Photo of Prof Andy Jones

Prof Andy Jones Bsc, MRes, PhD

Professor of Bioinformatics Functional and Comparative Genomics

    Publications

    2018

    Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants. (Journal article)

    Al-Momani, S., Qi, D., Ren, Z., & Jones, A. R. (2018). Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants.. Journal of proteomics, 181, 152-159. doi:10.1016/j.jprot.2018.04.011

    DOI: 10.1016/j.jprot.2018.04.011

    The effect of immunogenetic variability on human health: bioinformatics investigations from different perspectives (Thesis / Dissertation)

    Takeshita, L. Y. C. (2018, April 10). The effect of immunogenetic variability on human health: bioinformatics investigations from different perspectives.

    The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data (Journal article)

    Menschaert, G., Wang, X., Jones, A. R., Ghali, F., Fenyo, D., Olexiouk, V., . . . Vizcaino, J. A. (2018). The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. GENOME BIOLOGY, 19. doi:10.1186/s13059-017-1377-x

    DOI: 10.1186/s13059-017-1377-x

    phpMs: A PHP-Based Mass Spectrometry Utilities Library (Journal article)

    Collins, A., & Jones, A. R. (2018). phpMs: A PHP-Based Mass Spectrometry Utilities Library. JOURNAL OF PROTEOME RESEARCH, 17(3), 1309-1313. doi:10.1021/acs.jproteome.7b00783

    DOI: 10.1021/acs.jproteome.7b00783

    2017

    Chapter 11: Data Formats of the Proteomics Standards Initiative (Chapter)

    Vizcaíno, J. A., Perkins, S., Jones, A. R., & Deutsch, E. W. (2017). Chapter 11: Data Formats of the Proteomics Standards Initiative. In New Developments in Mass Spectrometry (Vol. 2017-January, pp. 231-258). doi:10.1039/9781782626732-00229

    DOI: 10.1039/9781782626732-00229

    Chapter 15: Proteogenomics: Proteomics for Genome Annotation (Chapter)

    Ghali, F., & Jones, A. R. (2017). Chapter 15: Proteogenomics: Proteomics for Genome Annotation. In New Developments in Mass Spectrometry (Vol. 2017-January, pp. 367-384). doi:10.1039/9781782626732-00365

    DOI: 10.1039/9781782626732-00365

    Chapter 5: Protein Inference and Grouping (Chapter)

    Jones, A. R. (2017). Chapter 5: Protein Inference and Grouping. In New Developments in Mass Spectrometry (Vol. 2017-January, pp. 93-115). doi:10.1039/9781782626732-00093

    DOI: 10.1039/9781782626732-00093

    Estimating the Pertinent Information Present in Social Media, not just what an Algorithm Detects (Poster)

    Maskell, S., Sloane, R., Perkins, S., Heap, J., Hajne, J., Jones, A., & Pirmohamed, M. (2017). Estimating the Pertinent Information Present in Social Media, not just what an Algorithm Detects. Poster session presented at the meeting of Unknown Conference. Retrieved from http://gateway.webofknowledge.com/

    Evaluation of Parameters for Confident Phosphorylation Site Localization Using an Orbitrap Fusion Tribrid Mass Spectrometer (Journal article)

    Ferries, S., Perkins, S., Brownridge, P. J., Camphell, A., Eyers, P. A., Jones, A. R., & Eyers, C. E. (2017). Evaluation of Parameters for Confident Phosphorylation Site Localization Using an Orbitrap Fusion Tribrid Mass Spectrometer. JOURNAL OF PROTEOME RESEARCH, 16(9), 3448-3459. doi:10.1021/acs.jproteome.7b00337

    DOI: 10.1021/acs.jproteome.7b00337

    Extensive non-canonical phosphorylation in human cells revealed using strong-anion exchange-mediated phosphoproteomics (Journal article)

    Hardman, G., Perkins, S., Ruan, Z., Kannan, N., Brownridge, P., Byrne, D., . . . Eyers, C. E. (n.d.). Extensive non-canonical phosphorylation in human cells revealed using strong-anion exchange-mediated phosphoproteomics. BioRxiv. doi:10.1101/202820

    DOI: 10.1101/202820

    Genome-wide association study of nevirapine hypersensitivity in a sub-Saharan African HIV-infected population (Journal article)

    Carr, D. F., Bourgeois, S., Chaponda, M., Takeshita, L. Y., Morris, A. P., Castro, E. M. C., . . . Pirmohamed, M. (2017). Genome-wide association study of nevirapine hypersensitivity in a sub-Saharan African HIV-infected population. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 72(4), 1152-1162. doi:10.1093/jac/dkw545

    DOI: 10.1093/jac/dkw545

    Human leucocyte antigen-adverse drug reaction associations: from a perspective of ethnicity (Journal article)

    Ghattaoraya, G. S., Middleton, D., Santos, E. J. M., Dickson, R., Jones, A. R., & Alfirevic, A. (2017). Human leucocyte antigen-adverse drug reaction associations: from a perspective of ethnicity. INTERNATIONAL JOURNAL OF IMMUNOGENETICS, 44(1), 7-26. doi:10.1111/iji.12304

    DOI: 10.1111/iji.12304

    KIR/HLA-DB: A REPOSITORY FOR THE ANALYSIS OF KIR AND HLA LIGANDS IN WORLDWIDE POPULATIONS (Conference Paper)

    Gonzalez-Galarza, F. F., Serna-Valverde, A. L., Ortega-Rivera, N. D., Jones, A. R., & Middleton, D. (2017). KIR/HLA-DB: A REPOSITORY FOR THE ANALYSIS OF KIR AND HLA LIGANDS IN WORLDWIDE POPULATIONS. In HUMAN IMMUNOLOGY Vol. 78 (pp. 121). doi:10.1016/j.humimm.2017.06.152

    DOI: 10.1016/j.humimm.2017.06.152

    Looking Longitudinally in Twitter: Reading More than 140 Characters (Poster)

    Maskell, S., Sloane, R., Hajne, J., Heap, J., Perkins, S., Griffith, E., . . . Pirmohamed, M. (2017). Looking Longitudinally in Twitter: Reading More than 140 Characters. Poster session presented at the meeting of Unknown Conference. Retrieved from http://gateway.webofknowledge.com/

    Neopeptide Analyser: A software tool for neopeptide discovery in proteomics data. (Journal article)

    Peffers, M., Jones, A. R., McCabe, A., & Anderson, J. (2017). Neopeptide Analyser: A software tool for neopeptide discovery in proteomics data.. Wellcome open research, 2, 24. doi:10.12688/wellcomeopenres.11275.1

    DOI: 10.12688/wellcomeopenres.11275.1

    Proteomics Standards Initiative: Fifteen Years of Progress and Future Work (Journal article)

    Deutsch, E. W., Orchard, S., Binz, P. -A., Bittremieux, W., Eisenacher, M., Hermjakob, H., . . . Jones, A. R. (2017). Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. JOURNAL OF PROTEOME RESEARCH, 16(12), 4288-4298. doi:10.1021/acs.jproteome.7b00370

    DOI: 10.1021/acs.jproteome.7b00370

    The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics (Journal article)

    Vizcaino, J. A., Mayer, G., Perkins, S., Barsnes, H., Vaudel, M., Perez-Riverol, Y., . . . Jones, A. R. (2017). The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics. MOLECULAR & CELLULAR PROTEOMICS, 16(7), 1275-1285. doi:10.1074/mcp.M117.068429

    DOI: 10.1074/mcp.M117.068429

    Using phosphoproteomics to decipher the syndecan-3 network (Conference Paper)

    Jones, F. K., Jones, A. R., & Pisconti, A. (2017). Using phosphoproteomics to decipher the syndecan-3 network. In INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY Vol. 98 (pp. A9-A10). Retrieved from http://gateway.webofknowledge.com/

    nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data (Journal article)

    Schober, D., Jacob, D., Wilson, M., Cruz, J. A., Marcu, A., Grant, J. R., . . . Neumann, S. (2018). nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data. ANALYTICAL CHEMISTRY, 90(1), 649-656. doi:10.1021/acs.analchem.7b02795

    DOI: 10.1021/acs.analchem.7b02795

    2016

    A web resource for mining HLA associations with adverse drug reactions: HLA-ADR. (Journal article)

    Ghattaoraya, G. S., Dundar, Y., González-Galarza, F. F., Maia, M. H. T., Santos, E. J. M., da Silva, A. L. S., . . . Jones, A. R. (2016). A web resource for mining HLA associations with adverse drug reactions: HLA-ADR.. Database : the journal of biological databases and curation, 2016. doi:10.1093/database/baw069

    DOI: 10.1093/database/baw069

    2015

    A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: Application to emerging infectious diseases (Journal article)

    Oyarzun, P., Ellis, J. J., Gonzalez-Galarza, F. F., Jones, A. R., Middleton, D., Boden, M., & Kobe, B. (2015). A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: Application to emerging infectious diseases. VACCINE, 33(10), 1267-1273. doi:10.1016/j.vaccine.2015.01.040

    DOI: 10.1016/j.vaccine.2015.01.040

    A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum (Journal article)

    Krishna, R., Xia, D., Sanderson, S., Shanmugasundram, A., Vermont, S., Bernal, A., . . . Jones, A. R. (2015). A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum. PROTEOMICS, 15(15), 2618-2628. doi:10.1002/pmic.201400553

    DOI: 10.1002/pmic.201400553

    Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data (Journal article)

    Melos dos Santos, E. J., McCabe, A., Gonzalez-Galarza, F. F., Jones, A. R., & Middleton, D. (2016). Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data. HUMAN IMMUNOLOGY, 77(3), 238-248. doi:10.1016/j.humimm.2015.11.013

    DOI: 10.1016/j.humimm.2015.11.013

    Computational phosphoproteomics: From identification to localization (Journal article)

    Lee, D. C. H., Jones, A. R., & Hubbard, S. J. (2015). Computational phosphoproteomics: From identification to localization. PROTEOMICS, 15(5-6), 950-963. doi:10.1002/pmic.201400372

    DOI: 10.1002/pmic.201400372

    Development of data representation standards by the human proteome organization proteomics standards initiative (Journal article)

    Deutsch, E. W., Albar, J. P., Binz, P. -A., Eisenacher, M., Jones, A. R., Mayer, G., . . . Hermjakob, H. (2015). Development of data representation standards by the human proteome organization proteomics standards initiative. JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION, 22(3), 495-506. doi:10.1093/jamia/ocv001

    DOI: 10.1093/jamia/ocv001

    Development of data representation standards by the human proteome organization proteomics standards initiative (Journal article)

    Deutsch, E. W., Albar, J. P., Binz, P. -A., Eisenacher, M., Jones, A. R., Mayer, G., . . . Hermjakob, H. (2015). Development of data representation standards by the human proteome organization proteomics standards initiative. Journal of the American Medical Informatics Association : JAMIA, 22(3), 495-506. doi:10.1093/jamia/ocv001

    DOI: 10.1093/jamia/ocv001

    Embedding standards in metabolomics: the Metabolomics Society data standards task group (Journal article)

    Salek, R. M., Arita, M., Dayalan, S., Ebbels, T., Jones, A. R., Neumann, S., . . . Vizcaino, J. -A. (2015). Embedding standards in metabolomics: the Metabolomics Society data standards task group. METABOLOMICS, 11(4), 782-783. doi:10.1007/s11306-015-0821-8

    DOI: 10.1007/s11306-015-0821-8

    Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics (Journal article)

    Fan, J., Saha, S., Barker, G., Heesom, K. J., Ghali, F., Jones, A. R., . . . Bessant, C. (2015). Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics. MOLECULAR & CELLULAR PROTEOMICS, 14(11), 3087-3093. doi:10.1074/mcp.O115.048777

    DOI: 10.1074/mcp.O115.048777

    IPeak: An open source tool to combine results from multiple MS/MS search engines (Journal article)

    Wen, B., Du, C., Li, G., Ghali, F., Jones, A. R., Kall, L., . . . Wang, J. (2015). IPeak: An open source tool to combine results from multiple MS/MS search engines. PROTEOMICS, 15(17), 2916-2920. doi:10.1002/pmic.201400208

    DOI: 10.1002/pmic.201400208

    Representation of selected-reaction monitoring data in the mzQuantML data standard (Journal article)

    Qi, D., Lawless, C., Teleman, J., Levander, F., Holman, S. W., Hubbard, S., & Jones, A. R. (2015). Representation of selected-reaction monitoring data in the mzQuantML data standard. PROTEOMICS, 15(15), 2592-2596. doi:10.1002/pmic.201400281

    DOI: 10.1002/pmic.201400281

    The mzqLibrary - An open source Java library supporting the HUPO-PSI quantitative proteomics standard (Journal article)

    Qi, D., Zhang, H., Fan, J., Perkins, S., Pisconti, A., Simpson, D. M., . . . Jones, A. R. (2015). The mzqLibrary - An open source Java library supporting the HUPO-PSI quantitative proteomics standard. PROTEOMICS, 15(18), 3152-3162. doi:10.1002/pmic.201400535

    DOI: 10.1002/pmic.201400535

    2014

    A standardized framing for reporting protein identifications in mzIdentML 1.2 (Journal article)

    Seymour, S. L., Farrah, T., Binz, P. -A., Chalkley, R. J., Cottrell, J. S., Searle, B. C., . . . Jones, A. R. (2014). A standardized framing for reporting protein identifications in mzIdentML 1.2. PROTEOMICS, 14(21-22), 2389-2399. doi:10.1002/pmic.201400080

    DOI: 10.1002/pmic.201400080

    A standardized framing for reporting protein identifications in mzIdentML 1.2. (Journal article)

    Seymour, S. L., Farrah, T., Binz, P. -A., Chalkley, R. J., Cottrell, J. S., Searle, B. C., . . . Jones, A. R. (2014). A standardized framing for reporting protein identifications in mzIdentML 1.2.. PROTEOMICS, epub a, pmic.201400080.

    A tutorial for software development in quantitative proteomics using PSI standard formats (Journal article)

    Gonzalez-Galarza, F. F., Qi, D., Fan, J., Bessant, C., & Jones, A. R. (2014). A tutorial for software development in quantitative proteomics using PSI standard formats. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1844(1), 88-97. doi:10.1016/j.bbapap2013.04.004

    DOI: 10.1016/j.bbapap2013.04.004

    A tutorial for software development in quantitative proteomics using PSI standard formats. (Journal article)

    Gonzalez-Galarza, F. F., Qi, D., Fan, J., Bessant, C., & Jones, A. R. (2014). A tutorial for software development in quantitative proteomics using PSI standard formats.. Biochimica et biophysica acta, 1844(1 Pt A), 88-97. doi:10.1016/j.bbapap.2013.04.004

    DOI: 10.1016/j.bbapap.2013.04.004

    Allele Frequencies Database (Journal article)

    Takeshita, L. Y. C., Jones, A. R., Gonzalez-Galarza, F. F., & Middleton, D. (2014). Allele Frequencies Database. TRANSFUSION MEDICINE AND HEMOTHERAPY, 41(5), 352-355. doi:10.1159/000368056

    DOI: 10.1159/000368056

    Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations (Journal article)

    Gonzalez-Galarza, F. F., Takeshita, L. Y. C., Santos, E. J. M., Kempson, F., Thomaz Maia, M. H., Soares da Silva, A. L., . . . Middleton, D. (2015). Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations. NUCLEIC ACIDS RESEARCH, 43(D1), D784-D788. doi:10.1093/nar/gku1166

    DOI: 10.1093/nar/gku1166

    Controlled vocabularies and ontologies in proteomics: Overview, principles and practice (Journal article)

    Mayer, G., Jones, A. R., Binz, P. -A., Deutsch, E. W., Orchard, S., Montecchi-Palazzi, L., . . . Eisenacher, M. (2014). Controlled vocabularies and ontologies in proteomics: Overview, principles and practice. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1844(1), 98-107. doi:10.1016/j.bbapap.2013.02.017

    DOI: 10.1016/j.bbapap.2013.02.017

    Guidelines for reporting quantitative mass spectrometry based experiments in proteomics (Journal article)

    Martinez-Bartolome, S., Deutsch, E. W., Binz, P. -A., Jones, A. R., Eisenacher, M., Mayer, G., . . . Albar, J. P. (2013). Guidelines for reporting quantitative mass spectrometry based experiments in proteomics. JOURNAL OF PROTEOMICS, 95, 84-88. doi:10.1016/j.jprot.2013.02.026

    DOI: 10.1016/j.jprot.2013.02.026

    How to submit MS proteomics data to ProteomeXchange via the PRIDE database (Journal article)

    Ternent, T., Csordas, A., Qi, D., Gomez-Baena, G., Beynon, R. J., Jones, A. R., . . . Vizcaino, J. A. (2014). How to submit MS proteomics data to ProteomeXchange via the PRIDE database. PROTEOMICS, 14(20), 2233-2241. doi:10.1002/pmic.201400120

    DOI: 10.1002/pmic.201400120

    Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany. (Journal article)

    Orchard, S., Albar, J. P., Binz, P. -A., Kettner, C., Jones, A. R., Salek, R. M., . . . Hermjakob, H. (2014). Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.. Proteomics, 14(21-22), 2363-2368. doi:10.1002/pmic.201470164

    DOI: 10.1002/pmic.201470164

    Numerical Compression Schemes for Proteomics Mass Spectrometry Data (Journal article)

    Teleman, J., Dowsey, A. W., Gonzalez-Galarza, F. F., Perkins, S., Pratt, B., Roest, H. L., . . . Levander, F. (2014). Numerical Compression Schemes for Proteomics Mass Spectrometry Data. MOLECULAR & CELLULAR PROTEOMICS, 13(6), 1537-1542. doi:10.1074/mcp.O114.037879

    DOI: 10.1074/mcp.O114.037879

    Numerical Compression Schemes for Proteomics Mass Spectrometry Data (Journal article)

    Teleman, J., Dowsey, A. W., Gonzalez-Galarza, F. F., Perkins, S., Pratt, B., Röst, H. L., . . . Levander, F. (2014). Numerical Compression Schemes for Proteomics Mass Spectrometry Data. Molecular & Cellular Proteomics, 13(6), 1537-1542. doi:10.1074/mcp.O114.037879

    DOI: 10.1074/mcp.O114.037879

    ProteoAnnotator - Open source proteogenomics annotation software supporting PSI standards (Journal article)

    Ghali, F., Krishna, R., Perkins, S., Collins, A., Xia, D., Wastling, J., & Jones, A. R. (2014). ProteoAnnotator - Open source proteogenomics annotation software supporting PSI standards. PROTEOMICS, 14(23-24), 2731-2741. doi:10.1002/pmic.201400265

    DOI: 10.1002/pmic.201400265

    ProteomeXchange provides globally coordinated proteomics data submission and dissemination (Journal article)

    Vizcaino, J. A., Deutsch, E. W., Wang, R., Csordas, A., Reisinger, F., Rios, D., . . . Hermjakob, H. (2014). ProteomeXchange provides globally coordinated proteomics data submission and dissemination. NATURE BIOTECHNOLOGY, 32(3), 223-226. doi:10.1038/nbt.2839

    DOI: 10.1038/nbt.2839

    Standardization and Guidelines: How to submit MS proteomics data to ProteomeXchange via the PRIDE database. (Journal article)

    Ternent, T., Csordas, A., Qi, D., Gómez-Baena, G., Beynon, R. J., Jones, A. R., . . . Vizcaíno, J. A. (2014). Standardization and Guidelines: How to submit MS proteomics data to ProteomeXchange via the PRIDE database.. PROTEOMICS, epub a, pmic.201400120.

    The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary (Journal article)

    Mayer, G., Montecchi-Palazzi, L., Ovelleiro, D., Jones, A. R., Binz, P. -A., Deutsch, E. W., . . . Grp, H. U. P. O. -P. S. I. (2013). The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. doi:10.1093/database/bat009

    DOI: 10.1093/database/bat009

    The jmzQuantML programming interface and validator for the mzQuantML data standard (Journal article)

    Qi, D., Krishna, R., & Jones, A. R. (2014). The jmzQuantML programming interface and validator for the mzQuantML data standard. PROTEOMICS, 14(6), 685-688. doi:10.1002/pmic.201300281

    DOI: 10.1002/pmic.201300281

    The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience. (Journal article)

    Griss, J., Jones, A. R., Sachsenberg, T., Walzer, M., Gatto, L., Hartler, J., . . . Hermjakob, H. (2014). The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience.. Molecular & Cellular Proteomics, epub a, mcp.O113.036681.

    jmzTab: A Java interface to the mzTab data standard (Journal article)

    Xu, Q. -W., Griss, J., Wang, R., Jones, A. R., Hermjakob, H., & Vizcaino, J. A. (2014). jmzTab: A Java interface to the mzTab data standard. PROTEOMICS, 14(11), 1328-1332. doi:10.1002/pmic.201300560

    DOI: 10.1002/pmic.201300560

    2013

    16(th) IHIW: extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles. (Conference Paper)

    Gonzalez-Galarza, F. F., Mack, S. J., Hollenbach, J., Fernandez-Vina, M., Setterholm, M., Kempenich, J., . . . HLA Rare Allele Consortium. (2013). 16(th) IHIW: extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles.. In International journal of immunogenetics Vol. 40 (pp. 60-65). doi:10.1111/iji.12030

    DOI: 10.1111/iji.12030

    16th IHIW: Extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles (Journal article)

    Gonzalez-Galarza, F. F., Mack, S. J., Hollenbach, J., Fernandez-Vina, M., Setterholm, M., Kempenich, J., . . . Consortium, H. L. A. R. A. (2013). 16th IHIW: Extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles. INTERNATIONAL JOURNAL OF IMMUNOGENETICS, 40(1), 60-65. doi:10.1111/iji.12030

    DOI: 10.1111/iji.12030

    A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations (Journal article)

    Takeshita, L. Y. C., Gonzalez-Galarza, F. F., dos Santos, E. J. M., Maia, M. H. T., Rahman, M. M., Zain, S. M. S., . . . Jones, A. R. (2013). A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. doi:10.1093/database/bat021

    DOI: 10.1093/database/bat021

    A guide for integration of proteomic data standards into laboratory workflows (Journal article)

    Alberto Medina-Aunon, J., Krishna, R., Ghali, F., Albar, J. P., & Jones, A. R. (2013). A guide for integration of proteomic data standards into laboratory workflows. PROTEOMICS, 13, 480-492. Retrieved from http://dx.doi.org/10.1002/pmic.201200268

    Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites (Journal article)

    Shanmugasundram, A., Gonzalez-Galarza, F. F., Wastling, J. M., Vasieva, O., & Jones, A. R. (2013). Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites. NUCLEIC ACIDS RESEARCH, 41(D1), D706-D713. doi:10.1093/nar/gks1139

    DOI: 10.1093/nar/gks1139

    Preparing to Work with Big Data in Proteomics - A Report on the HUPO-PSI Spring Workshop April 15-17, 2013, Liverpool, UK (Journal article)

    Orchard, S., Binz, P. -A., Jones, A. R., Vizcaino, J. A., Deutsch, E. W., & Hermjakob, H. (2013). Preparing to Work with Big Data in Proteomics - A Report on the HUPO-PSI Spring Workshop April 15-17, 2013, Liverpool, UK. PROTEOMICS, 13(20), 2931-2937. doi:10.1002/pmic.201370166

    DOI: 10.1002/pmic.201370166

    The mzQuantML Data Standard for Mass Spectrometry-based Quantitative Studies in Proteomics (Journal article)

    Walzer, M., Qi, D., Mayer, G., Uszkoreit, J., Eisenacher, M., Sachsenberg, T., . . . Jones, A. R. (2013). The mzQuantML Data Standard for Mass Spectrometry-based Quantitative Studies in Proteomics. MOLECULAR & CELLULAR PROTEOMICS, 12(8), 2332-2340. doi:10.1074/mcp.O113.028506

    DOI: 10.1074/mcp.O113.028506

    Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML (Journal article)

    Ghali, F., Krishna, R., Lukasse, P., Martinez-Bartolome, S., Reisinger, F., Hermjakob, H., . . . Jones, A. R. (2013). Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML. MOLECULAR & CELLULAR PROTEOMICS, 12(11), 3026-3035. doi:10.1074/mcp.O113.029777

    DOI: 10.1074/mcp.O113.029777

    2012

    A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis (Journal article)

    Gonzalez-Galarza, F. F., Lawless, C., Hubbard, S. J., Fan, J., Bessant, C., Hermjakob, H., & Jones, A. R. (2012). A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 16(9), 431-442. doi:10.1089/omi.2012.0022

    DOI: 10.1089/omi.2012.0022

    A Software Toolkit and Interface for Performing Stable Isotope Labeling and Top3 Quantification Using Progenesis LC-MS (Journal article)

    Qi, D., Brownridge, P., Xia, D., Mackay, K., Gonzalez-Galarza, F. F., Kenyani, J., . . . Jones, A. R. (2012). A Software Toolkit and Interface for Performing Stable Isotope Labeling and Top3 Quantification Using Progenesis LC-MS. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 16(9), 489-495. doi:10.1089/omi.2012.0042

    DOI: 10.1089/omi.2012.0042

    Bioinformatics Challenges and Solutions in Proteomics as Quantitative Methods Mature (Journal article)

    Jones, A. R. (2012). Bioinformatics Challenges and Solutions in Proteomics as Quantitative Methods Mature. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 16(9), 429-430. doi:10.1089/omi.2012.0051

    DOI: 10.1089/omi.2012.0051

    FDRAnalysis: A Tool for the Integrated Analysis of Tandem Mass Spectrometry Identification Results from Multiple Search Engines (Journal article)

    Wedge, D. C., Krishna, R., Blackhurst, P., Siepen, J. A., Jones, A. R., & Hubbard, S. J. (2011). FDRAnalysis: A Tool for the Integrated Analysis of Tandem Mass Spectrometry Identification Results from Multiple Search Engines. JOURNAL OF PROTEOME RESEARCH, 10(4), 2088-2094. doi:10.1021/pr101157s

    DOI: 10.1021/pr101157s

    In silico analysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers (Journal article)

    Alfirevic, A., Gonzalez-Galarza, F., Bell, C., Martinsson, K., Platt, V., Bretland, G., . . . Pirmohamed, M. (2012). In silico analysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers. GENOME MEDICINE, 4. doi:10.1186/gm350

    DOI: 10.1186/gm350

    In silico analysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers. (Journal article)

    Alfirevic, A., Gonzalez-Galarza, F., Bell, C., Martinsson, K., Platt, V., Bretland, G., . . . Pirmohamed, M. (2012). In silico analysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers.. Genome Medicine, 4, 51. Retrieved from http://genomemedicine.com/content/4/6/51/abstract

    Software for analysing ion mobility mass spectrometry data to improve peptide identification (Journal article)

    Xia, D., Ghali, F., Gaskell, S. J., O'Cualain, R., Sims, P. F. G., & Jones, A. R. (2012). Software for analysing ion mobility mass spectrometry data to improve peptide identification. PROTEOMICS, 12(12), 1912-1916. doi:10.1002/pmic.201200029

    DOI: 10.1002/pmic.201200029

    Software for analysing ion mobility mass spectrometry data to improve peptide identification (Journal article)

    Xia, D., Ghali, F., Gaskell, S. J., O'Cualain, R., Sims, P. F. G., & Jones, A. R. (2012). Software for analysing ion mobility mass spectrometry data to improve peptide identification. PROTEOMICS, 12(12), 1912-1916. doi:10.1002/pmic.201200029

    DOI: 10.1002/pmic.201200029

    Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop (Journal article)

    Orchard, S., Binz, P. -A., Borchers, C., Gilson, M. K., Jones, A. R., Nicola, G., . . . Hermjakob, H. (2012). Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop. PROTEOMICS, 12(18), 2767-2772. doi:10.1002/pmic.201270126

    DOI: 10.1002/pmic.201270126

    The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results (Journal article)

    Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O., Siepen, J., Hubbard, S. J., . . . Creasy, D. (2012). The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results. MOLECULAR & CELLULAR PROTEOMICS, 11(7). doi:10.1074/mcp.M111.014381

    DOI: 10.1074/mcp.M111.014381

    The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience (Journal article)

    Griss, J., Jones, A. R., Sachsenberg, T., Walzer, M., Gatto, L., Hartler, J., . . . Hermjakob, H. (2014). The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience. MOLECULAR & CELLULAR PROTEOMICS, 13(10), 2765-2775. doi:10.1074/mcp.O113.036681

    DOI: 10.1074/mcp.O113.036681

    jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data (Journal article)

    Reisinger, F., Krishna, R., Ghali, F., Rios, D., Hermjakob, H., Vizcaino, J. A., & Jones, A. R. (2012). jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. PROTEOMICS, 12(6), 790-794. doi:10.1002/pmic.201100577

    DOI: 10.1002/pmic.201100577

    2011

    A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics (Journal article)

    Kenyani, J., Medina-Aunon, J. A., Martinez-Bartolomé, S., Albar, J. -P., Wastling, J. M., & Jones, A. R. (2011). A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics. BMC Research Notes, 4(1), 86. doi:10.1186/1756-0500-4-86

    DOI: 10.1186/1756-0500-4-86

    A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics. (Journal article)

    Kenyani, J., Medina-Aunon, J. A., Martinez-Bartolomé, S., Albar, J. -P., Wastling, J. M., & Jones, A. R. (2011). A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics.. BMC research notes, 4, 86. doi:10.1186/1756-0500-4-86

    DOI: 10.1186/1756-0500-4-86

    Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations (Journal article)

    Gonzalez-Galarza, F. F., Christmas, S., Middleton, D., & Jones, A. R. (2011). Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. NUCLEIC ACIDS RESEARCH, 39, D913-D919. doi:10.1093/nar/gkq1128

    DOI: 10.1093/nar/gkq1128

    Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations (Journal article)

    Gonzalez-Galarza, F. F., Christmas, S., Middleton, D., & Jones, A. R. (2011). Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Research, 39(Database), D913-D919. doi:10.1093/nar/gkq1128

    DOI: 10.1093/nar/gkq1128

    Bioinformatics in Animal Proteomics (Chapter)

    Blakeley, P., Wright, J. C., Hubbard, S. J., & Jones, A. R. (2011). Bioinformatics in Animal Proteomics. In Methods in Animal Proteomics (pp. 103-119). doi:10.1002/9780470960660.ch5

    DOI: 10.1002/9780470960660.ch5

    FDRAnalysis: A Tool for the Integrated Analysis of Tandem Mass Spectrometry Identification Results from Multiple Search Engines. (Journal article)

    Wedge, D. C., Krishna, R., Blackhurst, P., Siepen, J. A., Jones, A. R., & Hubbard, S. J. (2011). FDRAnalysis: A Tool for the Integrated Analysis of Tandem Mass Spectrometry Identification Results from Multiple Search Engines.. J Proteome Res., 10(4), 2088-2094. Retrieved from http://pubs.acs.org/doi/abs/10.1021/pr101157s

    The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards (Journal article)

    Alberto Medina-Aunon, J., Martinez-Bartolome, S., Lopez-Garcia, M. A., Salazar, E., Navajas, R., Jones, A. R., . . . Albar, J. P. (2011). The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards. MOLECULAR & CELLULAR PROTEOMICS, 10(10). doi:10.1074/mcp.M111.008334

    DOI: 10.1074/mcp.M111.008334

    The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards (Journal article)

    Medina-Aunon, J. A., Martínez-Bartolomé, S., López-García, M. A., Salazar, E., Navajas, R., Jones, A. R., . . . Albar, J. P. (2011). The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards. Molecular & Cellular Proteomics, 10(10), M111.008334. doi:10.1074/mcp.M111.008334

    DOI: 10.1074/mcp.M111.008334

    2010

    An introduction to proteome bioinformatics. (Chapter)

    Jones, A. R., & Hubbard, S. J. (2010). An introduction to proteome bioinformatics.. In Unknown Book (Vol. 604, pp. 1-5). doi:10.1007/978-1-60761-444-9_1

    DOI: 10.1007/978-1-60761-444-9_1

    Guidelines for reporting the use of column chromatography in proteomics (Journal article)

    Jones, A. R., Carroll, K., Knight, D., MacLellan, K., Domann, P. J., Legido-Quigley, C., . . . Paton, N. W. (2010). Guidelines for reporting the use of column chromatography in proteomics. NATURE BIOTECHNOLOGY, 28(7), 654. doi:10.1038/nbt0710-654a

    DOI: 10.1038/nbt0710-654a

    Guidelines for reporting the use of gel image informatics in proteomics (Journal article)

    Hoogland, C., O'Gorman, M., Bogard, P., Gibson, F., Berth, M., Cockell, S. J., . . . Jones, A. R. (2010). Guidelines for reporting the use of gel image informatics in proteomics. NATURE BIOTECHNOLOGY, 28(7), 655-656. doi:10.1038/nbt0710-655

    DOI: 10.1038/nbt0710-655

    Managing experimental data using FuGE. (Chapter)

    Jones, A. R., & Lister, A. L. (2010). Managing experimental data using FuGE.. In Unknown Book (Vol. 604, pp. 333-343). doi:10.1007/978-1-60761-444-9_23

    DOI: 10.1007/978-1-60761-444-9_23

    Methods in Molecular Biology (Book)

    Hubbard, S. J., & Jones, A. R. (Eds.) (2010). Methods in Molecular Biology. New York: Humana Press.

    Semi-automatic tool to describe, store and compare proteomics experiments based on MIAPE compliant reports (Journal article)

    Martinez-Bartolome, S., Alberto Medina-Aunon, J., Jones, A. R., & Albar, J. P. (2010). Semi-automatic tool to describe, store and compare proteomics experiments based on MIAPE compliant reports. PROTEOMICS, 10(6), 1256-1260. doi:10.1002/pmic.200900367

    DOI: 10.1002/pmic.200900367

    Tackling Quantitation: A Report on the Annual Spring Workshop of the HUPO-PSI (Journal article)

    Orchard, S., Jones, A., Albar, J. -P., Cho, S. Y., Kwon, K. -H., Lee, C., & Hermjakob, H. (2010). Tackling Quantitation: A Report on the Annual Spring Workshop of the HUPO-PSI. PROTEOMICS, 10(17), 3062-3066. doi:10.1002/pmic.201090075

    DOI: 10.1002/pmic.201090075

    Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea. (Journal article)

    Orchard, S., Jones, A., Albar, J. -P., Cho, S. Y., Kwon, K. -H., Lee, C., & Hermjakob, H. (2010). Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea.. Proteomics, 10(17), 3062-3066. doi:10.1002/pmic.201090075

    DOI: 10.1002/pmic.201090075

    The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative (Journal article)

    Gibson, F., Hoogland, C., Martinez-Bartolome, S., Alberto Medina-Aunon, J., Pablo Albar, J., Babnigg, G., . . . Jones, A. R. (2010). The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative. PROTEOMICS, 10(17), 3073-3081. doi:10.1002/pmic.201000120

    DOI: 10.1002/pmic.201000120

    XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments (Journal article)

    Swertz, M. A., van der Velde, K. J., Tesson, B. M., Scheltema, R. A., Arends, D., Vera, G., . . . GEN2PHEN, G. -T. -P. (2010). XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. GENOME BIOLOGY, 11(3). doi:10.1186/gb-2010-11-3-r27

    DOI: 10.1186/gb-2010-11-3-r27

    2009

    Annual Spring Meeting of the Proteomics Standards Initiative (Journal article)

    Orchard, S., Deutsch, E. W., Binz, P. -A., Jones, A. R., Creasy, D., Montechi-Palazzi, L., . . . Hermjakob, H. (2009). Annual Spring Meeting of the Proteomics Standards Initiative. PROTEOMICS, 9(19), 4429-4432. doi:10.1002/pmic.200900407

    DOI: 10.1002/pmic.200900407

    FuGEFlow: data model and markup language for flow cytometry (Journal article)

    Qian, Y., Tchuvatkina, O., Spidlen, J., Wilkinson, P., Gasparetto, M., Jones, A. R., . . . Brinkman, R. R. (2009). FuGEFlow: data model and markup language for flow cytometry. BMC BIOINFORMATICS, 10. doi:10.1186/1471-2105-10-184

    DOI: 10.1186/1471-2105-10-184

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

    Jones, A. R., Siepen, J. A., Hubbard, S. J., & Paton, N. W. (2009). Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. PROTEOMICS, 9(5), 1220-1229. doi:10.1002/pmic.200800473

    DOI: 10.1002/pmic.200800473

    Modeling and Managing Experimental Data Using FuGE (Journal article)

    Jones, A. R., Lister, A. L., Hermida, L., Wilkinson, P., Eisenacher, M., Belhajjame, K., . . . Paton, N. W. (2009). Modeling and Managing Experimental Data Using FuGE. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 13(3), 239-251. doi:10.1089/omi.2008.0080

    DOI: 10.1089/omi.2008.0080

    The PSI semantic validator: A framework to check MIAPE compliance of proteomics data (Journal article)

    Montecchi-Palazzi, L., Kerrien, S., Reisinger, F., Aranda, B., Jones, A. R., Martens, L., & Hermjakob, H. (2009). The PSI semantic validator: A framework to check MIAPE compliance of proteomics data. PROTEOMICS, 9(22), 5112-5119. doi:10.1002/pmic.200900189

    DOI: 10.1002/pmic.200900189

    2008

    A toolkit for capturing and sharing FuGE experiments (Journal article)

    Belhajjame, K., Jones, A. R., & Paton, N. W. (2008). A toolkit for capturing and sharing FuGE experiments. BIOINFORMATICS, 24(22), 2647-2649. doi:10.1093/bioinformatics/btn496

    DOI: 10.1093/bioinformatics/btn496

    Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain (Journal article)

    Orchard, S., Albar, J. -P., Deutsch, E. W., Binz, P. -A., Jones, A. R., Creasy, D., & Hermjakob, H. (2008). Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain. PROTEOMICS, in pre, NA. Retrieved from http://dx.doi.org/10.1002/pmic.200800555

    Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain (Journal article)

    Orchard, S., Albar, J. -P., Deutsch, E. W., Binz, P. -A., Jones, A. R., Creasy, D., & Hermjakob, H. (2008). Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain. PROTEOMICS, 8(20), 4168-4172. doi:10.1002/pmic.200800555

    DOI: 10.1002/pmic.200800555

    Guidelines for reporting the use of gel electrophoresis in proteomics (Journal article)

    Gibson, F., Anderson, L., Babnigg, G., Baker, M., Berth, M., Binz, P. -A., . . . Jones, A. R. (2008). Guidelines for reporting the use of gel electrophoresis in proteomics. NATURE BIOTECHNOLOGY, 26(8), 863-864. doi:10.1038/nbt0808-863

    DOI: 10.1038/nbt0808-863

    Minimum Reporting Guidelines for Proteomics Released by the Proteomics Standards Initiative (Journal article)

    Jones, A. R., & Orchard, S. (2008). Minimum Reporting Guidelines for Proteomics Released by the Proteomics Standards Initiative. MOLECULAR & CELLULAR PROTEOMICS, 7(10), 2067-2068. doi:10.1074/mcp.H800010-MCP200

    DOI: 10.1074/mcp.H800010-MCP200

    Modulation of the host cell proteome by the intracellular apicomplexan parasite Toxoplasma gondii (Journal article)

    Nelson, M. M., Jones, A. R., Carmen, J. C., Sinai, A. P., Burchmore, R., & Wastling, J. A. (2008). Modulation of the host cell proteome by the intracellular apicomplexan parasite Toxoplasma gondii. INFECTION AND IMMUNITY, 76(2), 828-844. doi:10.1128/IAI.01115-07

    DOI: 10.1128/IAI.01115-07

    The Proteome of Toxoplasma gondii: Integration with the genome to give Insights into Gene Expression and Annotation (Journal article)

    Xia, D., Sanderson, S. J., Jones, A. R., Prieto, J. H., Yates, J., Bromley, E., . . . Wastling, J. M. (2008). The Proteome of Toxoplasma gondii: Integration with the genome to give Insights into Gene Expression and Annotation. Genome Biology, 9(7), R116. Retrieved from http://genomebiology.com/2008/9/7/R116

    The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation (Journal article)

    Xia, D., Sanderson, S. J., Jones, A. R., Prieto, J. H., Yates, J. R., Bromley, E., . . . Wastling, J. M. (2008). The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation. GENOME BIOLOGY, 9(7). doi:10.1186/gb-2008-9-7-r116

    DOI: 10.1186/gb-2008-9-7-r116

    2007

    An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ (TM) (Journal article)

    Siepen, J. A., Swainston, N., Jones, A. R., Hart, S. R., Hermjakob, H., Jones, P., & Hubbard, S. J. (2007). An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ (TM). PROTEOME SCIENCE, 5. doi:10.1186/1477-5956-5-4

    DOI: 10.1186/1477-5956-5-4

    An update on data standards for gel electrophoresis. (Journal article)

    Jones, A. R., & Gibson, F. (2007). An update on data standards for gel electrophoresis.. Proteomics, 7 Suppl 1, 35-40. doi:10.1002/pmic.200700171

    DOI: 10.1002/pmic.200700171

    Capture and analysis of quantitative proteomic data (Journal article)

    Lau, K. W., Jones, A. R., Swainston, N., Siepen, J. A., & Hubbard, S. J. (2007). Capture and analysis of quantitative proteomic data. PROTEOMICS, 7(16), 2787-2799. doi:10.1002/pmic.200700127

    DOI: 10.1002/pmic.200700127

    Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA. (Journal article)

    Orchard, S., Taylor, C. F., Jones, P., Montechi-Palazzo, L., Binz, P. -A., Jones, A. R., . . . Hermjakob, H. (2007). Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.. Proteomics, 7(3), 337-339. doi:10.1002/pmic.200600915

    DOI: 10.1002/pmic.200600915

    Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France. (Journal article)

    Orchard, S., Montechi-Palazzi, L., Deutsch, E. W., Binz, P. -A., Jones, A. R., Paton, N., . . . Hermjakob, H. (2007). Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France.. Proteomics, 7(19), 3436-3440. doi:10.1002/pmic.200700658

    DOI: 10.1002/pmic.200700658

    Storing, searching, and disseminating experimental proteomics data (Chapter)

    Paton, N. W., Jones, A. R., Garwood, C., Garwood, K., & Oliver, S. (2007). Storing, searching, and disseminating experimental proteomics data. In Introduction to Systems Biology (pp. 472-483). doi:10.1007/978-1-59745-531-2_24

    DOI: 10.1007/978-1-59745-531-2_24

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

    Jones, A. R., Miller, M., Aebersold, R., Apweiler, R., Ball, C. A., Brazma, A., . . . Pizarro, A. (2007). The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. NATURE BIOTECHNOLOGY, 25(10), 1127-1133. doi:10.1038/nbt1347

    DOI: 10.1038/nbt1347

    The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006. (Journal article)

    Orchard, S., Jones, A. R., Stephan, C., & Binz, P. -A. (2007). The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006.. Proteomics, 7(7), 1006-1008. doi:10.1002/pmic.200700014

    DOI: 10.1002/pmic.200700014

    The minimum information about a proteomics experiment (MIAPE) (Journal article)

    Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P. -A., Jr, J. R. K., Jones, A. R., . . . Hermjakob, H. (2007). The minimum information about a proteomics experiment (MIAPE). NATURE BIOTECHNOLOGY, 25(8), 887-893. doi:10.1038/nbt1329

    DOI: 10.1038/nbt1329

    2006

    A strategy capitalizing on synergies: The Reporting Structure for Biological Investigation (RSBI) working group (Journal article)

    Sansone, S. -A., Rocca-Serra, P., Tong, W., Fostel, J., Morrison, N., Jones, A. R., & Members, R. S. B. I. (2006). A strategy capitalizing on synergies: The Reporting Structure for Biological Investigation (RSBI) working group. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 10(2), 164-171. doi:10.1089/omi.2006.10.164

    DOI: 10.1089/omi.2006.10.164

    Data access and integration in the ISPIDER proteomics grid (Journal article)

    Zamboulis, L., Fan, H., Belhajjame, K., Siepen, J., Jones, A., Martin, N., . . . Paton, N. W. (2006). Data access and integration in the ISPIDER proteomics grid. DATA INTEGRATION IN THE LIFE SCIENCES, PROCEEDINGS, 4075, 3-18. Retrieved from http://gateway.webofknowledge.com/

    FuGE: Functional Genomics Experiment Object Model (Journal article)

    Jones, A. R., Pizarro, A., Spellman, P., Miller, M., & Grp, F. W. (2006). FuGE: Functional Genomics Experiment Object Model. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 10(2), 179-184. doi:10.1089/omi.2006.10.179

    DOI: 10.1089/omi.2006.10.179

    Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA. (Journal article)

    Orchard, S., Apweiler, R., Barkovich, R., Field, D., Garavelli, J. S., Horn, D., . . . Hermjakob, H. (2006). Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.. Proteomics, 6(16), 4439-4443. doi:10.1002/pmic.200600452

    DOI: 10.1002/pmic.200600452

    Proteomics data representation and management (Chapter)

    Paton, N. W., Jones, A., & Oliver, S. G. (2006). Proteomics data representation and management. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Wiley.

    Visualisation and analysis of proteomic data from the procyclic form of Trypanosoma brucei (Journal article)

    Jones, A., Faldas, A., Foucher, A., Hunt, E., Tait, A., Wastling, J. M., & Turner, C. M. (2006). Visualisation and analysis of proteomic data from the procyclic form of Trypanosoma brucei. PROTEOMICS, 6(1), 259-267. doi:10.1002/pmic.200500119

    DOI: 10.1002/pmic.200500119

    2005

    An analysis of extensible modelling for functional genomics data (Journal article)

    Jones, A. R., & Paton, N. W. (2005). An analysis of extensible modelling for functional genomics data. BMC BIOINFORMATICS, 6. doi:10.1186/1471-2105-6-235

    DOI: 10.1186/1471-2105-6-235

    2004

    An object model and database for functional genomics (Journal article)

    Jones, A., Hunt, E., Wastling, J. M., Pizarro, A., & Stoeckert, C. J. (2004). An object model and database for functional genomics. BIOINFORMATICS, 20(10), 1583-1590. doi:10.1093/bioinformatics/bth

    DOI: 10.1093/bioinformatics/bth

    An object model and database for functional genomics (Journal article)

    Jones, A., Hunt, E., Wastling, J., Piazarro, A., & Stoeckert, C. J. (2004). An object model and database for functional genomics. Bioinformatics, 20(10), 1583-1590. doi:10.1093/bioinformatics/bth130

    DOI: 10.1093/bioinformatics/bth130

    2003

    Proposal for a standard representation of two-dimensional gel electrophoresis data (Journal article)

    Jones, A., Wastling, J., & Hunt, E. (2003). Proposal for a standard representation of two-dimensional gel electrophoresis data. COMPARATIVE AND FUNCTIONAL GENOMICS, 4(5), 492-501. doi:10.1002/cfg.323

    DOI: 10.1002/cfg.323

    Undated

    Proteomic and transcriptomic analysis of the Protozoan Parasite Neospora caninum (Thesis / Dissertation)

    Vermont, S. J. (n.d.). Proteomic and transcriptomic analysis of the Protozoan Parasite Neospora caninum. (PhD Thesis, University of Liverpool).

    The development of a database and bioinformatics applications for the investigation of immune genes (Thesis / Dissertation)

    Gonzalez Galarza, F. (n.d.). The development of a database and bioinformatics applications for the investigation of immune genes. (PhD Thesis, University of Liverpool).
    Untitled Document