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Items: 1 to 20 of 35

1.

Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions.

Bianchi V, Ceol A, Ogier AG, de Pretis S, Galeota E, Kishore K, Bora P, Croci O, Campaner S, Amati B, Morelli MJ, Pelizzola M.

Front Genet. 2016 May 6;7:75. doi: 10.3389/fgene.2016.00075. eCollection 2016.

2.

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.

BMC Bioinformatics. 2016 Mar 2;17 Suppl 4:54. doi: 10.1186/s12859-016-0908-x.

3.

LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer.

Melloni GE, de Pretis S, Riva L, Pelizzola M, Céol A, Costanza J, Müller H, Zammataro L.

BMC Bioinformatics. 2016 Feb 9;17:80. doi: 10.1186/s12859-016-0935-7.

4.

The MI bundle: enabling network and structural biology in genome visualization tools.

Céol A, Müller H.

Bioinformatics. 2015 Nov 15;31(22):3679-81. doi: 10.1093/bioinformatics/btv431. Epub 2015 Jul 25.

5.

dSysMap: exploring the edgetic role of disease mutations.

Mosca R, Tenorio-Laranga J, Olivella R, Alcalde V, Céol A, Soler-López M, Aloy P.

Nat Methods. 2015 Mar;12(3):167-8. doi: 10.1038/nmeth.3289. No abstract available.

PMID:
25719824
6.

The EHEC-host interactome reveals novel targets for the translocated intimin receptor.

Blasche S, Arens S, Ceol A, Siszler G, Schmidt MA, Häuser R, Schwarz F, Wuchty S, Aloy P, Uetz P, Stradal T, Koegl M.

Sci Rep. 2014 Dec 18;4:7531. doi: 10.1038/srep07531.

7.

SMITH: a LIMS for handling next-generation sequencing workflows.

Venco F, Vaskin Y, Ceol A, Muller H.

BMC Bioinformatics. 2014;15 Suppl 14:S3. doi: 10.1186/1471-2105-15-S14-S3. Epub 2014 Nov 27.

8.

A second-generation protein-protein interaction network of Helicobacter pylori.

Häuser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P.

Mol Cell Proteomics. 2014 May;13(5):1318-29. doi: 10.1074/mcp.O113.033571. Epub 2014 Mar 13.

9.

AnnotateGenomicRegions: a web application.

Zammataro L, DeMolfetta R, Bucci G, Ceol A, Muller H.

BMC Bioinformatics. 2014;15 Suppl 1:S8. doi: 10.1186/1471-2105-15-S1-S8. Epub 2014 Jan 10.

10.

The binary protein-protein interaction landscape of Escherichia coli.

Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P.

Nat Biotechnol. 2014 Mar;32(3):285-90. doi: 10.1038/nbt.2831. Epub 2014 Feb 23.

11.

3did: a catalog of domain-based interactions of known three-dimensional structure.

Mosca R, Céol A, Stein A, Olivella R, Aloy P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D374-9. doi: 10.1093/nar/gkt887. Epub 2013 Sep 29.

12.

Towards a detailed atlas of protein-protein interactions.

Mosca R, Pons T, Céol A, Valencia A, Aloy P.

Curr Opin Struct Biol. 2013 Dec;23(6):929-40. doi: 10.1016/j.sbi.2013.07.005. Epub 2013 Jul 26. Review.

PMID:
23896349
13.

Interactome3D: adding structural details to protein networks.

Mosca R, Céol A, Aloy P.

Nat Methods. 2013 Jan;10(1):47-53. doi: 10.1038/nmeth.2289. Epub 2012 Dec 16.

PMID:
23399932
14.

NetAligner--a network alignment server to compare complexes, pathways and whole interactomes.

Pache RA, Céol A, Aloy P.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W157-61. doi: 10.1093/nar/gks446. Epub 2012 May 22.

15.

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.

Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.

Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637. No abstract available.

16.

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.

J Biol Chem. 2011 Feb 11;286(6):4173-85. doi: 10.1074/jbc.M110.157420. Epub 2010 Dec 1.

17.

3did: identification and classification of domain-based interactions of known three-dimensional structure.

Stein A, Céol A, Aloy P.

Nucleic Acids Res. 2011 Jan;39(Database issue):D718-23. doi: 10.1093/nar/gkq962. Epub 2010 Oct 21.

18.

The FEBS Letters/BioCreative II.5 experiment: making biological information accessible.

Leitner F, Chatr-aryamontri A, Mardis SA, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A.

Nat Biotechnol. 2010 Sep;28(9):897-9. doi: 10.1038/nbt0910-897. No abstract available.

PMID:
20829821
19.

Recurated protein interaction datasets.

Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H.

Nat Methods. 2009 Dec;6(12):860-1. doi: 10.1038/nmeth1209-860. No abstract available.

PMID:
19935838
20.

MINT, the molecular interaction database: 2009 update.

Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G.

Nucleic Acids Res. 2010 Jan;38(Database issue):D532-9. doi: 10.1093/nar/gkp983. Epub 2009 Nov 6.

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