<?xml version="1.0"?>
<doi_batch xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.crossref.org/schema/4.4.0" xmlns:fr="http://www.crossref.org/fundref.xsd" xmlns:ct="http://www.crossref.org/clinicaltrials.xsd" xmlns:ai="http://www.crossref.org/AccessIndicators.xsd" xmlns:rel="http://www.crossref.org/relations.xsd" xmlns:jats="http://www.ncbi.nlm.nih.gov/JATS1" version="4.4.0" xsi:schemaLocation="http://www.crossref.org/schema/4.4.0 crossref4.4.0.xsd">
  <head>
    <doi_batch_id>TODENTJ-25-03-2019_TODENTJ-4-67</doi_batch_id>
    <timestamp>1553505154</timestamp>
    <depositor>
      <depositor_name>Bentham Open</depositor_name>
      <email_address>doi@benthamopen.net</email_address>
    </depositor>
    <registrant>Bentham Open</registrant>
  </head>
  <body>
    <journal>
      <journal_metadata language="en">
        <full_title>The Open Dentistry Journal</full_title>
        <abbrev_title>TODENTJ</abbrev_title>
        <issn media_type="print">1874-2106</issn>
      </journal_metadata>
      <journal_issue>
        <publication_date media_type="print">
          <month>7</month>
          <day>16</day>
          <year>2010</year>
        </publication_date>
        <journal_volume>
          <volume>4</volume>
        </journal_volume>
        <issue>1</issue>
      </journal_issue>
      <journal_article publication_type="full_text">
        <titles>
          <title>Bioinformatics and Data Mining Studies in Oral Genomics and  Proteomics: New Trends and Challenges </title>
        </titles>
        <contributors>
          <person_name contributor_role="author" sequence="first">
            <given_name>Luca</given_name>
            <surname>Giacomelli</surname>
          </person_name>
          <person_name contributor_role="author" sequence="additional">
            <given_name>Ugo</given_name>
            <surname>Covani</surname>
          </person_name>
        </contributors>
        <jats:abstract>
                <jats:p>Genomics and proteomics have promised to change the practice of dentistry and oral pathology, allowing the identification and the characterization of risk factors and therapeutic targets at a molecular level. However, mass-scale molecular genomics and proteomics suffer from some pitfalls: gene/protein expression are significant only if inserted in a detailed network of molecular pathways and gene/gene, gene/protein and protein/protein interactions. </jats:p>
                <jats:p>The proper analysis of these complex pictures requires the contribution of theoretical disciplines, like bioinformatics and data mining. In particular, data-mining of existing information could become a strong starting point to formulate new targeted hypotheses and to plan <jats:italic>ad hoc</jats:italic> experimentation.</jats:p>
                <jats:p>In this review, advantages and disadvantages of the above-mentioned disciplines and their potential in oral pathology are discussed. The leader gene approach is a new data mining algorithm, recently applied to some oral diseases and their correlation with systemic conditions. The preliminary results of the application of the leader gene approach to the correlation between periodontitis and heart ischemia at a molecular level are presented for the first time.</jats:p>
            </jats:abstract>
        <publication_date>
          <month>7</month>
          <day>16</day>
          <year>2010</year>
        </publication_date>
        <pages>
          <first_page>67</first_page>
          <last_page>71</last_page>
        </pages>
        <publisher_item>
          <identifier id_type="sici">TODENTJ-4-67</identifier>
        </publisher_item>
        <crossmark>
          <crossmark_version>1</crossmark_version>
          <crossmark_policy>10.2174/crossmark_policy</crossmark_policy>
          <crossmark_domains>
            <crossmark_domain>
              <domain>opendentistryjournal.com</domain>
            </crossmark_domain>
            <crossmark_domain>
              <domain>benthamopen.com</domain>
            </crossmark_domain>
          </crossmark_domains>
          <crossmark_domain_exclusive>true</crossmark_domain_exclusive>
          <custom_metadata>
            <assertion name="review_status" label="Review Status" group_name="peer_review_details" group_label="Peer Review Details" order="0">Peer Reviewed</assertion>
            <assertion name="review_process" label="Review Process" group_name="peer_review_details" group_label="Peer Review Details" order="1">Single blind</assertion>
            <assertion name="screening_status" label="Screening Status" group_name="plagiarism_screening" group_label="Plagiarism Screening" order="0">Checked with iThenticate</assertion>
            <assertion name="received" label="Received" group_name="publication_history" group_label="Publication History" order="0">2009-9-2</assertion>
            <assertion name="revised" label="Revised" group_name="publication_history" group_label="Publication History" order="1">2009-10-1</assertion>
            <assertion name="accepted" label="Accepted" group_name="publication_history" group_label="Publication History" order="2">2009-10-1</assertion>
            <assertion name="published" label="Published" group_name="publication_history" group_label="Publication History" order="3">2010-7-16</assertion>
            <ai:program name="AccessIndicators">
              <ai:license_ref>http://creativecommons.org/licenses/by-nc/3.0/</ai:license_ref>
            </ai:program>
          </custom_metadata>
        </crossmark>
        <doi_data>
          <doi>10.2174/1874210601004010067</doi>
          <timestamp>1553505154</timestamp>
          <resource>https://opendentistryjournal.com/VOLUME/4/PAGE/67/</resource>
          <collection property="crawler-based">
            <item crawler="google">
              <resource>https://opendentistryjournal.com/contents/volumes/V4/TODENTJ-4-67/TODENTJ-4-67.pdf</resource>
            </item>
            <item crawler="msn">
              <resource>https://opendentistryjournal.com/contents/volumes/V4/TODENTJ-4-67/TODENTJ-4-67.pdf</resource>
            </item>
            <item crawler="altavista">
              <resource>https://opendentistryjournal.com/contents/volumes/V4/TODENTJ-4-67/TODENTJ-4-67.pdf</resource>
            </item>
            <item crawler="yahoo">
              <resource>https://opendentistryjournal.com/contents/volumes/V4/TODENTJ-4-67/TODENTJ-4-67.pdf</resource>
            </item>
            <item crawler="scirus">
              <resource>https://opendentistryjournal.com/contents/volumes/V4/TODENTJ-4-67/TODENTJ-4-67.pdf</resource>
            </item>
            <item crawler="iParadigms">
              <resource>https://opendentistryjournal.com/contents/volumes/V4/TODENTJ-4-67/TODENTJ-4-67.pdf</resource>
            </item>
          </collection>
          <collection property="text-mining">
            <item>
              <resource mime_type="application/pdf">https://opendentistryjournal.com/contents/volumes/V4/TODENTJ-4-67/TODENTJ-4-67.pdf</resource>
            </item>
            <item>
              <resource mime_type="application/xml">https://opendentistryjournal.com/contents/volumes/V4/TODENTJ-4-67/TODENTJ-4-67.xml</resource>
            </item>
          </collection>
        </doi_data>
        <citation_list>
          <citation key="refR1">
            <journal_title>J Am Dent Assoc</journal_title>
            <author>Garcia I</author>
            <volume>139</volume>
            <first_page>392</first_page>
            <cYear>2008</cYear>
            <unstructured_citation>
                    Garcia I, Tabak LA. 
                    Beyond the "omics": translating science into improved health 
                    J Am Dent Assoc  
                    2008; 
                    139
                    : 392-5.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR2">
            <journal_title>J Periodontol</journal_title>
            <author>Covani U</author>
            <volume>79</volume>
            <first_page>1974</first_page>
            <cYear>2008</cYear>
            <unstructured_citation>
                    Covani U, Marconcini S, Giacomelli L, Sivozhelevov V, Barone A, Nicolini C. 
                    Bioinformatic prediction of leader genes in human periodontitis 
                    J Periodontol  
                    2008; 
                    79
                    : 1974-83.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR3">
            <journal_title>J Periodontal Res</journal_title>
            <author>Steinberg T</author>
            <volume>41</volume>
            <first_page>426</first_page>
            <cYear>2006</cYear>
            <unstructured_citation>
                    Steinberg T, Dannewitz B, Tomakidi P, et al. 
                    Analysis of interleukin-1beta-modulated mRNA gene transcription in human gingival keratinocytes by epithelia-specific cDNA microarrays 
                    J Periodontal Res  
                    2006; 
                    41
                    : 426-6.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR4">
            <journal_title>J Periodontol</journal_title>
            <author>Vardar-Sengul S</author>
            <volume>80</volume>
            <first_page>833</first_page>
            <cYear>2009</cYear>
            <unstructured_citation>
                    Vardar-Sengul S, Arora S, Baylas H, Mercola D. 
                    Expression profile of human gingival fibroblasts induced by interleukin-1beta reveals central role of nuclear factor-kappa B in stabilizing human gingival fibroblasts during inflammation 
                    J Periodontol  
                    2009; 
                    80
                    : 833-49.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR5">
            <journal_title>BMC Med Genomics</journal_title>
            <author>Beikler T</author>
            <volume>1</volume>
            <first_page>30</first_page>
            <cYear>2008</cYear>
            <unstructured_citation>
                    Beikler T, Peters U, Prior K, Eisenacher M, Flemmig TF. 
                    Gene expression in periodontal tissues following treatment 
                    BMC Med Genomics  
                    2008; 
                    1
                    : 30.
                </unstructured_citation>
          </citation>
          <citation key="refR6">
            <journal_title>J Clin Microbiol</journal_title>
            <author>Igboin CO</author>
            <cYear>2009</cYear>
            <unstructured_citation>
                    Igboin CO, Griffen AL, Leys EJ. 
                    Analysis of Porphyromonas gingivalis strain diversity 
                    J Clin Microbiol 
                    2009.
                    
                 [Epub ahead of print]</unstructured_citation>
          </citation>
          <citation key="refR7">
            <journal_title>Eur J Clin Microbiol Infect Dis</journal_title>
            <author>Preza D</author>
            <cYear>2009</cYear>
            <unstructured_citation>
                    Preza D, Olsen I, Willumsen T, Grinde B, Paster BJ. 
                    Diversity and site-specificity of the oral microflora in the elderly 
                    Eur J Clin Microbiol Infect Dis 
                    2009.
                    
                 [Epub ahead of print]</unstructured_citation>
          </citation>
          <citation key="refR8">
            <journal_title>Mol Cells</journal_title>
            <author>Chung J</author>
            <volume>27</volume>
            <first_page>257</first_page>
            <cYear>2009</cYear>
            <unstructured_citation>
                    Chung J, Choi MJ, Jeong SY, Oh JS, Kim HK. 
                    Chemokines gene expression of RAW 264.7 cells by Actinobacillus actinomycetemcomitans lipopolysaccharide using microarray and RT-PCR analysis 
                    Mol Cells  
                    2009; 
                    27
                    : 257-61.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR9">
            <journal_title>J Oral Pathol Med</journal_title>
            <author>Tao XA</author>
            <volume>38</volume>
            <first_page>427</first_page>
            <cYear>2009</cYear>
            <unstructured_citation>
                    Tao XA, Li CY, Xia J, et al. 
                    Differential gene expression profiles of whole lesions from patients with oral lichen planus 
                    J Oral Pathol Med  
                    2009; 
                    38
                    : 427-33.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR10">
            <journal_title>J Am Dent Assoc</journal_title>
            <author>Diehl SR</author>
            <volume>137</volume>
            <first_page>710</first_page>
            <cYear>2006</cYear>
            <unstructured_citation>
                    Diehl SR. 
                    Pulling teeth into the genomics era 
                    J Am Dent Assoc  
                    2006; 
                    137
                    : 710-2.
                    
                    
                 714 passim</unstructured_citation>
          </citation>
          <citation key="refR11">
            <journal_title>J Periodontal Res</journal_title>
            <author>Wu Y</author>
            <volume>44</volume>
            <first_page>636</first_page>
            <cYear>2009</cYear>
            <unstructured_citation>
                    Wu Y, Shu R, Luo LJ, Ge LH, Xie YF. 
                    Initial comparison of proteomic profiles of whole unstimulated saliva obtained from generalized aggressive periodontitis patients and healthy control subjects 
                    J Periodontal Res  
                    2009; 
                    44
                    : 636-44.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR12">
            <journal_title>Oral Oncol</journal_title>
            <author>Yan SK</author>
            <volume>44</volume>
            <first_page>477</first_page>
            <cYear>2008</cYear>
            <unstructured_citation>
                    Yan SK, Wei BJ, Lin ZY, Yang Y, Zhou ZT, Zhang WD. 
                    A metabonomic approach to the diagnosis of oral squamous cell carcinoma, oral lichen planus and oral leukoplakia 
                    Oral Oncol  
                    2008; 
                    44
                    : 477-83.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR13">
            <journal_title>Ann N Y Acad Sci</journal_title>
            <author>Tanke HJ</author>
            <volume>1098</volume>
            <first_page>330</first_page>
            <cYear>2007</cYear>
            <unstructured_citation>
                    Tanke HJ. 
                    Genomics and proteomics: the potential role of oral diagnostics 
                    Ann N Y Acad Sci  
                    2007; 
                    1098
                    : 330-4.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR14">
            <journal_title>AMIA Annu Symp Proc</journal_title>
            <author>Giacomelli L</author>
            <volume>963</volume>
            <cYear>2007</cYear>
            <unstructured_citation>
                    Giacomelli L, Marconcini S, Derchi G, Barone A, Covani U. 
                    Leader genes: a data mining approach for molecular genomics 
                    AMIA Annu Symp Proc  
                    2007; 
                    963
                </unstructured_citation>
          </citation>
          <citation key="refR15">
            <journal_title>Nat Genet</journal_title>
            <author>Lehner B</author>
            <volume>38</volume>
            <first_page>896</first_page>
            <cYear>2006</cYear>
            <unstructured_citation>
                    Lehner B, Crombie C, Tischler J, Fortunato A, Fraser AG. 
                    Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways 
                    Nat Genet  
                    2006; 
                    38
                    : 896-903.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR16">
            <journal_title>J Cell Biochem</journal_title>
            <author>Sivozhelezov V</author>
            <volume>97</volume>
            <first_page>1137</first_page>
            <cYear>2006</cYear>
            <unstructured_citation>
                    Sivozhelezov V, Giacomelli L, Tripathi S, Nicolini C. 
                    Gene expression in the cell cycle of human T lymphocytes: predicted gene and protein networks 
                    J Cell Biochem  
                    2006; 
                    97
                    : 1137-50.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR17">
            <journal_title>J Cell Biochem</journal_title>
            <author>Giacomelli L</author>
            <volume>99</volume>
            <first_page>1326</first_page>
            <cYear>2006</cYear>
            <unstructured_citation>
                    Giacomelli L, Nicolini C. 
                    Gene expression in human T lymphocytes: experimental and bioinformatics analysis 
                    J Cell Biochem  
                    2006; 
                    99
                    : 1326-33.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR18">
            <journal_title>J Cell Biochem</journal_title>
            <author>Sivozhelezov V</author>
            <volume>103</volume>
            <first_page>1693</first_page>
            <cYear>2008</cYear>
            <unstructured_citation>
                    Sivozhelezov V, Braud C, Giacomelli L, et al. 
                    Immunosuppressive drug-free operational immune tollerance in human kidney transplant recipient: II Non-statistical gene microarray analysis 
                    J Cell Biochem  
                    2008; 
                    103
                    : 1693-706.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR19">
            <journal_title>J Periodontol</journal_title>
            <author>Covani U</author>
            <cYear>2009</cYear>
            <unstructured_citation>
                    Covani U, Marconcini S, Derchi G, Barone A, Giacomelli L. 
                    Relationship between human periodontitis and type 2 diabetes at a genomic level: a data-mining study 
                    J Periodontol 
                    2009.
                </unstructured_citation>
          </citation>
          <citation key="refR20">
            <journal_title>J Dent Educ</journal_title>
            <author>Wright JT</author>
            <volume>66</volume>
            <first_page>659</first_page>
            <cYear>2002</cYear>
            <unstructured_citation>
                    Wright JT, Hart TC. 
                    The genome projects: implications for dental practice and education 
                    J Dent Educ  
                    2002; 
                    66
                    : 659-71.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR21">
            <journal_title>Adv Dent Res</journal_title>
            <author>Kuo WP</author>
            <volume>17</volume>
            <first_page>89</first_page>
            <cYear>2003</cYear>
            <unstructured_citation>
                    Kuo WP. 
                    Overview of bioinformatics and its application to oral genomics 
                    Adv Dent Res  
                    2003; 
                    17
                    : 89-94.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR22">
            <journal_title>AI Magazine</journal_title>
            <author>Fayyad U</author>
            <volume>17</volume>
            <first_page>37</first_page>
            <cYear>1996</cYear>
            <unstructured_citation>
                    Fayyad U, Piatetsky-Shapiro G, Smyth P. 
                    From data mining to knowledge discovery in databases 
                    AI Magazine  
                    1996; 
                    17
                    : 37-54.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR23">
            <journal_title>Int J Med Inform</journal_title>
            <author>Käkilehto T</author>
            <cYear>2009</cYear>
            <unstructured_citation>
                    Käkilehto T, Salo S, Larmas M. 
                    Data mining of clinical oral health documents for analysis of the longevity of different restorative materials in Finland 
                    Int J Med Inform 
                    2009.
                    
                 [Epub ahead of print]</unstructured_citation>
          </citation>
          <citation key="refR24">
            <journal_title>J Oral Sci</journal_title>
            <author>Tamaki Y</author>
            <volume>51</volume>
            <first_page>61</first_page>
            <cYear>2009</cYear>
            <unstructured_citation>
                    Tamaki Y, Nomura Y, Katsumura S, et al. 
                    Construction of a dental caries prediction model by data mining 
                    J Oral Sci  
                    2009; 
                    51
                    : 61-8.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR25">
            <journal_title>J Clin Periodontol</journal_title>
            <author>Hettne KM</author>
            <volume>34</volume>
            <first_page>1016</first_page>
            <cYear>2007</cYear>
            <unstructured_citation>
                    Hettne KM, Weeber M, Laine ML, et al. 
                    Automatic mining of the literature to generate new hypotheses for the possible link between periodontitis and atherosclerosis: lipopolysaccharide as a case study 
                    J Clin Periodontol  
                    2007; 
                    34
                    : 1016-24.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR26">
            <unstructured_citation>
                    Marconcini S, Giacomelli L, Covani U, Barone A, Nicolini C. 
                    Leader genes in osteogenesis 
                    10th CCT international meting Faenza 
                    2006 May 23-27; 
                    
                    
                </unstructured_citation>
          </citation>
          <citation key="refR27">
            <journal_title>Nucleic Acids Res</journal_title>
            <author>von Mering C</author>
            <volume>35</volume>
            <first_page>D358</first_page>
            <cYear>2007</cYear>
            <unstructured_citation>
                    von Mering C, Jensen LJ, Kuhn M, et al. 
                    STRING 7-recent developments in the integration and prediction of protein interactions 
                    Nucleic Acids Res  
                    2007; 
                    35
                    (Database issue)
                    : D358-62.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR28">
            <journal_title>Med Oral</journal_title>
            <author>Luis-Delgado O</author>
            <volume>9</volume>
            <first_page>131-7</first_page>
            <cYear>2004</cYear>
            <unstructured_citation>
                    Luis-Delgado O, Echevarría-García JJ, Berini-Aytés L, Gay-Escoda C. 
                    Periodontitis as a risk factor in patients with ischemic heart disease 
                    Med Oral  
                    2004; 
                    9
                    : 131-7-125-31.
                    
                </unstructured_citation>
          </citation>
          <citation key="refR29">
            <journal_title>BMC Med Genet</journal_title>
            <author>Zhou B</author>
            <volume>10</volume>
            <first_page>47</first_page>
            <cYear>2009</cYear>
            <unstructured_citation>
                    Zhou B, Rao L, Peng Y, et al. 
                    Functional polymorphism of the NFKB1 gene promoter is related to the risk of dilated cardiomyopathy 
                    BMC Med Genet  
                    2009; 
                    10
                    : 47.
                </unstructured_citation>
          </citation>
        </citation_list>
      </journal_article>
    </journal>
  </body>
</doi_batch>
