2024
What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species. (Journal article)
Basenko, E. Y., Shanmugasundram, A., Böhme, U., Starns, D., Wilkinson, P. A., Davison, H. R., . . . Jones, A. (2024). What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species.. Genetics, iyae035. doi:10.1093/genetics/iyae035DOI: 10.1093/genetics/iyae035
Mukkawar, V., Roy, D., Sue-Ob, K., Jones, A., Zhang, C., Kumar Bhagat, P., . . . Sadanandom, A. (2024). SUMOylation of OsPSTOL1 is essential for regulating phosphate starvation responses in rice and <i>Arabidopsis</i>.. Frontiers in plant science, 15, 1274610. doi:10.3389/fpls.2024.1274610DOI: 10.3389/fpls.2024.1274610
2023
Daly, L. A., Byrne, D. P., Perkins, S., Brownridge, P. J., McDonnell, E., Jones, A. R., . . . Eyers, C. E. (2023). Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides.. Journal of proteome research, 22(12), 3754-3772. doi:10.1021/acs.jproteome.3c00425DOI: 10.1021/acs.jproteome.3c00425
Huang, F., Grauslys, A., Huokko, T., Caamaño Gutiérrez, E., Jones, A. R., & Liu, L. (n.d.). Dynamic changes in the thylakoid proteome of cyanobacteria during light-regulated thylakoid membrane development. Plants, 12(23). doi:10.3390/plants12233967DOI: 10.3390/plants12233967
Alvarez-Jarreta, J., Amos, B., Aurrecoechea, C., Bah, S., Barba, M., Barreto, A., . . . Zheng, J. (2023). VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023.. Nucleic acids research, gkad1003. doi:10.1093/nar/gkad1003DOI: 10.1093/nar/gkad1003
Russomanno, G., Sison-Young, R., Livoti, L. A., Coghlan, H., Jenkins, R. E., Kunnen, S. J., . . . Copple, I. M. (2023). A systems approach reveals species differences in hepatic stress response capacity. TOXICOLOGICAL SCIENCES. doi:10.1093/toxsci/kfad085DOI: 10.1093/toxsci/kfad085
Contreras-Moreira, B., Saraf, S., Naamati, G., Casas, A. M., Amberkar, S. S., Flicek, P., . . . Dyer, S. (2023). GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation.. Genome biology, 24(1), 223. doi:10.1186/s13059-023-03071-zDOI: 10.1186/s13059-023-03071-z
Camacho, O. M., Ramsbottom, K. A., Collins, A., & Jones, A. R. (2023). Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets. JOURNAL OF PROTEOME RESEARCH, 22(6), 1828-1842. doi:10.1021/acs.jproteome.2c00823DOI: 10.1021/acs.jproteome.2c00823
Jones, A. R., Deutsch, E. W., & Vizcaino, J. A. (2023). Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future. PROTEOMICS, 23(7-8). doi:10.1002/pmic.202200014DOI: 10.1002/pmic.202200014
Prakash, A., Garcia-Seisdedos, D., Wang, S., Kundu, D. J., Collins, A., George, N., . . . Vizcaino, J. A. (2023). Integrated View of Baseline Protein Expression in Human Tissues. JOURNAL OF PROTEOME RESEARCH, 22(3), 729-742. doi:10.1021/acs.jproteome.2c00406DOI: 10.1021/acs.jproteome.2c00406
Deutsch, E. W., Vizcaino, J. A., Jones, A. R., Binz, P. -A., Lam, H., Klein, J., . . . Orchard, S. E. (2023). Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. JOURNAL OF PROTEOME RESEARCH. doi:10.1021/acs.jproteome.2c00637DOI: 10.1021/acs.jproteome.2c00637
Shanmugasundram, A., Starns, D., Böhme, U., Amos, B., Wilkinson, P. A., Harb, O. S., . . . Jones, A. R. (2023). TriTrypDB: An integrated functional genomics resource for kinetoplastida.. PLoS neglected tropical diseases, 17(1), e0011058. doi:10.1371/journal.pntd.0011058DOI: 10.1371/journal.pntd.0011058
2022
Assessing multiple evidence streams to decide on confidence for identification of post-translational modifications, within and across data sets (Preprint)
DOI: 10.1101/2022.12.15.520504
Effective tree-based classification for automated flow cytometry data analysis on samples with suspected haematological malignancy (Preprint)
DOI: 10.1101/2022.12.07.22283209
Jones, F. K., Phillips, A. M., Jones, A. R., & Pisconti, A. (2022). The INSR/AKT/mTOR pathway regulates the pace of myogenesis in a syndecan-3-dependent manner. MATRIX BIOLOGY, 113, 61-82. doi:10.1016/j.matbio.2022.09.004DOI: 10.1016/j.matbio.2022.09.004
Understanding SUMO-mediated adaptive responses in plants to improve crop productivity. (Journal article)
Clark, L., Sue-Ob, K., Mukkawar, V., Jones, A. R., & Sadanandom, A. (2022). Understanding SUMO-mediated adaptive responses in plants to improve crop productivity.. Essays in biochemistry, EBC20210068. doi:10.1042/ebc20210068DOI: 10.1042/ebc20210068
Ramsbottom, K. A., Prakash, A., Riverol, Y. P., Camacho, O. M., Martin, M. -J., Vizcaino, J. A., . . . Jones, A. R. (2022). Method for Independent Estimation of the False Localization Rate for Phosphoproteomics. JOURNAL OF PROTEOME RESEARCH. doi:10.1021/acs.jproteome.1c00827DOI: 10.1021/acs.jproteome.1c00827
Wang, S., Garcia-Seisdedos, D. R., Prakash, A., Kundu, D. J., Collins, A., George, N., . . . Vizcaino, J. A. (2022). Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues. PLOS COMPUTATIONAL BIOLOGY, 18(6). doi:10.1371/journal.pcbi.1010174DOI: 10.1371/journal.pcbi.1010174
Kalyuzhnyy, A., Eyers, P. A., Eyers, C. E., Bowler-Barnett, E., Martin, M. J., Sun, Z., . . . Jones, A. R. (2022). Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. JOURNAL OF PROTEOME RESEARCH, 21(6), 1510-1524. doi:10.1021/acs.jproteome.2c00131DOI: 10.1021/acs.jproteome.2c00131
Amos, B., Aurrecoechea, C., Barba, M., Barreto, A., Basenko, E. Y., Bazant, W., . . . Zheng, J. (2022). VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. NUCLEIC ACIDS RESEARCH, 50(D1), D898-D911. doi:10.1093/nar/gkab929DOI: 10.1093/nar/gkab929
2021
Pearngam, P., Sriswasdi, S., Pisitkun, T., & Jones, A. R. (2021). MHCVision: estimation of global and local false discovery rate for MHC class I peptide binding prediction. BIOINFORMATICS, 37(21), 3830-3838. doi:10.1093/bioinformatics/btab479DOI: 10.1093/bioinformatics/btab479
Ramsbottom, K., Prakash, A., Riverol, Y. P., Camacho, O. M., Martin, M., Vizcaíno, J. A., . . . Jones, A. (2021). A method for independent estimation of false localisation rate for phosphoproteomics. doi:10.1101/2021.10.18.464791DOI: 10.1101/2021.10.18.464791
Meyer, B., Chiaravalli, J., Gellenoncourt, S., Brownridge, P., Bryne, D. P., Daly, L. A., . . . Emmott, E. (2021). Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-25796-wDOI: 10.1038/s41467-021-25796-w
Myall, A. C., Perkins, S., Rushton, D., David, J., Spencer, P., Jones, A. R., & Antczak, P. (2021). An OMICs-based meta-analysis to support infection state stratification. BIOINFORMATICS, 37(16), 2347-2355. doi:10.1093/bioinformatics/btab089DOI: 10.1093/bioinformatics/btab089
A snapshot of human leukocyte antigen (HLA) diversity using data from the Allele Frequency Net Database (Journal article)
Gonzalez-Galarza, F. F., McCabe, A., dos Santos, E. J. M., Jones, A. R., & Middleton, D. (2021). A snapshot of human leukocyte antigen (HLA) diversity using data from the Allele Frequency Net Database. HUMAN IMMUNOLOGY, 82(7), 496-504. doi:10.1016/j.humimm.2020.10.004DOI: 10.1016/j.humimm.2020.10.004
McCabe, A., & Jones, A. R. (2021). lcmsWorld: High-Performance 3D Visualization Software for Mass Spectrometry. Journal of Proteome Research, 20(4), 1981-1985. doi:10.1021/acs.jproteome.0c00618DOI: 10.1021/acs.jproteome.0c00618
Oyarzun, P., Kashyap, M., Fica, V., Salas-Burgos, A., Gonzalez-Galarza, F. F., McCabe, A., . . . Kobe, B. (2021). A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach. FRONTIERS IN IMMUNOLOGY, 12. doi:10.3389/fimmu.2021.598778DOI: 10.3389/fimmu.2021.598778
Campbell, A. E., Franco, C. F., Ling-I, S., Corbin, E. K., Perkins, S., Kalyuzhnyy, A., . . . Eyers, C. E. (2021). Temporal modulation of the NF-kappa B ReIA network in response to different types of DNA damage. Biochemical Journal, 478(3), 533-551. doi:10.1042/BCJ20200627DOI: 10.1042/BCJ20200627
Bhamber, R. S., Jankevics, A., Deutsch, E. W., Jones, A. R., & Dowsey, A. W. (2021). mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements. JOURNAL OF PROTEOME RESEARCH, 20(1), 172-183. doi:10.1021/acs.jproteome.0c00192DOI: 10.1021/acs.jproteome.0c00192
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 (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, 63. doi:10.1016/j.trim.2020.101332DOI: 10.1016/j.trim.2020.101332
Myall, A., Perkins, S., David, J., Spencer, P., Jones, A., & Antczak, P. (2020). Machine learning to uncover differentiable signatures of bacterial and viral infections. In INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES Vol. 101 (pp. 189). doi:10.1016/j.ijid.2020.09.506DOI: 10.1016/j.ijid.2020.09.506
Ashwood, C., Bittremieux, W., Deutsch, E. W., Doncheva, N. T., Dorfer, V., Gabriels, R., . . . Willems, S. (2020). Proceedings of the EuBIC-MS 2020 Developers’ Meeting. In EuPA Open Proteomics Vol. 24 (pp. 1-6). Elsevier BV. doi:10.1016/j.euprot.2020.11.001DOI: 10.1016/j.euprot.2020.11.001
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, 28(11), 1259-1268. doi:10.1016/j.str.2020.09.011DOI: 10.1016/j.str.2020.09.011
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. doi:10.1016/j.trim.2020.101310DOI: 10.1016/j.trim.2020.101310
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/bcj20200309DOI: 10.1042/bcj20200309
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., Jankevics, A., Deutsch, E., Jones, A., & Dowsey, A. (2020). mzMLb: a future-proof raw mass spectrometry data format based on standards-compliant mzML and optimized for speed and storage requirements. doi:10.1101/2020.02.13.947218DOI: 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.0220754DOI: 10.1371/journal.pone.0220754
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/gkz1029DOI: 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 HISTIDINE PHOSPHORYLATION (Vol. 2077, pp. 237-250). doi:10.1007/978-1-4939-9884-5_16DOI: 10.1007/978-1-4939-9884-5_16
2019
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(21). doi:10.15252/embj.2018100847DOI: 10.15252/embj.2018100847
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/giz091DOI: 10.1093/gigascience/giz091
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.8b04310DOI: 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.RA118.000832DOI: 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.2018.08.003DOI: 10.1016/j.molimm.2018.08.003
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.2018.04.011DOI: 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.7b00783DOI: 10.1021/acs.jproteome.7b00783
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-xDOI: 10.1186/s13059-017-1377-x
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.7b02795DOI: 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 HLA TYPING: METHODS AND PROTOCOLS (Vol. 1802, pp. 49-62). doi:10.1007/978-1-4939-8546-3_4DOI: 10.1007/978-1-4939-8546-3_4
2017
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.7b00370DOI: 10.1021/acs.jproteome.7b00370
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.7b00337DOI: 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.2017.06.152DOI: 10.1016/j.humimm.2017.06.152
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.M117.068429DOI: 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 https://www.webofscience.com/
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.11275.1DOI: 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/dkw545DOI: 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.12304DOI: 10.1111/iji.12304
Data Formats of the Proteomics Standards Initiative (Chapter)
Vizcaino, J. A., Perkins, S., Jones, A. R., & Deutsch, E. W. (2017). Data Formats of the Proteomics Standards Initiative. In PROTEOME INFORMATICS (Vol. 5, pp. 231-258). Retrieved from https://www.webofscience.com/
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 https://www.webofscience.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 https://www.webofscience.com/
Protein Inference and Grouping (Chapter)
Jones, A. R. (2017). Protein Inference and Grouping. In PROTEOME INFORMATICS (Vol. 5, pp. 93-115). Retrieved from https://www.webofscience.com/
Proteogenomics: Proteomics for Genome Annotation (Chapter)
Ghali, F., & Jones, A. R. (2017). Proteogenomics: Proteomics for Genome Annotation. In PROTEOME INFORMATICS (Vol. 5, pp. 367-384). Retrieved from https://www.webofscience.com/
2016
Data Formats of the Proteomics Standards Initiative (Chapter)
Vizcaíno, J. A., Perkins, S., Jones, A. R., & Deutsch, E. W. (2016). Data Formats of the Proteomics Standards Initiative. In Proteome Informatics (pp. 229-258). The Royal Society of Chemistry. doi:10.1039/9781782626732-00229DOI: 10.1039/9781782626732-00229
Protein Inference and Grouping (Chapter)
Jones, A. R. (2016). Protein Inference and Grouping. In Proteome Informatics (pp. 93-115). The Royal Society of Chemistry. doi:10.1039/9781782626732-00093DOI: 10.1039/9781782626732-00093
Proteogenomics: Proteomics for Genome Annotation (Chapter)
Ghali, F., & Jones, A. R. (2016). Proteogenomics: Proteomics for Genome Annotation. In Proteome Informatics (pp. 365-384). The Royal Society of Chemistry. doi:10.1039/9781782626732-00365DOI: 10.1039/9781782626732-00365
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, baw069. doi:10.1093/database/baw069DOI: 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.2015.11.013DOI: 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.O115.048777DOI: 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.201400208DOI: 10.1002/pmic.201400208
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.201400535DOI: 10.1002/pmic.201400535
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/s11306-015-0821-8DOI: 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.201400553DOI: 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.201400281DOI: 10.1002/pmic.201400281
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/ocv001DOI: 10.1093/jamia/ocv001
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.2015.01.040DOI: 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.201400372DOI: 10.1002/pmic.201400372
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.201400265DOI: 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:10.1159/000368056DOI: 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/gku1166DOI: 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.201400080DOI: 10.1002/pmic.201400080
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.201470164DOI: 10.1002/pmic.201470164
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.201400120DOI: 10.1002/pmic.201400120
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.O113.036681DOI: 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.2013.04.004DOI: 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.2013.02.017DOI: 10.1016/j.bbapap.2013.02.017
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.O114.037879DOI: 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.2839DOI: 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., . . . VizcaÃno, 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.201300281DOI: 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.201300560DOI: 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.2013.02.026DOI: 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.O113.029777DOI: 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.201370166DOI: 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.O113.028506DOI: 10.1074/mcp.O113.028506
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., . . . Eisenacher, M. (2013). The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. doi:10.1093/database/bat009DOI: 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.12030DOI: 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., . . . Middleton, D. (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.12030DOI: 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.201200268DOI: 10.1002/pmic.201200268
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/bat021DOI: 10.1093/database/bat021
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/gks1139DOI: 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.2012.0022DOI: 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.2012.0042DOI: 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.2012.0051DOI: 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.201270126DOI: 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.M111.014381DOI: 10.1074/mcp.M111.014381
<i>In silico</i> 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). <i>In silico</i> 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/gm350DOI: 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.201200029DOI: 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.201200029DOI: 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.201100577DOI: 10.1002/pmic.201100577
Quantitative proteomics and data analysis (Journal article)
Beynon, R., Hubbard, S., & Jones, A. (2012). Quantitative proteomics and data analysis. The Biochemist, 34(1), 61-62. doi:10.1042/bio03401061DOI: 10.1042/bio03401061
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:10.1186/1756-0500-4-86DOI: 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.M111.008334DOI: 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.m111.008334DOI: 10.1074/mcp.m111.008334
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). Retrieved from https://www.webofscience.com/
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/pr101157sDOI: 10.1021/pr101157s
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:10.1186/1756-0500-4-86DOI: 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(Database), D913-D919. doi:10.1093/nar/gkq1128DOI: 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, D913-D919. doi:10.1093/nar/gkq1128DOI: 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
Boegelein, T., Rao, A., Jones, A. R., & Tatlock, G. J. (2011). Selective Laser Melting of Oxide Dispersion Strengthened Steels. (ASME 2011 Pressure Vessels and Piping Conference). Retrieved from http://dx.doi.org/10.1115/pvp2011-57892DOI: 10.1115/pvp2011-57892
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.201090075DOI: 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.201090075DOI: 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.201000120DOI: 10.1002/pmic.201000120
Microstructural evolution in friction stir welding of nanostructured ODS alloys (Journal article)
Chen, C. -L., Tatlock, G. J., & Jones, A. R. (2010). Microstructural evolution in friction stir welding of nanostructured ODS alloys. Journal of Alloys and Compounds, 504, S460-S466. doi:10.1016/j.jallcom.2010.02.192DOI: 10.1016/j.jallcom.2010.02.192
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., . . . Jansen, R. C. (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-r27DOI: 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.200900367DOI: 10.1002/pmic.200900367
An Introduction to Proteome Bioinformatics (Chapter)
Jones, A. R., & Hubbard, S. J. (2010). An Introduction to Proteome Bioinformatics. In PROTEOME BIOINFORMATICS (Vol. 604, pp. 1-5). doi:10.1007/978-1-60761-444-9_1DOI: 10.1007/978-1-60761-444-9_1
Effect of Strain Heterogeneity on the Recrystallization Behavior of an Oxide Dispersion Strengthened Ferritic Alloy (Journal article)
Chen, C. L., Tatlock, G. J., & Jones, A. R. (n.d.). Effect of Strain Heterogeneity on the Recrystallization Behavior of an Oxide Dispersion Strengthened Ferritic Alloy. Materials Science Forum, 638-642, 3833-3838. doi:10.4028/www.scientific.net/msf.638-642.3833DOI: 10.4028/www.scientific.net/msf.638-642.3833
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/nbt0710-654aDOI: 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/nbt0710-655DOI: 10.1038/nbt0710-655
Managing Experimental Data Using FuGE (Chapter)
Jones, A. R., & Lister, A. L. (2010). Managing Experimental Data Using FuGE. In PROTEOME BIOINFORMATICS (Vol. 604, pp. 333-343). doi:10.1007/978-1-60761-444-9_23DOI: 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.200900189DOI: 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.200900407DOI: 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:10.1186/1471-2105-10-184DOI: 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.2008.0080DOI: 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.200800473DOI: 10.1002/pmic.200800473
Effect of annealing temperatures on the secondary re-crystallization of extruded PM2000 steel bar. (Journal article)
Chen, C. -L., Tatlock, G. J., & Jones, A. R. (2009). Effect of annealing temperatures on the secondary re-crystallization of extruded PM2000 steel bar.. Journal of microscopy, 233(3), 474-481. doi:10.1111/j.1365-2818.2009.03134.xDOI: 10.1111/j.1365-2818.2009.03134.x
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/btn496DOI: 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.200800555DOI: 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-MCP200DOI: 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/nbt0808-863DOI: 10.1038/nbt0808-863
The proteome of <i>Toxoplasma gondii</i>:: 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 <i>Toxoplasma gondii</i>:: integration with the genome provides novel insights into gene expression and annotation. GENOME BIOLOGY, 9(7). doi:10.1186/gb-2008-9-7-r116DOI: 10.1186/gb-2008-9-7-r116
Modulation of the host cell proteome by the intracellular apicomplexan parasite <i>Toxoplasma gondii</i> (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 <i>Toxoplasma gondii</i>. INFECTION AND IMMUNITY, 76(2), 828-844. doi:10.1128/IAI.01115-07DOI: 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_24DOI: 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.200700658DOI: 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/nbt1347DOI: 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.200700171DOI: 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.200700127DOI: 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., Julian, R. K. J., Jones, A. R., . . . Hermjakob, H. (2007). The minimum information about a proteomics experiment (MIAPE). NATURE BIOTECHNOLOGY, 25(8), 887-893. doi:10.1038/nbt1329DOI: 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.200700014DOI: 10.1002/pmic.200700014
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ™ (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™. PROTEOME SCIENCE, 5. doi:10.1186/1477-5956-5-4DOI: 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.200600915DOI: 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. (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.2006.10.164DOI: 10.1089/omi.2006.10.164
FuGE: Functional Genomics Experiment Object Model (Journal article)
Jones, A. R., Pizarro, A., Spellman, P., & Miller, M. (2006). FuGE: Functional Genomics Experiment Object Model. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 10(2), 179-184. doi:10.1089/omi.2006.10.179DOI: 10.1089/omi.2006.10.179
Data access and integration in the ISPIDER proteomics grid (Journal article)
Zamboulis, L., Hao, F., 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 https://www.webofscience.com/
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.200600452DOI: 10.1002/pmic.200600452
Visualisation and analysis of proteomic data from the procyclic form of <i>Trypanosoma brucei</i> (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 <i>Trypanosoma brucei</i>. PROTEOMICS, 6(1), 259-267. doi:10.1002/pmic.200500119DOI: 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:10.1186/1471-2105-6-235DOI: 10.1186/1471-2105-6-235
Proteomics data representation and management (Chapter)
Paton, N. W., Jones, A., & Oliver, S. G. (2005). Proteomics data representation and management. Wiley. doi:10.1002/047001153x.g408316DOI: 10.1002/047001153x.g408316
On suitability of novel fluidised bed technique for separation of metallic powders during commercial powder metallurgical processing (Journal article)
Ritherdon, J., Dechsiri, C., Jones, A. R., Hoffmann, A. C., & Wright, I. G. (2005). On suitability of novel fluidised bed technique for separation of metallic powders during commercial powder metallurgical processing. Powder Metallurgy, 48(2), 199-202. doi:10.1179/003258905x37639DOI: 10.1179/003258905x37639
2004
Electron microscopy of defects in oxide-dispersion strengthened ferritic alloys (Conference Paper)
Chen, Y. L., & Jones, A. R. (2004). Electron microscopy of defects in oxide-dispersion strengthened ferritic alloys. In Institute of Physics Conference Series Vol. 179 (pp. 253-256).
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/bth130DOI: 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/bth130DOI: 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.323DOI: 10.1002/cfg.323
Grain Boundary Mobility in Fe-Base Oxide Dispersion Strengthened PM2000 Alloy (Journal article)
Capdevila, C., Chen, Y. L., Jones, A. R., & Bhadeshia, H. K. D. H. (2003). Grain Boundary Mobility in Fe-Base Oxide Dispersion Strengthened PM2000 Alloy. ISIJ International, 43(5), 777-783. doi:10.2355/isijinternational.43.777DOI: 10.2355/isijinternational.43.777
Oxidation of mechanically alloyed powders during processing: origins and control (Journal article)
Ritherdon, J., Jones, A. R., & Wright, I. G. (2003). Oxidation of mechanically alloyed powders during processing: origins and control. Powder Metallurgy, 46(4), 319-323. doi:10.1179/003258903225008562DOI: 10.1179/003258903225008562
2002
Origin of porosity in oxide-dispersion-strengthened alloys produced by mechanical alloying (Journal article)
Chen, Y. L., Jones, A. R., & Miller, U. (2002). Origin of porosity in oxide-dispersion-strengthened alloys produced by mechanical alloying. Metallurgical and Materials Transactions A, 33(8), 2713-2718. doi:10.1007/s11661-002-0393-xDOI: 10.1007/s11661-002-0393-x
The microstructure and recrystallization of flow-formed oxide-dispersion-strengthened ferritic alloy: Part I. Deformation structure (Journal article)
Chen, Y. L., & Jones, A. R. (2002). The microstructure and recrystallization of flow-formed oxide-dispersion-strengthened ferritic alloy: Part I. Deformation structure. Metallurgical and Materials Transactions A, 33(12), 3777-3785. doi:10.1007/s11661-002-0250-yDOI: 10.1007/s11661-002-0250-y
The microstructure and recrystallization of flow-formed oxide-dispersion-strengthened ferritic alloy: Part II. Recrystallization behavior (Journal article)
Chen, Y. L., Jones, A. R., Pond, R. C., & Miller, U. (2002). The microstructure and recrystallization of flow-formed oxide-dispersion-strengthened ferritic alloy: Part II. Recrystallization behavior. Metallurgical and Materials Transactions A, 33(12), 3787-3794. doi:10.1007/s11661-002-0251-xDOI: 10.1007/s11661-002-0251-x
2001
Measurement of proteases using chemiluminescence-resonance-energy-transfer chimaeras between green fluorescent protein and aequorin. (Journal article)
Waud, J. P., Bermúdez Fajardo, A., Sudhaharan, T., Trimby, A. R., Jeffery, J., Jones, A., & Campbell, A. K. (2001). Measurement of proteases using chemiluminescence-resonance-energy-transfer chimaeras between green fluorescent protein and aequorin.. The Biochemical journal, 357(Pt 3), 687-697. doi:10.1042/0264-6021:3570687DOI: 10.1042/0264-6021:3570687
Heterogeneous deformation and recrystallisation of iron base oxide dispersion strengthened PM2000 alloy (Journal article)
Capdevila, C., Chen, Y. L., Lassen, N. C. K., Jones, A. R., & Bhadeshia, H. K. D. H. (2001). Heterogeneous deformation and recrystallisation of iron base oxide dispersion strengthened PM2000 alloy. Materials Science and Technology, 17(6), 693-699. doi:10.1179/026708301101510410DOI: 10.1179/026708301101510410
Reduction in defect content of ODS alloys (Journal article)
Ritherdon, J., & Jones, A. R. (2001). Reduction in defect content of ODS alloys. Materials at High Temperatures, 18(3), 177-184. doi:10.1179/mht.2001.020DOI: 10.1179/mht.2001.020
Reduction of porosity in oxide dispersion-strengthened alloys produced by powder metallurgy (Journal article)
Chen, Y. L., & Jones, A. R. (2001). Reduction of porosity in oxide dispersion-strengthened alloys produced by powder metallurgy. Metallurgical and Materials Transactions A, 32(8), 2077-2085. doi:10.1007/s11661-001-0019-8DOI: 10.1007/s11661-001-0019-8
The Recovery and Recrystallisation of a Mechanically Alloyed ODS-Fe<sub>3</sub>Al Alloy (Conference Paper)
Ritherdon, J., Jones, A. R., & Wright, I. G. (n.d.). The Recovery and Recrystallisation of a Mechanically Alloyed ODS-Fe<sub>3</sub>Al Alloy. In Materials Science Forum Vol. 360-362 (pp. 217-222). Trans Tech Publications, Ltd.. doi:10.4028/www.scientific.net/msf.360-362.217DOI: 10.4028/www.scientific.net/msf.360-362.217
1999
Evidence of in situ stability of the type IV collagen triple helix in human inflammatory bowel disease using a denaturation specific epitope antibody. (Journal article)
Wheatcroft, A. C., Hollander, A. P., Croucher, L. J., Jones, A., Taylor, C. J., & Evans, G. S. (1999). Evidence of in situ stability of the type IV collagen triple helix in human inflammatory bowel disease using a denaturation specific epitope antibody.. Matrix biology : journal of the International Society for Matrix Biology, 18(4), 361-372. doi:10.1016/s0945-053x(99)00028-1DOI: 10.1016/s0945-053x(99)00028-1
Reduction in defect content of oxide dispersion strengthened alloys (Journal article)
Jones, A. R., & Ritherdon, J. (1999). Reduction in defect content of oxide dispersion strengthened alloys. Materials at High Temperatures, 16(4), 181-188. doi:10.1179/mht.1999.017DOI: 10.1179/mht.1999.017
1993
New enhanced performance stainless steel (Journal article)
Hamerton, R. G., Jaeger, D. M., & Jones, A. R. (1993). New enhanced performance stainless steel. Materials World, 1(1), 9-10.
