| Year |
Citation |
Score |
| 2024 |
Basenko EY, Shanmugasundram A, Böhme U, Starns D, Wilkinson PA, Davison HR, Crouch K, Maslen G, Harb OS, Amos B, McDowell MA, Kissinger JC, Roos DS, Jones A. What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species. Genetics. PMID 38529759 DOI: 10.1093/genetics/iyae035 |
0.35 |
|
| 2023 |
Ramsbottom KA, Prakash A, Riverol YP, Camacho OM, Sun Z, Kundu DJ, Bowler-Barnett E, Martin M, Fan J, Chebotarov D, McNally KL, Deutsch EW, Vizcaíno JA, Jones AR. A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome. Biorxiv : the Preprint Server For Biology. PMID 38014076 DOI: 10.1101/2023.11.17.567512 |
0.316 |
|
| 2023 |
Shanmugasundram A, Starns D, Böhme U, Amos B, Wilkinson PA, Harb OS, Warrenfeltz S, Kissinger JC, McDowell MA, Roos DS, Crouch K, Jones AR. TriTrypDB: An integrated functional genomics resource for kinetoplastida. Plos Neglected Tropical Diseases. 17: e0011058. PMID 36656904 DOI: 10.1371/journal.pntd.0011058 |
0.32 |
|
| 2022 |
Prakash A, García-Seisdedos D, Wang S, Kundu DJ, Collins A, George N, Moreno P, Papatheodorou I, Jones AR, Vizcaíno JA. Integrated View of Baseline Protein Expression in Human Tissues. Journal of Proteome Research. PMID 36577097 DOI: 10.1021/acs.jproteome.2c00406 |
0.323 |
|
| 2022 |
Jones AR, Deutsch EW, Vizcaíno JA. Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future. Proteomics. e2200014. PMID 36074795 DOI: 10.1002/pmic.202200014 |
0.322 |
|
| 2018 |
Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA. The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. Genome Biology. 19: 12. PMID 29386051 DOI: 10.1186/S13059-017-1377-X |
0.38 |
|
| 2017 |
Peffers M, Jones AR, McCabe A, Anderson J. Neopeptide Analyser: A software tool for neopeptide discovery in proteomics data. Wellcome Open Research. 2: 24. PMID 28503667 DOI: 10.12688/wellcomeopenres.11275.1 |
0.328 |
|
| 2015 |
Fan J, Saha S, Barker G, Heesom KJ, Ghali F, Jones AR, Matthews DA, Bessant C. Galaxy Integrated Omics: Web-based standards-compliant workflows for proteomics informed by transcriptomics. Molecular & Cellular Proteomics : McP. PMID 26269333 DOI: 10.1074/mcp.O115.048777 |
0.366 |
|
| 2015 |
Qi D, Zhang H, Fan J, Perkins S, Pisconti A, Simpson DM, Bessant C, Hubbard S, Jones AR. The mzqLibrary - An open source Java library supporting the HUPO-PSI quantitative proteomics standard. Proteomics. PMID 26037908 DOI: 10.1002/pmic.201400535 |
0.332 |
|
| 2015 |
Krishna R, Xia D, Sanderson S, Shanmugasundram A, Vermont S, Bernal A, Daniel-Naguib G, Ghali F, Brunk BP, Roos DS, Wastling JM, Jones AR. A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum. Proteomics. PMID 25867681 DOI: 10.1002/pmic.201400553 |
0.629 |
|
| 2015 |
Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H. Development of data representation standards by the human proteome organization proteomics standards initiative. Journal of the American Medical Informatics Association : Jamia. 22: 495-506. PMID 25726569 DOI: 10.1093/Jamia/Ocv001 |
0.345 |
|
| 2014 |
Ghali F, Krishna R, Perkins S, Collins A, Xia D, Wastling J, Jones AR. ProteoAnnotator--open source proteogenomics annotation software supporting PSI standards. Proteomics. 14: 2731-41. PMID 25297486 DOI: 10.1002/pmic.201400265 |
0.661 |
|
| 2014 |
Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR. A standardized framing for reporting protein identifications in mzIdentML 1.2. Proteomics. 14: 2389-99. PMID 25092112 DOI: 10.1002/Pmic.201400080 |
0.31 |
|
| 2014 |
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, et al. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Molecular & Cellular Proteomics : McP. 13: 2765-75. PMID 24980485 DOI: 10.1074/Mcp.O113.036681 |
0.316 |
|
| 2014 |
Gonzalez-Galarza FF, Qi D, Fan J, Bessant C, Jones AR. A tutorial for software development in quantitative proteomics using PSI standard formats. Biochimica Et Biophysica Acta. 1844: 88-97. PMID 23584085 DOI: 10.1016/j.bbapap.2013.04.004 |
0.327 |
|
| 2013 |
Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H. Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK. Proteomics. 13: 2931-7. PMID 24108681 DOI: 10.1002/Pmic.201370166 |
0.317 |
|
| 2013 |
Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, ... Jones AR, et al. The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Molecular & Cellular Proteomics : McP. 12: 2332-40. PMID 23599424 DOI: 10.1074/Mcp.O113.028506 |
0.36 |
|
| 2013 |
Martínez-Bartolomé S, Deutsch EW, Binz PA, Jones AR, Eisenacher M, Mayer G, Campos A, Canals F, Bech-Serra JJ, Carrascal M, Gay M, Paradela A, Navajas R, Marcilla M, Hernáez ML, et al. Guidelines for reporting quantitative mass spectrometry based experiments in proteomics Journal of Proteomics. 95: 84-88. PMID 23500130 DOI: 10.1016/J.Jprot.2013.02.026 |
0.368 |
|
| 2013 |
Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, VizcaÃno JA, Hermjakob H, Stephan C, Meyer HE, et al. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database : the Journal of Biological Databases and Curation. 2013: bat009. PMID 23482073 DOI: 10.1093/Database/Bat009 |
0.334 |
|
| 2013 |
Shanmugasundram A, Gonzalez-Galarza FF, Wastling JM, Vasieva O, Jones AR. Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites. Nucleic Acids Research. 41: D706-13. PMID 23193253 DOI: 10.1093/nar/gks1139 |
0.598 |
|
| 2012 |
Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H. Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA. Proteomics. 12: 2767-72. PMID 22969026 DOI: 10.1002/Pmic.201270126 |
0.315 |
|
| 2012 |
Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, et al. The mzIdentML data standard for mass spectrometry-based proteomics results. Molecular & Cellular Proteomics : McP. 11: M111.014381. PMID 22375074 DOI: 10.1074/Mcp.M111.014381 |
0.338 |
|
| 2011 |
Medina-Aunon JA, Martínez-Bartolomé S, López-García MA, Salazar E, Navajas R, Jones AR, Paradela A, Albar JP. The ProteoRed MIAPE web toolkit: a user-friendly framework to connect and share proteomics standards. Molecular & Cellular Proteomics : McP. 10: M111.008334. PMID 21983993 DOI: 10.1074/mcp.M111.008334 |
0.312 |
|
| 2011 |
Kenyani J, Medina-Aunon JA, Martinez-Bartolomé S, Albar JP, Wastling JM, Jones AR. 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. PMID 21443781 DOI: 10.1186/1756-0500-4-86 |
0.638 |
|
| 2010 |
Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR. The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. Proteomics. 10: 3073-81. PMID 20677327 DOI: 10.1002/Pmic.201000120 |
0.334 |
|
| 2010 |
Jones A, Wastling J, Hunt E. Proposal for a standard representation of two-dimensional gel electrophoresis data. Comparative and Functional Genomics. 4: 492-501. PMID 18628860 DOI: 10.1002/cfg.323 |
0.637 |
|
| 2009 |
Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H. The PSI semantic validator: A framework to check MIAPE compliance of proteomics data Proteomics. 9: 5112-5119. PMID 19834897 DOI: 10.1002/Pmic.200900189 |
0.313 |
|
| 2009 |
Orchard S, Deutsch EW, Binz PA, Jones AR, Creasy D, Montechi-Palazzi L, Corthals G, Hermjakob H. Annual spring meeting of the proteomics standards initiative Proteomics. 9: 4429-4432. PMID 19670378 DOI: 10.1002/Pmic.200900407 |
0.303 |
|
| 2008 |
Xia D, Sanderson SJ, Jones AR, Prieto JH, Yates JR, Bromley E, Tomley FM, Lal K, Sinden RE, Brunk BP, Roos DS, Wastling JM. The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation. Genome Biology. 9: R116. PMID 18644147 DOI: 10.1186/Gb-2008-9-7-R116 |
0.634 |
|
| 2007 |
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, et al. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology. 25: 1127-33. PMID 17921998 DOI: 10.1038/Nbt1347 |
0.376 |
|
| 2007 |
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, et al. The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology. 25: 887-93. PMID 17687369 DOI: 10.1038/Nbt1329 |
0.321 |
|
| 2007 |
Lau KW, Jones AR, Swainston N, Siepen JA, Hubbard SJ. Capture and analysis of quantitative proteomic data. Proteomics. 7: 2787-99. PMID 17640002 DOI: 10.1002/pmic.200700127 |
0.324 |
|
| 2007 |
Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ. An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. Proteome Science. 5: 4. PMID 17270041 DOI: 10.1186/1477-5956-5-4 |
0.335 |
|
| 2006 |
Jones AR, Pizarro A, Spellman P, Miller M. FuGE: Functional Genomics Experiment Object Model Omics a Journal of Integrative Biology. 10: 179-184. PMID 16901224 DOI: 10.1089/Omi.2006.10.179 |
0.325 |
|
| 2006 |
Jones A, Faldas A, Foucher A, Hunt E, Tait A, Wastling JM, Turner CM. Visualisation and analysis of proteomic data from the procyclic form of Trypanosoma brucei. Proteomics. 6: 259-67. PMID 16302277 DOI: 10.1002/Pmic.200500119 |
0.635 |
|
| 2004 |
Jones A, Hunt E, Wastling JM, Pizarro A, Stoeckert CJ. An object model and database for functional genomics Bioinformatics. 20: 1583-1590. PMID 15145818 DOI: 10.1093/Bioinformatics/Bth130 |
0.65 |
|
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