Consiglio Nazionale delle Ricerche

Institute of Food Science

Bioinformatics Laboratory

 

GROUP  RESULTS
 
 
         

 

 

Here you can find the list (in reverse date order) of publications of our Laboratory, from the start of its activities (2001) up today.

 

 
 
  • Scafuri B, Varriale A, Facchiano A, D'Auria S, Raggi ME, Marabotti A. (2017)
    Binding of mycotoxins to proteins involved in neuronal plasticity: a combined in silico/wet investigation.
    Sci Rep. 2017 Nov 9;7(1):15156. doi: 10.1038/s41598-017-15148-4. PMID: 29123130.

  • d'Acierno A, Scafuri B, Facchiano A, Marabotti A. (2017)
    The evolution of a Web resource: The Galactosemia Proteins Database 2.0.
    Hum Mutat. 2017 Sep 29. doi: 10.1002/humu.23346. [Epub ahead of print] PMID: 28961353.

  • D'Arcangelo D, Facchiano A, Facchiano AM. (2017)
    Role of "shared epitope" and other citrullination-sites in rheumatoid arthritis and in melanoma.
    Expert Opin Ther Targets. 2017 Oct;21(10):993-994. doi: 10.1080/14728222.2017.1370776. PMID: 28836878.

  • Gogliettino M, Cocca E, Fusco C, Agrillo B, Riccio A, Balestrieri M, Facchiano A, Pepe A, Palmieri G. (2017)
    Unusual Antioxidant Properties of 26S Proteasome Isolated from Cold-Adapted Organisms.
    Int J Mol Sci. 2017 Jul 25;18(8). pii: E1605. doi: 10.3390/ijms18081605. PMID: 28757562.

  • Buonocore F, Stocchi V, Nunez-Ortiz N, Randelli E, Gerdol M, Pallavicini A, Facchiano A, Bernini C, Guerra L, Scapigliati G, Picchietti S. (2017)
    Immunoglobulin T from sea bass (Dicentrarchus labrax L.): molecular characterization, tissue localization and expression after nodavirus infection.
    BMC Mol Biol. 2017 Mar 15;18(1):8. doi: 10.1186/s12867-017-0085-0. PMID: 28298204.

  • De Masi L, Castaldo D, Pignone D, Servillo L, Facchiano A. (2017)
    Experimental Evidence and In Silico Identification of Tryptophan Decarboxylase in Citrus Genus.
    Molecules. 2017 Feb 11;22(2). pii: E272. doi: 10.3390/molecules22020272. PMID: 28208655.

  • Cordella M, Tabolacci C, Rossi S, Senatore C, Facchiano AM, D'Arcangelo D, Facchiano A, Facchiano F. (2016)
    Transglutaminase type 2 affects cell migration through post-translational modification of platelet-derived growth factor-BB.
    Amino Acids. 2017 Mar;49(3):473-481. doi: 10.1007/s00726-016-2331-z. Epub 2016 Sep 16. PMID: 27633721

  • D'Arcangelo D, Facchiano F, Nassa G, Stancato A, Antonini A, Rossi S, Senatore C, Cordella M, Tabolacci C, Salvati A, Tarallo R, Weisz A, Facchiano AM, Facchiano A. (2016)
    PDGFR-alpha inhibits melanoma growth via CXCL10/IP-10: a multi-omics approach.
    Oncotarget. 2016 Nov 22;7(47):77257-77275. doi: 10.18632/oncotarget.12629. PMID: 27764787

  • Scafuri B, Marabotti A, Carbone V, Minasi P, Dotolo S, Facchiano A. (2016)
    A theoretical study on predicted protein targets of apple polyphenols and possible mechanisms of chemoprevention in colorectal cancer.
    Sci Rep. 2016 Sep 2;6:32516. doi: 10.1038/srep32516. PMID: 27587238

  • Picart-Palmade L, Chevalier-Lucia D, Lange R, Facchiano A, Pennacchio A, Staiano M, D'Auria S. (2016)
    The fluorescent monomeric protein Kusabira Orange. Pressure effect on its structure and stability.
    Biochemistry and Biophysics Reports 2016, 7, 138-143. doi:10.1016/j.bbrep.2016.06.002

  • Falcigno L, Palmieri G, Balestrieri M, Proroga YTR, Facchiano A, Riccio A, Capuano F, Marrone R, Campanile G, Anastasio A. (2016)
    NMR and computational data of two novel antimicrobial peptides.
    Data in Brief 2016, 8, 562-569. doi:10.1016/j.dib.2016.06.009 PMID: 27508217

  • Ricciardi A, De Filippis F, Zotta T, Facchiano A, Ercolini D, Parente E. (2016)
    Polymorphism of the phosphoserine phosphatase gene in Streptococcus thermophilus and its potential use for typing and monitoring of population diversity.
    Int J Food Microbiol. 2016 Jul 27;236:138-147. doi: 10.1016/j.ijfoodmicro.2016.07.031. PMID: 27497152

  • Palmieri G, Balestrieri M, Proroga YT, Falcigno L, Facchiano A, Riccio A, Capuano F, Marrone R, Neglia G, Anastasio A. (2016)
    New antimicrobial peptides against foodborne pathogens: From in silico design to experimental evidence.
    Food Chem. 2016 Nov 15;211:546-54. doi: 10.1016/j.foodchem.2016.05.100. Epub 2016 May 17. PMID: 27283665

  • Dubey A, Facchiano A, Ramteke PW, Marabotti A. (2016)
    In silico approach to find chymase inhibitors among biogenic compounds.
    Future Med Chem. 2016, 8, 841-851. PMID: 27173139

  • Dubey A, Marabotti A, Ramteke PW, Facchiano A. (2016)
    Interaction of human chymase with ginkgolides, terpene trilactones of Ginkgo biloba investigated by molecular docking simulations.
    Biochem Biophys Res Commun. 2016, 473, 449-454. doi: 10.1016/j.bbrc.2016.03.028. PMID: 26975469

  • Romano P, Profumo A, Rocco M, Mangerini R, Ferri F, Facchiano A. (2016)
    Geena 2, improved automated analysis of MALDI/TOF mass spectra.
    BMC Bioinformatics 2016 Mar 2;17 Suppl 4:61. doi: 10.1186/s12859-016-0911-2. PMID: 26961516

  • Gogliettino M, Balestrieri M, Riccio A, Facchiano A, Fusco C, Cecere Palazzo V, Rossi M, Cocca E, Palmieri G. (2016)
    Uncommon functional properties of the first piscine 26S proteasome from the Antarctic notothenioid Trematomus bernacchii.
    Biosci Rep., 2016. Apr 15;36(2). pii: e00320. DOI: 10.1042/BSR20160022
    PMID: 26933238

  • Scafuri B., Facchiano A., Marabotti A. (2015)
    Inverse docking approaches.
    In: From medicinal chemistry to food science. A transfer of in silico methods applications. P.Cozzini ed., Nova Publisher, New York, USA, 2015, Chapter 5, pp. 81-104.

  • Del Prete E, Dotolo S, Marabotti A, Facchiano A. (2015)
    Basic exploratory proteins analysis with statistical methods applied on structural features.
    In: Mathematical Models in Biology. V.Zazzu et al. (eds.) Springer International Publishing Switzerland 2015. pp. 173-187. DOI 10.1007/978-3-319-23497-7_13.

  • 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 doi: 10.1186/1471-2105-16-S9-S1. PMID: 26050789

  • Riccio A, Gogliettino M, Palmieri G, Balestrieri M, Facchiano A, Rossi M, Palumbo S, Monti G, Cocca E. (2015)
    A New APEH Cluster with Antioxidant Functions in the Antarctic Hemoglobinless Icefish Chionodraco hamatus.
    PLoS One, 2015 May 6;10(5):e0125594. doi: 10.1371/journal.pone.0125594. eCollection 2015. PMID: 25946123

  • Viggiano E, Marabotti A, Burlina AP, Cazzorla C, D'Apice MR, Giordano L, Fasan I, Novelli G, Facchiano A, Burlina AB. (2015)
    Clinical and molecular spectra in galactosemic patients from neonatal screening in northeastern Italy: Structural and functional characterization of new variations in the galactose-1-phosphate uridyltransferase (GALT) gene.
    Gene, 2015, 559 (2), 112- 118. doi: 10.1016/j.gene.2015.01.013. [Epub ahead of print] PMID: 25592817

  • Facchiano AM, Facchiano F, Facchiano A. (2015)
    The role of chemical elements in melanoma.
    New Horizons in Translational Medicine, 2 (3) 73-80. available online 27 Nov 2014. doi:10.1016/j.nhtm.2014.11.056

  • Siciliano RA, Mazzeo MF, Spada V, Facchiano A, d'Acierno A, Stocchero M, De Franciscis P, Colacurci N, Sannolo N, Miraglia N. (2014) Rapid peptidomic profiling of peritoneal fluid by MALDI-TOF mass spectrometry for the identification of biomarkers of endometriosis.
    Gynecol Endocrinol. 2014, Aug 11:1-5. PMID: 25111755

  • d'Acierno A, Facchiano A, Marabotti A. (2014)
    GALT Protein Database: querying structural and functional features of GALT enzyme.
    Hum Mutat. 2014, 35, 1060-1067. doi: 10.1002/humu.22613. [Epub ahead of print] PMID: 24990533

  • Buonocore F, Randelli E, Trisolino P, Facchiano A, de Pascale D, Scapigliati G. (2014)
    Molecular characterization, gene structure and antibacterial activity of a g-type lysozyme from the European sea bass (Dicentrarchus labrax L.).
    Mol Immunol. 2014, 62, 10-18. doi: 10.1016/j.molimm.2014.05.009. PMID: 24929449

  • Gogliettino M, Riccio A, Balestrieri M, Cocca E, Facchiano A, D'Arco TM, Tesoro C, Rossi M, Palmieri G. (2014)
    A novel class of bifunctional Acylpeptide Hydrolases: potential role in the antioxidant defense systems of the Antarctic fish Trematomus bernacchii.
    FEBS J 2014, 281, 401-415. doi: 10.1111/febs.12610. PMID: 24206103

  • 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. doi: 10.1186/1471-2105-14-S7-S1. PMID: 23815154

  • Profumo A, Mangerini R, Rubagotti A, Romano P, Damonte G, Guglielmini P, Facchiano A, Ferri F, Ricci F, Rocco M, Boccardo F. (2013)
    Complement C3f serum levels may predict breast cancer risk in women with gross cystic disease of the breast.
    J Proteomics 2013, 85, 44-52. doi: 10.1016/j.jprot.2013.04.029. PMID: 23639844

  • Garrisi VM, Tommasi S, Facchiano A, Bongarzone I, De Bortoli M, Cremona M, Cafagna V, Abbate I, Tufaro A, Quaranta M, Paradiso A. (2013)
    Proteomic profile in familial breast cancer patients.
    Clin. Biochem. 2013, 46, 259-265. doi: 10.1016/j.clinbiochem.2012.11.003. Epub 2012 Nov 13. PMID: 23159292

  • Facchiano F, D'Arcangelo D, Lentini A, Rossi S, Senatore C, Pannellini T, Tabolacci C, Facchiano AM, Facchiano A, Beninati S. (2013)
    Tissue transglutaminase activity protects from cutaneous melanoma metastatic dissemination: an in vivo study.
    Amino Acids 2013, 44, 53-61. doi: 10.1007/s00726-012-1351-6. Epub 2012 Jul 11. PMID: 22782215

  • Facchiano A, Festa P, Marabotti A, Milanesi L, Musacchia F. (2012)
    Solving biclustering with a GRASP-like metaheuristic: Two case-studies on gene expression analysis.
    Lecture Notes in Computer Science - Lecture Notes in Bioinformatics LNCS-LNBI, 7548, 253-267. DOI 10.1007/978-3-642-35686-5_21

  • Buonocore F, Castro R, Randelli E, Lefranc MP, Six A, Kuhl H, Reinhardt R, Facchiano A, Boudinot P, Scapigliati G. (2012)
    Diversity, Molecular Characterization and Expression of T Cell Receptor in a Teleost Fish, the Sea Bass (Dicentrarchus labrax, L).
    PLoS One 2012;7(10):e47957. doi: 10.1371/journal.pone.0047957. PMID: 23133531

  • Tedeschi F, Di Maro A, Facchiano A, Costantini S, Chambery A, Bruni N, Capuzzi V, Ficca AG, Poerio E. (2012)
    Wheat Subtilisin/Chymotrypsin Inhibitor (WSCI) as a scaffold for novel serine protease inhibitors with a given specificity.
    Mol Biosyst. 2012, 8, 3335-3343. doi: 10.1039/c2mb25320h. PMID: 23090387

  • Boutron A, Marabotti A, Facchiano A, Cheillan D, Zater M, Oliveira C, Costa C, Labrune P, Brivet M; French Galactosemia Working Group.(2012)
    Mutation spectrum in the French cohort of galactosemic patients and structural simulation of 27 novel missense variations.
    Mol Genet Metab. 2012, 107, 438-447. doi: 10.1016/j.ymgme.2012.07.025. PMID: 22944367

  • Tang M, Facchiano A, Rachamadugu R, Calderon F, Mao R, Milanesi L, Marabotti A, Lai K. (2012)
    Correlation assessment among clinical phenotypes, expression analysis and molecular modeling of 14 novel variations in the human galactose-1-phosphate uridylyltransferase gene.
    Hum Mutat. 2012, 33, 1107-1115. doi: 10.1002/humu.22093. PMID: 22461411

  • Salzano M, Marabotti A, Milanesi L, Facchiano A. (2011)
    Human aryl-hydrocarbon receptor and its interaction with dioxin and physiological ligands investigated by molecular modelling and docking simulations.
    Biochem Biophys Res Commun. 2011, 413, 176-181. PMID: 21871440
    Erratum in: Biochem Biophys Res Commun. 2012 Feb 24;418(4):852.

  • Mangerini R, Romano P, Facchiano A, Damonte G, Muselli M, Rocco M, Boccardo F, Profumo A. (2011)
    The application of atmospheric pressure matrix-assisted laser desorption/ionization to the analysis of long-term cryopreserved serum peptidome.
    Anal Biochem. 2011, 417, 174-81. doi: 10.1016/j.ab.2011.06.021. Epub 2011 Jun 22. PMID: 21756868

  • Cacciapuoti G, Marabotti A, Fuccio F, Porcelli M. (2011)
    Unraveling the structural and functional differences between purine nucleoside phosphorylase and 5'-deoxy-5'-methylthioadenosine phosphorylase from the archaeon Pyrococcus furiosus.
    Biochim Biophys Acta 2011, 1814, 1358-66. doi: 10.1016/j.bbapap.2011.06.001. Epub 2011 Jun 13. PMID: 21683167

  • Tarallo R, Bamundo A, Nassa G, Nola E, Paris O, Ambrosino C, Facchiano A, Baumann M, Nyman TA, Weisz A. (2011)
    Identification of proteins associated with ligand-activated estrogen receptor in human breast cancer cell nuclei by tandem affinity purification and nano LC-MS/MS.
    Proteomics 2011, 11, 172-179. PMID: 21182205

  • Costantini S, Facchiano AM, Randelli E, Casani D, Scapigliati G, Buonocore F. (2010)
    3D modelling of three pro-inflammatory molecules in selected fish species.
    Curr. Pharm. Des. 2010, 16, 4203-4212. PMID: 21184658

  • Marabotti A, Facchiano A. (2010)
    Critical assessment of side chain conformation prediction in modelling of single point amino acid mutation.
    Adv Exp Med Biol. 2010, 680, 283-289. PMID: 20865511

  • Marabotti A, Facchiano A. (2010)
    The misuse of terms in scientific literature.
    Bioinformatics, 2010, 26, 2498. PMID: 20696735

  • Paladino A, Colonna G, Facchiano AM, Costantini S. (2010)
    Functional hypothesis on miraculin' sweetness by a molecular dynamics approach.
    Biochem Biophys Res Commun. 2010, 396, 726-730. PMID: 20451498

  • Buonocore F, Randelli E, Facchiano AM, Pallavicini A, Modonut M, Scapigliati G. (2010)
    Molecular and structural characterisation of a macrophage migration inhibitory factor from sea bass (Dicentrarchus labrax L.).
    Vet Immunol Immunopathol. 2010, 136, 297-304. PMID: 20363032

  • Scire' A, Marabotti A, Staiano M, Iozzino L, Luchansky MS, Der BS, Dattelbaum JD, Tanfani F, D'Auria S. (2010)
    Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima. 2. Molecular organization and structural stability.
    Mol Biosyst. 2010, 6, 687-690. PMID: 20237647

  • D'Imperio M, Corte AD, Facchiano A, Di Michele M, Ferrandina G, Donati MB, Rotilio D. (2010)
    Standardized sample preparation phases for a quantitative measurement of plasma peptidome profiling by MALDI-TOF.
    J Proteomics 2010, 73, 1355-1367. PMID: 20227539

  • Facchiano F, Deloye F, Doussau F, Innamorati G, Ashton AC, Dolly JO, Beninati S, Facchiano A, Luini A, Poulain B, Benfenati F. (2010)
    Transglutaminase participates in the blockade of neurotransmitter release by tetanus toxin: evidence for a novel biological function.
    Amino Acids 2010, 39, 257-269. PMID: 20084413

  • Facchiano A, Marabotti A. (2010)
    Analysis of galactosemia-linked mutations of GALT enzyme using a computational biology approach.
    Proteins Eng Des Sel. 2010, 23, 103-113. PMID: 20008339

  • Ceccarelli M, d'Acierno A, Facchiano A. (2009)
    A scale space approach for unsupervised feature selection in mass spectra classification for ovarian cancer detection.
    BMC Bioinformatics 2009 Oct 15;10 Suppl 12:S9. PMID: 19828085

  • D'Auria S, Aurilia V, Marabotti A, Gonnelli M, Strambini G. (2009)
    Structure and Dynamics of Cold-Adapted Enzymes as Investigated by Phosphorescence Spectroscopy and Molecular Dynamics Studies. 2. The Case of an Esterase from Pseudoalteromonas haloplanktis.
    J Phys Chem B. 2009, 113, 13171-178. PMID: 19754077

  • Marchal S, Staiano M, Marabotti A, Vitale A, Varriale A, Lange R, D'Auria S. (2009)
    Pressure Effects on the Structure and Stability of the Hyperthermophilic Trehalose/Maltose-Binding Protein from Thermococcus litoralis.
    J Phys Chem B 2009, 113, 12804-12808. PMID: 19711955

  • Buonocore F, Randelli E, Scala V, Belardinelli MC, Casani D, Facchiano AM, Costantini S, Scapigliati G. (2009)
    Evolution of cell-mediated immune defences: Cloning and structural characterisation of the T cell receptor beta chain from the icefish Chionodraco hamatus (Perciformes: Channichthyidae)
    Italian Journal of Zoology, 2009, 76, 258-268. DOI: 10.1080/11250000802364632

  • Ceccarelli M, d'Acierno A, Facchiano A (2009)
    A machine learning approach to mass spectra classification with unsupervised feature selection.
    In: "Computational Intelligence Methods for Bioinformatics and Biostatistics." F Masulli, R Tagliaferri and GM Verkhiver (Eds.) CINN 2008, LNBI 5488, pp.242-252, 2009. Springer-Verlag Berlin Heidelberg 2009.

  • Faraone D, Aguzzi MS, Toietta G, Facchiano AM, Facchiano F, Magenta A, Martelli F, Truffa S, Cesareo E, Ribatti D, Capogrossi MC, Facchiano A. (2009)
    Platelet-derived growth factor-receptor alpha strongly inhibits melanoma growth in vitro and in vivo.
    Neoplasia 2009, 11, 732-742. PMID: 19649203

  • d'Acierno A, Facchiano A, Marabotti A. (2009)
    GALT Protein Database, a bioinformatics resource for the management and analysis of structural features of a galactosemia-related protein and its mutants.
    Genomics Proteomics Bioinformatics 2009, 7, 71-76. PMID: 19591794

  • Costantini S, Facchiano A. (2009)
    Computational methods for protein structural class prediction.
    In: "Computational Biology: New Research." Editor: Alona S. Russe. Nova Science Publishers, 2009. ISBN: 978-1-60692-040-4. pp.315-340.

  • Scire A, Marabotti A, Staiano M, Briand L, Varriale A, Bertoli E, Tanfani F, D'Auria S. (2009)
    Structure and Stability of a Rat Odorant-Binding Protein: Another Brick in the Wall.
    J Proteome Res. 2009, 8, 4005-4013. PMID: 19537758

  • Costantini S, Facchiano AM. (2009)
    Human Prion Protein Helices: Studying their Stability by Molecular Dynamics Simulations.
    Protein Pept Lett. 2009, 16, 1057-1062. PMID: 19508225

  • Bruni N, Di Maro A, Costantini S, Chambery A, Facchiano AM, Ficca AG, Parente A, Poerio E. (2009)
    Redesigning the reactive site loop of the Wheat Subtilisin/Chymotrypsin Inhibitor (WSCI) by site-directed mutagenesis: a protein-protein interaction study by affinity chromatography and molecular modeling.
    Biochimie 2009, 91, 1112-1122. PMID: 19500644

  • Aurilia V, Rioux-Dube' JF, Marabotti A, Pezolet M, D'Auria S. (2009)
    Structure and Dynamics of Cold-Adapted Enzymes as Investigated by FT-IR Spectroscopy and MD. The Case of an Esterase from Pseudoalteromonas haloplanktis.
    J Phys Chem B. 2009, 113, 7753-7761. PMID: 19435327

  • Camarca A, Anderson RP, Mamone G, Fierro O, Facchiano A, Costantini S, Zanzi D, Sidney J, Auricchio S, Sette A, Troncone R, Gianfrani C. (2009)
    Intestinal T cell responses to gluten peptides are largely heterogeneous: implications for a peptide-based therapy in celiac disease.
    J Immunol. 2009, 182, 4158-4166. PMID: 19299713

  • Marabotti A, Facchiano A,(2009)
    When it comes to homology, bad habits die hard.
    Trends Biochem Sci. 2009, 34, 98-99. PMID: 19181528

  • Santarpia L, Sherman SI, Marabotti A, Clayman GL, El-Naggar AK. (2009)
    Detection and molecular characterization of a novel BRAF activated domain mutation in follicular variant of papillary thyroid carcinoma.
    Hum Pathol. 2009, 40, 827-833. PMID: 19200582

  • Casani D, Randelli E, Costantini S, Facchiano AM, Zou J, Martin S, Secombes CJ, Scapigliati G, Buonocore F.(2009)
    Molecular characterisation and structural analysis of an interferon homologue in sea bass (Dicentrarchus labrax L.).
    Mol Immunol 2009, 46, 943-952. PMID: 18952288

  • Costantini S, Facchiano AM. (2009)
    Prediction of the protein structural class by specific peptide frequencies.
    Biochimie 2009, 91, 226-229. PMID: 18957316

  • Porcelli M, Peluso I, Marabotti A, Facchiano A, Cacciapuoti G. (2009)
    Biochemical characterization and homology modeling of a purine-specific ribonucleoside hydrolase from the archaeon Sulfolobus solfataricus: Insights into mechanisms of protein stabilization.
    Arch Biochem Biophys. 2009, 483, 55-65. PMID: 19121283

  • Di Maro A, Chambery A, Carafa V, Costantini S, Colonna G, Parente A. (2009)
    Structural characterization and comparative modeling of PD-Ls 1-3, type 1 ribosome-inactivating proteins from summer leaves of Phytolacca dioica L.
    Biochimie 2009, 91, 352-363. PMID: 19014994

  • Facchiano A, Facchiano F. (2009)
    Transglutaminases and their substrates in biology and human diseases: 50 years of growing.
    Amino Acids 2009, 36, 599-614. PMID: 18597041

  • Costantini S, Autiero I, Colonna G.(2008)
    On new challange for the Bioinformatics.
    Bioinformation, 2008, 3, 238-239.

  • Costantini S, Colonna G, Facchiano AM. (2008)
    ESBRI: a web server for evaluating salt bridges in proteins.
    Bioinformation, 2008, 3, 137-138. PMID: 19238252

  • Marabotti A. (2008)
    Modeling the Conformation of Side Chains in Proteins: Approaches, Problems and Possible Developments.
    Curr Chem Biol. 2008, 2, 200-214. Abstract

  • Lepretti M, Costantini S, Ammirato G, Giuberti G, Caraglia M, Facchiano AM, Metafora S, Stiuso P. (2008)
    The N-terminal 1-16 peptide derived in vivo from protein seminal vesicle protein IV modulates alpha-thrombin activity: potential clinical implications.
    Exp Mol Med. 2008, 40, 541-549. PMID: 18985012

  • Marabotti A, Scire' A, Staiano M, Crescenzo R, Aurilia V, Tanfani F, D'Auria S. (2008)
    Wild-Type and Mutant Bovine Odorant-Binding Proteins To Probe the Role of the Quaternary Structure Organization in the Protein Thermal Stability.
    J Proteome Res. 2008, 7, 5221-5229. PMID: 19367721 PMID: 18954134

  • Costantini S, Buonocore F, Facchiano AM. (2008)
    Molecular modelling of co-receptor CD8alphaalpha and its complex with MHC class I and T-cell receptor in sea bream (Sparus aurata).
    Fish Shellfish Immunol. 2008, 25, 782-790. PMID: 18951040

  • Scire' A, Marabotti A, Aurilia V, Staiano M, Ringhieri P, Iozzino L, Crescenzo R, Tanfani F, D'Auria S. (2008)
    Molecular strategies for protein stabilization: The case of a trehalose/maltose-binding protein from Thermus thermophilus.
    Proteins 2008, 73, 839-850. PMID: 18506781

  • Mucherino A, Costantini S, di Serafino D, D'Apuzzo M, Facchiano A, Colonna G. (2008)
    Understanding the role of the topology in protein folding by computational inverse folding experiments.
    Comput Biol Chem. 2008, 32, 233-239. PMID: 18479970.

  • Costantini S, Paladino A, Facchiano AM. (2008)
    CALCOM: A software for calculating the center of mass of proteins.
    Bioinformation, 2008, 2, 271-272. PMID: 18478078.

  • Mutarelli M, Cicatiello L, Ferraro L, Grober OM, Ravo M, Facchiano AM, Angelini C, Weisz A. (2008)
    Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells.
    BMC Bioinformatics, 2008, 9, Suppl.2:S12. PMID: 18387200.

  • Buonocore F, Randelli E, Casani D, Guerra L, Picchietti S, Costantini S, Facchiano AM, Zou J, Secombes CJ, Scapigliati G. (2008)
    A CD4 homologue in sea bass (Dicentrarchus labrax): Molecular characterization and structural analysis.
    Mol Immunol. 2008, 45, 3168-3177. PMID: 18403019.

  • Marabotti A, Spyrakis F, Facchiano A, Cozzini P, Alberti S, Kellogg GE, Mozzarelli A. (2008)
    Energy-based prediction of amino acid-nucleotide base recognition.
    J Comput Chem. 2008, 29, 1955-1969. PMID: 18366021.

  • Porcelli M, Concilio L, Peluso I, Marabotti A, Facchiano A, Cacciapuoti G. (2008)
    Pyrimidine-specific ribonucleoside hydrolase from the archaeon Sulfolobus solfataricus- biochemical characterization and homology modeling.
    FEBS J. 2008, 275, 1900-1914. PMID: 18355316.

  • Ravo M, Mutarelli M, Ferraro L, Grober OM, Paris O, Tarallo R, Vigilante A, Cimino D, De Bortoli M, Nola E, Cicatiello L, Weisz A. (2008)
    Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays.
    Lab Invest. 2008 Apr;88(4):430-40. PMID: 18305565

  • Costantini S, Colonna G, Facchiano AM.(2008)
    FASMA: A Service to Format and Analyze Sequences in Multiple Alignments.
    Genomics Proteomics Bioinformatics. 2007, 5, 253-255. PMID: 18267307

  • Marabotti A, Lefevre T, Staiano M, Crescenzo R, Varriale A, Rossi M, Pezolet M, D'Auria S. (2008)
    Mutant bovine odorant-binding protein: Temperature affects the protein stability and dynamics as revealed by infrared spectroscopy and molecular dynamics simulations.
    Proteins. 2008, 72, 769-778. PMID: 18260099

  • D'Auria S, Staiano M, Varriale A, Gonnelli M, Marabotti A, Rossi M, Strambini GB. (2008)
    The Tryptophan Phosphorescence of Porcine and Mutant Bovine Odorant-Binding Proteins: A Probe for the Local Protein Structure and Dynamics.
    J Proteome Res. 2008, 7, 1151-1158. PMID: 18232631

  • Paladino A, Costantini S, Colonna G, Facchiano AM.(2008)
    Molecular modelling of miraculin: Structural analyses and functional hypotheses.
    Biochem Biophys Res Commun. 2008, 367, 26-32. PMID: 18158914.

  • de Maria S, Metafora V, Metafora S, Ravagnan G, Carteni M, Pontoni G, Facchiano A, Lepretti M, Severino B, Caliendo G, Santagada V, Langer I, Robberecht P. (2008)
    Effect of positive charge in VIP (16)gamma-glutamyl diamino derivatives on hVPAC1 and hVPAC2 receptor function.
    J Pept Sci., 2008, 14, 102-109. PMID: 17883247

  • Randelli E, Scala V, Casani D, Costantini S, Facchiano A, Mazzini M, Scapigliati G, Buonocore F. (2008)
    T cell receptor beta chain from sea bream (Sparus aurata): Molecular cloning, expression and modelling of the complexes with MHC class I.
    Mol Immunol. 2008, 45, 2017-2027. PMID: 18035419

  • D'Auria S, Staiano M, Varriale A, Gonnelli M, Marabotti A, Rossi M and Strambini GB. (2008)
    The differences in the microenvironment of the two tryptophan residues of the glutamine-binding protein from E. coli shed light on the binding properties and the structural dynamics of the protein.
    Proteins, 2008, 71, 743-750. PMID: 17979189

  • Stepanenko OV, Marabotti A, Kuznetsova IM, Turoverov KK, Fini C, Varriale A, Staiano M, Rossi M, and D'Auria S. (2008)
    Hydrophobic interactions and ionic networks play an important role in thermal stability and denaturation mechanism of the porcine Odorant-Binding Protein.
    Proteins, 2008, 71, 35-44. PMID: 17918730

  • Angelini C, De Canditiis D, Mutarelli M, Pensky M. (2007)
    A Bayesian approach to estimation and testing in time-course microarray experiments.
    Stat Appl Genet Mol Biol. 2007;6:Article24. PMID: 17910530

  • Staiano M, D'Auria S, Varriale A, Rossi M, Marabotti A, Fini C, Stepanenko OV, Kuznetsova IM, Turoverov KK. (2007)
    Stability and Dynamics of the Porcine Odorant-Binding Protein.
    Biochemistry, 2007, 46, 11120-11127. PMID: 17845011

  • Costantini S, Colonna G, Facchiano A. (2007)
    PreSSAPro: a software for the prediction of secondary structure by amino acid properties.
    Comput Biol Chem., 2007, 31, 389-392. PMID: 17888742

  • Gianfrani C, Siciliano R, Facchiano AM, Camarca A, Mazzeo FM, Costantini S, Savati VM, Maurano F, Mazzarella G, Iaquinto G, Bergamo P, Rossi M. (2007)
    Transamidation of wheat flour inhibitsthe response to gliadin of intestinal T cells in celiac disease.
    Gastroenterology 2007, 133, 780-789. PMID: 17678925

  • Buonocore F, Randelli E, Bird S, Secombes CJ, Facchiano A, Costantini S, Scapigliati G. (2007)
    Interleukin-10 expression by real-time PCR and homology modelling analysis in the European sea bass (Dicentrarchu Labrax L.).
    Aquaculture 2007, 270, 512-522. Abstract

  • Costantini S, Colonna G, Facchiano AM (2007)
    Simulation of conformational changes occurring when a protein interacts with its receptor.
    Comput Biol Chem. 2007, 31, 196-206. PMID: 17500035

  • Buonocore F, Randelli E, Casani D, Costantini S, Facchiano A, Scapigliati G, Stet RJ. (2007)
    Molecular cloning, differential expression and 3D structural analysis of the MHC class-II beta chain from sea bass (Dicentrarchus labrax L.).
    Fish Shelfish Immunol. 2007, 23, 853-866. PMID: 17493833

  • Fessas D, Staiano M, Barbiroli A, Marabotti A, Schiraldi A, Varriale A, Rossi M, D'Auria S.(2007)
    Molecular adaptation strategies to high temperature and thermal denaturation mechanism of the D-trehalose/D-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis.
    Proteins: Structure, Function, and Bioinformatics 2007, 67, 1002-1009. PMID: 17373708

  • Cannavo' S, Karl M, Santarpia L, Facchiano A, Marabotti A, Trimarchi F and Benvenga S
    Identification of a novel point mutation in the ligand-binding domain of the human glucocorticoidreceptor (hGR) in a patient with glucocorticoid resistance
    Int J Disabil Human Develop, 2007, 6,105-112.

  • Costantini S, Facchiano AM, Colonna G. (2007)
    Evaluation of the structural quality of modeled proteins by using globularity criteria.
    BMC Struct Biol. 2007, 7:9. PMID: 17346357

  • Ceci G, Mucherino A, D'Apuzzo M, Di Serafino D, Costantini S, Facchiano A, Colonna G. (2007)
    Computational methods for protein fold prediction: an ab-initio topological approach.
    In: Data Mining in Biomedicine, Eds. P.M. Pardalos, V.L. Boginski, A. Vazacopoulos, 2007, Springer. ISBN: 978-0-387-69318-7, pp. 391-430.

  • de Champdore' M, Staiano M, Marabotti A, Facchiano A, Varriale A, Scognamiglio V, Aquino G, Cocozza I, Vitale A, Ringhieri P, Iozzino L, Parracino A, Aurilia V, Rossi M and D'Auria S. (2007)
    Proteins from Thermophiles for the Design of Advanced Fluorescence Biosensors. Glucose sensing as Model.
    Proceedings of International Symposium on Extremophiles and Their Applications, Vol. 2005 (2007) pp. 302-309.

  • Spyrakis F, Cozzini P,Bertoli C, Marabotti A, Kellogg GE, Mozzarelli A (2007)
    Energetics of the protein-DNA-water interaction.
    BMC Structural Biology, 2007, 7, 4. PMID: 17214883.

  • Ronga L, Palladino P, Costantini S, Facchiano A, Ruvo M, Benedetti E, Ragone R, Rossi F (2007)
    Conformational diseases and structure-toxicity relationships: lessons from prion-derived peptides.
    Current Protein and Peptide Science, 8, 83-90. PMID: 17305562

  • Marabotti A, Colonna G, Facchiano A (2007)
    A new computational strategy to analyze the interactions of ERalpha and ERbeta with different ERE sequences.
    Journal of Computational Chemistry, 28, 1031-1041. PMID: 17269124

  • Chambery A, Pisante M, Di Maro A, Di Zazzo E, Ruvo M, Costantini S, Colonna G and Parente A. (2007)
    Invariant Ser211 is involved in the catalysis of PD-L4, type I RIP from (Phytolacca dioica) leaves.
    Proteins: Structure, Function and Bioinformatics, 67, 209-218. PMID: 17243169

  • Palladino P, Ronga L, Tizzano B, Rossi F, Ragone R, Tancredi T, Saviano G, Facchiano A, Costantini S, Ruvo M, Benedetti E.(2006) Prion Protein Misfolding: Conformational Stability of the alpha2-helix.
    Understanding Biology using Peptides, (Sylvie F. Blondelle, ed.), 2006, American Peptide Symposia, 9, 575-576.

  • Marabotti A, Ausili A, Staiano M, Scire' A, Tanfani F, Parracino A, Varriale A, Rossi M and D'Auria S. (2006)
    Pressure affects the structure and the dynamics of the D-Galactose/D-Glucose-Binding Protein from Escherichia coli by perturbing the C-terminal domain of the protein.
    Biochemistry, 45, 11885-11894. PMID: 17002289

  • Dosi R, Di Maro A, Chambery A, Colonna G, Costantini S, Geraci G, Parente A. (2006)
    Characterization and kinetics studies of water buffalo (Bubalus bubalus) myoglobin.
    Comparative Biochemistry and Physiology Part B, 145, 230-238. PMID: 16959515

  • Facchiano AM, Costantini S, Di Maro A, Panichi D, Chambery A, Parente A, Di Gennaro S, Poerio E. (2006)
    Modelling the 3D structure of WSCI. Probing the reactive site of the inhibitor with two susceptible proteinases, by time-course analysis and molecular dynamics simulations.
    Biological Chemistry, 387, 931-940. PMID: 16913843

  • Costantini S, Facchiano A, Marabotti A.(2006)
    La predizione della struttura delle proteine.
    Compositi e Nanotecnologie, 2, 43-47.

  • Mutarelli M, Facchiano F, Colonna G, Facchiano A. (2006)
    Gene expression analysis by integration of microarrays technology, bioinformatics tools and biocomputing methods.
    Compositi e Nanotecnologie, 2, 13-18.

  • Mutarelli M, Facchiano F, Colonna G, Facchiano A. (2006)
    Bioinformatics tools for the analysis of gene expression by microarrays.
    Recent Devel. Nucleic Acid Res., 2, 175-200.

  • Costantini S, Colonna G, Facchiano A. (2006)
    Amino acid propensities for secondary structures are influenced by the protein structural class.
    Biochemical and Biophysical Research Communications, 342, 441-451. PMID: 16487481

  • Scafoglio C, Ambrosino C, Cicatiello L, Altucci L, Ardovino M, Bontempo P, Medici N, Molinari AM, Nebbioso A, Facchiano A, Calogero RA, Elkon R, Menini N, Ponzone R, Biglia N, Sismondi P, De Bortoli M, and Weisz A. (2006)
    Comparative gene expression profiling reveals partially overlapping but distinct genomic actions of different antiestrogens in human breast cancer cells.
    J Cellular Biochem, 98, 1163-1184. PMID: 16514628

  • Herman P, Staiano M, Marabotti A, Varriale A, Scire' A, Tanfani F, Vecer J, Rossi M and D'Auria S. (2006)
    D-Trehalose/D-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis. The binding of trehalose and maltose results in different protein conformational states.
    Proteins: Structure, Function, and Bioinformatics, 63, 754-767. PMID: 16532450

  • D'Auria S, Ausili A, Marabotti A, Varriale A, Scognamiglio V, Staiano M, Bertoli E, Rossi M and Tanfani F. (2006)
    Binding of glucose to the D-galactose/D-glucose-binding protein from Escherichia coli restores the native protein secondary structure and the thermostability that are lost upon calcium depletion.
    Journal of Biochemistry, 139, 213-221. PMID: 16452309

  • Mazzeo MF, Sorrentino A, Gaita M, Cacace G, Di Stasio M, Facchiano A, Comi G, Malorni A and Siciliano RA. (2006)
    MALDI-TOF mass spectrometry for the discrimination of foodborne microorganisms.
    Applied and Environmental Microbiology, 72, 1631-1638. PMID: 16461665

  • Mannini R, Rivieccio V, D'Auria S, Tanfani F, Ausili A, Facchiano A, Pedone C and Grimaldi G. (2006)
    Structure/function of KRAB repression domains: structural properties of KRAB modules inferred from hydrodynamic, circular dichroism and FTIR spectroscopic analyses
    Proteins: Structure, Function, and Bioinformatics, 62, 604-616. PMID: 16385564

  • Marabotti A, Herman P, Staiano M, Varriale A, de Champdore M, Rossi M, Gryczynski Z, D'Auria S. (2006)
    Pressure Effect on the Stability and the Conformational Dynamics of the D-Galactose/D-Glucose-Binding Protein from Escherichia coli.
    Proteins: Structure, Function, and Bioinformatics, 62, 193-201. PMID: 16294341

  • Facchiano F, Facchiano A, Facchiano A. (2006)
    The role of transglutaminase-2 and its substrates in human diseases.
    Frontiers in Biosciences, 11, 1758-1773. PMID: 16368554

  • Buonocore F, Randelli E, Bird S, Secombes CJ, Costantini S, Facchiano A, Mazzini M, Scapigliati G. (2006)
    The CD8alpha from sea bass (Dicentrarchus labrax L.): cloning, expression and 3D modelling.
    Fish Shellfish Immunol., 20, 637-646. PMID: 16230027

  • Stiuso P, Marabotti A, Facchiano A, Lepretti M, Dicitore A, Ferranti P, Carteni M. (2006)
    Assessment of the conformational features of vasoactive intestinal peptide in solution by limited proteolysis experiments.
    Biopolymers, 81, 110-119. PMID: 16224772

  • Facchiano F, Facchiano A. (2005)
    Transglutaminases and their substrates.
    Prog Exp Tumor Res. , 38, 37-57. PMID: 15746528

  • Costantini S., Colonna G., Rossi M., and Facchiano A.M. (2005)
    Modelling of HLA-DQ2 and simulations of its interaction with gluten peptides to explain molecular recognition in celiac disease.
    J. of Molecular Graphics and Modelling, 23, 419-431. PMID: 15781184

  • Marabotti A. and Facchiano A.M. (2005)
    Homology modelling studies on human galactose-1-phosphate uridylyltransferase and on its galactosemia-related mutant Q188R provide an explanation of molecular effects of the mutation on homo- and heterodimers.
    J. Med. Chem., 48, 773-779. PMID: 15689161

  • D'Auria S, Scire A, Varriale A, Scognamiglio V, Staiano M, Ausili A, Marabotti A, Rossi M, Tanfani F. (2005)
    Binding of glutamine to glutamine-binding protein from Escherichia coli induces changes in protein structure and increases protein stability.
    Proteins: Structure, Function, and Bioinformatics, 58, 80-87. PMID: 15517590

  • Cozzini P, Fornabaio M, Marabotti A, Abraham DJ, Kellogg GE, Mozzarelli A. (2004)
    Free energy of ligand binding to protein: evaluation of the contribution of water molecules by computational methods.
    Curr Med Chem., 11, 3093-3118. PMID: 15579003

  • Staiano M, Sapio M, Scognamiglio V, Marabotti A, Facchiano AM, Bazzicalupo P, Rossi M, D'Auria S. (2004)
    A Thermostable Sugar-Binding Protein from the Archaeon Pyrococcus horikoshii as a Probe for the Development of a Stable Fluorescence Biosensor for Diabetic Patients.
    Biotechnol Prog. 2004 20, 1572-1577. PMID: 15458346

  • Marabotti A, D'Auria S, Rossi M, Facchiano AM (2004)
    Theoretical model of the three-dimensional structure of a sugar binding protein from Pyrococcus horikoshii: structural analysis and sugar binding simulations.
    Biochem J. 2004, 380, 677-684. PMID: 15015939

  • Costantini S, Colonna G, Rossi M, Facchiano AM (2004)
    Binding od gluten peptides to the coeliac disease-associated HLA-DQ2 molecule by computational methods.
    In: The Gluten Proteins. Lafiandra, Masci, D'Ovidio Eds. The Royal Society of Chemistry, Cambridge, UK 2004, pp. 391-394.

  • Cicatiello L, Scafoglio C, Altucci L, Cancemi M, Natoli G, Facchiano A, Iazzetti G, Calogero R, Biglia N, De Bortoli M, Sfiligoi C, Sismondi P, Bresciani F and Weisz A.(2004)
    A genomic view of estrogen actions in human breast cancer cells by expression profiling of the hormone responsive transcriptome
    J. Mol. Endocrinology, 2004, 32, 719-775. PMID: 15171711

  • Weisz A, Basile W, Scafoglio C, Altucci L, Bresciani F, Facchiano A, Sismondi P, Cicatiello L, De Bortoli M. (2004)
    Molecular identification of ER -positive breast cancer cells by the expression profile of an intrinsic set of estrogen regulated genes.
    Journal of Cellular Physiology, 2004, 200, 440-450. PMID: 15254972

  • Scapigliati G, Costantini S, Colonna G, Facchiano A, Buonocore F, Bossu' P, Cunningham C, Holland JW, Secombes CJ. (2004)
    Modelling of fish interleukin-1 and its receptor.
    Developmental and Comparative Immunology, 2004, 8, 429-441. PMID: 15062642

  • Caporale C, Caruso C, Colonna G, Facchiano A, Ferranti P, Mamone G, Picariello G, Colonna F, Metafora S, Stiuso P. (2004)
    Structural properties of the protein SV-IV.
    European Journal of Biochemistry, 2004, 271, 263-271. PMID: 14717694

  • Caporale C, Facchiano A, Leonardi L, Bertini L, Chilosi G, Buonocore V, Caruso C.
    Comparing the modelled structures of PR-4 proteins from wheat (2003)
    Journal of Molecular Model (Online), 2003, 9, 9-15. PMID: 12638007

  • Facchiano AM, Facchiano A, Facchiano F. (2003)
    ASC (Active Sequences Collection) database: a new tool to assign functions to protein sequences.
    Nucleic Acids Research, 2003 31, 379-382. PMID: 12520027

  • Facchiano A, Russo K, Facchiano AM, De Marchis F, Facchiano F, Ribatti D, Aguzzi MS, Capogrossi MC (2003)
    Identification of a novel domain of fibroblast growth factor- 2 controlling its angiogenic properties.
    J Biol Chem. 2003, 278, 8751-8760. PMID: 12496262

  • Stiuso P, Libondi T, Facchiano A, Colicchio P, Ferranti P, Lilla S, and Colonna G.(2002)
    Alteration in the ubiquitin structure and function in the human lens: a possible mechanism of senile cataractogenesis.
    FEBS Letters,, 2002, 531, 162-167. PMID: 12417305

  • Martin ACR, Facchiano AM, Cuff AL, Hernandez-Boussard T, Olivier M, Hainaut P, Thornton JM.(2002)
    Integrating Mutation Data and Structural Analysis of the p53 Tumour-Suppressor Protein
    Human Mutation, 2002, 19, 149-164. PMID: 11793474

  • Russo K, Ragone R, Facchiano AM, Capogrossi MC, Facchiano A. (2002)
    Platelet-derived growth factor-BB and basic fibroblast growth factor directly interact in vitro with high affinity.
    J Biol Chem., 2002, 277, 1284-1291. PMID: 11694520

  • De Maria S, Metafora S, Metafora V, Morelli F, Robberecht P, Waelbroeck M, Stiuso P, De Rosa A, Cozzolino A, Esposito C, Facchiano A, Carteni M. (2002)
    Transglutaminase-mediated polyamination of vasoactive intestinal peptide (VIP) Gln16residue modulates VIP/PACAP receptor activity.
    Eur J Biochem 2002, Jul;269(13):3211-3219 PMID: 1208406

  • Facchiano AM, Stiuso P, Chiusano ML, Caraglia M, Giuberti G, Marra M, Abbruzzese A, and Colonna G. (2001)
    Homology modelling of the human eukaryotic initiation factor 5A (eIF-5A).
    Protein Engineering, 14, 881-890. PMID: 11742107

  • Ferranti P, Facchiano A, Zappacosta F, Vincenti D, Rullo R, Masala B and Di Luccia A.(2001)
    Primary Structure of alpha-Globin Chains from River Buffalo (Bubalus Bubalis L.) Hemoglobins
    J. Protein Chemistry, 20(2), 171-179. PMID: 11563698

  • Cicatiello L, Facchiano A, Calogero R, De Bortoli M, Bresciani F, and Weisz A.(2001)
    Gene expression monitoring in hormone-responsive human breast cancer cells during estrogen-induced cell cycle progression.
    Nature Genetics "Oncogenomics Conference - Dissecting cancer through genome research".
    January 25-27, 2001, Tucson, Arizona, USA.
    Abstract

   

 

 

     
     
   

 

   
    Copyright 2002 CNR - INSTITUTE OF FOOD SCIENCE -  BIOINFORMATICS LABORATORY
    Last Update:
Monday, June 28, 2004