Proteomics and proteogenomics approaches for oral diseases

Advances in Protein Chemistry and Structural Biology

Volumn 95, Issue , 2014, Pages 125-162

  Bragazzi, Nicola Luigi ^a,b   Pechkova, Eugenia ^a,b   Nicolini, Claudio ^a,b,c  

^a UNIVERSITY OF GENOA   (Italy)

^b Nanoworld Institute Fondazione ELBA Nicolini   (Italy)

^c ARIZONA STATE UNIVERSITY   (United States)

Author keywords

Anodic porous alumina; Genomics; Label free technologies; Mass spectrometry; Nanodentistry; Nanogenomics; Nanomedicine; Nanoproteomics; Nucleic acid programmable protein arrays; Oral diseases; Personalized dentistry; Proteomics; Quartz crystal microbalance with dissipation factor monitoring

Indexed keywords

ALUMINUM OXIDE; BIOMATERIAL;

BIOFILM; BIOINFORMATICS; CLINICAL PROTOCOL; DENTAL CARIES; DENTISTRY; DEVELOPING COUNTRY; GENOMICS; GINGIVITIS; HUMAN; LICHEN PLANUS; MASS SPECTROMETRY; MEDICAL ETHICS; MOUTH CANCER; MOUTH CAVITY; MOUTH DISEASE; NANOBIOTECHNOLOGY; NANOGENOMICS; NANOMEDICINE; NANOPROTEOMICS; NUCLEIC ACID ANALYSIS; PERIODONTITIS; PRIORITY JOURNAL; PROTEOGENOMICS; PROTEOMICS; REVIEW; SALIVA; TOOTH PLAQUE; TRANSLATIONAL RESEARCH;

GENOMICS; HUMANS; MOUTH DISEASES; NANOMEDICINE; PROTEOMICS;

EID: 84903600093     PISSN: 18761623     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-800453-1.00004-X     Document Type: Chapter

References (199)

1. J.Y. Ai, B. Smith, and D.T. Wong Bioinformatics advances in saliva diagnostics International Journal of Oral Science 4 2 2012 85 87
2. S.K. Al-Tarawneh, M.B. Border, C.F. Dibble, and S. Bencharit Defining salivary biomarkers using mass spectrometry-based proteomics: A systematic review OMICS 15 6 2011 353 361
3. F.M. Amado, R.P. Ferreira, and R. Vitorino One decade of salivary proteomics: Current approaches and outstanding challenges Clinical Biochemistry 46 6 2013 506 517
4. K.S. Anderson, N. Ramachandran, J. Wong, J.V. Raphael, E. Hainsworth, and G. Demirkan et al. Application of protein microarrays for multiplexed detection of antibodies to tumor antigens in breast cancer Journal of Proteome Research 7 4 2008 1490 1499
5. K.S. Anderson, S. Sibani, G. Wallstrom, J. Qiu, E.A. Mendoza, and J. Raphael et al. Protein microarray signature of autoantibody biomarkers for the early detection of breast cancer Journal of Proteome Research 10 1 2011 85 96
6. K.S. Anderson, J. Wong, A. Vitonis, C.P. Crum, P.M. Sluss, and J. Labaer et al. p53 autoantibodies as potential detection and prognostic biomarkers in serous ovarian cancer Cancer Epidemiology, Biomarkers & Prevention 19 3 2010 859 868
7. J.O. Andreasen Oral lichen planus. 1. A clinical evaluation of 115 cases Oral Surgery, Oral Medicine, and Oral Pathology 25 1 1968 31 42
8. J.P. Arrais, N. Rosa, J. Melo, E.D. Coelho, D. Amaral, and M.J. Correia et al. OralCard: A bioinformatic tool for the study of oral proteome Archives of Oral Biology 58 7 2013 762 772
9. J. Bánóczy, and A. Rugg-Gunn Epidemiology and prevention of dental caries Acta Medicine Academica 42 2 2013 105 107
10. C.W. Bassim, K.S. Ambatipudi, J.W. Mays, D.A. Edwards, S. Swatkoski, and H. Fassil et al. Quantitative salivary proteomic differences in oral chronic graft-versus-host disease Journal of Clinical Immunology 32 6 2012 1390 1399
11. K.G. Becker, K.C. Barnes, T.J. Bright, and S.A. Wang The genetic association database Nature Genetics 36 5 2004 431 432
12. L. Belmonte, R. Spera, and C. Nicolini SpADS: An R script for mass spectrometry data preprocessing before data mining Journal of Computer Science and Systems Biology 6 2013 298 304
13. S. Bencharit, S.K. Altarawneh, S.S. Baxter, J. Carlson, G.F. Ross, and M.B. Border et al. Elucidating role of salivary proteins in denture stomatitis using a proteomic approach Molecular BioSystems 8 12 2012 3216 3223
14. D.A. Benson, I. Karsch-Mizrachi, K. Clark, D.J. Lipman, J. Ostell, and E.W. Sayers GenBank Nucleic Acids Research 40 2012 D48 D53 (Database issue)
15. N.L. Bragazzi Children, adolescents, and young adults participatory medicine: Involving them in the health care process as a strategy for facing the infertility issue The American Journal of Bioethics 13 3 2013 43 44
16. N.L. Bragazzi From P0 to P6 medicine, a model of highly participatory, narrative, interactive, and "augmented" medicine: Some considerations on Salvatore Iaconesi's clinical story Patient Preference and Adherence 7 2013 353 359
17. N.L. Bragazzi Rethinking psychiatry with OMICS science in the age of personalized P5 medicine: Ready for psychiatome? Philosophy, Ethics, and Humanities in Medicine 8 1 2013 4
18. N. Bragazzi, L. Giacomelli, V. Sivozhelezov, and C. Nicolini LeaderGene: A fast data-mining tool for molecular genomics Journal of Proteomics & Bioinformatics 4 4 2011 083 085
19. N.L. Bragazzi, and C. Nicolini A leader genes approach-based tool for molecular genomics: From gene-ranking to gene-network systems biology and biotargets predictions Journal of Computer Science and Systems Biology 6 2013 165 176
20. C. Braud, D. Baeten, M. Giral, A. Pallier, J. Ashton-Chess, and C. Braudeau et al. Immunosuppressive drug-free operational immune tolerancein human kidney transplant recipients: Part I Blood gene expression statistical analysis. Journal of Cellular Biochemistry 103 6 2008 1681 1692
21. C. Cafiero, and S. Matarasso Predictive, preventive, personalised and participatory periodontology: 'The 5Ps age' has already started The EPMA Journal 4 1 2013 16 10.1186/1878-5085-4-16
22. M. Carbone, P.G. Arduino, M. Carrozzo, S. Gandolfo, M.R. Argiolas, and G. Bertolusso et al. Course of oral lichen planus: A retrospective study of 808 northern Italian patients Oral Diseases 15 3 2009 235 243
23. A. Ceroni, S. Sibani, A. Baiker, V.R. Pothineni, S.M. Bailer, and J. LaBaer et al. Systematic analysis of the IgG antibody immune response against varicella zoster virus (VZV) using a self-assembled protein microarray Molecular BioSystems 6 9 2010 1604 1610
24. T. Chen, K. Abbey, W.J. Deng, and M.C. Cheng The bioinformatics resource for oral pathogens Nucleic Acids Research 33 2005 W734 W740 (Web Server issue)
25. Y.T. Chen, Y.M. Chong, C.W. Cheng, C.L. Ho, H.W. Tsai, and F.H. Kasten et al. Identification of novel tumor markers for oral squamous cell carcinoma using glycoproteomic analysis Clinica Chimica Acta 420 2013 45 53
26. T. Chen, W.H. Yu, J. Izard, O.V. Baranova, A. Lakshmanan, and F.E. Dewhirst The Human Oral Microbiome Database: A web accessible resource for investigating oral microbe taxonomic and genomic information Database (Oxford) 2010 2010, baq013
27. W.C. Cheng, M.L. Tsai, C.W. Chang, C.L. Huang, C.R. Chen, and W.Y. Shu et al. Microarray meta-analysis database (M(2)DB): A uniformly pre-processed, quality controlled, and manually curated human clinical microarray database BMC Bioinformatics 11 2010 421
28. A.H. Choi, B. Ben-Nissan, J.P. Matinlinna, and R.C. Conway Current perspectives: Calcium phosphate nanocoatings and nanocomposite coatings in dentistry Journal of Dental Research 92 10 2013 853 859
29. U. Covani, L. Giacomelli, A. Krajewski, A. Ravaglioli, L. Spotorno, and P. Loria et al. Biomaterials for orthopedics: A roughness analysis by atomic force microscopy Journal of Biomedical Materials Research. Part A 82 3 2007 723 730
30. U. Covani, S. Marconcini, L. Giacomelli, V. Sivozhelevov, A. Barone, and C. Nicolini Bioinformatic prediction of leader genes in human periodontitis Journal of Periodontology 79 10 2008 Oct 1974 1983
31. U. Covani, S. Marconcini, G. Derchi, A. Barone, and L. Giacomelli Relationship between human periodontitis and type 2 diabetes at a genomic level: A data-mining study Journal of Periodontology 80 8 2009 1265 1273
32. B. Cuevas-Córdoba, and J. Santiago-García Saliva: A fluid of study for OMICS Omics: A Journal of Integrative Biology 18 2 2014 87 97
33. T. Deepa, and N. Thirrunavukkarasu Saliva as a potential diagnostic tool Indian Journal of Medical Sciences 64 7 2010 293 306
34. D. De La Iglesia, S. Chiesa, J. Kern, V. Maojo, F. Martin-Sanchez, and G. Potamias et al. Nanoinformatics: New challenges for biomedical informatics at the nano level Studies in Health Technology and Informatics 150 2009 987 991
35. F.E. Dewhirst, T. Chen, J. Izard, B.J. Paster, A.C. Tanner, and W.H. Yu et al. The human oral microbiome Journal of Bacteriology 192 19 2010 5002 5017
36. D.V. Dimitrov, and J. Hoeng Systems approaches to computational modeling of the oral microbiome Frontiers in Physiology 4 2013 172
37. R. Doǧan, R. Leaman, and Z. Lu NCBI disease corpus: A resource for disease name recognition and concept normalization Journal of Biomedical Informatics 47 2014 1 10 10.1016/j.jbi.2013.12.006 pii: S1532-0464(13)00197-4
38. A.E. Duran-Pinedo, B. Paster, R. Teles, and J. Frias-Lopez Correlation network analysis applied to complex biofilm communities PLoS One 6 12 2011 e28438
39. R. Edgar, M. Domrachev, and A.E. Lash Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Research 30 1 2002 207 210
40. A. Franceschini, D. Szklarczyk, S. Frankild, M. Kuhn, M. Simonovic, and A. Roth et al. STRING v9.1: Protein-protein interaction networks, with increased coverage and integration Nucleic Acids Research 41 Database issue 2013 D808 D815
41. T. Fiorini, C. Susin, J.M. da Rocha, P. Weidlich, P. Vianna, and C.H. Moreira et al. Effect of nonsurgical periodontal therapy on serum and gingival crevicular fluid cytokine levels during pregnancy and postpartum Journal of Periodontal Research 48 1 2013 126 133
42. R.A. Freitas Jr. Nanodentistry The Journal of the American Dental Association 131 11 2000 1559 1565
43. N.S. Gadewal, and S.M. Zingde Database and interaction network of genes involved in oral cancer: Version II Bioinformation 6 4 2011 169 170
44. S. Gaiser, H. Deyhle, O. Bunk, S.N. White, and B. Müller Understanding nano-anatomy of healthy and carious human teeth: A prerequisite for nanodentistry Biointerphases 7 1-4 2012 4
45. S. Gandolfo, L. Richiardi, M. Carrozzo, R. Broccoletti, M. Carbone, and M. Pagano et al. Risk of oral squamous cell carcinoma in 402 patients with oral lichen planus: A follow-up study in an Italian population Oral Oncology 40 1 2004 77 83
46. I. Garcia, R. Kuska, and M.J. Somerman Expanding the foundation for personalized medicine: Implications and challenges for dentistry Journal of Dental Research 92 7 Suppl 2013 3S 10S
47. M.A. Ghannoum, R.J. Jurevic, P.K. Mukherjee, F. Cui, M. Sikaroodi, and A. Naqvi et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals PLoS Pathogen 6 1 2010 e1000713
48. L. Giacomelli, and C. Nicolini Gene expression of human T lymphocytes cell cycle: Experimental and bioinformatic analysis Journal of Cellular Biochemistry 99 5 2006 1326 1333
49. L. Giacomelli, O. Oluwadara, G. Chiappe, A. Barone, F. Chiappelli, and U. Covani Relationship between human oral lichen planus and oral squamous cell carcinoma at a genomic level: A datamining study Bioinformation 4 6 2009 258 262
50. L. Giacomelli, and U. Covani Bioinformatics and data mining studies in oral genomics and proteomics: New trends and challenges The Open Dentistry Journal 4 2010 67 71
51. W.V. Giannobile Our duty to promote global oral health Journal of Dental Research 92 7 2013 573 574
52. D.S. Gibson, J. Qiu, E.A. Mendoza, K. Barker, M.E. Rooney, and J. LaBaer Circulating and synovial antibody profiling of juvenile arthritis patients by nucleic acid programmable protein arrays Arthritis Research & Therapy 14 2 2012 R77
53. E. Glaab, J.M. Garibaldi, and N. Krasnogor ArrayMining: A modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization BMC Bioinformatics 10 2009 358
54. I. Glurich, A. Acharya, S.K. Shukla, G.R. Nycz, and M.H. Brilliant The oral-systemic personalized medicine model at Marshfield Clinic Oral Diseases 19 1 2013 1 17
55. K. Gokul, M. Faizuddin, and A.R. Pradeep Estimation of the level of tumor necrosis factor-α in gingival crevicular fluid and serum in periodontal health & disease: A biochemical study Indian Journal of Dental Research 23 3 2012 348 352
56. A.L. Griffen, C.J. Beall, N.D. Firestone, E.L. Gross, J.M. Difranco, and J.H. Hardman et al. CORE: A phylogenetically-curated 16S rDNA database of the core oral microbiome PLoS One 6 4 2011 e19051
57. Y.A. Guzman, D. Sakellari, M. Arsenakis, and C.A. Floudas Proteomics for the discovery of biomarkers and diagnosis of periodontitis: A critical review Expert Review of Proteomics 11 1 2014 31 41
58. H. Haririan, K. Bertl, M. Laky, W.D. Rausch, M. Böttcher, and M. Matejka et al. Salivary and serum chromogranin A and α-amylase in periodontal health and disease Journal of Periodontology 83 10 2012 1314 1321
59. T.C. Hart, P.M. Corby, M. Hauskrecht, O. Hee Ryu, R. Pelikan, and M. Valko et al. Identification of microbial and proteomic biomarkers in early childhood caries International Journal of Dentistry 2011 2011 196721
60. M.N. Hegde, N.D. Hegde, A. Ashok, and S. Shetty Biochemical indicators of dental caries in saliva: An in vivo study Caries Research 48 2 2014 170 173
61. A. Heider, and R. Alt VirtualArray: A R/bioconductor package to merge raw data from different microarray platforms BMC Bioinformatics 14 2013 75
62. J.A. Horst, U. Pieper, A. Sali, L. Zhan, G. Chopra, and R. Samudrala et al. Strategic protein target analysis for developing drugs to stop dental caries Advances in Dental Research 24 2 2012 86 93
63. G. Houlihan, P. Gatti-Lafranconi, M. Kaltenbach, D. Lowe, and F. Hollfelder An experimental framework for improved selection of binding proteins using SNAP display Journal of Immunological Methods 405 2014 47 56 10.1016/j.jim.2014.01.006 pii: S0022-1759(14)00016-7
64. W.W. Hsiao, K.L. Li, Z. Liu, C. Jones, C.M. Fraser-Liggett, and A.F. Fouad Microbial transformation from normal oral microbiota to acute endodontic infections BMC Genomics 13 2012 345
65. S. Hu, M. Arellano, P. Boontheung, J. Wang, H. Zhou, and J. Jiang et al. Salivary proteomics for oral cancer biomarker discovery Clinical Cancer Research 14 19 2008 6246 6252
66. S. Hu, and D.T. Wong Oral cancer proteomics Current Opinion in Molecular Therapeutics 9 5 2007 467 476
67. C.M. Huang Comparative proteomic analysis of human whole saliva Archives of Oral Biology 49 12 2004 951 962
68. C. Huttenhower, and O. Hofmann A quick guide to large-scale genomic data mining PLoS Computational Biology 6 5 2010 e1000779
69. M. Jágr, A. Eckhardt, S. Pataridis, and I. Mikšík Comprehensive proteomic analysis of human dentin European Journal of Oral Sciences 120 4 2012 259 268
70. P. Jagtap, T. McGowan, S. Bandhakavi, Z.J. Tu, S. Seymour, and T.J. Griffin et al. Deep metaproteomic analysis of human salivary supernatant Proteomics 12 7 2012 992 1001
71. G. Jaiswal, V. Deo, M. Bhongade, and S. Jaiswal Serum alkaline phosphatase: A potential marker in the progression of periodontal disease in cirrhosis patients Quintessence International 42 4 2011 345 348
72. M. Jessri, and C.S. Farah Next generation sequencing and its application in deciphering head and neck cancer Oral Oncology 50 2014 247 253 10.1016/j.oraloncology.2013.12.017 pii: S1368-8375(13)00805-1
73. W. Jiang, Z. Ling, X. Lin, Y. Chen, J. Zhang, and J. Yu et al. Pyrosequencing analysis of oral microbiota shifting in various caries states in childhood Microbial Ecology 67 4 2014 962 969
74. R. Joseph, S. Rajappan, S.G. Nath, and B.J. Paul Association between chronic periodontitis and rheumatoid arthritis: A hospital-based case-control study Rheumatology International 33 1 2013 103 109
75. V. Jovanovic, L. Giacomelli, V. Sivozhelezov, N. Degauque, D. Lair, and J.P. Soulillou et al. AKT1 leader gene and downstream targets are involved in a rat model of kidney allograft tolerance Journal of Cellular Biochemistry 111 3 2010 709 719
76. N. Kalema, S.D. Boon, A. Cattamanchi, J.L. Davis, A. Andama, and W. Katagira et al. Oral antimicrobial rinse to reduce mycobacterial culture contamination among tuberculosis suspects in Uganda: A prospective study PLoS One 7 7 2012 e38888
77. R. Kanaparthy, and A. Kanaparthy The changing face of dentistry: nanotechnology International Journal of Nanomedicine 6 2011 2799 2804 10.2147/IJN.S24353. Epub 2011 Nov 9
78. M. Karlsson, E. Pålsgård, P.R. Wilshaw, and L. Di Silvio Initial in vitro interaction of osteoblasts with nano-porous alumina Biomaterials 24 18 2003 3039 3046
79. P. Kellam, and R.A. Weiss Infectogenomics: Insights from the host genome into infectious diseases Cell 124 4 2006 695 697
80. D.K. Kim, K. Kerman, H.M. Hiep, M. Saito, S. Yamamura, and Y. Takamura et al. Label-free optical detection of aptamer-protein interactions using gold-capped oxide nanostructures Analytical Biochemistry 379 1 2008 1 7
81. M.I. Klein, J. Xiao, B. Lu, C.M. Delahunty, J.R. Yates 3rd., and H. Koo Streptococcus mutans protein synthesis during mixed-species biofilm development by high-throughput quantitative proteomics PLoS One 7 9 2012 e45795
82. T. Kobayashi, M. Okada, S. Ito, D. Kobayashi, K. Ishida, and A. Kojima et al. Assessment of interleukin-6 receptor inhibition therapy on periodontal condition in patients with rheumatoid arthritis and chronic periodontitis Journal of Periodontology 85 1 2014 57 67
83. F.H. Kobeissy, B. Gulbakan, A. Alawieh, P. Karam, Z. Zhang, and J.D. Guingab-Cagmat et al. Post-genomics nanotechnology is gaining momentum: Nanoproteomics and applications in life sciences Omics: A Journal of Integrative Biology 18 2 2014 111 131
84. Y. Kodama, E. Kaminuma, S. Saruhashi, K. Ikeo, H. Sugawara, and Y. Tateno et al. Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies Advances in Experimental Medicine and Biology 680 2010 125 135
85. K.S. Kornman, and G.W. Duff Personalized medicine: Will dentistry ride the wave or watch from the beach? Journal of Dental Research 91 7 Suppl 2012 8S 11S
86. R.B. Krishna Prasad, A. Sharma, and H.M. Babu An insight into salivary markers in oral cancer Dental Research Journal 10 3 2013 287 295
87. M. Kuboniwa, G.D. Tribble, E.L. Hendrickson, A. Amano, R.J. Lamont, and M. Hackett Insights into the virulence of oral biofilms: Discoveries from proteomics Expert Review of Proteomics 9 3 2012 311 323
88. M.L. Laine, V. Moustakis, L. Koumakis, G. Potamias, and B.G. Loos Modeling susceptibility to periodontitis Journal of Dental Research 92 1 2013 45 50
89. I.B. Lamster, and J.K. Ahlo Analysis of gingival crevicular fluid as applied to the diagnosis of oral and systemic diseases Annals of the New York Academy of Sciences 1098 2007 216 229
90. H.S. Le, Z.N. Oltvai, and Z. Bar-Joseph Cross-species queries of large gene expression databases Bioinformatics 26 19 2010 2416 2423
91. S.Y. Lee, H.R. Park, N.H. Cho, Y.P. Choi, S.Y. Rha, and S.W. Park et al. Identifying genes related to radiation resistance in oral squamous cell carcinoma cell lines International Journal of Oral and Maxillofacial Surgery 42 2 2013 169 176
92. J.A. Lemos, J. Abranches, and R.A. Burne Responses of cariogenic streptococci to environmental stresses Current Issues in Molecular Biology 7 1 2005 95 107
93. J.A. Lemos, and R.A. Burne A model of efficiency: Stress tolerance by Streptococcus mutans Microbiology 154 Pt 11 2008 3247 3255
94. A.E. Levine, and D.L. Steffen OrCGDB: A database of genes involved in oral cancer Nucleic Acids Research 29 1 2001 300 302
95. Y. Li, M.A. St John, X. Zhou, Y. Kim, U. Sinha, and R.C. Jordan et al. Salivary transcriptome diagnostics for oral cancer detection Clinical Cancer Research 10 24 2004 8442 8450
96. J. Li, W. Wang, Y. Wang, and A.P. Zeng Two-dimensional gel-based proteomic of the caries causative bacterium Streptococcus mutans UA159 and insight into the inhibitory effect of carolacton Proteomics 13 23-24 2013 3470 3477
97. B. Liu, L.L. Faller, N. Klitgord, V. Mazumdar, M. Ghodsi, and D.D. Sommer et al. Deep sequencing of the oral microbiome reveals signatures of periodontal disease PLoS One 7 6 2012 e37919
98. S.K. Mallineni, S. Nuvvula, J.P. Matinlinna, C.K. Yiu, and N.M. King Biocompatibility of various dental materials in contemporary dentistry: A narrative insight Journal of Investigative and Clinical Dentistry 4 1 2013 9 19
99. S.S. Mantri, and S.P. Mantri The nano era in dentistry Journal of Natural Science, Biology, and Medicine 4 1 2013 39 44
100. R. Manzano-Román, V. Díaz-Martín, M. González-González, S. Matarraz, A.F. Álvarez-Prado, and J. LaBaer et al. Self-assembled protein arrays from an Ornithodoros moubata salivary gland expression library Journal of Proteome Research 11 12 2012 5972 5982
101. S. Marconcini, U. Covani, A. Barone, O. Vittorio, M. Curcio, and S. Barbuti et al. Real-time quantitative polymerase chain reaction analysis of patients with refractory chronic periodontitis Journal of Periodontology 82 7 2011 1018 1024
102. S. Marconcini, A.M. Genovesi, O. Marchisio, F. Gelpi, A. Barone, and C. Corega et al. In vivo study of titanium healing screws surface modifications after different debridment procedure Minerva Stomatologica 2014 (Epub ahead of print)
103. A. Marimuthu, S. Chavan, G. Sathe, N.A. Sahasrabuddhe, S.M. Srikanth, and S. Renuse et al. Identification of head and neck squamous cell carcinoma biomarker candidates through proteomic analysis of cancer cell secretome Biochimica et Biophysica Acta 1834 11 2013 2308 2316
104. H. Masuda, and K. Fukuda Ordered metal nanohole arrays made by a two-step replication of honeycomb structures of anodic alumina Science 268 1995 1466 1468
105. J.H. Matse, J. Yoshizawa, X. Wang, D. Elashoff, J.G. Bolscher, and E.C. Veerman et al. Discovery and prevalidation of salivary extracellular microRNA biomarkers panel for the noninvasive detection of benign and malignant parotid gland tumors Clinical Cancer Research 19 11 2013 3032 3038
106. V. Mazumdar, E.S. Snitkin, S. Amar, and D. Segrè Metabolic network model of a human oral pathogen Journal of Bacteriology 191 1 2009 74 90
107. B.E. McCartan, and C.M. Healy The reported prevalence of oral lichen planus: A review and critique Journal of Oral Pathology & Medicine 37 8 2008 447 453
108. J.H. Meurman, S.J. Janket, M. Qvarnström, and P. Nuutinen Dental infections and serum inflammatory markers in patients with and without severe heart disease Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology, and Endodontics 96 6 2003 695 700
109. S. Miersch, X. Bian, G. Wallstrom, S. Sibani, T. Logvinenko, and C.H. Wasserfall et al. Serological autoantibody profiling of type 1 diabetes by protein arrays Journal of Proteomics 94 2013 486 496
110. S. Mitra, S. Das, S. Ghosal, and J. Chakrabarti HNOCDB: A comprehensive database of genes and miRNAs relevant to head and neck and oral cancer Oral Oncology 48 2 2012 117 119
111. W.R. Montor, J. Huang, Y. Hu, E. Hainsworth, S. Lynch, and J.W. Kronish et al. Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays Infection and Immunity 77 11 2009 4877 4886
112. Y. Moreau, and L.C. Tranchevent Computational tools for prioritizing candidate genes: Boosting disease gene discovery Nature Reviews. Genetics 13 8 2012 523 536
113. Y. Nakano, Y. Shibata, M. Kawada, M. Kojima, H. Fukamachi, and Y. Shibata et al. A searchable database for proteomes of oral microorganisms Oral Microbiology and Immunology 20 6 2005 344 348
114. J. Nan, E. Brostromer, X.Y. Liu, O. Kristensen, and X.D. Su Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans: Implication of antibiotic resistance PLoS One 4 10 2009 e7245
115. A. Nand, A. Gautam, J.B. Pérez, A. Merino, and J. Zhu Emerging technology of in situ cell free expression protein microarrays Protein & Cell 3 2 2012 84 88
116. NCBI Resource Coordinators Database resources of the National Center for Biotechnology Information Nucleic Acids Research 42 1 2014 D7 D17
117. L. Nibali, N. Donos, and B. Henderson Periodontal infectogenomics Journal of Medical Microbiology 58 Pt 10 2009 1269 1274
118. C. Nicolini Nanogenomics for medicine Nanomedicine (London, England) 1 2 2006 147 152
119. C. Nicolini, R. Spera, E. Stura, S. Fiordoro, and L. Giacomelli Gene expression in the cell cycle of human T-lymphocytes: II Experimental determination by DNASER technology Journal of Cellular Biochemistry 97 5 2006 1151 1159
120. C. Nicolini Nanogenomics in medicine Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology 2 1 2010 59 76
121. C. Nicolini, M. Adami, M. Sartore, N.L. Bragazzi, V. Bavastrello, and R. Spera et al. Prototypes of newly conceived inorganic and biological sensors for health and environmental applications Sensors (Basel, Switzerland) 12 12 2012 17112 17127
122. C. Nicolini, N. Bragazzi, and E. Pechkova Nanoproteomics enabling personalized nanomedicine Advanced Drug Delivery Reviews 64 13 2012 1522 1531
123. C. Nicolini, N. Bragazzi, and E. Pechkova From nanobiotechnology to organic and biological monitoring of health and environment for biosafety Journal of Bioanalysis & Biomedicine 5 2013 108 117
124. C. Nicolini, T.B. Correia, E. Stura, C. Larosa, R. Spera, and E. Pechkova Atomic force microscopy and anodic porous allumina of nucleic acid programmable protein arrays Recent Patents on Biotechnology 7 2 2013 112 121
125. C. Nicolini, and E. Pechkova An overview of nanotechnology-based functional proteomics for cancer and cell cycle progression Anticancer Research 30 6 2010 2073 2080
126. C. Nicolini, and E. Pechkova Nanoproteomics for nanomedicine Nanomedicine (London, England) 5 5 2010 677 682
127. C. Nicolini, M. Singh, R. Spera, and L. Felli Analysis of gene expression on anodic porous alumina microarrays Bioengineered 4 5 2013 332 337
128. C. Nicolini, R. Spera, F. Festa, L. Belmonte, S. Chong, and E. Pechkova et al. Mass spectrometry and florescence analysis of SNAP-NAPPA arrays expressed using E. coli cell-free expression system Journal of Nanomedicine & Nanotechnology 4 5 2013 181 195
129. Y. Ogawa, Y. Miura, A. Harazono, M. Kanai-Azuma, Y. Akimoto, and H. Kawakami et al. Proteomic analysis of two types of exosomes in human whole saliva Biological & Pharmaceutical Bulletin 34 1 2011 13 23
130. M. Okada, T. Kobayashi, S. Ito, T. Yokoyama, A. Abe, and A. Murasawa et al. Periodontal treatment decreases levels of antibodies to Porphyromonas gingivalis and citrulline in patients with rheumatoid arthritis and periodontitis Journal of Periodontology 84 12 2013 e74 e84
131. B. Orlando, N. Bragazzi, and C. Nicolini Bioinformatics and systems biology analysis of genes network involved in OLP (Oral Lichen Planus) pathogenesis Archives of Oral Biology 58 6 2013 664 673
132. S.T. Ozak, and P. Ozkan Nanotechnology and dentistry European Journal of Dentistry 7 1 2013 145 151
133. S.P. Patel, and P.A. Raju Resistin in serum and gingival crevicular fluid as a marker of periodontal inflammation and its correlation with single-nucleotide polymorphism in human resistin gene at -420 Contemporary Clinical Dentistry 4 2 2013 192 197
134. E. Pechkova, S. Chong, S. Tripathi, and C. Nicolini Cell free expression and APA for NAPPA and protein crystallography: Functional proteomics and nanotechnology-based microarrays C. Nicolini, J. LaBaer, Pan stanford series on nanobiotechnology 2 2010 Thomson ISI Web of Science London - New York - Singapore 121 147
135. P.E. Petersen Oral cancer prevention and control - The approach of the World Health Organization Oral Oncology 45 4-5 2009 454 460
136. S.N. Peterson, E. Snesrud, N.J. Schork, and W.A. Bretz Dental caries pathogenicity: A genomic and metagenomic perspective International Dental Journal 61 Suppl 1 2011 11 22
137. T.K. Pham, S. Roy, J. Noirel, I. Douglas, P.C. Wright, and G.P. Stafford A quantitative proteomic analysis of biofilm adaptation by the periodontal pathogen Tannerella forsythia Proteomics 10 17 2010 3130 3141
138. A.R. Pradeep, M. Kumari, N. Kalra, and N. Priyanka Correlation of MCP-4 and high-sensitivity C-reactive protein as a marker of inflammation in obesity and chronic periodontitis Cytokine 61 3 2013 772 777
139. A.R. Pradeep, N.M. Raghavendra, M.V. Prasad, R. Kathariya, S.P. Patel, and A. Sharma Gingival crevicular fluid and serum visfatin concentration: Their relationship in periodontal health and disease Journal of Periodontology 82 9 2011 1314 1319
140. D. Preza, B. Thiede, I. Olsen, and B. Grinde The proteome of the human parotid gland secretion in elderly with and without root caries Acta Odontologica Scandinavica 67 3 2009 161 169
141. M. Racapé, N. Bragazzi, V. Sivozhelezov, R. Danger, E. Pechkova, and J.P. Duong Van Huyen et al. SMILE silencing and PMA activation gene networks in HeLa cells: Comparison with kidney transplantation gene networks Journal of Cellular Biochemistry 113 6 2012 1820 1832
142. N.M. Raghavendra, A.R. Pradeep, R. Kathariya, A. Sharma, N.S. Rao, and S.B. Naik Effect of non surgical periodontal therapy on gingival crevicular fluid and serum visfatin concentration in periodontal health and disease Disease Markers 32 6 2012 383 388
143. N. Ramachandran, E. Hainsworth, B. Bhullar, S. Eisenstein, B. Rosen, and A.Y. Lau et al. Self-assembling protein microarrays Science 305 5680 2004 86 90
144. N. Rappaport, N. Nativ, G. Stelzer, M. Twik, Y. Guan-Golan, and T.I. Stein et al. MalaCards: An integrated compendium for diseases and their annotation Database 2013 2013 bat018
145. R. Rappuoli Reverse vaccinology Current Opinion in Microbiology 3 5 2000 445 450
146. S. Razzouk, and O. Termechi Host genome, epigenome, and oral microbiome interactions: Toward personalized periodontal therapy Journal of Periodontology 84 9 2013 1266 1271
147. P.J. Reddy, R. Jain, Y.K. Paik, R. Downey, A.S. Ptolemy, and V. Ozdemir et al. Personalized medicine in the age of pharmacoproteomics: A close up on India and need for social science engagement for responsible innovation in post-proteomic biology Current Pharmacogenomics and Personalized Medicine 9 1 2011 67 75
148. G. Reshmi, S. Charles, P. James, V.S. Jijith, R. Prathibha, and S. Ramachandran et al. OrCa-dB: A complete catalogue of molecular and clinical information in oral carcinogenesis Oral Oncology 48 6 2012 e19
149. D. Richards Oral diseases affect some 3.9 billion people Evidence-Based Dentistry 14 2 2013 35
150. D.J. Riley, V. Bavastrello, U. Covani, A. Barone, and C. Nicolini An in-vitro study of the sterilization of titanium dental implants using low intensity UV-radiation Dental Materials 21 8 2005 756 760
151. A. Rolfs, W.R. Montor, S.S. Yoon, Y. Hu, B. Bhullar, and F. Kelley et al. Production and sequence validation of a complete full length ORF collection for the pathogenic bacterium Vibrio cholerae Proceedings of the National Academy of Sciences of the United States of America 105 11 2008 4364 4369
152. N. Rosa, M.J. Correia, J.P. Arrais, P. Lopes, J. Melo, and J.L. Oliveira et al. From the salivary proteome to the OralOme: Comprehensive molecular oral biology Archives of Oral Biology 57 7 2012 853 864
153. B.C. Ross, L. Czajkowski, D. Hocking, M. Margetts, E. Webb, and L. Rothel et al. Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis Vaccine 19 30 2001 4135 4142
154. S. Ruhl The scientific exploration of saliva in the post-proteomic era: From database back to basic function Expert Review of Proteomics 9 1 2012 85 96
155. G. Rustici, N. Kolesnikov, M. Brandizi, T. Burdett, M. Dylag, and I. Emam et al. ArrayExpress update - Trends in database growth and links to data analysis tools Nucleic Acids Research 41 Database issue 2013 D987 D990
156. M. Salerno, F. Caneva-Soumetz, L. Pastorino, N. Patra, A. Diaspro, and C. Ruggiero Adhesion and proliferation of osteoblast-like cells on anodic porous alumina substrates with different morphology IEEE Transactions on Nanobioscience 12 2 2013 106 111
157. M. Salerno, L. Giacomelli, and C. Larosa Biomaterials for the programming of cell growth in oral tissues: The possible role of APA Bioinformation 5 7 2011 291 293
158. L. Sbordone, C. Sbordone, N. Filice, G. Menchini-Fabris, M. Baldoni, and P. Toti Gene clustering analysis in human osseous remodeling Journal of Periodontology 80 12 2009 1998 2009
159. T.K. Schleyer Dental informatics: An emerging biomedical informatics discipline Journal of Dental Education 67 11 2003 1193 1200
160. T. Schleyer, U. Mattsson, R. Ní Ríordáin, V. Brailo, M. Glick, and R.B. Zain et al. Advancing oral medicine through informatics and information technology: A proposed framework and strategy Oral Diseases 17 Suppl 1 2011 85 94
161. K. Schwarzberg, R. Le, B. Bharti, S. Lindsay, G. Casaburi, and F. Salvatore et al. The personal human oral microbiome obscures the effects of treatment on periodontal disease PLoS One 9 1 2014 e86708
162. A. Sharma, A.R. Pradeep, N.M. Raghavendra, P. Arjun, and R. Kathariya Gingival crevicular fluid and serum cystatin c levels in periodontal health and disease Disease Markers 32 2 2012 101 107
163. N. Shenar, J. Martinez, and C. Enjalbal Laser desorption/ionization mass spectrometry on porous silica and alumina for peptide mass fingerprinting Journal of the American Society for Mass Spectrometry 19 5 2008 632 644
164. S. Sibani, and J. LaBaer Immunoprofiling using NAPPA protein microarrays Methods in Molecular Biology 723 2011 149 161
165. S. Silverman Jr., M. Gorsky, and F. Lozada-Nur A prospective follow-up study of 570 patients with oral lichen planus: Persistence, remission, and malignant association Oral Surgery, Oral Medicine, and Oral Pathology 60 1 1985 30 34
166. V. Sivozhelezov, C. Braud, L. Giacomelli, E. Pechkova, M. Giral, and J.P. Soulillou et al. Immunosuppressive drug-free operational immune tolerance in human kidney transplants recipients. Part II. Non-statistical gene microarray
167. V. Sivozhelezov, L. Giacomelli, S. Tripathi, and C. Nicolini Gene expression in the cell cycle of human T lymphocytes: I. Predicted gene and protein networks Journal of Cellular Biochemistry 97 5 2006 1137 1150
168. V. Sivozhelezov, R. Spera, L. Giacomelli, E. Hainsworth, J. Labaer, and N.L. Bragazzi et al. Bioinformatics and fluorescence DNASER for NAPPA studies on cell transformation and cell cycle Functional Proteomics and Nanotechnology-Based Microarrays Vol. 2 2009 31 59
169. S.J. Skates, M.A. Gillette, J. LaBaer, S.A. Carr, L. Anderson, and D.C. Liebler et al. Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies Journal of Proteome Research 12 12 2013 5383 5394
170. Y. Song, Y. Ju, Y. Morita, and G. Song Effect of the nanostructure of porous alumina on growth behavior of MG63 osteoblast-like cells Journal of Bioscience and Bioengineering 116 4 2013 509 515
171. R. Spera, F. Badino, E. Hainsworth, M. Fuentes, S. Srivastava, and J. LaBaer et al. Label free detection of NAPPA via mass spectrometry J. LaBaer, C. Nicolini, Functional Proteomics and Nanotechnology-Based Microarrays 2010 Pan Stanford Publishing 61 78 (Chapter)
172. R. Spera, T.T.B. Correia, and C. Nicolini NAPPA based nanogravimetric biosensor: Preliminary characterization Sensors and Actuators, B: Chemical 182 2013 682 688
173. R. Spera, F. Festa, N.L. Bragazzi, E. Pechkova, J. LaBaer, and C. Nicolini Conductometric monitoring of protein-protein interactions Journal of Proteome Research 12 12 2013 5535 5547
174. R. Spera, J. Labaer, and C. Nicolini MALDI-TOF characterization of NAPPA-generated proteins Journal of Mass Spectrometry 46 9 2011 960 965
175. G. Stelzer, I. Dalah, T.I. Stein, Y. Satanower, N. Rosen, and N. Nativ et al. In-silico human genomics with GeneCards Human Genomics 5 6 2011 709 717
176. K. Strimbu, and J.A. Tavel What are biomarkers? Current Opinion in HIV and AIDS 5 6 2010 463 466
177. E. Stura, D. Bruzzese, F. Valerio, V. Grasso, P. Perlo, and C. Nicolini Anodic porous alumina as mechanical stability enhancer for LDL-cholesterol sensitive electrodes Biosensors & Bioelectronics 23 5 2007 655 660
178. N.M. Sundar, V. Krishnan, S. Krishnaraj, V.T. Hemalatha, and M.N. Alam Comparison of the salivary and the serum nitric oxide levels in chronic and aggressive periodontitis: A biochemical study Journal of Clinical and Diagnostic Research 7 6 2013 1223 1227
179. A. Suzuki, T. Takai-Igarashi, Y. Numabe, and H. Tanaka Development of a database and ontology for pathogenic pathways in periodontitis In Silico Biology 9 4 2009 233 243
180. A. Thanawastien, W.R. Montor, J. Labaer, J.J. Mekalanos, and S.S. Yoon Vibrio cholerae proteome-wide screen for immunostimulatory proteins identifies phosphatidylserine decarboxylase as a novel Toll-like receptor 4 agonist PLoS Pathogen 5 8 2009 e1000556
181. M. Thorat, A.R. Pradeep, and G. Garg Correlation of levels of oncostatin M cytokine in crevicular fluid and serum in periodontal disease International Journal of Oral Science 2 4 2010 198 207
182. C.L. Tung, S.T. Lin, H.C. Chou, Y.W. Chen, H.C. Lin, and C.L. Tung et al. Proteomics-based identification of plasma biomarkers in oral squamous cell carcinoma Journal of Pharmaceutical and Biomedical Analysis 75 2013 7 17
183. W.G. Wade The oral microbiome in health and disease Pharmacological Research 69 1 2013 137 143
184. Y. Wang, X. Xia, and Y. Guo Porous anodic alumina membrane as a sample support for MALDI-TOF MS analysis of salt-containing proteins Journal of the American Society for Mass Spectrometry 16 9 2005 1488 1492
185. Q. Wang, P. Jia, K.T. Cuenco, E. Feingold, M.L. Marazita, and L. Wang et al. Multi-dimensional prioritization of dental caries candidate genes and its enriched dense network modules PLoS One 8 10 2013 e76666
186. C.B. Wiebe, and E.E. Putnins The periodontal disease classification system of the American Academy of Periodontology - An update Journal of the Canadian Dental Association 66 11 2000 594 597
187. D. Wong Salivary Diagnostics 2009 Wiley-Blackwell 978-0-8138-0664-8 (320 pages)
188. C. Wright, S. Sibani, D. Trudgian, R. Fischer, B. Kessler, and J. LaBaer et al. Detection of multiple autoantibodies in patients with ankylosing spondylitis using nucleic acid programmable protein arrays Molecular & Cellular Proteomics 11 2 2012 M9.00384
189. G. Xie, P.S. Chain, C.C. Lo, K.L. Liu, J. Gans, and J. Merritt et al. Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing Molecular Oral Microbiology 25 6 2010 391 405
190. V. Xue, T. Burdett, M. Lukk, J. Taylor, A. Brazma, and H. Parkinson MageComet - Web application for harmonizing existing large-scale experiment descriptions Bioinformatics 28 10 2012 1402 1403
191. L.L. Yang, X.Q. Liu, W. Liu, B. Cheng, and M.T. Li Comparative analysis of whole saliva proteomes for the screening of biomarkers for oral lichen planus Inflammation Research 55 10 2006 405 407
192. W.H. Yu, H. Hu, Q. Zhou, Y. Xia, and S. Amar Bioinformatics analysis of macrophages exposed to Porphyromonas gingivalis: Implications in acute vs. chronic infections PLoS One 5 12 2010 e15613
193. Z. Zainal-Abidin, P.D. Veith, S.G. Dashper, Y. Zhu, D.V. Catmull, and Y.Y. Chen et al. Differential proteomic analysis of a polymicrobial biofilm Journal of Proteome Research 11 9 2012 4449 4464
194. R. Zandparsa Latest biomaterials and technology in dentistry Dental Clinics of North America 58 1 2014 113 134
195. S. Zehetbauer, T. Wojahn, K.A. Hiller, G. Schmalz, and S. Ruhl Resemblance of salivary protein profiles between children with early childhood caries and caries-free controls European Journal of Oral Sciences 117 4 2009 369 373
196. Y. Zhan, R. Zhang, H. Lv, X. Song, X. Xu, and L. Chai et al. Prioritization of candidate genes for periodontitis using multiple computational tools Journal of Periodontology 2014 (Epub ahead of print)
197. A. Zhang, H. Sun, P. Wang, and X. Wang Salivary proteomics in biomedical research Clinica Chimica Acta 415 2013 261 265
198. J. Zheng, J. Stoyanovich, E. Manduchi, J. Liu, and C.J. Stoeckert Jr. AnnotCompute: Annotation-based exploration and meta-analysis of genomics experiments Database 2011 2011 bar045
199. V. Zijnge, T. Kieselbach, and J. Oscarsson Proteomics of protein secretion by Aggregatibacter actinomycetemcomitans PLoS One 7 7 2012 e41662