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List of works by Simon J. Hubbard

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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

scientific article
A comprehensive collection of chicken cDNAs

scientific article published in November 2002
Global translational responses to oxidative stress impact upon multiple levels of protein synthesis.

scientific article published on 18 July 2006
The structural aspects of limited proteolysis of native proteins

scientific article published on February 17, 1998
BioMart Central Portal: an open database network for the biological community

scientific article
The mzIdentML data standard for mass spectrometry-based proteomics results

scientific article (publication date: July 2012)
A systematic approach to modeling, capturing, and disseminating proteomics experimental data

scientific article
The chicken as a model for large-scale analysis of vertebrate gene function.

scientific article
Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways

scientific article published on November 2005
Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis

scientific article
Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures.

scientific article
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

scientific article published on 8 December 2004
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast.

scientific article
Differential Expression of Ion Channel Transcripts in Atrial Muscle and Sinoatrial Node in Rabbit

scientific article published on 02 November 2006
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article
Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi

scientific article
CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches

scientific article
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

scientific article published on March 2009
Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy.

scientific article published on 28 June 2011
Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics

scientific article published on January 2007
Cavities and packing at protein interfaces

scientific article published on December 1994
Global mRNA selection mechanisms for translation initiation.

scientific article
Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies

scientific article published on 15 October 2012
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis

scientific article published on 17 July 2012
Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins

scientific article
Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring.

scientific article published on 10 January 2016
Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting

scientific article
Prediction of missed proteolytic cleavages for the selection of surrogate peptides for quantitative proteomics

scientific article published on 17 July 2012
Effect of polymorphisms on ligand binding by mouse major urinary proteins

scientific article
Capture and analysis of quantitative proteomic data

scientific article
PEDRo: a database for storing, searching and disseminating experimental proteomics data

scientific article
Comparative bioinformatic analysis of complete proteomes and protein parameters for cross-species identification in proteomics

scientific article published in October 2002
UKPMC: a full text article resource for the life sciences

scientific article
Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

scientific article
A Functional Role for Protein Cavities in Domain:Domain Motions

scientific article published on 01 August 1996
Analysis of the trypanosome flagellar proteome using a combined electron transfer/collisionally activated dissociation strategy

scientific article published on 3 September 2008
Conservation of Orientation and Sequence in Protein Domain–Domain Interactions

scientific article published on 16 December 2004
Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p

scientific article
Investigating protein isoforms via proteomics: a feasibility study

scientific article published on March 2010
Conceptual modelling of genomic information

scientific article
The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation

scientific article published on 14 May 2015
The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response.

scientific article
Puf3p induces translational repression of genes linked to oxidative stress

scientific article published on 25 October 2013
Detection of internal cavities in globular proteins.

scientific article
Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides

scientific article published in May 2009
Quantitative analysis of chaperone network throughput in budding yeast.

scientific article published on 15 March 2013
FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines

scientific article published on 21 February 2011
e-Fungi: a data resource for comparative analysis of fungal genomes

scientific article
Human and mouse homo-oligomeric meprin A metalloendopeptidase: substrate and inhibitor specificities

scientific article published in November 2007

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