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Bioinformatic assessment of mass spectrometric chemical derivatisation techniques for proteome database searching.
Published in:
Proteomics, 2001, v. 1, n. 11, p. 1368, doi. 10.1002/1615-9861(200111)1:11<1368::AID-PROT1368>3.0.CO;2-U
By:
- Sidhu, Khushwant S.;
- Sangvanich, Polkit;
- Brancia, Francesco L.;
- Sullivan, Anthony G.;
- Gaskell, Simon J.;
- Wolkenhauer, Olaf;
- Oliver, Stephen G.;
- Hubbard, Simon J.
Publication type:
Article
Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.
Published in:
Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01380-9
By:
- Walzer, Mathias;
- García-Seisdedos, David;
- Prakash, Ananth;
- Brack, Paul;
- Crowther, Peter;
- Graham, Robert L.;
- George, Nancy;
- Mohammed, Suhaib;
- Moreno, Pablo;
- Papatheodorou, Irene;
- Hubbard, Simon J.;
- Vizcaíno, Juan Antonio
Publication type:
Article
Pride Wizard: generation of standards compliant quantitative proteomics data.
Published in:
2007
By:
- Swainston, Neil;
- Siepen, Jennifer A.;
- Jones, Andrew R.;
- Hart, Sarah R.;
- Hermjakob, Henning;
- Jones, Phil;
- Hubbard, Simon J.
Publication type:
Abstract
Understanding the Role of Yeast Yme1 in Mitochondrial Function Using Biochemical and Proteomics Analyses.
Published in:
International Journal of Molecular Sciences, 2022, v. 23, n. 22, p. 13694, doi. 10.3390/ijms232213694
By:
- Kan, Kwan Ting;
- Nelson, Michael G.;
- Grant, Chris M.;
- Hubbard, Simon J.;
- Lu, Hui
Publication type:
Article
Glycolytic flux in Saccharomyces cerevisiae is dependent on RNA polymerase III and its negative regulator Maf1.
Published in:
Biochemical Journal, 2019, v. 476, n. 7, p. 1053, doi. 10.1042/BCJ20180701
By:
- Szatkowska, Roza;
- Garcia-Albornoz, Manuel;
- Roszkowska, Katarzyna;
- Holman, Stephen W.;
- Furmanek, Emil;
- Hubbard, Simon J.;
- Beynon, Robert J.;
- Adamczyk, Malgorzata
Publication type:
Article
Puf3p induces translational repression of genes linked to oxidative stress.
Published in:
Nucleic Acids Research, 2014, v. 42, n. 2, p. 1026, doi. 10.1093/nar/gkt948
By:
- Rowe, William;
- Kershaw, Christopher J.;
- Castelli, Lydia M.;
- Costello, Joseph L.;
- Ashe, Mark P.;
- Grant, Christopher M.;
- Sims, Paul F. G.;
- Pavitt, Graham D.;
- Hubbard, Simon J.
Publication type:
Article
UKPMC: a full text article resource for the life sciences.
Published in:
Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D58, doi. 10.1093/nar/gkq1063
By:
- McEntyre, Johanna R.;
- Ananiadou, Sophia;
- Andrews, Stephen;
- Black, William J.;
- Boulderstone, Richard;
- Buttery, Paula;
- Chaplin, David;
- Chevuru, Sandeepreddy;
- Cobley, Norman;
- Coleman, Lee-Ann;
- Davey, Paul;
- Gupta, Bharti;
- Haji-Gholam, Lesley;
- Hawkins, Craig;
- Horne, Alan;
- Hubbard, Simon J.;
- Kim, Jee-Hyub;
- Lewin, Ian;
- Lyte, Vic;
- MacIntyre, Ross
Publication type:
Article
Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins.
Published in:
Nucleic Acids Research, 2010, v. 38, n. 22, p. 8039, doi. 10.1093/nar/gkq686
By:
- Cridge, Andrew G.;
- Castelli, Lydia M.;
- Smirnova, Julia B.;
- Selley, Julian N.;
- Rowe, William;
- Hubbard, Simon J.;
- McCarthy, John E.G.;
- Ashe, Mark P.;
- Grant, Christopher M.;
- Pavitt, Graham D.
Publication type:
Article
ISPIDER Central: an integrated database web-server for proteomics.
Published in:
Nucleic Acids Research, 2008, v. 36, n. suppl_2, p. W485, doi. 10.1093/nar/gkn196
By:
- Siepen, Jennifer A.;
- Belhajjame, Khalid;
- Selley, Julian N.;
- Embury, Suzanne M.;
- Paton, Norman W.;
- Goble, Carole A.;
- Oliver, Stephen G.;
- Stevens, Robert;
- Zamboulis, Lucas;
- Martin, Nigel;
- Poulovassillis, Alexandra;
- Jones, Philip;
- Côté, Richard;
- Hermjakob, Henning;
- Pentony, Melissa M.;
- Jones, David T.;
- Orengo, Christine A.;
- Hubbard, Simon J.
Publication type:
Article
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Published in:
Nature Biotechnology, 2007, v. 25, n. 10, p. 1127, doi. 10.1038/nbt1347
By:
- Jones, Andrew R.;
- Miller, Michael;
- Aebersold, Ruedi;
- Apweiler, Rolf;
- Ball, Catherine A.;
- Brazma, Alvis;
- DeGreef, James;
- Hardy, Nigel;
- Hermjakob, Henning;
- Hubbard, Simon J.;
- Hussey, Peter;
- Igra, Mark;
- Jenkins, Helen;
- Julian, Jr., Randall K.;
- Laursen, Kent;
- Oliver, Stephen G.;
- Paton, Norman W.;
- Sansone, Susanna-Assunta;
- Sarkans, Ugis;
- Stoeckert, Jr., Christian J.
Publication type:
Article
Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal.
Published in:
PLoS ONE, 2008, v. 3, n. 6, p. 1, doi. 10.1371/journal.pone.0002300
By:
- Soanes, Darren M.;
- Alam, Intikhab;
- Cornell, Mike;
- Han Min Wong;
- Hedeler, Cornelia;
- Paton, Norman W.;
- Rattray, Magnus;
- Hubbard, Simon J.;
- Oliver, Stephen G.;
- Talbot, Nicholas J.
Publication type:
Article
Improved prediction for N-termini of α-helices using empirical information.
Published in:
Proteins, 2004, v. 57, n. 2, p. 322, doi. 10.1002/prot.20218
By:
- Wilson, Claire L.;
- Boardman, Paul E.;
- Doig, Andrew J.;
- Hubbard, Simon J.
Publication type:
Article
Absolute protein quantification of the yeast chaperome under conditions of heat shock.
Published in:
Proteomics, 2016, v. 16, n. 15/16, p. 2128, doi. 10.1002/pmic.201500503
By:
- Mackenzie, Rebecca J.;
- Lawless, Craig;
- Holman, Stephen W.;
- Lanthaler, Karin;
- Beynon, Robert J.;
- Grant, Chris M.;
- Hubbard, Simon J.;
- Eyers, Claire E.
Publication type:
Article
Quantitative proteomics and network analysis of SSA1 and SSB1 deletion mutants reveals robustness of chaperone HSP70 network in Saccharomyces cerevisiae.
Published in:
Proteomics, 2015, v. 15, n. 18, p. 3126, doi. 10.1002/pmic.201400527
By:
- Jarnuczak, Andrew F.;
- Eyers, Claire E.;
- Schwartz, Jean ‐ Marc;
- Grant, Christopher M.;
- Hubbard, Simon J.
Publication type:
Article
Focus on Quantitative Proteomics.
Published in:
2015
By:
- Lilley, Kathryn S.;
- Beynon, Robert J.;
- Eyers, Claire E.;
- Hubbard, Simon J.
Publication type:
Editorial
Computational phosphoproteomics: From identification to localization.
Published in:
Proteomics, 2015, v. 15, n. 5/6, p. 950, doi. 10.1002/pmic.201400372
By:
- Lee, Dave C. H.;
- Jones, Andrew R.;
- Hubbard, Simon J.
Publication type:
Article
Quantitative analysis of chaperone network throughput in budding yeast.
Published in:
Proteomics, 2013, v. 13, n. 8, p. 1276, doi. 10.1002/pmic.201200412
By:
- Brownridge, Philip;
- Lawless, Craig;
- Payapilly, Aishwarya B.;
- Lanthaler, Karin;
- Holman, Stephen W.;
- Harman, Victoria M.;
- Grant, Christopher M.;
- Beynon, Robert J.;
- Hubbard, Simon J.
Publication type:
Article
Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy.
Published in:
Proteomics, 2011, v. 11, n. 15, p. 2957, doi. 10.1002/pmic.201100039
By:
- Brownridge, Philip;
- Holman, Stephen W.;
- Gaskell, Simon J.;
- Grant, Christopher M.;
- Harman, Victoria M.;
- Hubbard, Simon J.;
- Lanthaler, Karin;
- Lawless, Craig;
- O'cualain, Ronan;
- Sims, Paul;
- Watkins, Rachel;
- Beynon, Robert J.
Publication type:
Article
Investigating protein isoforms via proteomics: A feasibility study.
Published in:
Proteomics, 2010, v. 10, n. 6, p. 1127, doi. 10.1002/pmic.200900445
By:
- Blakeley, Paul;
- Siepen, Jennifer A.;
- Lawless, Craig;
- Hubbard, Simon J.
Publication type:
Article
Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).
Published in:
Proteomics, 2009, v. 9, n. 15, p. 3928, doi. 10.1002/pmic.200900247
By:
- Eisenacher, Martin;
- Martens, Lennart;
- Hardt, Tanja;
- Kohl, Michael;
- Barsnes, Harald;
- Helsens, Kenny;
- Häkkinen, Jari;
- Levander, Fredrik;
- Aebersold, Ruedi;
- Vandekerckhove, Joël;
- Dunn, Michael J.;
- Lisacek, Frederique;
- Siepen, Jennifer A.;
- Hubbard, Simon J.;
- Binz, Pierre-Alain;
- Blüggel, Martin;
- Thiele, Herbert;
- Cottrell, John;
- Meyer, Helmut E.;
- Apweiler, Rolf
Publication type:
Article
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines.
Published in:
Proteomics, 2009, v. 9, n. 5, p. 1220, doi. 10.1002/pmic.200800473
By:
- Jones, Andrew R.;
- Siepen, Jennifer A.;
- Hubbard, Simon J.;
- Paton, Norman W.
Publication type:
Article
Capture and analysis of quantitative proteomic data.
Published in:
Proteomics, 2007, v. 7, n. 16, p. 2787, doi. 10.1002/pmic.200700127
By:
- Lau, King Wai;
- Jones, Andrew R.;
- Swainston, Neil;
- Siepen, Jennifer A.;
- Hubbard, Simon J.
Publication type:
Article
Comparative bioinformatic analysis of complete proteomes and protein parameters for cross-species identification in proteomics.
Published in:
Proteomics, 2002, v. 2, n. 10, p. 1392, doi. 10.1002/1615-9861(200210)2:10<1392::AID-PROT1392>3.0.CO;2-L
By:
- Lester, Patrick J.;
- Hubbard, Simon J.
Publication type:
Article
Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting.
Published in:
Proteomics, 2002, v. 2, n. 2, p. 157, doi. 10.1002/1615-9861(200202)2:2<157::AID-PROT157>3.0.CO;2-M
By:
- Pratt, Julie M.;
- Robertson, Duncan H. L.;
- Gaskell, Simon J.;
- Riba-Garcia, Isabel;
- Hubbard, Simon J.;
- Sidhu, Khushwant;
- Oliver, Stephen G.;
- Butler, Philip;
- Hayes, Andrew;
- Petty, June;
- Beynon, Robert J.
Publication type:
Article
The chicken as a model for large-scale analysis of vertebrate gene function.
Published in:
Nature Reviews Genetics, 2003, v. 4, n. 2, p. 87, doi. 10.1038/nrg998
By:
- Brown, William R. A.;
- Hubbard, Simon J.;
- Tickle, Cheryll;
- Wilson, Stuart A.
Publication type:
Article
Cytosolic aspartate aminotransferase moonlights as a ribosome-binding modulator of Gcn2 activity during oxidative stress.
Published in:
eLife, 2022, p. 1, doi. 10.7554/eLife.73466
By:
- Crawford, Robert A.;
- Ashe, Mark P.;
- Hubbard, Simon J.;
- Pavitt, Graham D.
Publication type:
Article
Yeast Protein Kinase A Isoforms: A Means of Encoding Specificity in the Response to Diverse Stress Conditions?
Published in:
Biomolecules (2218-273X), 2022, v. 12, n. 7, p. N.PAG, doi. 10.3390/biom12070958
By:
- Creamer, Declan R.;
- Hubbard, Simon J.;
- Ashe, Mark P.;
- Grant, Chris M.
Publication type:
Article
Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger.
Published in:
BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-61
By:
- Wright, James C.;
- Sugden, Deana;
- Francis-McIntyre, Sue;
- Riba-Garcia, Isabel;
- Gaskell, Simon J.;
- Grigoriev, Igor V.;
- Baker, Scott E.;
- Beynon, Robert J.;
- Hubbard, Simon J.
Publication type:
Article
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast.
Published in:
BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-7
By:
- Lawless, Craig;
- Pearson, Richard D.;
- Selley, Julian N.;
- Smirnova, Julia B.;
- Grant, Christopher M.;
- Ashe, Mark P.;
- Pavitt, Graham D.;
- Hubbard, Simon J.
Publication type:
Article
Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor.
Published in:
BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-79
By:
- Laing, Emma;
- Sidhu, Khushwant;
- Hubbard, Simon J.
Publication type:
Article
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes.
Published in:
BMC Genomics, 2007, v. 8, p. 97, doi. 10.1186/1471-2164-8-97
By:
- Alam, Intikhab;
- Hubbard, Simon J;
- Oliver, Stephen G;
- Rattray, Magnus
Publication type:
Article
A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics.
Published in:
Electrophoresis, 2001, v. 22, n. 3, p. 552, doi. 10.1002/1522-2683(200102)22:3<552::AID-ELPS552>3.0.CO;2-C
By:
- Brancia, Francesco L.;
- Butt, Amna;
- Beynon, Robert J.;
- Hubbard, Simon J.;
- Gaskell, Simon J.;
- Oliver, Stephen G.
Publication type:
Article
PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d649, doi. 10.1093/nar/gkj066
By:
- McLaughlin, Thomas;
- Siepen, Jennifer A.;
- Selley, Julian;
- Lynch, Jennifer A.;
- Lau, King Wai;
- Yin, Hujun;
- Gaskell, Simon J.;
- Hubbard, Simon J.
Publication type:
Article
SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences.
Published in:
Nucleic Acids Research, 2003, v. 31, n. 13, p. 3572, doi. 10.1093/nar/gkg511
By:
- Boardman, Paul E.;
- Oliver, Stephen G.;
- Hubbard, Simon J.
Publication type:
Article
A critical assessment of the secondary structure α-helices and their termini in proteins.
Published in:
Protein Engineering, 2002, v. 15, n. 7, p. 545, doi. 10.1093/protein/15.7.545
By:
- Wilson, Claire L.;
- Hubbard, Simon J.;
- Doig, Andrew J.
Publication type:
Article
Model Parameterization with Quantitative Proteomics: Case Study with Trehalose Metabolism in Saccharomyces cerevisiae.
Published in:
Processes, 2021, v. 9, n. 1, p. 139, doi. 10.3390/pr9010139
By:
- Yap, Chuan Fu;
- Garcia-Albornoz, Manuel;
- Jarnuczak, Andrew F.;
- Hubbard, Simon J.;
- Schwartz, Jean-Marc
Publication type:
Article
Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome.
Published in:
Frontiers in Plant Science, 2017, p. 1, doi. 10.3389/fpls.2017.01239
By:
- Miller, Matthew A. E.;
- O'Cualain, Ronan;
- Selley, Julian;
- Knight, David;
- Karim, Mohd F.;
- Hubbard, Simon J.;
- Johnson, Giles N.
Publication type:
Article
Global mRNA selection mechanisms for translation initiation.
Published in:
Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-014-0559-z
By:
- Costello, Joseph;
- Castelli, Lydia M.;
- Rowe, William;
- Kershaw, Christopher J.;
- Talavera, David;
- Mohammad-Qureshi, Sarah S.;
- Sims, Paul F. G.;
- Grant, Christopher M.;
- Pavitt, Graham D.;
- Hubbard, Simon J.;
- Ashe, Mark P.
Publication type:
Article
Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides.
Published in:
Rapid Communications in Mass Spectrometry: RCM, 2009, v. 23, n. 10, p. 1508, doi. 10.1002/rcm.4032
By:
- Lau, King Wai;
- Hart, Sarah R.;
- Lynch, Jennifer A.;
- Wong, Stephen C. C.;
- Hubbard, Simon J.;
- Gaskell, Simon J.
Publication type:
Article
Disease modeling of core pre-mRNA splicing factor haploinsufficiency.
Published in:
Human Molecular Genetics, 2019, v. 28, n. 22, p. 3704, doi. 10.1093/hmg/ddz169
By:
- Wood, Katherine A;
- Rowlands, Charlie F;
- Qureshi, Wasay Mohiuddin Shaikh;
- Thomas, Huw B;
- Buczek, Weronika A;
- Briggs, Tracy A;
- Hubbard, Simon J;
- Hentges, Kathryn E;
- Newman, William G;
- O'Keefe, Raymond T
Publication type:
Article
Ribosomal flavours: an acquired taste for specific mRNAs?
Published in:
Biochemical Society Transactions, 2018, v. 46, n. 6, p. 1529, doi. 10.1042/BST20180160
By:
- Bates, Christian;
- Hubbard, Simon J.;
- Ashe, Mark P.
Publication type:
Article
Conceptual modelling of genomic information.
Published in:
Bioinformatics, 2000, v. 16, n. 6, p. 548, doi. 10.1093/bioinformatics/16.6.548
By:
- Paton, Norman W.;
- Khan, Shakeel A.;
- Hayes, Andrew;
- Moussouni, Fouzia;
- Brass, Andy;
- Eilbeck, Karen;
- Goble, Carole A.;
- Hubbard, Simon J.;
- Oliver, Stephen G.
Publication type:
Article
Paralogous translation factors target distinct mRNAs to differentially regulate tolerance to oxidative stress in yeast.
Published in:
Nucleic Acids Research, 2023, v. 51, n. 16, p. 8820, doi. 10.1093/nar/gkad568
By:
- Cunningham, Joanne;
- Sfakianos, Aristeidis P;
- Kritsiligkou, Paraskevi;
- Kershaw, Christopher J;
- Whitmarsh, Alan J;
- Hubbard, Simon J;
- Ashe, Mark P;
- Grant, Chris M
Publication type:
Article
Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses.
Published in:
Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1338-4
By:
- Costello, Joseph L.;
- Kershaw, Christopher J.;
- Castelli, Lydia M.;
- Talavera, David;
- Rowe, William;
- Sims, Paul F. G.;
- Ashe, Mark P.;
- Grant, Christopher M.;
- Hubbard, Simon J.;
- Pavitt, Graham D.
Publication type:
Article
The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation.
Published in:
PLoS Genetics, 2015, v. 11, n. 5, p. 1, doi. 10.1371/journal.pgen.1005233
By:
- Castelli, Lydia M.;
- Talavera, David;
- Kershaw, Christopher J.;
- Mohammad-Qureshi, Sarah S.;
- Costello, Joseph L.;
- Rowe, William;
- Sims, Paul F. G.;
- Grant, Christopher M.;
- Hubbard, Simon J.;
- Ashe, Mark P.;
- Pavitt, Graham D.
Publication type:
Article
The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response.
Published in:
PLoS Genetics, 2015, v. 11, n. 1, p. 1, doi. 10.1371/journal.pgen.1004903
By:
- Kershaw, Christopher J.;
- Costello, Joseph L.;
- Castelli, Lydia M.;
- Talavera, David;
- Rowe, William;
- Sims, Paul F. G.;
- Ashe, Mark P.;
- Hubbard, Simon J.;
- Pavitt, Graham D.;
- Grant, Chris M.
Publication type:
Article
Effect of polymorphisms on ligand binding by mouse major urinary proteins.
Published in:
Protein Science: A Publication of the Protein Society, 2001, v. 10, n. 2, p. 411, doi. 10.1110/ps.31701
By:
- Darwish Marie, Amr;
- Veggerby, Christina;
- Robertson, Duncan H.L.;
- Gaskell, Simon J.;
- Hubbard, Simon J.;
- Martinsen, Line;
- Hurst, Jane L.;
- Beynon, Robert J.
Publication type:
Article
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.
Published in:
Proteome Science, 2007, v. 5, p. 1, doi. 10.1186/1477-5956-5-4
By:
- Siepen, Jennifer A.;
- Swainston, Neil;
- Jones, Andrew R.;
- Hart, Sarah R.;
- Hermjakob, Henning;
- Jones, Philip;
- Hubbard, Simon J.
Publication type:
Article
Human and mouse homo-oligomeric meprin A metalloendopeptidase: substrate and inhibitor specificities.
Published in:
Biological Chemistry, 2007, v. 388, n. 11, p. 1163, doi. 10.1515/BC.2007.156
By:
- Bylander, John E.;
- Bertenshaw, Greg P.;
- Matters, Gail L.;
- Hubbard, Simon J.;
- Bond, Judith S.
Publication type:
Article

Found: 49