.) 2008;484():319-32.
2008: Darren M Soanes; Intikhab Alam; Mike Cornell; Han Min Wong; Cornelia Hedeler; Norman W Paton; Magnus Rattray; Simon Hubbard; Stephen G Oliver; Nicholas J Talbot
Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis.
PloS one 2008;3(6):e2300.
2008: Emma Laing; Khushwant Sidhu; Simon Hubbard
Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor.
BMC genomics 2008;9():79.
2007: Michael Cornell; Intikhab Alam; Darren M Soanes; Han Min Wong; Cornelia Hedeler; Norman W Paton; Magnus Rattray; Simon Hubbard; Nicholas J Talbot; Stephen G Oliver
Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi.
Genome research 2007;17(12):1809-22.
2007: John E Bylander; Greg P Bertenshaw; Gail L Matters; Simon Hubbard; Judith S Bond
Human and mouse homo-oligomeric meprin A metalloendopeptidase: substrate and inhibitor specificities.
Biological chemistry 2007;388(11):1163-72.
2007: Andrew R Jones; Michael Miller; Ruedi Aebersold; Rolf Apweiler; Catherine A Ball; Alvis Brazma; James Degreef; Nigel Hardy; Henning Hermjakob; Simon Hubbard; Peter Hussey; Mark Igra; Helen Jenkins; Randall K Julian; Kent Laursen; Stephen G Oliver; Norman W Paton; Susanna-Assunta Sansone; Ugis Sarkans; Christian J Stoeckert; Christopher Taylor; Patricia L Whetzel; Joseph A White; Paul Spellman; Angel Pizarro
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Nature biotechnology 2007;25(10):1127-33.
2007: King Wai Lau; Andrew R Jones; Neil Swainston; Jennifer A Siepen; Simon Hubbard
Capture and analysis of quantitative proteomic data.
Proteomics 2007;7(16):2787-99.
2007: Cornelia Hedeler; Han Min Wong; Michael Cornell; Intikhab Alam; Darren M Soanes; Magnus Rattray; Simon Hubbard; Nicholas J Talbot; Stephen G Oliver; Norman W Paton
e-Fungi: a data resource for comparative analysis of fungal genomes.
BMC genomics 2007;8():426.
2007: H Tang; T Heeley; R Morlec; Simon Hubbard
Characterising alternate splicing and tissue specific expression in the chicken from ESTs.
Cytogenetic and genome research 2007;117(1-4):268-77.
2007: Intikhab Alam; Simon Hubbard; Stephen G Oliver; Magnus Rattray
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes.
BMC genomics 2007;8():97.
2007: Jennifer A Siepen; Neil Swainston; Andrew R Jones; Sarah Hart; Henning Hermjakob; Philip Jones; Simon Hubbard
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.
Proteome science 2007;5():4.
2007: Jennifer A Siepen; Emma-Jayne Keevil; David Knight; Simon Hubbard
Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.
Journal of proteome research 2007;6(1):399-408.
2006: James Tellez; Halina Dobrzynski; Ian D Greener; Gillian M Graham; Emma Laing; Haruo Honjo; Simon Hubbard; Mark R Boyett; Rudolf Billeter
Differential expression of ion channel transcripts in atrial muscle and sinoatrial node in rabbit.
Circulation research 2006;99(12):1384-93.
2006: Daniel Shenton; Julia B Smirnova; Julian N Selley; Kathleen Carroll; Simon Hubbard; Graham D Pavitt; Mark Ashe; Chris M Grant
Global translational responses to oxidative stress impact upon multiple levels of protein synthesis.
The Journal of biological chemistry 2006;281(39):29011-21.
2006: Emma Laing; Vassilis Mersinias; Colin P Smith; Simon Hubbard
Analysis of gene expression in operons of Streptomyces coelicolor.
Genome biology 2006;7(6):R46.
2006: Thomas McLaughlin; Jennifer A Siepen; Julian N Selley; Jennifer A Lynch; King Wai Lau; Hujun Yin; Simon J Gaskell; Simon Hubbard
PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns.
Nucleic acids research 2006;34(Database issue):D649-54.
2005: Julia B Smirnova; Julian N Selley; Fatima Sanchez Cabo; Kathleen Carroll; A Alan Eddy; John E G McCarthy; Simon Hubbard; Graham D Pavitt; Chris M Grant; Mark Ashe
Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways.
Molecular and cellular biology 2005;25(21):9340-9.
2005: Stephen J Littler; Simon Hubbard
Conservation of orientation and sequence in protein domain--domain interactions.
Journal of molecular biology 2005;345(5):1265-79.
2005: Simon Hubbard; Darren V Grafham; Kevin J Beattie; Ian M Overton; Stuart R McLaren; Michael D R Croning; Paul E Boardman; James K Bonfield; Joan Burnside; Robert M Davies; Elizabeth R Farrell; Matthew D Francis; Sam Griffiths-Jones; Sean Humphray; Christopher Hyland; Carol E Scott; Haizhou Tang; Ruth G Taylor; Cheryll Tickle; William R A Brown; Ewan Birney; Jane Rogers; Stuart A Wilson
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.
Genome research 2005;15(1):174-83.
2004: Gane Ka-Shu Wong; Bin Liu; Jun Wang; Yong Zhang; Xu Yang; Zengjin Zhang; Qingshun Meng; Jun Zhou; Dawei Li; Jingjing Zhang; Ximiao He; Songgang Li; Longhua Ran; Heng Li; Jianguo Zhang; Ruiqiang Li; Shengting Li; Hongkun Zheng; Wei Lin; Guangyuan Li; Xiaoling Wang; Wenming Zhao; Jun Li; Chen Ye; Mingtao Dai; Jue Ruan; Yan Zhou; Yuanzhe Li; Ximiao He; Yunze Zhang; Jing Wang; Xiangang Huang; Wei Tong; Jie Chen; Jia Ye; Chen Chen; Ning Wei; Guoqing Li; Le Dong; Fengdi Lan; Yongqiao Sun; Zhenpeng Zhang; Zheng Yang; Yingpu Yu; Yanqing Huang; Dandan He; Yan Xi; Dong Wei; Qiuhui Qi; Wenjie Li; Jianping Shi; Miaoheng Wang; Fei Xie; Jianjun Wang; Xiaowei Zhang; Pei Wang; Yiqiang Zhao; Ning Li; Ning Yang; Wei Dong; Songnian Hu; Changqing Zeng; Weimou Zheng; Bailin Hao; Ladeana W Hillier; Shiaw-Pyng Yang; Wesley C Warren; Richard K Wilson; Mikael Brandström; Hans Ellegren; Richard P M A Crooijmans; Jan J van der Poel; Henk Bovenhuis; Martien A M Groenen; Ivan Ovcharenko; Laurie Gordon; Lisa Stubbs; Susan Lucas; Tijana Glavina; Andrea Aerts; Pete Kaiser; Lisa Rothwell; John R Young; Sally Rogers; Brian A Walker; Andy van Hateren; Jim Kaufman; Nat Bumstead; Susan Lamont; Huaijun Zhou; Paul M Hocking; David Morrice; Dirk-Jan de Koning; Andy Law; Neil Bartley; David W Burt; Henry Hunt; Hans H Cheng; Ulrika Gunnarsson; Per Wahlberg; Leif Andersson; Ellen Kindlund; Martti T Tammi; Björn Andersson; Caleb Webber; Chris P Ponting; Ian M Overton; Paul E Boardman; Haizhou Tang; Simon Hubbard; Stuart A Wilson; Jun Yu; Jian Wang; Huanming Yang
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.
Nature 2004;432(7018):717-22.
2004: Claire L Wilson; Paul E Boardman; Andrew J Doig; Simon Hubbard
Improved prediction for N-termini of alpha-helices using empirical information.
Proteins 2004;57(2):322-30.
2004: Kevin L Garwood; Thomas McLaughlin; Christopher Garwood; Scott Joens; Norman Morrison; Christopher Taylor; Kathleen Carroll; Caroline Evans; Anthony D Whetton; Sarah Hart; David Stead; Zhikang Yin; Alistair J P Brown; Andy Hesketh; Keith F Chater; Lena Hansson; Muriel Mewissen; Peter Ghazal; Julie Howard; Kathryn S Lilley; Simon J Gaskell; Andrew Brass; Simon Hubbard; Stephen G Oliver; Norman W Paton
PEDRo: a database for storing, searching and disseminating experimental proteomics data.
BMC genomics 2004;5():68.
2003: Paul E Boardman; Stephen G Oliver; Simon Hubbard
SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences.
Nucleic acids research 2003;31(13):3572-5.
2003: Christopher Taylor; Norman W Paton; Kevin L Garwood; Paul D Kirby; David Stead; Zhikang Yin; Eric Deutsch; Laura Selway; Janet Walker; Isabel Riba; shabaz mohammed; Michael J Deery; Julie A Howard; Tom P J Dunkley; Ruedi Aebersold; Douglas B Kell; Kathryn S Lilley; Peter Roepstorff; John R Yates; Andrew Brass; Alistair J P Brown; Phillip Cash; Simon J Gaskell; Simon Hubbard; Stephen G Oliver
A systematic approach to modeling, capturing, and disseminating proteomics experimental data.
Nature biotechnology 2003;21(3):247-54.
2003: William R A Brown; Simon Hubbard; Cheryll Tickle; Stuart A Wilson
The chicken as a model for large-scale analysis of vertebrate gene function.
Nature reviews. Genetics 2003;4(2):87-98.
2002: Paul E Boardman; Juan José Sanz-Ezquerro; Ian M Overton; David W Burt; Elizabeth Bosch; Willy T Fong; Cheryll Tickle; William R A Brown; Stuart A Wilson; Simon Hubbard
A comprehensive collection of chicken cDNAs.
Current biology : CB 2002;12(22):1965-9.
2002: Patrick J Lester; Simon Hubbard
Comparative bioinformatic analysis of complete proteomes and protein parameters for cross-species identification in proteomics.
Proteomics 2002;2(10):1392-405.
2002: Claire L Wilson; Simon Hubbard; Andrew J Doig
A critical assessment of the secondary structure alpha-helices and their termini in proteins.
Protein engineering 2002;15(7):545-54.
2002: Julie M Pratt; Duncan H L Robertson; Simon J Gaskell; Isabel Riba; Simon Hubbard; Khushwant Sidhu; Stephen G Oliver; Philip Butler; Andrew Hayes; June Petty; Robert Beynon
Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting.
Proteomics 2002;2(2):157-63.
2001: K S Sidhu; Polkit Sangvanich; Francesco L Brancia; A G Sullivan; Simon J Gaskell; O Wolkenhaue; Stephen G Oliver; Simon Hubbard
Bioinformatic assessment of mass spectrometric chemical derivatisation techniques for proteome database searching.
Proteomics 2001;1(11):1368-77.
2001: Greg P Bertenshaw; Boris Turk; Simon Hubbard; Gail L Matters; John E Bylander; Jacqueline M Crisman; Lewis C Cantley; Judith S Bond
Marked differences between metalloproteases meprin A and B in substrate and peptide bond specificity.
The Journal of biological chemistry 2001;276(16):13248-55.
2001: A Darwish Marie; C Veggerby; Duncan H L Robertson; Simon J Gaskell; Simon Hubbard; L Martinsen; Jane L Hurst; Robert Beynon
Effect of polymorphisms on ligand binding by mouse major urinary proteins.
Protein science : a publication of the Protein Society 2001;10(2):411-7.
2001: Francesco L Brancia; Amna Butt; Robert Beynon; Simon Hubbard; Simon J Gaskell; Stephen G Oliver
A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics.
Electrophoresis 2001;22(3):552-9.
2001: K C Woodwark; Simon Hubbard; S G Oliver
Sequence search algorithms for single pass sequence identification: does one size fit all?
Comparative and functional genomics 2001;2(1):4-9.
2000: Norman W Paton; S A Khan; Andrew Hayes; F Moussouni; Andrew Brass; K Eilbeck; Carole Goble; Simon Hubbard; Stephen G Oliver
Conceptual modelling of genomic information.
Bioinformatics (Oxford, England) 2000;16(6):548-57.
1999: C Wu; Duncan H L Robertson; Simon Hubbard; Simon J Gaskell; Robert Beynon
Proteolysis of native proteins. Trapping of a reaction intermediate.
The Journal of biological chemistry 1999;274(2):1108-15.
1998: J H Kanan; Simon Hubbard; S J Minter; Stephen G Oliver
Use of fortuitous in vitro mutations in a synthetic Cu-Zn superoxide dismutase gene to illuminate protein structure-function relationships.
Protein engineering 1998;11(11):1083-8.
1998: Simon Hubbard; Robert Beynon; J M Thornton
Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures.
Protein engineering 1998;11(5):349-59.
1998: Simon Hubbard
The structural aspects of limited proteolysis of native proteins.
Biochimica et biophysica acta 1998;1382(2):191-206.
1996: Simon Hubbard; P Argos
A functional role for protein cavities in domain: domain motions.
Journal of molecular biology 1996;261(2):289-300.
1995: A H Juffer; Frank Eisenhaber; Simon Hubbard; Dirk Walther; P Argos
Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding.
Protein science : a publication of the Protein Society 1995;4(12):2499-509.
1995: Simon Hubbard; P Argos
Detection of internal cavities in globular proteins.
Protein engineering 1995;8(10):1011-5.
1995: Simon Hubbard; P Argos
Evidence on close packing and cavities in proteins.
Current opinion in biotechnology 1995;6(4):375-81.
1995: D Ellison; J Hinton; Simon Hubbard; Robert Beynon
Limited proteolysis of native proteins: the interaction between avidin and proteinase K.
Protein science : a publication of the Protein Society 1995;4(7):1337-45.
1994: Simon Hubbard; P Argos
Cavities and packing at protein interfaces.
Protein science : a publication of the Protein Society 1994;3(12):2194-206.
1994: Simon Hubbard; K H Gross; P Argos
Intramolecular cavities in globular proteins.
Protein engineering 1994;7(5):613-26.
1994: Simon Hubbard; F Eisenmenger; Janet M Thornton
Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.
Protein science : a publication of the Protein Society 1994;3(5):757-68.
1992: Simon Hubbard; Janet M Thornton; S F Campbell
Substrate recognition by proteinases.
Faraday discussions 1992;(93):13-23.
1991: Simon Hubbard; S F Campbell; Janet M Thornton
Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors.
Journal of molecular biology 1991;220(2):507-30.