Back to the home page of the Bioinformatics and Computational Laboratory at CNR-ISA, Avellino, Italy

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

Warning: this page may be not updated and not correctly linking to original article pages!

1. Gallucci A, Giordano D, Facchiano A, Villano C, Carputo D, Aversano R. (2024)
   Transmembrane proteins in grape immunity: current knowledge and methodological advances.
   Front Plant Sci. 2024 15:1515163. doi: 10.3389/fpls.2024.1515163. PMID: 39759230.
   
   
2. Giordano D, Argenio MA, Scafuri B, Carbone V, Bonora S, D'Arminio N, Marabotti A, Facchiano A. (2024)
   Theoretical study based on molecular docking to investigate the potential interaction of known antiviral food components with SARS-CoV-2 proteins.
   Food Bioscience. 2024 62:105415. doi: 10.1016/j.fbio.2024.105415. PMID: ...
   
   
3. Giordano D, D'Arminio N, Marabotti A, Facchiano A. (2024)
   Algorithms for Structure Comparison and Analysis: Docking.
   Reference Module in Life Sciences, Elsevier 2024. ISBN 9780128096338, doi: 10.1016/B978-0-323-95502-7.00149-4.
   
   
4. D'Arminio N, Giordano D, Facchiano A, Marabotti A. (2024)
   Algorithms for Structure Comparison and Analysis: Prediction of Structures of Proteins.
   Reference Module in Life Sciences, Elsevier 2024. ISBN 9780128096338, doi: 10.1016/B978-0-323-95502-7.00114-7.
   
   
5. Giordano D, d'Acierno A, Marabotti A, Iovino P, Iacomino G, Facchiano A. (2024)
   Bioinformatics Study on Site-Specific Variations of Eotaxin-3, a Key Chemokine in Eosinophilic Esophagitis (EoE)
   Genes (Basel). 2024 Aug 14;15(8):1073. doi: 10.3390/genes15081073. PMID: 39202432
   
   
6. Maresca V, Capasso L, Rigano D, Stornaiuolo M, Sirignano C, Piacente S, Cerulli A, Marallo N, Basile A, Nebbioso A, Giordano D, Facchiano A, De Masi L, Bontempo P. (2024)
   Health-Promoting Effects, Phytochemical Constituents and Molecular Genetic Profile of the Purple Carrot 'Purple Sun' (Daucus carota L.).
   Nutrients 2024 Aug 1;16(15):2505. doi: 10.3390/nu16152505. PMID: 39125387
   
   
7. Chacon-Millan P, Lama S, Del Gaudio N, Gravina AG, Federico A, Pellegrino R, Luce A, Altucci L, Facchiano A, Caraglia M, Stiuso P. (2024)
   A Combination of Microarray-Based Profiling and Biocomputational Analysis Identified miR331-3p and hsa-let-7d-5p as Potential Biomarkers of Ulcerative Colitis Progression to Colorectal Cancer.
   Int J Mol Sci. 2024 May 23:25(11)5699. doi: 10.3390/ijms25115699. PMID: 38891888
   
   
8. Giordano D, Bonora S, D'Orsi I, D'Alelio D, Facchiano A. (2024)
   Structural and Functional Characterization of Lipoxygenases from Diatoms by Bioinformatics and Modelling Studies.
   Biomolecules. 2024 Feb 25;14(3):276. doi: 10.3390/biom14030276 PMID: 38540697
   
   
9. Facchiano A, Heider D, Mutarelli M.(2024)
   Editorial: Artificial intelligence and bioinformatics applications for omics and multi-omics studies.
   Front. Genet., 2024, 15:1371473. doi: 10.3389/fgene.2024.1371473. PMID: 38352165
   
   
10. Giordano D, Facchiano A, Minasi P, D'Agostino N, Parisi M, Carbone V. (2023)
    Phenolic Compounds and Capsaicinoids in Three Capsicum annuum Varieties: From Analytical Characterization to In Silico Hypotheses on Biological Activity.
    Molecules 2023 28(19):6772. doi: 10.3390/molecules28196772. PMID: 37836615.
    
    
11. Lintas C, Facchiano A, Azzarà A, Cassano I, Tabolacci C, Galasso C, Gurrieri F. (2023)
    Deletion of a Single Lysine Residue at Position 292 of CAMK2A Disrupts Protein Function, Causing Severe Epileptic Encephalopathy and Intellectual Disability.
    Genes 2023 14(7):1353. doi:10.3390/genes14071353 PMID: 37510258.
    
    
12. Giordano D, Scafuri B, De Masi L, Capasso L, Maresca V, Altucci L, Nebbioso A, Facchiano A, Bontempo P. (2023)
    Sirtuin Inhibitor Cambinol Induces Cell Differentiation and Differently Interferes with SIRT1 and 2 at the Substrate Binding Site.
    Biomedicines 2023, 11(6), 1624. doi: 10.3390/biomedicines11061624 PMID: 37371719.
    
    
13. Giordano D, Facchiano A, Moccia S, Meola AMI, Russo GL, Spagnuolo C. (2023)
    Molecular Docking of Natural Compounds for Potential Inhibition of AhR.
    Foods 2023, 12(10), 1953. doi: 10.3390/foods12101953 PMID: 37238771.
    
    
14. Licata L, Via A, Turina P, Babbi G, Benevenuta S, Carta C, Casadio R, Cicconardi A, Facchiano A, Fariselli P, Giordano D, Isidori F, Marabotti A, Martelli PL, Pascarella S, Pinelli M, Pippucci T, Russo R, Savojardo C, Scafuri B, Valeriani L, Capriotti E. (2023)
    Resources and tools for rare disease variant interpretation.
    Front. Mol. Biosci., 10 May 2023, Volume 10 - 2023. doi: 10.3389/fmolb.2023.1169109 PMID: 37234922.
    
    
15. Giordano D, Facchiano A, Carbone V.(2023)
    Food Plant Secondary Metabolites Antiviral Activity
    Enyclopedia. Available online: https://encyclopedia.pub/entry/42358
    
    
16. D'Arminio N, Giordano D, Scafuri B, Facchiano A, Marabotti A.(2023)
    Standardizing macromolecular structure files: further efforts are needed.
    Trends Biochem Sci. 2023. Published online:April 06, 2023. doi: 10.1016/j.tibs.2023.03.002. PMID: 37031054.
    
    
17. Agliata A, Giordano D, Bardozzo F, Bottiglieri S, Facchiano A, Tagliaferri R. (2023)
    Machine Learning as a Support for the Diagnosis of Type 2 Diabetes.
    Int. J. Mol. Sci. 2023, 24(7), 6775. doi: 10.3390/ijms24076775. PMID: 37047748.
    
    
18. Giordano D, Facchiano A, Carbone V.(2023)
    Food Plant Secondary Metabolites Antiviral Activity and Their Possible Roles in SARS-CoV-2 Treatment: An Overview.
    Molecules 2023 Mar 8;28(6):2470. doi: 10.3390/molecules28062470. PMID: 36985442.
    
    
19. Tabolacci C, Giordano D, Rossi S, Cordella M, D'Arcangelo D, Moschella F, D'Atri S, Biffoni M, Facchiano A, Facchiano F. (2022).
    Identification of Dihydrolipoamide Dehydrogenase as Potential Target of Vemurafenib-Resistant Melanoma Cells.
    Molecules 2022 Nov 12; 27(22):7800. doi: 10.3390/molecules27227800. PMID: 36431901.
    
    
20. D'Arminio N, Giordano D, Scafuri B, Biancaniello C, Petrillo M, Facchiano A, Marabotti A. (2022)
    In Silico Analysis of the Effects of Omicron Spike Amino Acid Changes on the Interactions with Human Proteins.
    Molecules 2022 Jul 28;27(15):4827. doi: 10.3390/molecules27154827. PMID: 35956778.
    
    
21. Giordano D, Langini C, Caflisch A, Marabotti A, Facchiano A. (2022)
    Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis.
    Comput Struct Biotechnol J 2022, 20:3924-3934. doi: 10.1016/j.csbj.2022.07.024. PMID: 35950183.
    
    
22. Giordano D, Biancaniello C, Argenio MA, Facchiano A. (2022)
    Drug Design by Pharmacophore and Virtual Screening Approach.
    Pharmaceuticals 2022, 15(5), 646. doi: 10.3390/ph15050646. PMID: 35631472.
    
    
23. Biancaniello C, D'Argenio A, Giordano D, Dotolo S, Scafuri B, Marabotti A, d'Acierno A, Tagliaferri R, Facchiano A. (2022)
    Investigating the Effects of Amino Acid Variations in Human Menin.
    Molecules, 27, 1747. doi: 10.3390/molecules27051747. PMID: 35268848.
    
    
24. De Masi L, Argenio MA, Giordano D, Facchiano A. (2022)
    Molecular Aspects of Spike-ACE2 Interaction.
    Encyclopedia, 2(1), 96-108. doi: 10.3390/encyclopedia2010007.
    
    
25. Cervellera C, Russo M, Dotolo S, Facchiano A, Russo GL. (2021)
    STL1, a New AKT Inhibitor, Synergizes with Flavonoid Quercetin in Enhancing Cell Death in A Chronic Lymphocytic Leukemia Cell Line.
    Molecules, 26 (19), 5810. doi:10.3390/molecules26195810. PMID: 34641354.
    
    
26. Giordano D, De Masi L, Argenio MA, Facchiano A. (2021)
    Structural Dissection of Viral Spike-Protein Binding of SARS-CoV-2 and SARS-CoV-1 to the Human Angiotensin-Converting Enzyme 2 (ACE2) as Cellular Receptor.
    Biomedicines, 9(8):1038. doi:10.3390/biomedicines9081038. PMID: 34440241.
    
    
27. Marabotti A, Romano P, Facchiano A. (2021)
    Editorial: Computational Proteomics and Integration of Data Resources for Advanced Studies in Life Sciences.
    Front. Genet.,2021 Jul 23;12:729013. doi:10.3389/fgene.2021.729013. PMID: 34367266.
    
    
28. Tomaipitinca L, Petrungaro S, D'Acunzo P, Facchiano A, Dubey A, Rizza S, Giulitti F, Gaudio E, Filippini A, Ziparo E, Cecconi F, Giampietri C. (2021)
    c-FLIP regulates autophagy by interacting with Beclin-1 and influencing its stability.
    Cell Death Dis. 2021 Jul 8;12(7):686. doi: 10.1038/s41419-021-03957-5. PMID: 34238932.
    
    
29. Marabotti A, Del Prete E, Scafuri B, Facchiano A (2021)
    Performance of Web tools for predicting changes in protein stability caused by mutations.
    BMC Bioinformatics 22(Suppl 7):345. doi: 10.1186/s12859-021-04238-w. PMID: 34225665.
    
    
30. Rossi S, Giordano D, Mazzeo MF, Maurano F, Luongo D, Facchiano A, Siciliano RA, Rossi M (2021)
    Transamidation Down-Regulates Intestinal Immunity of Recombinant .-Gliadin in HLA-DQ8 Transgenic Mice.
    Int. J. Mol. Sci. 2021, 22(13), 7019; doi: 10.3390/ijms22137019. PMID: 34209932.
    
    
31. Giordano D, Facchiano A, D'Auria S, Loreto F. (2021).
    A hypothesis on the capacity of plant odorant-binding proteins to bind volatile isoprenoids based on in silico evidences.
    Elife 2021 Jun 23;10:e66741. doi: 10.7554/eLife.66741. PMID: 34161230.
    
    
32. Dotolo S, Marabotti A, Rachiglio AM, Esposito Abate R, Benedetto M, Ciardiello F, De Luca A, Normanno N, Facchiano A, Tagliaferri R. (2021).
    A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine.
    Brief Bioinform. 2021 Nov 5;22(6):bbab180. doi: 10.1093/bib/bbab180. PMID: 34050359.
    
    
33. Marabotti A, Scafuri B, Facchiano A. (2021)
    Predicting the stability of mutant proteins by computational approaches: an overview.
    Brief Bioinform. 2021 May 20;22(3):bbaa074. doi: 10.1093/bib/bbaa074. Published online 3 June 2020. PMID: 32496523
    
    
34. Del Prete E, Facchiano A, Profumo A , Angelini C, Romano P. (2021)
    GeenaR: A Web Tool for Reproducible MALDI-TOF Analysis.
    Front Genet 2021 Mar 29;12:635814. doi: 10.3389/fgene.2021.635814. PMID: 33854526
    
    
35. Dotolo S, Marabotti A, Facchiano A, Tagliaferri R. (2021).
    A review on drug repurposing applicable to COVID-19.
    Brief Bioinform. 2021 Mar 22;22(2):726-741. doi: 10.1093/bib/bbaa288. Published online 5 November 2020. PMID: 33147623
    
    
36. Dotolo S, Cervellera C, Russo M, Russo GL, Facchiano A. (2021)
    Virtual Screening of Natural Compounds as Potential PI 3 K-AKT1 Signaling Pathway Inhibitors and Experimental Validation.
    Molecules 2021 Jan 18;26(2):492. doi: 10.3390/molecules26020492. PMID: 33477701
    
    
37. Scafuri B, Bontempo P, Altucci L, De Masi L, Facchiano A. (2020)
    Molecular Docking Simulations on Histone Deacetylases (HDAC)-1 and -2 to Investigate the Flavone Binding.
    Biomedicines 2020 Dec 4;8(12):E568. doi: 10.3390/biomedicines8120568. PMID: 33291755
    
    
38. Facchiano A, Facchiano F, Facchiano A. (2020)
    An investigation into the molecular basis of cancer comorbidities in coronavirus infection.
    FEBS Open Bio 2020 Sep 24:10.1002/2211-5463.12984. doi: 10.1002/2211-5463.12984. Online ahead of print. PMID: 32970391
    
    
39. Facchiano A, Facchiano A, Bartoli M, Ricci A, Facchiano F. (2020)
    Reply to Jakovac: About COVID-19 and Vitamin D.
    Am J Physiol Endocrinol Metab. 2020 Jun 1;318(6):E838. doi: 10.1152/ajpendo.00185.2020. PMID: 32432923
    
    
40. Chicco D, Heider D, Facchiano A. (2020)
    Editorial: Artificial Intelligence Bioinformatics: Development and Application of Tools for Omics and Inter-Omics Studies.
    Front Genet. 2020 Apr 9;11:309. doi: 10.3389/fgene.2020.00309. eCollection 2020. PMID: 32328085
    
    
41. Soriano AA, de Cristofaro T, Di Palma T, Dotolo S, Gokulnath P, Izzo A, Calì G, Facchiano A, Zannini M.(2019)
    PAX8 expression in high-grade serous ovarian cancer positively regulates attachment to ECM via Integrin beta3.
    Cancer Cell Int. 2019 Nov 20;19:303. PMID: 31832016
    
    
42. Colonna V, D'Agostino N, Garrison E, Albrechtsen A, Meisner J, Facchiano A, Cardi T, Tripodi P. (2019)
    Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites.
    Sci Rep. 2019 Jul 11;9(1):10067. doi: 10.1038/s41598-019-46136-5. PMID: 31296904
    
    
43. Facchiano A, Pignone D, Servillo L, Castaldo D, De Masi L. (2019)
    Structure and Ligands Interactions of Citrus Tryptophan Decarboxylase by Molecular Modeling and Docking Simulations.
    Biomolecules 2019 Mar 26;9(3). pii: E117. doi: 10.3390/biom9030117. PMID: 30917613
    
    
44. Giordano D, Facchiano A. (2019)
    Classification of microbial transglutaminases by evaluation of evolution trees, sequence motifs, secondary structure topology and conservation of potential catalytic residues.
    Biochem Biophys Res Commun. 2019, 509(2), 506-513. doi: 10.1016/j.bbrc.2018.12.121. PMID: 30595384
    Corrigendum: Biochem Biophys Res Commun. 2019 Mar 26;511(1):205. doi: 10.1016/j.bbrc.2019.02.058. PMID: 30777328
    
    
45. Dubey A, Dotolo S, Ramteke PW, Facchiano A, Marabotti A. (2019)
    Searching for Chymase Inhibitors among Chamomile Compounds Using a Computational-Based Approach.
    Biomolecules 2019 9(1), 5. doi: 10.3390/biom9010005. PMID: 30583487
    
    
46. Del Prete E, Facchiano A, Liò P. (2018)
    Bioinformatics methodologies for coeliac disease and its comorbidities.
    Briefing in Bioinformatics 2018 Nov. 16 doi: 10.1093/bib/bby109. PMID: 30452543
    
    
47. Romano P, Profumo A, Facchiano A. (2018)
    Pre-Processing MALDI/TOF Mass Spectra by Using Geena 2.
    Curr Protoc Bioinformatics 2018 Dec;64(1):e59. doi: 10.1002/cpbi.59. PMID: 30422396
    
    
48. Facchiano A, Di Giulio M. (2018)
    The genetic code is not an optimal code in a model taking into account both the biosynthetic relationships between amino acids and their physicochemical properties.
    J Theor Biol. 2018 Dec 14;459:45-51. doi: 10.1016/j.jtbi.2018.09.021. Epub 2018 Sep 20.
    PMID: 30243564
    
    
49. Martano M, Stiuso P, Facchiano A, De Maria S, Vanacore D, Restucci B, Rubini C, Caraglia M, Ravagnan G, Lo Muzio L. (2018)
    Aryl hydrocarbon receptor, a tumor grade.associated marker of oral cancer, is directly downregulated by polydatin: A pilot study.
    Oncology Reports 2018 Sep;40(3):1435-1442. doi: 10.3892/or.2018.6555.
    PMID: 30015848
    
    
50. d'Acierno A, Scafuri B, Facchiano A, Marabotti A. (2018)
    The evolution of a Web resource: The Galactosemia Proteins Database 2.0.
    Hum Mutat. 2018 Jan;39(1):52-60. doi: 10.1002/humu.23346.
    PMID: 28961353
    
    
51. 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
    
    
52. 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
    
    
53. 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
    
    
54. 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
    
    
55. 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: 27808487
    
    
56. 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
    
    
57. 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
    
    
58. 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
    
    
59. 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. PMID: 28955900
    
    
60. 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
    
    
61. 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
    
    
62. 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
    
    
63. 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
    
    
64. 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
    
    
65. 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
    
    
66. 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.
    
    
67. Ricciardi A, De Filippis F, Zotta T, Facchiano A, Ercolini D, Parente E. (2015)
    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 Nov 7;236:138-47. doi: 10.1016/j.ijfoodmicro.2016.07.031 PMID: 27497152
    
    
68. Del Prete E, Dotolo S, Marabotti A, Facchiano A. (2015)
    Statistical Analysis of Protein Structural Features: Relationships and PCA Grouping.
    Lecture Notes in Bioinformatics 8623, 33-43. doi: 10.1007/978-3-319-24462-4_3.
    
    
69. 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
    
    
70. 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.
    
    
71. 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
    
    
72. Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW; GOBLET Consortium. (2015)
    GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.
    PLoS Comput Biol. 2015 Apr 9;11(4):e1004143. doi: 10.1371/journal.pcbi.1004143.
    PMID: 25856076
    
    
73. 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, 112-118. doi: 10.1016/j.gene.2015.01.013. [Epub ahead of print] PMID: 25592817
    
    
74. Facchiano AM, Facchiano F, Facchiano A. (2015)
    The role of chemical elements in melanoma.
    New Horizons in Translational Medicine, 2, 73-80. doi:10.1016/j.nhtm.2014.11.056
    Link to journal abstract
    
    
75. 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
    
    
76. 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. PMID: 24990533
    
    
77. 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
    
    
78. 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
    
    
79. 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
    
    
80. 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
    
    
81. 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
    
    
82. 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
    
    
83. 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
    Link to abstract
    
    
84. 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
    
    
85. 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
    
    
86. 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
    
    
87. 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
    
    
88. 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
    
    
89. 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(2):174-181. PMID: 21756868
    
    
90. 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(10):1358-1366. PMID: 21683167
    
    
91. 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
    
    
92. 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
    
    
93. 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
    
    
94. Marabotti A, Facchiano A. (2010)
    The misuse of terms in scientific literature.
    Bioinformatics, 2010, 26, 2498. PMID: 20696735
    
    
95. 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
    
    
96. 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
    
    
97. 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
    
    
98. 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
    
    
99. 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
    
    
100. 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. Epub 2009 Dec 11. PMID: 20008339
     
     
101. 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
     
     
102. 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
     
     
103. 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
     
     
104. 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
     
     
105. 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.
     
     
106. 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
     
     
107. 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
     
     
108. 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.
     
     
109. 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
     
     
110. 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
     
     
111. 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
     
     
112. 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
     
     
113. 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. class=GramE>2009, 182, 4158-4166. PMID: 19299713
     
     
114. Marabotti A, Facchiano A,(2009)
     When it comes to homology, bad habits die hard.
     Trends Biochem Sci. 2009, 34, 98-99. PMID: 19181528
     
     
115. 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
     
     
116. 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
     
     
117. Costantini S, Facchiano AM. (2009)
     Prediction of the protein structural class by specific peptide frequencies.
     Biochimie 2009, 91, 226-229. PMID: 18957316
     
     
118. 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
     
     
119. 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
     
     
120. Costantini S, Autiero I, Colonna G.(2008)
     On new challange for the Bioinformatics.
     Bioinformation, 2008, 3, 238-239.
     
     
121. Costantini S, Colonna G, Facchiano AM. (2008)
     ESBRI: a web server for evaluating salt bridges in proteins.
     Bioinformation, 2008, 3, 137-138. PMID: 19238252
     
     
122. Marabotti A. (2008)
     Modeling the Conformation of Side Chains in Proteins: Approaches, Problems and Possible Developments.
     Curr Chem Biol. 2008, 2, 200-214. Abstract
     
     
123. 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
     
     
124. 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
     
     
125. 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
     
     
126. Facchiano A, Facchiano F. (2008)
     Transglutaminases and their substrates in biology and human diseases: 50 years of growing.
     Amino Acids 2008, Jul.3 [Epub ahead ofprint] PMID: 18597041
     
     
127. 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
     
     
128. 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.
     
     
129. 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
     
     
130. 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
     
     
131. 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
     
     
132. 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
     
     
133. 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
     
     
134. 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
     
     
135. 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
     
     
136. 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
     
     
137. 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
     
     
138. 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
     
     
139. 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
     
     
140. 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
     
     
141. 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
     
     
142. 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
     
     
143. 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
     
     
144. 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
     
     
145. 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
     
     
146. 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
     
     
147. 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
     
     
148. 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
     
     
149. 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
     
     
150. 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
     
     
151. Cannavo' S, Karl M, Santarpia L, Facchiano A, Marabotti A, Trimarchi F and Benvenga S (2007)
     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.
     
     
152. 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
     
     
153. 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.
     
     
154. 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.
     
     
155. 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
     
     
156. 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
     
     
157. 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
     
     
158. 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
     
     
159. 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.
     
     
160. 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
     
     
161. 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
     
     
162. 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
     
     
163. Costantini S, Facchiano A, Marabotti A.(2006)
     La predizione della struttura delle proteine.
     Compositi e Nanotecnologie, 2, 43-47.
     
     
164. 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.
     
     
165. 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.
     
     
166. 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
     
     
167. 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
     
     
168. 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
     
     
169. 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
     
     
170. 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
     
     
171. 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
     
     
172. 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
     
     
173. 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
     
     
174. 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
     
     
175. 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
     
     
176. Facchiano F, Facchiano A. (2005)
     Transglutaminases and their substrates.
     Prog Exp Tumor Res. 38, 37-57. PMID: 15746528
     
     
177. 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
     
     
178. 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
     
     
179. 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
     
     
180. 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
     
     
181. 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
     
     
182. 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
     
     
183. Costantini S, Colonna G, Rossi M, Facchiano AM (2004)
     Binding of 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.
     
     
184. 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
     
     
185. 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
     
     
186. 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
     
     
187. 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
     
     
188. Caporale C, Facchiano A, Leonardi L, Bertini L, Chilosi G, Buonocore V, Caruso C. (2003)
     Comparing the modelled structures of PR-4 proteins from wheat.
     Journal of Molecular Model (Online), 2003, 9, 9-15. PMID: 12638007
     
     
189. 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
     
     
190. 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
     
     
191. 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
     
     
192. 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
     
     
193. 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
     
     
194. 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
     
     
195. 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
     
     
196. 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
     
     
197. 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.
     Nat Genet 27 (Suppl 4), 95 (2001). doi: 10.1038/87358.
     Nature Genetics "Oncogenomics Conference - Dissecting cancer through genome research". January 25-27, 2001, Tucson, Arizona, USA.
     Abstract