Photo of Prof Andy Jones

Prof Andy Jones Bsc, MRes, PhD

Professor of Bioinformatics Functional and Comparative Genomics

Publications

Selected Publications

  1. Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets (Journal article - 2019)
  2. Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants (Journal article - 2018)
  3. MzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics (Journal article - 2019)
  4. Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations. (Journal article - 2014)
  5. ProteomeXchange provides globally coordinated proteomics data submission and dissemination (Journal article - 2014)

2020

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. (Journal article)

Leitner, A., Bonvin, A. M. J. J., Borchers, C. H., Chalkley, R. J., Chamot-Rooke, J., Combe, C. W., . . . Rappsilber, J. (2020). Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry.. Structure. doi:10.1016/j.str.2020.09.011

DOI: 10.1016/j.str.2020.09.011

Investigating complement mediated interference in class I HLA-specific antibodies following renal transplantation. (Journal article)

Goldsmith, P., Lowe, D., Wong, C., Howse, M., Ridgway, D., Hammad, A., . . . Jones, A. (2020). Investigating complement mediated interference in class I HLA-specific antibodies following renal transplantation.. Transplant immunology, 62, 101310. doi:10.1016/j.trim.2020.101310

DOI: 10.1016/j.trim.2020.101310

Investigating the relationship between class I HLA-specific immunoglobulin-G subclasses, Pan-IgG single antigen bead assays and complement mediated interference in sera from renal transplant recipients. (Journal article)

Goldsmith, P., Lowe, D., Wong, C., Ridgway, D., Howse, M., Hammad, A., . . . Jones, A. (2020). Investigating the relationship between class I HLA-specific immunoglobulin-G subclasses, Pan-IgG single antigen bead assays and complement mediated interference in sera from renal transplant recipients.. Transplant immunology, 101332. doi:10.1016/j.trim.2020.101332

DOI: 10.1016/j.trim.2020.101332

Temporal modulation of the NF-?B RelA network in response to different types of DNA damage (Journal article)

Campbell, A., Franco, C. F., Su, L. -I., Perkins, S., Jones, A., Brownridge, P., . . . Eyers, C. (2020). Temporal modulation of the NF-?B RelA network in response to different types of DNA damage. doi:10.1101/2020.08.11.246504

DOI: 10.1101/2020.08.11.246504

Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics (Journal article)

Byrne, D. P., Clarke, C. J., Brownridge, P. J., Kalyuzhnyy, A., Perkins, S., Campbell, A., . . . Eyers, C. E. (2020). Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics. The Biochemical journal, 477(13), 2451-2475. doi:10.1042/bcj20200309

DOI: 10.1042/bcj20200309

Baseline factors associated with early and late death in intracerebral haemorrhage survivors (Journal article)

Banerjee, G., Ambler, G., Wilson, D., Hostettler, I. C., Shakeshaft, C., Lunawat, S., . . . Collaborators, C. (2020). Baseline factors associated with early and late death in intracerebral haemorrhage survivors. EUROPEAN JOURNAL OF NEUROLOGY, 27(7), 1257-1263. doi:10.1111/ene.14238

DOI: 10.1111/ene.14238

mzMLb: a future-proof raw mass spectrometry data format based on standards-compliant mzML and optimized for speed and storage requirements (Journal article)

Bhamber, R. S., Jankevics, A., Deutsch, E. W., Jones, A. R., & Dowsey, A. W. (n.d.). mzMLb: a future-proof raw mass spectrometry data format based on standards-compliant mzML and optimized for speed and storage requirements. doi:10.1101/2020.02.13.947218

DOI: 10.1101/2020.02.13.947218

Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles (Journal article)

Ramsbottom, K. A., Carr, D. F., Rigden, D. J., & Jones, A. R. (2020). Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles. PLOS ONE, 15(2). doi:10.1371/journal.pone.0220754

DOI: 10.1371/journal.pone.0220754

Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools (Journal article)

Gonzalez-Galarza, F. F., McCabe, A., Santos, E. J. M. D., Jones, J., Takeshita, L., Ortega-Rivera, N. D., . . . Jones, A. R. (n.d.). Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools. Nucleic Acids Research. doi:10.1093/nar/gkz1029

DOI: 10.1093/nar/gkz1029

Proteome Bioinformatics Methods for Studying Histidine Phosphorylation. (Chapter)

Jones, A. R., & Camacho, O. M. (2020). Proteome Bioinformatics Methods for Studying Histidine Phosphorylation.. In Unknown Book (Vol. 2077, pp. 237-250). doi:10.1007/978-1-4939-9884-5_16

DOI: 10.1007/978-1-4939-9884-5_16

2019

VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock (Journal article)

Pereira, S. S., Heap, J., Jones, A. R., & Jackson, A. P. (2019). VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock. GIGASCIENCE, 8(9). doi:10.1093/gigascience/giz091

DOI: 10.1093/gigascience/giz091

Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation (Journal article)

Hardman, G., Perkins, S., Brownridge, P., Clarke, C., Byrne, D., Campbell, A., . . . Eyers, C. (2019). Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation. The EMBO Journal, 38. doi:10.15252/embj.2018100847

DOI: 10.15252/embj.2018100847

MzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics (Journal article)

Hoffmann, N., Rein, J., Sachsenberg, T., Hartler, J., Haug, K., Mayer, G., . . . Jones, A. R. (2019). MzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics. Analytical Chemistry, 91(5), 3302-3310. doi:10.1021/acs.analchem.8b04310

DOI: 10.1021/acs.analchem.8b04310

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets (Journal article)

Ren, Z., Qi, D., Pugh, N., Li, K., Wen, B., Zhou, R., . . . Jones, A. R. (2019). Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets. Molecular and Cellular Proteomics, 18(1), 86-98. doi:10.1074/mcp.RA118.000832

DOI: 10.1074/mcp.RA118.000832

2018

Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions (Journal article)

Ramsbottom, K. A., Carr, D. F., Jones, A. R., & Rigden, D. J. (2018). Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions. MOLECULAR IMMUNOLOGY, 101, 488-499. doi:10.1016/j.molimm.2018.08.003

DOI: 10.1016/j.molimm.2018.08.003

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

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

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

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

Allele Frequency Net Database. (Chapter)

Gonzalez-Galarza, F. F., McCabe, A., Melo Dos Santos, E. J., Takeshita, L., Ghattaoraya, G., Jones, A. R., & Middleton, D. (2018). Allele Frequency Net Database.. In Unknown Book (Vol. 1802, pp. 49-62). doi:10.1007/978-1-4939-8546-3_4

DOI: 10.1007/978-1-4939-8546-3_4

2017

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

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

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/

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/

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

Ferries., Perkins, S., Brownridge., Campbell, A., Eyers, P., Jones, A., & 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

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

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/

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

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., Morris, A., Cornejo Castro, E. M., . . . 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(01), 7-26. doi:10.1111/iji.12304

DOI: 10.1111/iji.12304

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

Vizcaíno, J. A., Perkins, S., Jones, A. R., & Deutsch, E. W. (n.d.). Chapter 11. Data Formats of the Proteomics Standards Initiative. In Proteome Informatics (pp. 229-258). Royal Society of Chemistry. doi:10.1039/9781782626732-00229

DOI: 10.1039/9781782626732-00229

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

Ghali, F., & Jones, A. R. (n.d.). Chapter 15. Proteogenomics: Proteomics for Genome Annotation. In Proteome Informatics (pp. 365-384). Royal Society of Chemistry. doi:10.1039/9781782626732-00365

DOI: 10.1039/9781782626732-00365

Chapter 5. Protein Inference and Grouping (Chapter)

Jones, A. R. (n.d.). Chapter 5. Protein Inference and Grouping. In Proteome Informatics (pp. 93-115). Royal Society of Chemistry. doi:10.1039/9781782626732-00093

DOI: 10.1039/9781782626732-00093

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

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

2015

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

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

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(5), 2618-2628. doi:10.1002/pmic.201400553

DOI: 10.1002/pmic.201400553

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

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

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

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

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

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)

González-Galarza, F. F., Takeshita, L. Y. C., Santos, E. J. M., Kempson, F., Maia, M. H. T., Silva, A. L. S. D., . . . Middleton, D. (2014). 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

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

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, 13(10). doi:10.1074/mcp.O113.036681

DOI: 10.1074/mcp.O113.036681

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.bbapap.2013.04.004

DOI: 10.1016/j.bbapap.2013.04.004

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

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

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, 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 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

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

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

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

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

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

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

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 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. J. (2013). A guide for integration of proteomic data standards into laboratory workflows. PROTEOMICS, 13(3-4), 480-492. doi:10.1002/pmic.201200268

DOI: 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

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

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

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

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

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

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

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). doi:10.1186/1756-0500-4-86

DOI: 10.1186/1756-0500-4-86

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

Bioinformatics in Animal Proteomics (Chapter)

Blakeley, P., Wright, J. C., Hubbard, S. J., & Jones, A. R. (n.d.). Bioinformatics in Animal Proteomics. In Methods in Animal Proteomics (pp. 103-119). Wiley-Blackwell. 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. JOURNAL OF PROTEOME RESEARCH, 10(4), 2088-2094. doi:10.1021/pr101157s

DOI: 10.1021/pr101157s

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

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

2010

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

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

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.

2009

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

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

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

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

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, 8(20), 4168-4172. doi:10.1002/pmic.200800555

DOI: 10.1002/pmic.200800555

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

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

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

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

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

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

2007

Storing, Searching, and Disseminating Experimental Proteomics Data (Chapter)

Paton, N. W., Jones, A. R., Garwood, C., Garwood, K., & Oliver, S. (n.d.). Storing, Searching, and Disseminating Experimental Proteomics Data. In Introduction to Systems Biology (pp. 472-483). Humana Press. doi:10.1007/978-1-59745-531-2_24

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

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

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

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

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

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

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

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

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

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

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/

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/bth130

DOI: 10.1093/bioinformatics/bth130

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