68) Vecchione L, Diano L, Campagnolo L, Rocchi L, Ferre' F, Mehta JL, Novelli G, Amati F. (2012). Functional characterization and expression analysis of novel alternative splicing isoforms of Olr1 gene during mouse embryogenesis. Gene. 491:5-12. Epub 2011 Oct 2. .

67) Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Spath GF, Zilberstein D, Helmer-Citterich M. (2011). PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae. BMC Genomics. 12:614. [Epub ahead of print] .

66) Parca L, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M (2011). Phosfinder: a web server for the identification of phosphate binding sites on protein structures. Nucl. Acids Res. 39(Web Server issue):W278-282. May 26. [Epub ahead of print] .

65) Schmidt-Arras,D., Leclercq, O., Gherardini, P.F., Helmer-Citterich, M., Faigle, W., Loew, D., Spaeth, G. (2011). Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani. J Proteomics, 74(9):1644-1651. Mar 26. [Epub ahead of print]. .

64) Via, A., Diella, F., Gibson, TJ., Helmer-Citterich, M. (2011). From sequence to structural analysis in protein phosphorylation motifs. Frontiers in Bioscience, 16: 1261-1275 .

63) Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A (2011). Phospho3D 2.0: An enhanced database of three-dimensional structures of phosphorylation sites. Nucl. Acids Res., 39 (Database issue): D268-71. Epub 2010 Oct 21 .

62) Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G (2010). Phosphate binding-sites identification in protein structures. Nucl. Acids Res., Oct 24. [Epub ahead of print] .

61) Gherardini, PF, Ausiello, A, Helmer-Citterich, M. (2010). Superpose3D: a local structural comparison program that allows for user-defined structure representations. PLoS One, 5(8): e11988 .

60) Hem, S, Gherardini, PF, Fortea, JO, Hourdel, V, Morales, MA, Watanabe, R, Pescher, P, Kuzyk, MA, Smith, D, Borchers, CH, Zilberstein, D, Helmer-Citterich, M, Namane, A, Spaeth GF (2010). Identification of Leishmania-specific protein phosphorylation sites by LC-MS/MS and comparative genomics analyses. Proteomics, 21: 3868-6883. .

59) 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, Spaeth GF (2010). Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite differentiation, proliferation, and viability. PLoS Negl Trop Dis., 4(6):e729 .

58) Gherardini, PF, Ausiello, G, Russell, RB, Helmer-Citterich, M (2010). Modular architecture of nucleotide binding pockets. Nucl. Acids Res., 38: 3809-3816. [Epub 2010 Feb 25] .

57) Gould, C., Diella, F., Via, A., Puntervoll, P., Gemuend, C., Michael, S., Sayadi, A., Bryne, JC., Chica, C., Davey, N., Haslam, N., Budd, A., Hughes, T., Pas, J., Rychlewski, L., Trave', G., Aasland, R., Helmer-Citterich, M., Linding, R., Gibson, TJ. (2010) ELM: The status of the 2010 Eukaryotic Linear Motif Resource. Nucl. Acids Res., 38(Database issue):D167-180. Epub 2009 Nov 17 .

56) Via, A., Gould, C.M., Gemuend, C., Gibson, TJ, Helmer-Citterich, M. (2009) A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinformatics, 10(1):351 .

55) Ausiello, G., Gherardini, P.F., Gatti, E., Incani, O., Helmer-Citterich, M. (2009). Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics, 10:182 .

54) Gherardini P.F., Helmer-Citterich M. (2008) Structure-based function prediction: approaches and applications. Briefings in Proteomics and Functional Genomics, 7:291-302 .

53) Ausiello G., Gherardini P.F., Marcatili P., Tramontano A., , Via A., Helmer-Citterich M. (2008) FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics, 9, Suppl.2: S2.

52) Gherardini P.F., Wass M.N., Helmer-Citterich M., Sternberg M.E. (2007) Convergent evolution of enzyme active sites is not a rare phenomenon. J. Mol. Biol., 372: 817-845.

51) Via A., Peluso D., Gherardini P.F., de Rinaldis E., Colombo T., Ausiello G., Helmer-Citterich M. (2007) 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucleic Acid Res. 35(Web Server issue):W416-419.

50) Ferraro E., Peluso D., Via A., Ausiello G., Helmer-Citterich M. (2007) SH3-Hunter: discovery of SH3 domain interaction sites in proteins. Nucleic Acid Res. 35(Web Server issue):W451-454.

49) Ausiello G., Peluso D., Via A. and Helmer-Citterich M. (2007) Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinformatics, 8(Suppl.1): S24.

48) Casadio R., Helmer-Citterich M., Pesole G. (2007). Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics, 8 (Suppl.1): S1.

47) Via A., Gherardini F., Ferraro E., Ausiello G., Scalia Tomba G. and Helmer-Citterich M. (2007) False occurrences of functional motifs in protein sequences highlight evolutionary constraints. BMC Bioinformatics. Mar 1;8(1):68 [Epub ahead of print].

46) Zanzoni A., Ausiello G., Via A.,Gherardini P.F., Helmer-Citterich M. (2007) Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Res.Jan; 35(Database issue):D229-31.

45) Ferraro E., Via A., Ausiello G., Helmer-Citterich M. (2006) A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity. Bioinformatics. 22(19):2333-2339.

44) Ausiello G., Via A., Helmer-Citterich M. (2005) Query3d: a new method for high-throughput analysis of functional residuesin protein structures. BMC Bioinformatics. Dec 1;6 Suppl 4:S5.

43) Ferraro E., Via A., Ausiello G., Helmer-Citterich M. (2005) A neural strategy for the inference of SH3 domain-peptide interactionspecificity. BMC Bioinformatics. Dec 1;6 Suppl 4:S13.

42) Helmer-Citterich M., Casadio R., Guffanti A., Mauri G., Milanesi L., Pesole G., Valle, G., Saccone, C. (2005). Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society. BMC Bioinformatics, 6(Suppl 4):S1.

41) Ferre' F., Ausiello G., Zanzoni A., Helmer-Citterich M. (2005) Functional annotation by identification of local surfacesimilarities: a novel tool for structural genomics. BMC Bioinformatics. Aug 2;6(1):194

40) Ausiello G., Zanzoni A., Peluso D., ViaA., Helmer-Citterich M. (2005) pdbFun: mass selection and fastcomparison of annotated PDB residues. Nucleic Acids Res., Jul 1;33(WebServer issue):W133-7.

39) Via A., Zanzoni A., Helmer-Citterich M. (2005) Seq2Struct: aresource for establishing sequence-structure links.Bioinformatics. 21(4):551-3.

38) Diella F., Cameron S., Gemund C., Linding R., Via A., KusterB., Sicheritz-Ponten T., Blom N., Gibson T.J. (2004) Phospho.ELM: A databaseof experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics. 5:79.

37) Via A., Helmer-Citterich M. (2004) A structural studyfor the optimisation of functional motifs encoded in protein sequences. BMCBioinformatics. 2004 Apr 30;5(1):50.

36) Ferre' F., Ausiello G., Zanzoni A.,Helmer-Citterich M. (2004) SURFACE: a database of protein surface regions forfunctional annotation. Nucleic Acids Res., Jan 1;32(1);D240-244.

35) Cesareni G., Helmer-Citterich M. (2003) Searching the MINT database for protein interaction information. Curr Protoc Bioinformatics, Chapter 8:Unit 8.5. John Wiley & Sons, Inc.

34) Ferre' F., Via A., Ausiello G., Brannetti B., Zanzoni A., Helmer-Citterich M. (2003) Development ofcomputational tools for the inference of protein interaction specificityrules and functional annotation using structural information. Comparativeand Functional Genomics, Aug 1;4:416-419. [Abstract]

33) Brannetti B., Helmer-Citterich M. (2003) iSPOT: a webtool to infer the interaction specificity of families of protein modules.Nucleic Acids Res. Jul 1;31(13):3709-11.

32)Puntervoll P., Linding R., Gemund C., Chabanis-Davidson S.,Mattingsdal M., Cameron S., Martin D.M., Ausiello G., Brannetti B., CostantiniA.,Ferre' F., Maselli V., Via A., Cesareni G., Diella F., Superti-FurgaG., Wyrwicz L.,Ramu C., McGuigan C., Gudavalli R., Letunic I., Bork P., Rychlewski L., Kuster B.,Helmer-Citterich M., Hunter W.N., Aasland R., Gibson T.J. (2003) ELM server: anew resource for investigating short functional sites in modular eukaryoticproteins.Nucleic Acids Res. Jul 1;31(13):3625-30.

31) Politou A.S., Spadaccini R., Joseph C., Brannetti B., Guerrini R.,Helmer-Citterich M., Salvadori S., Temussi P.A. and Pastore A. (2002). The SH3domain of nebulin binds selectively to type II peptides: theoreticalprediction and experimental validation. J.Mol.Biol., 316(2):305-15.

30) Zanzoni, A., Montecchi-Palazzi,L., Quondam, M., Ausiello, G., Helmer-Citterich, M. and Cesareni,G. (2002) MINT: a Molecular INTeraction database. FEBS Letters, 513(1);135-140. [Abstract]

29) Tong A.H., Drees B., Nardelli G., Bader G.D., Brannetti B., Castagnoli L., Evangelista M., Ferracuti S., Nelson B., Paoluzi S., Quondam M., Zucconi A.,Hogue C.W., Fields S., Boone C. and Cesareni G. (2002). A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.Science, 295(5553):321-4

28) Brannetti B., Zanzoni A.,Montecchi-Palazzi L., Cesareni G. and Helmer-Citterich M. (2001).iSPOT: a web tool for the analysis and recognition of protein domain specificity. Comparative and Functional Genomics,2:314-318. [Abstract]

27) Vaccaro P., Brannetti B.,Montecchi-Palazzi L., Helmer-Citterich M., Cesareni G. and DenteL. (2001). Distinct Binding Specificity of hINADL PDZ Domains. J Biol Chem,276(45):42122-30.

26) Citarella F., Velthuis H.,Helmer-Citterich M. and Hack C.E. (2000). Identification of a binding sitefor negatively charged surfaces in the fibronectin type II domain of humanfactor XII: an immunochemical and homology modeling approach. Thrombosisand Haemostasis, 84:1057-1065.

25) Via A., Ferre' F., Brannetti B. and Helmer-Citterich M. (2000) Protein surface similarities:a survey of methods to describe and compare protein surfaces. Cell. Mol.LifeSci., 57, 1970-1977.

24) Via A., Ferre' F., Brannetti B., Valencia A. and Helmer-Citterich M. (2000). 3D view of thesurface motif associated to the Ploop structure: cis and transcases of convergent evolution. J.Mol.Biol., 303, 455-465.

23) Brannetti B., Via A., Cestra G., Cesareni G. and Helmer-Citterich M. SH3-SPOT (2000): an algorithmto predict preferred ligands of different members of the SH3 gene family.J.Mol.Biol, 298, 313-328.

22) De Rinaldis M., Ausiello G.,Cesareni G. and Helmer-Citterich M. (1998) Three-dimensional profiles:a new tool to identify protein surface similarities.  J.Mol.Biol.,284,1211-1221.

21) Soucek L., Helmer-Citterich M., Sacco A., Jucker R., Cesareni G. and Nasi S. (1998) Designand properties of a Myc derivative that efficiently homodimerizes. Oncogene,17:2463-2472.

20) Murali R., Helmer-Citterich M., Sharkey D.J., Scalice E., Daiss J. and Murthy K. (1998) Structuralstudies on a inhibitory antibody against Thermus aquaticus DNA polymerasesuggest mode of inhibition. Prot. Eng., 11(2):79-86.

19) Quondam M., Barbato C., Pickford A.,Helmer-Citterich M. and Macino G. (1997) Structural conservation in prenyltransferases:structural analysis and modeling of Neurospora crassa geranylgeranylpyrophosphate synthase. Prot. Eng., 10, 1047-1055.

18) Pazos F., Helmer-Citterich M.,Ausiello G. and Valencia A. (1997).Protein docking with sequences. Correlatedmutations contain information about protein-protein interaction. J.Mol.Biol.,271, 511-523.

17) Ausiello G., Cesareni G. andHelmer-Citterich M. (1997). ESCHER: a new docking procedure applied to thereconstruction of protein tertiary structure. Proteins, 28, 556-567.

16) Zappavigna V., Falciola L.,Helmer-Citterich M., Mavilio F. and Bianchi M.E. (1996) HMG1 cooperates withHOX proteins in DNA binding and transcriptional activation. EMBO Journal,15, 4981 - 4991.

15) Sinclair J., Park J., Helmer-Citterich M.and Sippl M. (1995). Frontiers of protein structure prediction: Group 4 Report. http://www.mrc-cpe.cam.ac.uk/irbm-course95/reports

14) Hubbard T., Tramontano A., Barton G.,Jones D., Sippl M., Valencia A., Lesk A., Moult J., Rost B., Sander C.,Schneider R., Lahm A., Leplae R., Buta C., Eisenstein M., Fjellstörm,O.,Floeckner H., Grossman G., Hansen J., Helmer-Citterich M., Joergensen F.S.,Marchler-Bauer A., Osuna J., Park J., Reinhardt A., Ribas de Pouplana L.,Rojo-Dominguez A., Saudek V., Sinclair J., Sturrock S., Venclovas C., Vinals C.(1996). Update on protein structure prediction: results of the IRBM 1995workshop. Folding and Design, 1, 55-63.

13) Cesareni G., Minenkova O., Dente L.,Iannolo G., Zucconi A., Helmer-Citterich M., Lanfrancotti, A., Castagnoli,L.and Vetriani,C. (1995). Phage display of peptide libraries: Structuraland functional constraints in the display of peptides on filamentous phagecapsids. in Combinatorial Libraries: Synthesis, screening and applicationpotential. Cortese,R. ed., de Gruyter.

12) Helmer-Citterich M.,Rovida E., Luzzago A. and Tramontano A. (1995). Modelling antibody antigeninteractions: ferritin as a case study. Molecular Immunology, 32, 1001-1010.

11) Helmer-Citterich M. andTramontano A. (1994). PUZZLE: a new method for automated protein dockingbased on surface shape complementarity. J.Mol.Biol., 235, 1021-1031.

10) Marvin D.A., Hale R.D., Nave C.and Helmer-Citterich M. (1994). Molecular models and structuralcomparisons of native and mutant class I filamentous bacteriophages Ff(fd, f1, M13), If1 and IKe. J.Mol.Biol., 235, 260-286.

9) Cesareni G., Helmer-Citterich M. and Castagnoli L. (1991). Control of ColE1 replication by antisenseRNA. TIG, 7, 230-235.

8) Cesareni G., Castagnoli L.,Felici F., Helmer-Citterich M., Jappelli , R., Tataseo, P., Gonfloni,S. and Musacchio, A. (1990) Protein vectors and oligopeptide librariesfor the selection of clones with specific binding properties. In RecombinantDNA technologies in Industry and Agriculture: state of the art in Italy.Amaldi, F., De Felice, M., Di Fonzo, N., Merlin, P., Polsinelli, M. andViotti, A. ed., pg.332-339.

7) Helmer-Citterich M. (1988). Il presunto secondo codice. Sapere, 8/9, 79-84.

6) Helmer-Citterich M., Anceschi M.,Banner D.W. and Cesareni G. (1988). Control of ColE1 replication: Low affinityspecific binding of Rop to RNAI and RNAII. EMBO Journal, 2, 557-566

5) Cesareni G., Anceschi M., Castagnoli L.,Felici F., Helmer-Citterich M., Hughes J., Kirk D., Murray J., Rossi N.,Scarpa M. and Spinelli L.(1986). E.coli plasmid stability and controlof copy number. Fifth International Symposium on the Genetics of IndustrialMicroorganisms, 1986, M.Alacevic, D.Hranueli, Z.Toman (eds);

4) Burger G., Helmer-Citterich M.,Nelson M.A., Werner S. and Macino G. (1985).  RNA processing in Neurosporacrassa mitochondria: transfer RNAs punctuate a large precursor transcript.EMBO Journal, 4,197-204.

3) Macino G., Helmer-Citterich M.,Morelli G. and Nelson M.A. (1984). The ATPase subunit 6 and 8 genes ofNeurosporacrassa mitochondria. in "H-ATP synthase: structure, function, regulation"ed: S.Papa, K.Altendorf, L.Ernster, L.Packer - ICSU Press and AdriaticaEditrice.

2) Helmer-Citterich M., Morelli G.and Macino G. (1983). Nucleotide sequence and intron structure of the apocytochromebgene of Neurospora crassa mitochondria. EMBO Journal, 8,1235-1242.

1) Helmer-Citterich M.,Morelli G., Nelson M.A. and Macino G. (1983). Expression of split genesof the Neurospora crassa mitochondrial genome.  in "Mitochondria1983", ed.R.J. Schweyen, K.Wolf, F.Kaudewitz, 357-369.;

Centro di Bioinformatica Molecolare - Università di Roma - Tor Vergata

Last update: 26/9/2011