-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
2
-
-
4644309196
-
The functions of animal microRNAs
-
Ambros V. 2004. The functions of animal microRNAs. Nature 431:350-355.
-
(2004)
Nature
, vol.431
, pp. 350-355
-
-
Ambros, V.1
-
3
-
-
43449118038
-
Evolution of plant microRNAs and their targets
-
Axtell MJ, Bowman JL. 2008. Evolution of plant microRNAs and their targets. Trends Plant Sci. 13:343-349.
-
(2008)
Trends Plant Sci.
, vol.13
, pp. 343-349
-
-
Axtell, M.J.1
Bowman, J.L.2
-
4
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297.
-
(2004)
Cell.
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
5
-
-
58249088751
-
MicroRNAs: Target recognition and regulatory functions
-
Bartel DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136:215-233.
-
(2009)
Cell.
, vol.136
, pp. 215-233
-
-
Bartel, D.P.1
-
6
-
-
33845452609
-
Insect microRNAs: Structure, function and evolution
-
Behura SK. 2007. Insect microRNAs: structure, function and evolution. Insect Biochem Mol Biol. 37:3-9.
-
(2007)
Insect Biochem. Mol. Biol.
, vol.37
, pp. 3-9
-
-
Behura, S.K.1
-
7
-
-
22844440427
-
Identification of hundreds of conserved and nonconserved human microRNAs
-
Bentwich I, et al. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet. 37:766-770.
-
(2005)
Nat. Genet.
, vol.37
, pp. 766-770
-
-
Bentwich, I.1
-
8
-
-
35348933779
-
Mammalian mirtron genes
-
Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC. 2007. Mammalian mirtron genes. Mol Cell. 28:328-336.
-
(2007)
Mol. Cell.
, vol.28
, pp. 328-336
-
-
Berezikov, E.1
Chung, W.J.2
Willis, J.3
Cuppen, E.4
Lai, E.C.5
-
9
-
-
73349122299
-
Evolutionary flux of canonical microRNAs and mirtrons in Drosophila
-
Berezikov E, et al. 2010. Evolutionary flux of canonical microRNAs and mirtrons in Drosophila. Nat Genet. 42:6-9.
-
(2010)
Nat. Genet.
, vol.42
, pp. 6-9
-
-
Berezikov, E.1
-
10
-
-
10244243802
-
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
-
Bonnet E, Wuyts J, Rouze P, Van de Peer Y. 2004. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20:2911-2917.
-
(2004)
Bioinformatics
, vol.20
, pp. 2911-2917
-
-
Bonnet, E.1
Wuyts, J.2
Rouze, P.3
Van De Peer, Y.4
-
11
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
Clark AG, et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218.
-
(2007)
Nature
, vol.450
, pp. 203-218
-
-
Clark, A.G.1
-
12
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
13
-
-
48249142558
-
Sequence variation of micro-RNAs and their binding sites in Arabidopsis
-
Ehrenreich IM, Purugganan MD. 2008. Sequence variation of micro-RNAs and their binding sites in Arabidopsis. Plant Physiol. 146:1974-1982.
-
(2008)
Plant Physiol.
, vol.146
, pp. 1974-1982
-
-
Ehrenreich, I.M.1
Purugganan, M.D.2
-
14
-
-
0036961560
-
Changing effective population size and the McDonald-Kreitman test
-
Eyre-Walker A. 2002. Changing effective population size and the McDonald-Kreitman test. Genetics 162:2017-2024.
-
(2002)
Genetics
, vol.162
, pp. 2017-2024
-
-
Eyre-Walker, A.1
-
15
-
-
57049169777
-
Evolution of Arabidopsis thaliana microRNAs from random sequences
-
Felippes FF, Schneeberger K, Dezulian T, Huson DH, Weigel D. 2008. Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA 14:2455-2459.
-
(2008)
RNA
, vol.14
, pp. 2455-2459
-
-
Felippes, F.F.1
Schneeberger, K.2
Dezulian, T.3
Huson, D.H.4
Weigel, D.5
-
16
-
-
54149095553
-
Biological principles of microRNA-mediated regulation: Shared themes amid diversity
-
Flynt AS, Lai EC. 2008. Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat Rev Genet. 9:831-842.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 831-842
-
-
Flynt, A.S.1
Lai, E.C.2
-
18
-
-
34548361941
-
Molecular evolution of Drosophila odorant receptor genes
-
Guo S, Kim J. 2007. Molecular evolution of Drosophila odorant receptor genes. Mol Biol Evol. 24:1198-1207.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1198-1207
-
-
Guo, S.1
Kim, J.2
-
19
-
-
33744520104
-
Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex
-
Han J, et al. 2006. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125:887-901.
-
(2006)
Cell.
, vol.125
, pp. 887-901
-
-
Han, J.1
-
20
-
-
45249106003
-
Near neutrality leading edge of the neutral theory of molecular evolution
-
Hughes AL. 2008. Near neutrality leading edge of the neutral theory of molecular evolution. Ann N Y Acad Sci. 1133:162-179.
-
(2008)
Ann. N. Y. Acad. Sci.
, vol.1133
, pp. 162-179
-
-
Hughes, A.L.1
-
21
-
-
0000732090
-
Evolution of protein molecules
-
Munro HM, editor, New York: Academic
-
Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In: Munro HM, editor. Mammalian protein metabolism. New York: Academic. p. 21-132
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
22
-
-
58649116227
-
The molecular machines that mediate microRNA maturation
-
Lau PW, MacRae IJ. 2009. The molecular machines that mediate microRNA maturation. J Cell Mol Med. 13:54-60.
-
(2009)
J. Cell. Mol. Med.
, vol.13
, pp. 54-60
-
-
Lau, P.W.1
MacRae, I.J.2
-
23
-
-
0027751663
-
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
-
Lee RC, Feinbaum RL, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843-854.
-
(1993)
Cell.
, vol.75
, pp. 843-854
-
-
Lee, R.C.1
Feinbaum, R.L.2
Ambros, V.3
-
24
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
Lewis BP, Burge CB, Bartel DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15-20.
-
(2005)
Cell.
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
25
-
-
33947309774
-
Evolution of plant microRNA gene families
-
Li A, Mao L. 2007. Evolution of plant microRNA gene families. Cell Res. 17:212-218.
-
(2007)
Cell. Res.
, vol.17
, pp. 212-218
-
-
Li, A.1
Mao, L.2
-
26
-
-
33751118533
-
MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila
-
Li Y, Wang F, Lee JA, Gao FB. 2006. MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila. Genes Dev. 20:2793-2805.
-
(2006)
Genes Dev.
, vol.20
, pp. 2793-2805
-
-
Li, Y.1
Wang, F.2
Lee, J.A.3
Gao, F.B.4
-
27
-
-
48249150513
-
Adaptive evolution of newly emerged micro-RNA genes in Drosophila
-
Lu J, et al. 2008a. Adaptive evolution of newly emerged micro-RNA genes in Drosophila. Mol Biol Evol. 25:929-938.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 929-938
-
-
Lu, J.1
-
28
-
-
39749083331
-
The birth and death of microRNA genes in Drosophila
-
Lu J, et al. 2008b. The birth and death of microRNA genes in Drosophila. Nat Genet. 40:351-355.
-
(2008)
Nat. Genet.
, vol.40
, pp. 351-355
-
-
Lu, J.1
-
29
-
-
33749153857
-
Biological function of unannotated transcription during the early development of Drosophila melanogaster
-
Manak JR, et al. 2006. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet. 38:1151-1158.
-
(2006)
Nat. Genet.
, vol.38
, pp. 1151-1158
-
-
Manak, J.R.1
-
30
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews DH, Sabina J, Zuker M, Turner DH. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol. 288:911-940.
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
31
-
-
0026428610
-
Adaptive protein evolution at the Adh locus in Drosophila
-
McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
-
(1991)
Nature
, vol.351
, pp. 652-654
-
-
McDonald, J.H.1
Kreitman, M.2
-
32
-
-
0024297806
-
Jockey, a mobile Drosophila element similar to mammalian LINEs, is transcribed from the internal promoter by RNA polymerase II
-
Mizrokhi LJ, Georgieva SG, Ilyin YV. 1988. jockey, a mobile Drosophila element similar to mammalian LINEs, is transcribed from the internal promoter by RNA polymerase II. Cell 54:685-691.
-
(1988)
Cell.
, vol.54
, pp. 685-691
-
-
Mizrokhi, L.J.1
Georgieva, S.G.2
Ilyin, Y.V.3
-
33
-
-
27944477670
-
Concerted and birth-and-death evolution of multigene families
-
Nei M, Rooney AP. 2005. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet. 39:121-152.
-
(2005)
Annu. Rev. Genet.
, vol.39
, pp. 121-152
-
-
Nei, M.1
Rooney, A.P.2
-
34
-
-
34249844953
-
Evolutionary dynamics of olfactory receptor genes in Drosophila species
-
Nozawa M, Nei M. 2007. Evolutionary dynamics of olfactory receptor genes in Drosophila species. Proc Natl Acad Sci USA. 104:7122-7127.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 7122-7127
-
-
Nozawa, M.1
Nei, M.2
-
35
-
-
34447107760
-
The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila
-
Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC. 2007. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130:89-100.
-
(2007)
Cell.
, vol.130
, pp. 89-100
-
-
Okamura, K.1
Hagen, J.W.2
Duan, H.3
Tyler, D.M.4
Lai, E.C.5
-
36
-
-
34250776711
-
A family of human microRNA genes from miniature inverted-repeat transposable elements
-
Piriyapongsa J, Jordan IK. 2007. A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS One. 2: e203.
-
(2007)
PLoS One
, vol.2
-
-
Piriyapongsa, J.1
Jordan, I.K.2
-
37
-
-
42449099982
-
Dual coding of siRNAs and miRNAs by plant transposable elements
-
Piriyapongsa J, Jordan IK. 2008. Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14:814-821.
-
(2008)
RNA
, vol.14
, pp. 814-821
-
-
Piriyapongsa, J.1
Jordan, I.K.2
-
38
-
-
0034708122
-
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
-
Reinhart BJ, et al. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901-906.
-
(2000)
Nature
, vol.403
, pp. 901-906
-
-
Reinhart, B.J.1
-
39
-
-
34447097693
-
Intronic microRNA precursors that bypass Drosha processing
-
Ruby JG, Jan CH, Bartel DP. 2007a. Intronic microRNA precursors that bypass Drosha processing. Nature 448:83-86.
-
(2007)
Nature
, vol.448
, pp. 83-86
-
-
Ruby, J.G.1
Jan, C.H.2
Bartel, D.P.3
-
40
-
-
38149071979
-
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila micro-RNAs
-
Ruby JG, et al. 2007b. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila micro-RNAs. Genome Res. 17:1850-1864.
-
(2007)
Genome Res.
, vol.17
, pp. 1850-1864
-
-
Ruby, J.G.1
-
41
-
-
52049125422
-
Polytene chromosomal maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps
-
Schaeffer SW, et al. 2008. Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps. Genetics 179:1601-1655.
-
(2008)
Genetics
, vol.179
, pp. 1601-1655
-
-
Schaeffer, S.W.1
-
42
-
-
51449085579
-
Origins and evolution of eukaryotic RNA interference
-
Shabalina SA, Koonin EV. 2008. Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol. 23:578-587.
-
(2008)
Trends Ecol. Evol.
, vol.23
, pp. 578-587
-
-
Shabalina, S.A.1
Koonin, E.V.2
-
43
-
-
37249025294
-
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
-
DOI 10.1101/gr.6593807
-
Stark A, et al. 2007. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res. 17:1865-1879. (Pubitemid 351360009)
-
(2007)
Genome Research
, vol.17
, Issue.12
, pp. 1865-1879
-
-
Stark, A.1
Kheradpour, P.2
Parts, L.3
Brennecke, J.4
Hodges, E.5
Hannon, G.J.6
Kellis, M.7
-
44
-
-
1242352089
-
Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks
-
Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol. 21:36-44.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 36-44
-
-
Tamura, K.1
Subramanian, S.2
Kumar, S.3
-
45
-
-
2342450524
-
Molecular evolution of a microRNA cluster
-
Tanzer A, Stadler PF. 2004. Molecular evolution of a microRNA cluster. J Mol Biol. 339:327-335.
-
(2004)
J. Mol. Biol.
, vol.339
, pp. 327-335
-
-
Tanzer, A.1
Stadler, P.F.2
-
46
-
-
36048973464
-
Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: Purifying selection and birth-and-death evolution
-
Vieira FG, Sanchez-Gracia A, Rozas J. 2007. Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution. Genome Biol. 8: R235.
-
(2007)
Genome Biol.
, vol.8
-
-
Vieira, F.G.1
Sanchez-Gracia, A.2
Rozas, J.3
-
47
-
-
60149086351
-
Origin, biogenesis, and activity of plant microRNAs
-
Voinnet O. 2009. Origin, biogenesis, and activity of plant microRNAs. Cell 136:669-687.
-
(2009)
Cell.
, vol.136
, pp. 669-687
-
-
Voinnet, O.1
-
48
-
-
0028820333
-
A new method of inference of ancestral nucleotide and amino acid sequences
-
Yang Z, Kumar S, Nei M. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.
-
(1995)
Genetics
, vol.141
, pp. 1641-1650
-
-
Yang, Z.1
Kumar, S.2
Nei, M.3
-
49
-
-
52149090746
-
MicroRNAs in the Hox network: An apparent link to posterior prevalence
-
Yekta S, Tabin CJ, Bartel DP. 2008. MicroRNAs in the Hox network: an apparent link to posterior prevalence. Nat Rev Genet. 9:789-796.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 789-796
-
-
Yekta, S.1
Tabin, C.J.2
Bartel, D.P.3
-
50
-
-
0032584099
-
Positive Darwinian selection after gene duplication in primate ribonuclease genes
-
Zhang J, Rosenberg HF, Nei M. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci USA. 95:3708-3713.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 3708-3713
-
-
Zhang, J.1
Rosenberg, H.F.2
Nei, M.3
-
51
-
-
50649110065
-
A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
-
Zhu QH, et al. 2008. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res. 18:1456-1465.
-
(2008)
Genome Res.
, vol.18
, pp. 1456-1465
-
-
Zhu, Q.H.1
|