-
1
-
-
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
-
2
-
-
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
-
3
-
-
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
-
4
-
-
22844440427
-
Identification of hundreds of conserved and nonconserved human microRNAs
-
(13 co-authors)
-
Bentwich I, Avniel A, Karov Y, et al. (13 co-authors). 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
Avniel, A.2
Karov, Y.3
-
5
-
-
33751548288
-
Diversity of microRNAs in human and chimpanzee brain
-
Berezikov E, Thuemmler F, van Laake LW, Kondova I, Bontrop R, Cuppen E, Plasterk RH. 2006. Diversity of microRNAs in human and chimpanzee brain. Nat Genet. 38:1375-1377.
-
(2006)
Nat Genet
, vol.38
, pp. 1375-1377
-
-
Berezikov, E.1
Thuemmler, F.2
Van Laake, L.W.3
Kondova, I.4
Bontrop, R.5
Cuppen, E.6
Plasterk, R.H.7
-
6
-
-
67249136441
-
C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts
-
Bortolin-Cavaille ML, Dance M, Weber M, Cavaille J. 2009. C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts. Nucleic Acids Res. 37:3464-3473.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 3464-3473
-
-
Bortolin-Cavaille, M.L.1
Dance, M.2
Weber, M.3
Cavaille, J.4
-
7
-
-
0037096916
-
Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region
-
Cavaille J, Seitz H, Paulsen M, Ferguson-Smith AC, Bachellerie JP. 2002. Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region. Hum Mol Genet. 11:1527-1538.
-
(2002)
Hum Mol Genet
, vol.11
, pp. 1527-1538
-
-
Cavaille, J.1
Seitz, H.2
Paulsen, M.3
Ferguson-Smith, A.C.4
Bachellerie, J.P.5
-
8
-
-
36549051577
-
Aligning multiple whole genomes with mercator and mavid
-
Dewey CN. 2007. Aligning multiple whole genomes with mercator and mavid. Methods Mol Biol. 395:221-236.
-
(2007)
Methods Mol Biol
, vol.395
, pp. 221-236
-
-
Dewey, C.N.1
-
10
-
-
84862025220
-
The dark side of a success story: MicroRNAs of the C19MC cluster in human tumours
-
Flor I, Bullerdiek J. 2012. The dark side of a success story: microRNAs of the C19MC cluster in human tumours. J Pathol. 227:270-274.
-
(2012)
J Pathol
, vol.227
, pp. 270-274
-
-
Flor, I.1
Bullerdiek, J.2
-
11
-
-
84862009479
-
In hepatocellular carcinoma miR-519d is upregulated by p53 and DNA hypomethylation and targets CDKN1A/p21, PTEN, AKT3 and TIMP2
-
(15 co-authors)
-
Fornari F, Milazzo M, Chieco P, et al. (15 co-authors). 2012. In hepatocellular carcinoma miR-519d is upregulated by p53 and DNA hypomethylation and targets CDKN1A/p21, PTEN, AKT3 and TIMP2. J Pathol. 227:275-285.
-
(2012)
J Pathol
, vol.227
, pp. 275-285
-
-
Fornari, F.1
Milazzo, M.2
Chieco, P.3
-
12
-
-
45849111603
-
Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals
-
Glazov EA, McWilliam S, Barris WC, Dalrymple BP. 2008. Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Mol Biol Evol. 25:939-948.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 939-948
-
-
Glazov, E.A.1
McWilliam, S.2
Barris, W.C.3
Dalrymple, B.P.4
-
14
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P. 1994. Fast folding and comparison of RNA secondary structures. Monatsh Chem. 125:167-188.
-
(1994)
Monatsh Chem
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, S.4
Tacker, M.5
Schuster, P.6
-
15
-
-
79551634894
-
PHAST and RPHAST: Phylogenetic analysis with space/time models
-
Hubisz MJ, Pollard KS, Siepel A. 2011. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 12:41-51.
-
(2011)
Brief Bioinform
, vol.12
, pp. 41-51
-
-
Hubisz, M.J.1
Pollard, K.S.2
Siepel, A.3
-
16
-
-
78650501446
-
MicroRNA networks alter to conform to transcription factor networks adding redundancy and reducing the repertoire of target genes for coordinated regulation
-
Iwama H, Murao K, Imachi H, Ishida T. 2011. MicroRNA networks alter to conform to transcription factor networks adding redundancy and reducing the repertoire of target genes for coordinated regulation. Mol Biol Evol. 28:639-646.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 639-646
-
-
Iwama, H.1
Murao, K.2
Imachi, H.3
Ishida, T.4
-
17
-
-
78651293534
-
MiRBase: Integrating microRNA annotation and deep-sequencing data
-
Kozomara A, Griffiths-Jones S. 2011. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39: D152-D157.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
18
-
-
79960130696
-
TimeTree2: Species divergence times on the iPhone
-
Kumar S, Hedges SB. 2011. TimeTree2: species divergence times on the iPhone. Bioinformatics 27:2023-2024.
-
(2011)
Bioinformatics
, vol.27
, pp. 2023-2024
-
-
Kumar, S.1
Hedges, S.B.2
-
19
-
-
34250877841
-
A mammalian microRNA expression atlas based on small RNA library sequencing
-
(51 co-authors)
-
Landgraf P, Rusu M, Sheridan R, et al. (51 co-authors). 2007. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129:1401-1414.
-
(2007)
Cell
, vol.129
, pp. 1401-1414
-
-
Landgraf, P.1
Rusu, M.2
Sheridan, R.3
-
20
-
-
79956222869
-
Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene
-
Lehnert S, Kapitonov V, Thilakarathne PJ, Schuit FC. 2011. Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene. BMC Genomics 12:257.
-
(2011)
BMC Genomics
, vol.12
, pp. 257
-
-
Lehnert, S.1
Kapitonov, V.2
Thilakarathne, P.J.3
Schuit, F.C.4
-
21
-
-
77249128400
-
Evolution of an X-linked primate-specific micro RNA cluster
-
Li J, Liu Y, Dong D, Zhang Z. 2010. Evolution of an X-linked primate-specific micro RNA cluster. Mol Biol Evol. 27:671-683.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 671-683
-
-
Li, J.1
Liu, Y.2
Dong, D.3
Zhang, Z.4
-
22
-
-
66249117657
-
Lowly expressed human microRNA genes evolve rapidly
-
Liang H, Li WH. 2009. Lowly expressed human microRNA genes evolve rapidly. Mol Biol Evol. 26:1195-1198.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1195-1198
-
-
Liang, H.1
Li, W.H.2
-
23
-
-
39749083331
-
The birth and death of microRNA genes in Drosophila
-
Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM,Wu CI. 2008. 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
Shen, Y.2
Wu, Q.3
Kumar, S.4
He, B.5
Shi, S.6
Carthew, R.W.7
Wang, S.M.8
Wu, C.I.9
-
24
-
-
70349697160
-
Placental mammals (Eutheria)
-
Hedges SB, Kumar S, editors New York: Oxford University Press
-
Marphy WJ, Eizirk E. 2009. Placental mammals (Eutheria). In: Hedges SB, Kumar S, editors. The timetree of life. New York: Oxford University Press. p. 471-474.
-
(2009)
The Timetree of Life
, pp. 471-474
-
-
Marphy, W.J.1
Eizirk, E.2
-
25
-
-
77958462907
-
Origins and evolution of microRNA genes in Drosophila species
-
Nozawa M, Miura S, Nei M. 2010. Origins and evolution of microRNA genes in Drosophila species. Genome Biol Evol. 2:180-189.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 180-189
-
-
Nozawa, M.1
Miura, S.2
Nei, M.3
-
26
-
-
54949108148
-
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
-
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. 2008. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res. 18:1814-1828.
-
(2008)
Genome Res
, vol.18
, pp. 1814-1828
-
-
Paten, B.1
Herrero, J.2
Beal, K.3
Fitzgerald, S.4
Birney, E.5
-
27
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
(16 co-authors)
-
Siepel A, Bejerano G, Pedersen JS, et al. (16 co-authors). 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15:1034-1050.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
-
28
-
-
1542510106
-
Phylogenetic estimation of contextdependent substitution rates by maximum likelihood
-
Siepel A, Haussler D. 2004. Phylogenetic estimation of contextdependent substitution rates by maximum likelihood. Mol Biol Evol. 21:468-488.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 468-488
-
-
Siepel, A.1
Haussler, D.2
-
29
-
-
2442666425
-
The Ensembl core software libraries
-
Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E. 2004. The Ensembl core software libraries. Genome Res. 14:929-933.
-
(2004)
Genome Res
, vol.14
, pp. 929-933
-
-
Stabenau, A.1
McVicker, G.2
Melsopp, C.3
Proctor, G.4
Clamp, M.5
Birney, E.6
-
30
-
-
79951675256
-
Primates (Primates)
-
Hedges SB, Kumar S, editors New York: Oxford University Press
-
SteiperME, Young NM. 2009. Primates (Primates). In: Hedges SB, Kumar S, editors. The timetree of life. New York: Oxford University Press. p. 482-486.
-
(2009)
The Timetree of Life
, pp. 482-486
-
-
Steiper, M.E.1
Young, N.M.2
-
32
-
-
62549128139
-
A census of human transcription factors: Function, expression and evolution
-
Vaquerizas JM. 2009. A census of human transcription factors: function, expression and evolution. Nat Rev Genet. 10: 252-263.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 252-263
-
-
Vaquerizas, J.M.1
-
33
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
34
-
-
34248196026
-
Rapid evolution of an X-linked microRNA cluster in primates
-
Zhang R, Peng Y, Wang W, Su B. 2007. Rapid evolution of an X-linked microRNA cluster in primates. Genome Res. 17:612-617.
-
(2007)
Genome Res
, vol.17
, pp. 612-617
-
-
Zhang, R.1
Peng, Y.2
Wang, W.3
Su, B.4
-
35
-
-
45849126048
-
Molecular evolution of a primatespecific microRNA family
-
Zhang R, Wang YQ, Su B. 2008. Molecular evolution of a primatespecific microRNA family. Mol Biol Evol. 25:1493-1502.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1493-1502
-
-
Zhang, R.1
Wang, Y.Q.2
Su, B.3
-
36
-
-
80053148609
-
Genome-wide impact of a recently expanded microRNA cluster in mouse
-
Zheng GX, Ravi A, Gould GM, Burge CB, Sharp PA. 2011. Genome-wide impact of a recently expanded microRNA cluster in mouse. Proc Natl Acad Sci USA. 108:15804-15809.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 15804-15809
-
-
Zheng, G.X.1
Ravi, A.2
Gould, G.M.3
Burge, C.B.4
Sharp, P.A.5
|