Publications
Selected publications
- Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome. (Journal article - 2024)
- What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species. (Journal article - 2024)
- VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023. (Journal article - 2023)
- GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation. (Journal article - 2023)
- Integrated View of Baseline Protein Expression in Human Tissues (Journal article - 2023)
- Method for Independent Estimation of the False Localization Rate for Phosphoproteomics (Journal article - 2022)
- Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues (Journal article - 2022)
2024
Phosphorylation in the <i>Plasmodium falciparum</i> Proteome: A Meta-Analysis of Publicly Available Data Sets.
Camacho, O. J. M., Ramsbottom, K. A., Prakash, A., Sun, Z., Perez Riverol, Y., Bowler-Barnett, E., . . . Jones, A. R. (2024). Phosphorylation in the <i>Plasmodium falciparum</i> Proteome: A Meta-Analysis of Publicly Available Data Sets.. Journal of proteome research, 23(12), 5326-5341. doi:10.1021/acs.jproteome.4c00418
The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.
Klein, J., Lam, H., Mak, T. D., Bittremieux, W., Perez-Riverol, Y., Gabriels, R., . . . Deutsch, E. W. (2024). The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.. Analytical chemistry. doi:10.1021/acs.analchem.4c04091
Integrated View of Baseline Protein Expression in Human Tissues using public Data Independent Acquisition datasets
Charting the evolutionary path of the SUMO modification system in plants reveals molecular hardwiring of development to stress adaptation.
Ghosh, S., Mellado Sanchez, M., Sue-Ob, K., Roy, D., Jones, A., Blazquez, M. A., & Sadanandom, A. (2024). Charting the evolutionary path of the SUMO modification system in plants reveals molecular hardwiring of development to stress adaptation.. The Plant cell, 36(9), 3131-3144. doi:10.1093/plcell/koae192
The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF
mzIdentML 1.3.0 - Essential progress on the support of crosslinking and other identifications based on multiple spectra.
Combe, C. W., Kolbowski, L., Fischer, L., Koskinen, V., Klein, J., Leitner, A., . . . Rappsilber, J. (2024). mzIdentML 1.3.0 - Essential progress on the support of crosslinking and other identifications based on multiple spectra.. Proteomics, e2300385. doi:10.1002/pmic.202300385
Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.
Ramsbottom, K. A., Prakash, A., Perez-Riverol, Y., Camacho, O. M., Sun, Z., Kundu, D. J., . . . Jones, A. R. (2024). Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.. Journal of proteome research, 23(7), 2518-2531. doi:10.1021/acs.jproteome.4c00187
Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues.
Wang, S., Collins, A., Prakash, A., Fexova, S., Papatheodorou, I., Jones, A. R., & Vizcaíno, J. A. (2024). Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues.. Journal of proteome research. doi:10.1021/acs.jproteome.3c00741
What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species.
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/iyae035
SUMOylation of OsPSTOL1 is essential for regulating phosphate starvation responses in rice and <i>Arabidopsis</i>.
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.2024.1274610
Allele Frequency Net Database.
Gonzalez-Galarza, F. F., McCabe, A., Melo Dos Santos, E. J., Ghattaoraya, G., Jones, A. R., & Middleton, D. (2024). Allele Frequency Net Database.. In Unknown Book (Vol. 2809, pp. 19-36). doi:10.1007/978-1-0716-3874-3_2
Corrigendum: SUMOylation of OsPSTOL1 is essential for regulating phosphate starvation responses in rice and <i>Arabidopsis</i>.
Mukkawar, V., Roy, D., Sue-Ob, K., Jones, A., Zhang, C., Bhagat, P. K., . . . Sadanandom, A. (2024). Corrigendum: SUMOylation of OsPSTOL1 is essential for regulating phosphate starvation responses in rice and <i>Arabidopsis</i>.. Frontiers in plant science, 15, 1412657. doi:10.3389/fpls.2024.1412657
2023
Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides.
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.3c00425
Dynamic changes in the thylakoid proteome of cyanobacteria during light-regulated thylakoid membrane development
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/plants12233967
Phosphorylation in the<i>Plasmodium falciparum</i>proteome: A meta-analysis of publicly available data sets
A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome.
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023.
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/gkad1003
MicroAge Mission: Examining the Effects of Microgravity and Electrical Stimulation on the Proteome of Human Tissue-Engineered Muscle Constructs
Jones, S., Shigdar, S., Hemmings, K., Hoettges, K., Henstock, J., McArdle, C., . . . McArdle, A. (2023). MicroAge Mission: Examining the Effects of Microgravity and Electrical Stimulation on the Proteome of Human Tissue-Engineered Muscle Constructs. Free Radical Biology and Medicine, 208, S55. doi:10.1016/j.freeradbiomed.2023.10.125
A systems approach reveals species differences in hepatic stress response capacity
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/kfad085
mzIdentML 1.3.0 - Essential progress on the support of crosslinking and other identifications based on multiple spectra
GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation.
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-z
Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets
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.2c00823
Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future
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.202200014
Integrated View of Baseline Protein Expression in Human Tissues
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.2c00406
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
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.2c00637
TriTrypDB: An integrated functional genomics resource for kinetoplastida.
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.0011058
2022
Assessing multiple evidence streams to decide on confidence for identification of post-translational modifications, within and across data sets
Effective tree-based classification for automated flow cytometry data analysis on samples with suspected haematological malignancy
The Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
The INSR/AKT/mTOR pathway regulates the pace of myogenesis in a syndecan-3-dependent manner
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.2022.09.004
Understanding SUMO-mediated adaptive responses in plants to improve crop productivity.
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/ebc20210068
Method for Independent Estimation of the False Localization Rate for Phosphoproteomics
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.1c00827
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues
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.1010174
Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation
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.2c00131
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center
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/gkab929
2021
MHCVision: estimation of global and local false discovery rate for MHC class I peptide binding prediction
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/btab479
A method for independent estimation of false localisation rate for phosphoproteomics
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:10.1101/2021.10.18.464791
Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential
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-w
An OMICs-based meta-analysis to support infection state stratification
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/btab089
A snapshot of human leukocyte antigen (HLA) diversity using data from the Allele Frequency Net Database
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.2020.10.004
lcmsWorld: High-Performance 3D Visualization Software for Mass Spectrometry
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.0c00618
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
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.2021.598778
Temporal modulation of the NF-kappa B ReIA network in response to different types of DNA damage
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/BCJ20200627
mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements
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.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
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.2020.101332
Machine learning to uncover differentiable signatures of bacterial and viral infections
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.2020.09.506
Proceedings of the EuBIC-MS 2020 Developers’ Meeting
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.2020.11.001
Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry
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.2020.09.011
Investigating complement mediated interference in class I HLA-specific antibodies following renal transplantation
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.2020.101310
SDC3 acts as a timekeeper of myogenic differentiation by regulating the insulin/AKT/mTOR axis in muscle stem cell progeny
Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics
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
Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signaling networks using SILAC-based phosphoproteomics
mzMLb: a future-proof raw mass spectrometry data format based on standards-compliant mzML and optimized for speed and storage requirements
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:10.1101/2020.02.13.947218
Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles
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
Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools
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
Proteome Bioinformatics Methods for Studying Histidine Phosphorylation
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_16
2019
Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation
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.2018100847
VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock
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
Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles
MzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics
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
Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets
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
2018
VAPPER: High-throughput Variant Antigen Profiling in African trypanosomes
Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions
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
Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants
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
Improvements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics datasets
Ren, Z., Qi, D., Pugh, N., Li, K., Wen, B., Zhou, R., . . . Jones, A. (2018). Improvements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics datasets. doi:10.1101/300426
Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with Adverse Drug Reactions
phpMs: A PHP-Based Mass Spectrometry Utilities Library
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
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
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
nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data
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
Allele Frequency Net Database
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_4
2017
Comparative Qualitative Phosphoproteomics Analysis Identifies Shared Phosphorylation Motifs and Associated Biological Processes in Flowering Plants
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
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
Evaluation of Parameters for Confident Phosphorylation Site Localization using an Orbitrap Fusion Tribrid Mass Spectrometer
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
KIR/HLA-DB: A REPOSITORY FOR THE ANALYSIS OF KIR AND HLA LIGANDS IN WORLDWIDE POPULATIONS
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
The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics
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
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
Using phosphoproteomics to decipher the syndecan-3 network
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/
Neopeptide Analyser: A software tool for neopeptide discovery in proteomics data.
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
Genome-Wide Association Study of Nevirapine Hypersensitivity in a sub-Saharan African HIV-infected Population
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
Human leucocyte antigen-adverse drug reaction associations: from a perspective of ethnicity
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
Data Formats of the Proteomics Standards Initiative
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
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
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
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
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
Chapter 11 Data Formats of the Proteomics Standards Initiative
Vizcaíno, J. A., Perkins, S., Jones, A. R., & Deutsch, E. W. (2016). Chapter 11 Data Formats of the Proteomics Standards Initiative. In Proteome Informatics (pp. 229-258). Royal Society of Chemistry (RSC). doi:10.1039/9781782626732-00229
Chapter 15 Proteogenomics: Proteomics for Genome Annotation
Ghali, F., & Jones, A. R. (2016). Chapter 15 Proteogenomics: Proteomics for Genome Annotation. In Proteome Informatics (pp. 365-384). Royal Society of Chemistry (RSC). doi:10.1039/9781782626732-00365
Data Formats of the Proteomics Standards Initiative
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:10.1039/9781782626732-00229
Protein Inference and Grouping
Jones, A. R. (2016). Protein Inference and Grouping. In Proteome Informatics (pp. 93-115). The Royal Society of Chemistry. doi:10.1039/9781782626732-00093
Proteogenomics: Proteomics for Genome Annotation
Ghali, F., & Jones, A. R. (2016). Proteogenomics: Proteomics for Genome Annotation. In Proteome Informatics (pp. 365-384). The Royal Society of Chemistry. doi:10.1039/9781782626732-00365
A web resource for mining HLA associations with adverse drug reactions: HLA-ADR.
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/baw069
Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data
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
2015
Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics
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
IPeak: An open source tool to combine results from multiple MS/MS search engines
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
The mzqLibrary - An open source Java library supporting the HUPO-PSI quantitative proteomics standard
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
Embedding standards in metabolomics: the Metabolomics Society data standards task group
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
A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum.
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
Representation of selected-reaction monitoring data in the mzQuantML data standard
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
Development of data representation standards by the human proteome organization proteomics standards initiative
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
A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: Application to emerging infectious diseases
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
Computational phosphoproteomics: From identification to localization
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
2014
ProteoAnnotator – Open source proteogenomics annotation software supporting PSI standards
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
Allele Frequencies Database
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
Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations.
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
A standardized framing for reporting protein identifications in mzIdentML 1.2
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
Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.
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
How to submit MS proteomics data to ProteomeXchange via the PRIDE database
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
The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience.
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
A tutorial for software development in quantitative proteomics using PSI standard formats
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
Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
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
Numerical Compression Schemes for Proteomics Mass Spectrometry Data
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
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
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
Standardization and Guidelines: How to submit MS proteomics data to ProteomeXchange via the PRIDE database.
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
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
jmzTab: A Java interface to the mzTab data standard
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
2013
Guidelines for reporting quantitative mass spectrometry based experiments in proteomics
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
Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML
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
Preparing to Work with Big Data in Proteomics - A Report on the HUPO-PSI Spring Workshop April 15-17, 2013, Liverpool, UK
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
The mzQuantML Data Standard for Mass Spectrometry-based Quantitative Studies in Proteomics
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
The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary
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/bat009
16(th) IHIW: extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles.
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
16th IHIW: Extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles
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.12030
A guide for integration of proteomic data standards into laboratory workflows
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
A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations
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
FuGE
Wilkinson, P., & Jones, A. R. (2013). FuGE. In Encyclopedia of Systems Biology (pp. 762-765). Springer New York. doi:10.1007/978-1-4419-9863-7_1094
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites
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
Relational Database
Jones, A. R. (2013). Relational Database. In Encyclopedia of Systems Biology (pp. 1838). Springer New York. doi:10.1007/978-1-4419-9863-7_1427
Relational Database Schema
Jones, A. R. (2013). Relational Database Schema. In Encyclopedia of Systems Biology (pp. 1838). Springer New York. doi:10.1007/978-1-4419-9863-7_1428
Unified Modeling Language (UML)
Jones, A. R. (2013). Unified Modeling Language (UML). In Encyclopedia of Systems Biology (pp. 2319). Springer New York. doi:10.1007/978-1-4419-9863-7_1426
XML
Jones, A. R. (2013). XML. In Encyclopedia of Systems Biology (pp. 2365). Springer New York. doi:10.1007/978-1-4419-9863-7_1424
XML Schema
Jones, A. R. (2013). XML Schema. In Encyclopedia of Systems Biology (pp. 2365-2366). Springer New York. doi:10.1007/978-1-4419-9863-7_1425
2012
A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis
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
A Software Toolkit and Interface for Performing Stable Isotope Labeling and Top3 Quantification Using Progenesis LC-MS
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
Bioinformatics Challenges and Solutions in Proteomics as Quantitative Methods Mature
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
Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop
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
The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results
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
<i>In silico</i> analysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers
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/gm350
Software for analysing ion mobility mass spectrometry data to improve peptide identification
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
Software for analysing ion mobility mass spectrometry data to improve peptide identification
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
jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data
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
Quantitative proteomics and data analysis
Beynon, R., Hubbard, S., & Jones, A. (2012). Quantitative proteomics and data analysis. The Biochemist, 34(1), 61-62. doi:10.1042/bio03401061
In silico analysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers.
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
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
The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards
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
The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards
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
Bioinformatics in Animal Proteomics
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
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
A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics.
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
Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations
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
Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations
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
FDRAnalysis: A Tool for the Integrated Analysis of Tandem Mass Spectrometry Identification Results from Multiple Search Engines.
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
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
Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea.
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
The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative
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
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
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-r27
Semi-automatic tool to describe, store and compare proteomics experiments based on MIAPE compliant reports
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
An Introduction to Proteome Bioinformatics
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_1
Guidelines for reporting the use of column chromatography in proteomics
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
Guidelines for reporting the use of gel image informatics in proteomics
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
Managing Experimental Data Using FuGE
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_23
Methods in Molecular Biology
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
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
Annual Spring Meeting of the Proteomics Standards Initiative
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
FuGEFlow: data model and markup language for flow cytometry
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
Modeling and Managing Experimental Data Using FuGE
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
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
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
Effect of annealing temperatures on the secondary re-crystallization of extruded PM2000 steel bar.
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.x
2008
A toolkit for capturing and sharing FuGE experiments
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
Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain
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
Minimum Reporting Guidelines for Proteomics Released by the Proteomics Standards Initiative
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
Guidelines for reporting the use of gel electrophoresis in proteomics
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
The proteome of <i>Toxoplasma gondii</i>:: integration with the genome provides novel insights into gene expression and annotation
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-r116
Modulation of the host cell proteome by the intracellular apicomplexan parasite <i>Toxoplasma gondii</i>
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.01115-07
Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain
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
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
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
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.
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
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
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
An update on data standards for gel electrophoresis.
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
Capture and analysis of quantitative proteomic data
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
The minimum information about a proteomics experiment (MIAPE)
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/nbt1329
Pride Wizard: generation of standards compliant quantitative proteomics data
Swainston, N., Siepen, J. A., Jones, A. R., Hart, S. R., Hermjakob, H., Jones, P., & Hubbard, S. J. (2007). Pride Wizard: generation of standards compliant quantitative proteomics data. BMC Systems Biology, 1(S1). doi:10.1186/1752-0509-1-s1-p27
The HUPO Pre-Congress Proteomics Standards Initiative Workshop HUPO 5th Annual World Congress Long Beach, CA, USA 28 October-1 November 2006
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
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ™
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:10.1186/1477-5956-5-4
Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.
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
2006
A strategy capitalizing on synergies: The Reporting Structure for Biological Investigation (RSBI) working group
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.2006.10.164
FuGE: Functional Genomics Experiment Object Model
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.2006.10.179
Data access and integration in the ISPIDER proteomics grid
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.
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
Visualisation and analysis of proteomic data from the procyclic form of <i>Trypanosoma brucei</i>
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.200500119
2005
An analysis of extensible modelling for functional genomics data
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
Proteomics data representation and management
Paton, N. W., Jones, A., & Oliver, S. G. (2005). Proteomics data representation and management. Wiley. doi:10.1002/047001153x.g408316
2004
An object model and database for functional genomics
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
An object model and database for functional genomics
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
2003
Proposal for a standard representation of two-dimensional gel electrophoresis data
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