-
1
-
-
33646928347
-
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
-
Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. 2006. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441: 87-90.
-
(2006)
Nature
, vol.441
, pp. 87-90
-
-
Bejerano, G.1
Lowe, C.B.2
Ahituv, N.3
King, B.4
Siepel, A.5
Salama, S.R.6
Rubin, E.M.7
Kent, W.J.8
Haussler, D.9
-
2
-
-
71749094924
-
Transposable elements in gene regulation and in the evolution of vertebrate genomes
-
Bourque G. 2009. Transposable elements in gene regulation and in the evolution of vertebrate genomes. Curr Opin Genet Dev 19: 607-612.
-
(2009)
Curr Opin Genet Dev
, vol.19
, pp. 607-612
-
-
Bourque, G.1
-
3
-
-
55549117831
-
Evolution of the mammalian transcription factor binding repertoire via transposable elements
-
Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew JL, Ruan Y, Wei CL, Ng HH, et al. 2008. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 18: 1752-1762.
-
(2008)
Genome Res
, vol.18
, pp. 1752-1762
-
-
Bourque, G.1
Leong, B.2
Vega, V.B.3
Chen, X.4
Lee, Y.L.5
Srinivasan, K.G.6
Chew, J.L.7
Ruan, Y.8
Wei, C.L.9
Ng, H.H.10
-
4
-
-
0014690698
-
Gene regulation for higher cells: A theory
-
Britten RJ, Davidson EH. 1969. Gene regulation for higher cells: A theory. Science 165: 349-357.
-
(1969)
Science
, vol.165
, pp. 349-357
-
-
Britten, R.J.1
Davidson, E.H.2
-
5
-
-
0029077187
-
Mesoderm-specific B104 expression in the Drosophila embryo is mediated by internal cis-acting elements of thetransposon
-
Bronner G, Taubert H, Jackle H. 1995. Mesoderm-specific B104 expression in the Drosophila embryo is mediated by internal cis-acting elements of thetransposon. Chromosoma 103: 669-675.
-
(1995)
Chromosoma
, vol.103
, pp. 669-675
-
-
Bronner, G.1
Taubert, H.2
Jackle, H.3
-
6
-
-
38549096565
-
JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update
-
DOI 10.1093/nar/gkm955
-
Bryne JC, Valen E, Tang MHE, Marstrand T,Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A. 2008. JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update. Nucleic Acids Res 36: D102-D106. (Pubitemid 351149704)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Bryne, J.C.1
Valen, E.2
Tang, M.-H.E.3
Marstrand, T.4
Winther, O.5
Da, P.I.6
Krogh, A.7
Lenhard, B.8
Sandelin, A.9
-
7
-
-
0030298436
-
High-efficiency full-length cDNA cloning by biotinylated CAP trapper
-
DOI 10.1006/geno.1996.0567
-
Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M, Shibata K, Sasaki N, Izawa M, et al. 1996. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37: 327-336. (Pubitemid 26386957)
-
(1996)
Genomics
, vol.37
, Issue.3
, pp. 327-336
-
-
Carninci, P.1
Kvam, C.2
Kitamura, A.3
Ohsumi, T.4
Okazaki, Y.5
Itoh, M.6
Kamiya, M.7
Shibata, K.8
Sasaki, N.9
Izawa, M.10
Muramatsu, M.11
Hayashizaki, Y.12
Schneider, C.13
-
8
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
DOI 10.1038/ng1789, PII N1789
-
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CAM, Taylor MS, Engstrom PG, Frith MC, et al. 2006. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635. (Pubitemid 43927303)
-
(2006)
Nature Genetics
, vol.38
, Issue.6
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
Ponjavic, J.6
Semple, C.A.M.7
Taylor, M.S.8
Engstrom, P.G.9
Frith, M.C.10
Forrest, A.R.R.11
Alkema, W.B.12
Tan, S.L.13
Plessy, C.14
Kodzius, R.15
Ravasi, T.16
Kasukawa, T.17
Fukuda, S.18
Kanamori-Katayama, M.19
Kitazume, Y.20
Kawaji, H.21
Kai, C.22
Nakamura, M.23
Konno, H.24
Nakano, K.25
Mottagui-Tabar, S.26
Arner, P.27
Chesi, A.28
Gustincich, S.29
Persichetti, F.30
Suzuki, H.31
Grimmond, S.M.32
Wells, C.A.33
Orlando, V.34
Wahlestedt, C.35
Liu, E.T.36
Harbers, M.37
Kawai, J.38
Bajic, V.B.39
Hume, D.A.40
Hayashizaki, Y.41
more..
-
9
-
-
70350232064
-
Endogenous retroviral LTRs as promoters for human genes: A critical assessment
-
Cohen CJ, Lock WM, Mager DL. 2009. Endogenous retroviral LTRs as promoters for human genes: A critical assessment. Gene 448: 105-114.
-
(2009)
Gene
, vol.448
, pp. 105-114
-
-
Cohen, C.J.1
Lock, W.M.2
Mager, D.L.3
-
10
-
-
0028618784
-
Spatially regulated expression of retrovirus-like transposons during Drosophila melanogaster embryogenesis
-
Ding D, Lipshitz HD. 1994. Spatially regulated expression of retrovirus-like transposons during Drosophila melanogaster embryogenesis. Genet Res 64: 167-181.
-
(1994)
Genet Res
, vol.64
, pp. 167-181
-
-
Ding, D.1
Lipshitz, H.D.2
-
11
-
-
84871941421
-
Landscape of transcription in human cells
-
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi AM, Tanzer A, Lagarde J, LinW, Schlesinger F, et al. 2012. Landscape of transcription in human cells. Nature 41: 563-571.
-
(2012)
Nature
, vol.41
, pp. 563-571
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
Dobin, A.4
Lassmann, T.5
Mortazavi, A.M.6
Tanzer, A.7
Lagarde, J.8
Lin, W.9
Schlesinger, F.10
-
12
-
-
84871809302
-
STAR: Ultrafast universal RNA-seq aligner
-
doi: 10.1093/bioinformatics/bts635
-
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2012. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics doi: 10.1093/bioinformatics/bts635.
-
(2012)
Bioinformatics
-
-
Dobin, A.1
Davis, C.A.2
Schlesinger, F.3
Drenkow, J.4
Zaleski, C.5
Jha, S.6
Batut, P.7
Chaisson, M.8
Gingeras, T.R.9
-
13
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Bernstein, B.E.1
Birney, E.2
Dunham, I.3
Green, E.D.4
Gunter, C.5
Snyder, M.6
-
14
-
-
84871979228
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X,Wang L, Issner R, Coyne M, et al. 2011.Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 489: 101-108.
-
(2011)
Nature
, vol.489
, pp. 101-108
-
-
Ernst, J.1
Kheradpour, P.2
Mikkelsen, T.S.3
Shoresh, N.4
Ward, L.D.5
Epstein, C.B.6
Zhang, X.7
Wang, L.8
Issner, R.9
Coyne, M.10
-
15
-
-
67349173665
-
The regulated retrotransposon transcriptome of mammalian cells
-
Faulkner GJ, Kimura Y, Daub CO,Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, et al. 2009. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41: 563-571.
-
(2009)
Nat Genet
, vol.41
, pp. 563-571
-
-
Faulkner, G.J.1
Kimura, Y.2
Daub, C.O.3
Wani, S.4
Plessy, C.5
Irvine, K.M.6
Schroder, K.7
Cloonan, N.8
Steptoe, A.L.9
Lassmann, T.10
-
16
-
-
42349096534
-
Transposable elements and the evolution of regulatory networks
-
DOI 10.1038/nrg2337, PII NRG2337
-
Feschotte C. 2008. Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9: 397-405. (Pubitemid 351556062)
-
(2008)
Nature Reviews Genetics
, vol.9
, Issue.5
, pp. 397-405
-
-
Feschotte, C.1
-
17
-
-
33747299885
-
Comparative genomics of Drosophila and human core promoters
-
doi: 10.1186/gb-2006-7-7-r53.
-
FitzGerald PC, Sturgill D, Shyakhtenko A, Oliver B, Vinson C. 2006. Comparative genomics of Drosophila and human core promoters. Genome Biol 7: R53. doi: 10.1186/gb-2006-7-7-r53.
-
(2006)
Genome Biol
, vol.7
-
-
FitzGerald, P.C.1
Sturgill, D.2
Shyakhtenko, A.3
Oliver, B.4
Vinson, C.5
-
18
-
-
79953300078
-
FIMO: Scanning for occurrences of a given motif
-
Grant CE, Bailey TL, Noble WS. 2011. FIMO: Scanning for occurrences of a given motif. Bioinformatics 27: 1017-1018.
-
(2011)
Bioinformatics
, vol.27
, pp. 1017-1018
-
-
Grant, C.E.1
Bailey, T.L.2
Noble, W.S.3
-
19
-
-
79953043801
-
The developmental transcriptome of Drosophila melanogaster
-
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, et al. 2010. The developmental transcriptome of Drosophila melanogaster. Nature 471: 473-479
-
(2010)
Nature
, vol.471
, pp. 473-479
-
-
Graveley, B.R.1
Brooks, A.N.2
Carlson, J.W.3
Duff, M.O.4
Landolin, J.M.5
Yang, L.6
Artieri, C.G.7
Van Baren, M.J.8
Boley, N.9
Booth, B.W.10
-
20
-
-
0027328728
-
Determination of messenger RNA 5'-ends by reverse transcription of the cap structure
-
Hirzmann J, Luo D, Hahnen J, Hobom G. 1993. Determination of messenger-Rna 5′-ends by reverse transcription of the cap structure. Nucleic Acids Res 21: 3597-3598. (Pubitemid 23241512)
-
(1993)
Nucleic Acids Research
, vol.21
, Issue.15
, pp. 3597-3598
-
-
Hirzmann, J.1
Luo, D.2
Hahnen, J.3
Hobom, G.4
-
21
-
-
79551610291
-
Genome-wide analysis of promoter architecture in Drosophila melanogaster
-
Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, et al. 2011. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res 21: 182-192.
-
(2011)
Genome Res
, vol.21
, pp. 182-192
-
-
Hoskins, R.A.1
Landolin, J.M.2
Brown, J.B.3
Sandler, J.E.4
Takahashi, H.5
Lassmann, T.6
Yu, C.7
Booth, B.W.8
Zhang, D.9
Wan, K.H.10
-
22
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
-
(2009)
Nat Protoc
, vol.4
, pp. 44-57
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
23
-
-
79959403670
-
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
-
Islam S, Kjallquist U, Moliner A, Zajac P, Fan JB, Lonnerberg P, Linnarsson S. 2011. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res 21: 1160-1167.
-
(2011)
Genome Res
, vol.21
, pp. 1160-1167
-
-
Islam, S.1
Kjallquist, U.2
Moliner, A.3
Zajac, P.4
Fan, J.B.5
Lonnerberg, P.6
Linnarsson, S.7
-
24
-
-
84871952979
-
Non-autonomous family of Helitrons: A consensus sequence
-
Kapitonov V, Jurka J. 2007. Non-autonomous family of Helitrons: A consensus sequence. Repbase 7: 313.
-
(2007)
Repbase
, vol.7
, pp. 313
-
-
Kapitonov, V.1
Jurka, J.2
-
25
-
-
34250160256
-
RNA maps reveal new RNA classes and a possible function for pervasive transcription
-
DOI 10.1126/science.1138341
-
Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R,Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, et al. 2007a. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316: 1484-1488. (Pubitemid 46906616)
-
(2007)
Science
, vol.316
, Issue.5830
, pp. 1484-1488
-
-
Kapranov, P.1
Cheng, J.2
Dike, S.3
Nix, D.A.4
Duttagupta, R.5
Willingham, A.T.6
Stadler, P.F.7
Hertel, J.8
Hackermuller, J.9
Hofacker, I.L.10
Bell, I.11
Cheung, E.12
Drenkow, J.13
Dumais, E.14
Patel, S.15
Helt, G.16
Ganesh, M.17
Ghosh, S.18
Piccolboni, A.19
Sementchenko, V.20
Tammana, H.21
Gingeras, T.R.22
more..
-
26
-
-
34249088350
-
Genome-wide transcription and the implications for genomic organization
-
DOI 10.1038/nrg2083, PII NRG2083
-
Kapranov P, Willingham AT, Gingeras TR. 2007b. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8: 413-423. (Pubitemid 46789245)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.6
, pp. 413-423
-
-
Kapranov, P.1
Willingham, A.T.2
Gingeras, T.R.3
-
27
-
-
84988044467
-
CAGE: Cap analysis of gene expression
-
Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D, Imamura K, Kai C, Harbers M, et al. 2006. CAGE: Cap analysis of gene expression. Nat Methods 3: 211-222.
-
(2006)
Nat Methods
, vol.3
, pp. 211-222
-
-
Kodzius, R.1
Kojima, M.2
Nishiyori, H.3
Nakamura, M.4
Fukuda, S.5
Tagami, M.6
Sasaki, D.7
Imamura, K.8
Kai, C.9
Harbers, M.10
-
28
-
-
0030857802
-
Twist-mediated activation of the NK-4 homeobox gene in the visceral mesoderm of Drosophila requires two distinct clusters of E-box regulatory elements
-
DOI 10.1074/jbc.272.28.17531
-
Lee YM, Park T, Schulz RA, Kim Y. 1997. Twist-mediated activation of the NK-4 homeobox gene in the visceral mesoderm of Drosophila requires two distinct clusters of E-box regulatory elements. J Biol Chem 272: 17531-17541. (Pubitemid 27311186)
-
(1997)
Journal of Biological Chemistry
, vol.272
, Issue.28
, pp. 17531-17541
-
-
Lee, Y.M.1
Park, T.2
Schulz, R.A.3
Kim, Y.4
-
29
-
-
80054973803
-
A high-resolutionmap of human evolutionary constraint using 29 mammals
-
Lindblad-Toh K,Garber M, Zuk O, Lin MF, Parker BJ,Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, et al. 2011. A high-resolutionmap of human evolutionary constraint using 29 mammals. Nature 478: 476-482.
-
(2011)
Nature
, vol.478
, pp. 476-482
-
-
Lindblad-Toh, K.1
Garber, M.2
Zuk, O.3
Lin, M.F.4
Parker, B.J.5
Washietl, S.6
Kheradpour, P.7
Ernst, J.8
Jordan, G.9
Mauceli, E.10
-
30
-
-
28044446960
-
Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome
-
doi: 10.1186/1741-7007-3-24
-
Lipatov M, Lenkov K, Petrov DA, Bergman CM. 2005. Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol 3: 24. doi: 10.1186/1741-7007-3-24.
-
(2005)
BMC Biol
, vol.3
, pp. 24
-
-
Lipatov, M.1
Lenkov, K.2
Petrov, D.A.3
Bergman, C.M.4
-
31
-
-
3342927934
-
Role of transposable elements in heterochromatin and epigenetic control
-
DOI 10.1038/nature02651
-
Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476. (Pubitemid 38987911)
-
(2004)
Nature
, vol.430
, Issue.6998
, pp. 471-476
-
-
Lippman, Z.1
Gendrel, A.-V.2
Black, M.3
Vaughn, M.W.4
Dedhia, N.5
McCombie, W.R.6
Lavine, K.7
Mittal, V.8
May, B.9
Kasschau, K.B.10
Carrington, J.C.11
Doerge, R.W.12
Colot, V.13
Martienssen, R.14
-
32
-
-
80055010534
-
Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
-
Lynch VJ, Leclerc RD, May G, Wagner GP. 2011. Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet 43: 1154-1158.
-
(2011)
Nat Genet
, vol.43
, pp. 1154-1158
-
-
Lynch, V.J.1
Leclerc, R.D.2
May, G.3
Wagner, G.P.4
-
33
-
-
84863458292
-
Embryonic stem cell potency fluctuates with endogenous retrovirus activity
-
Macfarlan TS, Gifford WD, Driscoll S, Lettieri K, Rowe HM, Bonanomi D, Firth A, Singer O, Trono D, Pfaff SL. 2012. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487: 57-63.
-
(2012)
Nature
, vol.487
, pp. 57-63
-
-
Macfarlan, T.S.1
Gifford, W.D.2
Driscoll, S.3
Lettieri, K.4
Rowe, H.M.5
Bonanomi, D.6
Firth, A.7
Singer, O.8
Trono, D.9
Pfaff, S.L.10
-
34
-
-
84863537088
-
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
-
Marbach D, Roy S, Ay F,Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. 2012. Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Res 22: 1334-1349.
-
(2012)
Genome Res
, vol.22
, pp. 1334-1349
-
-
Marbach, D.1
Roy, S.2
Ay, F.3
Meyer, P.E.4
Candeias, R.5
Kahveci, T.6
Bristow, C.A.7
Kellis, M.8
-
36
-
-
0028822316
-
Dorsal-ventral patterning genes restrict NK-2 homeobox gene expression to the ventral half of the central nervous system of Drosophila embryos
-
Mellerick DM, Nirenberg M. 1995. Dorsal-ventral patterning genes restrict NK-2 homeobox gene expression to the ventral half of the central nervous system of Drosophila embryos. Dev Biol 171: 306-316.
-
(1995)
Dev Biol
, vol.171
, pp. 306-316
-
-
Mellerick, D.M.1
Nirenberg, M.2
-
37
-
-
0028230861
-
Ingrowth by photoreceptor axons induces transcription of a retrotransposon in the developing Drosophila brain
-
Mozer BA, Benzer S. 1994. Ingrowth by photoreceptor axons induces transcription of a retrotransposon in the developing Drosophila brain. Development 120: 1049-1058. (Pubitemid 24150032)
-
(1994)
Development
, vol.120
, Issue.5
, pp. 1049-1058
-
-
Mozer, B.A.1
Benzer, S.2
-
38
-
-
70350515004
-
Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
-
Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka T,Wessler SR. 2009. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461: 1130-1232.
-
(2009)
Nature
, vol.461
, pp. 1130-1232
-
-
Naito, K.1
Zhang, F.2
Tsukiyama, T.3
Saito, H.4
Hancock, C.N.5
Richardson, A.O.6
Okumoto, Y.7
Tanisaka, T.8
Wessler, S.R.9
-
39
-
-
79953046943
-
A cis-regulatory map ofthe Drosophila genome
-
Negre N, Brown CD, Ma LJ, Bristow CA, Miller SW,Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, et al. 2011. A cis-regulatory map ofthe Drosophila genome. Nature 471: 527-531.
-
(2011)
Nature
, vol.471
, pp. 527-531
-
-
Negre, N.1
Brown, C.D.2
Ma, L.J.3
Bristow, C.A.4
Miller, S.W.5
Wagner, U.6
Kheradpour, P.7
Eaton, M.L.8
Loriaux, P.9
Sealfon, R.10
-
40
-
-
77954716355
-
A paired-end sequencing strategy to map the complex landscape of transcription initiation
-
Ni T, Corcoran DL, Rach EA, Song S, Spana EP, Gao Y, Ohler U, Zhu J. 2010. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods 7: 521-527.
-
(2010)
Nat Methods
, vol.7
, pp. 521-527
-
-
Ni, T.1
Corcoran, D.L.2
Rach, E.A.3
Song, S.4
Spana, E.P.5
Gao, Y.6
Ohler, U.7
Zhu, J.8
-
41
-
-
0036251775
-
Many human genes are transcribed from the antisense promoter of L1 retrotransposon
-
DOI 10.1006/geno.2002.6758
-
Nigumann P, Redik K, Matlik K, Speek M. 2002. Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics 79: 628-634. (Pubitemid 34499478)
-
(2002)
Genomics
, vol.79
, Issue.5
, pp. 628-634
-
-
Nigumann, P.1
Redik, K.2
Matlik, K.3
Speek, M.4
-
42
-
-
0023282178
-
Developmental expression of Drosophila melanogaster retrovirus-like transposable elements
-
Parkhurst SM, Corces VG. 1987. Developmental expression of Drosophila melanogaster retrovirus-like transposable elements. EMBO J 6: 419-424.
-
(1987)
EMBO J
, vol.6
, pp. 419-424
-
-
Parkhurst, S.M.1
Corces, V.G.2
-
43
-
-
5044251591
-
Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos
-
DOI 10.1016/j.devcel.2004.09.004, PII S1534580704003259
-
Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D, Knowles BB. 2004. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell 7: 597-606. (Pubitemid 39341844)
-
(2004)
Developmental Cell
, vol.7
, Issue.4
, pp. 597-606
-
-
Peaston, A.E.1
Evsikov, A.V.2
Graber, J.H.3
De Vries, W.N.4
Holbrook, A.E.5
Solter, D.6
Knowles, B.B.7
-
44
-
-
79953729211
-
Population genomics of transposable elements in Drosophila melanogaster
-
Petrov DA, Fiston-Lavier AS, Lipatov M, Lenkov K, Gonzalez J. 2011. Population genomics of transposable elements in Drosophila melanogaster. Mol Biol Evol 28: 1633-1644.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 1633-1644
-
-
Petrov, D.A.1
Fiston-Lavier, A.S.2
Lipatov, M.3
Lenkov, K.4
Gonzalez, J.5
-
45
-
-
78149276744
-
Permutation P-values should never be zero: Calculating exact P-values when permutations are randomly drawn
-
doi: 10.2202/1544-6115.1585
-
Phipson B, Smyth GK. 2010. Permutation P-values should never be zero: Calculating exact P-values when permutations are randomly drawn. Stat Appl Genet Mol Biol 9: Article39. doi: 10.2202/1544-6115.1585.
-
(2010)
Stat Appl Genet Mol Biol
, vol.9
-
-
Phipson, B.1
Smyth, G.K.2
-
46
-
-
77954738647
-
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
-
Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J, Olivarius S, Lazarevic D, et al. 2010. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods 7: 528-534.
-
(2010)
Nat Methods
, vol.7
, pp. 528-534
-
-
Plessy, C.1
Bertin, N.2
Takahashi, H.3
Simone, R.4
Salimullah, M.5
Lassmann, T.6
Vitezic, M.7
Severin, J.8
Olivarius, S.9
Lazarevic, D.10
-
47
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. 2010. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
48
-
-
68049107475
-
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
-
doi: 10.1186/gb-2009-10-7-r73
-
Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U. 2009. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol 10: R73. doi: 10.1186/gb-2009-10-7-r73.
-
(2009)
Genome Biol
, vol.10
-
-
Rach, E.A.1
Yuan, H.Y.2
Majoros, W.H.3
Tomancak, P.4
Ohler, U.5
-
49
-
-
78049387387
-
Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo
-
Rouget C, Papin C, Boureux A, Meunier AC, Franco B, Robine N, Lai EC, Pelisson A, Simonelig M. 2010. Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467: 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
-
-
0040891824
-
Differential regulation of the two transcripts from the Drosophila gap segmentation gene hunchback
-
Schroder C, Tautz D, Seifert E, Jackle H. 1988. Differential regulation of the two transcripts from the Drosophila gap segmentation gene hunchback. EMBO J 7: 2881-2887.
-
(1988)
EMBO J
, vol.7
, pp. 2881-2887
-
-
Schroder, C.1
Tautz, D.2
Seifert, E.3
Jackle, H.4
-
51
-
-
84864462544
-
A map of the cis-regulatory sequences in the mouse genome
-
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S,Wagner U, Dixon J, Lee L, Lobanenkov VV, et al. 2012. A map of the cis-regulatory sequences in the mouse genome. Nature 488: 116-120.
-
(2012)
Nature
, vol.488
, pp. 116-120
-
-
Shen, Y.1
Yue, F.2
McCleary, D.F.3
Ye, Z.4
Edsall, L.5
Kuan, S.6
Wagner, U.7
Dixon, J.8
Lee, L.9
Lobanenkov, V.V.10
-
52
-
-
65149083962
-
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
-
Suzuki H, Forrest ARR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJL, et al. 2009. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41: 553-562.
-
(2009)
Nat Genet
, vol.41
, pp. 553-562
-
-
Suzuki, H.1
Forrest, A.R.R.2
Van Nimwegen, E.3
Daub, C.O.4
Balwierz, P.J.5
Irvine, K.M.6
Lassmann, T.7
Ravasi, T.8
Hasegawa, Y.9
De Hoon, M.J.L.10
-
53
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
54
-
-
0029936218
-
Control of expression of the I factor, a LINE-like transposable element in Drosophila melanogaster
-
Udomkit A, Forbes S, McLean C, Arkhipova I, Finnegan DJ. 1996. Control of expression of the I factor, a LINE-like transposable element in Drosophila melanogaster. EMBO J 15: 3174-3181. (Pubitemid 26187764)
-
(1996)
EMBO Journal
, vol.15
, Issue.12
, pp. 3174-3181
-
-
Udomkit, A.1
Forbes, S.2
McLean, C.3
Arkhipova, I.4
Finnegan, D.J.5
-
55
-
-
0141561907
-
Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions
-
DOI 10.1016/j.tig.2003.08.004
-
van de Lagemaat LN, Landry JR, Mager DL, Medstrand P. 2003. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet 19: 530-536. (Pubitemid 37204911)
-
(2003)
Trends in Genetics
, vol.19
, Issue.10
, pp. 530-536
-
-
Van De, L.L.N.1
Landry, J.-R.2
Mager, D.L.3
Medstrand, P.4
-
56
-
-
0031468348
-
Regulation of the twist target gene tinman by modular cis-regulatory elements during early mesoderm development
-
Yin Z, Xu XL, Frasch M. 1997. Regulation of the twist target gene tinman by modular cis-regulatory elements during early mesoderm development. Development 124: 4971-4982. (Pubitemid 28025123)
-
(1997)
Development
, vol.124
, Issue.24
, pp. 4971-4982
-
-
Yin, Z.1
Xu, X.-L.2
Frasch, M.3
-
57
-
-
0035498955
-
biniou (FoxF), a central component in a regulatory network controlling visceral mesoderm development and midgut morphogenesis in Drosophila
-
Zaffran S, Kuchler A, Lee HH, Frasch M. 2001. biniou (FoxF), a central component in a regulatory network controlling visceral mesoderm development and midgut morphogenesis in Drosophila. Genes Dev 15: 2900-2915. (Pubitemid 33042059)
-
(2001)
Genes and Development
, vol.15
, Issue.21
, pp. 2900-2915
-
-
Zaffran, S.1
Kuchler, A.2
Lee, H.-H.3
Frasch, M.4
-
58
-
-
0024652566
-
Substrate specificity of T4 RNA-ligase. The effect of the nucleotide composition of substrates and the size of phosphate donor on the effectiveness of intermolecular ligation
-
Zhenodarova SM, Kliagina VP, Maistrenko FG, Pustoshilova NM, Smolianinova OA. 1989. Substrate specificity of T4 RNA-ligase. The effect of the nucleotide composition of substrates and the size of phosphate donor on the effectiveness of intermolecular ligation. Bioorg Khim 15: 478-483.
-
(1989)
Bioorg Khim
, vol.15
, pp. 478-483
-
-
Zhenodarova, S.M.1
Kliagina, V.P.2
Maistrenko, F.G.3
Pustoshilova, N.M.4
Smolianinova, O.A.5
|