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Items: 37

1.

The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes.

Romano P, Céol A, Dräger A, Fiannaca A, Giugno R, La Rosa M, Milanesi L, Pfeffer U, Rizzo R, Shin SY, Xia J, Urso A.

BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):125. doi: 10.1186/s12859-019-2681-0.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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
8.

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.

9.

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.

10.

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.

11.

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.

12.

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):285-290. doi: 10.1038/nbt.2831. Epub 2014 Feb 23.

13.

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.

14.

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
15.

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
16.

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.

17.

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.

18.

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.

19.

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.

20.

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
21.

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
22.

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.

23.

VirusMINT: a viral protein interaction database.

Chatr-aryamontri A, Ceol A, Peluso D, Nardozza A, Panni S, Sacco F, Tinti M, Smolyar A, Castagnoli L, Vidal M, Cusick ME, Cesareni G.

Nucleic Acids Res. 2009 Jan;37(Database issue):D669-73. doi: 10.1093/nar/gkn739. Epub 2008 Oct 30.

24.

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.

Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H.

Genome Biol. 2008;9 Suppl 2:S5. doi: 10.1186/gb-2008-9-s2-s5. Epub 2008 Sep 1.

25.

Searching the protein interaction space through the MINT database.

Chatr-Aryamontri A, Zanzoni A, Ceol A, Cesareni G.

Methods Mol Biol. 2008;484:305-17. doi: 10.1007/978-1-59745-398-1_20.

PMID:
18592188
26.

Searching the MINT database for protein interaction information.

Cesareni G, Chatr-aryamontri A, Licata L, Ceol A.

Curr Protoc Bioinformatics. 2008 Jun;Chapter 8:Unit 8.5. doi: 10.1002/0471250953.bi0805s22. Review.

PMID:
18551417
27.

Protein interactions: integration leads to belief.

Chatr-Aryamontri A, Ceol A, Licata L, Cesareni G.

Trends Biochem Sci. 2008 Jun;33(6):241-2; author reply 242-3. doi: 10.1016/j.tibs.2008.04.002. Epub 2008 May 9. No abstract available.

PMID:
18472267
28.

Linking entries in protein interaction database to structured text: the FEBS Letters experiment.

Ceol A, Chatr-Aryamontri A, Licata L, Cesareni G.

FEBS Lett. 2008 Apr 9;582(8):1171-7. doi: 10.1016/j.febslet.2008.02.071. Epub 2008 Mar 6. Review.

29.

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.

BMC Biol. 2007 Oct 9;5:44.

30.

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.

Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H.

Proteomics. 2007 Sep;7 Suppl 1:28-34.

PMID:
17893861
31.

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.

Nat Biotechnol. 2007 Aug;25(8):894-8. Review.

PMID:
17687370
32.

MINT: the Molecular INTeraction database.

Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G.

Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4. Epub 2006 Nov 29.

33.

DOMINO: a database of domain-peptide interactions.

Ceol A, Chatr-aryamontri A, Santonico E, Sacco R, Castagnoli L, Cesareni G.

Nucleic Acids Res. 2007 Jan;35(Database issue):D557-60. Epub 2006 Nov 29.

34.

HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms.

Persico M, Ceol A, Gavrila C, Hoffmann R, Florio A, Cesareni G.

BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S21.

35.

Comparative interactomics.

Cesareni G, Ceol A, Gavrila C, Palazzi LM, Persico M, Schneider MV.

FEBS Lett. 2005 Mar 21;579(8):1828-33. Review.

36.

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.

Nat Biotechnol. 2004 Feb;22(2):177-83.

PMID:
14755292
37.

[Description of a simple method for the bacteriological examination of urine. Preliminary note].

Avantey S, Stevenin F, Ceol A, Saggiorato R.

Quad Sclavo Diagn. 1980 Jun;16(2):227-30. Italian. No abstract available.

PMID:
7017797

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