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List of works by Simon J. Hubbard

A Functional Role for Protein Cavities in Domain:Domain Motions

scientific article published on 01 August 1996

A comprehensive collection of chicken cDNAs

scientific article published in November 2002

A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis

scientific article published on 17 July 2012

A critical assessment of the secondary structure alpha-helices and their termini in proteins.

scientific article

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

scientific article

A kingdom-specific protein domain HMM library for improved annotation of fungal genomes

scientific article

A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae

scientific article published on 01 February 2020

A quantitative and temporal map of proteostasis during heat shock in Saccharomyces cerevisiae

scientific article published on 16 January 2018

A systematic approach to modeling, capturing, and disseminating proteomics experimental data

scientific article

Absolute protein quantification of the yeast chaperome under conditions of heat shock

scientific article published on 2 June 2016

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

scientific article published on 15 October 2012

An Introduction to Proteome Bioinformatics

scientific article published on 01 January 2010

An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ

scientific article (publication date: February 2007)

Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics.

scientific article published on 25 July 2016

Analysis of the trypanosome flagellar proteome using a combined electron transfer/collisionally activated dissociation strategy

scientific article published on 3 September 2008

Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions.

scientific article

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

scientific article

BioMart Central Portal: an open database network for the biological community

scientific article

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

scientific article

Capture and analysis of quantitative proteomic data

scientific article

Cavities and packing at protein interfaces

scientific article published on December 1994

Characterising alternate splicing and tissue specific expression in the chicken from ESTs

scientific article

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

scientific article published in October 2002

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

scientific article

Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis

scientific article

Computational approaches to peptide identification via tandem MS.

scientific article published in January 2010

Computational phosphoproteomics: from identification to localization

scientific article

Conceptual modelling of genomic information

scientific article

Conservation of Orientation and Sequence in Protein Domain–Domain Interactions

scientific article published on 16 December 2004

Cross species proteomics.

scientific article published on January 2010

Data Access and Integration in the ISPIDER Proteomics Grid

Detection of internal cavities in globular proteins.

scientific article

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

scientific article published on 02 November 2006

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

scientific article published on 10 January 2016

Disease modeling of core pre-mRNA splicing factor haploinsufficiency

scientific article published on 01 November 2019

Distributions of ion series in ETD and CID spectra: making a comparison

scientific article published in January 2011

Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome

scientific article

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses

scientific article published on 27 October 2017

Effect of polymorphisms on ligand binding by mouse major urinary proteins

scientific article

Evidence on close packing and cavities in proteins.

scientific article

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

scientific article

Expression screening and annotation of a zebrafish myoblast cDNA library

scientific article

FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines

scientific article published on 21 February 2011

Focus on Quantitative Proteomics

article

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).

scientific article

Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy.

scientific article published on 28 June 2011

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

Global mRNA selection mechanisms for translation initiation.

scientific article

Global translational responses to oxidative stress impact upon multiple levels of protein synthesis.

scientific article published on 18 July 2006

Glycolytic flux in is dependent on RNA polymerase III and its negative regulator Maf1

scientific article published on 04 April 2019

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

scientific article published in November 2007

ISPIDER Central: an integrated database web-server for proteomics

scientific article published on 25 April 2008

Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins

scientific article

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

scientific article published on March 2009

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

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

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

scientific article

PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns

scientific article

PepSeeker: mining information from proteomic data

scientific article

Peptide detectability following ESI mass spectrometry

Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor

scientific article

Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics

scientific article published on January 2007

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

scientific article published on 17 July 2012

Proteolysis of Native Proteins

scientific article published in Journal of Biological Chemistry

Puf3p induces translational repression of genes linked to oxidative stress

scientific article published on 25 October 2013

Quantitative analysis of chaperone network throughput in budding yeast.

scientific article published on 15 March 2013

Quantitative proteomics and network analysis of SSA1 and SSB1 deletion mutants reveals robustness of chaperone HSP70 network in Saccharomyces cerevisiae

scientific article published on 16 February 2015

Recent developments in proteome informatics for mass spectrometry analysis

scientific article published on February 2009

Representation of selected-reaction monitoring data in the mzQuantML data standard

scientific article published on 5 June 2015

Ribosomal flavours: an acquired taste for specific mRNAs?

scientific article published on 12 November 2018

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

scientific article

Sequence search algorithms for single pass sequence identification: does one size fit all?

scientific article published on January 2001

SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences

scientific article

Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting

scientific article

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

scientific article published on 14 May 2015

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article

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

scientific article

The mzIdentML data standard for mass spectrometry-based proteomics results

scientific article (publication date: July 2012)

The mzqLibrary--An open source Java library supporting the HUPO-PSI quantitative proteomics standard.

scientific article published on 2 June 2015

The structural aspects of limited proteolysis of native proteins ⬇️

scientific article published on February 17, 1998

The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response.

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

UKPMC: a full text article resource for the life sciences

scientific article

Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast.

scientific article

Use of fortuitous in vitro mutations in a synthetic Cu-Zn superoxide dismutase gene to illuminate protein structure-function relationships.

scientific article

Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

scientific article published on 10 February 2022

e-Fungi: a data resource for comparative analysis of fungal genomes

scientific article

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