Publications, Books, Book chapters, others...




- Parca L, Ariano B, Cabibbo A, Paoletti M, Tamburrini A, Palmeri A, Ausiello G, Helmer-Citterich M. (2018). Kinome-wide identification of phosphorylation networks in Eukaryotic proteomes. Bioinformatics. [Epub ahead of print] (free full-text)


- Pietrosanto M, Adinolfi M, Casula R, Ausiello G, Ferrè F, Helmer-Citterich M. (2017). BEAM web server: A tool for structural RNA motif discovery. Bioinformatics. [Epub ahead of print] (free full-text)


- El Hachem M, Fortugno P, Palmeri A, Helmer-Citterich M, Diociaiuti A, Proto V, Boldrini R, Zambruno G, Castiglia D (2016). Structural Defects of Laminin β3 N-terminus Underlie Junctional Epidermolysis Bullosa with Altered Granulation Tissue Response. Acta Derm Venereol,  in press. (free full-text)


- Pietrosanto M, Mattei E, Helmer-Citterich M, Ferrè F. (2016). A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications. Nucleic Acids Res. 44(18):8600-8609. (free-full-text)


- Mongiardi MP, Savino M, Falchetti ML, Illi B, Bozzo F, Valle C, Helmer-Citterich M, Ferrè F, Nasi S, Levi A. (2016). c-MYC inhibition impairs hypoxia response in glioblastoma multiforme. Oncotarget, doi:10.18632/oncotarget.8921. [Epub ahead of print] PMID: 27119353.


- Tabolacci E, Mancano G, Lanni S, Palumbo F, Goracci M, Ferrè F, Helmer-Citterich M, Neri G. (2016). 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. (free full-text)


- 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 Mar 25;80(4):938-49.


- 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. (2015). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. [Epub ahead of print] PubMed PMID: 26538599. (free full-text)


- Morini E, Rizzacasa B, Pucci S, Polidoro C, Ferrè F, Caporossi D, Helmer-Citterich M, Novelli G, Amati F. (2015). The human rs1050286 polymorphism alters LOX-1 expression through modifying miR-24 binding. J Cell Mol Med., 20(1):181-187 PubMed PMID: 26542080. (free full-text)


- 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. (2015). Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling. Cell, pii: S0092-8674(15)01108-3.


- Ferrè F, Colantoni A, Helmer-Citterich M. (2015). Revealing protein-lncRNA interaction. Brief Bioinform., pii: bbv031. [Epub ahead of print] (free full-text)


- Mattei E, Pietrosanto M, Ferrè F, Helmer-Citterich M. (2015). Web-Beagle: a web server for the alignment of RNA secondary structures. Nucleic Acids Res., pii: gkv489. (free full-text)


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


- 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, Gretzmeier C, Helmer-Citterich M, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, and Cecconi F. (2015). AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-MYC dephosphorylation and degradation. Nature Cell Biology, 17:20-30.


- Palmeri A, Ferrè F, Helmer-Citterich M. (2014). Exploiting holistic approaches to model specificity in protein phosphorylation. Front Genet. 5:315 (free full-text)


- Ferrè F, Palmeri A, Helmer-Citterich M. (2014). Computational methods for analysis and inference of kinase/inhibitor relationships. Front Genet. 5:196 (free full-text).


- Palmeri A, Helmer-Citterich M, Gherardini PF (2014). A proteome-wide domain-centric perspective on protein phosphorylation. Mol. Cell. proteomics:13,9; 2198-2212 (free full-text).


- Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M. (2014). A novel approach to represent and compare RNA secondary structures. Nucleic Acids Res. 2014 Apr 21. [Epub ahead of print] (free full-text).


- Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Myler PJ, Zilberstein D. (2014) Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends. Mol. Cell. Proteomics, 13:1787-1799.  (free full-text).


- Lanni S, Goracci M, Borrelli L, Mancano G, Chiurazzi P, Moscato U, Ferre' F, Helmer-Citterich M, Tabolacci E, Neri G. (2013). Role of CTCF Protein in Regulating FMR1 Locus Transcription. PLoS Genet. 2013 Jul;9(7):e1003601. (free full-test)


- Bianchi V, Colantoni A, Calderone A, Ausiello G, Ferre' F, Helmer-Citterich M. (2013). DBATE: DataBase of Alternative Transcripts Expression. Database, 2013:bat050. (free full-text)


- Colantoni A, Bianchi V, Gherardini PF, Scalia Tomba G, Ausiello G, Helmer-Citterich M, Ferre' F. (2013). Alternative splicing tends to avoid partial removals of protein-protein interaction sites. BMC Genomics, 14:379. (free full-text)


- Parca L, Ferre' F, Ausiello G, Helmer Citterich M. Nucleos: a web server for the identification of nucleotide-binding sites in protein structures. Nucl Acids Res 2013 May 22. [Epub ahead of print] PubMed PMID: 23703207 (free full-text).


- Bianchi V, Mangone I, Ferre' F, Helmer-Citterich M, Ausiello G. The webPDBinder server for the identification of ligand binding sites on protein structures. Nucl Acids Res 2013 Jun 3. [Epub ahead of print] PubMed PMID: 23737450 (free full-text).


- Tsigankov P, Gherardini PF, Helmer Citterich M, Spaeth GF, Zilberstein D. (2013). Phosphoproteomic analysis of differentiating Leishmania parasites reveals unique stage-specific phosphorylation motif. J Proteome Res., 12:3405-3412.


- Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Spaeth GF. (2013). Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound. J Proteomics., 86:97-104.


- Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G. (2013). Exploring the diversity of SPRY/B30.2-mediated interactions. TiBS, 38(1):38-46. (abstract)


- Tuppo L, Alessandri C, Pomponi D, Picone D, Tamburrini M, Ferrara R, Petriccione M, Mangone I, Palazzo P, Liso M, Giangrieco I, Crescenzo R, Bernardi ML, Zennaro D, Helmer-Citterich M, Mari A, Ciardiello MA. (2013). Peamaclein - A new peach allergenic protein: similarities, differences and misleading features compared to Pru p 3. Clinical And Experimental Allergy, 43(1):128-140. (abstract)


- Gherardini PF, Helmer-Citterich M. (2012). Experimental and computational methods for the analysis and modeling of signaling networks. N. Biotechnol, S1871-6784(12)00864-3. (abstract)


- Parca L, Gherardini PF, Truglio M, Mangone I, Ferre' F, Helmer-Citterich M, Ausiello G. (2012). Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PLoS One, 7(11):e50240. (free full-text)


- Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini A, Castagnoli L, Cesareni C. Mapping the human phosphatome on growth pathways. Mol. Syst. Biol., 8:603. (free full-text)


- Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P (2012). Deciphering a global network of functionally associated post-translational modifications. Mol. Syst. Biol, 8:599. (free full-text)


- Giaco' L, Amicosante M, Fraziano M, Gherardini PF, Ausiello G, Helmer-Citterich M, Colizzi V, Cabibbo A. (2012). B-Pred, a structure based B-cell epitopes prediction server. Adv Appl Bioinform Chem, 5:11-21. (free-full-text)


- Fioravanti F, Helmer-Citterich M, Nardelli E. (2012). Modeling Gene Regulatory Network Motifs using Statecharts. BMC Bioinformatics, 13(Suppl 4):S20. (free full-text).


- Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G. (2012). Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. BMC Bioinformatics, 13(Suppl 4):S17. (free full-text).


- Tsigankov P, Gherardini PF, Helmer-Citterich M, Zilberstein D. (2012) What have proteomics taught us about Leishmania development inside its host? Parasitology, 28:1-12.


- Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Spaeth GF, Zilberstein D, Helmer-Citterich M. (2011). PhosTryp: a phosphorylation sites predictor specific for parasitic protozoa of the family trypanosomatidae. BMC Genomics, 12:614. (abstract, free full-text).


- 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]. (free full-text)


- 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].


- 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 (free full-text).


- 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 (free full-text).


- Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G (2010). Phosphate binding-sites identification in protein structures. Nucl. Acids Res., 39(4):1231-1242. Oct 24. [Epub ahead of print] (free full-text).


- 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 (free full-text).


- 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.


- 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 (free full-text).


- 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] (free full-text).


- 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 (free full-text).


- 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 (free full-text).


- 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 (free full-text).highlyaccessed-large


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

- 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): S1 (free full-text).

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

- Ferraro, E., Peluso, D., Via, A., Ausiello, G., Helmer-Citterich, M. (2007) SH3-Hunter: discovery of SH3 domain interaction sites in proteins. Nucl. Acids Res., 35:W451-454 (free full-text).

- 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. Nucl. Acids Res., 35:W416-419 (free full-text).

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

- Via, A., Gherardini, P.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, 8:68 (free-fulltext).

- Zanzoni, A., Ausiello, G., Via, A., Gherardini, P.F., Helmer-Citterich, M. (2007). Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucl. Acids Res., 35:D229-D231 (free full-text).

- 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, 22:2333-2339.

- Ferraro, E., Via, A., Ausiello, G., Helmer-Citterich, M. (2005).
A neural strategy for the inference of SH3 domain-peptide interaction specificity. BMC Bioinformatics, 6(Suppl 4):S13 (free full-text).

- Ausiello, G., Via, A., Helmer-Citterich, M. (2005). Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics, 6(Suppl 4):S5 (free full-text).

- Ferre', F., Ausiello, G., Zanzoni, A., Helmer-Citterich, M. (2005). Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinformatics, 6:19. (free full-text)

- Ausiello, G., Zanzoni, A., Peluso, D., Via, A., Helmer-Citterich, M. (2005) pdbFun: Mass selection and fast comparison of annotated PDB residues. Nucl.Acids Res., 33:133-137. (free full-text)

- Via, A., Zanzoni, A., Helmer-Citterich, M (2005). Seq2Struct: a resource for establishing sequence-structure links. Bioinformatics, 21:551-552. Epub 2004 Sep 28.

- Via, A, Helmer-Citterich, M (2004). A structural study for the optimisation of functional motifs encoded in protein sequences BMC Bioinformatics, 5, 50. (abstract, free full-text)

- Ferre', F., Ausiello, G., Zanzoni, A., Helmer-Citterich, M. (2004). SURFACE: a database of protein surface regions for functional annotation (abstract, freefull-text). Nucl.Acids Res., 32, 240-244.

- Ferre', F., Via, A., Ausiello, G., Brannetti, B., Zanzoni, A., Helmer-Citterich, M. (2003).
Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information. Comparative and Functional Genomics, 4, 416-419 . (abstract)

- 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.

- Brannetti, B., Helmer-Citterich, M. (2003) iSPOT: a web tool to infer the interaction specificity of families of protein modules. (abstract, free full-text) Nucl. Acids Res., 31: 3709-3711.

- Puntervoll, P., Linding, R., Gemuend, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D.M.A., Ausiello, G., Brannetti, B., Costantini, A., Ferre', F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P., Rychlewski, Kuester, B., Helmer-Citterich, M., Hunter, W.N., Aasland, R. and Gibson, T. (2003) ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. (abstract, free full-text) Nucl. Acids Res., 31: 3625-3630

- Politou, A.S., Spadaccini, R., Joseph, C., Brannetti, B., Guerrini, R., Helmer-Citterich, M., Salvadori, S., Temussi, P.A. and Pastore, A. (2002). The SH3 domain of nebulin binds selectively to type II peptides: theoretical prediction and experimental validation.
J Mol Biol. 316:305-315. (abstract)


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


- 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.


- Vaccaro, P., Brannetti, B., Montecchi Palazzi, L., Philipp, S., Helmer Citterich, M., Cesareni, G. and Dente, L. (2001). Distinct binding specificity of the multiple PDZ domains of the human INADL, a human protein with homology to INAD from Drosophila melanogaster. (abstract, free full-text) J.Biol.Chem., 276, 42122-42130.


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


- 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.Life Sci., 57, 1970-1977. (abstract)


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


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


- 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. (abstract)


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


- Murali, R., Helmer Citterich, M., Sharkey, D.J., Scalice, E., Daiss, J. and Murthy, K. (1998) Structural studies on a inhibitory antibody against Thermus aquaticus DNA polymerase suggest mode of inhibition. (abstract, full-text) Prot. Eng., 11(2):79-86.


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


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


- Ausiello,G., Cesareni,G. and Helmer Citterich,M. (1997). ESCHER: a new docking procedure applied to the reconstruction of protein tertiary structure. Proteins, 28, 556-567. (abstract)


- Zappavigna,V., Falciola,L., Helmer Citterich,M., Mavilio,F. and Bianchi,M.E. (1996) HMG1 cooperates with HOX proteins in DNA binding and transcriptional activation. EMBO Journal, 15, 4981 - 4991.  (abstract, free full-text)


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


- Helmer Citterich,M. and Tramontano,A. (1994). PUZZLE: a new method for automated protein docking based on surface shape complementarity. J.Mol.Biol., 235, 1021-1031. (abstract)


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


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


- Helmer Citterich,M., Anceschi,M., Banner,D.W. and Cesareni,G. (1988). Control of ColE1 replication: Low affinity specific binding of Rop to RNAI and RNAII. EMBO Journal, 7, 557-566. (abstract, free full-text)


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


- Helmer Citterich,M., Morelli,G. and Macino,G. (1983). Nucleotide sequence and intron structure of the apocytochrome b gene of Neurospora crassa mitochondria. EMBO Journal, 2,1235-1242. (abstract, free full-text)




Helmer Citterich M, Ferrè F, Pavesi G, Romualdi C, Pesole G (2018) Fondamenti di Bioinformatica – ed Zanichelli


Valle, G., Helmer-Citterich, M., Attimonelli, M., Pesole, G. (2003) Introduzione alla Bioinformatica - ed. Zanichelli

The Internet for Cell and Molecular Biologists - ed. A. Cabibbo, R.P. Grant, M. Helmer-Citterich, Horizon Scientific Press, 368 pages, Publication date: April 2002 ISBN: 1-898486-32-8 (hbk).


Books chapters

- 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: Structural and functional constraints in the display of peptides on filamentous phage capsids. in Combinatorial Libraries: Synthesis, screening and application potential. Cortese,R. ed., de Gruyter.

- Pizzi, E., Helmer-Citterich, M., Tramontano, A. (1994). Structural and dynamic models of biomedicl interest. in: A. Colosimo (ed.) Structural and dynamic models of biomedical interest, CISB, Rome.


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


- 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 control of copy number. Fifth International Symposium on the Genetics of Industrial Microorganisms, 1986, M.Alacevic, D.Hranueli, Z.Toman (eds);


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


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






- Facchiano A, Angelini C, Bosotti R, Guffanti A, Marabotti A, Marangoni R, Pascarella S, Romano P, Zanzoni A, Helmer-Citterich M. (2015). Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics.

2015;16 Suppl 9:S1 (free full-text)


- Gissi C, Romano P, Ferro A, Giugno R, Pulvirenti A, Facchiano A, Helmer-Citterich M. (2013). Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics. 2013;14 Suppl 7:S1 (free full-text)


- Romano P, Helmer-Citterich M. (2012). Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of  Bioinformatics. BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:I1 (free full-text)


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


- 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 (free full-text).

- 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., Fjellstr^m,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 1995 workshop. Folding and Design, 1, 55-63.

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