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Volumn 4 JAN, Issue , 2014, Pages

Current challenges in the bioinformatics of single cell genomics

Author keywords

CNV; DNA sequencing; RNA sequencing; Single cell analysis; SNP

Indexed keywords

TRANSCRIPTOME;

EID: 84893710389     PISSN: None     EISSN: 2234943X     Source Type: Journal    
DOI: 10.3389/fonc.2014.00007     Document Type: Review
Times cited : (40)

References (99)
  • 1
    • 18344396798 scopus 로고    scopus 로고
    • Comprehensive human genome amplification using multiple displacement amplification
    • doi:10.1073/pnas.082089499
    • Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, et al. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A (2002) 99(8):5261-6. doi:10.1073/pnas.082089499
    • (2002) Proc Natl Acad Sci U S A , vol.99 , Issue.8 , pp. 5261-5266
    • Dean, F.B.1    Hosono, S.2    Fang, L.3    Wu, X.4    Faruqi, A.F.5    Bray-Ward, P.6
  • 2
    • 34248678989 scopus 로고    scopus 로고
    • Whole-genome multiple displacement amplification from single cells
    • doi:10.1038/nprot.2006.326
    • Spits C, Le Caignec C, De Rycke M, Van Haute L, Van Steirteghem A, Liebaers I, et al. Whole-genome multiple displacement amplification from single cells. Nat Protoc (2006) 1(4):1965-70. doi:10.1038/nprot.2006.326
    • (2006) Nat Protoc , vol.1 , Issue.4 , pp. 1965-1970
    • Spits, C.1    Le Caignec, C.2    De Rycke, M.3    Van Haute, L.4    Van Steirteghem, A.5    Liebaers, I.6
  • 3
    • 35748983784 scopus 로고    scopus 로고
    • Single-cell genomic sequencing using multiple displacement amplification
    • doi:10.1016/j.mib.2007.08.005
    • Lasken RS. Single-cell genomic sequencing using multiple displacement amplification. Curr Opin Microbiol (2007) 10(5):510-6. doi:10.1016/j.mib.2007.08.005
    • (2007) Curr Opin Microbiol , vol.10 , Issue.5 , pp. 510-516
    • Lasken, R.S.1
  • 4
    • 84871461434 scopus 로고    scopus 로고
    • Genome-wide detection of single-nucleotide and copy-number variations of a single human cell
    • doi:10.1126/science.1229164
    • Zong C, Lu S, Chapman AR, Xie XS. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science (2012) 338(6114):1622-6. doi:10.1126/science.1229164
    • (2012) Science , vol.338 , Issue.6114 , pp. 1622-1626
    • Zong, C.1    Lu, S.2    Chapman, A.R.3    Xie, X.S.4
  • 5
    • 84882455458 scopus 로고    scopus 로고
    • Single-cell sequencing-based technologies will revolutionize whole-organism science
    • doi:10.1038/nrg3542
    • Shapiro E, Biezuner T, Linnarsson S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet (2013) 14(9):618-30. doi:10.1038/nrg3542
    • (2013) Nat Rev Genet , vol.14 , Issue.9 , pp. 618-630
    • Shapiro, E.1    Biezuner, T.2    Linnarsson, S.3
  • 6
    • 84881439152 scopus 로고    scopus 로고
    • Single-cell analysis: toward the clinic
    • doi:10.1186/gm478
    • Speicher MR. Single-cell analysis: toward the clinic. Genome Med (2013) 5(8):1-3. doi:10.1186/gm478
    • (2013) Genome Med , vol.5 , Issue.8 , pp. 1-3
    • Speicher, M.R.1
  • 7
    • 0042021843 scopus 로고    scopus 로고
    • Single-cell sequencing and mini-sequencing for preimplantation genetic diagnosis
    • doi:10.1002/pd.658
    • Bermudez MG, Piyamongkol W, Tomaz S, Dudman E, Sherlock JK, Wells D. Single-cell sequencing and mini-sequencing for preimplantation genetic diagnosis. Prenat Diagn (2003) 23(8):669-77. doi:10.1002/pd.658
    • (2003) Prenat Diagn , vol.23 , Issue.8 , pp. 669-677
    • Bermudez, M.G.1    Piyamongkol, W.2    Tomaz, S.3    Dudman, E.4    Sherlock, J.K.5    Wells, D.6
  • 8
    • 84883134780 scopus 로고    scopus 로고
    • Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
    • doi:10.1038/nature12364
    • Xue Z, Huang K, Cai C, Cai L, Jiang CY, Feng Y, et al. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature (2013) 500(7464):593-7. doi:10.1038/nature12364
    • (2013) Nature , vol.500 , Issue.7464 , pp. 593-597
    • Xue, Z.1    Huang, K.2    Cai, C.3    Cai, L.4    Jiang, C.Y.5    Feng, Y.6
  • 9
    • 84876122754 scopus 로고    scopus 로고
    • The future is now: single-cell genomics of bacteria and archaea
    • doi:10.1111/1574-6976.12015
    • Blainey PC. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev (2013) 37(3):407-27. doi:10.1111/1574-6976.12015
    • (2013) FEMS Microbiol Rev , vol.37 , Issue.3 , pp. 407-427
    • Blainey, P.C.1
  • 10
    • 84878724342 scopus 로고    scopus 로고
    • Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage
    • doi:10.1038/ncomms2884
    • Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, et al. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun (2013) 4:1854. doi:10.1038/ncomms2884
    • (2013) Nat Commun , vol.4 , pp. 1854
    • Dodsworth, J.A.1    Blainey, P.C.2    Murugapiran, S.K.3    Swingley, W.D.4    Ross, C.A.5    Tringe, S.G.6
  • 11
    • 84865318505 scopus 로고    scopus 로고
    • Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
    • doi:10.1038/ismej.2012.59
    • Mason OU, Hazen TC, Borglin S, Chain PS, Dubinsky EA, Fortney JL, et al. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J (2012) 6(9):1715-27. doi:10.1038/ismej.2012.59
    • (2012) ISME J , vol.6 , Issue.9 , pp. 1715-1727
    • Mason, O.U.1    Hazen, T.C.2    Borglin, S.3    Chain, P.S.4    Dubinsky, E.A.5    Fortney, J.L.6
  • 12
    • 45849153461 scopus 로고    scopus 로고
    • Genomic sequencing of single microbial cells from environmental samples
    • doi:10.1016/j.mib.2008.05.006
    • Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS. Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol (2008) 11(3):198-204. doi:10.1016/j.mib.2008.05.006
    • (2008) Curr Opin Microbiol , vol.11 , Issue.3 , pp. 198-204
    • Ishoey, T.1    Woyke, T.2    Stepanauskas, R.3    Novotny, M.4    Lasken, R.S.5
  • 13
    • 84877865227 scopus 로고    scopus 로고
    • Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing
    • doi:10.1158/0008-5472.CAN-12-4140
    • Heitzer E, Auer M, Gasch C, Pichler M, Ulz P, Hoffmann EM, et al. Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res (2013) 73(10):2965-75. doi:10.1158/0008-5472.CAN-12-4140
    • (2013) Cancer Res , vol.73 , Issue.10 , pp. 2965-2975
    • Heitzer, E.1    Auer, M.2    Gasch, C.3    Pichler, M.4    Ulz, P.5    Hoffmann, E.M.6
  • 14
    • 84886379960 scopus 로고    scopus 로고
    • Going with the flow: from circulating tumor cells to DNA
    • doi:10.1126/scitranslmed.3006305
    • Bidard F-C, Weigelt B, Reis-Filho JS. Going with the flow: from circulating tumor cells to DNA. Sci Transl Med (2013) 5(207):s14-14. doi:10.1126/scitranslmed.3006305
    • (2013) Sci Transl Med , vol.5 , Issue.207
    • Bidard, F.-C.1    Weigelt, B.2    Reis-Filho, J.S.3
  • 15
    • 84864880991 scopus 로고    scopus 로고
    • Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
    • doi:10.1038/nbt.2282
    • Ramsköld D, Luo S, Wang Y-C, Li R, Deng Q, Faridani OR, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol (2012) 30(8):777-82. doi:10.1038/nbt.2282
    • (2012) Nat Biotechnol , vol.30 , Issue.8 , pp. 777-782
    • Ramsköld, D.1    Luo, S.2    Wang, Y.-C.3    Li, R.4    Deng, Q.5    Faridani, O.R.6
  • 16
    • 83255177150 scopus 로고    scopus 로고
    • Single-cell dissection of transcriptional heterogeneity in human colon tumors
    • doi:10.1038/nbt.2038
    • Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, et al. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol (2011) 29(12):1120-7. doi:10.1038/nbt.2038
    • (2011) Nat Biotechnol , vol.29 , Issue.12 , pp. 1120-1127
    • Dalerba, P.1    Kalisky, T.2    Sahoo, D.3    Rajendran, P.S.4    Rothenberg, M.E.5    Leyrat, A.A.6
  • 17
    • 84860214990 scopus 로고    scopus 로고
    • Intra-tumour heterogeneity: a looking glass for cancer?
    • doi:10.1038/nrc3261
    • Marusyk A, Almendro V, Polyak K. Intra-tumour heterogeneity: a looking glass for cancer? Nat Rev Cancer (2012) 12(5):323-34. doi:10.1038/nrc3261
    • (2012) Nat Rev Cancer , vol.12 , Issue.5 , pp. 323-334
    • Marusyk, A.1    Almendro, V.2    Polyak, K.3
  • 18
    • 79953766940 scopus 로고    scopus 로고
    • Tumour evolution inferred by single-cell sequencing
    • doi:10.1038/nature09807
    • Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, et al. Tumour evolution inferred by single-cell sequencing. Nature (2011) 472(7341):90-4. doi:10.1038/nature09807
    • (2011) Nature , vol.472 , Issue.7341 , pp. 90-94
    • Navin, N.1    Kendall, J.2    Troge, J.3    Andrews, P.4    Rodgers, L.5    McIndoo, J.6
  • 19
    • 84863230091 scopus 로고    scopus 로고
    • Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor
    • doi:10.1016/j.cell.2012.02.025
    • Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, et al. Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 148(5):886-95. doi:10.1016/j.cell.2012.02.025
    • (2012) Cell , vol.148 , Issue.5 , pp. 886-895
    • Xu, X.1    Hou, Y.2    Yin, X.3    Bao, L.4    Tang, A.5    Song, L.6
  • 20
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • The 1000 Genomes Project Consortium doi:10.1038/nature11632
    • The 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature (2012) 491:1. doi:10.1038/nature11632
    • (2012) Nature , vol.491 , pp. 1
  • 21
    • 0033863391 scopus 로고    scopus 로고
    • SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease
    • doi:10.1086/303003
    • Martin ER, Lai EH, Gilbert JR, Rogala AR, Afshari A, Riley J, et al. SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease. Am J Hum Genet (2000) 67(2):383-94. doi:10.1086/303003
    • (2000) Am J Hum Genet , vol.67 , Issue.2 , pp. 383-394
    • Martin, E.R.1    Lai, E.H.2    Gilbert, J.R.3    Rogala, A.R.4    Afshari, A.5    Riley, J.6
  • 22
    • 3242713277 scopus 로고    scopus 로고
    • A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis
    • doi:10.1086/422827
    • Begovich AB, Carlton VE, Honigberg LA, Schrodi SJ, Chokkalingam AP, Alexander HC, et al. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am J Hum Genet (2004) 75(2):330-7. doi:10.1086/422827
    • (2004) Am J Hum Genet , vol.75 , Issue.2 , pp. 330-337
    • Begovich, A.B.1    Carlton, V.E.2    Honigberg, L.A.3    Schrodi, S.J.4    Chokkalingam, A.P.5    Alexander, H.C.6
  • 23
    • 33750892139 scopus 로고    scopus 로고
    • Common single nucleotide polymorphisms in TCF7L2 are reproducibly associated with type 2 diabetes and reduce the insulin response to glucose in nondiabetic individuals
    • doi:10.2337/db06-0381
    • Saxena R, Gianniny L, Burtt NP, Lyssenko V, Giuducci C, Sjögren M, et al. Common single nucleotide polymorphisms in TCF7L2 are reproducibly associated with type 2 diabetes and reduce the insulin response to glucose in nondiabetic individuals. Diabetes (2006) 55(10):2890-5. doi:10.2337/db06-0381
    • (2006) Diabetes , vol.55 , Issue.10 , pp. 2890-2895
    • Saxena, R.1    Gianniny, L.2    Burtt, N.P.3    Lyssenko, V.4    Giuducci, C.5    Sjögren, M.6
  • 24
    • 0035503537 scopus 로고    scopus 로고
    • A single nucleotide polymorphism in the matrix metalloproteinase-1 promoter enhances lung cancer susceptibility
    • Zhu Y, Spitz MR, Lei L, Mills GB, Wu X. A single nucleotide polymorphism in the matrix metalloproteinase-1 promoter enhances lung cancer susceptibility. Cancer Res (2001) 61(21):7825-9.
    • (2001) Cancer Res , vol.61 , Issue.21 , pp. 7825-7829
    • Zhu, Y.1    Spitz, M.R.2    Lei, L.3    Mills, G.B.4    Wu, X.5
  • 25
    • 33751329250 scopus 로고    scopus 로고
    • Global variation in copy number in the human genome
    • doi:10.1038/nature05329
    • Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, et al. Global variation in copy number in the human genome. Nature (2006) 444(7118):444-54. doi:10.1038/nature05329
    • (2006) Nature , vol.444 , Issue.7118 , pp. 444-454
    • Redon, R.1    Ishikawa, S.2    Fitch, K.R.3    Feuk, L.4    Perry, G.H.5    Andrews, T.D.6
  • 26
    • 70350221909 scopus 로고    scopus 로고
    • Copy number variation in human health, disease, and evolution
    • doi:10.1146/annurev.genom.9.081307.164217
    • Zhang F, Gu W, Hurles ME, Lupski JR. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet (2009) 10:451-81. doi:10.1146/annurev.genom.9.081307.164217
    • (2009) Annu Rev Genomics Hum Genet , vol.10 , pp. 451-481
    • Zhang, F.1    Gu, W.2    Hurles, M.E.3    Lupski, J.R.4
  • 27
    • 34547730931 scopus 로고    scopus 로고
    • Copy number variant in the candidate tumor suppressor gene MTUS1 and familial breast cancer risk
    • doi:10.1093/carcin/bgm033
    • Frank B, Bermejo JL, Hemminki K, Sutter C, Wappenschmidt B, Meindl A, et al. Copy number variant in the candidate tumor suppressor gene MTUS1 and familial breast cancer risk. Carcinogenesis (2007) 28(7):1442-5. doi:10.1093/carcin/bgm033
    • (2007) Carcinogenesis , vol.28 , Issue.7 , pp. 1442-1445
    • Frank, B.1    Bermejo, J.L.2    Hemminki, K.3    Sutter, C.4    Wappenschmidt, B.5    Meindl, A.6
  • 28
    • 67349182343 scopus 로고    scopus 로고
    • Autism genome-wide copy number variation reveals ubiquitin and neuronal genes
    • doi:10.1038/nature07953
    • Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, et al. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature (2009) 459(7246):569-73. doi:10.1038/nature07953
    • (2009) Nature , vol.459 , Issue.7246 , pp. 569-573
    • Glessner, J.T.1    Wang, K.2    Cai, G.3    Korvatska, O.4    Kim, C.E.5    Wood, S.6
  • 29
    • 34250841166 scopus 로고    scopus 로고
    • Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans
    • doi:10.1086/518257
    • Yang Y, Chung EK, Wu YL, Savelli SL, Nagaraja HN, Zhou B, et al. Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am J Hum Genet (2007) 80(6):1037-54. doi:10.1086/518257
    • (2007) Am J Hum Genet , vol.80 , Issue.6 , pp. 1037-1054
    • Yang, Y.1    Chung, E.K.2    Wu, Y.L.3    Savelli, S.L.4    Nagaraja, H.N.5    Zhou, B.6
  • 30
    • 61849115785 scopus 로고    scopus 로고
    • Copy number variation in the human genome and its implication in autoimmunity
    • doi:10.1111/j.1365-2249.2008.03865.x
    • Schaschl H, Aitman T, Vyse T. Copy number variation in the human genome and its implication in autoimmunity. Clin Exp Immunol (2009) 156(1):12-6. doi:10.1111/j.1365-2249.2008.03865.x
    • (2009) Clin Exp Immunol , vol.156 , Issue.1 , pp. 12-16
    • Schaschl, H.1    Aitman, T.2    Vyse, T.3
  • 31
    • 84883474570 scopus 로고    scopus 로고
    • Single-cell DNA-methylation analysis reveals epigenetic chimerism in preimplantation embryos
    • doi:10.1126/science.1240617
    • Lorthongpanich C, Cheow LF, Balu S, Quake SR, Knowles BB, Burkholder WF, et al. Single-cell DNA-methylation analysis reveals epigenetic chimerism in preimplantation embryos. Science (2013) 341(6150):1110-2. doi:10.1126/science.1240617
    • (2013) Science , vol.341 , Issue.6150 , pp. 1110-1112
    • Lorthongpanich, C.1    Cheow, L.F.2    Balu, S.3    Quake, S.R.4    Knowles, B.B.5    Burkholder, W.F.6
  • 32
    • 84871447495 scopus 로고    scopus 로고
    • Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing
    • doi:10.1126/science.1229112
    • Lu S, Zong C, Fan W, Yang M, Li J, Chapman AR, et al. Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science (2012) 338(6114):1627-30. doi:10.1126/science.1229112
    • (2012) Science , vol.338 , Issue.6114 , pp. 1627-1630
    • Lu, S.1    Zong, C.2    Fan, W.3    Yang, M.4    Li, J.5    Chapman, A.R.6
  • 33
    • 0026755807 scopus 로고
    • Whole genome amplification from a single cell: implications for genetic analysis
    • doi:10.1073/pnas.89.13.5847
    • Zhang L, Cui X, Schmitt K, Hubert R, Navidi W, Arnheim N. Whole genome amplification from a single cell: implications for genetic analysis. Proc Natl Acad Sci U S A (1992) 89(13):5847-51. doi:10.1073/pnas.89.13.5847
    • (1992) Proc Natl Acad Sci U S A , vol.89 , Issue.13 , pp. 5847-5851
    • Zhang, L.1    Cui, X.2    Schmitt, K.3    Hubert, R.4    Navidi, W.5    Arnheim, N.6
  • 34
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • doi:10.1093/bioinformatics/btp120
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 25:1105-11. doi:10.1093/bioinformatics/btp120
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 35
    • 0027446875 scopus 로고
    • Fidelity of phi 29 DNA polymerase, Comparison between protein-primed initiation and DNA polymerization
    • Esteban J, Salas M, Blanco L. Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. J Biol Chem (1993) 268(4):2719-26.
    • (1993) J Biol Chem , vol.268 , Issue.4 , pp. 2719-2726
    • Esteban, J.1    Salas, M.2    Blanco, L.3
  • 36
    • 84875160584 scopus 로고    scopus 로고
    • Single-cell sequencing in its prime
    • doi:10.1038/nbt.2523
    • Lasken RS. Single-cell sequencing in its prime. Nat Biotechnol (2013) 31(3):211-2. doi:10.1038/nbt.2523
    • (2013) Nat Biotechnol , vol.31 , Issue.3 , pp. 211-212
    • Lasken, R.S.1
  • 37
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    • doi:10.1101/gr.107524.110
    • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 20(9):1297-303. doi:10.1101/gr.107524.110
    • (2010) Genome Res , vol.20 , Issue.9 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3    Sivachenko, A.4    Cibulskis, K.5    Kernytsky, A.6
  • 38
    • 34548084253 scopus 로고    scopus 로고
    • SNPdetector: a software tool for sensitive and accurate SNP detection
    • doi:10.1371/journal.pcbi.0010053
    • Zhang J, Wheeler DA, Yakub I, Wei S, Sood R, Rowe W, et al. SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol (2005) 1(5):e53. doi:10.1371/journal.pcbi.0010053
    • (2005) PLoS Comput Biol , vol.1 , Issue.5
    • Zhang, J.1    Wheeler, D.A.2    Yakub, I.3    Wei, S.4    Sood, R.5    Rowe, W.6
  • 39
    • 66449114324 scopus 로고    scopus 로고
    • SNP detection for massively parallel whole-genome resequencing
    • doi:10.1101/gr.088013.108
    • Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, et al. SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 19(6):1124-32. doi:10.1101/gr.088013.108
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 1124-1132
    • Li, R.1    Li, Y.2    Fang, X.3    Yang, H.4    Wang, J.5    Kristiansen, K.6
  • 40
    • 69949122158 scopus 로고    scopus 로고
    • VarScan: variant detection in massively parallel sequencing of individual and pooled samples
    • doi:10.1093/bioinformatics/btp373
    • Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (2009) 25(17):2283-5. doi:10.1093/bioinformatics/btp373
    • (2009) Bioinformatics , vol.25 , Issue.17 , pp. 2283-2285
    • Koboldt, D.C.1    Chen, K.2    Wylie, T.3    Larson, D.E.4    McLellan, M.D.5    Mardis, E.R.6
  • 41
    • 64849083125 scopus 로고    scopus 로고
    • CNV-seq, a new method to detect copy number variation using high-throughput sequencing
    • doi:10.1186/1471-2105-10-80
    • Xie C, Tammi M. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics (2009) 10(1):80. doi:10.1186/1471-2105-10-80
    • (2009) BMC Bioinformatics , vol.10 , Issue.1 , pp. 80
    • Xie, C.1    Tammi, M.2
  • 42
    • 35948984173 scopus 로고    scopus 로고
    • PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    • doi:10.1101/gr.6861907
    • Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res (2007) 17(11):1665-74. doi:10.1101/gr.6861907
    • (2007) Genome Res , vol.17 , Issue.11 , pp. 1665-1674
    • Wang, K.1    Li, M.2    Hadley, D.3    Liu, R.4    Glessner, J.5    Grant, S.F.6
  • 43
    • 79951748341 scopus 로고    scopus 로고
    • CNAseg - a novel framework for identification of copy number changes in cancer from second-generation sequencing data
    • doi:10.1093/bioinformatics/btq587
    • Ivakhno S, Royce T, Cox AJ, Evers DJ, Cheetham RK, Tavaré S. CNAseg - a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics (2010) 26(24):3051-8. doi:10.1093/bioinformatics/btq587
    • (2010) Bioinformatics , vol.26 , Issue.24 , pp. 3051-3058
    • Ivakhno, S.1    Royce, T.2    Cox, A.J.3    Evers, D.J.4    Cheetham, R.K.5    Tavaré, S.6
  • 44
    • 79551621409 scopus 로고    scopus 로고
    • ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads
    • doi:10.1371/journal.pone.0016327
    • Miller CA, Hampton O, Coarfa C, Milosavljevic A. ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One (2011) 6(1):e16327. doi:10.1371/journal.pone.0016327
    • (2011) PLoS One , vol.6 , Issue.1
    • Miller, C.A.1    Hampton, O.2    Coarfa, C.3    Milosavljevic, A.4
  • 45
    • 84861400043 scopus 로고    scopus 로고
    • MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
    • doi:10.1093/nar/gks003
    • Klambauer G, Schwarzbauer K, Mayr A, Clevert D-A, Mitterecker A, Bodenhofer U, et al. MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res (2012) 40(9):e69-e. doi:10.1093/nar/gks003
    • (2012) Nucleic Acids Res , vol.40 , Issue.9
    • Klambauer, G.1    Schwarzbauer, K.2    Mayr, A.3    Clevert, D.-A.4    Mitterecker, A.5    Bodenhofer, U.6
  • 46
    • 0038781878 scopus 로고    scopus 로고
    • Unbiased whole-genome amplification directly from clinical samples
    • doi:10.1101/gr.816903
    • Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z, Wu X, et al. Unbiased whole-genome amplification directly from clinical samples. Genome Res (2003) 13(5):954-64. doi:10.1101/gr.816903
    • (2003) Genome Res , vol.13 , Issue.5 , pp. 954-964
    • Hosono, S.1    Faruqi, A.F.2    Dean, F.B.3    Du, Y.4    Sun, Z.5    Wu, X.6
  • 47
    • 48349105094 scopus 로고    scopus 로고
    • Impact of whole genome amplification on analysis of copy number variants
    • doi:10.1093/nar/gkn378
    • Pugh T, Delaney A, Farnoud N, Flibotte S, Griffith M, Li H, et al. Impact of whole genome amplification on analysis of copy number variants. Nucleic Acids Res (2008) 36(13):e80-e. doi:10.1093/nar/gkn378
    • (2008) Nucleic Acids Res , vol.36 , Issue.13
    • Pugh, T.1    Delaney, A.2    Farnoud, N.3    Flibotte, S.4    Griffith, M.5    Li, H.6
  • 48
    • 84861033754 scopus 로고    scopus 로고
    • Genome-wide copy number analysis of single cells
    • doi:10.1038/nprot.2012.039
    • Baslan T, Kendall J, Rodgers L, Cox H, Riggs M, Stepansky A, et al. Genome-wide copy number analysis of single cells. Nat Protoc (2012) 7(6):1024-41. doi:10.1038/nprot.2012.039
    • (2012) Nat Protoc , vol.7 , Issue.6 , pp. 1024-1041
    • Baslan, T.1    Kendall, J.2    Rodgers, L.3    Cox, H.4    Riggs, M.5    Stepansky, A.6
  • 49
    • 0028546845 scopus 로고
    • Wavelet transform domain filters: a spatially selective noise filtration technique
    • doi:10.1109/83.336245
    • Xu Y, Weaver JB, Healy DM, Lu J. Wavelet transform domain filters: a spatially selective noise filtration technique. Image Proc IEEE Trans (1994) 3(6):747-58. doi:10.1109/83.336245
    • (1994) Image Proc IEEE Trans , vol.3 , Issue.6 , pp. 747-758
    • Xu, Y.1    Weaver, J.B.2    Healy, D.M.3    Lu, J.4
  • 50
    • 0018455310 scopus 로고
    • Suppression of acoustic noise in speech using spectral subtraction
    • doi:10.1109/TASSP.1979.1163209
    • Boll S. Suppression of acoustic noise in speech using spectral subtraction. Acoust Speech Signal Proc IEEE Trans (1979) 27(2):113-20. doi:10.1109/TASSP.1979.1163209
    • (1979) Acoust Speech Signal Proc IEEE Trans , vol.27 , Issue.2 , pp. 113-120
    • Boll, S.1
  • 51
    • 77749323185 scopus 로고    scopus 로고
    • RNA-Seq analysis to capture the transcriptome landscape of a single cell
    • doi:10.1038/nprot.2009.236
    • Tang F, Barbacioru C, Nordman E, Li B, Xu N, Bashkirov VI, et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc (2010) 5(3):516-35. doi:10.1038/nprot.2009.236
    • (2010) Nat Protoc , vol.5 , Issue.3 , pp. 516-535
    • Tang, F.1    Barbacioru, C.2    Nordman, E.3    Li, B.4    Xu, N.5    Bashkirov, V.I.6
  • 52
    • 84862999381 scopus 로고    scopus 로고
    • Differentiation of single cell derived human mesenchymal stem cells into cells with a neuronal phenotype: RNA and microRNA expression profile
    • doi:10.1007/s11033-011-1180-9
    • Crobu F, Latini V, Marongiu MF, Sogos V, Scintu F, Porcu S, et al. Differentiation of single cell derived human mesenchymal stem cells into cells with a neuronal phenotype: RNA and microRNA expression profile. Mol Biol Rep (2012) 39(4):3995-4007. doi:10.1007/s11033-011-1180-9
    • (2012) Mol Biol Rep , vol.39 , Issue.4 , pp. 3995-4007
    • Crobu, F.1    Latini, V.2    Marongiu, M.F.3    Sogos, V.4    Scintu, F.5    Porcu, S.6
  • 53
    • 84954396263 scopus 로고    scopus 로고
    • Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data
    • doi:10.1186/gb-2013-14-1-r7
    • Kim JK, Marioni JC. Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data. Genome Biol (2013) 14(1):R7. doi:10.1186/gb-2013-14-1-r7
    • (2013) Genome Biol , vol.14 , Issue.1
    • Kim, J.K.1    Marioni, J.C.2
  • 54
    • 45249120816 scopus 로고    scopus 로고
    • Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells
    • doi:10.1186/1471-2164-9-268
    • Subkhankulova T, Gilchrist MJ, Livesey FJ. Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells. BMC Genomics (2008) 9:268. doi:10.1186/1471-2164-9-268
    • (2008) BMC Genomics , vol.9 , pp. 268
    • Subkhankulova, T.1    Gilchrist, M.J.2    Livesey, F.J.3
  • 56
    • 84866953427 scopus 로고    scopus 로고
    • Yanai ICEL-. Seq: single-cell RNA-Seq by multiplexed linear amplification
    • doi:10.1016/j.celrep.2012.08.003
    • Hashimshony T, Wagner F, Sher N, Yanai ICEL-. Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Reports (2012) 2(3):666-73. doi:10.1016/j.celrep.2012.08.003
    • (2012) Cell Reports , vol.2 , Issue.3 , pp. 666-673
    • Hashimshony, T.1    Wagner, F.2    Sher, N.3
  • 57
    • 67349146589 scopus 로고    scopus 로고
    • mRNA-Seq whole-transcriptome analysis of a single cell
    • doi:10.1038/nmeth.1315
    • Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods (2009) 6(5):377-82. doi:10.1038/nmeth.1315
    • (2009) Nat Methods , vol.6 , Issue.5 , pp. 377-382
    • Tang, F.1    Barbacioru, C.2    Wang, Y.3    Nordman, E.4    Lee, C.5    Xu, N.6
  • 58
    • 84887101406 scopus 로고    scopus 로고
    • Smart-seq2 for sensitive full-length transcriptome profiling in single cells
    • doi:10.1038/nmeth.2639
    • Picelli S, Björklund ÅK, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods (2013) 10:1096-8. doi:10.1038/nmeth.2639
    • (2013) Nat Methods , vol.10 , pp. 1096-1098
    • Picelli, S.1    Björklund, Å.K.2    Faridani, O.R.3    Sagasser, S.4    Winberg, G.5    Sandberg, R.6
  • 59
    • 84872194966 scopus 로고    scopus 로고
    • Two methods for full-length RNA sequencing for low quantities of cells and single cells
    • doi:10.1073/pnas.1217322109
    • Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, et al. Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci U S A (2013) 110(2):594-9. doi:10.1073/pnas.1217322109
    • (2013) Proc Natl Acad Sci U S A , vol.110 , Issue.2 , pp. 594-599
    • Pan, X.1    Durrett, R.E.2    Zhu, H.3    Tanaka, Y.4    Li, Y.5    Zi, X.6
  • 60
    • 84876085773 scopus 로고    scopus 로고
    • Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity
    • doi:10.1186/gb-2013-14-4-r31
    • Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, et al. Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity. Genome Biol (2013) 14(4):R31. doi:10.1186/gb-2013-14-4-r31
    • (2013) Genome Biol , vol.14 , Issue.4
    • Sasagawa, Y.1    Nikaido, I.2    Hayashi, T.3    Danno, H.4    Uno, K.D.5    Imai, T.6
  • 61
    • 84878997106 scopus 로고    scopus 로고
    • Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
    • doi:10.1038/nature12172
    • Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature (2013) 498(7453):236-40. doi:10.1038/nature12172
    • (2013) Nature , vol.498 , Issue.7453 , pp. 236-240
    • Shalek, A.K.1    Satija, R.2    Adiconis, X.3    Gertner, R.S.4    Gaublomme, J.T.5    Raychowdhury, R.6
  • 62
    • 84882582801 scopus 로고    scopus 로고
    • Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments
    • doi:10.1038/nbt.2642
    • Wills QF, Livak KJ, Tipping AJ, Enver T, Goldson AJ, Sexton DW, et al. Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments. Nat Biotechnol (2013) 31(8):748-52. doi:10.1038/nbt.2642
    • (2013) Nat Biotechnol , vol.31 , Issue.8 , pp. 748-752
    • Wills, Q.F.1    Livak, K.J.2    Tipping, A.J.3    Enver, T.4    Goldson, A.J.5    Sexton, D.W.6
  • 63
    • 84893910301 scopus 로고    scopus 로고
    • Quantitative assessment of single-cell RNA-sequencing methods
    • doi:10.1038/nmeth.2694
    • Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, Rothenberg ME, et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods (2013) 11(1):41-6. doi:10.1038/nmeth.2694
    • (2013) Nat Methods , vol.11 , Issue.1 , pp. 41-46
    • Wu, A.R.1    Neff, N.F.2    Kalisky, T.3    Dalerba, P.4    Treutlein, B.5    Rothenberg, M.E.6
  • 64
    • 84880213158 scopus 로고    scopus 로고
    • Single-cell paired-end genome sequencing reveals structural variation per cell cycle
    • doi:10.1093/nar/gkt345
    • Voet T, Kumar P, Van Loo P, Cooke SL, Marshall J, Lin M-L, et al. Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res (2013) 41(12):6119-38. doi:10.1093/nar/gkt345
    • (2013) Nucleic Acids Res , vol.41 , Issue.12 , pp. 6119-6138
    • Voet, T.1    Kumar, P.2    Van Loo, P.3    Cooke, S.L.4    Marshall, J.5    Lin, M.-L.6
  • 65
    • 84887109584 scopus 로고    scopus 로고
    • Accounting for technical noise in single-cell RNA-seq experiments
    • doi:10.1038/nmeth.2645
    • Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, et al. Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods (2013) 10(11):1093-5. doi:10.1038/nmeth.2645
    • (2013) Nat Methods , vol.10 , Issue.11 , pp. 1093-1095
    • Brennecke, P.1    Anders, S.2    Kim, J.K.3    Kołodziejczyk, A.A.4    Zhang, X.5    Proserpio, V.6
  • 66
    • 84875811525 scopus 로고    scopus 로고
    • Methods, challenges and potentials of single cell RNA-seq
    • doi:10.3390/biology1030658
    • Hebenstreit D. Methods, challenges and potentials of single cell RNA-seq. Biology (2012) 1(3):658-67. doi:10.3390/biology1030658
    • (2012) Biology , vol.1 , Issue.3 , pp. 658-667
    • Hebenstreit, D.1
  • 67
    • 84893007623 scopus 로고    scopus 로고
    • Single-cell transcriptomics for drug target discovery
    • doi:10.1016/j.coph.2013.04.011
    • Spaethling JM, Eberwine JH. Single-cell transcriptomics for drug target discovery. Curr Opin Pharmacol (2013) 13(5):786-90. doi:10.1016/j.coph.2013.04.011
    • (2013) Curr Opin Pharmacol , vol.13 , Issue.5 , pp. 786-790
    • Spaethling, J.M.1    Eberwine, J.H.2
  • 68
    • 84890060756 scopus 로고    scopus 로고
    • SAMstrt: Statistical test for differential expression in single-cell transcriptome with spike-in normalization
    • doi:10.1093/bioinformatics/btt511
    • Katayama S, Töhönen V, Linnarsson S, Kere J. SAMstrt: Statistical test for differential expression in single-cell transcriptome with spike-in normalization. Bioinformatics (2013) 29(22):2943-5. doi:10.1093/bioinformatics/btt511
    • (2013) Bioinformatics , vol.29 , Issue.22 , pp. 2943-2945
    • Katayama, S.1    Töhönen, V.2    Linnarsson, S.3    Kere, J.4
  • 69
    • 84887237209 scopus 로고    scopus 로고
    • Investigating intratumour heterogeneity by single-cell sequencing
    • doi:10.1038/aja.2013.106
    • Ren S-C, Qu M, Sun Y-H. Investigating intratumour heterogeneity by single-cell sequencing. Asian J Androl (2013) 15(6):729-34. doi:10.1038/aja.2013.106
    • (2013) Asian J Androl , vol.15 , Issue.6 , pp. 729-734
    • Ren, S.-C.1    Qu, M.2    Sun, Y.-H.3
  • 70
    • 84883743509 scopus 로고    scopus 로고
    • Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells
    • doi:10.1038/nsmb.2660
    • Yan L, Yang M, Guo H, Yang L, Wu J, Li R, et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol (2013) 20(9):1131-9. doi:10.1038/nsmb.2660
    • (2013) Nat Struct Mol Biol , vol.20 , Issue.9 , pp. 1131-1139
    • Yan, L.1    Yang, M.2    Guo, H.3    Yang, L.4    Wu, J.5    Li, R.6
  • 71
    • 80052745094 scopus 로고    scopus 로고
    • Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
    • doi:10.1093/bioinformatics/btr427
    • Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, et al. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics (2011) 27(18):2518-28. doi:10.1093/bioinformatics/btr427
    • (2011) Bioinformatics , vol.27 , Issue.18 , pp. 2518-2528
    • Grant, G.R.1    Farkas, M.H.2    Pizarro, A.D.3    Lahens, N.F.4    Schug, J.5    Brunk, B.P.6
  • 72
    • 77955443472 scopus 로고    scopus 로고
    • Detection of splice junctions from paired-end RNA-seq data by SpliceMap
    • doi:10.1093/nar/gkq211
    • Au KF, Jiang H, Lin L, Xing Y, Wong WH. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res (2010) 38(14):4570-8. doi:10.1093/nar/gkq211
    • (2010) Nucleic Acids Res , vol.38 , Issue.14 , pp. 4570-4578
    • Au, K.F.1    Jiang, H.2    Lin, L.3    Xing, Y.4    Wong, W.H.5
  • 73
    • 78649345104 scopus 로고    scopus 로고
    • MapSplice: accurate mapping of RNA-seq reads for splice junction discovery
    • doi:10.1093/nar/gkq622
    • Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, et al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res (2010) 38(18):e178. doi:10.1093/nar/gkq622
    • (2010) Nucleic Acids Res , vol.38 , Issue.18
    • Wang, K.1    Singh, D.2    Zeng, Z.3    Coleman, S.J.4    Huang, Y.5    Savich, G.L.6
  • 74
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • doi:10.1093/bioinformatics/btq057
    • Wu TD, Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics (2010) 26(7):873-81. doi:10.1093/bioinformatics/btq057
    • (2010) Bioinformatics , vol.26 , Issue.7 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2
  • 75
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - the BLAST-like alignment tool
    • doi:10.1101/gr.229202
    • Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res (2002) 12(4):656-64. doi:10.1101/gr.229202
    • (2002) Genome Res , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1
  • 76
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • doi:10.1038/nmeth.1923
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 9(4):357-9. doi:10.1038/nmeth.1923
    • (2012) Nat Methods , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 77
    • 40049104732 scopus 로고    scopus 로고
    • SOAP: short oligonucleotide alignment program
    • doi:10.1093/bioinformatics/btn025
    • Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 24(5):713-4. doi:10.1093/bioinformatics/btn025
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 713-714
    • Li, R.1    Li, Y.2    Kristiansen, K.3    Wang, J.4
  • 78
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • doi:10.1093/bioinformatics/btp324
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 25(14):1754-60. doi:10.1093/bioinformatics/btp324
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 79
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • doi:10.1038/nmeth.1226
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 5(7):621-8. doi:10.1038/nmeth.1226
    • (2008) Nat Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 80
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • doi:10.1038/nbt.1621
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 28(5):511-5. doi:10.1038/nbt.1621
    • (2010) Nat Biotechnol , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    van Baren, M.J.6
  • 81
    • 84871809302 scopus 로고    scopus 로고
    • STAR: ultrafast universal RNA-seq aligner
    • doi:10.1093/bioinformatics/bts635
    • Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (2013) 29(1):15-21. doi:10.1093/bioinformatics/bts635
    • (2013) Bioinformatics , vol.29 , Issue.1 , pp. 15-21
    • Dobin, A.1    Davis, C.A.2    Schlesinger, F.3    Drenkow, J.4    Zaleski, C.5    Jha, S.6
  • 82
    • 74549125753 scopus 로고    scopus 로고
    • An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
    • doi:10.1371/journal.pcbi.1000598
    • Ramsköld D, Wang ET, Burge CB, Sandberg R. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol (2009) 5(12):e1000598. doi:10.1371/journal.pcbi.1000598
    • (2009) PLoS Comput Biol , vol.5 , Issue.12
    • Ramsköld, D.1    Wang, E.T.2    Burge, C.B.3    Sandberg, R.4
  • 83
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    • doi:10.1186/1471-2105-12-323
    • Li B, Dewey C. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics (2011) 12(1):323. doi:10.1186/1471-2105-12-323
    • (2011) BMC Bioinformatics , vol.12 , Issue.1 , pp. 323
    • Li, B.1    Dewey, C.2
  • 84
    • 78649714014 scopus 로고    scopus 로고
    • Analysis and design of RNA sequencing experiments for identifying isoform regulation
    • doi:10.1038/nmeth.1528
    • Katz Y, Wang ET, Airoldi EM, Burge CB. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods (2010) 7(12):1009-15. doi:10.1038/nmeth.1528
    • (2010) Nat Methods , vol.7 , Issue.12 , pp. 1009-1015
    • Katz, Y.1    Wang, E.T.2    Airoldi, E.M.3    Burge, C.B.4
  • 85
    • 33746747476 scopus 로고    scopus 로고
    • Machine learning in bioinformatics: a brief survey and recommendations for practitioners
    • doi:10.1016/j.compbiomed.2005.09.002
    • Bhaskar H, Hoyle DC, Singh S. Machine learning in bioinformatics: a brief survey and recommendations for practitioners. Comput Biol Med (2006) 36(10):1104-25. doi:10.1016/j.compbiomed.2005.09.002
    • (2006) Comput Biol Med , vol.36 , Issue.10 , pp. 1104-1125
    • Bhaskar, H.1    Hoyle, D.C.2    Singh, S.3
  • 86
    • 70349608338 scopus 로고    scopus 로고
    • Probabilistic models and machine learning in structural bioinformatics
    • doi:10.1177/0962280208099492
    • Hamelryck T. Probabilistic models and machine learning in structural bioinformatics. Stat Methods Med Res (2009) 18(5):505-26. doi:10.1177/0962280208099492
    • (2009) Stat Methods Med Res , vol.18 , Issue.5 , pp. 505-526
    • Hamelryck, T.1
  • 88
    • 80052199067 scopus 로고    scopus 로고
    • Machine learning models in protein bioinformatics
    • doi:10.2174/138920311796957621
    • Kurgan L, Zhou Y. Machine learning models in protein bioinformatics. Curr Protein Pept Sci (2011) 12(6):455. doi:10.2174/138920311796957621
    • (2011) Curr Protein Pept Sci , vol.12 , Issue.6 , pp. 455
    • Kurgan, L.1    Zhou, Y.2
  • 90
    • 84870348120 scopus 로고    scopus 로고
    • Applying bioinformatics to proteomics: is machine learning the answer to biomarker discovery for PD and MSA?
    • doi:10.1002/mds.25189
    • Mattison HA, Stewart T, Zhang J. Applying bioinformatics to proteomics: is machine learning the answer to biomarker discovery for PD and MSA? Mov Disord (2012) 27(13):1595-7. doi:10.1002/mds.25189
    • (2012) Mov Disord , vol.27 , Issue.13 , pp. 1595-1597
    • Mattison, H.A.1    Stewart, T.2    Zhang, J.3
  • 91
    • 77649209688 scopus 로고    scopus 로고
    • Machine learning in biomedicine and bioinformatics
    • Peterson LE, Chen XW. Machine learning in biomedicine and bioinformatics. Int J Data Min Bioinform (2009) 3(4):363-4.
    • (2009) Int J Data Min Bioinform , vol.3 , Issue.4 , pp. 363-364
    • Peterson, L.E.1    Chen, X.W.2
  • 92
    • 61449205119 scopus 로고    scopus 로고
    • Computational intelligence and machine learning in bioinformatics
    • doi:10.1016/j.artmed.2008.08.014
    • Valentini G, Tagliaferri R, Masulli F. Computational intelligence and machine learning in bioinformatics. Artif Intell Med (2009) 45(2-3):91-6. doi:10.1016/j.artmed.2008.08.014
    • (2009) Artif Intell Med , vol.45 , Issue.2-3 , pp. 91-96
    • Valentini, G.1    Tagliaferri, R.2    Masulli, F.3
  • 93
    • 84894441508 scopus 로고    scopus 로고
    • Single-cell analysis of embryoid body heterogeneity using microfluidic trapping array
    • doi:10.1007/s10544-013-9807-3
    • Wilson JL, Suri S, Singh A, Rivet CA, Lu H, McDevitt TC. Single-cell analysis of embryoid body heterogeneity using microfluidic trapping array. Biomed Microdevices (2013). doi:10.1007/s10544-013-9807-3
    • (2013) Biomed Microdevices
    • Wilson, J.L.1    Suri, S.2    Singh, A.3    Rivet, C.A.4    Lu, H.5    McDevitt, T.C.6
  • 94
    • 84890281380 scopus 로고    scopus 로고
    • Single cell heterogeneity: why unstable genomes are incompatible with average profiles
    • doi:10.4161/cc.26580
    • Abdallah BY, Horne SD, Stevens JB, Liu G, Ying AY, Vanderhyden B, et al. Single cell heterogeneity: why unstable genomes are incompatible with average profiles. Cell Cycle (2013) 12(23). doi:10.4161/cc.26580
    • (2013) Cell Cycle , vol.12 , Issue.23
    • Abdallah, B.Y.1    Horne, S.D.2    Stevens, J.B.3    Liu, G.4    Ying, A.Y.5    Vanderhyden, B.6
  • 95
    • 76649128993 scopus 로고    scopus 로고
    • Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype
    • doi:10.1172/JCI40724
    • Park SY, Gonen M, Kim HJ, Michor F, Polyak K. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. J Clin Invest (2010) 120(2):636-44. doi:10.1172/JCI40724
    • (2010) J Clin Invest , vol.120 , Issue.2 , pp. 636-644
    • Park, S.Y.1    Gonen, M.2    Kim, H.J.3    Michor, F.4    Polyak, K.5
  • 96
    • 84863229772 scopus 로고    scopus 로고
    • Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm
    • doi:10.1016/j.cell.2012.02.028
    • Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, et al. Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 148(5):873-85. doi:10.1016/j.cell.2012.02.028
    • (2012) Cell , vol.148 , Issue.5 , pp. 873-885
    • Hou, Y.1    Song, L.2    Zhu, P.3    Zhang, B.4    Tao, Y.5    Xu, X.6
  • 97
    • 77956412152 scopus 로고    scopus 로고
    • Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis
    • doi:10.1016/j.stem.2010.03.015
    • Tang F, Barbacioru C, Bao S, Lee C, Nordman E, Wang X, et al. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell (2010) 6(5):468-78. doi:10.1016/j.stem.2010.03.015
    • (2010) Cell Stem Cell , vol.6 , Issue.5 , pp. 468-478
    • Tang, F.1    Barbacioru, C.2    Bao, S.3    Lee, C.4    Nordman, E.5    Wang, X.6
  • 98
    • 84864258558 scopus 로고    scopus 로고
    • Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm
    • doi:10.1016/j.cell.2012.06.030
    • Wang J, Fan HC, Behr B, Quake SR. Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell (2012) 150(2):402-12. doi:10.1016/j.cell.2012.06.030
    • (2012) Cell , vol.150 , Issue.2 , pp. 402-412
    • Wang, J.1    Fan, H.C.2    Behr, B.3    Quake, S.R.4
  • 99
    • 84890055556 scopus 로고    scopus 로고
    • Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells
    • doi:10.1038/nbt.2720
    • Gole J, Gore A, Richards A, Chiu Y-J, Fung H-L, Bushman D, et al. Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat Biotechnol (2013) 31(12):1126-32. doi:10.1038/nbt.2720
    • (2013) Nat Biotechnol , vol.31 , Issue.12 , pp. 1126-1132
    • Gole, J.1    Gore, A.2    Richards, A.3    Chiu, Y.-J.4    Fung, H.-L.5    Bushman, D.6


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