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Searching the protein interaction space through the MINT database.
Chatr-Aryamontri A, Zanzoni A, Ceol A, Cesareni G. Chatr-Aryamontri A, et al. Among authors: ceol a. Methods Mol Biol. 2008;484:305-17. doi: 10.1007/978-1-59745-398-1_20. Methods Mol Biol. 2008. PMID: 18592188
Protein-protein interaction databases are thus becoming a major resource for investigating biological networks and pathways. ...The MINT database aims at storing, in a structured format, information about protein-protein interactions (PPIs) by extracting experimenta …
Protein-protein interaction databases are thus becoming a major resource for investigating biological networks and pathways. ...The M …
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. Sivade Dumousseau M, et al. Among authors: ceol a. BMC Bioinformatics. 2018 Apr 11;19(1):134. doi: 10.1186/s12859-018-2118-1. BMC Bioinformatics. 2018. PMID: 29642841 Free PMC article.
Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks.
Céol A, Verhoef LG, Wade M, Muller H. Céol A, et al. BMC Bioinformatics. 2016 Mar 2;17 Suppl 4(Suppl 4):54. doi: 10.1186/s12859-016-0908-x. BMC Bioinformatics. 2016. PMID: 26961139 Free PMC article.
Interactome3D: adding structural details to protein networks.
Mosca R, Céol A, Aloy P. Mosca R, et al. Among authors: ceol a. Nat Methods. 2013 Jan;10(1):47-53. doi: 10.1038/nmeth.2289. Epub 2012 Dec 16. Nat Methods. 2013. PMID: 23399932
Unlike static databases, Interactome3D also allows biologists to upload newly discovered interactions and pathways in any species, select the best combination of structural templates and build three-dimensional models in a fully automated manner. Finally, we illustrate the …
Unlike static databases, Interactome3D also allows biologists to upload newly discovered interactions and pathways in any species, select th …
Towards a detailed atlas of protein-protein interactions.
Mosca R, Pons T, Céol A, Valencia A, Aloy P. Mosca R, et al. Among authors: ceol a. Curr Opin Struct Biol. 2013 Dec;23(6):929-40. doi: 10.1016/j.sbi.2013.07.005. Epub 2013 Jul 26. Curr Opin Struct Biol. 2013. PMID: 23896349 Review.
The net result will be the definition of a detailed atlas spanning the universe of protein interactions to guide the everyday work of the biologist....
The net result will be the definition of a detailed atlas spanning the universe of protein interactions to guide the everyday work of …
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Kerrien S, et al. Among authors: ceol a. BMC Biol. 2007 Oct 9;5:44. doi: 10.1186/1741-7007-5-44. BMC Biol. 2007. PMID: 17925023 Free PMC article.
BACKGROUND: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. ...MITAB2.5 is a simpler format app …
BACKGROUND: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previousl …
The minimum information required for reporting a molecular interaction experiment (MIMIx).
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H. Orchard S, et al. Among authors: ceol a. Nat Biotechnol. 2007 Aug;25(8):894-8. doi: 10.1038/nbt1324. Nat Biotechnol. 2007. PMID: 17687370 Review.
A wealth of molecular interaction data is available in the literature, ranging from large-scale datasets to a single interaction confirmed by several different techniques. These data are all too often reported either as free text or in tables of variable format, and
A wealth of molecular interaction data is available in the literature, ranging from large-scale datasets to a single interacti
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R. Hermjakob H, et al. Among authors: ceol a. Nat Biotechnol. 2004 Feb;22(2):177-83. doi: 10.1038/nbt926. Nat Biotechnol. 2004. PMID: 14755292
A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the inter
A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large
MINT: the Molecular INTeraction database.
Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G. Chatr-aryamontri A, et al. Among authors: ceol a. Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4. doi: 10.1093/nar/gkl950. Epub 2006 Nov 29. Nucleic Acids Res. 2007. PMID: 17135203 Free PMC article.
The new version of MINT is based on a completely remodeled database structure, which offers more efficient data exploration and analysis, and is characterized by entries with a richer annotation. ...MINT now includes, as an integrated addition, HomoMINT, a da …
The new version of MINT is based on a completely remodeled database structure, which offers more efficient data exploration and analy …
Identification of new substrates of the protein-tyrosine phosphatase PTP1B by Bayesian integration of proteome evidence.
Ferrari E, Tinti M, Costa S, Corallino S, Nardozza AP, Chatraryamontri A, Ceol A, Cesareni G, Castagnoli L. Ferrari E, et al. Among authors: ceol a. J Biol Chem. 2011 Feb 11;286(6):4173-85. doi: 10.1074/jbc.M110.157420. Epub 2010 Dec 1. J Biol Chem. 2011. PMID: 21123182 Free PMC article.
We describe here a system wide strategy to infer physiological substrates of protein-tyrosine phosphatases. Here we integrate, by a Bayesian model, proteome wide evidence about in vitro substrate preference, as determined by a novel high-density peptide chip …
We describe here a system wide strategy to infer physiological substrates of protein-tyrosine phosphatases. Here we integrate, by …
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