Publications

70: Pietrosanto M, Mattei E, Helmer-Citterich M, Ferrè F. A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications. Nucleic Acids Res. 2016 Oct 14;44(18):8600-8609. PubMed PMID: 27580722; PubMed Central PMCID: PMC5062999.

69: Mongiardi MP, Savino M, Falchetti ML, Illi B, Bozzo F, Valle C, Helmer-Citterich M, Ferrè F, Nasi S, Levi A. c-MYC inhibition impairs hypoxia response in glioblastoma multiforme. Oncotarget. 2016 May 31;7(22):33257-71. doi: 10.18632/oncotarget.8921. PubMed PMID: 27119353; PubMed Central PMCID: PMC5078092.

68: Tabolacci E, Mancano G, Lanni S, Palumbo F, Goracci M, Ferrè F, Helmer-Citterich M, Neri G. Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells. Epigenetics Chromatin. 2016 Mar 24;9:12. doi: 10.1186/s13072-016-0060-x. PubMed PMID: 27014370; PubMed Central PMCID: PMC4806452.

67: Mango R, Luchetti A, Sangiuolo R, Ferradini V, Briglia N, Giardina E, Ferrè F, Helmer Citterich M, Romeo F, Novelli G, Sangiuolo F. Next Generation Sequencing and Linkage Analysis for the Molecular Diagnosis of a Novel Overlapping Syndrome Characterized by Hypertrophic Cardiomyopathy and Typical Electrical Instability of Brugada Syndrome. Circ J. 2016;80(4):938-49. doi: 10.1253/circj.CJ-15-0685. PubMed PMID: 26960954.

66: Morini E, Rizzacasa B, Pucci S, Polidoro C, Ferrè F, Caporossi D, Helmer Citterich M, Novelli G, Amati F. The human rs1050286 polymorphism alters LOX-1 expression through modifying miR-24 binding. J Cell Mol Med. 2016 Jan;20(1):181-7. doi: 10.1111/jcmm.12716. PubMed PMID: 26542080; PubMed Central PMCID: PMC4717858.

65: Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116. PubMed PMID: 26538599; PubMed Central PMCID: PMC4702812.

64: Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R. Kinome-wide decoding of network-attacking mutations rewiring cancer signaling. Cell. 2015 Sep 24;163(1):202-17. doi: 10.1016/j.cell.2015.08.056. PubMed PMID: 26388441; PubMed Central PMCID: PMC4644236.

63: Facchiano A, Angelini C, Bosotti R, Guffanti A, Marabotti A, Marangoni R, Pascarella S, Romano P, Zanzoni A, Helmer-Citterich M. Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics. 2015;16 Suppl 9:S1. doi: 10.1186/1471-2105-16-S9-S1. PubMed PMID: 26050789; PubMed Central PMCID: PMC4464032.

62: Ferrè F, Colantoni A, Helmer-Citterich M. Revealing protein-lncRNA interaction. Brief Bioinform. 2016 Jan;17(1):106-16. doi: 10.1093/bib/bbv031. Review. PubMed PMID: 26041786; PubMed Central PMCID: PMC4719072.

61: Mattei E, Pietrosanto M, Ferrè F, Helmer-Citterich M. Web-Beagle: a web server for the alignment of RNA secondary structures. Nucleic Acids Res. 2015 Jul 1;43(W1):W493-7. doi: 10.1093/nar/gkv489. PubMed PMID: 25977293; PubMed Central PMCID: PMC4489221.

60: Cianfanelli V, Fuoco C, Lorente M, Salazar M, Quondamatteo F, Gherardini PF, De Zio D, Nazio F, Antonioli M, D'Orazio M, Skobo T, Bordi M, Rohde M, Dalla Valle L, Helmer-Citterich M, Gretzmeier C, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, Cecconi F. AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nat Cell Biol. 2015 May;17(5):706. doi: 10.1038/ncb3171. PubMed PMID: 25925585.

59: Mattei E, Helmer-Citterich M, Ferrè F. A simple protocol for the inference of RNA global pairwise alignments. Methods Mol Biol. 2015;1269:39-47. doi: 10.1007/978-1-4939-2291-8_3. PubMed PMID: 25577371.

58: Cianfanelli V, Fuoco C, Lorente M, Salazar M, Quondamatteo F, Gherardini PF, De Zio D, Nazio F, Antonioli M, D'Orazio M, Skobo T, Bordi M, Rohde M, Dalla Valle L, Helmer-Citterich M, Gretzmeier C, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, Cecconi F. AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nat Cell Biol. 2015 Jan;17(1):20-30. doi: 10.1038/ncb3072. Erratum in: Nat Cell Biol. 2015 May;17(5):706. PubMed PMID: 25438055; PubMed Central PMCID: PMC4976803.

57: Palmeri A, Ferrè F, Helmer-Citterich M. Exploiting holistic approaches to model specificity in protein phosphorylation. Front Genet. 2014 Sep 30;5:315. doi: 10.3389/fgene.2014.00315. Review. PubMed PMID: 25324856; PubMed Central PMCID: PMC4179730.

56: Ferrè F, Palmeri A, Helmer-Citterich M. Computational methods for analysis and inference of kinase/inhibitor relationships. Front Genet. 2014 Jun 30;5:196. doi: 10.3389/fgene.2014.00196. Review. PubMed PMID: 25071826; PubMed Central PMCID: PMC4075008.

55: Palmeri A, Ausiello G, Ferrè F, Helmer-Citterich M, Gherardini PF. A Proteome-wide Domain-centric Perspective on Protein Phosphorylation. Mol Cell Proteomics. 2014 Sep;13(9):2198-212. doi: 10.1074/mcp.M114.039990. PubMed PMID: 24830415; PubMed Central PMCID: PMC4159644.

54: Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M. A novel approach to represent and compare RNA secondary structures. Nucleic Acids Res. 2014 Jun;42(10):6146-57. doi: 10.1093/nar/gku283. PubMed PMID: 24753415; PubMed Central PMCID: PMC4041456.

53: Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Myler PJ, Zilberstein D. Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends. Mol Cell Proteomics. 2014 Jul;13(7):1787-99. doi: 10.1074/mcp.M114.037705. PubMed PMID: 24741111; PubMed Central PMCID: PMC4083115.

52: Lanni S, Goracci M, Borrelli L, Mancano G, Chiurazzi P, Moscato U, Ferrè F, Helmer-Citterich M, Tabolacci E, Neri G. Role of CTCF protein in regulating FMR1 locus transcription. PLoS Genet. 2013;9(7):e1003601. doi: 10.1371/journal.pgen.1003601. PubMed PMID: 23874213; PubMed Central PMCID: PMC3715420.

51: Gissi C, Romano P, Ferro A, Giugno R, Pulvirenti A, Facchiano A, Helmer-Citterich M. Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics. 2013;14 Suppl 7:S1. doi: 10.1186/1471-2105-14-S7-S1. PubMed PMID: 23815154; PubMed Central PMCID: PMC3633006.

50: Bianchi V, Colantoni A, Calderone A, Ausiello G, Ferrè F, Helmer-Citterich M. DBATE: database of alternative transcripts expression. Database (Oxford). 2013 Jul 9;2013:bat050. doi: 10.1093/database/bat050. PubMed PMID: 23842462.

49: Colantoni A, Bianchi V, Gherardini PF, Tomba GS, Ausiello G, Helmer-Citterich M, Ferrè F. Alternative splicing tends to avoid partial removals of protein-protein interaction sites. BMC Genomics. 2013 Jun 7;14:379. doi: 10.1186/1471-2164-14-379. PubMed PMID: 23758645; PubMed Central PMCID: PMC3700808.

48: Bianchi V, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G. webPDBinder: a server for the identification of ligand binding sites on protein structures. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W308-13. doi: 10.1093/nar/gkt457. PubMed PMID: 23737450; PubMed Central PMCID: PMC3692056.

47: Parca L, Ferré F, Ausiello G, Helmer-Citterich M. Nucleos: a web server for the identification of nucleotide-binding sites in protein structures. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W281-5. doi: 10.1093/nar/gkt390. PubMed PMID: 23703207; PubMed Central PMCID: PMC3692072.

46: Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Zilberstein D. Phosphoproteomic analysis of differentiating Leishmania parasites reveals a unique stage-specific phosphorylation motif. J Proteome Res. 2013 Jul 5;12(7):3405-12. doi: 10.1021/pr4002492. PubMed PMID: 23688256.

45: Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Späth GF. Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound. J Proteomics. 2013 Jun 28;86:97-104. doi: 10.1016/j.jprot.2013.05.002. PubMed PMID: 23684787.

44: Parca L, Gherardini PF, Truglio M, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G. Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PLoS One. 2012;7(11):e50240. doi: 10.1371/journal.pone.0050240. PubMed PMID: 23209685; PubMed Central PMCID: PMC3507729.

43: Gherardini PF, Helmer-Citterich M. Experimental and computational methods for the analysis and modeling of signaling networks. N Biotechnol. 2013 Mar 25;30(3):327-32. doi: 10.1016/j.nbt.2012.11.007. Review. PubMed PMID: 23165097.

42: Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G. Exploring the diversity of SPRY/B30.2-mediated interactions. Trends Biochem Sci. 2013 Jan;38(1):38-46. doi: 10.1016/j.tibs.2012.10.001. Review. PubMed PMID: 23164942.

41: Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G. Mapping the human phosphatome on growth pathways. Mol Syst Biol. 2012;8:603. doi: 10.1038/msb.2012.36. PubMed PMID: 22893001; PubMed Central PMCID: PMC3435503.

40: Giacò L, Amicosante M, Fraziano M, Gherardini PF, Ausiello G, Helmer-Citterich M, Colizzi V, Cabibbo A. B-Pred, a structure based B-cell epitopes prediction server. Adv Appl Bioinform Chem. 2012;5:11-21. doi: 10.2147/AABC.S30620. PubMed PMID: 22888263; PubMed Central PMCID: PMC3413014.

39: Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P. Deciphering a global network of functionally associated post-translational modifications. Mol Syst Biol. 2012 Jul 17;8:599. doi: 10.1038/msb.2012.31. PubMed PMID: 22806145; PubMed Central PMCID: PMC3421446.

38: Fioravanti F, Helmer-Citterich M, Nardelli E. Modeling gene regulatory network motifs using Statecharts. BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S20. doi: 10.1186/1471-2105-13-S4-S20. PubMed PMID: 22536967; PubMed Central PMCID: PMC3434443.

37: Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G. Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S17. doi: 10.1186/1471-2105-13-S4-S17. PubMed PMID: 22536963; PubMed Central PMCID: PMC3434446.

36: Romano P, Helmer-Citterich M. Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics. BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:I1. doi: 10.1186/1471-2105-13-S4-I1. PubMed PMID: 22536954; PubMed Central PMCID: PMC3314567.

35: Tsigankov P, Gherardini PF, Helmer-Citterich M, Zilberstein D. What has proteomics taught us about Leishmania development? Parasitology. 2012 Aug;139(9):1146-57. doi: 10.1017/S0031182012000157. Review. PubMed PMID: 22369930.

34: Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Späth GF, Zilberstein D, Helmer-Citterich M. PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae. BMC Genomics. 2011 Dec 19;12:614. doi: 10.1186/1471-2164-12-614. PubMed PMID: 22182631; PubMed Central PMCID: PMC3285042.

33: Parca L, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M. Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W278-82. doi: 10.1093/nar/gkr389. PubMed PMID: 21622655; PubMed Central PMCID: PMC3125782.

32: Schmidt-Arras D, Leclercq O, Gherardini PF, Helmer-Citterich M, Faigle W, Loew D, Späth GF. Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani. J Proteomics. 2011 Aug 24;74(9):1644-51. doi: 10.1016/j.jprot.2011.03.024. PubMed PMID: 21443974.

31: Via A, Diella F, Gibson TJ, Helmer-Citterich M. From sequence to structural analysis in protein phosphorylation motifs. Front Biosci (Landmark Ed). 2011 Jan 1;16:1261-75. Review. PubMed PMID: 21196230.

30: Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G. Phosphate binding sites identification in protein structures. Nucleic Acids Res. 2011 Mar;39(4):1231-42. doi: 10.1093/nar/gkq987. PubMed PMID: 20974634; PubMed Central PMCID: PMC3045618.

29: Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A. Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Res. 2011 Jan;39(Database issue):D268-71. doi: 10.1093/nar/gkq936. PubMed PMID: 20965970; PubMed Central PMCID: PMC3013787.

28: Hem S, Gherardini PF, Osorio y Fortéa J, Hourdel V, Morales MA, Watanabe R, Pescher P, Kuzyk MA, Smith D, Borchers CH, Zilberstein D, Helmer-Citterich M, Namane A, Späth GF. Identification of Leishmania-specific protein phosphorylation sites by LC-ESI-MS/MS and comparative genomics analyses. Proteomics. 2010 Nov;10(21):3868-83. doi: 10.1002/pmic.201000305. PubMed PMID: 20960452.

27: Gherardini PF, Ausiello G, Helmer-Citterich M. Superpose3D: a local structural comparison program that allows for user-defined structure representations. PLoS One. 2010 Aug 5;5(8):e11988. doi: 10.1371/journal.pone.0011988. PubMed PMID: 20700534; PubMed Central PMCID: PMC2916828.

26: Yau WL, Blisnick T, Taly JF, Helmer-Citterich M, Schiene-Fischer C, Leclercq O, Li J, Schmidt-Arras D, Morales MA, Notredame C, Romo D, Bastin P, Späth GF. Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite proliferation and viability. PLoS Negl Trop Dis. 2010 Jun 29;4(6):e729. doi: 10.1371/journal.pntd.0000729. PubMed PMID: 20614016; PubMed Central PMCID: PMC2894131.

25: Gherardini PF, Ausiello G, Russell RB, Helmer-Citterich M. Modular architecture of nucleotide-binding pockets. Nucleic Acids Res. 2010 Jun;38(11):3809-16. doi: 10.1093/nar/gkq090. PubMed PMID: 20185567; PubMed Central PMCID: PMC2887960.

24: Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ. ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80. doi: 10.1093/nar/gkp1016. PubMed PMID: 19920119; PubMed Central PMCID: PMC2808914.

23: Via A, Gould CM, Gemünd C, Gibson TJ, Helmer-Citterich M. A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinformatics. 2009 Oct 24;10:351. doi: 10.1186/1471-2105-10-351. PubMed PMID: 19852836; PubMed Central PMCID: PMC2774702.

22: Ausiello G, Gherardini PF, Gatti E, Incani O, Helmer-Citterich M. Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics. 2009 Jun 15;10:182. doi: 10.1186/1471-2105-10-182. PubMed PMID: 19527512; PubMed Central PMCID: PMC2704211.

21: Ferrè F, Via A, Ausiello G, Brannetti B, Zanzoni A, Helmer-Citterich M. Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information. Comp Funct Genomics. 2003;4(4):416-9. doi: 10.1002/cfg.304. PubMed PMID: 18629081; PubMed Central PMCID: PMC2447366.

20: Gherardini PF, Helmer-Citterich M. Structure-based function prediction: approaches and applications. Brief Funct Genomic Proteomic. 2008 Jul;7(4):291-302. doi: 10.1093/bfgp/eln030. Review. PubMed PMID: 18599513.

19: Cesareni G, Helmer-Citterich M. Searching the MINT database for protein interaction information. Curr Protoc Bioinformatics. 2003 Aug;Chapter 8:Unit 8.5. doi: 10.1002/0471250953.bi0805s02. PubMed PMID: 18428712.

18: Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M. FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S2. doi: 10.1186/1471-2105-9-S2-S2. PubMed PMID: 18387204; PubMed Central PMCID: PMC2323665.

17: Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ. Convergent evolution of enzyme active sites is not a rare phenomenon. J Mol Biol. 2007 Sep 21;372(3):817-45. PubMed PMID: 17681532.

16: Via A, Peluso D, Gherardini PF, de Rinaldis E, Colombo T, Ausiello G, Helmer-Citterich M. 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W416-9. PubMed PMID: 17488847; PubMed Central PMCID: PMC1933223.

15: Ferraro E, Peluso D, Via A, Ausiello G, Helmer-Citterich M. SH3-Hunter: discovery of SH3 domain interaction sites in proteins. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W451-4. PubMed PMID: 17485474; PubMed Central PMCID: PMC1933191.

14: Ausiello G, Peluso D, Via A, Helmer-Citterich M. Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S24. PubMed PMID: 17430569; PubMed Central PMCID: PMC1885854.

13: Via A, Gherardini PF, Ferraro E, Ausiello G, Scalia Tomba G, Helmer-Citterich M. False occurrences of functional motifs in protein sequences highlight evolutionary constraints. BMC Bioinformatics. 2007 Mar 1;8:68. PubMed PMID: 17331242; PubMed Central PMCID: PMC1821045.

12: Zanzoni A, Ausiello G, Via A, Gherardini PF, Helmer-Citterich M. Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Res. 2007 Jan;35(Database issue):D229-31. PubMed PMID: 17142231; PubMed Central PMCID: PMC1669737.

11: Ausiello G, Via A, Helmer-Citterich M. Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S5. PubMed PMID: 16351754; PubMed Central PMCID: PMC1866380.

10: Ferraro E, Via A, Ausiello G, Helmer-Citterich M. A neural strategy for the inference of SH3 domain-peptide interaction specificity. BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S13. PubMed PMID: 16351739; PubMed Central PMCID: PMC1866395.

9: Ferrè F, Ausiello G, Zanzoni A, Helmer-Citterich M. Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinformatics. 2005 Aug 2;6:194. PubMed PMID: 16076399; PubMed Central PMCID: PMC1190158.

8: Ausiello G, Zanzoni A, Peluso D, Via A, Helmer-Citterich M. pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W133-7. PubMed PMID: 15980442; PubMed Central PMCID: PMC1160259.

7: Via A, Zanzoni A, Helmer-Citterich M. Seq2Struct: a resource for establishing sequence-structure links. Bioinformatics. 2005 Feb 15;21(4):551-3. PubMed PMID: 15454411.

6: Via A, Helmer-Citterich M. A structural study for the optimisation of functional motifs encoded in protein sequences. BMC Bioinformatics. 2004 Apr 30;5:50. PubMed PMID: 15119965; PubMed Central PMCID: PMC420233.

5: Ferrè F, Ausiello G, Zanzoni A, Helmer-Citterich M. SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D240-4. PubMed PMID: 14681403; PubMed Central PMCID: PMC308788.

4: Brannetti B, Helmer-Citterich M. iSPOT: A web tool to infer the interaction specificity of families of protein modules. Nucleic Acids Res. 2003 Jul 1;31(13):3709-11. PubMed PMID: 12824399; PubMed Central PMCID: PMC168998.

3: Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Küster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. 2003 Jul 1;31(13):3625-30. PubMed PMID: 12824381; PubMed Central PMCID: PMC168952.

2: Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. MINT: a Molecular INTeraction database. FEBS Lett. 2002 Feb 20;513(1):135-40. Review. PubMed PMID: 11911893.

1: Politou AS, Spadaccini R, Joseph C, Brannetti B, Guerrini R, Helmer-Citterich M, Salvadori S, Temussi PA, Pastore A. The SH3 domain of nebulin binds selectively to type II peptides: theoretical prediction and experimental validation. J Mol Biol. 2002 Feb 15;316(2):305-15. PubMed PMID: 11851340.