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Volumn 36, Issue 4, 2014, Pages 407-418

Opening the genetic toolbox of niche model organisms with high throughput techniques: Novel proteins in regeneration as a case study

Author keywords

High throughput; Newt; Next generation sequencing; Niche model organism; Regeneration

Indexed keywords

CELL MARKER; CONTIG; PROTEOME; TRANSCRIPTOME;

EID: 84896701909     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.201300093     Document Type: Article
Times cited : (7)

References (85)
  • 1
    • 3142615372 scopus 로고    scopus 로고
    • The RNAi revolution
    • Novina CD, Sharp PA. 2004. The RNAi revolution. Nature 430: 161-4.
    • (2004) Nature , vol.430 , pp. 161-164
    • Novina, C.D.1    Sharp, P.A.2
  • 2
    • 84875372911 scopus 로고    scopus 로고
    • Natural RNA circles function as efficient microRNA sponges
    • Hansen TB, Jensen TI, Clausen BH, Bramsen JB, et al. 2013. Natural RNA circles function as efficient microRNA sponges. Nature 495: 384-8.
    • (2013) Nature , vol.495 , pp. 384-388
    • Hansen, T.B.1    Jensen, T.I.2    Clausen, B.H.3    Bramsen, J.B.4
  • 3
    • 84864880991 scopus 로고    scopus 로고
    • Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
    • Ramskold D, Luo S, Wang YC, Li R, et al. 2012. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol 30: 777-82.
    • (2012) Nat Biotechnol , vol.30 , pp. 777-782
    • Ramskold, D.1    Luo, S.2    Wang, Y.C.3    Li, R.4
  • 4
    • 33645544764 scopus 로고    scopus 로고
    • An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis
    • Kurimoto K, Yabuta Y, Ohinata Y, Ono Y, et al. 2006. An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res 34: e42.
    • (2006) Nucleic Acids Res , vol.34
    • Kurimoto, K.1    Yabuta, Y.2    Ohinata, Y.3    Ono, Y.4
  • 5
    • 84866096861 scopus 로고    scopus 로고
    • Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators
    • Bodenmiller B, Zunder ER, Finck R, Chen TJ, et al. 2012. Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators. Nat Biotechnol 30: 858-67.
    • (2012) Nat Biotechnol , vol.30 , pp. 858-867
    • Bodenmiller, B.1    Zunder, E.R.2    Finck, R.3    Chen, T.J.4
  • 6
    • 84878633937 scopus 로고    scopus 로고
    • Orbitrap mass spectromery
    • Zubarev RA, Makarov A. 2013. Orbitrap mass spectromery. Anal Chem 85: 5288-96.
    • (2013) Anal Chem , vol.85 , pp. 5288-5296
    • Zubarev, R.A.1    Makarov, A.2
  • 7
    • 47549099572 scopus 로고    scopus 로고
    • SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function
    • Kruger M, Moser M, Ussar S, Thievessen I, et al. 2008. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134: 353-64.
    • (2008) Cell , vol.134 , pp. 353-364
    • Kruger, M.1    Moser, M.2    Ussar, S.3    Thievessen, I.4
  • 8
    • 77958018495 scopus 로고    scopus 로고
    • The SILAC fly allows for accurate protein quantification in vivo
    • Sury MD, Chen JX, Selbach M. 2010. The SILAC fly allows for accurate protein quantification in vivo. Mol Cell Proteomics 9: 2173-83.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 2173-2183
    • Sury, M.D.1    Chen, J.X.2    Selbach, M.3
  • 9
    • 84871860708 scopus 로고    scopus 로고
    • Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples
    • Boersema PJ, Geiger T, Wisniewski JR, Mann M. 2013. Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples. Mol Cell Proteomics 12: 158-71.
    • (2013) Mol Cell Proteomics , vol.12 , pp. 158-171
    • Boersema, P.J.1    Geiger, T.2    Wisniewski, J.R.3    Mann, M.4
  • 10
    • 84861157792 scopus 로고    scopus 로고
    • Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles
    • Deeb SJ, D'Souza RC, Cox J, Schmidt-Supprian M, et al. 2012. Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles. Mol Cell Proteomics 11: 77-89.
    • (2012) Mol Cell Proteomics , vol.11 , pp. 77-89
    • Deeb, S.J.1    D'Souza, R.C.2    Cox, J.3    Schmidt-Supprian, M.4
  • 11
    • 77952226764 scopus 로고    scopus 로고
    • Super-SILAC mix for quantitative proteomics of human tumor tissue
    • Geiger T, Cox J, Ostasiewicz P, Wisniewski JR, et al. 2010. Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods 7: 383-5.
    • (2010) Nat Methods , vol.7 , pp. 383-385
    • Geiger, T.1    Cox, J.2    Ostasiewicz, P.3    Wisniewski, J.R.4
  • 12
    • 84865604070 scopus 로고    scopus 로고
    • Quantitative mass spectrometry in proteomics
    • Bantscheff M, Kuster B. 2012. Quantitative mass spectrometry in proteomics. Anal Bioanal Chem 404: 937-8.
    • (2012) Anal Bioanal Chem , vol.404 , pp. 937-938
    • Bantscheff, M.1    Kuster, B.2
  • 13
    • 84857790643 scopus 로고    scopus 로고
    • Proteomics: bases for protein complexity understanding
    • Rotilio D, Della Corte A, D'Imperio M, Coletta W, et al. 2012. Proteomics: bases for protein complexity understanding. Thromb Res 129: 257-62.
    • (2012) Thromb Res , vol.129 , pp. 257-262
    • Rotilio, D.1    Della Corte, A.2    D'Imperio, M.3    Coletta, W.4
  • 14
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, Attiya S, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-80.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3    Attiya, S.4
  • 15
    • 33751077282 scopus 로고    scopus 로고
    • Analysis of one million base pairs of Neanderthal DNA
    • Green RE, Krause J, Ptak SE, Briggs AW, et al. 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444: 330-6.
    • (2006) Nature , vol.444 , pp. 330-336
    • Green, R.E.1    Krause, J.2    Ptak, S.E.3    Briggs, A.W.4
  • 16
    • 24644462173 scopus 로고    scopus 로고
    • Accurate multiplex polony sequencing of an evolved bacterial genome
    • Shendure J, Porreca GJ, Reppas NB, Lin X, et al. 2005. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728-32.
    • (2005) Science , vol.309 , pp. 1728-1732
    • Shendure, J.1    Porreca, G.J.2    Reppas, N.B.3    Lin, X.4
  • 17
    • 41749104588 scopus 로고    scopus 로고
    • Single-molecule DNA sequencing of a viral genome
    • Harris TD, Buzby PR, Babcock H, Beer E, et al. 2008. Single-molecule DNA sequencing of a viral genome. Science 320: 106-9.
    • (2008) Science , vol.320 , pp. 106-109
    • Harris, T.D.1    Buzby, P.R.2    Babcock, H.3    Beer, E.4
  • 18
    • 44949200024 scopus 로고    scopus 로고
    • Parallel confocal detection of single molecules in real time
    • Lundquist PM, Zhong CF, Zhao P, Tomaney AB, et al. 2008. Parallel confocal detection of single molecules in real time. Opt Lett 33: 1026-8.
    • (2008) Opt Lett , vol.33 , pp. 1026-1028
    • Lundquist, P.M.1    Zhong, C.F.2    Zhao, P.3    Tomaney, A.B.4
  • 19
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-9.
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1    Balasubramanian, S.2    Swerdlow, H.P.3    Smith, G.P.4
  • 20
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 21
    • 84873801934 scopus 로고    scopus 로고
    • High-throughput sequencing for biology and medicine
    • Soon WW, Hariharan M, Snyder MP. 2013. High-throughput sequencing for biology and medicine. Mol Syst Biol 9: 640.
    • (2013) Mol Syst Biol , vol.9 , pp. 640
    • Soon, W.W.1    Hariharan, M.2    Snyder, M.P.3
  • 22
    • 80054757012 scopus 로고    scopus 로고
    • Performance comparison of exome DNA sequencing technologies
    • Clark MJ, Chen R, Lam HY, Karczewski KJ, et al. 2011. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol 29: 908-14.
    • (2011) Nat Biotechnol , vol.29 , pp. 908-914
    • Clark, M.J.1    Chen, R.2    Lam, H.Y.3    Karczewski, K.J.4
  • 23
    • 48749124117 scopus 로고    scopus 로고
    • ChIPping away at gene regulation
    • Massie CE, Mills IG. 2008. ChIPping away at gene regulation. EMBO Rep 9: 337-43.
    • (2008) EMBO Rep , vol.9 , pp. 337-343
    • Massie, C.E.1    Mills, I.G.2
  • 24
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Waterston RH, Lindblad-Toh K, Birney E, Rogers J, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-62.
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1    Lindblad-Toh, K.2    Birney, E.3    Rogers, J.4
  • 26
    • 79959875909 scopus 로고    scopus 로고
    • De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
    • Adamidi C, Wang Y, Gruen D, Mastrobuoni G, et al. 2011. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Res 21: 1193-200.
    • (2011) Genome Res , vol.21 , pp. 1193-1200
    • Adamidi, C.1    Wang, Y.2    Gruen, D.3    Mastrobuoni, G.4
  • 27
    • 34447254707 scopus 로고    scopus 로고
    • Positional identity of adult stem cells in salamander limb regeneration
    • Kumar A, Gates PB, Brockes JP. 2007. Positional identity of adult stem cells in salamander limb regeneration. C R Biol 330: 485-90.
    • (2007) C R Biol , vol.330 , pp. 485-490
    • Kumar, A.1    Gates, P.B.2    Brockes, J.P.3
  • 28
    • 38349023585 scopus 로고    scopus 로고
    • Molecular basis for the nerve dependence of limb regeneration in an adult vertebrate
    • Kumar A, Godwin JW, Gates PB, Garza-Garcia AA, et al. 2007. Molecular basis for the nerve dependence of limb regeneration in an adult vertebrate. Science 318: 772-7.
    • (2007) Science , vol.318 , pp. 772-777
    • Kumar, A.1    Godwin, J.W.2    Gates, P.B.3    Garza-Garcia, A.A.4
  • 29
    • 84873948069 scopus 로고    scopus 로고
    • A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration
    • Looso M, Preussner J, Sousounis K, Bruckskotten M, et al. 2013. A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration. Genome Biol 14: R16.
    • (2013) Genome Biol , vol.14
    • Looso, M.1    Preussner, J.2    Sousounis, K.3    Bruckskotten, M.4
  • 30
    • 84876083730 scopus 로고    scopus 로고
    • A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens
    • Abdullayev I, Kirkham M, Bjorklund AK, Simon A, et al. 2013. A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens. Exp Cell Res 319: 1187-97.
    • (2013) Exp Cell Res , vol.319 , pp. 1187-1197
    • Abdullayev, I.1    Kirkham, M.2    Bjorklund, A.K.3    Simon, A.4
  • 31
    • 72549089941 scopus 로고    scopus 로고
    • Proteomic analysis of blastema formation in regenerating axolotl limbs
    • Rao N, Jhamb D, Milner DJ, Li B, et al. 2009. Proteomic analysis of blastema formation in regenerating axolotl limbs. BMC Biol 7: 83.
    • (2009) BMC Biol , vol.7 , pp. 83
    • Rao, N.1    Jhamb, D.2    Milner, D.J.3    Li, B.4
  • 32
    • 84879639724 scopus 로고    scopus 로고
    • Integrative "omics"-approach discovers dynamic and regulatory features of bacterial stress responses
    • Berghoff BA, Konzer A, Mank NN, Looso M, et al. 2013. Integrative "omics"-approach discovers dynamic and regulatory features of bacterial stress responses. PLoS Genet 9: e1003576.
    • (2013) PLoS Genet , vol.9
    • Berghoff, B.A.1    Konzer, A.2    Mank, N.N.3    Looso, M.4
  • 33
    • 84870748269 scopus 로고    scopus 로고
    • Generation of albino Xenopus tropicalis using zinc-finger nucleases
    • Nakajima K, Nakajima T, Takase M, Yaoita Y. 2012. Generation of albino Xenopus tropicalis using zinc-finger nucleases. Dev Growth Differ 54: 777-84.
    • (2012) Dev Growth Differ , vol.54 , pp. 777-784
    • Nakajima, K.1    Nakajima, T.2    Takase, M.3    Yaoita, Y.4
  • 34
    • 84867904873 scopus 로고    scopus 로고
    • Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases (TALENs)
    • Lei Y, Guo X, Liu Y, Cao Y, et al. 2012. Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases (TALENs). Proc Natl Acad Sci USA 109: 17484-9.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 17484-17489
    • Lei, Y.1    Guo, X.2    Liu, Y.3    Cao, Y.4
  • 35
    • 84875353107 scopus 로고    scopus 로고
    • TALEN-based gene disruption in the dengue vector Aedes aegypti
    • Aryan A, Anderson MA, Myles KM, Adelman ZN. 2013. TALEN-based gene disruption in the dengue vector Aedes aegypti. PLoS One 8: e60082.
    • (2013) PLoS One , vol.8
    • Aryan, A.1    Anderson, M.A.2    Myles, K.M.3    Adelman, Z.N.4
  • 36
    • 84875332105 scopus 로고    scopus 로고
    • Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest
    • Keeling CI, Yuen MM, Liao NY, Roderick Docking T, et al. 2013. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biol 14: R27.
    • (2013) Genome Biol , vol.14
    • Keeling, C.I.1    Yuen, M.M.2    Liao, N.Y.3    Roderick Docking, T.4
  • 37
    • 84879020737 scopus 로고    scopus 로고
    • The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
    • Shaffer HB, Minx P, Warren DE, Shedlock AM, et al. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol 14: R28.
    • (2013) Genome Biol , vol.14
    • Shaffer, H.B.1    Minx, P.2    Warren, D.E.3    Shedlock, A.M.4
  • 38
    • 35348932160 scopus 로고    scopus 로고
    • Wasp gene expression supports an evolutionary link between maternal behavior and eusociality
    • Toth AL, Varala K, Newman TC, Miguez FE, et al. 2007. Wasp gene expression supports an evolutionary link between maternal behavior and eusociality. Science 318: 441-4.
    • (2007) Science , vol.318 , pp. 441-444
    • Toth, A.L.1    Varala, K.2    Newman, T.C.3    Miguez, F.E.4
  • 39
    • 71049176982 scopus 로고    scopus 로고
    • Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species
    • Genome KCoS. 2009. Genome 10K: a proposal to obtain whole-genome sequence for 10, 000 vertebrate species. J Hered 100: 659-74.
    • (2009) J Hered , vol.100 , pp. 659-674
    • Genome, KC.1
  • 40
    • 84859165788 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
    • Pagani I, Liolios K, Jansson J, Chen IM, et al. 2012. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40: D571-9.
    • (2012) Nucleic Acids Res , vol.40
    • Pagani, I.1    Liolios, K.2    Jansson, J.3    Chen, I.M.4
  • 41
    • 77954450225 scopus 로고    scopus 로고
    • De novo characterization of a whitefly transcriptome and analysis of its gene expression during development
    • Wang XW, Luan JB, Li JM, Bao YY, et al. 2010. De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11: 400.
    • (2010) BMC Genomics , vol.11 , pp. 400
    • Wang, X.W.1    Luan, J.B.2    Li, J.M.3    Bao, Y.Y.4
  • 42
    • 41149167170 scopus 로고    scopus 로고
    • Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
    • 1636-147
    • Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, et al. 2008. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17: 1636-147.
    • (2008) Mol Ecol , vol.17
    • Vera, J.C.1    Wheat, C.W.2    Fescemyer, H.W.3    Frilander, M.J.4
  • 43
    • 66749182204 scopus 로고    scopus 로고
    • Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
    • Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, et al. 2009. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 10: 219.
    • (2009) BMC Genomics , vol.10 , pp. 219
    • Meyer, E.1    Aglyamova, G.V.2    Wang, S.3    Buchanan-Carter, J.4
  • 44
    • 13344269000 scopus 로고    scopus 로고
    • From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis
    • Wilkins MR, Pasquali C, Appel RD, Ou K, et al. 1996. From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (N Y) 14: 61-5.
    • (1996) Biotechnology (N Y) , vol.14 , pp. 61-65
    • Wilkins, M.R.1    Pasquali, C.2    Appel, R.D.3    Ou, K.4
  • 45
    • 84873724658 scopus 로고    scopus 로고
    • A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis
    • Picotti P, Clement-Ziza M, Lam H, Campbell DS, et al. 2013. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature 494: 266-70.
    • (2013) Nature , vol.494 , pp. 266-270
    • Picotti, P.1    Clement-Ziza, M.2    Lam, H.3    Campbell, D.S.4
  • 46
    • 84874232489 scopus 로고    scopus 로고
    • The coming age of complete, accurate, and ubiquitous proteomes
    • Mann M, Kulak NA, Nagaraj N, Cox J. 2013. The coming age of complete, accurate, and ubiquitous proteomes. Mol Cell 49: 583-90.
    • (2013) Mol Cell , vol.49 , pp. 583-590
    • Mann, M.1    Kulak, N.A.2    Nagaraj, N.3    Cox, J.4
  • 47
    • 84876181417 scopus 로고    scopus 로고
    • Transcriptome analysis of newt lens regeneration reveals distinct gradients in gene expression patterns
    • Sousounis K, Looso M, Maki N, Ivester CJ, et al. 2013. Transcriptome analysis of newt lens regeneration reveals distinct gradients in gene expression patterns. PLoS One 8: e61445.
    • (2013) PLoS One , vol.8
    • Sousounis, K.1    Looso, M.2    Maki, N.3    Ivester, C.J.4
  • 48
    • 84878722381 scopus 로고    scopus 로고
    • Stable isotope labelling in zebrafish allows in vivo monitoring of cardiac morphogenesis
    • Konzer A, Ruhs A, Braun H, Jungblut B, et al. 2013. Stable isotope labelling in zebrafish allows in vivo monitoring of cardiac morphogenesis. Mol Cell Proteomics 12: 1502-12.
    • (2013) Mol Cell Proteomics , vol.12 , pp. 1502-1512
    • Konzer, A.1    Ruhs, A.2    Braun, H.3    Jungblut, B.4
  • 49
    • 84876314836 scopus 로고    scopus 로고
    • Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10,000 proteins
    • Wisniewski JR, Dus K, Mann M. 2013. Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10, 000 proteins. Proteomics Clin Appl 7: 225-33.
    • (2013) Proteomics Clin Appl , vol.7 , pp. 225-233
    • Wisniewski, J.R.1    Dus, K.2    Mann, M.3
  • 50
    • 2642523613 scopus 로고    scopus 로고
    • The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches
    • Habermann B, Oegema J, Sunyaev S, Shevchenko A. 2004. The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches. Mol Cell Proteomics 3: 238-49.
    • (2004) Mol Cell Proteomics , vol.3 , pp. 238-249
    • Habermann, B.1    Oegema, J.2    Sunyaev, S.3    Shevchenko, A.4
  • 51
    • 48849097490 scopus 로고    scopus 로고
    • Protein identification pipeline for the homology-driven proteomics
    • Junqueira M, Spirin V, Balbuena TS, Thomas H, et al. 2008. Protein identification pipeline for the homology-driven proteomics. J Proteomics 71: 346-56.
    • (2008) J Proteomics , vol.71 , pp. 346-356
    • Junqueira, M.1    Spirin, V.2    Balbuena, T.S.3    Thomas, H.4
  • 52
    • 84870210594 scopus 로고    scopus 로고
    • Survey of the camel urinary proteome by shotgun proteomics using a multiple database search strategy
    • Alhaider AA, Bayoumy N, Argo E, Gader AG, et al. 2012. Survey of the camel urinary proteome by shotgun proteomics using a multiple database search strategy. Proteomics 12: 3403-6.
    • (2012) Proteomics , vol.12 , pp. 3403-3406
    • Alhaider, A.A.1    Bayoumy, N.2    Argo, E.3    Gader, A.G.4
  • 53
    • 76949094959 scopus 로고    scopus 로고
    • Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish
    • Borchardt T, Looso M, Bruckskotten M, Weis P, et al. 2010. Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish. BMC Genomics 11: 4.
    • (2010) BMC Genomics , vol.11 , pp. 4
    • Borchardt, T.1    Looso, M.2    Bruckskotten, M.3    Weis, P.4
  • 54
    • 84867459034 scopus 로고    scopus 로고
    • Conus consors snail venom proteomics proposes functions, pathways, and novel families involved in its venomic system
    • Leonardi A, Biass D, Kordis D, Stocklin R, et al. 2012. Conus consors snail venom proteomics proposes functions, pathways, and novel families involved in its venomic system. J Proteome Res 11: 5046-58.
    • (2012) J Proteome Res , vol.11 , pp. 5046-5058
    • Leonardi, A.1    Biass, D.2    Kordis, D.3    Stocklin, R.4
  • 55
    • 77953155113 scopus 로고    scopus 로고
    • Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry
    • Looso M, Borchardt T, Kruger M, Braun T. 2010. Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry. Mol Cell Proteomics 9: 1157-66.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 1157-1166
    • Looso, M.1    Borchardt, T.2    Kruger, M.3    Braun, T.4
  • 56
    • 0141884306 scopus 로고    scopus 로고
    • Peptide and protein de novo sequencing by mass spectrometry
    • Standing KG. 2003. Peptide and protein de novo sequencing by mass spectrometry. Curr Opin Struct Biol 13: 595-601.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 595-601
    • Standing, K.G.1
  • 57
    • 2642585189 scopus 로고    scopus 로고
    • Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome
    • Liska AJ, Popov AV, Sunyaev S, Coughlin P, et al. 2004. Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome. Proteomics 4: 2707-21.
    • (2004) Proteomics , vol.4 , pp. 2707-2721
    • Liska, A.J.1    Popov, A.V.2    Sunyaev, S.3    Coughlin, P.4
  • 58
    • 84879488712 scopus 로고    scopus 로고
    • De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration
    • Wu CH, Tsai MH, Ho CC, Chen CY, et al. 2013. De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration. BMC Genomics 14: 434.
    • (2013) BMC Genomics , vol.14 , pp. 434
    • Wu, C.H.1    Tsai, M.H.2    Ho, C.C.3    Chen, C.Y.4
  • 59
    • 77950200829 scopus 로고    scopus 로고
    • Zebrafish heart regeneration occurs by cardiomyocyte dedifferentiation and proliferation
    • Jopling C, Sleep E, Raya M, Marti M, et al. 2010. Zebrafish heart regeneration occurs by cardiomyocyte dedifferentiation and proliferation. Nature 464: 606-9.
    • (2010) Nature , vol.464 , pp. 606-609
    • Jopling, C.1    Sleep, E.2    Raya, M.3    Marti, M.4
  • 60
  • 61
    • 84879344080 scopus 로고    scopus 로고
    • Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish
    • Meng F, Braasch I, Phillips JB, Lin X, et al. 2013. Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish. Mol Biol Evol 30: 1527-43.
    • (2013) Mol Biol Evol , vol.30 , pp. 1527-1543
    • Meng, F.1    Braasch, I.2    Phillips, J.B.3    Lin, X.4
  • 62
    • 84874214846 scopus 로고    scopus 로고
    • Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes
    • Ferreira PG, Patalano S, Chauhan R, Ffrench-Constant R, et al. 2013. Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biol 14: R20.
    • (2013) Genome Biol , vol.14
    • Ferreira, P.G.1    Patalano, S.2    Chauhan, R.3    Ffrench-Constant, R.4
  • 63
    • 84863510246 scopus 로고    scopus 로고
    • De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system
    • Peterson MP, Whittaker DJ, Ambreth S, Sureshchandra S, et al. 2012. De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. BMC Genomics 13: 305.
    • (2012) BMC Genomics , vol.13 , pp. 305
    • Peterson, M.P.1    Whittaker, D.J.2    Ambreth, S.3    Sureshchandra, S.4
  • 64
    • 84877071493 scopus 로고    scopus 로고
    • Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program
    • Knapp D, Schulz H, Rascon CA, Volkmer M, et al. 2013. Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program. PLoS One 8: e61352.
    • (2013) PLoS One , vol.8
    • Knapp, D.1    Schulz, H.2    Rascon, C.A.3    Volkmer, M.4
  • 65
    • 84876007237 scopus 로고    scopus 로고
    • Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema
    • Stewart R, Rascon CA, Tian S, Nie J, et al. 2013. Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema. PLoS Comput Biol 9: e1002936.
    • (2013) PLoS Comput Biol , vol.9
    • Stewart, R.1    Rascon, C.A.2    Tian, S.3    Nie, J.4
  • 66
    • 70349909714 scopus 로고    scopus 로고
    • Bilaterian phylogeny: a broad sampling of 13 nuclear genes provides a new Lophotrochozoa phylogeny and supports a paraphyletic basal acoelomorpha
    • Paps J, Baguna J, Riutort M. 2009. Bilaterian phylogeny: a broad sampling of 13 nuclear genes provides a new Lophotrochozoa phylogeny and supports a paraphyletic basal acoelomorpha. Mol Biol Evol 26: 2397-406.
    • (2009) Mol Biol Evol , vol.26 , pp. 2397-2406
    • Paps, J.1    Baguna, J.2    Riutort, M.3
  • 67
    • 39649084637 scopus 로고    scopus 로고
    • Bioinformatics challenges of new sequencing technology
    • Pop M, Salzberg SL. 2008. Bioinformatics challenges of new sequencing technology. Trends Genet 24: 142-9.
    • (2008) Trends Genet , vol.24 , pp. 142-149
    • Pop, M.1    Salzberg, S.L.2
  • 68
    • 80755159050 scopus 로고    scopus 로고
    • How to apply de Bruijn graphs to genome assembly
    • Compeau PE, Pevzner PA, Tesler G. 2011. How to apply de Bruijn graphs to genome assembly. Nat Biotechnol 29: 987-91.
    • (2011) Nat Biotechnol , vol.29 , pp. 987-991
    • Compeau, P.E.1    Pevzner, P.A.2    Tesler, G.3
  • 69
    • 79952178131 scopus 로고    scopus 로고
    • High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    • Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, et al. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 108: 1513-8.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 1513-1518
    • Gnerre, S.1    Maccallum, I.2    Przybylski, D.3    Ribeiro, F.J.4
  • 70
    • 84859768479 scopus 로고    scopus 로고
    • Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
    • Schulz MH, Zerbino DR, Vingron M, Birney E. 2012. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28: 1086-92.
    • (2012) Bioinformatics , vol.28 , pp. 1086-1092
    • Schulz, M.H.1    Zerbino, D.R.2    Vingron, M.3    Birney, E.4
  • 71
    • 35348988679 scopus 로고    scopus 로고
    • Paired-end mapping reveals extensive structural variation in the human genome
    • Korbel JO, Urban AE, Affourtit JP, Godwin B, et al. 2007. Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420-6.
    • (2007) Science , vol.318 , pp. 420-426
    • Korbel, J.O.1    Urban, A.E.2    Affourtit, J.P.3    Godwin, B.4
  • 72
    • 84877801923 scopus 로고    scopus 로고
    • A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly
    • Francis WR, Christianson LM, Kiko R, Powers ML, et al. 2013. A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly. BMC Genomics 14: 167.
    • (2013) BMC Genomics , vol.14 , pp. 167
    • Francis, W.R.1    Christianson, L.M.2    Kiko, R.3    Powers, M.L.4
  • 73
    • 84888437648 scopus 로고    scopus 로고
    • SILAC proteomics of planarians identifies Ncoa5 as a conserved component of pluripotent stem cells
    • Böser A, Drexler HC, Reuter H, Guangming W, et al. 2013. SILAC proteomics of planarians identifies Ncoa5 as a conserved component of pluripotent stem cells. Cell Rep 5: 1142-55.
    • (2013) Cell Rep , vol.5 , pp. 1142-1155
    • Böser, A.1    Drexler, H.C.2    Reuter, H.3    Guangming, W.4
  • 74
    • 84866137157 scopus 로고    scopus 로고
    • Spiked-in pulsed in vivo labeling identifies a new member of the CCN family in regenerating newt hearts
    • Looso M, Michel CS, Konzer A, Bruckskotten M, et al. 2012. Spiked-in pulsed in vivo labeling identifies a new member of the CCN family in regenerating newt hearts. J Proteome Res 11: 4693-704.
    • (2012) J Proteome Res , vol.11 , pp. 4693-4704
    • Looso, M.1    Michel, C.S.2    Konzer, A.3    Bruckskotten, M.4
  • 75
    • 84879335696 scopus 로고    scopus 로고
    • Reconstitution of the myocardium in regenerating newt hearts is preceded by transient deposition of extracellular matrix components
    • Piatkowski T, Muhlfeld C, Borchardt T, Braun T. 2013. Reconstitution of the myocardium in regenerating newt hearts is preceded by transient deposition of extracellular matrix components. Stem Cells Dev 22: 1921-31.
    • (2013) Stem Cells Dev , vol.22 , pp. 1921-1931
    • Piatkowski, T.1    Muhlfeld, C.2    Borchardt, T.3    Braun, T.4
  • 76
    • 33845708407 scopus 로고    scopus 로고
    • Re-programming of newt cardiomyocytes is induced by tissue regeneration
    • Laube F, Heister M, Scholz C, Borchardt T, et al. 2006. Re-programming of newt cardiomyocytes is induced by tissue regeneration. J Cell Sci 119: 4719-29.
    • (2006) J Cell Sci , vol.119 , pp. 4719-4729
    • Laube, F.1    Heister, M.2    Scholz, C.3    Borchardt, T.4
  • 77
    • 79955507001 scopus 로고    scopus 로고
    • Recapitulation of developmental cardiogenesis governs the morphological and functional regeneration of adult newt hearts following injury
    • Witman N, Murtuza B, Davis B, Arner A, et al. 2011. Recapitulation of developmental cardiogenesis governs the morphological and functional regeneration of adult newt hearts following injury. Dev Biol 354: 67-76.
    • (2011) Dev Biol , vol.354 , pp. 67-76
    • Witman, N.1    Murtuza, B.2    Davis, B.3    Arner, A.4
  • 78
    • 33847257790 scopus 로고    scopus 로고
    • CCN1 protects cardiac myocytes from oxidative stress via beta1 integrin-Akt pathway
    • Yoshida Y, Togi K, Matsumae H, Nakashima Y, et al. 2007. CCN1 protects cardiac myocytes from oxidative stress via beta1 integrin-Akt pathway. Biochem Biophys Res Commun 355: 611-8.
    • (2007) Biochem Biophys Res Commun , vol.355 , pp. 611-618
    • Yoshida, Y.1    Togi, K.2    Matsumae, H.3    Nakashima, Y.4
  • 79
    • 84871519181 scopus 로고    scopus 로고
    • TALENs: a widely applicable technology for targeted genome editing
    • Joung JK, Sander JD. 2013. TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14: 49-55.
    • (2013) Nat Rev Mol Cell Biol , vol.14 , pp. 49-55
    • Joung, J.K.1    Sander, J.D.2
  • 80
    • 84873729095 scopus 로고    scopus 로고
    • Multiplex genome engineering using CRISPR/Cas systems
    • Cong L, Ran FA, Cox D, Lin S, et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819-23.
    • (2013) Science , vol.339 , pp. 819-823
    • Cong, L.1    Ran, F.A.2    Cox, D.3    Lin, S.4
  • 81
    • 84873734105 scopus 로고    scopus 로고
    • RNA-guided human genome engineering via Cas9
    • Mali P, Yang L, Esvelt KM, Aach J, et al. 2013. RNA-guided human genome engineering via Cas9. Science 339: 823-6.
    • (2013) Science , vol.339 , pp. 823-826
    • Mali, P.1    Yang, L.2    Esvelt, K.M.3    Aach, J.4
  • 82
    • 66249100555 scopus 로고    scopus 로고
    • Transposon-mediated genome manipulation in vertebrates
    • Ivics Z, Li MA, Mates L, Boeke JD, et al. 2009. Transposon-mediated genome manipulation in vertebrates. Nat Methods 6: 415-22.
    • (2009) Nat Methods , vol.6 , pp. 415-422
    • Ivics, Z.1    Li, M.A.2    Mates, L.3    Boeke, J.D.4
  • 83
    • 0033985437 scopus 로고    scopus 로고
    • Engineering mouse chromosomes with Cre-loxP: range, efficiency, and somatic applications
    • Zheng B, Sage M, Sheppeard EA, Jurecic V, et al. 2000. Engineering mouse chromosomes with Cre-loxP: range, efficiency, and somatic applications. Mol Cell Biol 20: 648-55.
    • (2000) Mol Cell Biol , vol.20 , pp. 648-655
    • Zheng, B.1    Sage, M.2    Sheppeard, E.A.3    Jurecic, V.4
  • 85
    • 84893763187 scopus 로고    scopus 로고
    • Fundamental differences in dedifferentiation and stem cell recruitment during skeletal muscle regeneration in two salamander species
    • in press doi: 10.1016/j.stem.2013.11.007.
    • Sandoval-Guzman T, Wang H, Khattak S, Schuez M, et al. 2013. Fundamental differences in dedifferentiation and stem cell recruitment during skeletal muscle regeneration in two salamander species. Cell Stem Cell, in press doi: 10.1016/j.stem.2013.11.007.
    • (2013) Cell Stem Cell
    • Sandoval-Guzman, T.1    Wang, H.2    Khattak, S.3    Schuez, M.4


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