-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
77953801618
-
Target RNA-directed trimming and tailing of small silencing RNAs
-
S.L. Ameres, M.D. Horwich, J.H. Hung, J. Xu, M. Ghildiyal, Z. Weng, and P.D. Zamore Target RNA-directed trimming and tailing of small silencing RNAs Science 328 2010 1534 1539
-
(2010)
Science
, vol.328
, pp. 1534-1539
-
-
Ameres, S.L.1
Horwich, M.D.2
Hung, J.H.3
Xu, J.4
Ghildiyal, M.5
Weng, Z.6
Zamore, P.D.7
-
3
-
-
33745402414
-
A novel class of small RNAs bind to MILI protein in mouse testes
-
A. Aravin, D. Gaidatzis, S. Pfeffer, M. Lagos-Quintana, P. Landgraf, N. Iovino, P. Morris, M.J. Brownstein, S. Kuramochi-Miyagawa, and T. Nakano A novel class of small RNAs bind to MILI protein in mouse testes Nature 442 2006 203 207
-
(2006)
Nature
, vol.442
, pp. 203-207
-
-
Aravin, A.1
Gaidatzis, D.2
Pfeffer, S.3
Lagos-Quintana, M.4
Landgraf, P.5
Iovino, N.6
Morris, P.7
Brownstein, M.J.8
Kuramochi-Miyagawa, S.9
Nakano, T.10
-
4
-
-
84868089881
-
The Paramecium germline genome provides a niche for intragenic parasitic DNA: Evolutionary dynamics of internal eliminated sequences
-
O. Arnaiz, N. Mathy, C. Baudry, S. Malinsky, J.M. Aury, C. Denby Wilkes, O. Garnier, K. Labadie, B.E. Lauderdale, and A. Le Mouel The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences PLoS Genet. 8 2012 e1002984
-
(2012)
PLoS Genet.
, vol.8
, pp. 1002984
-
-
Arnaiz, O.1
Mathy, N.2
Baudry, C.3
Malinsky, S.4
Aury, J.M.5
Denby Wilkes, C.6
Garnier, O.7
Labadie, K.8
Lauderdale, B.E.9
Le Mouel, A.10
-
5
-
-
84863611417
-
PiRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans
-
A. Ashe, A. Sapetschnig, E.M. Weick, J. Mitchell, M.P. Bagijn, A.C. Cording, A.L. Doebley, L.D. Goldstein, N.J. Lehrbach, and J. Le Pen piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans Cell 150 2012 88 99
-
(2012)
Cell
, vol.150
, pp. 88-99
-
-
Ashe, A.1
Sapetschnig, A.2
Weick, E.M.3
Mitchell, J.4
Bagijn, M.P.5
Cording, A.C.6
Doebley, A.L.7
Goldstein, L.D.8
Lehrbach, N.J.9
Le Pen, J.10
-
6
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
7
-
-
79960056273
-
Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling
-
K. Bouhouche, J.F. Gout, A. Kapusta, M. Bétermier, and E. Meyer Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling Nucleic Acids Res. 39 2011 4249 4264
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 4249-4264
-
-
Bouhouche, K.1
Gout, J.F.2
Kapusta, A.3
Bétermier, M.4
Meyer, E.5
-
8
-
-
33947273235
-
Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila
-
J. Brennecke, A.A. Aravin, A. Stark, M. Dus, M. Kellis, R. Sachidanandam, and G.J. Hannon Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila Cell 128 2007 1089 1103
-
(2007)
Cell
, vol.128
, pp. 1089-1103
-
-
Brennecke, J.1
Aravin, A.A.2
Stark, A.3
Dus, M.4
Kellis, M.5
Sachidanandam, R.6
Hannon, G.J.7
-
9
-
-
57149104113
-
An epigenetic role for maternally inherited piRNAs in transposon silencing
-
J. Brennecke, C.D. Malone, A.A. Aravin, R. Sachidanandam, A. Stark, and G.J. Hannon An epigenetic role for maternally inherited piRNAs in transposon silencing Science 322 2008 1387 1392
-
(2008)
Science
, vol.322
, pp. 1387-1392
-
-
Brennecke, J.1
Malone, C.D.2
Aravin, A.A.3
Sachidanandam, R.4
Stark, A.5
Hannon, G.J.6
-
10
-
-
33947720638
-
MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline
-
M.A. Carmell, A. Girard, H.J. van de Kant, D. Bourc'his, T.H. Bestor, D.G. de Rooij, and G.J. Hannon MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline Dev. Cell 12 2007 503 514
-
(2007)
Dev. Cell
, vol.12
, pp. 503-514
-
-
Carmell, M.A.1
Girard, A.2
Van De Kant, H.J.3
Bourc'His, D.4
Bestor, T.H.5
De Rooij, D.G.6
Hannon, G.J.7
-
11
-
-
0029953126
-
Non-Mendelian, heritable blocks to DNA rearrangement are induced by loading the somatic nucleus of Tetrahymena thermophila with germ line-limited DNA
-
D.L. Chalker, and M.C. Yao Non-Mendelian, heritable blocks to DNA rearrangement are induced by loading the somatic nucleus of Tetrahymena thermophila with germ line-limited DNA Mol. Cell. Biol. 16 1996 3658 3667
-
(1996)
Mol. Cell. Biol.
, vol.16
, pp. 3658-3667
-
-
Chalker, D.L.1
Yao, M.C.2
-
12
-
-
69749100606
-
Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila
-
M.T. Couvillion, S.R. Lee, B. Hogstad, C.D. Malone, L.A. Tonkin, R. Sachidanandam, G.J. Hannon, and K. Collins Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila Genes Dev. 23 2009 2016 2032
-
(2009)
Genes Dev.
, vol.23
, pp. 2016-2032
-
-
Couvillion, M.T.1
Lee, S.R.2
Hogstad, B.3
Malone, C.D.4
Tonkin, L.A.5
Sachidanandam, R.6
Hannon, G.J.7
Collins, K.8
-
13
-
-
84858714140
-
Whole genome studies of Tetrahymena
-
K. Collins, Academic Press New York
-
R.S. Coyne, N.A. Stover, and W. Miao Whole genome studies of Tetrahymena K. Collins, Methods in Cell Biology 2012 Academic Press New York 53 81
-
(2012)
Methods in Cell Biology
, pp. 53-81
-
-
Coyne, R.S.1
Stover, N.A.2
Miao, W.3
-
14
-
-
79953310937
-
SHRiMP2: Sensitive yet practical SHort Read Mapping
-
M. David, M. Dzamba, D. Lister, L. Ilie, and M. Brudno SHRiMP2: sensitive yet practical SHort Read Mapping Bioinformatics 27 2011 1011 1012
-
(2011)
Bioinformatics
, vol.27
, pp. 1011-1012
-
-
David, M.1
Dzamba, M.2
Lister, D.3
Ilie, L.4
Brudno, M.5
-
15
-
-
0029103019
-
Epigenetic self-regulation of developmental excision of an internal eliminated sequence on Paramecium tetraurelia
-
S. Duharcourt, A. Butler, and E. Meyer Epigenetic self-regulation of developmental excision of an internal eliminated sequence on Paramecium tetraurelia Genes Dev. 9 1995 2065 2077
-
(1995)
Genes Dev.
, vol.9
, pp. 2065-2077
-
-
Duharcourt, S.1
Butler, A.2
Meyer, E.3
-
16
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
R. Edgar, M. Domrachev, and A.E. Lash Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res. 30 2002 207 210
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
-
17
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
R.C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
18
-
-
79959298599
-
PiRNA profiling during specific stages of mouse spermatogenesis
-
H. Gan, X. Lin, Z. Zhang, W. Zhang, S. Liao, L. Wang, and C. Han piRNA profiling during specific stages of mouse spermatogenesis RNA 17 2011 1191 1203
-
(2011)
RNA
, vol.17
, pp. 1191-1203
-
-
Gan, H.1
Lin, X.2
Zhang, Z.3
Zhang, W.4
Liao, S.5
Wang, L.6
Han, C.7
-
19
-
-
33745336617
-
A germline-specific class of small RNAs binds mammalian Piwi proteins
-
A. Girard, R. Sachidanandam, G.J. Hannon, and M.A. Carmell A germline-specific class of small RNAs binds mammalian Piwi proteins Nature 442 2006 199 202
-
(2006)
Nature
, vol.442
, pp. 199-202
-
-
Girard, A.1
Sachidanandam, R.2
Hannon, G.J.3
Carmell, M.A.4
-
20
-
-
55249115975
-
Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals
-
A. Grimson, M. Srivastava, B. Fahey, B.J. Woodcroft, H.R. Chiang, N. King, B.M. Degnan, D.S. Rokhsar, and D.P. Bartel Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals Nature 455 2008 1193 1197
-
(2008)
Nature
, vol.455
, pp. 1193-1197
-
-
Grimson, A.1
Srivastava, M.2
Fahey, B.3
Woodcroft, B.J.4
Chiang, H.R.5
King, N.6
Degnan, B.M.7
Rokhsar, D.S.8
Bartel, D.P.9
-
21
-
-
33745621037
-
A novel class of small RNAs in mouse spermatogenic cells
-
S.T. Grivna, E. Beyret, Z. Wang, and H. Lin A novel class of small RNAs in mouse spermatogenic cells Genes Dev. 20 2006 1709 1714
-
(2006)
Genes Dev.
, vol.20
, pp. 1709-1714
-
-
Grivna, S.T.1
Beyret, E.2
Wang, Z.3
Lin, H.4
-
22
-
-
84856239588
-
Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint
-
S.G. Gu, J. Pak, S. Guang, J.M. Maniar, S. Kennedy, and A. Fire Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint Nat. Genet. 44 2012 157 164
-
(2012)
Nat. Genet.
, vol.44
, pp. 157-164
-
-
Gu, S.G.1
Pak, J.2
Guang, S.3
Maniar, J.M.4
Kennedy, S.5
Fire, A.6
-
23
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
S. Guindon, J.F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, and O. Gascuel New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 Syst. Biol. 59 2010 307 321
-
(2010)
Syst. Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
24
-
-
34047154356
-
A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish
-
S. Houwing, L.M. Kamminga, E. Berezikov, D. Cronembold, A. Girard, H. van den Elst, D.V. Filippov, H. Blaser, E. Raz, and C.B. Moens A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish Cell 129 2007 69 82
-
(2007)
Cell
, vol.129
, pp. 69-82
-
-
Houwing, S.1
Kamminga, L.M.2
Berezikov, E.3
Cronembold, D.4
Girard, A.5
Van Den Elst, H.6
Filippov, D.V.7
Blaser, H.8
Raz, E.9
Moens, C.B.10
-
25
-
-
34247259831
-
Mouse Piwi-interacting RNAs are 2′-O-methylated at their 3′ termini
-
Y. Kirino, and Z. Mourelatos Mouse Piwi-interacting RNAs are 2′-O-methylated at their 3′ termini Nat. Struct. Mol. Biol. 14 2007 347 348
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 347-348
-
-
Kirino, Y.1
Mourelatos, Z.2
-
26
-
-
62549159996
-
2′-O-methylation stabilizes Piwi-associated small RNAs and ensures DNA elimination in Tetrahymena
-
H.M. Kurth, and K. Mochizuki 2′-O-methylation stabilizes Piwi-associated small RNAs and ensures DNA elimination in Tetrahymena RNA 15 2009 675 685
-
(2009)
RNA
, vol.15
, pp. 675-685
-
-
Kurth, H.M.1
Mochizuki, K.2
-
27
-
-
33746527679
-
Characterization of the piRNA complex from rat testes
-
N.C. Lau, A.G. Seto, J. Kim, S. Kuramochi-Miyagawa, T. Nakano, D.P. Bartel, and R.E. Kingston Characterization of the piRNA complex from rat testes Science 313 2006 363 367
-
(2006)
Science
, vol.313
, pp. 363-367
-
-
Lau, N.C.1
Seto, A.G.2
Kim, J.3
Kuramochi-Miyagawa, S.4
Nakano, T.5
Bartel, D.P.6
Kingston, R.E.7
-
28
-
-
84863624978
-
C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts
-
H.C. Lee, W. Gu, M. Shirayama, E. Youngman, D. Conte Jr.; and C.C. Mello C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts Cell 150 2012 78 87
-
(2012)
Cell
, vol.150
, pp. 78-87
-
-
Lee, H.C.1
Gu, W.2
Shirayama, M.3
Youngman, E.4
Conte, Jr.D.5
Mello, C.C.6
-
29
-
-
29944442623
-
Two classes of endogenous small RNAs in Tetrahymena thermophila
-
S.R. Lee, and K. Collins Two classes of endogenous small RNAs in Tetrahymena thermophila Genes Dev. 20 2006 28 33
-
(2006)
Genes Dev.
, vol.20
, pp. 28-33
-
-
Lee, S.R.1
Collins, K.2
-
30
-
-
44849120634
-
Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia
-
G. Lepère, M. Bétermier, E. Meyer, and S. Duharcourt Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia Genes Dev. 22 2008 1501 1512
-
(2008)
Genes Dev.
, vol.22
, pp. 1501-1512
-
-
Lepère, G.1
Bétermier, M.2
Meyer, E.3
Duharcourt, S.4
-
31
-
-
63349109487
-
Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia
-
G. Lepère, M. Nowacki, V. Serrano, J.F. Gout, G. Guglielmi, S. Duharcourt, and E. Meyer Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia Nucleic Acids Res. 37 2009 903 915
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 903-915
-
-
Lepère, G.1
Nowacki, M.2
Serrano, V.3
Gout, J.F.4
Guglielmi, G.5
Duharcourt, S.6
Meyer, E.7
-
32
-
-
23944493378
-
Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis
-
J. Li, Z. Yang, B. Yu, J. Liu, and X. Chen Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis Curr. Biol. 15 2005 1501 1507
-
(2005)
Curr. Biol.
, vol.15
, pp. 1501-1507
-
-
Li, J.1
Yang, Z.2
Yu, B.3
Liu, J.4
Chen, X.5
-
33
-
-
1242319537
-
Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena
-
Y. Liu, K. Mochizuki, and M.A. Gorovsky Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena Proc. Natl. Acad. Sci. USA 101 2004 1679 1684
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 1679-1684
-
-
Liu, Y.1
Mochizuki, K.2
Gorovsky, M.A.3
-
34
-
-
34250735582
-
RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena
-
Y. Liu, S.D. Taverna, T.L. Muratore, J. Shabanowitz, D.F. Hunt, and C.D. Allis RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena Genes Dev. 21 2007 1530 1545
-
(2007)
Genes Dev.
, vol.21
, pp. 1530-1545
-
-
Liu, Y.1
Taverna, S.D.2
Muratore, T.L.3
Shabanowitz, J.4
Hunt, D.F.5
Allis, C.D.6
-
35
-
-
60149098474
-
Small RNAs as guardians of the genome
-
C.D. Malone, and G.J. Hannon Small RNAs as guardians of the genome Cell 136 2009 656 668
-
(2009)
Cell
, vol.136
, pp. 656-668
-
-
Malone, C.D.1
Hannon, G.J.2
-
36
-
-
65249148019
-
RNA-mediated chromatin-based silencing in plants
-
M. Matzke, T. Kanno, L. Daxinger, B. Huettel, and A.J. Matzke RNA-mediated chromatin-based silencing in plants Curr. Opin. Cell Biol. 21 2009 367 376
-
(2009)
Curr. Opin. Cell Biol.
, vol.21
, pp. 367-376
-
-
Matzke, M.1
Kanno, T.2
Daxinger, L.3
Huettel, B.4
Matzke, A.J.5
-
37
-
-
4444383501
-
Conjugation-specific small RNAs in Tetrahymena have predicted properties of scan (scn) RNAs involved in genome rearrangement
-
K. Mochizuki, and M.A. Gorovsky Conjugation-specific small RNAs in Tetrahymena have predicted properties of scan (scn) RNAs involved in genome rearrangement Genes Dev. 18 2004 2068 2073
-
(2004)
Genes Dev.
, vol.18
, pp. 2068-2073
-
-
Mochizuki, K.1
Gorovsky, M.A.2
-
38
-
-
0037145031
-
Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in Tetrahymena
-
K. Mochizuki, N.A. Fine, T. Fujisawa, and M.A. Gorovsky Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in Tetrahymena Cell 110 2002 689 699
-
(2002)
Cell
, vol.110
, pp. 689-699
-
-
Mochizuki, K.1
Fine, N.A.2
Fujisawa, T.3
Gorovsky, M.A.4
-
39
-
-
48449094455
-
The pathway to detangle a scrambled gene
-
M. Möllenbeck, Y. Zhou, A.R. Cavalcanti, F. Jönsson, B.P. Higgins, W.J. Chang, S. Juranek, T.G. Doak, G. Rozenberg, H.J. Lipps, and L.F. Landweber The pathway to detangle a scrambled gene PLoS ONE 3 2008 e2330
-
(2008)
PLoS ONE
, vol.3
, pp. 2330
-
-
Möllenbeck, M.1
Zhou, Y.2
Cavalcanti, A.R.3
Jönsson, F.4
Higgins, B.P.5
Chang, W.J.6
Juranek, S.7
Doak, T.G.8
Rozenberg, G.9
Lipps, H.J.10
Landweber, L.F.11
-
40
-
-
38049186458
-
RNA-mediated epigenetic programming of a genome-rearrangement pathway
-
M. Nowacki, V. Vijayan, Y. Zhou, K. Schotanus, T.G. Doak, and L.F. Landweber RNA-mediated epigenetic programming of a genome-rearrangement pathway Nature 451 2008 153 158
-
(2008)
Nature
, vol.451
, pp. 153-158
-
-
Nowacki, M.1
Vijayan, V.2
Zhou, Y.3
Schotanus, K.4
Doak, T.G.5
Landweber, L.F.6
-
41
-
-
66149132301
-
A functional role for transposases in a large eukaryotic genome
-
M. Nowacki, B.P. Higgins, G.M. Maquilan, E.C. Swart, T.G. Doak, and L.F. Landweber A functional role for transposases in a large eukaryotic genome Science 324 2009 935 938
-
(2009)
Science
, vol.324
, pp. 935-938
-
-
Nowacki, M.1
Higgins, B.P.2
Maquilan, G.M.3
Swart, E.C.4
Doak, T.G.5
Landweber, L.F.6
-
42
-
-
34247199896
-
The 3′ termini of mouse Piwi-interacting RNAs are 2′-O-methylated
-
T. Ohara, Y. Sakaguchi, T. Suzuki, H. Ueda, K. Miyauchi, and T. Suzuki The 3′ termini of mouse Piwi-interacting RNAs are 2′-O-methylated Nat. Struct. Mol. Biol. 14 2007 349 350
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 349-350
-
-
Ohara, T.1
Sakaguchi, Y.2
Suzuki, T.3
Ueda, H.4
Miyauchi, K.5
Suzuki, T.6
-
43
-
-
33846527241
-
Distinct populations of primary and secondary effectors during RNAi in C. elegans
-
J. Pak, and A. Fire Distinct populations of primary and secondary effectors during RNAi in C. elegans Science 315 2007 241 244
-
(2007)
Science
, vol.315
, pp. 241-244
-
-
Pak, J.1
Fire, A.2
-
44
-
-
80052019696
-
Estimating the timing of early eukaryotic diversification with multigene molecular clocks
-
L.W. Parfrey, D.J. Lahr, A.H. Knoll, and L.A. Katz Estimating the timing of early eukaryotic diversification with multigene molecular clocks Proc. Natl. Acad. Sci. USA 108 2011 13624 13629
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 13624-13629
-
-
Parfrey, L.W.1
Lahr, D.J.2
Knoll, A.H.3
Katz, L.A.4
-
45
-
-
0033570886
-
A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability
-
V. Patzel, U. Steidl, R. Kronenwett, R. Haas, and G. Sczakiel A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability Nucleic Acids Res. 27 1999 4328 4334
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4328-4334
-
-
Patzel, V.1
Steidl, U.2
Kronenwett, R.3
Haas, R.4
Sczakiel, G.5
-
46
-
-
0034574433
-
Genome gymnastics: Unique modes of DNA evolution and processing in ciliates
-
D.M. Prescott Genome gymnastics: unique modes of DNA evolution and processing in ciliates Nat. Rev. Genet. 1 2000 191 198
-
(2000)
Nat. Rev. Genet.
, vol.1
, pp. 191-198
-
-
Prescott, D.M.1
-
47
-
-
84860320656
-
A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity
-
P. Rajasethupathy, I. Antonov, R. Sheridan, S. Frey, C. Sander, T. Tuschl, and E.R. Kandel A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity Cell 149 2012 693 707
-
(2012)
Cell
, vol.149
, pp. 693-707
-
-
Rajasethupathy, P.1
Antonov, I.2
Sheridan, R.3
Frey, S.4
Sander, C.5
Tuschl, T.6
Kandel, E.R.7
-
48
-
-
72649094955
-
A broadly conserved pathway generates 3'UTR-directed primary piRNAs
-
N. Robine, N.C. Lau, S. Balla, Z. Jin, K. Okamura, S. Kuramochi-Miyagawa, M.D. Blower, and E.C. Lai A broadly conserved pathway generates 3'UTR-directed primary piRNAs Curr. Biol. 19 2009 2066 2076
-
(2009)
Curr. Biol.
, vol.19
, pp. 2066-2076
-
-
Robine, N.1
Lau, N.C.2
Balla, S.3
Jin, Z.4
Okamura, K.5
Kuramochi-Miyagawa, S.6
Blower, M.D.7
Lai, E.C.8
-
49
-
-
78049387387
-
Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo
-
C. Rouget, C. Papin, A. Boureux, A.C. Meunier, B. Franco, N. Robine, E.C. Lai, A. Pelisson, and M. Simonelig Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo Nature 467 2010 1128 1132
-
(2010)
Nature
, vol.467
, pp. 1128-1132
-
-
Rouget, C.1
Papin, C.2
Boureux, A.3
Meunier, A.C.4
Franco, B.5
Robine, N.6
Lai, E.C.7
Pelisson, A.8
Simonelig, M.9
-
50
-
-
33747369856
-
Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome
-
K. Saito, K.M. Nishida, T. Mori, Y. Kawamura, K. Miyoshi, T. Nagami, H. Siomi, and M.C. Siomi Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome Genes Dev. 20 2006 2214 2222
-
(2006)
Genes Dev.
, vol.20
, pp. 2214-2222
-
-
Saito, K.1
Nishida, K.M.2
Mori, T.3
Kawamura, Y.4
Miyoshi, K.5
Nagami, T.6
Siomi, H.7
Siomi, M.C.8
-
51
-
-
34347378274
-
Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi- interacting RNAs at their 3′ ends
-
K. Saito, Y. Sakaguchi, T. Suzuki, T. Suzuki, H. Siomi, and M.C. Siomi Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi- interacting RNAs at their 3′ ends Genes Dev. 21 2007 1603 1608
-
(2007)
Genes Dev.
, vol.21
, pp. 1603-1608
-
-
Saito, K.1
Sakaguchi, Y.2
Suzuki, T.3
Suzuki, T.4
Siomi, H.5
Siomi, M.C.6
-
52
-
-
70449519397
-
A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila
-
K. Saito, S. Inagaki, T. Mituyama, Y. Kawamura, Y. Ono, E. Sakota, H. Kotani, K. Asai, H. Siomi, and M.C. Siomi A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila Nature 461 2009 1296 1299
-
(2009)
Nature
, vol.461
, pp. 1296-1299
-
-
Saito, K.1
Inagaki, S.2
Mituyama, T.3
Kawamura, Y.4
Ono, Y.5
Sakota, E.6
Kotani, H.7
Asai, K.8
Siomi, H.9
Siomi, M.C.10
-
53
-
-
84864757507
-
Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena
-
U.E. Schoeberl, H.M. Kurth, T. Noto, and K. Mochizuki Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena Genes Dev. 26 2012 1729 1742
-
(2012)
Genes Dev.
, vol.26
, pp. 1729-1742
-
-
Schoeberl, U.E.1
Kurth, H.M.2
Noto, T.3
Mochizuki, K.4
-
54
-
-
34249805994
-
The coming of age for Piwi proteins
-
A.G. Seto, R.E. Kingston, and N.C. Lau The coming of age for Piwi proteins Mol. Cell 26 2007 603 609
-
(2007)
Mol. Cell
, vol.26
, pp. 603-609
-
-
Seto, A.G.1
Kingston, R.E.2
Lau, N.C.3
-
55
-
-
84863631177
-
PiRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline
-
M. Shirayama, M. Seth, H.C. Lee, W. Gu, T. Ishidate, D. Conte Jr.; and C.C. Mello piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline Cell 150 2012 65 77
-
(2012)
Cell
, vol.150
, pp. 65-77
-
-
Shirayama, M.1
Seth, M.2
Lee, H.C.3
Gu, W.4
Ishidate, T.5
Conte, Jr.D.6
Mello, C.C.7
-
56
-
-
33846524902
-
Secondary siRNAs result from unprimed RNA synthesis and form a distinct class
-
T. Sijen, F.A. Steiner, K.L. Thijssen, and R.H. Plasterk Secondary siRNAs result from unprimed RNA synthesis and form a distinct class Science 315 2007 244 247
-
(2007)
Science
, vol.315
, pp. 244-247
-
-
Sijen, T.1
Steiner, F.A.2
Thijssen, K.L.3
Plasterk, R.H.4
-
57
-
-
44849108310
-
RNA-mediated DNA modifications and RNA-templated DNA repair
-
F. Storici RNA-mediated DNA modifications and RNA-templated DNA repair Curr. Opin. Mol. Ther. 10 2008 224 230
-
(2008)
Curr. Opin. Mol. Ther.
, vol.10
, pp. 224-230
-
-
Storici, F.1
-
58
-
-
79551634514
-
Structural basis for piRNA 2′-O-methylated 3′-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains
-
Y. Tian, D.K. Simanshu, J.B. Ma, and D.J. Patel Structural basis for piRNA 2′-O-methylated 3′-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains Proc. Natl. Acad. Sci. USA 108 2011 903 910
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 903-910
-
-
Tian, Y.1
Simanshu, D.K.2
Ma, J.B.3
Patel, D.J.4
-
59
-
-
33746502166
-
A distinct small RNA pathway silences selfish genetic elements in the germline
-
V.V. Vagin, A. Sigova, C. Li, H. Seitz, V. Gvozdev, and P.D. Zamore A distinct small RNA pathway silences selfish genetic elements in the germline Science 313 2006 320 324
-
(2006)
Science
, vol.313
, pp. 320-324
-
-
Vagin, V.V.1
Sigova, A.2
Li, C.3
Seitz, H.4
Gvozdev, V.5
Zamore, P.D.6
-
60
-
-
0942279635
-
RNAi-mediated targeting of heterochromatin by the RITS complex
-
A. Verdel, S. Jia, S. Gerber, T. Sugiyama, S. Gygi, S.I. Grewal, and D. Moazed RNAi-mediated targeting of heterochromatin by the RITS complex Science 303 2004 672 676
-
(2004)
Science
, vol.303
, pp. 672-676
-
-
Verdel, A.1
Jia, S.2
Gerber, S.3
Sugiyama, T.4
Gygi, S.5
Grewal, S.I.6
Moazed, D.7
-
61
-
-
0037072661
-
Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi
-
T.A. Volpe, C. Kidner, I.M. Hall, G. Teng, S.I. Grewal, and R.A. Martienssen Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi Science 297 2002 1833 1837
-
(2002)
Science
, vol.297
, pp. 1833-1837
-
-
Volpe, T.A.1
Kidner, C.2
Hall, I.M.3
Teng, G.4
Grewal, S.I.5
Martienssen, R.A.6
-
62
-
-
80052521105
-
Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles
-
J. Wang, B. Czech, A. Crunk, A. Wallace, M. Mitreva, G.J. Hannon, and R.E. Davis Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles Genome Res. 21 2011 1462 1477
-
(2011)
Genome Res.
, vol.21
, pp. 1462-1477
-
-
Wang, J.1
Czech, B.2
Crunk, A.3
Wallace, A.4
Mitreva, M.5
Hannon, G.J.6
Davis, R.E.7
-
63
-
-
0028031830
-
RNA-directed de novo methylation of genomic sequences in plants
-
M. Wassenegger, S. Heimes, L. Riedel, and H.L. Sänger RNA-directed de novo methylation of genomic sequences in plants Cell 76 1994 567 576
-
(1994)
Cell
, vol.76
, pp. 567-576
-
-
Wassenegger, M.1
Heimes, S.2
Riedel, L.3
Sänger, H.L.4
-
64
-
-
33745599586
-
Identification and characterization of two novel classes of small RNAs in the mouse germline: Retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes
-
T. Watanabe, A. Takeda, T. Tsukiyama, K. Mise, T. Okuno, H. Sasaki, N. Minami, and H. Imai Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes Genes Dev. 20 2006 1732 1743
-
(2006)
Genes Dev.
, vol.20
, pp. 1732-1743
-
-
Watanabe, T.1
Takeda, A.2
Tsukiyama, T.3
Mise, K.4
Okuno, T.5
Sasaki, H.6
Minami, N.7
Imai, H.8
-
65
-
-
79956052873
-
Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus
-
T. Watanabe, S. Tomizawa, K. Mitsuya, Y. Totoki, Y. Yamamoto, S. Kuramochi-Miyagawa, N. Iida, Y. Hoki, P.J. Murphy, and A. Toyoda Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus Science 332 2011 848 852
-
(2011)
Science
, vol.332
, pp. 848-852
-
-
Watanabe, T.1
Tomizawa, S.2
Mitsuya, K.3
Totoki, Y.4
Yamamoto, Y.5
Kuramochi-Miyagawa, S.6
Iida, N.7
Hoki, Y.8
Murphy, P.J.9
Toyoda, A.10
-
66
-
-
84862777814
-
A role for small RNAs in DNA double-strand break repair
-
W. Wei, Z. Ba, M. Gao, Y. Wu, Y. Ma, S. Amiard, C.I. White, J.M. Rendtlew Danielsen, Y.G. Yang, and Y. Qi A role for small RNAs in DNA double-strand break repair Cell 149 2012 101 112
-
(2012)
Cell
, vol.149
, pp. 101-112
-
-
Wei, W.1
Ba, Z.2
Gao, M.3
Wu, Y.4
Ma, Y.5
Amiard, S.6
White, C.I.7
Rendtlew Danielsen, J.M.8
Yang, Y.G.9
Qi, Y.10
-
67
-
-
0030807656
-
Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax
-
D.J. Witherspoon, T.G. Doak, K.R. Williams, A. Seegmiller, J. Seger, and G. Herrick Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax Mol. Biol. Evol. 14 1997 696 706
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 696-706
-
-
Witherspoon, D.J.1
Doak, T.G.2
Williams, K.R.3
Seegmiller, A.4
Seger, J.5
Herrick, G.6
-
68
-
-
0038581529
-
Programmed DNA deletion as an RNA-guided system of genome defense
-
M.C. Yao, P. Fuller, and X. Xi Programmed DNA deletion as an RNA-guided system of genome defense Science 300 2003 1581 1584
-
(2003)
Science
, vol.300
, pp. 1581-1584
-
-
Yao, M.C.1
Fuller, P.2
Xi, X.3
-
69
-
-
84865010587
-
Mating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27 nt small RNAs derived from the parental macronucleus
-
A.M. Zahler, Z.T. Neeb, A. Lin, and S. Katzman Mating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27 nt small RNAs derived from the parental macronucleus PLoS ONE 7 2012 e42371
-
(2012)
PLoS ONE
, vol.7
, pp. 42371
-
-
Zahler, A.M.1
Neeb, Z.T.2
Lin, A.3
Katzman, S.4
-
70
-
-
24644446398
-
Ribo-gnome: The big world of small RNAs
-
P.D. Zamore, and B. Haley Ribo-gnome: the big world of small RNAs Science 309 2005 1519 1524
-
(2005)
Science
, vol.309
, pp. 1519-1524
-
-
Zamore, P.D.1
Haley, B.2
-
71
-
-
57149118220
-
Small RNAs with 5′-polyphosphate termini associate with a Piwi-related protein and regulate gene expression in the single-celled eukaryote Entamoeba histolytica
-
H. Zhang, G.M. Ehrenkaufer, J.M. Pompey, J.A. Hackney, and U. Singh Small RNAs with 5′-polyphosphate termini associate with a Piwi-related protein and regulate gene expression in the single-celled eukaryote Entamoeba histolytica PLoS Pathog. 4 2008 e1000219
-
(2008)
PLoS Pathog.
, vol.4
, pp. 1000219
-
-
Zhang, H.1
Ehrenkaufer, G.M.2
Pompey, J.M.3
Hackney, J.A.4
Singh, U.5
-
72
-
-
75949108066
-
Galaxy: A web-based genome analysis tool for experimentalists
-
Chapter 19, Unit 19, 10.1-21
-
Blankenberg, D.; Von Kuster, G.; Coraor, N.; Ananda, G.; Lazarus, R.; Mangan, M.; Nekrutenko, A.; and Taylor, J. (2010). Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. Chapter 19, Unit 19, 10.1-21.
-
(2010)
Curr. Protoc. Mol. Biol.
-
-
Blankenberg, D.1
Von Kuster, G.2
Coraor, N.3
Ananda, G.4
Lazarus, R.5
Mangan, M.6
Nekrutenko, A.7
Taylor, J.8
-
73
-
-
79953310937
-
SHRiMP2: Sensitive yet practical SHort Read Mapping
-
David, M.; Dzamba, M.; Lister, D.; Ilie, L.; and Brudno, M. (2011). SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics 27, 1011-1012.
-
(2011)
Bioinformatics
, vol.27
, pp. 1011-1012
-
-
David, M.1
Dzamba, M.2
Lister, D.3
Ilie, L.4
Brudno, M.5
-
74
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
Giardine, B.; Riemer, C.; Hardison, R.C.; Burhans, R.; Elnitski, L.; Shah, P.; Zhang, Y.; Blankenberg, D.; Albert, I.; Taylor, J.; et al. (2005). Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451-1455.
-
(2005)
Genome Res.
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
-
75
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks, J.; Nekrutenko, A.; and Taylor, J.; Galaxy Team (2010). Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86.
-
(2010)
Genome Biol.
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
76
-
-
35348896591
-
The Chlamydomonas genome reveals the evolution of key animal and plant functions
-
Merchant, S.S.; Prochnik, S.E.; Vallon, O.; Harris, E.H.; Karpowicz, S.J.; Witman, G.B.; Terry, A.; Salamov, A.; Fritz-Laylin, L.K.; Maréchal-Drouard, L.; et al. (2007). The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318, 245-250.
-
(2007)
Science
, vol.318
, pp. 245-250
-
-
Merchant, S.S.1
Prochnik, S.E.2
Vallon, O.3
Harris, E.H.4
Karpowicz, S.J.5
Witman, G.B.6
Terry, A.7
Salamov, A.8
Fritz-Laylin, L.K.9
Maréchal-Drouard, L.10
-
77
-
-
84864968493
-
The Oxytricha trifallax mitochondrial genome
-
Swart, E.C.; Nowacki, M.; Shum, J.; Stiles, H.; Higgins, B.P.; Doak, T.G.; Schotanus, K.; Magrini, V.J.; Minx, P.; Mardis, E.R.; and Landweber, L.F. (2012). The Oxytricha trifallax mitochondrial genome. Genome Biol. Evol. 4, 136-154.
-
(2012)
Genome Biol. Evol.
, vol.4
, pp. 136-154
-
-
Swart, E.C.1
Nowacki, M.2
Shum, J.3
Stiles, H.4
Higgins, B.P.5
Doak, T.G.6
Schotanus, K.7
Magrini, V.J.8
Minx, P.9
Mardis, E.R.10
And Landweber, L.F.11
|