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Volumn 17, Issue 9, 2016, Pages

Omics-based strategies in precision medicine: Toward a paradigm shift in inborn errors of metabolism investigations

Author keywords

Bioinformatics; Biomarkers; Chemometrics; Data integration; Inborn errors of metabolism; Machine learning; Mass spectrometry; Next generation sequencing; Omics; Precision medicine

Indexed keywords

DNA POLYMERASE;

EID: 84987749377     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms17091555     Document Type: Review
Times cited : (140)

References (188)
  • 1
    • 84923762812 scopus 로고    scopus 로고
    • New initiative on precision medicine
    • [CrossRef] [PubMed]
    • Collins, F.S.; Varmus, H. A new initiative on precision medicine. N. Engl. J. Med. 2015, 372, 793-795. [CrossRef] [PubMed]
    • (2015) N. Engl. J. Med , vol.372 , pp. 793-795
    • Collins, F.S.1    Varmus, H.A.2
  • 2
    • 33745588546 scopus 로고    scopus 로고
    • The limits of reductionism in medicine: Could systems biology offer an alternative
    • [CrossRef] [PubMed]
    • Ahn, A.C.; Tewari, M.; Poon, C.S.; Phillips, R.S. The limits of reductionism in medicine: Could systems biology offer an alternative? PLoS Med. 2006, 3, e208. [CrossRef] [PubMed]
    • (2006) Plos Med , pp. 3
    • Ahn, A.C.1    Tewari, M.2    Poon, C.S.3    Phillips, R.S.4
  • 3
    • 10044298236 scopus 로고    scopus 로고
    • Reductionism and complexity in molecular biology: Scientists now have the tools to unravel biological and overcome the limitations of reductionism
    • [CrossRef] [PubMed]
    • Van Regenmortel M.H. Reductionism and complexity in molecular biology: Scientists now have the tools to unravel biological and overcome the limitations of reductionism. EMBO Rep. 2004, 5, 1016-1020. [CrossRef] [PubMed]
    • (2004) EMBO Rep , vol.5 , pp. 1016-1020
    • van Regenmortel, M.H.1
  • 4
    • 84904286951 scopus 로고    scopus 로고
    • Complex systems biology of networks: The riddle and the challenge
    • Springer Berlin Heidelberg: Heidelberg, Germany
    • Aon, M.A. Complex systems biology of networks: The riddle and the challenge. In Systems Biology of Metabolic and Signaling Networks; Springer Berlin Heidelberg: Heidelberg, Germany, 2014; pp. 19-35.
    • (2014) In Systems Biology of Metabolic and Signaling Networks , pp. 19-35
    • Aon, M.A.1
  • 5
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • [CrossRef] [PubMed]
    • Kitano, H. Systems biology: A brief overview. Science 2002, 295, 1662-1664. [CrossRef] [PubMed]
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 6
    • 33646893457 scopus 로고    scopus 로고
    • Inborn errors of metabolism: The flux from mendelian to complex diseases
    • [CrossRef] [PubMed]
    • Lanpher, B.; Brunetti-Pierri, N.; Lee, B. Inborn errors of metabolism: The flux from mendelian to complex diseases. Nat. Rev. Genet. 2006, 7, 449-460. [CrossRef] [PubMed]
    • (2006) Nat. Rev. Genet , vol.7 , pp. 449-460
    • Lanpher, B.1    Brunetti-Pierri, N.2    Lee, B.3
  • 7
    • 68049140098 scopus 로고
    • The structure of DNA. Cold Spring Harb
    • [CrossRef] [PubMed]
    • Watson, J.D.; Crick, F.H. The structure of DNA. Cold Spring Harb. Symp. Quant. Biol. 1953, 18, 123-131. [CrossRef] [PubMed]
    • (1953) Symp. Quant. Biol , vol.18 , pp. 123-131
    • Watson, J.D.1    Crick, F.H.2
  • 8
    • 84968903135 scopus 로고    scopus 로고
    • Coming of age: Ten years of next-generation sequencing technologies
    • [CrossRef] [PubMed]
    • Goodwin, S.; McPherson, J.D.; McCombie W.R. Coming of age: Ten years of next-generation sequencing technologies. Nat. Rev. Genet. 2016, 17, 333-351. [CrossRef] [PubMed]
    • (2016) Nat. Rev. Genet , vol.17 , pp. 333-351
    • Goodwin, S.1    McPherson, J.D.2    McCombie, W.R.3
  • 12
    • 79251645624 scopus 로고    scopus 로고
    • Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease
    • [CrossRef] [PubMed]
    • Worthey, E.A.; Mayer, A.N.; Syverson, G.D.; Helbling, D.; Bonacci, B.B.; Decker, B.; Serpe, J.M.; Dasu, T.; Tschannen, M.R.; Veith, R.L. et al. Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med. 2011, 13, 255-262. [CrossRef] [PubMed]
    • (2011) Genet. Med , vol.13 , pp. 255-262
    • Worthey, E.A.1    Mayer, A.N.2    Syverson, G.D.3    Helbling, D.4    Bonacci, B.B.5    Decker, B.6    Serpe, J.M.7    Dasu, T.8    Tschannen, M.R.9    Veith, R.L.10
  • 13
    • 84958928645 scopus 로고    scopus 로고
    • Clinical implications of omics and systems medicine: Focus on predictive and individualized treatment
    • [CrossRef] [PubMed]
    • Benson, M. Clinical implications of omics and systems medicine: Focus on predictive and individualized treatment. J. Intern. Med. 2016, 279, 229-240. [CrossRef] [PubMed]
    • (2016) J. Intern. Med , vol.279 , pp. 229-240
    • Benson, M.1
  • 16
    • 77952574849 scopus 로고    scopus 로고
    • Uncovering the roles of rare variants in common disease through whole-genome sequencing
    • [CrossRef] [PubMed]
    • Cirulli, E.T.; Goldstein, D.B. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat. Rev. Genet. 2010, 11, 415-425. [CrossRef] [PubMed]
    • (2010) Nat. Rev. Genet , vol.11 , pp. 415-425
    • Cirulli, E.T.1    Goldstein, D.B.2
  • 17
    • 84949627233 scopus 로고    scopus 로고
    • Exome and genome sequencing: A revolution for the discovery and diagnosis of monogenic disorders
    • [CrossRef] [PubMed]
    • Stranneheim, H.; Wedell, A. Exome and genome sequencing: A revolution for the discovery and diagnosis of monogenic disorders. J. Intern. Med. 2016, 279, 3-15. [CrossRef] [PubMed]
    • (2016) J. Intern. Med , vol.279 , pp. 3-15
    • Stranneheim, H.1    Wedell, A.2
  • 19
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • [CrossRef] [PubMed]
    • Mortazavi, A.; Williams, B.A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5, 621-628. [CrossRef] [PubMed]
    • (2008) Nat. Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 21
    • 0017681196 scopus 로고
    • DNA sequencing with chain-terminating inhibitors
    • [CrossRef] [PubMed]
    • Sanger, F.; Nicklen, S.; Coulson, A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 1977, 74, 5463-5467. [CrossRef] [PubMed]
    • (1977) Proc. Natl. Acad. Sci. USA , vol.74 , pp. 5463-5467
    • Sanger, F.1    Nicklen, S.2    Coulson, A.R.3
  • 27
    • 84929662757 scopus 로고    scopus 로고
    • High-throughput sequencing technologies
    • [CrossRef] [PubMed]
    • Reuter, J.A.; Spacek, D.V.; Snyder, M.P. High-throughput sequencing technologies. Mol. Cell 2015, 58, 586-597. [CrossRef] [PubMed]
    • (2015) Mol. Cell , vol.58 , pp. 586-597
    • Reuter, J.A.1    Spacek, D.V.2    Snyder, M.P.3
  • 29
    • 84879627975 scopus 로고    scopus 로고
    • Next-generation sequencing platforms
    • [CrossRef] [PubMed]
    • Mardis, E.R. Next-generation sequencing platforms. Annu. Rev. Anal. Chem. 2013, 6, 287-303. [CrossRef] [PubMed]
    • (2013) Annu. Rev. Anal. Chem , vol.6 , pp. 287-303
    • Mardis, E.R.1
  • 30
    • 85027949514 scopus 로고    scopus 로고
    • Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients
    • [CrossRef] [PubMed]
    • Lim, E.C.; Brett, M.; Lai, A.H.; Lee, S.P.; Tan, E.S.; Jamuar, S.S.; Ng, I.S.; Tan, E.C. Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients. Hum. Genom. 2015, 9, 33. [CrossRef] [PubMed]
    • (2015) Hum. Genom , vol.9 , pp. 33
    • Lim, E.C.1    Brett, M.2    Lai, A.H.3    Lee, S.P.4    Tan, E.S.5    Jamuar, S.S.6    Ng, I.S.7    Tan, E.C.8
  • 31
    • 84903618205 scopus 로고    scopus 로고
    • Use of whole-exome sequencing to determine the genetic basis of multiple mitochondrial respiratory chain complex deficiencies
    • [CrossRef] [PubMed]
    • Taylor, R.W.; Pyle, A.; Griffin, H.; Blakely, E.L.; Duff, J.; He, L.; Smertenko, T.; Alston, C.L.; Neeve, V.C.; Best, A. et al. Use of whole-exome sequencing to determine the genetic basis of multiple mitochondrial respiratory chain complex deficiencies. JAMA 2014, 312, 68-77. [CrossRef] [PubMed]
    • (2014) JAMA , vol.312 , pp. 68-77
    • Taylor, R.W.1    Pyle, A.2    Griffin, H.3    Blakely, E.L.4    Duff, J.5    He, L.6    Smertenko, T.7    Alston, C.L.8    Neeve, V.C.9    Best, A.10
  • 32
    • 84948712119 scopus 로고    scopus 로고
    • Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes
    • [CrossRef] [PubMed]
    • Howard, H.C.; Knoppers, B.M.; Cornel, M.C.; Wright Clayton, E.; Senecal, K.; Borry, P. Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. Eur. J. Hum. Genet. 2015, 23, 1593-1600. [CrossRef] [PubMed]
    • (2015) Eur. J. Hum. Genet , vol.23 , pp. 1593-1600
    • Howard, H.C.1    Knoppers, B.M.2    Cornel, M.C.3    Wright Clayton, E.4    Senecal, K.5    Borry, P.6
  • 33
    • 84982270082 scopus 로고    scopus 로고
    • Towards precision medicine
    • [CrossRef] [PubMed]
    • Ashley, E.A. Towards precision medicine. Nat. Rev. Genet. 2016, 17, 507-522. [CrossRef] [PubMed]
    • (2016) Nat. Rev. Genet , vol.17 , pp. 507-522
    • Ashley, E.A.1
  • 34
    • 84987741834 scopus 로고    scopus 로고
    • A precision metric for clinical genome sequencing
    • [CrossRef]
    • Goldfeder, R.L.; Ashley, E.A. A precision metric for clinical genome sequencing. bioRxiv 2016, 051490. [CrossRef]
    • (2016) Biorxiv
    • Goldfeder, R.L.1    Ashley, E.A.2
  • 35
    • 34249337761 scopus 로고    scopus 로고
    • Perceptions of epigenetics
    • [CrossRef] [PubMed]
    • Bird, A. Perceptions of epigenetics. Nature 2007, 447, 396-398. [CrossRef] [PubMed]
    • (2007) Nature , vol.447 , pp. 396-398
    • Bird, A.1
  • 36
    • 84895446627 scopus 로고    scopus 로고
    • Epigenetics: The language of the cell?
    • [CrossRef] [PubMed]
    • Huang, B.; Jiang, C.; Zhang, R. Epigenetics: The language of the cell? Epigenomics 2014, 6, 73-88. [CrossRef] [PubMed]
    • (2014) Epigenomics , vol.6 , pp. 73-88
    • Huang, B.1    Jiang, C.2    Zhang, R.3
  • 37
    • 84921421088 scopus 로고    scopus 로고
    • A comprehensive view of the epigenetic landscape. Part II: Histone post-translational modification, nucleosome level, and chromatin regulation by ncRNAs
    • [CrossRef] [PubMed]
    • Sadakierska-Chudy, A.; Filip, M. A comprehensive view of the epigenetic landscape. Part II: Histone post-translational modification, nucleosome level, and chromatin regulation by ncRNAs. Neurotox. Res. 2015, 27, 172-197. [CrossRef] [PubMed]
    • (2015) Neurotox. Res , vol.27 , pp. 172-197
    • Sadakierska-Chudy, A.1    Filip, M.2
  • 38
    • 84922004823 scopus 로고    scopus 로고
    • Comprehensive view of the epigenetic landscape part I: DNA methylation, passive and active DNA demethylation pathways and histone variants
    • [CrossRef] [PubMed]
    • Sadakierska-Chudy, A.; Kostrzewa, R.M.; Filip, M. A comprehensive view of the epigenetic landscape part I: DNA methylation, passive and active DNA demethylation pathways and histone variants. Neurotox. Res. 2015, 27, 84-97. [CrossRef] [PubMed]
    • (2015) Neurotox. Res , vol.27 , pp. 84-97
    • Sadakierska-Chudy, A.1    Kostrzewa, R.M.2    Filip, M.A.3
  • 40
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • [CrossRef] [PubMed]
    • Barski, A.; Cuddapah, S.; Cui, K.; Roh, T.Y.; Schones, D.E.; Wang, Z.; Wei, G.; Chepelev, I.; Zhao, K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129, 823-837. [CrossRef] [PubMed]
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.Y.4    Schones, D.E.5    Wang, Z.6    Wei, G.7    Chepelev, I.8    Zhao, K.9
  • 41
    • 44849121274 scopus 로고    scopus 로고
    • Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions
    • [CrossRef] [PubMed]
    • Yaragatti, M.; Basilico, C.; Dailey, L. Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions. Genome Res. 2008, 18, 930-938. [CrossRef] [PubMed]
    • (2008) Genome Res , vol.18 , pp. 930-938
    • Yaragatti, M.1    Basilico, C.2    Dailey, L.3
  • 44
    • 84908207355 scopus 로고    scopus 로고
    • Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
    • [CrossRef] [PubMed]
    • Meyer, C.A.; Liu, X.S. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat. Rev. Genet. 2014, 15, 709-721. [CrossRef] [PubMed]
    • (2014) Nat. Rev. Genet , vol.15 , pp. 709-721
    • Meyer, C.A.1    Liu, X.S.2
  • 45
    • 84871403110 scopus 로고    scopus 로고
    • Epigenome-wide analysis in familial hypercholesterolemia identified new loci associated with high-density lipoprotein cholesterol concentration
    • [CrossRef] [PubMed]
    • Guay, S.P.; Voisin, G.; Brisson, D.; Munger, J.; Lamarche, B.; Gaudet, D.; Bouchard, L. Epigenome-wide analysis in familial hypercholesterolemia identified new loci associated with high-density lipoprotein cholesterol concentration. Epigenomics 2012, 4, 623-639. [CrossRef] [PubMed]
    • (2012) Epigenomics , vol.4 , pp. 623-639
    • Guay, S.P.1    Voisin, G.2    Brisson, D.3    Munger, J.4    Lamarche, B.5    Gaudet, D.6    Bouchard, L.7
  • 46
    • 57749195712 scopus 로고    scopus 로고
    • RNA-seq: A revolutionary tool for transcriptomics
    • [CrossRef] [PubMed]
    • Wang, Z.; Gerstein, M.; Snyder, M. RNA-seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10, 57-63. [CrossRef] [PubMed]
    • (2009) Nat. Rev. Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 52
    • 84953738781 scopus 로고    scopus 로고
    • Toward merging untargeted and targeted methods in mass spectrometry-based metabolomics and lipidomics
    • [CrossRef] [PubMed]
    • Cajka, T.; Fiehn, O. Toward merging untargeted and targeted methods in mass spectrometry-based metabolomics and lipidomics. Anal. Chem. 2015, 88, 524-545. [CrossRef] [PubMed]
    • (2015) Anal. Chem , vol.88 , pp. 524-545
    • Cajka, T.1    Fiehn, O.2
  • 53
    • 84930067094 scopus 로고    scopus 로고
    • Clinical protein mass spectrometry
    • [CrossRef] [PubMed]
    • Scherl, A. Clinical protein mass spectrometry. Methods 2015, 81, 3-14. [CrossRef] [PubMed]
    • (2015) Methods , vol.81 , pp. 3-14
    • Scherl, A.1
  • 55
    • 84975521607 scopus 로고    scopus 로고
    • Advanced multidimensional separations in mass spectrometry: Navigating the big data deluge
    • [CrossRef] [PubMed]
    • May, J.C.; McLean, J.A. Advanced multidimensional separations in mass spectrometry: Navigating the big data deluge. Annu. Rev. Anal. Chem. 2016, 9, 387-409. [CrossRef] [PubMed]
    • (2016) Annu. Rev. Anal. Chem , vol.9 , pp. 387-409
    • May, J.C.1    McLean, J.A.2
  • 56
    • 84990253074 scopus 로고    scopus 로고
    • Optimization of a liquid chromatography ion mobility-mass spectrometry method for untargeted metabolomics using experimental design and multivariate data analysis
    • [CrossRef] [PubMed]
    • Tebani, A.; Schmitz-Afonso, I.; Rutledge, D.N.; Gonzalez, B.J.; Bekri, S.; Afonso, C. Optimization of a liquid chromatography ion mobility-mass spectrometry method for untargeted metabolomics using experimental design and multivariate data analysis. Anal. Chim. Acta 2016, 913, 55-62. [CrossRef] [PubMed]
    • (2016) Anal. Chim. Acta , vol.913 , pp. 55-62
    • Tebani, A.1    Schmitz-Afonso, I.2    Rutledge, D.N.3    Gonzalez, B.J.4    Bekri, S.5    Afonso, C.6
  • 57
    • 0031398974 scopus 로고    scopus 로고
    • Protein identification in the post-genome era: The rapid rise of proteomics
    • [CrossRef]
    • James, P. Protein identification in the post-genome era: The rapid rise of proteomics. Quart. Rev. Biophys. 1997, 30, 279-331. [CrossRef]
    • (1997) Quart. Rev. Biophys , vol.30 , pp. 279-331
    • James, P.1
  • 58
    • 84910679144 scopus 로고    scopus 로고
    • Proteome-wide post-translational modification statistics: Frequency analysis and curation of the swiss-prot database
    • [CrossRef] [PubMed]
    • Khoury, G.A.; Baliban, R.C.; Floudas, C.A. Proteome-wide post-translational modification statistics: Frequency analysis and curation of the swiss-prot database. Sci. Rep. 2011, 1, 90. [CrossRef] [PubMed]
    • (2011) Sci. Rep , vol.1 , pp. 90
    • Khoury, G.A.1    Baliban, R.C.2    Floudas, C.A.3
  • 60
    • 84960384497 scopus 로고    scopus 로고
    • Clinical applications of ms-based protein quantification
    • [CrossRef] [PubMed]
    • Sabbagh, B.; Mindt, S.; Neumaier, M.; Findeisen, P. Clinical applications of ms-based protein quantification. Proteom. Clin. Appl. 2016, 10, 323-345. [CrossRef] [PubMed]
    • (2016) Proteom. Clin. Appl , vol.10 , pp. 323-345
    • Sabbagh, B.1    Mindt, S.2    Neumaier, M.3    Findeisen, P.4
  • 62
    • 84939267729 scopus 로고    scopus 로고
    • Urine proteomic analysis in cystinuric children with renal stones
    • 217.e1-217.e6[CrossRef] [PubMed]
    • Kovacevic, L.; Lu, H.; Goldfarb, D.S.; Lakshmanan, Y.; Caruso, J.A. Urine proteomic analysis in cystinuric children with renal stones. J. Pediatr. Urol. 2015, 11, 217.e1-217.e6. [CrossRef] [PubMed]
    • (2015) J. Pediatr. Urol , vol.11
    • Kovacevic, L.1    Lu, H.2    Goldfarb, D.S.3    Lakshmanan, Y.4    Caruso, J.A.5
  • 63
    • 84950119296 scopus 로고    scopus 로고
    • Proteomic discovery and development of a multiplexed targeted mrm-lc-ms/ms assay for urine biomarkers of extracellular matrix disruption in mucopolysaccharidoses I, II, and VI
    • [CrossRef] [PubMed]
    • Heywood, W.E.; Camuzeaux, S.; Doykov, I.; Patel, N.; Preece, R.L.; Footitt, E.; Cleary, M.; Clayton, P.; Grunewald, S.; Abulhoul, L. et al. Proteomic discovery and development of a multiplexed targeted mrm-lc-ms/ms assay for urine biomarkers of extracellular matrix disruption in mucopolysaccharidoses I, II, and VI. Anal. Chem. 2015, 87, 12238-12244. [CrossRef] [PubMed]
    • (2015) Anal. Chem , vol.87 , pp. 12238-12244
    • Heywood, W.E.1    Camuzeaux, S.2    Doykov, I.3    Patel, N.4    Preece, R.L.5    Footitt, E.6    Cleary, M.7    Clayton, P.8    Grunewald, S.9    Abulhoul, L.10
  • 65
    • 84879446684 scopus 로고    scopus 로고
    • Bringing proteomics into the clinic: The need for the field to finally take itself seriously
    • [CrossRef] [PubMed]
    • Martens, L. Bringing proteomics into the clinic: The need for the field to finally take itself seriously. Proteom. Clin. Appl. 2013, 7, 388-391. [CrossRef] [PubMed]
    • (2013) Proteom. Clin. Appl , vol.7 , pp. 388-391
    • Martens, L.1
  • 66
    • 50249099816 scopus 로고    scopus 로고
    • Metabolic phenotyping in health and disease
    • [CrossRef] [PubMed]
    • Holmes, E.; Wilson, I.D.; Nicholson, J.K. Metabolic phenotyping in health and disease. Cell 2008, 134, 714-717. [CrossRef] [PubMed]
    • (2008) Cell , vol.134 , pp. 714-717
    • Holmes, E.1    Wilson, I.D.2    Nicholson, J.K.3
  • 67
    • 0032168794 scopus 로고    scopus 로고
    • Systematic functional analysis of the yeast genome
    • [CrossRef]
    • Oliver, S.G.; Winson, M.K.; Kell, D.B.; Baganz, F. Systematic functional analysis of the yeast genome. Trends Biotechnol. 1998, 16, 373-378. [CrossRef]
    • (1998) Trends Biotechnol , vol.16 , pp. 373-378
    • Oliver, S.G.1    Winson, M.K.2    Kell, D.B.3    Baganz, F.4
  • 68
    • 0032694577 scopus 로고    scopus 로고
    • Metabonomics”: Understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data
    • [CrossRef] [PubMed]
    • Nicholson, J.K.; Lindon, J.C.; Holmes, E. “Metabonomics”: Understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 1999, 29, 1181-1189. [CrossRef] [PubMed]
    • (1999) Xenobiotica , vol.29 , pp. 1181-1189
    • Nicholson, J.K.1    Lindon, J.C.2    Holmes, E.3
  • 69
    • 84869049715 scopus 로고    scopus 로고
    • Metabolic phenotyping in clinical and surgical environments
    • [CrossRef] [PubMed]
    • Nicholson, J.K.; Holmes, E.; Kinross, J.M.; Darzi, A.W.; Takats, Z.; Lindon, J.C. Metabolic phenotyping in clinical and surgical environments. Nature 2012, 491, 384-392. [CrossRef] [PubMed]
    • (2012) Nature , vol.491 , pp. 384-392
    • Nicholson, J.K.1    Holmes, E.2    Kinross, J.M.3    Darzi, A.W.4    Takats, Z.5    Lindon, J.C.6
  • 70
    • 84950326824 scopus 로고    scopus 로고
    • Biochemical insights from population studies with genetics and metabolomics
    • [CrossRef] [PubMed]
    • Suhre, K.; Raffler, J.; Kastenmüller, G. Biochemical insights from population studies with genetics and metabolomics. Arch. Biochem. Biophys. 2016, 589, 168-176. [CrossRef] [PubMed]
    • (2016) Arch. Biochem. Biophys , vol.589 , pp. 168-176
    • Suhre, K.1    Raffler, J.2    Kastenmüller, G.3
  • 71
    • 85039998984 scopus 로고    scopus 로고
    • Analytical methods in untargeted metabolomics: State of the art in 2015
    • [CrossRef] [PubMed]
    • Alonso, A.; Marsal, S.; Julia, A. Analytical methods in untargeted metabolomics: State of the art in 2015. Front. Bioeng. Biotechnol. 2015, 3, 23. [CrossRef] [PubMed]
    • (2015) Front. Bioeng. Biotechnol , vol.3 , pp. 23
    • Alonso, A.1    Marsal, S.2    Julia, A.3
  • 73
    • 84869485096 scopus 로고    scopus 로고
    • Metabonomics of newborn screening dried blood spot samples: A novel approach in the screening and diagnostics of inborn errors of metabolism. Anal
    • [CrossRef] [PubMed]
    • Denes, J.; Szabo, E.; Robinette, S.L.; Szatmari, I.; Szonyi, L.; Kreuder, J.G.; Rauterberg, E.W.; Takats, Z. Metabonomics of newborn screening dried blood spot samples: A novel approach in the screening and diagnostics of inborn errors of metabolism. Anal. Chem. 2012, 84, 10113-10120. [CrossRef] [PubMed]
    • (2012) Chem , vol.84 , pp. 10113-10120
    • Denes, J.1    Szabo, E.2    Robinette, S.L.3    Szatmari, I.4    Szonyi, L.5    Kreuder, J.G.6    Rauterberg, E.W.7    Takats, Z.8
  • 74
    • 84973236606 scopus 로고    scopus 로고
    • NMR-based screening for inborn errors of metabolism: Initial results from a study on turkish neonates
    • [PubMed]
    • Aygen, S.; Durr, U.; Hegele, P.; Kunig, J.; Spraul, M.; Schafer, H.; Krings, D.; Cannet, C.; Fang, F.; Schutz, B. et al. NMR-based screening for inborn errors of metabolism: Initial results from a study on turkish neonates. JIMD Rep. 2014, 16, 101-111. [PubMed]
    • (2014) JIMD Rep , vol.16 , pp. 101-111
    • Aygen, S.1    Durr, U.2    Hegele, P.3    Kunig, J.4    Spraul, M.5    Schafer, H.6    Krings, D.7    Cannet, C.8    Fang, F.9    Schutz, B.10
  • 76
    • 84979022687 scopus 로고    scopus 로고
    • Clinical metabolomics: The new metabolic window for inborn errors of metabolism investigations in the post-genomic era
    • [CrossRef] [PubMed]
    • Tebani, A.; Abily-Donval, L.; Afonso, C.; Marret, S.; Bekri, S. Clinical metabolomics: The new metabolic window for inborn errors of metabolism investigations in the post-genomic era. Int. J. Mol. Sci. 2016, 17, 1167. [CrossRef] [PubMed]
    • (2016) Int. J. Mol. Sci , vol.1167 , pp. 17
    • Tebani, A.1    Abily-Donval, L.2    Afonso, C.3    Marret, S.4    Bekri, S.5
  • 77
    • 78549246207 scopus 로고    scopus 로고
    • Phenomics: The next challenge
    • [CrossRef] [PubMed]
    • Houle, D.; Govindaraju, D.R.; Omholt, S. Phenomics: The next challenge. Nat. Rev. Genet. 2010, 11, 855-866. [CrossRef] [PubMed]
    • (2010) Nat. Rev. Genet , vol.11 , pp. 855-866
    • Houle, D.1    Govindaraju, D.R.2    Omholt, S.3
  • 78
    • 70450223891 scopus 로고    scopus 로고
    • Common disorders are quantitative traits. Nat
    • [CrossRef] [PubMed]
    • Plomin, R.; Haworth, C.M.; Davis, O.S. Common disorders are quantitative traits. Nat. Rev. Genet. 2009, 10, 872-878. [CrossRef] [PubMed]
    • (2009) Rev. Genet , vol.10 , pp. 872-878
    • Plomin, R.1    Haworth, C.M.2    Davis, O.S.3
  • 79
    • 84958659058 scopus 로고    scopus 로고
    • Unravelling the human genome-phenome relationship using phenome-wide association studies
    • [CrossRef] [PubMed]
    • Bush, W.S.; Oetjens, M.T.; Crawford, D.C. Unravelling the human genome-phenome relationship using phenome-wide association studies. Nat. Rev. Genet. 2016, 17, 129-145. [CrossRef] [PubMed]
    • (2016) Nat. Rev. Genet , vol.17 , pp. 129-145
    • Bush, W.S.1    Oetjens, M.T.2    Crawford, D.C.3
  • 81
    • 0038670579 scopus 로고    scopus 로고
    • The human phenome project
    • [CrossRef] [PubMed]
    • Freimer, N.; Sabatti, C. The human phenome project. Nat. Genet. 2003, 34, 15-21. [CrossRef] [PubMed]
    • (2003) Nat. Genet , vol.34 , pp. 15-21
    • Freimer, N.1    Sabatti, C.2
  • 82
    • 0036775142 scopus 로고    scopus 로고
    • Phenomics: Fiction or the future
    • [CrossRef]
    • Gerlai, R. Phenomics: Fiction or the future? Trends Neurosci. 2002, 25, 506-509. [CrossRef]
    • (2002) Trends Neurosci , vol.25 , pp. 506-509
    • Gerlai, R.1
  • 85
    • 84925031191 scopus 로고    scopus 로고
    • Methods of integrating data to uncover genotype-phenotype interactions
    • [CrossRef] [PubMed]
    • Ritchie, M.D.; Holzinger, E.R.; Li, R.; Pendergrass, S.A.; Kim, D. Methods of integrating data to uncover genotype-phenotype interactions. Nat. Rev. Genet. 2015, 16, 85-97. [CrossRef] [PubMed]
    • (2015) Nat. Rev. Genet , vol.16 , pp. 85-97
    • Ritchie, M.D.1    Holzinger, E.R.2    Li, R.3    Pendergrass, S.A.4    Kim, D.5
  • 86
    • 41649090385 scopus 로고    scopus 로고
    • “Deep phenotyping”: Characterizing populations in the era of genomics and systems biology
    • [CrossRef] [PubMed]
    • Tracy, R.P. “Deep phenotyping”: Characterizing populations in the era of genomics and systems biology. Curr. Opin. Lipidol. 2008, 19, 151-157. [CrossRef] [PubMed]
    • (2008) Curr. Opin. Lipidol , vol.19 , pp. 151-157
    • Tracy, R.P.1
  • 87
    • 84962310114 scopus 로고    scopus 로고
    • Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams
    • [CrossRef] [PubMed]
    • Shameer, K.; Badgeley, M.A.; Miotto, R.; Glicksberg, B.S.; Morgan, J.W.; Dudley, J.T. Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. Brief. Bioinform. 2016. [CrossRef] [PubMed]
    • (2016) Brief. Bioinform
    • Shameer, K.1    Badgeley, M.A.2    Miotto, R.3    Glicksberg, B.S.4    Morgan, J.W.5    Dudley, J.T.6
  • 89
    • 84947870697 scopus 로고    scopus 로고
    • Integrative phenotyping framework (IPF): Integrative clustering of multiple omics data identifies novel lung disease subphenotypes
    • [CrossRef] [PubMed]
    • Kim, S.; Herazo-Maya, J.D.; Kang, D.D.; Juan-Guardela, B.M.; Tedrow, J.; Martinez, F.J.; Sciurba, F.C.; Tseng, G.C.; Kaminski, N. Integrative phenotyping framework (iPF): Integrative clustering of multiple omics data identifies novel lung disease subphenotypes. BMC Genom. 2015, 16, 1-11. [CrossRef] [PubMed]
    • (2015) BMC Genom , vol.16 , pp. 1-11
    • Kim, S.1    Herazo-Maya, J.D.2    Kang, D.D.3    Juan-Guardela, B.M.4    Tedrow, J.5    Martinez, F.J.6    Sciurba, F.C.7    Tseng, G.C.8    Kaminski, N.9
  • 91
    • 84955254841 scopus 로고    scopus 로고
    • A next generation multiscale view of inborn errors of metabolism
    • [CrossRef] [PubMed]
    • Argmann, C.A.; Houten, S.M.; Zhu, J.; Schadt, E.E. A next generation multiscale view of inborn errors of metabolism. Cell Metab. 2016, 23, 13-26. [CrossRef] [PubMed]
    • (2016) Cell Metab , vol.23 , pp. 13-26
    • Argmann, C.A.1    Houten, S.M.2    Zhu, J.3    Schadt, E.E.4
  • 92
    • 84948703087 scopus 로고    scopus 로고
    • Methods for biological data integration: Perspectives and challenges
    • [CrossRef] [PubMed]
    • Gligorijevic, V.; Przulj, N. Methods for biological data integration: Perspectives and challenges. J. R. Soc. Interface 2015, 12, 112. [CrossRef] [PubMed]
    • (2015) J. R. Soc. Interface , vol.12 , pp. 112
    • Gligorijevic, V.1    Przulj, N.2
  • 93
    • 84941365835 scopus 로고    scopus 로고
    • Genomic, proteomic, and metabolomic data integration strategies
    • [PubMed]
    • Wanichthanarak, K.; Fahrmann, J.F.; Grapov, D. Genomic, proteomic, and metabolomic data integration strategies. Biomark. Insights 2015, 10, 1-6. [PubMed]
    • (2015) Biomark. Insights , vol.10 , pp. 1-6
    • Wanichthanarak, K.1    Fahrmann, J.F.2    Grapov, D.3
  • 95
    • 84939795842 scopus 로고    scopus 로고
    • Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: Prostate cancer as a case
    • [CrossRef] [PubMed]
    • Liu, W.; Bai, X.; Liu, Y.; Wang, W.; Han, J.; Wang, Q.; Xu, Y.; Zhang, C.; Zhang, S.; Li, X. et al. Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: Prostate cancer as a case. Sci. Rep. 2015, 5, 13192. [CrossRef] [PubMed]
    • (2015) Sci. Rep , vol.5 , pp. 13192
    • Liu, W.1    Bai, X.2    Liu, Y.3    Wang, W.4    Han, J.5    Wang, Q.6    Xu, Y.7    Zhang, C.8    Zhang, S.9    Li, X.10
  • 100
    • 82755192534 scopus 로고    scopus 로고
    • Improving validation practices in “omics” research
    • [CrossRef] [PubMed]
    • Ioannidis, J.P.; Khoury, M.J. Improving validation practices in “omics” research. Science 2011, 334, 1230-1232. [CrossRef] [PubMed]
    • (2011) Science , vol.334 , pp. 1230-1232
    • Ioannidis, J.P.1    Khoury, M.J.2
  • 101
    • 84893152857 scopus 로고    scopus 로고
    • Toward more transparent and reproducible omics studies through a common metadata checklist and data publications
    • [CrossRef] [PubMed]
    • Kolker, E.; Ozdemir, V.; Martens, L.; Hancock, W.; Anderson, G.; Anderson, N.; Aynacioglu, S.; Baranova, A.; Campagna, S.R.; Chen, R. et al. Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. Omics 2014, 18, 10-14. [CrossRef] [PubMed]
    • (2014) Omics , vol.18 , pp. 10-14
    • Kolker, E.1    Ozdemir, V.2    Martens, L.3    Hancock, W.4    Anderson, G.5    Anderson, N.6    Aynacioglu, S.7    Baranova, A.8    Campagna, S.R.9    Chen, R.10
  • 105
    • 84867341623 scopus 로고    scopus 로고
    • The importance of experimental design and QC samples in large-scale and MS-driven untargeted metabolomic studies of humans
    • [CrossRef] [PubMed]
    • Dunn, W.B.; Wilson, I.D.; Nicholls, A.W.; Broadhurst, D. The importance of experimental design and QC samples in large-scale and MS-driven untargeted metabolomic studies of humans. Bioanalysis 2012, 4, 2249-2264. [CrossRef] [PubMed]
    • (2012) Bioanalysis , vol.4 , pp. 2249-2264
    • Dunn, W.B.1    Wilson, I.D.2    Nicholls, A.W.3    Broadhurst, D.4
  • 107
    • 79954452136 scopus 로고    scopus 로고
    • Cancer biomarker discovery: Opportunities and pitfalls in analytical methods
    • [CrossRef] [PubMed]
    • Issaq, H.J.; Waybright, T.J.; Veenstra, T.D. Cancer biomarker discovery: Opportunities and pitfalls in analytical methods. Electrophoresis 2011, 32, 967-975. [CrossRef] [PubMed]
    • (2011) Electrophoresis , vol.32 , pp. 967-975
    • Issaq, H.J.1    Waybright, T.J.2    Veenstra, T.D.3
  • 108
    • 84944279233 scopus 로고    scopus 로고
    • Constrained randomization and multivariate effect projections improve information extraction and biomarker pattern discovery in metabolomics studies involving dependent samples
    • [CrossRef] [PubMed]
    • Jonsson, P.; Wuolikainen, A.; Thysell, E.; Chorell, E.; Stattin, P.; Wikstrom, P.; Antti, H. Constrained randomization and multivariate effect projections improve information extraction and biomarker pattern discovery in metabolomics studies involving dependent samples. Metabolomics 2015, 11, 1667-1678. [CrossRef] [PubMed]
    • (2015) Metabolomics , vol.11 , pp. 1667-1678
    • Jonsson, P.1    Wuolikainen, A.2    Thysell, E.3    Chorell, E.4    Stattin, P.5    Wikstrom, P.6    Antti, H.7
  • 113
    • 79951810290 scopus 로고    scopus 로고
    • The importance of phase information for human genomics
    • [CrossRef] [PubMed]
    • Tewhey, R.; Bansal, V.; Torkamani, A.; Topol, E.J.; Schork, N.J. The importance of phase information for human genomics. Nat. Rev. Genet. 2011, 12, 215-223. [CrossRef] [PubMed]
    • (2011) Nat. Rev. Genet , vol.12 , pp. 215-223
    • Tewhey, R.1    Bansal, V.2    Torkamani, A.3    Topol, E.J.4    Schork, N.J.5
  • 117
    • 64449088698 scopus 로고    scopus 로고
    • Continuous base identification for single-molecule nanopore DNA sequencing
    • [CrossRef] [PubMed]
    • Clarke, J.; Wu, H.-C.; Jayasinghe, L.; Patel, A.; Reid, S.; Bayley, H. Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 2009, 4, 265-270. [CrossRef] [PubMed]
    • (2009) Nat. Nanotechnol , vol.4 , pp. 265-270
    • Clarke, J.1    Wu, H.-C.2    Jayasinghe, L.3    Patel, A.4    Reid, S.5    Bayley, H.6
  • 118
    • 84957096258 scopus 로고    scopus 로고
    • Mass spectral databases for LC/MS-and GC/MS-based metabolomics: State of the field and future prospects
    • [CrossRef]
    • Vinaixa, M.; Schymanski, E.L.; Neumann, S.; Navarro, M.; Salek, R.M.; Yanes, O. Mass spectral databases for LC/MS-and GC/MS-based metabolomics: State of the field and future prospects. TrAC Trends Anal. Chem. 2016, 78, 23-35. [CrossRef]
    • (2016) Trac Trends Anal. Chem , vol.78 , pp. 23-35
    • Vinaixa, M.1    Schymanski, E.L.2    Neumann, S.3    Navarro, M.4    Salek, R.M.5    Yanes, O.6
  • 120
    • 84858439862 scopus 로고    scopus 로고
    • Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
    • [CrossRef] [PubMed]
    • Vogel, C.; Marcotte, E.M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet. 2012, 13, 227-232. [CrossRef] [PubMed]
    • (2012) Nat. Rev. Genet , vol.13 , pp. 227-232
    • Vogel, C.1    Marcotte, E.M.2
  • 121
    • 85012822290 scopus 로고    scopus 로고
    • Computational quality control tools for mass spectrometry proteomics
    • [CrossRef] [PubMed]
    • Bittremieux, W.; Valkenborg, D.; Martens, L.; Laukens, K. Computational quality control tools for mass spectrometry proteomics. Proteomics 2016. [CrossRef] [PubMed]
    • (2016) Proteomics
    • Bittremieux, W.1    Valkenborg, D.2    Martens, L.3    Laukens, K.4
  • 123
    • 76649109590 scopus 로고    scopus 로고
    • An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers
    • [CrossRef] [PubMed]
    • Whiteaker, J.R.; Zhao, L.; Anderson, L.; Paulovich, A.G. An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol. Cell. Proteom. 2010, 9, 184-196. [CrossRef] [PubMed]
    • (2010) Mol. Cell. Proteom , vol.9 , pp. 184-196
    • Whiteaker, J.R.1    Zhao, L.2    Anderson, L.3    Paulovich, A.G.4
  • 124
    • 84915822559 scopus 로고    scopus 로고
    • Four areas of engagement requiring strengthening in modern proteomics today
    • [CrossRef] [PubMed]
    • Fehniger, T.E.; Boja, E.S.; Rodriguez, H.; Baker, M.S.; Marko-Varga, G. Four areas of engagement requiring strengthening in modern proteomics today. J. Proteome Res. 2014, 13, 5310-5318. [CrossRef] [PubMed]
    • (2014) J. Proteome Res , vol.13 , pp. 5310-5318
    • Fehniger, T.E.1    Boja, E.S.2    Rodriguez, H.3    Baker, M.S.4    Marko-Varga, G.5
  • 125
    • 84899529765 scopus 로고    scopus 로고
    • Evaluation and comparison of multiple aligners for next-generation sequencing data analysis
    • [CrossRef] [PubMed]
    • Shang, J.; Zhu, F.; Vongsangnak W.; Tang, Y.; Zhang W.; Shen, B. Evaluation and comparison of multiple aligners for next-generation sequencing data analysis. BioMed Res. Int. 2014, 2014, 309650. [CrossRef] [PubMed]
    • (2014) Biomed Res. Int. 2014 , vol.309650
    • Shang, J.1    Zhu, F.2    Vongsangnak, W.3    Tang, Y.4    Zhang, W.5    Shen, B.6
  • 131
    • 84890326219 scopus 로고    scopus 로고
    • Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data
    • [CrossRef] [PubMed]
    • Spencer, D.H.; Tyagi, M.; Vallania, F.; Bredemeyer, A.J.; Pfeifer, J.D.; Mitra, R.D.; Duncavage, E.J. Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. J. Mol. Diagn. 2014, 16, 75-88. [CrossRef] [PubMed]
    • (2014) J. Mol. Diagn , vol.16 , pp. 75-88
    • Spencer, D.H.1    Tyagi, M.2    Vallania, F.3    Bredemeyer, A.J.4    Pfeifer, J.D.5    Mitra, R.D.6    Duncavage, E.J.7
  • 133
    • 84876783779 scopus 로고    scopus 로고
    • Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics
    • [PubMed]
    • Gullapalli, R.R.; Desai, K.V.; Santana-Santos, L.; Kant, J.A.; Becich, M.J. Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics. J. Pathol. Inform. 2012, 3, 40. [PubMed]
    • (2012) J. Pathol. Inform , vol.3 , pp. 40
    • Gullapalli, R.R.1    Desai, K.V.2    Santana-Santos, L.3    Kant, J.A.4    Becich, M.J.5
  • 134
    • 84870721324 scopus 로고    scopus 로고
    • File formats commonly used in mass spectrometry proteomics
    • [CrossRef] [PubMed]
    • Deutsch, E.W. File formats commonly used in mass spectrometry proteomics. Mol. Cell. Proteom. 2012, 11, 1612-1621. [CrossRef] [PubMed]
    • (2012) Mol. Cell. Proteom , vol.11 , pp. 1612-1621
    • Deutsch, E.W.1
  • 135
    • 84952863976 scopus 로고    scopus 로고
    • Updates in metabolomics tools and resources: 2014-2015
    • [CrossRef] [PubMed]
    • Misra, B.B.; van der Hooft, J.J. Updates in metabolomics tools and resources: 2014-2015. Electrophoresis 2016, 37, 86-110. [CrossRef] [PubMed]
    • (2016) Electrophoresis , vol.37 , pp. 86-110
    • Misra, B.B.1    van Der Hooft, J.J.2
  • 137
    • 84954509878 scopus 로고    scopus 로고
    • US food and drug administration perspectives on clinical mass spectrometry
    • [CrossRef] [PubMed]
    • Lathrop, J.T.; Jeffery, D.A.; Shea, Y.R.; Scholl, P.F.; Chan, M.M. US food and drug administration perspectives on clinical mass spectrometry. Clin. Chem. 2016, 62, 41-47. [CrossRef] [PubMed]
    • (2016) Clin. Chem , vol.62 , pp. 41-47
    • Lathrop, J.T.1    Jeffery, D.A.2    Shea, Y.R.3    Scholl, P.F.4    Chan, M.M.5
  • 139
    • 84929001104 scopus 로고    scopus 로고
    • The genotype-tissue expression (GTEX) pilot analysis: Multitissue gene regulation in humans
    • GTEx Consortium. The genotype-tissue expression (GTEX) pilot analysis: Multitissue gene regulation in humans. Science 2015, 348, 648-660.
    • (2015) Science , vol.348 , pp. 648-660
  • 141
    • 84922675982 scopus 로고    scopus 로고
    • Network-based approach for analyzing intra-and interfluid metabolite associations in human blood, urine, and saliva, [CrossRef] [PubMed]
    • Do, K.T.; Kastenmüller, G.; Mook-Kanamori, D.O.; Yousri, N.A.; Theis, F.J.; Suhre, K.; Krumsiek, J. Network-based approach for analyzing intra-and interfluid metabolite associations in human blood, urine, and saliva. J. Proteome Res. 2015, 14, 1183-1194. [CrossRef] [PubMed]
    • (2015) J. Proteome Res , vol.14 , pp. 1183-1194
    • Do, K.T.1    Kastenmüller, G.2    Mook-Kanamori, D.O.3    Yousri, N.A.4    Theis, F.J.5    Suhre, K.6    Krumsiek, J.7
  • 142
    • 84964747508 scopus 로고    scopus 로고
    • An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies
    • [CrossRef] [PubMed]
    • McGregor, K.; Bernatsky, S.; Colmegna, I.; Hudson, M.; Pastinen, T.; Labbe, A.; Greenwood, C.M.T. An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies. Genome Biol. 2016, 17, 1-17. [CrossRef] [PubMed]
    • (2016) Genome Biol , vol.17 , pp. 1-17
    • McGregor, K.1    Bernatsky, S.2    Colmegna, I.3    Hudson, M.4    Pastinen, T.5    Labbe, A.6    Greenwood, C.M.T.7
  • 143
    • 84923292191 scopus 로고    scopus 로고
    • Computational analysis of cell-to-cell heterogeneity in single-cell RNA-Sequencing data reveals hidden subpopulations of cells. Nat
    • [CrossRef] [PubMed]
    • Buettner, F.; Natarajan, K.N.; Casale, F.P.; Proserpio, V.; Scialdone, A.; Theis, F.J.; Teichmann, S.A.; Marioni, J.C.; Stegle, O. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-Sequencing data reveals hidden subpopulations of cells. Nat. Biotechnol. 2015, 33, 155-160. [CrossRef] [PubMed]
    • (2015) Biotechnol , vol.33 , pp. 155-160
    • Buettner, F.1    Natarajan, K.N.2    Casale, F.P.3    Proserpio, V.4    Scialdone, A.5    Theis, F.J.6    Teichmann, S.A.7    Marioni, J.C.8    Stegle, O.9
  • 144
    • 84900824657 scopus 로고    scopus 로고
    • Reference-free cell mixture adjustments in analysis of DNA methylation data
    • [CrossRef] [PubMed]
    • Houseman, E.A.; Molitor, J.; Marsit, C.J. Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics 2014, 30, 1431-1439. [CrossRef] [PubMed]
    • (2014) Bioinformatics , vol.30 , pp. 1431-1439
    • Houseman, E.A.1    Molitor, J.2    Marsit, C.J.3
  • 145
    • 84969504939 scopus 로고    scopus 로고
    • Multi-omics of single cells: Strategies and applications
    • [CrossRef] [PubMed]
    • Bock, C.; Farlik, M.; Sheffield, N.C. Multi-omics of single cells: Strategies and applications. Trends Biotechnol. 2016, 34, 605-608. [CrossRef] [PubMed]
    • (2016) Trends Biotechnol , vol.34 , pp. 605-608
    • Bock, C.1    Farlik, M.2    Sheffield, N.C.3
  • 146
    • 0035100888 scopus 로고    scopus 로고
    • Biomarkers and surrogate endpoints: Preferred definitions and conceptual framework
    • Biomarkers Definitions Working Group. Biomarkers and surrogate endpoints: Preferred definitions and conceptual framework. Clin. Pharmacol. Ther. 2001, 69, 89-95.
    • (2001) Clin. Pharmacol. Ther , vol.69 , pp. 89-95
  • 150
    • 84856441294 scopus 로고    scopus 로고
    • What is the difference between “predictive and prognostic biomarkers
    • Brünner, N. What is the difference between “predictive and prognostic biomarkers”? Can you give some examples. Connection 2009, 13, 18.
    • (2009) Can You Give Some Examples. Connection , vol.13 , pp. 18
    • Brünner, N.1
  • 151
    • 0038004636 scopus 로고    scopus 로고
    • Clinical biomarkers in drug discovery and development
    • [CrossRef] [PubMed]
    • Frank, R.; Hargreaves, R. Clinical biomarkers in drug discovery and development. Nat. Rev. Drug Discov. 2003, 2, 566-580. [CrossRef] [PubMed]
    • (2003) Nat. Rev. Drug Discov , vol.2 , pp. 566-580
    • Frank, R.1    Hargreaves, R.2
  • 153
    • 0001710505 scopus 로고
    • Analysis of a complex of statistical variables into principal components
    • [CrossRef]
    • Hotelling, H. Analysis of a complex of statistical variables into principal components. J. Educ. Psychol. 1933, 24, 417. [CrossRef]
    • (1933) J. Educ. Psychol , vol.24 , pp. 417
    • Hotelling, H.1
  • 154
    • 84879467778 scopus 로고    scopus 로고
    • Independent components analysis with the jade algorithm
    • [CrossRef]
    • Rutledge, D.N.; Bouveresse, D.J.-R. Independent components analysis with the jade algorithm. TrAC Trends Anal. Chem. 2013, 50, 22-32. [CrossRef]
    • (2013) Trac Trends Anal. Chem , vol.50 , pp. 22-32
    • Rutledge, D.N.1    Bouveresse, D.J.2
  • 155
    • 0001138328 scopus 로고
    • Algorithm as 136: A k-means clustering algorithm
    • [CrossRef]
    • Hartigan, J.A.; Wong, M.A. Algorithm as 136: A k-means clustering algorithm. J. R. Stat. Soc. Ser. C 1979, 28, 100-108. [CrossRef]
    • (1979) J. R. Stat. Soc. Ser. C , vol.28 , pp. 100-108
    • Hartigan, J.A.1    Wong, M.A.2
  • 156
    • 0014129195 scopus 로고
    • Hierarchical clustering schemes
    • [CrossRef] [PubMed]
    • Johnson, S.C. Hierarchical clustering schemes. Psychometrika 1967, 32, 241-254. [CrossRef] [PubMed]
    • (1967) Psychometrika , vol.32 , pp. 241-254
    • Johnson, S.C.1
  • 157
    • 0025489075 scopus 로고
    • The self-organizing map
    • [CrossRef]
    • Kohonen, T. The self-organizing map. Proc. IEEE 1990, 78, 1464-1480. [CrossRef]
    • (1990) Proc. IEEE , vol.78 , pp. 1464-1480
    • Kohonen, T.1
  • 158
    • 0035965476 scopus 로고    scopus 로고
    • Pls-regression: A basic tool of chemometrics
    • [CrossRef]
    • Wold, S.; Sjöström, M.; Eriksson, L. Pls-regression: A basic tool of chemometrics. Chemom. Intell. Lab. Syst. 2001, 58, 109-130. [CrossRef]
    • (2001) Chemom. Intell. Lab. Syst , vol.58 , pp. 109-130
    • Wold, S.1    Sjöström, M.2    Eriksson, L.3
  • 159
    • 0036083139 scopus 로고    scopus 로고
    • Orthogonal projections to latent structures (O-PLS)
    • [CrossRef]
    • Trygg, J.; Wold, S. Orthogonal projections to latent structures (O-PLS). J. Chemom. 2002, 16, 119-128. [CrossRef]
    • (2002) J. Chemom , vol.16 , pp. 119-128
    • Trygg, J.1    Wold, S.2
  • 160
    • 34249753618 scopus 로고
    • Support-vector networks
    • [CrossRef]
    • Cortes, C.; Vapnik, V. Support-vector networks. Mach. Learn. 1995, 20, 273-297. [CrossRef]
    • (1995) Mach. Learn , vol.20 , pp. 273-297
    • Cortes, C.1    Vapnik, V.2
  • 162
    • 84987718199 scopus 로고    scopus 로고
    • Integration and visualization of translational medicine data for better understanding of human diseases
    • [CrossRef] [PubMed]
    • Satagopam, V.; Gu, W.; Eifes, S.; Gawron, P.; Ostaszewski, M.; Gebel, S.; Barbosa-Silva, A.; Balling, R.; Schneider, R. Integration and visualization of translational medicine data for better understanding of human diseases. Big Data 2016, 4, 97-108. [CrossRef] [PubMed]
    • (2016) Big Data , vol.4 , pp. 97-108
    • Satagopam, V.1    Gu, W.2    Eifes, S.3    Gawron, P.4    Ostaszewski, M.5    Gebel, S.6    Barbosa-Silva, A.7    Balling, R.8    Schneider, R.9
  • 163
    • 84957426178 scopus 로고    scopus 로고
    • Topological data analysis: A promising big data exploration tool in biology, analytical chemistry and physical chemistry
    • [CrossRef] [PubMed]
    • Offroy, M.; Duponchel, L. Topological data analysis: A promising big data exploration tool in biology, analytical chemistry and physical chemistry. Anal. Chim. Acta 2016, 910, 1-11. [CrossRef] [PubMed]
    • (2016) Anal. Chim. Acta , vol.910 , pp. 1-11
    • Offroy, M.1    Duponchel, L.2
  • 165
    • 70049091784 scopus 로고    scopus 로고
    • Topology and data
    • [CrossRef]
    • Carlsson, G. Topology and data. Bull. Am. Math. Soc. 2009, 46, 255-308. [CrossRef]
    • (2009) Bull. Am. Math. Soc , vol.46 , pp. 255-308
    • Carlsson, G.1
  • 167
    • 84938360711 scopus 로고    scopus 로고
    • Computational tools for parsimony phylogenetic analysis of omics data
    • [CrossRef] [PubMed]
    • Salazar, J.; Amri, H.; Noursi, D.; Abu-Asab, M. Computational tools for parsimony phylogenetic analysis of omics data. Omics J. Integr. Biol. 2015, 19, 471-477. [CrossRef] [PubMed]
    • (2015) Omics J. Integr. Biol , vol.19 , pp. 471-477
    • Salazar, J.1    Amri, H.2    Noursi, D.3    Abu-Asab, M.4
  • 168
    • 84954408826 scopus 로고    scopus 로고
    • Unmet needs: Research helps regulators do their jobs
    • 315ps22[CrossRef] [PubMed]
    • Altman, R.B.; Khuri, N.; Salit, M.; Giacomini, K.M. Unmet needs: Research helps regulators do their jobs. Sci. Transl. Med. 2015, 7, 315ps22. [CrossRef] [PubMed]
    • (2015) Sci. Transl. Med , vol.7
    • Altman, R.B.1    Khuri, N.2    Salit, M.3    Giacomini, K.M.4
  • 169
    • 84969219444 scopus 로고    scopus 로고
    • The need for global regulatory harmonization: A public health imperative
    • 338ed6[CrossRef] [PubMed]
    • Zerhouni, E.; Hamburg, M. The need for global regulatory harmonization: A public health imperative. Sci. Transl. Med. 2016, 8, 338ed6. [CrossRef] [PubMed]
    • (2016) Sci. Transl. Med , vol.8
    • Zerhouni, E.1    Hamburg, M.2
  • 171
    • 84890526744 scopus 로고    scopus 로고
    • Genetic data and electronic health records: A discussion of ethical, logistical and technological considerations
    • [CrossRef] [PubMed]
    • Shoenbill, K.; Fost, N.; Tachinardi, U.; Mendonca, E.A. Genetic data and electronic health records: A discussion of ethical, logistical and technological considerations. J. Am. Med. Inform. Assoc. 2014, 21, 171-180. [CrossRef] [PubMed]
    • (2014) J. Am. Med. Inform. Assoc , vol.21 , pp. 171-180
    • Shoenbill, K.1    Fost, N.2    Tachinardi, U.3    Mendonca, E.A.4
  • 172
    • 78651394465 scopus 로고    scopus 로고
    • Bring on the biomarkers
    • [CrossRef] [PubMed]
    • Poste, G. Bring on the biomarkers. Nature 2011, 469, 156-157. [CrossRef] [PubMed]
    • (2011) Nature , vol.469 , pp. 156-157
    • Poste, G.1
  • 173
    • 84959496982 scopus 로고    scopus 로고
    • Integrative methods for analyzing big data in precision medicine
    • [CrossRef] [PubMed]
    • Gligorijevic, V.; Malod-Dognin, N.; Przulj, N. Integrative methods for analyzing big data in precision medicine. Proteomics 2016, 16, 741-758. [CrossRef] [PubMed]
    • (2016) Proteomics , vol.16 , pp. 741-758
    • Gligorijevic, V.1    Malod-Dognin, N.2    Przulj, N.3
  • 175
    • 84944743064 scopus 로고    scopus 로고
    • Databases for multilevel biophysiology research available at physiome.jp
    • [CrossRef] [PubMed]
    • Asai, Y.; Abe, T.; Li, L.; Oka, H.; Nomura, T.; Kitano, H. Databases for multilevel biophysiology research available at physiome.jp. Front. Physiol. 2015, 6, 251. [CrossRef] [PubMed]
    • (2015) Front. Physiol , vol.6 , pp. 251
    • Asai, Y.1    Abe, T.2    Li, L.3    Oka, H.4    Nomura, T.5    Kitano, H.6
  • 178
    • 85009243668 scopus 로고    scopus 로고
    • Pathology informatics essentials for residents: A flexible informatics curriculum linked to accreditation council for graduate medical education milestones
    • [PubMed]
    • Henricks, W.H.; Karcher, D.S.; Harrison, J.H.; Sinard, J.H.; Riben, M.W.; Boyer, P.J.; Plath, S.; Thompson, A.; Pantanowitz, L. Pathology informatics essentials for residents: A flexible informatics curriculum linked to accreditation council for graduate medical education milestones. J. Pathol. Inform. 2016, 7, 27. [PubMed]
    • (2016) J. Pathol. Inform , vol.7 , pp. 27
    • Henricks, W.H.1    Karcher, D.S.2    Harrison, J.H.3    Sinard, J.H.4    Riben, M.W.5    Boyer, P.J.6    Plath, S.7    Thompson, A.8    Pantanowitz, L.9
  • 181
    • 84957628653 scopus 로고    scopus 로고
    • Translational bioinformatics and clinical research (Biomedical) informatics
    • [CrossRef] [PubMed]
    • Sirintrapun, S.J.; Zehir, A.; Syed, A.; Gao, J.; Schultz, N.; Cheng, D.T. Translational bioinformatics and clinical research (biomedical) informatics. Clin. Lab. Med. 2016, 36, 153-181. [CrossRef] [PubMed]
    • (2016) Clin. Lab. Med , vol.36 , pp. 153-181
    • Sirintrapun, S.J.1    Zehir, A.2    Syed, A.3    Gao, J.4    Schultz, N.5    Cheng, D.T.6
  • 182
    • 84968813824 scopus 로고    scopus 로고
    • Deep patient: An unsupervised representation to predict the future of patients from the electronic health records
    • [CrossRef] [PubMed]
    • Miotto, R.; Li, L.; Kidd, B.A.; Dudley, J.T. Deep patient: An unsupervised representation to predict the future of patients from the electronic health records. Sci. Rep. 2016, 6, 26094. [CrossRef] [PubMed]
    • (2016) Sci. Rep , vol.6 , pp. 26094
    • Miotto, R.1    Li, L.2    Kidd, B.A.3    Dudley, J.T.4
  • 183
    • 84987713568 scopus 로고    scopus 로고
    • Bioinformatics methods and tools to advance clinical care. Findings from the yearbook 2015 section on bioinformatics and translational informatics
    • [CrossRef] [PubMed]
    • Soualmia, L.F.; Lecroq, T. Bioinformatics methods and tools to advance clinical care. Findings from the yearbook 2015 section on bioinformatics and translational informatics. Yearb. Med. Inform. 2015, 10, 170-173. [CrossRef] [PubMed]
    • (2015) Yearb. Med. Inform , vol.10 , pp. 170-173
    • Soualmia, L.F.1    Lecroq, T.2
  • 186
    • 84865768271 scopus 로고    scopus 로고
    • Compendium of inborn errors of metabolism mapped onto the human metabolic network
    • [CrossRef] [PubMed]
    • Sahoo, S.; Franzson, L.; Jonsson, J.J.; Thiele, I. A compendium of inborn errors of metabolism mapped onto the human metabolic network. Mol. BioSyst. 2012, 8, 2545-2558. [CrossRef] [PubMed]
    • (2012) Mol. Biosyst , vol.8 , pp. 2545-2558
    • Sahoo, S.1    Franzson, L.2    Jonsson, J.J.3    Thiele, I.A.4
  • 187
    • 84872037912 scopus 로고    scopus 로고
    • Chapter 5: Network biology approach to complex diseases
    • [CrossRef] [PubMed]
    • Cho, D.-Y.; Kim, Y.-A.; Przytycka, T.M. Chapter 5: Network biology approach to complex diseases. PLoS Comput. Biol. 2012, 8, e1002820. [CrossRef] [PubMed]
    • (2012) Plos Comput. Biol , vol.8
    • Cho, D.-Y.1    Kim, Y.-A.2    Przytycka, T.M.3
  • 188
    • 84864818817 scopus 로고    scopus 로고
    • Revolutionizing medicine in the 21st century through systems approaches
    • [CrossRef] [PubMed]
    • Hood, L.; Balling, R.; Auffray, C. Revolutionizing medicine in the 21st century through systems approaches. Biotechnol. J. 2012, 7, 992-1001. [CrossRef] [PubMed]
    • (2012) Biotechnol. J , vol.7 , pp. 992-1001
    • Hood, L.1    Balling, R.2    Auffray, C.3


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