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Page 1
A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome.
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. Ramsbottom KA, et al. Among authors: kundu dj. bioRxiv [Preprint]. 2023 Nov 17:2023.11.17.567512. doi: 10.1101/2023.11.17.567512. bioRxiv. 2023. Update in: J Proteome Res. 2024 Jul 5;23(7):2518-2531. doi: 10.1021/acs.jproteome.4c00187 PMID: 38014076 Free PMC article. Updated. Preprint.
The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA. Perez-Riverol Y, et al. Among authors: kundu dj. Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450. doi: 10.1093/nar/gky1106. Nucleic Acids Res. 2019. PMID: 30395289 Free PMC article.
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. Deutsch EW, et al. Among authors: kundu dj. Nucleic Acids Res. 2020 Jan 8;48(D1):D1145-D1152. doi: 10.1093/nar/gkz984. Nucleic Acids Res. 2020. PMID: 31686107 Free PMC article.
An integrated landscape of protein expression in human cancer.
Jarnuczak AF, Najgebauer H, Barzine M, Kundu DJ, Ghavidel F, Perez-Riverol Y, Papatheodorou I, Brazma A, Vizcaíno JA. Jarnuczak AF, et al. Among authors: kundu dj. Sci Data. 2021 Apr 23;8(1):115. doi: 10.1038/s41597-021-00890-2. Sci Data. 2021. PMID: 33893311 Free PMC article.
A proteomics sample metadata representation for multiomics integration and big data analysis.
Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y. Dai C, et al. Among authors: kundu dj. Nat Commun. 2021 Oct 6;12(1):5854. doi: 10.1038/s41467-021-26111-3. Nat Commun. 2021. PMID: 34615866 Free PMC article. Review.
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.
Perez-Riverol Y, Bai J, Bandla C, García-Seisdedos D, Hewapathirana S, Kamatchinathan S, Kundu DJ, Prakash A, Frericks-Zipper A, Eisenacher M, Walzer M, Wang S, Brazma A, Vizcaíno JA. Perez-Riverol Y, et al. Among authors: kundu dj. Nucleic Acids Res. 2022 Jan 7;50(D1):D543-D552. doi: 10.1093/nar/gkab1038. Nucleic Acids Res. 2022. PMID: 34723319 Free PMC article.
Expression Atlas update: gene and protein expression in multiple species.
Moreno P, Fexova S, George N, Manning JR, Miao Z, Mohammed S, Muñoz-Pomer A, Fullgrabe A, Bi Y, Bush N, Iqbal H, Kumbham U, Solovyev A, Zhao L, Prakash A, García-Seisdedos D, Kundu DJ, Wang S, Walzer M, Clarke L, Osumi-Sutherland D, Tello-Ruiz MK, Kumari S, Ware D, Eliasova J, Arends MJ, Nawijn MC, Meyer K, Burdett T, Marioni J, Teichmann S, Vizcaíno JA, Brazma A, Papatheodorou I. Moreno P, et al. Among authors: kundu dj. Nucleic Acids Res. 2022 Jan 7;50(D1):D129-D140. doi: 10.1093/nar/gkab1030. Nucleic Acids Res. 2022. PMID: 34850121 Free PMC article.
The ProteomeXchange consortium at 10 years: 2023 update.
Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. Deutsch EW, et al. Among authors: kundu dj. Nucleic Acids Res. 2023 Jan 6;51(D1):D1539-D1548. doi: 10.1093/nar/gkac1040. Nucleic Acids Res. 2023. PMID: 36370099 Free PMC article.
Integrated View of Baseline Protein Expression in Human Tissues.
Prakash A, García-Seisdedos D, Wang S, Kundu DJ, Collins A, George N, Moreno P, Papatheodorou I, Jones AR, Vizcaíno JA. Prakash A, et al. Among authors: kundu dj. J Proteome Res. 2023 Mar 3;22(3):729-742. doi: 10.1021/acs.jproteome.2c00406. Epub 2022 Dec 28. J Proteome Res. 2023. PMID: 36577097 Free PMC article.
13 results