메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers

Author keywords

Biomarkers; Classification; Computational; Ensemble; Genomics; Pipeline; Proteomics

Indexed keywords

ACUTE REJECTION; AGGREGATION METHODS; AREA UNDER THE CURVES; BEST VALUE; BIO-SAMPLES; BLOOD SAMPLES; CLASSIFICATION PERFORMANCE; CLINICAL USE; COMPUTATIONAL; ENSEMBLE; ENSEMBLE CLASSIFIERS; GENOMICS; INDIVIDUAL CLASSIFIERS; MICROARRAY DATA; MULTICENTER STUDY; PROTEOMIC; PROTEOMICS; RENAL TRANSPLANTS;

EID: 84870545296     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-326     Document Type: Article
Times cited : (32)

References (49)
  • 2
    • 33745004785 scopus 로고    scopus 로고
    • Biomarkers of cardiovascular disease: molecular basis and practical considerations
    • Vasan RS. Biomarkers of cardiovascular disease: molecular basis and practical considerations. Circulation 2006, 113:2335-2362.
    • (2006) Circulation , vol.113 , pp. 2335-2362
    • Vasan, R.S.1
  • 3
    • 72949100046 scopus 로고    scopus 로고
    • Biomarkers for the diagnosis, prognosis, and evaluation of treatment efficacy for traumatic brain injury
    • Dash PK, Zhao J, Hergenroeder G, Moore AN. Biomarkers for the diagnosis, prognosis, and evaluation of treatment efficacy for traumatic brain injury. Neurotherapeutics 2010, 7:100-114.
    • (2010) Neurotherapeutics , vol.7 , pp. 100-114
    • Dash, P.K.1    Zhao, J.2    Hergenroeder, G.3    Moore, A.N.4
  • 9
    • 79956352550 scopus 로고    scopus 로고
    • Advances of genomic science and systems biology in renal transplantation: a review
    • Perkins D, Verma M, Park KJ. Advances of genomic science and systems biology in renal transplantation: a review. Semin Immunopathol 2011, 33(2):211-218.
    • (2011) Semin Immunopathol , vol.33 , Issue.2 , pp. 211-218
    • Perkins, D.1    Verma, M.2    Park, K.J.3
  • 13
    • 67449135223 scopus 로고    scopus 로고
    • An integrative multi-platform analysis for discovering biomarkers of osteosarcoma
    • Li G, Zhang W, Zeng H, Chen L, Wang W, Liu J, Zhang Z, Cai Z. An integrative multi-platform analysis for discovering biomarkers of osteosarcoma. BMC Cancer 2009, 9:150.
    • (2009) BMC Cancer , vol.9 , pp. 150
    • Li, G.1    Zhang, W.2    Zeng, H.3    Chen, L.4    Wang, W.5    Liu, J.6    Zhang, Z.7    Cai, Z.8
  • 16
    • 75149176174 scopus 로고    scopus 로고
    • Ensemble-based classifiers
    • Rokach L. Ensemble-based classifiers. Artif Intell Rev 2010, 33:1-39.
    • (2010) Artif Intell Rev , vol.33 , pp. 1-39
    • Rokach, L.1
  • 17
    • 33748611921 scopus 로고    scopus 로고
    • Ensemble based systems in decision making
    • Polikar R. Ensemble based systems in decision making. Circ Syst Mag IEEE 2006, 6:21-45.
    • (2006) Circ Syst Mag IEEE , vol.6 , pp. 21-45
    • Polikar, R.1
  • 20
    • 59549093642 scopus 로고    scopus 로고
    • ArrayQualityMetrics-a bioconductor package for quality assessment of microarray data
    • Kauffmann A, Gentleman R, Huber W. ArrayQualityMetrics-a bioconductor package for quality assessment of microarray data. Bioinformatics 2009, 25:415-416.
    • (2009) Bioinformatics , vol.25 , pp. 415-416
    • Kauffmann, A.1    Gentleman, R.2    Huber, W.3
  • 23
    • 34548775883 scopus 로고    scopus 로고
    • RefPlus: an R package extending the RMA Algorithm
    • Harbron C, Chang K-M, South MC. RefPlus: an R package extending the RMA Algorithm. Bioinformatics 2007, 23:2493-2494.
    • (2007) Bioinformatics , vol.23 , pp. 2493-2494
    • Harbron, C.1    Chang, K.-M.2    South, M.C.3
  • 25
    • 33645823677 scopus 로고    scopus 로고
    • A new summarization method for Affymetrix probe level data
    • Hochreiter S, Clevert D-A, Obermayer K. A new summarization method for Affymetrix probe level data. Bioinformatics 2006, 22:943-949.
    • (2006) Bioinformatics , vol.22 , pp. 943-949
    • Hochreiter, S.1    Clevert, D.-A.2    Obermayer, K.3
  • 26
    • 77953095629 scopus 로고    scopus 로고
    • Independent filtering increases detection power for high-throughput experiments
    • Bourgon R, Gentleman R, Huber W. Independent filtering increases detection power for high-throughput experiments. Proc Nat Aca Sci USA 2010, 107:9546-9551.
    • (2010) Proc Nat Aca Sci USA , vol.107 , pp. 9546-9551
    • Bourgon, R.1    Gentleman, R.2    Huber, W.3
  • 27
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • Article 3
    • Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3. Article 3.
    • (2004) Stat Appl Genet Mol Biol , vol.3
    • Smyth, G.K.1
  • 28
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98:5116-5121.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 29
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc Series B (Methodological) 1995, 57:289-300.
    • (1995) J Royal Stat Soc Series B (Methodological) , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 30
    • 0043203327 scopus 로고    scopus 로고
    • Multiple hypothesis testing in microarray experiments
    • Dudoit, Shaffer JP, Boldrick JC. Multiple hypothesis testing in microarray experiments. Stat Sci 2003, 18:71-103.
    • (2003) Stat Sci , vol.18 , pp. 71-103
    • Dudoit1    Shaffer, J.P.2    Boldrick, J.C.3
  • 32
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Mach Learn 2001, 45:5-32.
    • (2001) Mach Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 33
    • 77950537175 scopus 로고    scopus 로고
    • Regularization paths for generalized linear models via coordinate descent
    • Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw 2010, 33:1-22.
    • (2010) J Stat Softw , vol.33 , pp. 1-22
    • Friedman, J.1    Hastie, T.2    Tibshirani, R.3
  • 35
    • 0037076272 scopus 로고    scopus 로고
    • Diagnosis of multiple cancer types by shrunken centroids of gene expression
    • Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 2002, 99:6567-6572.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 6567-6572
    • Tibshirani, R.1    Hastie, T.2    Narasimhan, B.3    Chu, G.4
  • 36
    • 69549090097 scopus 로고    scopus 로고
    • A model-based ensembling approach for developing QSARs
    • Zhang Q, Hughes-Oliver JM, Ng RT. A model-based ensembling approach for developing QSARs. J Chem Inform Model 2009, 49:1857-1865.
    • (2009) J Chem Inform Model , vol.49 , pp. 1857-1865
    • Zhang, Q.1    Hughes-Oliver, J.M.2    Ng, R.T.3
  • 37
    • 0037403516 scopus 로고    scopus 로고
    • Measures of diversity in classifier ensembles and their relationship with the ensemble accuracy
    • Kuncheva LI, Whitaker CJ. Measures of diversity in classifier ensembles and their relationship with the ensemble accuracy. Mach Learn 2003, 51:181-207.
    • (2003) Mach Learn , vol.51 , pp. 181-207
    • Kuncheva, L.I.1    Whitaker, C.J.2
  • 42
    • 84863325194 scopus 로고    scopus 로고
    • Diagnosing breast masses in digital mammography using feature selection and ensemble methods
    • Luo S-T, Cheng B-W. Diagnosing breast masses in digital mammography using feature selection and ensemble methods. J Med Syst 2010, 98(26):15149-15154.
    • (2010) J Med Syst , vol.98 , Issue.26 , pp. 15149-15154
    • Luo, S.-T.1    Cheng, B.-W.2
  • 43
    • 79551665221 scopus 로고    scopus 로고
    • Ensemble learning with active example selection for imbalanced biomedical data classification
    • Oh S, Lee MS, Zhang B-T. Ensemble learning with active example selection for imbalanced biomedical data classification. IEEE/ACM Trans Comput Biol Bioinform 2011, 8:316-325.
    • (2011) IEEE/ACM Trans Comput Biol Bioinform , vol.8 , pp. 316-325
    • Oh, S.1    Lee, M.S.2    Zhang, B.-T.3
  • 44
    • 84862651693 scopus 로고    scopus 로고
    • Mito-GSAAC: mitochondria prediction using genetic ensemble classifier and split amino acid composition
    • Afridi TH, Khan A, Lee YS. Mito-GSAAC: mitochondria prediction using genetic ensemble classifier and split amino acid composition. Amino Acids 2011, 42(4):1443-1454.
    • (2011) Amino Acids , vol.42 , Issue.4 , pp. 1443-1454
    • Afridi, T.H.1    Khan, A.2    Lee, Y.S.3
  • 46
    • 78649653097 scopus 로고    scopus 로고
    • Rejection and function and chronic allograft dysfunction
    • de Fijter JW. Rejection and function and chronic allograft dysfunction. Kidney Int Suppl 2010, 78(S119):S38-S41.
    • (2010) Kidney Int Suppl , vol.78 , Issue.S119
    • de Fijter, J.W.1
  • 47
    • 22544475586 scopus 로고    scopus 로고
    • GEMS: a system for automated cancer diagnosis and biomarker discovery from microarray gene expression data
    • Statnikov A, Tsamardinos I, Dosbayev Y, Aliferis CF. GEMS: a system for automated cancer diagnosis and biomarker discovery from microarray gene expression data. Int J Med Inform 2005, 74:491-503.
    • (2005) Int J Med Inform , vol.74 , pp. 491-503
    • Statnikov, A.1    Tsamardinos, I.2    Dosbayev, Y.3    Aliferis, C.F.4
  • 48
    • 58749086251 scopus 로고    scopus 로고
    • Mistakes in validating the accuracy of a prediction classifier in high-dimensional but small-sample microarray data
    • Lee S. Mistakes in validating the accuracy of a prediction classifier in high-dimensional but small-sample microarray data. Stat Methods Med Res 2008, 17:635-642.
    • (2008) Stat Methods Med Res , vol.17 , pp. 635-642
    • Lee, S.1
  • 49
    • 84861123691 scopus 로고    scopus 로고
    • Ten years of pathway analysis: current approaches and outstanding challenges
    • Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comp Bio 2012, 8(2).
    • (2012) PLoS Comp Bio , vol.8 , Issue.2
    • Khatri, P.1    Sirota, M.2    Butte, A.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.