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Items: 27

1.

Ribosomal protein RPL22/eL22 regulates the cell cycle by acting as an inhibitor of the CDK4-cyclin D complex.

Del Toro N, Fernandez-Ruiz A, Mignacca L, Kalegari P, Rowell MC, Igelmann S, Saint-Germain E, Benfdil M, Lopes-Paciencia S, Brakier-Gingras L, Bourdeau V, Ferbeyre G, Lessard F.

Cell Cycle. 2019 Mar - Apr;18(6-7):759-770. doi: 10.1080/15384101.2019.1593708. Epub 2019 Mar 28.

PMID:
30874462
2.

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium contributing authors, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P.

Nat Commun. 2019 Mar 4;10(1):1098. doi: 10.1038/s41467-019-08814-w.

3.

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, Touré V, Zobolas J, Licata L.

Bioinformatics. 2019 Feb 21. pii: btz132. doi: 10.1093/bioinformatics/btz132. [Epub ahead of print]

PMID:
30793173
4.

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

IMEx Consortium Curators, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P.

Nat Commun. 2019 Jan 2;10(1):10. doi: 10.1038/s41467-018-07709-6. Erratum in: Nat Commun. 2019 Mar 4;10(1):1098.

5.

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.

Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S.

Nucleic Acids Res. 2019 Jan 8;47(D1):D550-D558. doi: 10.1093/nar/gky1001.

6.

Senescence-associated ribosome biogenesis defects contributes to cell cycle arrest through the Rb pathway.

Lessard F, Igelmann S, Trahan C, Huot G, Saint-Germain E, Mignacca L, Del Toro N, Lopes-Paciencia S, Le Calvé B, Montero M, Deschênes-Simard X, Bury M, Moiseeva O, Rowell MC, Zorca CE, Zenklusen D, Brakier-Gingras L, Bourdeau V, Oeffinger M, Ferbeyre G.

Nat Cell Biol. 2018 Jul;20(7):789-799. doi: 10.1038/s41556-018-0127-y. Epub 2018 Jun 25.

PMID:
29941930
7.

JAMI: a Java library for molecular interactions and data interoperability.

Sivade Dumousseau M, Koch M, Shrivastava A, Alonso-López D, De Las Rivas J, Del-Toro N, Combe CW, Meldal BHM, Heimbach J, Rappsilber J, Sullivan J, Yehudi Y, Orchard S.

BMC Bioinformatics. 2018 Apr 11;19(1):133. doi: 10.1186/s12859-018-2119-0.

8.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S.

BMC Bioinformatics. 2018 Apr 11;19(1):134. doi: 10.1186/s12859-018-2118-1.

9.

Discovering and linking public omics data sets using the Omics Discovery Index.

Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.

Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. No abstract available.

10.

Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence.

Garin-Muga A, Odriozola L, Martínez-Val A, Del Toro N, Martínez R, Molina M, Cantero L, Rivera R, Garrido N, Dominguez F, Sanchez Del Pino MM, Vizcaíno JA, Corrales FJ, Segura V.

J Proteome Res. 2016 Nov 4;15(11):4101-4115. Epub 2016 Sep 15.

11.

2016 update of the PRIDE database and its related tools.

Vizcaíno JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.

Nucleic Acids Res. 2016 Dec 15;44(22):11033. Epub 2016 Sep 28. No abstract available.

12.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, Vizcaíno JA.

Nat Methods. 2016 Aug;13(8):651-656. Epub 2016 Jun 27.

13.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6.

14.

2016 update of the PRIDE database and its related tools.

Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.

Nucleic Acids Res. 2016 Jan 4;44(D1):D447-56. doi: 10.1093/nar/gkv1145. Epub 2015 Nov 2. Erratum in: Nucleic Acids Res. 2016 Dec 15;44(22):11033.

15.

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.

Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.

Bioinformatics. 2015 Sep 1;31(17):2903-5. doi: 10.1093/bioinformatics/btv250. Epub 2015 Apr 24.

16.

Introducing the PRIDE Archive RESTful web services.

Reisinger F, del-Toro N, Ternent T, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res. 2015 Jul 1;43(W1):W599-604. doi: 10.1093/nar/gkv382. Epub 2015 Apr 22.

17.

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

Villaveces JM, Jiménez RC, Porras P, Del-Toro N, Duesbury M, Dumousseau M, Orchard S, Choi H, Ping P, Zong NC, Askenazi M, Habermann BH, Hermjakob H.

Database (Oxford). 2015 Feb 4;2015. pii: bau131. doi: 10.1093/database/bau131. Print 2015.

18.

A comparative study of different protein immobilization methods for the construction of an efficient nano-structured lactate oxidase-SWCNT-biosensor.

Pagán M, Suazo D, Del Toro N, Griebenow K.

Biosens Bioelectron. 2015 Feb 15;64:138-46. doi: 10.1016/j.bios.2014.08.072. Epub 2014 Sep 3.

19.

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.

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, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.

Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30.

20.

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H.

Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63. doi: 10.1093/nar/gkt1115. Epub 2013 Nov 13.

21.

A new reference implementation of the PSICQUIC web service.

del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W601-6. doi: 10.1093/nar/gkt392. Epub 2013 May 13.

22.

BioJS: an open source JavaScript framework for biological data visualization.

Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.

Bioinformatics. 2013 Apr 15;29(8):1103-4. doi: 10.1093/bioinformatics/btt100. Epub 2013 Feb 23.

23.

[Comparative study of PTFE grafts in forearm vs cuffed permanent catheters].

Moyano MJ, Salgueira M, Aresté N, Escalera B, del Toro N, Jiménez-Víbora E, Martínez-Puerto AI, Molas JR, Palma A.

Nefrologia. 2006;26(5):594-9. Spanish.

24.

[Renal hyperparathyroidism's control after subtotal parathyroidectomy].

Jiménez Víbora E, Aresté N, Salgueira M, del Toro N, Jiménez García A, Villar JL, Palma A.

Nefrologia. 2005;25(4):416-21. Spanish.

25.

[Fatal outcome of a patient with Fabry disease in enzymatic treatment].

Moyano MJ, del Toro N, Amor J, Milán JA.

Nefrologia. 2005;25(2):207-8. Spanish. No abstract available.

26.

Enzyme replacement in the treatment of Fabry's disease. Is there a point-of-no-return?

del Toro N, Milán JA, Palma A.

Nephrol Dial Transplant. 2004 Apr;19(4):1018. No abstract available.

PMID:
15031378
27.

Vascular calcification in the uremic patient: a cardiovascular risk?

Salgueira M, del Toro N, Moreno-Alba R, Jiménez E, Aresté N, Palma A.

Kidney Int Suppl. 2003 Jun;(85):S119-21.

PMID:
12753281

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