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Volumn 14, Issue 1, 2013, Pages

Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals

Author keywords

Coral reef; Dinoflagellates; Expression profiling; microRNA (miRNA); mRNA; RNAseq; Scleractinian corals; Small interfering RNA (siRNA); Small RNA (smRNA); Symbiodinium; Symbiont

Indexed keywords

MESSENGER RNA; MICRORNA; TRANSCRIPTOME;

EID: 84885354418     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-704     Document Type: Article
Times cited : (94)

References (110)
  • 3
    • 33646923128 scopus 로고    scopus 로고
    • Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing
    • 10.1016/j.cell.2006.04.025, 16751098
    • Bühler M, Verdel A, Moazed D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 2006, 125:873-886. 10.1016/j.cell.2006.04.025, 16751098.
    • (2006) Cell , vol.125 , pp. 873-886
    • Bühler, M.1    Verdel, A.2    Moazed, D.3
  • 4
    • 70350778443 scopus 로고    scopus 로고
    • An epigenetic switch involving NF-Œ∫B, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation
    • 10.1016/j.cell.2009.10.014, 2783826, 19878981
    • Iliopoulos D, Hirsch HA, Struhl K. An epigenetic switch involving NF-Œ∫B, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation. Cell 2009, 139:693-706. 10.1016/j.cell.2009.10.014, 2783826, 19878981.
    • (2009) Cell , vol.139 , pp. 693-706
    • Iliopoulos, D.1    Hirsch, H.A.2    Struhl, K.3
  • 5
    • 58449134534 scopus 로고    scopus 로고
    • Small silencing RNAs: an expanding universe
    • 10.1038/nrg2504, 2724769, 19148191
    • Ghildiyal M, Zamore PD. Small silencing RNAs: an expanding universe. Nat Rev Genet 2009, 10:94-108. 10.1038/nrg2504, 2724769, 19148191.
    • (2009) Nat Rev Genet , vol.10 , pp. 94-108
    • Ghildiyal, M.1    Zamore, P.D.2
  • 6
    • 60149088848 scopus 로고    scopus 로고
    • Origins and mechanisms of miRNAs and siRNAs
    • 10.1016/j.cell.2009.01.035, 2675692, 19239886
    • Carthew RW, Sontheimer EJ. Origins and mechanisms of miRNAs and siRNAs. Cell 2009, 136:642-655. 10.1016/j.cell.2009.01.035, 2675692, 19239886.
    • (2009) Cell , vol.136 , pp. 642-655
    • Carthew, R.W.1    Sontheimer, E.J.2
  • 9
    • 23944514849 scopus 로고    scopus 로고
    • Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation
    • 10.1016/j.cell.2005.07.031, 16122423
    • Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 2005, 122:553-563. 10.1016/j.cell.2005.07.031, 16122423.
    • (2005) Cell , vol.122 , pp. 553-563
    • Bagga, S.1    Bracht, J.2    Hunter, S.3    Massirer, K.4    Holtz, J.5    Eachus, R.6    Pasquinelli, A.E.7
  • 11
    • 28044457883 scopus 로고    scopus 로고
    • MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function
    • 10.1073/pnas.0506482102, 1287990, 16287976
    • Humphreys DT, Westman BJ, Martin DIK, Preiss T. MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proc Natl Acad Sci U S A 2005, 102:16961-16966. 10.1073/pnas.0506482102, 1287990, 16287976.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 16961-16966
    • Humphreys, D.T.1    Westman, B.J.2    Martin, D.I.K.3    Preiss, T.4
  • 12
    • 73149089202 scopus 로고    scopus 로고
    • Transcriptional control of gene expression by MicroRNAs
    • 10.1016/j.cell.2009.12.023, 20085706
    • Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, Reski R, Frank W. Transcriptional control of gene expression by MicroRNAs. Cell 2010, 140:111-122. 10.1016/j.cell.2009.12.023, 20085706.
    • (2010) Cell , vol.140 , pp. 111-122
    • Khraiwesh, B.1    Arif, M.A.2    Seumel, G.I.3    Ossowski, S.4    Weigel, D.5    Reski, R.6    Frank, W.7
  • 14
    • 40949100837 scopus 로고    scopus 로고
    • A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases
    • 10.1038/nsmb.1399, 2990406, 18311151
    • Benetti R, Gonzalo S, Jaco I, Munoz P, Gonzalez S, Schoeftner S, Murchison E, Andl T, Chen T, Klatt P, et al. A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat Struct Mol Biol 2008, 15:268-279. 10.1038/nsmb.1399, 2990406, 18311151.
    • (2008) Nat Struct Mol Biol , vol.15 , pp. 268-279
    • Benetti, R.1    Gonzalo, S.2    Jaco, I.3    Munoz, P.4    Gonzalez, S.5    Schoeftner, S.6    Murchison, E.7    Andl, T.8    Chen, T.9    Klatt, P.10
  • 15
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: target recognition and regulatory functions
    • 10.1016/j.cell.2009.01.002, 3794896, 19167326
    • Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233. 10.1016/j.cell.2009.01.002, 3794896, 19167326.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 16
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are MicroRNA targets
    • 10.1016/j.cell.2004.12.035, 15652477
    • Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are MicroRNA targets. Cell 2005, 120:15-20. 10.1016/j.cell.2004.12.035, 15652477.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 18
    • 79959340052 scopus 로고    scopus 로고
    • The emerging world of small silencing RNAs in protozoan parasites
    • 10.1016/j.pt.2011.03.002, 3124596, 21497553
    • Atayde VD, Tschudi C, Ullu E. The emerging world of small silencing RNAs in protozoan parasites. Trends Parasitol 2011, 27:321-327. 10.1016/j.pt.2011.03.002, 3124596, 21497553.
    • (2011) Trends Parasitol , vol.27 , pp. 321-327
    • Atayde, V.D.1    Tschudi, C.2    Ullu, E.3
  • 19
    • 84866267741 scopus 로고    scopus 로고
    • Do miRNAs have a deep evolutionary history?
    • 10.1002/bies.201200055, 22847169
    • Tarver JE, Donoghue PC, Peterson KJ. Do miRNAs have a deep evolutionary history?. Bioessays 2012, 34:857-866. 10.1002/bies.201200055, 22847169.
    • (2012) Bioessays , vol.34 , pp. 857-866
    • Tarver, J.E.1    Donoghue, P.C.2    Peterson, K.J.3
  • 21
    • 84859996524 scopus 로고    scopus 로고
    • Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals
    • 10.1371/journal.pone.0035269, 3329448, 22529998
    • Bayer T, Aranda M, Sunagawa S, Yum LK, DeSalvo MK, Lindquist E, Coffroth MA, Voolstra CR, Medina M. Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PLoS ONE 2012, 7:e35269. 10.1371/journal.pone.0035269, 3329448, 22529998.
    • (2012) PLoS ONE , vol.7
    • Bayer, T.1    Aranda, M.2    Sunagawa, S.3    Yum, L.K.4    DeSalvo, M.K.5    Lindquist, E.6    Coffroth, M.A.7    Voolstra, C.R.8    Medina, M.9
  • 22
    • 78650582054 scopus 로고    scopus 로고
    • Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates
    • 10.1073/pnas.1007246107, 2993343, 21041634
    • Lin S, Zhang H, Zhuang Y, Tran B, Gill J. Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates. Proc Natl Acad Sci 2010, 107:20033-20038. 10.1073/pnas.1007246107, 2993343, 21041634.
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 20033-20038
    • Lin, S.1    Zhang, H.2    Zhuang, Y.3    Tran, B.4    Gill, J.5
  • 23
    • 0001584709 scopus 로고
    • Biochemistry of the dinoflagellate nucleus
    • Oxford: Blackwell, Taylor FJR
    • Rizzo PJ. Biochemistry of the dinoflagellate nucleus. The Biology of Dinoflagellates 1987, 143-173. Oxford: Blackwell, Taylor FJR.
    • (1987) The Biology of Dinoflagellates , pp. 143-173
    • Rizzo, P.J.1
  • 25
    • 0028951751 scopus 로고
    • Evidence that some dinoflagellates contain a ribulose-1,5-bisphosphate carboxylase/oxygenase related to that of the alpha-proteobacteria
    • 10.1098/rspb.1995.0040, 7740046
    • Whitney SM, Shaw DC, Yellowlees D. Evidence that some dinoflagellates contain a ribulose-1,5-bisphosphate carboxylase/oxygenase related to that of the alpha-proteobacteria. Proc Biol Sci 1995, 259:271-275. 10.1098/rspb.1995.0040, 7740046.
    • (1995) Proc Biol Sci , vol.259 , pp. 271-275
    • Whitney, S.M.1    Shaw, D.C.2    Yellowlees, D.3
  • 26
    • 0033536215 scopus 로고    scopus 로고
    • Single gene circles in dinoflagellate chloroplast genomes
    • 10.1038/22099, 10408440
    • Zhang Z, Green BR, Cavalier-Smith T. Single gene circles in dinoflagellate chloroplast genomes. Nature 1999, 400:155-159. 10.1038/22099, 10408440.
    • (1999) Nature , vol.400 , pp. 155-159
    • Zhang, Z.1    Green, B.R.2    Cavalier-Smith, T.3
  • 27
    • 84868643112 scopus 로고    scopus 로고
    • Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D
    • 10.1186/1471-2148-12-217, 3740780, 23145489
    • Ladner JT, Barshis DJ, Palumbi SR. Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D. BMC Evol Biol 2012, 12:217. 10.1186/1471-2148-12-217, 3740780, 23145489.
    • (2012) BMC Evol Biol , vol.12 , pp. 217
    • Ladner, J.T.1    Barshis, D.J.2    Palumbi, S.R.3
  • 28
    • 64549129565 scopus 로고    scopus 로고
    • Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium)
    • doi: 10.1016/j.cbd.2008.11.001. Epub 2008 Dec 6
    • Voolstra CR, Sunagawa S, Schwarz JA, Coffroth MA, Yellowlees D, Leggat W, Medina M. Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium). Comp Biochem Physiol Part D Genomics Proteomics 2008, doi: 10.1016/j.cbd.2008.11.001. Epub 2008 Dec 6.
    • (2008) Comp Biochem Physiol Part D Genomics Proteomics
    • Voolstra, C.R.1    Sunagawa, S.2    Schwarz, J.A.3    Coffroth, M.A.4    Yellowlees, D.5    Leggat, W.6    Medina, M.7
  • 29
    • 77950397835 scopus 로고    scopus 로고
    • Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression Due to bacterial presence
    • 10.1371/journal.pone.0009688, 2837391, 20300646
    • Moustafa A, Evans AN, Kulis DM, Hackett JD, Erdner DL, Anderson DM, Bhattacharya D. Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression Due to bacterial presence. PLoS ONE 2010, 5:e9688. 10.1371/journal.pone.0009688, 2837391, 20300646.
    • (2010) PLoS ONE , vol.5
    • Moustafa, A.1    Evans, A.N.2    Kulis, D.M.3    Hackett, J.D.4    Erdner, D.L.5    Anderson, D.M.6    Bhattacharya, D.7
  • 30
    • 0001462989 scopus 로고
    • Assimilation of photosynthetic products of zooxanthellae by a reef coral
    • Muscatine L, Cernichiari E. Assimilation of photosynthetic products of zooxanthellae by a reef coral. Biol Bull 1969, 137:506-523.
    • (1969) Biol Bull , vol.137 , pp. 506-523
    • Muscatine, L.1    Cernichiari, E.2
  • 31
    • 34247218626 scopus 로고    scopus 로고
    • The role of microorganisms in coral health, disease and evolution
    • 10.1038/nrmicro1635, 17384666
    • Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I. The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol 2007, 5:355-362. 10.1038/nrmicro1635, 17384666.
    • (2007) Nat Rev Microbiol , vol.5 , pp. 355-362
    • Rosenberg, E.1    Koren, O.2    Reshef, L.3    Efrony, R.4    Zilber-Rosenberg, I.5
  • 33
    • 50049109156 scopus 로고    scopus 로고
    • Differential gene expression during thermal stress and bleaching in the caribbean coral montastraea faveolata
    • 10.1111/j.1365-294X.2008.03879.x, 18662230
    • DeSalvo MK, Voolstra CR, Sunagawa S, Schwarz JA, Stillman JH, Coffroth MA, Szmant AM, Medina M. Differential gene expression during thermal stress and bleaching in the caribbean coral montastraea faveolata. Mol Ecol 2008, 17:3952-3971. 10.1111/j.1365-294X.2008.03879.x, 18662230.
    • (2008) Mol Ecol , vol.17 , pp. 3952-3971
    • DeSalvo, M.K.1    Voolstra, C.R.2    Sunagawa, S.3    Schwarz, J.A.4    Stillman, J.H.5    Coffroth, M.A.6    Szmant, A.M.7    Medina, M.8
  • 34
    • 71649110546 scopus 로고    scopus 로고
    • Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata
    • 10.1016/j.margen.2009.07.002, 21798184
    • Reyes-Bermudez A, Desalvo MK, Voolstra CR, Sunagawa S, Szmant AM, Iglesias-Prieto R, Medina M. Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata. Mar Genomics 2009, 2:149-159. 10.1016/j.margen.2009.07.002, 21798184.
    • (2009) Mar Genomics , vol.2 , pp. 149-159
    • Reyes-Bermudez, A.1    Desalvo, M.K.2    Voolstra, C.R.3    Sunagawa, S.4    Szmant, A.M.5    Iglesias-Prieto, R.6    Medina, M.7
  • 35
    • 74549224369 scopus 로고    scopus 로고
    • Effects of temperature on gene expression in embryos of the coral Montastraea faveolata
    • 10.1186/1471-2164-10-627, 2807443, 20030803
    • Voolstra CR, Schnetzer J, Peshkin L, Randall CJ, Szmant AM, Medina M. Effects of temperature on gene expression in embryos of the coral Montastraea faveolata. BMC Genomics 2009, 10:627. 10.1186/1471-2164-10-627, 2807443, 20030803.
    • (2009) BMC Genomics , vol.10 , pp. 627
    • Voolstra, C.R.1    Schnetzer, J.2    Peshkin, L.3    Randall, C.J.4    Szmant, A.M.5    Medina, M.6
  • 36
    • 65549099059 scopus 로고    scopus 로고
    • The host transcriptome remains unaltered during the establishment of coral-algal symbioses
    • 10.1111/j.1365-294X.2009.04167.x, 19317843
    • Voolstra CR, Schwarz JA, Schnetzer J, Sunagawa S, Desalvo MK, Szmant AM, Coffroth MA, Medina M. The host transcriptome remains unaltered during the establishment of coral-algal symbioses. Mol Ecol 2009, 18:1823-1833. 10.1111/j.1365-294X.2009.04167.x, 19317843.
    • (2009) Mol Ecol , vol.18 , pp. 1823-1833
    • Voolstra, C.R.1    Schwarz, J.A.2    Schnetzer, J.3    Sunagawa, S.4    Desalvo, M.K.5    Szmant, A.M.6    Coffroth, M.A.7    Medina, M.8
  • 37
    • 77950247237 scopus 로고    scopus 로고
    • Coral host transcriptomic states are correlated with Symbiodinium genotypes
    • 10.1111/j.1365-294X.2010.04534.x, 20149089
    • DeSalvo MK, Sunagawa S, Fisher PL, Voolstra CR, Iglesias-Prieto R, Medina M. Coral host transcriptomic states are correlated with Symbiodinium genotypes. Mol Ecol 2010, 19:1174-1186. 10.1111/j.1365-294X.2010.04534.x, 20149089.
    • (2010) Mol Ecol , vol.19 , pp. 1174-1186
    • DeSalvo, M.K.1    Sunagawa, S.2    Fisher, P.L.3    Voolstra, C.R.4    Iglesias-Prieto, R.5    Medina, M.6
  • 38
    • 77955284871 scopus 로고    scopus 로고
    • Location-specific responses to thermal stress in larvae of the reef-building coral Montastraea faveolata
    • 10.1371/journal.pone.0011221, 2890407, 20585643
    • Polato NR, Voolstra CR, Schnetzer J, DeSalvo MK, Randall CJ, Szmant AM, Medina M, Baums IB. Location-specific responses to thermal stress in larvae of the reef-building coral Montastraea faveolata. PLoS ONE 2010, 5:e11221. 10.1371/journal.pone.0011221, 2890407, 20585643.
    • (2010) PLoS ONE , vol.5
    • Polato, N.R.1    Voolstra, C.R.2    Schnetzer, J.3    DeSalvo, M.K.4    Randall, C.J.5    Szmant, A.M.6    Medina, M.7    Baums, I.B.8
  • 39
    • 79960084719 scopus 로고    scopus 로고
    • Differential sensitivity of coral larvae to natural levels of ultraviolet radiation during the onset of larval competence
    • 10.1111/j.1365-294X.2011.05153.x, 21689186
    • Aranda M, Banaszak AT, Bayer T, Luyten JR, Medina M, Voolstra CR. Differential sensitivity of coral larvae to natural levels of ultraviolet radiation during the onset of larval competence. Mol Ecol 2011, 20:2955-2972. 10.1111/j.1365-294X.2011.05153.x, 21689186.
    • (2011) Mol Ecol , vol.20 , pp. 2955-2972
    • Aranda, M.1    Banaszak, A.T.2    Bayer, T.3    Luyten, J.R.4    Medina, M.5    Voolstra, C.R.6
  • 40
    • 84891157526 scopus 로고    scopus 로고
    • Bacterial profiling of white plague disease in a comparative coral species framework
    • doi: 10.1038/ismej.2013.127. [Epub ahead of print]
    • Roder C, Arif C, Bayer T, Aranda M, Daniels C, Shibl A, Chavanich S, Voolstra CR. Bacterial profiling of white plague disease in a comparative coral species framework. ISME J 2013, doi: 10.1038/ismej.2013.127. [Epub ahead of print].
    • (2013) ISME J
    • Roder, C.1    Arif, C.2    Bayer, T.3    Aranda, M.4    Daniels, C.5    Shibl, A.6    Chavanich, S.7    Voolstra, C.R.8
  • 41
    • 77949674527 scopus 로고    scopus 로고
    • Threatened corals provide underexplored microbial habitats
    • 10.1371/journal.pone.0009554, 2832684, 20221265
    • Sunagawa S, Woodley CM, Medina M. Threatened corals provide underexplored microbial habitats. PLoS ONE 2010, 5:e9554. 10.1371/journal.pone.0009554, 2832684, 20221265.
    • (2010) PLoS ONE , vol.5
    • Sunagawa, S.1    Woodley, C.M.2    Medina, M.3
  • 42
    • 84855293838 scopus 로고    scopus 로고
    • MiRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
    • 10.1093/nar/gkr688, 3245920, 21911355
    • Friedlander MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 2012, 40:37-52. 10.1093/nar/gkr688, 3245920, 21911355.
    • (2012) Nucleic Acids Res , vol.40 , pp. 37-52
    • Friedlander, M.R.1    Mackowiak, S.D.2    Li, N.3    Chen, W.4    Rajewsky, N.5
  • 43
    • 41349114789 scopus 로고    scopus 로고
    • Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide
    • 10.1016/j.cell.2008.02.034, 2981139, 18342361
    • Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, et al. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 2008, 133:116-127. 10.1016/j.cell.2008.02.034, 2981139, 18342361.
    • (2008) Cell , vol.133 , pp. 116-127
    • Mi, S.1    Cai, T.2    Hu, Y.3    Chen, Y.4    Hodges, E.5    Ni, F.6    Wu, L.7    Li, S.8    Zhou, H.9    Long, C.10
  • 44
    • 18344369543 scopus 로고    scopus 로고
    • MicroRNA biogenesis: coordinated cropping and dicing
    • Kim VN. MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 2005, 6:376-385.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 376-385
    • Kim, V.N.1
  • 45
    • 39549115890 scopus 로고    scopus 로고
    • Cloning and characterization of microRNAs from wheat (Triticum aestivum L.)
    • 10.1186/gb-2007-8-6-r96, 2394755, 17543110
    • Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q. Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol 2007, 8:R96. 10.1186/gb-2007-8-6-r96, 2394755, 17543110.
    • (2007) Genome Biol , vol.8
    • Yao, Y.1    Guo, G.2    Ni, Z.3    Sunkar, R.4    Du, J.5    Zhu, J.K.6    Sun, Q.7
  • 46
    • 2942568227 scopus 로고    scopus 로고
    • A molecular timescale of eukaryote evolution and the rise of complex multicellular life
    • 10.1186/1471-2148-4-2, 341452, 15005799
    • Hedges S, Blair J, Venturi M, Shoe J. A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol Biol 2004, 4:2. 10.1186/1471-2148-4-2, 341452, 15005799.
    • (2004) BMC Evol Biol , vol.4 , pp. 2
    • Hedges, S.1    Blair, J.2    Venturi, M.3    Shoe, J.4
  • 48
    • 0035956856 scopus 로고    scopus 로고
    • Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms
    • 10.1073/pnas.051611498, 30166, 11226267
    • Nei M, Xu P, Glazko G. Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proc Natl Acad Sci 2001, 98:2497-2502. 10.1073/pnas.051611498, 30166, 11226267.
    • (2001) Proc Natl Acad Sci , vol.98 , pp. 2497-2502
    • Nei, M.1    Xu, P.2    Glazko, G.3
  • 49
    • 77955039174 scopus 로고    scopus 로고
    • The origin and early evolution of eukaryotes in the light of phylogenomics
    • 10.1186/gb-2010-11-5-209, 2898073, 20441612
    • Koonin E. The origin and early evolution of eukaryotes in the light of phylogenomics. Genome Biol 2010, 11:209. 10.1186/gb-2010-11-5-209, 2898073, 20441612.
    • (2010) Genome Biol , vol.11 , pp. 209
    • Koonin, E.1
  • 50
    • 48449104617 scopus 로고    scopus 로고
    • GOEAST: a web-based software toolkit for gene ontology enrichment analysis
    • 10.1093/nar/gkn276, 2447756, 18487275
    • Zheng Q, Wang XJ. GOEAST: a web-based software toolkit for gene ontology enrichment analysis. Nucleic Acids Res 2008, 36:W358-W363. 10.1093/nar/gkn276, 2447756, 18487275.
    • (2008) Nucleic Acids Res , vol.36
    • Zheng, Q.1    Wang, X.J.2
  • 51
    • 79960976768 scopus 로고    scopus 로고
    • UniProt knowledgebase: a hub of integrated protein data
    • bar009-bar009, 10.1093/database/bar009, 3070428, 21447597
    • Magrane M, UniProt C. UniProt knowledgebase: a hub of integrated protein data. Database 2011, 2011:bar009-bar009. 10.1093/database/bar009, 3070428, 21447597.
    • (2011) Database , vol.2011
    • Magrane, M.1    UniProt, C.2
  • 53
    • 3142613181 scopus 로고    scopus 로고
    • Single processing center models for human dicer and bacterial RNase III
    • 10.1016/j.cell.2004.06.017, 15242644
    • Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W. Single processing center models for human dicer and bacterial RNase III. Cell 2004, 118:57-68. 10.1016/j.cell.2004.06.017, 15242644.
    • (2004) Cell , vol.118 , pp. 57-68
    • Zhang, H.1    Kolb, F.A.2    Jaskiewicz, L.3    Westhof, E.4    Filipowicz, W.5
  • 54
    • 1842816517 scopus 로고    scopus 로고
    • Distinct roles for drosophila dicer-1 and dicer-2 in the siRNA/miRNA silencing pathways
    • 10.1016/S0092-8674(04)00261-2, 15066283
    • Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ, Carthew RW. Distinct roles for drosophila dicer-1 and dicer-2 in the siRNA/miRNA silencing pathways. Cell 2004, 117:69-81. 10.1016/S0092-8674(04)00261-2, 15066283.
    • (2004) Cell , vol.117 , pp. 69-81
    • Lee, Y.S.1    Nakahara, K.2    Pham, J.W.3    Kim, K.4    He, Z.5    Sontheimer, E.J.6    Carthew, R.W.7
  • 55
    • 2442679207 scopus 로고    scopus 로고
    • Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain
    • 10.1038/nature02519, 15152257
    • Ma JB, Ye K, Patel DJ. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 2004, 429:318-322. 10.1038/nature02519, 15152257.
    • (2004) Nature , vol.429 , pp. 318-322
    • Ma, J.B.1    Ye, K.2    Patel, D.J.3
  • 57
    • 70349939426 scopus 로고    scopus 로고
    • Structural insights into mechanisms of the small RNA methyltransferase HEN1
    • 10.1038/nature08433, 19812675
    • Huang Y, Ji L, Huang Q, Vassylyev DG, Chen X, Ma JB. Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 2009, 461:823-827. 10.1038/nature08433, 19812675.
    • (2009) Nature , vol.461 , pp. 823-827
    • Huang, Y.1    Ji, L.2    Huang, Q.3    Vassylyev, D.G.4    Chen, X.5    Ma, J.B.6
  • 58
    • 80053903465 scopus 로고    scopus 로고
    • Functional implications of microRNAs in acute myeloid leukemia by integrating microRNA and messenger RNA expression profiling
    • 10.1002/cncr.26096, 3154970, 21455993
    • Havelange V, Stauffer N, Heaphy CC, Volinia S, Andreeff M, Marcucci G, Croce CM, Garzon R. Functional implications of microRNAs in acute myeloid leukemia by integrating microRNA and messenger RNA expression profiling. Cancer 2011, 117:4696-4706. 10.1002/cncr.26096, 3154970, 21455993.
    • (2011) Cancer , vol.117 , pp. 4696-4706
    • Havelange, V.1    Stauffer, N.2    Heaphy, C.C.3    Volinia, S.4    Andreeff, M.5    Marcucci, G.6    Croce, C.M.7    Garzon, R.8
  • 59
    • 79957579613 scopus 로고    scopus 로고
    • Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques
    • doi: 10.1038/msb.2011.23
    • Su W-L, Kleinhanz RR, Schadt EE. Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques. Mol Syst Biol 2011, 7. doi: 10.1038/msb.2011.23.
    • (2011) Mol Syst Biol , vol.7
    • Su, W.-L.1    Kleinhanz, R.R.2    Schadt, E.E.3
  • 60
    • 77955902024 scopus 로고    scopus 로고
    • The widespread regulation of microRNA biogenesis, function and decay
    • Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 2010, 11:597-610.
    • (2010) Nat Rev Genet , vol.11 , pp. 597-610
    • Krol, J.1    Loedige, I.2    Filipowicz, W.3
  • 61
    • 84856467364 scopus 로고    scopus 로고
    • Identification of putative miRNAs from the deep-branching unicellular flagellates
    • 10.1016/j.ygeno.2011.11.002, 22120185
    • Huang PJ, Lin WC, Chen SC, Lin YH, Sun CH, Lyu PC, Tang P. Identification of putative miRNAs from the deep-branching unicellular flagellates. Genomics 2012, 99:101-107. 10.1016/j.ygeno.2011.11.002, 22120185.
    • (2012) Genomics , vol.99 , pp. 101-107
    • Huang, P.J.1    Lin, W.C.2    Chen, S.C.3    Lin, Y.H.4    Sun, C.H.5    Lyu, P.C.6    Tang, P.7
  • 63
    • 81755161586 scopus 로고    scopus 로고
    • A microRNA derived from an apparent canonical biogenesis pathway regulates variant surface protein gene expression in Giardia lamblia
    • 10.1261/rna.028118.111, 3222128, 22033329
    • Saraiya AA, Li W, Wang CC. A microRNA derived from an apparent canonical biogenesis pathway regulates variant surface protein gene expression in Giardia lamblia. RNA 2011, 17:2152-2164. 10.1261/rna.028118.111, 3222128, 22033329.
    • (2011) RNA , vol.17 , pp. 2152-2164
    • Saraiya, A.A.1    Li, W.2    Wang, C.C.3
  • 64
    • 34347355440 scopus 로고    scopus 로고
    • MiRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii
    • 10.1038/nature05903, 17538623
    • Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 2007, 447:1126-1129. 10.1038/nature05903, 17538623.
    • (2007) Nature , vol.447 , pp. 1126-1129
    • Molnar, A.1    Schwach, F.2    Studholme, D.J.3    Thuenemann, E.C.4    Baulcombe, D.C.5
  • 66
    • 78651293534 scopus 로고    scopus 로고
    • MiRBase: integrating microRNA annotation and deep-sequencing data
    • 10.1093/nar/gkq1027, 3013655, 21037258
    • Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:D152-D157. 10.1093/nar/gkq1027, 3013655, 21037258.
    • (2011) Nucleic Acids Res , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 67
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • 10.1038/ng2135, 17893677
    • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet 2007, 39:1278-1284. 10.1038/ng2135, 17893677.
    • (2007) Nat Genet , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 68
    • 67749132423 scopus 로고    scopus 로고
    • Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    • 2733940, 19536157
    • Chi SW, Zang JB, Mele A, Darnell RB. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 2009, 460:479-486. 2733940, 19536157.
    • (2009) Nature , vol.460 , pp. 479-486
    • Chi, S.W.1    Zang, J.B.2    Mele, A.3    Darnell, R.B.4
  • 70
    • 79959830057 scopus 로고    scopus 로고
    • Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition
    • 10.1186/1471-2164-12-346, 3149589, 21729317
    • Morey J, Monroe E, Kinney A, Beal M, Johnson J, Hitchcock G, Van Dolah F. Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition. BMC Genomics 2011, 12:346. 10.1186/1471-2164-12-346, 3149589, 21729317.
    • (2011) BMC Genomics , vol.12 , pp. 346
    • Morey, J.1    Monroe, E.2    Kinney, A.3    Beal, M.4    Johnson, J.5    Hitchcock, G.6    Van Dolah, F.7
  • 71
    • 34547558886 scopus 로고    scopus 로고
    • Microarray analysis of diurnal- and circadian-regulated genes in the Florida red-tide dinoflagellate Karenia brevis (Dinophyceae)
    • Van Dolah FM, Lidie KB, Morey JS, Brunelle SA, Ryan JC, Monroe EA, Haynes BL. Microarray analysis of diurnal- and circadian-regulated genes in the Florida red-tide dinoflagellate Karenia brevis (Dinophyceae). J Phycol 2007, 43:741-752.
    • (2007) J Phycol , vol.43 , pp. 741-752
    • Van Dolah, F.M.1    Lidie, K.B.2    Morey, J.S.3    Brunelle, S.A.4    Ryan, J.C.5    Monroe, E.A.6    Haynes, B.L.7
  • 72
    • 20444495969 scopus 로고    scopus 로고
    • Multiple modes of RNA recognition by zinc finger proteins
    • 10.1016/j.sbi.2005.04.004, 15963892
    • Hall TM. Multiple modes of RNA recognition by zinc finger proteins. Curr Opin Struct Biol 2005, 15:367-373. 10.1016/j.sbi.2005.04.004, 15963892.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 367-373
    • Hall, T.M.1
  • 73
    • 84859620899 scopus 로고    scopus 로고
    • The Trypanosoma brucei CCCH zinc finger proteins ZC3H12 and ZC3H13
    • 10.1016/j.molbiopara.2012.02.006, 22366391
    • Ouna BA, Stewart M, Helbig C, Clayton C. The Trypanosoma brucei CCCH zinc finger proteins ZC3H12 and ZC3H13. Mol Biochem Parasitol 2012, 183:184-188. 10.1016/j.molbiopara.2012.02.006, 22366391.
    • (2012) Mol Biochem Parasitol , vol.183 , pp. 184-188
    • Ouna, B.A.1    Stewart, M.2    Helbig, C.3    Clayton, C.4
  • 74
    • 76549101962 scopus 로고    scopus 로고
    • Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression
    • 10.1002/bies.200900122, 20091748
    • Mihailovich M, Militti C, Gabaldon T, Gebauer F. Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression. Bioessays 2010, 32:109-118. 10.1002/bies.200900122, 20091748.
    • (2010) Bioessays , vol.32 , pp. 109-118
    • Mihailovich, M.1    Militti, C.2    Gabaldon, T.3    Gebauer, F.4
  • 75
    • 0033637153 scopus 로고    scopus 로고
    • Genomic expression programs in the response of yeast cells to environmental changes
    • 10.1091/mbc.11.12.4241, 15070, 11102521
    • Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000, 11:4241-4257. 10.1091/mbc.11.12.4241, 15070, 11102521.
    • (2000) Mol Biol Cell , vol.11 , pp. 4241-4257
    • Gasch, A.P.1    Spellman, P.T.2    Kao, C.M.3    Carmel-Harel, O.4    Eisen, M.B.5    Storz, G.6    Botstein, D.7    Brown, P.O.8
  • 76
    • 41849143745 scopus 로고    scopus 로고
    • Rapid determination of the damage to photosynthesis caused by salt and osmotic stresses using delayed fluorescence of chloroplasts
    • 10.1039/b714209a, 18389153
    • Zhang L, Xing D. Rapid determination of the damage to photosynthesis caused by salt and osmotic stresses using delayed fluorescence of chloroplasts. Photochem Photobiol Sci 2008, 7:352-360. 10.1039/b714209a, 18389153.
    • (2008) Photochem Photobiol Sci , vol.7 , pp. 352-360
    • Zhang, L.1    Xing, D.2
  • 77
    • 57849155713 scopus 로고    scopus 로고
    • Salt stress inhibits photosystems II and I in cyanobacteria
    • 10.1007/s11120-008-9334-x, 18670904
    • Allakhverdiev SI, Murata N. Salt stress inhibits photosystems II and I in cyanobacteria. Photosynth Res 2008, 98:529-539. 10.1007/s11120-008-9334-x, 18670904.
    • (2008) Photosynth Res , vol.98 , pp. 529-539
    • Allakhverdiev, S.I.1    Murata, N.2
  • 78
    • 84870894088 scopus 로고    scopus 로고
    • Transcriptional response of two core photosystem genes in Symbiodinium spp. exposed to thermal stress
    • 10.1371/journal.pone.0050439, 3517614, 23236373
    • McGinley MP, Aschaffenburg MD, Pettay DT, Smith RT, LaJeunesse TC, Warner ME. Transcriptional response of two core photosystem genes in Symbiodinium spp. exposed to thermal stress. PLoS One 2012, 7:e50439. 10.1371/journal.pone.0050439, 3517614, 23236373.
    • (2012) PLoS One , vol.7
    • McGinley, M.P.1    Aschaffenburg, M.D.2    Pettay, D.T.3    Smith, R.T.4    LaJeunesse, T.C.5    Warner, M.E.6
  • 79
    • 1942422299 scopus 로고    scopus 로고
    • Dinoflagellate chloroplasts-where have all the genes gone?
    • 10.1016/j.tig.2004.03.008, 15109781
    • Koumandou VL, Nisbet RE, Barbrook AC, Howe CJ. Dinoflagellate chloroplasts-where have all the genes gone?. Trends Genet 2004, 20:261-267. 10.1016/j.tig.2004.03.008, 15109781.
    • (2004) Trends Genet , vol.20 , pp. 261-267
    • Koumandou, V.L.1    Nisbet, R.E.2    Barbrook, A.C.3    Howe, C.J.4
  • 80
    • 18044377963 scopus 로고    scopus 로고
    • Principles of microRNA-target recognition
    • 10.1371/journal.pbio.0030085, 1043860, 15723116
    • Brennecke J, Stark A, Russell RB, Cohen SM. Principles of microRNA-target recognition. PLoS Biol 2005, 3:e85. 10.1371/journal.pbio.0030085, 1043860, 15723116.
    • (2005) PLoS Biol , vol.3
    • Brennecke, J.1    Stark, A.2    Russell, R.B.3    Cohen, S.M.4
  • 81
    • 10644237968 scopus 로고    scopus 로고
    • RNAi-mediated pathways in the nucleus
    • 10.1038/nrg1500, 15630419
    • Matzke MA, Birchler JA. RNAi-mediated pathways in the nucleus. Nat Rev Genet 2005, 6:24-35. 10.1038/nrg1500, 15630419.
    • (2005) Nat Rev Genet , vol.6 , pp. 24-35
    • Matzke, M.A.1    Birchler, J.A.2
  • 83
    • 34548458193 scopus 로고    scopus 로고
    • Fine-tuning of the innate immune response by microRNAs
    • 10.1038/sj.icb.7100091, 17621315
    • Gantier MP, Sadler AJ, Williams BR. Fine-tuning of the innate immune response by microRNAs. Immunol Cell Biol 2007, 85:458-462. 10.1038/sj.icb.7100091, 17621315.
    • (2007) Immunol Cell Biol , vol.85 , pp. 458-462
    • Gantier, M.P.1    Sadler, A.J.2    Williams, B.R.3
  • 84
    • 0346094457 scopus 로고    scopus 로고
    • Prediction of mammalian MicroRNA targets
    • 10.1016/S0092-8674(03)01018-3, 14697198
    • Lewis BP, Shih I, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian MicroRNA targets. Cell 2003, 115:787-798. 10.1016/S0092-8674(03)01018-3, 14697198.
    • (2003) Cell , vol.115 , pp. 787-798
    • Lewis, B.P.1    Shih, I.2    Jones-Rhoades, M.W.3    Bartel, D.P.4    Burge, C.B.5
  • 85
    • 73049174685 scopus 로고
    • Studies of marine planktonic diatoms. I. Cyclotella nana hustedt and detonula confervacea cleve
    • 10.1139/m62-029, 13902807
    • Guillard RRL, Ryther JH. Studies of marine planktonic diatoms. I. Cyclotella nana hustedt and detonula confervacea cleve. Can J Microbiol 1962, 8:229-239. 10.1139/m62-029, 13902807.
    • (1962) Can J Microbiol , vol.8 , pp. 229-239
    • Guillard, R.R.L.1    Ryther, J.H.2
  • 87
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • 10.1101/gr.074492.107, 2336801, 18349386
    • Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829. 10.1101/gr.074492.107, 2336801, 18349386.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 90
    • 10244243802 scopus 로고    scopus 로고
    • Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
    • 10.1093/bioinformatics/bth374, 15217813
    • Bonnet E, Wuyts J, Rouze P, Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 2004, 20:2911-2917. 10.1093/bioinformatics/bth374, 15217813.
    • (2004) Bioinformatics , vol.20 , pp. 2911-2917
    • Bonnet, E.1    Wuyts, J.2    Rouze, P.3    Van de Peer, Y.4
  • 91
  • 92
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • 10.1186/gb-2009-10-3-r25, 2690996, 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 93
    • 84055178433 scopus 로고    scopus 로고
    • MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
    • Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinforma 2011, 12:491.
    • (2011) BMC Bioinforma , vol.12 , pp. 491
    • Holt, C.1    Yandell, M.2
  • 94
    • 33745626459 scopus 로고    scopus 로고
    • Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    • 10.1093/bioinformatics/btl140, 16606683
    • Alexa A, Rahnenführer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 2006, 22:1600-1607. 10.1093/bioinformatics/btl140, 16606683.
    • (2006) Bioinformatics , vol.22 , pp. 1600-1607
    • Alexa, A.1    Rahnenführer, J.2    Lengauer, T.3
  • 95
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • 10.1186/gb-2010-11-10-r106, 3218662, 20979621
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010, 11:R106. 10.1186/gb-2010-11-10-r106, 3218662, 20979621.
    • (2010) Genome Biol , vol.11
    • Anders, S.1    Huber, W.2
  • 96
    • 79952592810 scopus 로고    scopus 로고
    • A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
    • 10.1093/bioinformatics/btr011, 3051319, 21217122
    • Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 2011, 27:764-770. 10.1093/bioinformatics/btr011, 3051319, 21217122.
    • (2011) Bioinformatics , vol.27 , pp. 764-770
    • Marçais, G.1    Kingsford, C.2
  • 97
    • 78649358717 scopus 로고    scopus 로고
    • Quake: quality-aware detection and correction of sequencing errors
    • 10.1186/gb-2010-11-11-r116, 3156955, 21114842
    • Kelley D, Schatz M, Salzberg S. Quake: quality-aware detection and correction of sequencing errors. Genome Biol 2010, 11:R116. 10.1186/gb-2010-11-11-r116, 3156955, 21114842.
    • (2010) Genome Biol , vol.11
    • Kelley, D.1    Schatz, M.2    Salzberg, S.3
  • 98
    • 84859768479 scopus 로고    scopus 로고
    • Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
    • 10.1093/bioinformatics/bts094, 3324515, 22368243
    • Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 2012, 28:1086-1092. 10.1093/bioinformatics/bts094, 3324515, 22368243.
    • (2012) Bioinformatics , vol.28 , pp. 1086-1092
    • Schulz, M.H.1    Zerbino, D.R.2    Vingron, M.3    Birney, E.4
  • 99
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Meth 2012, 9:357-359.
    • (2012) Nat Meth , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 100
    • 84871946825 scopus 로고    scopus 로고
    • Streaming fragment assignment for real-time analysis of sequencing experiments
    • Roberts A, Pachter L. Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Meth 2013, 10:71-73.
    • (2013) Nat Meth , vol.10 , pp. 71-73
    • Roberts, A.1    Pachter, L.2
  • 101
    • 79951480123 scopus 로고    scopus 로고
    • Vienna, Austria: R Foundation for Statistical Computing, R Development Core Team
    • R Development Core Team R: A language and environment for statistical computing 2010, Vienna, Austria: R Foundation for Statistical Computing, R Development Core Team.
    • (2010) R: A language and environment for statistical computing
  • 105
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated Profile HMM Searches
    • 10.1371/journal.pcbi.1002195, 3197634, 22039361
    • Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol 2011, 7:e1002195. 10.1371/journal.pcbi.1002195, 3197634, 22039361.
    • (2011) PLoS Comput Biol , vol.7
    • Eddy, S.R.1
  • 106
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan-an integration platform for the signature-recognition methods in InterPro
    • 10.1093/bioinformatics/17.9.847, 11590104
    • Zdobnov EM, Apweiler R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848. 10.1093/bioinformatics/17.9.847, 11590104.
    • (2001) Bioinformatics , vol.17 , pp. 847-848
    • Zdobnov, E.M.1    Apweiler, R.2
  • 107
    • 36549003965 scopus 로고    scopus 로고
    • InterPro and InterProScan: tools for protein sequence classification and comparison
    • 10.1007/978-1-59745-515-2_5, 18025686
    • Mulder N, Apweiler R. InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol 2007, 396:59-70. 10.1007/978-1-59745-515-2_5, 18025686.
    • (2007) Methods Mol Biol , vol.396 , pp. 59-70
    • Mulder, N.1    Apweiler, R.2
  • 110
    • 1342288004 scopus 로고    scopus 로고
    • The jalview java alignment editor
    • 10.1093/bioinformatics/btg430, 14960472
    • Clamp M, Cuff J, Searle SM, Barton GJ. The jalview java alignment editor. Bioinformatics 2004, 20:426-427. 10.1093/bioinformatics/btg430, 14960472.
    • (2004) Bioinformatics , vol.20 , pp. 426-427
    • Clamp, M.1    Cuff, J.2    Searle, S.M.3    Barton, G.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.