-
1
-
-
0027386243
-
The zebrafish midblastula transition
-
Kane DA, Kimmel CB. The zebrafish midblastula transition. Development 1993, 119:447-456.
-
(1993)
Development
, vol.119
, pp. 447-456
-
-
Kane, D.A.1
Kimmel, C.B.2
-
2
-
-
56449123775
-
Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy
-
Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EH. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 2008, 322:1065-1069.
-
(2008)
Science
, vol.322
, pp. 1065-1069
-
-
Keller, P.J.1
Schmidt, A.D.2
Wittbrodt, J.3
Stelzer, E.H.4
-
3
-
-
0027226233
-
Commitment of cell fate in the early zebrafish embryo
-
Ho RK, Kimmel CB. Commitment of cell fate in the early zebrafish embryo. Science 1993, 261:109-111.
-
(1993)
Science
, vol.261
, pp. 109-111
-
-
Ho, R.K.1
Kimmel, C.B.2
-
4
-
-
0029045033
-
Stages of embryonic development of the zebrafish
-
Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF. Stages of embryonic development of the zebrafish. Dev Dyn 1995, 203:253-310.
-
(1995)
Dev Dyn
, vol.203
, pp. 253-310
-
-
Kimmel, C.B.1
Ballard, W.W.2
Kimmel, S.R.3
Ullmann, B.4
Schilling, T.F.5
-
5
-
-
80051555960
-
Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition
-
Aanes H, Winata CL, Lin CH, Chen JP, Srinivasan KG, Lee SG, et al. Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. Genome Res 2011, 21:1328-1338.
-
(2011)
Genome Res
, vol.21
, pp. 1328-1338
-
-
Aanes, H.1
Winata, C.L.2
Lin, C.H.3
Chen, J.P.4
Srinivasan, K.G.5
Lee, S.G.6
-
6
-
-
33645124258
-
Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs
-
Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van DS, Inoue K, et al. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 2006, 312:75-79.
-
(2006)
Science
, vol.312
, pp. 75-79
-
-
Giraldez, A.J.1
Mishima, Y.2
Rihel, J.3
Grocock, R.J.4
Van, D.S.5
Inoue, K.6
-
7
-
-
30544437719
-
Transcriptome analysis of zebrafish embryogenesis using microarrays
-
Mathavan S, Lee SG, Mak A, Miller LD, Murthy KR, Govindarajan KR, et al. Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS Genet 2005, 1:260-276.
-
(2005)
PLoS Genet
, vol.1
, pp. 260-276
-
-
Mathavan, S.1
Lee, S.G.2
Mak, A.3
Miller, L.D.4
Murthy, K.R.5
Govindarajan, K.R.6
-
8
-
-
64549129564
-
Developmental gene regulatory networks in the zebrafish embryo
-
Chan TM, Longabaugh W, Bolouri H, Chen HL, Tseng WF, Chao CH, et al. Developmental gene regulatory networks in the zebrafish embryo. Biochim Biophys Acta 2009, 1789:279-298.
-
(2009)
Biochim Biophys Acta
, vol.1789
, pp. 279-298
-
-
Chan, T.M.1
Longabaugh, W.2
Bolouri, H.3
Chen, H.L.4
Tseng, W.F.5
Chao, C.H.6
-
9
-
-
77950866717
-
Chromatin signature of embryonic pluripotency is established during genome activation
-
Vastenhouw NL, Zhang Y, Woods IG, Imam F, Regev A, Liu XS, et al. Chromatin signature of embryonic pluripotency is established during genome activation. Nature 2010, 464:922-926.
-
(2010)
Nature
, vol.464
, pp. 922-926
-
-
Vastenhouw, N.L.1
Zhang, Y.2
Woods, I.G.3
Imam, F.4
Regev, A.5
Liu, X.S.6
-
10
-
-
83455243023
-
Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation
-
Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Ostrup O, et al. Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation. Dev Cell 2011, 21:993-1004.
-
(2011)
Dev Cell
, vol.21
, pp. 993-1004
-
-
Lindeman, L.C.1
Andersen, I.S.2
Reiner, A.H.3
Li, N.4
Aanes, H.5
Ostrup, O.6
-
11
-
-
84864936117
-
Developmental features of DNA methylation during activation of the embryonic zebrafish genome
-
Andersen IS, Reiner AH, Aanes H, Alestrom P, Collas P. Developmental features of DNA methylation during activation of the embryonic zebrafish genome. Genome Biol 2012, 13:R65.
-
(2012)
Genome Biol
, vol.13
-
-
Andersen, I.S.1
Reiner, A.H.2
Aanes, H.3
Alestrom, P.4
Collas, P.5
-
12
-
-
84856214088
-
Epigenetic complexity during the zebrafish mid-blastula transition
-
Andersen IS, Ostrup O, Lindeman LC, Aanes H, Reiner AH, Mathavan S, et al. Epigenetic complexity during the zebrafish mid-blastula transition. Biochem Biophys Res Commun 2012, 417:1139-1144.
-
(2012)
Biochem Biophys Res Commun
, vol.417
, pp. 1139-1144
-
-
Andersen, I.S.1
Ostrup, O.2
Lindeman, L.C.3
Aanes, H.4
Reiner, A.H.5
Mathavan, S.6
-
13
-
-
84857836107
-
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
-
Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 2012, 22:577-591.
-
(2012)
Genome Res
, vol.22
, pp. 577-591
-
-
Pauli, A.1
Valen, E.2
Lin, M.F.3
Garber, M.4
Vastenhouw, N.L.5
Levin, J.Z.6
-
14
-
-
79956290756
-
The zebrafish transcriptome during early development
-
Vesterlund L, Jiao H, Unneberg P, Hovatta O, Kere J. The zebrafish transcriptome during early development. BMC Dev Biol 2011, 11:30.
-
(2011)
BMC Dev Biol
, vol.11
, pp. 30
-
-
Vesterlund, L.1
Jiao, H.2
Unneberg, P.3
Hovatta, O.4
Kere, J.5
-
15
-
-
0019423884
-
Altered expression of the calcitonin gene associated with RNA polymorphism
-
Rosenfeld MG, Amara SG, Roos BA, Ong ES, Evans RM. Altered expression of the calcitonin gene associated with RNA polymorphism. Nature 1981, 290:63-65.
-
(1981)
Nature
, vol.290
, pp. 63-65
-
-
Rosenfeld, M.G.1
Amara, S.G.2
Roos, B.A.3
Ong, E.S.4
Evans, R.M.5
-
16
-
-
0019961126
-
Calcitonin mRNA polymorphism: peptide switching associated with alternative RNA splicing events
-
Rosenfeld MG, Lin CR, Amara SG, Stolarsky L, Roos BA, Ong ES, et al. Calcitonin mRNA polymorphism: peptide switching associated with alternative RNA splicing events. Proc Natl Acad Sci U S A 1982, 79:1717-1721.
-
(1982)
Proc Natl Acad Sci U S A
, vol.79
, pp. 1717-1721
-
-
Rosenfeld, M.G.1
Lin, C.R.2
Amara, S.G.3
Stolarsky, L.4
Roos, B.A.5
Ong, E.S.6
-
17
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40:1413-1415.
-
(2008)
Nat Genet
, vol.40
, pp. 1413-1415
-
-
Pan, Q.1
Shai, O.2
Lee, L.J.3
Frey, B.J.4
Blencowe, B.J.5
-
18
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
-
19
-
-
80052223272
-
An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming
-
Gabut M, Samavarchi-Tehrani P, Wang X, Slobodeniuc V, O'Hanlon D, Sung HK, et al. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell 2011, 147:132-146.
-
(2011)
Cell
, vol.147
, pp. 132-146
-
-
Gabut, M.1
Samavarchi-Tehrani, P.2
Wang, X.3
Slobodeniuc, V.4
O'Hanlon, D.5
Sung, H.K.6
-
20
-
-
79551610956
-
Genome-wide analysis of alternative splicing in Caenorhabditis elegans
-
Ramani AK, Calarco JA, Pan Q, Mavandadi S, Wang Y, Nelson AC, et al. Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res 2011, 21:342-348.
-
(2011)
Genome Res
, vol.21
, pp. 342-348
-
-
Ramani, A.K.1
Calarco, J.A.2
Pan, Q.3
Mavandadi, S.4
Wang, Y.5
Nelson, A.C.6
-
22
-
-
12344281782
-
The implications of structured 5' untranslated regions on translation and disease
-
Pickering BM, Willis AE. The implications of structured 5' untranslated regions on translation and disease. Semin Cell Dev Biol 2005, 16:39-47.
-
(2005)
Semin Cell Dev Biol
, vol.16
, pp. 39-47
-
-
Pickering, B.M.1
Willis, A.E.2
-
23
-
-
69549135202
-
To localize or not to localize: mRNA fate is in 3'UTR ends
-
Andreassi C, Riccio A. To localize or not to localize: mRNA fate is in 3'UTR ends. Trends Cell Biol 2009, 19:465-474.
-
(2009)
Trends Cell Biol
, vol.19
, pp. 465-474
-
-
Andreassi, C.1
Riccio, A.2
-
24
-
-
77149175671
-
Regulation of alternative splicing by histone modifications
-
Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T. Regulation of alternative splicing by histone modifications. Science 2010, 327:996-1000.
-
(2010)
Science
, vol.327
, pp. 996-1000
-
-
Luco, R.F.1
Pan, Q.2
Tominaga, K.3
Blencowe, B.J.4
Pereira-Smith, O.M.5
Misteli, T.6
-
25
-
-
80455176999
-
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
-
Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 2011, 479:74-79.
-
(2011)
Nature
, vol.479
, pp. 74-79
-
-
Shukla, S.1
Kavak, E.2
Gregory, M.3
Imashimizu, M.4
Shutinoski, B.5
Kashlev, M.6
-
26
-
-
77952029221
-
Deciphering the splicing code
-
Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, et al. Deciphering the splicing code. Nature 2010, 465:53-59.
-
(2010)
Nature
, vol.465
, pp. 53-59
-
-
Barash, Y.1
Calarco, J.A.2
Gao, W.3
Pan, Q.4
Wang, X.5
Shai, O.6
-
27
-
-
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, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 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
-
28
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
29
-
-
79952709611
-
Improving RNA-Seq expression estimates by correcting for fragment bias
-
Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 2011, 12:R22.
-
(2011)
Genome Biol
, vol.12
-
-
Roberts, A.1
Trapnell, C.2
Donaghey, J.3
Rinn, J.L.4
Pachter, L.5
-
30
-
-
80051941094
-
Identification of novel transcripts in annotated genomes using RNA-Seq
-
Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 2011, 27:2325-2329.
-
(2011)
Bioinformatics
, vol.27
, pp. 2325-2329
-
-
Roberts, A.1
Pimentel, H.2
Trapnell, C.3
Pachter, L.4
-
31
-
-
84858077472
-
The Pfam protein families database
-
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, et al. The Pfam protein families database. Nucleic Acids Res 2012, 40:D290-D301.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
Boursnell, C.6
-
32
-
-
78651539141
-
Coding potential of the products of alternative splicing in human
-
Leoni G, Le PL, Ferre F, Raimondo D, Tramontano A. Coding potential of the products of alternative splicing in human. Genome Biol 2011, 12:R9.
-
(2011)
Genome Biol
, vol.12
-
-
Leoni, G.1
Le, P.L.2
Ferre, F.3
Raimondo, D.4
Tramontano, A.5
-
33
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 2006, 38:626-635.
-
(2006)
Nat Genet
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
Ponjavic, J.6
-
34
-
-
0035912718
-
A gene family required for human germ cell development evolved from an ancient meiotic gene conserved in metazoans
-
Xu EY, Moore FL, Pera RA. A gene family required for human germ cell development evolved from an ancient meiotic gene conserved in metazoans. Proc Natl Acad Sci U S A 2001, 98:7414-7419.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 7414-7419
-
-
Xu, E.Y.1
Moore, F.L.2
Pera, R.A.3
-
35
-
-
79954531148
-
Genome-wide analysis of translation reveals a critical role for deleted in azoospermia-like (Dazl) at the oocyte-to-zygote transition
-
Chen J, Melton C, Suh N, Oh JS, Horner K, Xie F, et al. Genome-wide analysis of translation reveals a critical role for deleted in azoospermia-like (Dazl) at the oocyte-to-zygote transition. Genes Dev 2011, 25:755-766.
-
(2011)
Genes Dev
, vol.25
, pp. 755-766
-
-
Chen, J.1
Melton, C.2
Suh, N.3
Oh, J.S.4
Horner, K.5
Xie, F.6
-
36
-
-
66249102331
-
Dazl functions in maintenance of pluripotency and genetic and epigenetic programs of differentiation in mouse primordial germ cells in vivo and in vitro
-
Haston KM, Tung JY, Reijo Pera RA. Dazl functions in maintenance of pluripotency and genetic and epigenetic programs of differentiation in mouse primordial germ cells in vivo and in vitro. PLoS One 2009, 4:e5654.
-
(2009)
PLoS One
, vol.4
-
-
Haston, K.M.1
Tung, J.Y.2
Reijo Pera, R.A.3
-
37
-
-
23044468281
-
The DAZL family proteins are PABP-binding proteins that regulate translation in germ cells
-
Collier B, Gorgoni B, Loveridge C, Cooke HJ, Gray NK. The DAZL family proteins are PABP-binding proteins that regulate translation in germ cells. EMBO J 2005, 24:2656-2666.
-
(2005)
EMBO J
, vol.24
, pp. 2656-2666
-
-
Collier, B.1
Gorgoni, B.2
Loveridge, C.3
Cooke, H.J.4
Gray, N.K.5
-
38
-
-
70449433489
-
DAZL relieves miRNA-mediated repression of germline mRNAs by controlling poly(A) tail length in zebrafish
-
Takeda Y, Mishima Y, Fujiwara T, Sakamoto H, Inoue K. DAZL relieves miRNA-mediated repression of germline mRNAs by controlling poly(A) tail length in zebrafish. PLoS One 2009, 4:e7513.
-
(2009)
PLoS One
, vol.4
-
-
Takeda, Y.1
Mishima, Y.2
Fujiwara, T.3
Sakamoto, H.4
Inoue, K.5
-
39
-
-
0037172993
-
Methylation of histone H3 Lys 4 in coding regions of active genes
-
Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS, et al. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A 2002, 99:8695-8700.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 8695-8700
-
-
Bernstein, B.E.1
Humphrey, E.L.2
Erlich, R.L.3
Schneider, R.4
Bouman, P.5
Liu, J.S.6
-
40
-
-
0037179716
-
Active genes are tri-methylated at K4 of histone H3
-
Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, et al. Active genes are tri-methylated at K4 of histone H3. Nature 2002, 419:407-411.
-
(2002)
Nature
, vol.419
, pp. 407-411
-
-
Santos-Rosa, H.1
Schneider, R.2
Bannister, A.J.3
Sherriff, J.4
Bernstein, B.E.5
Emre, N.C.6
-
41
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560.
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
-
42
-
-
33847084602
-
Genome regulation by polycomb and trithorax proteins
-
Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G. Genome regulation by polycomb and trithorax proteins. Cell 2007, 128:735-745.
-
(2007)
Cell
, vol.128
, pp. 735-745
-
-
Schuettengruber, B.1
Chourrout, D.2
Vervoort, M.3
Leblanc, B.4
Cavalli, G.5
-
43
-
-
78651364359
-
ZFIN: enhancements and updates to the Zebrafish Model Organism Database
-
Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Howe DG, et al. ZFIN: enhancements and updates to the Zebrafish Model Organism Database. Nucleic Acids Res 2011, 39:D822-D829.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Bradford, Y.1
Conlin, T.2
Dunn, N.3
Fashena, D.4
Frazer, K.5
Howe, D.G.6
-
44
-
-
69949156902
-
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos
-
Akkers RC, van Heeringen SJ, Jacobi UG, Janssen-Megens EM, Francoijs KJ, Stunnenberg HG, et al. A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. Dev Cell 2009, 17:425-434.
-
(2009)
Dev Cell
, vol.17
, pp. 425-434
-
-
Akkers, R.C.1
van Heeringen, S.J.2
Jacobi, U.G.3
Janssen-Megens, E.M.4
Francoijs, K.J.5
Stunnenberg, H.G.6
-
47
-
-
0037016668
-
Multi-PDZ domain protein 1 (MUPP1) is concentrated at tight junctions through its possible interaction with claudin-1 and junctional adhesion molecule
-
Hamazaki Y, Itoh M, Sasaki H, Furuse M, Tsukita S. Multi-PDZ domain protein 1 (MUPP1) is concentrated at tight junctions through its possible interaction with claudin-1 and junctional adhesion molecule. J Biol Chem 2002, 277:455-461.
-
(2002)
J Biol Chem
, vol.277
, pp. 455-461
-
-
Hamazaki, Y.1
Itoh, M.2
Sasaki, H.3
Furuse, M.4
Tsukita, S.5
-
48
-
-
78649980886
-
Molecular dissection of the migrating posterior lateral line primordium during early development in zebrafish
-
Gallardo VE, Liang J, Behra M, Elkahloun A, Villablanca EJ, Russo V, et al. Molecular dissection of the migrating posterior lateral line primordium during early development in zebrafish. BMC Dev Biol 2010, 10:120.
-
(2010)
BMC Dev Biol
, vol.10
, pp. 120
-
-
Gallardo, V.E.1
Liang, J.2
Behra, M.3
Elkahloun, A.4
Villablanca, E.J.5
Russo, V.6
-
50
-
-
77951936055
-
The tight junction component Claudin E is required for zebrafish epiboly
-
Siddiqui M, Sheikh H, Tran C, Bruce AE. The tight junction component Claudin E is required for zebrafish epiboly. Dev Dyn 2010, 239:715-722.
-
(2010)
Dev Dyn
, vol.239
, pp. 715-722
-
-
Siddiqui, M.1
Sheikh, H.2
Tran, C.3
Bruce, A.E.4
-
51
-
-
34547599504
-
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets
-
Foissac S, Sammeth M. ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res 2007, 35:W297-W299.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Foissac, S.1
Sammeth, M.2
-
52
-
-
78751470921
-
Structure and function of mammalian DNA methyltransferases
-
Jurkowska RZ, Jurkowski TP, Jeltsch A. Structure and function of mammalian DNA methyltransferases. Chembiochem 2011, 12:206-222.
-
(2011)
Chembiochem
, vol.12
, pp. 206-222
-
-
Jurkowska, R.Z.1
Jurkowski, T.P.2
Jeltsch, A.3
-
53
-
-
0033945861
-
DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci
-
Rountree MR, Bachman KE, Baylin SB. DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nat Genet 2000, 25:269-277.
-
(2000)
Nat Genet
, vol.25
, pp. 269-277
-
-
Rountree, M.R.1
Bachman, K.E.2
Baylin, S.B.3
-
54
-
-
78549288551
-
DNA methyltransferase 1-associated protein (DMAP1) is a co-repressor that stimulates DNA methylation globally and locally at sites of double strand break repair
-
Lee GE, Kim JH, Taylor M, Muller MT. DNA methyltransferase 1-associated protein (DMAP1) is a co-repressor that stimulates DNA methylation globally and locally at sites of double strand break repair. J Biol Chem 2010, 285:37630-37640.
-
(2010)
J Biol Chem
, vol.285
, pp. 37630-37640
-
-
Lee, G.E.1
Kim, J.H.2
Taylor, M.3
Muller, M.T.4
-
55
-
-
0343485074
-
Transient depletion of xDnmt1 leads to premature gene activation in Xenopus embryos
-
Stancheva I, Meehan RR. Transient depletion of xDnmt1 leads to premature gene activation in Xenopus embryos. Genes Dev 2000, 14:313-327.
-
(2000)
Genes Dev
, vol.14
, pp. 313-327
-
-
Stancheva, I.1
Meehan, R.R.2
-
56
-
-
43049108039
-
XDnmt1 regulates transcriptional silencing in pre-MBT Xenopus embryos independently of its catalytic function
-
Dunican DS, Ruzov A, Hackett JA, Meehan RR. xDnmt1 regulates transcriptional silencing in pre-MBT Xenopus embryos independently of its catalytic function. Development 2008, 135:1295-1302.
-
(2008)
Development
, vol.135
, pp. 1295-1302
-
-
Dunican, D.S.1
Ruzov, A.2
Hackett, J.A.3
Meehan, R.R.4
-
57
-
-
34247468830
-
The maternal-zygotic transition: death and birth of RNAs
-
Schier AF. The maternal-zygotic transition: death and birth of RNAs. Science 2007, 316:406-407.
-
(2007)
Science
, vol.316
, pp. 406-407
-
-
Schier, A.F.1
-
58
-
-
80051558092
-
Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
-
Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB, Gomez-Skarmeta JL, Stunnenberg HG, et al. Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Res 2011, 21:1313-1327.
-
(2011)
Genome Res
, vol.21
, pp. 1313-1327
-
-
Bogdanovic, O.1
Long, S.W.2
van Heeringen, S.J.3
Brinkman, A.B.4
Gomez-Skarmeta, J.L.5
Stunnenberg, H.G.6
-
59
-
-
77953566957
-
Concise review: isoforms of OCT4 contribute to the confusing diversity in stem cell biology
-
Wang X, Dai J. Concise review: isoforms of OCT4 contribute to the confusing diversity in stem cell biology. Stem Cells 2010, 28:885-893.
-
(2010)
Stem Cells
, vol.28
, pp. 885-893
-
-
Wang, X.1
Dai, J.2
-
60
-
-
81855183655
-
Single-molecule imaging of transcriptionally coupled and uncoupled splicing
-
Vargas DY, Shah K, Batish M, Levandoski M, Sinha S, Marras SA, et al. Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 2011, 147:1054-1065.
-
(2011)
Cell
, vol.147
, pp. 1054-1065
-
-
Vargas, D.Y.1
Shah, K.2
Batish, M.3
Levandoski, M.4
Sinha, S.5
Marras, S.A.6
-
61
-
-
84856120332
-
Understanding the language of Lys36 methylation at histone H3
-
Wagner EJ, Carpenter PB. Understanding the language of Lys36 methylation at histone H3. Nat Rev Mol Cell Biol 2012, 13:115-126.
-
(2012)
Nat Rev Mol Cell Biol
, vol.13
, pp. 115-126
-
-
Wagner, E.J.1
Carpenter, P.B.2
-
62
-
-
78650961149
-
Epigenetics in alternative pre-mRNA splicing
-
Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T. Epigenetics in alternative pre-mRNA splicing. Cell 2011, 144:16-26.
-
(2011)
Cell
, vol.144
, pp. 16-26
-
-
Luco, R.F.1
Allo, M.2
Schor, I.E.3
Kornblihtt, A.R.4
Misteli, T.5
-
63
-
-
79955475464
-
Unravelling the means to an end: RNA polymerase II transcription termination
-
Kuehner JN, Pearson EL, Moore C. Unravelling the means to an end: RNA polymerase II transcription termination. Nat Rev Mol Cell Biol 2011, 12:283-294.
-
(2011)
Nat Rev Mol Cell Biol
, vol.12
, pp. 283-294
-
-
Kuehner, J.N.1
Pearson, E.L.2
Moore, C.3
-
64
-
-
77953284100
-
Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation
-
Millevoi S, Vagner S. Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation. Nucleic Acids Res 2010, 38:2757-2774.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 2757-2774
-
-
Millevoi, S.1
Vagner, S.2
-
65
-
-
80052447253
-
Ending the message: poly(A) signals then and now
-
Proudfoot NJ. Ending the message: poly(A) signals then and now. Genes Dev 2011, 25:1770-1782.
-
(2011)
Genes Dev
, vol.25
, pp. 1770-1782
-
-
Proudfoot, N.J.1
-
66
-
-
80053413109
-
Transcriptional activity regulates alternative cleavage and polyadenylation
-
Ji Z, Luo W, Li W, Hoque M, Pan Z, Zhao Y, et al. Transcriptional activity regulates alternative cleavage and polyadenylation. Mol Syst Biol 2011, 7:534.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 534
-
-
Ji, Z.1
Luo, W.2
Li, W.3
Hoque, M.4
Pan, Z.5
Zhao, Y.6
-
67
-
-
80053137344
-
Neural-specific elongation of 3' UTRs during Drosophila development
-
Hilgers V, Perry MW, Hendrix D, Stark A, Levine M, Haley B. Neural-specific elongation of 3' UTRs during Drosophila development. Proc Natl Acad Sci U S A 2011, 108:15864-15869.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 15864-15869
-
-
Hilgers, V.1
Perry, M.W.2
Hendrix, D.3
Stark, A.4
Levine, M.5
Haley, B.6
-
68
-
-
66049104920
-
Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development
-
Ji Z, Lee JY, Pan Z, Jiang B, Tian B. Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A 2009, 106:7028-7033.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 7028-7033
-
-
Ji, Z.1
Lee, J.Y.2
Pan, Z.3
Jiang, B.4
Tian, B.5
-
69
-
-
84867163995
-
Extensive alternative polyadenylation during zebrafish development
-
Ulitsky I, Shkumatava A, Jan C, Subtelny AO, Koppstein D, Bell G, et al. Extensive alternative polyadenylation during zebrafish development. Genome Res 2012,
-
(2012)
Genome Res
-
-
Ulitsky, I.1
Shkumatava, A.2
Jan, C.3
Subtelny, A.O.4
Koppstein, D.5
Bell, G.6
-
70
-
-
67649109141
-
Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining
-
Turi A, Loglisci C, Salvemini E, Grillo G, Malerba D, D'Elia D. Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining. BMC Bioinformatics 2009, 10(Suppl 6):S25.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 6
-
-
Turi, A.1
Loglisci, C.2
Salvemini, E.3
Grillo, G.4
Malerba, D.5
D'Elia, D.6
-
71
-
-
0031767514
-
The K box, a conserved 3' UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts
-
Lai EC, Burks C, Posakony JW. The K box, a conserved 3' UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. Development 1998, 125:4077-4088.
-
(1998)
Development
, vol.125
, pp. 4077-4088
-
-
Lai, E.C.1
Burks, C.2
Posakony, J.W.3
-
72
-
-
23944473342
-
Structural and functional diversity generated by alternative mRNA splicing
-
Stetefeld J, Ruegg MA. Structural and functional diversity generated by alternative mRNA splicing. Trends Biochem Sci 2005, 30:515-521.
-
(2005)
Trends Biochem Sci
, vol.30
, pp. 515-521
-
-
Stetefeld, J.1
Ruegg, M.A.2
-
73
-
-
0034696822
-
MAGI-1 interacts with beta-catenin and is associated with cell-cell adhesion structures
-
Dobrosotskaya IY, James GL. MAGI-1 interacts with beta-catenin and is associated with cell-cell adhesion structures. Biochem Biophys Res Commun 2000, 270:903-909.
-
(2000)
Biochem Biophys Res Commun
, vol.270
, pp. 903-909
-
-
Dobrosotskaya, I.Y.1
James, G.L.2
-
74
-
-
84860718888
-
Beta-Catenin 1 and beta-catenin 2 play similar and distinct roles in left-right asymmetric development of zebrafish embryos
-
Zhang M, Zhang J, Lin SC, Meng A. beta-Catenin 1 and beta-catenin 2 play similar and distinct roles in left-right asymmetric development of zebrafish embryos. Development 2012, 139:2009-2019.
-
(2012)
Development
, vol.139
, pp. 2009-2019
-
-
Zhang, M.1
Zhang, J.2
Lin, S.C.3
Meng, A.4
-
75
-
-
0031460029
-
PDZ domain proteins: scaffolds for signaling complexes
-
Ranganathan R, Ross EM. PDZ domain proteins: scaffolds for signaling complexes. Curr Biol 1997, 7:R770-R773.
-
(1997)
Curr Biol
, vol.7
-
-
Ranganathan, R.1
Ross, E.M.2
-
76
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
77
-
-
77951770756
-
BEDTools: a flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
78
-
-
2642574503
-
-
Vienna, Austria: R foundation for statistical computing, ISBN 3-900051-07-0, URL, R Core Team. R
-
R Core Team. R A language and environment for statistical computing 2012, Vienna, Austria: R foundation for statistical computing, ISBN 3-900051-07-0, URLhttp://www.R-project.org/, R Core Team. R.
-
(2012)
A language and environment for statistical computing
-
-
-
79
-
-
78651271733
-
Integrative genomics viewer
-
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol 2011, 29:24-26.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
Thorvaldsdottir, H.2
Winckler, W.3
Guttman, M.4
Lander, E.S.5
Getz, G.6
-
80
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012, 7:562-578.
-
(2012)
Nat Protoc
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
-
81
-
-
0034201441
-
EMBOSS: the European Molecular Biology Open Software Suite
-
Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16:276-277.
-
(2000)
Trends Genet
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
82
-
-
75549083389
-
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
-
Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, et al. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 2010, 38:D75-D80.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Grillo, G.1
Turi, A.2
Licciulli, F.3
Mignone, F.4
Liuni, S.5
Banfi, S.6
-
83
-
-
73949158469
-
Fish'n ChIPs: chromatin immunoprecipitation in the zebrafish embryo
-
Lindeman LC, Vogt-Kielland LT, Alestrom P, Collas P. Fish'n ChIPs: chromatin immunoprecipitation in the zebrafish embryo. Methods Mol Biol 2009, 567:75-86.
-
(2009)
Methods Mol Biol
, vol.567
, pp. 75-86
-
-
Lindeman, L.C.1
Vogt-Kielland, L.T.2
Alestrom, P.3
Collas, P.4
-
84
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
85
-
-
77952857912
-
A signal-noise model for significance analysis of ChIP-seq with negative control
-
Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, et al. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics 2010, 26:1199-1204.
-
(2010)
Bioinformatics
, vol.26
, pp. 1199-1204
-
-
Xu, H.1
Handoko, L.2
Wei, X.3
Ye, C.4
Sheng, J.5
Wei, C.L.6
-
86
-
-
77954205689
-
Repitools: an R package for the analysis of enrichment-based epigenomic data
-
Statham AL, Strbenac D, Coolen MW, Stirzaker C, Clark SJ, Robinson MD. Repitools: an R package for the analysis of enrichment-based epigenomic data. Bioinformatics 2010, 26:1662-1663.
-
(2010)
Bioinformatics
, vol.26
, pp. 1662-1663
-
-
Statham, A.L.1
Strbenac, D.2
Coolen, M.W.3
Stirzaker, C.4
Clark, S.J.5
Robinson, M.D.6
-
87
-
-
77951947707
-
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
-
Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS, et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 2010, 11:237.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 237
-
-
Zhu, L.J.1
Gazin, C.2
Lawson, N.D.3
Pages, H.4
Lin, S.M.5
Lapointe, D.S.6
-
88
-
-
80055112955
-
RNA isolation from embryonic zebrafish and cDNA synthesis for gene expression analysis
-
Peterson SM, Freeman JL. RNA isolation from embryonic zebrafish and cDNA synthesis for gene expression analysis. J Vis Exp 2009,
-
(2009)
J Vis Exp
-
-
Peterson, S.M.1
Freeman, J.L.2
|