-
1
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
DOI 10.1038/nature05874, PII NATURE05874
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816. (Pubitemid 46920138)
-
(2007)
Nature
, vol.447
, Issue.7146
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
Margulies, E.H.6
Weng, Z.7
Snyder, M.8
Dermitzakis, E.T.9
Thurman, R.E.10
Kuehn, M.S.11
Taylor, C.M.12
Neph, S.13
Koch, C.M.14
Asthana, S.15
Malhotra, A.16
Adzhubei, I.17
Greenbaum, J.A.18
Andrews, R.M.19
Flicek, P.20
Boyle, P.J.21
Cao, H.22
Carter, N.P.23
Clelland, G.K.24
Davis, S.25
Day, N.26
Dhami, P.27
Dillon, S.C.28
Dorschner, M.O.29
Fiegler, H.30
Giresi, P.G.31
Goldy, J.32
Hawrylycz, M.33
Haydock, A.34
Humbert, R.35
James, K.D.36
Johnson, B.E.37
Johnson, E.M.38
Frum, T.T.39
Rosenzweig, E.R.40
Karnani, N.41
Lee, K.42
Lefebvre, G.C.43
Navas, P.A.44
Neri, F.45
Parker, S.C.J.46
Sabo, P.J.47
Sandstrom, R.48
Shafer, A.49
Vetrie, D.50
Weaver, M.51
Wilcox, S.52
Yu, M.53
Collins, F.S.54
Dekker, J.55
Lieb, J.D.56
Tullius, T.D.57
Crawford, G.E.58
Sunyaev, S.59
Noble, W.S.60
Dunham, I.61
Denoeud, F.62
Reymond, A.63
Kapranov, P.64
Rozowsky, J.65
Zheng, D.66
Castelo, R.67
Frankish, A.68
Harrow, J.69
Ghosh, S.70
Sandelin, A.71
Hofacker, I.L.72
Baertsch, R.73
Keefe, D.74
Dike, S.75
Cheng, J.76
Hirsch, H.A.77
Sekinger, E.A.78
Lagarde, J.79
Abril, J.F.80
Shahab, A.81
Flamm, C.82
Fried, C.83
Hackermuller, J.84
Hertel, J.85
Lindemeyer, M.86
Missal, K.87
Tanzer, A.88
Washietl, S.89
Korbel, J.90
Emanuelsson, O.91
Pedersen, J.S.92
Holroyd, N.93
Taylor, R.94
Swarbreck, D.95
Matthews, N.96
Dickson, M.C.97
Thomas, D.J.98
Weirauch, M.T.99
more..
-
2
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, et al. (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
-
3
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, et al. (2012) Landscape of transcription in human cells. Nature 489: 101-108.
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
Dobin, A.4
Lassmann, T.5
-
4
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. (2005) The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
-
6
-
-
60149099385
-
Evolution and functions of long noncoding RNAs
-
Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136: 629-641.
-
(2009)
Cell
, vol.136
, pp. 629-641
-
-
Ponting, C.P.1
Oliver, P.L.2
Reik, W.3
-
7
-
-
84867291885
-
Long noncoding RNA: Its physiological and pathological roles
-
Yan B, Wang Z (2012) Long noncoding RNA: its physiological and pathological roles. DNA and Cell Biology 31 Suppl 1: S34-41.
-
(2012)
DNA and Cell Biology
, vol.31
, Issue.SUPPL. 1
-
-
Yan, B.1
Wang, Z.2
-
8
-
-
0142104045
-
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
-
DOI 10.1038/nature01266
-
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573. (Pubitemid 35477049)
-
(2002)
Nature
, vol.420
, Issue.6915
, pp. 563-573
-
-
Hayashizaki, Y.1
Okazaki, Y.2
Furuno, M.3
Kasukawa, T.4
Adachi, J.5
Bono, H.6
Kondo, S.7
Nikaido, I.8
Osato, N.9
Saito, R.10
Suzuki, H.11
Yamanaka, I.12
Kiyosawa, H.13
Yagi, K.14
Tomaru, Y.15
Hasegawa, Y.16
Nogami, A.17
Schonbach, C.18
Gojobori, T.19
Baldarelli, R.20
Hill, D.P.21
Bult, C.22
Hume, D.A.23
Quackenbush, J.24
Schriml, L.M.25
Kanapin, A.26
Matsuda, H.27
Batalov, S.28
Beisel, K.W.29
Blake, J.A.30
Bradt, D.31
Brusic, V.32
Chothia, C.33
Corbani, L.E.34
Cousins, S.35
Dalla, E.36
Dragani, T.A.37
Fletcher, C.F.38
Forrest, A.39
Frazer, K.S.40
Gaasterland, T.41
Gariboldi, M.42
Gissi, C.43
Godzik, A.44
Gough, J.45
Grimmond, S.46
Gustincich, S.47
Hirokawa, N.48
Jackson, I.J.49
Jarvis, E.D.50
Kanai, A.51
Kawaji, H.52
Kawasawa, Y.53
Kedzierski, R.M.54
King, B.L.55
Konagaya, A.56
Kurochkin, I.V.57
Lee, Y.58
Lenhard, B.59
Lyons, P.A.60
Maglott, D.R.61
Maltais, L.62
Marchionni, L.63
McKenzie, L.64
Miki, H.65
Nagashima, T.66
Numata, K.67
Okido, T.68
Pavan, W.J.69
Pertea, G.70
Pesole, G.71
Petrovsky, N.72
Pillai, R.73
Pontius, J.U.74
Qi, D.75
Ramachandran, S.76
Ravasi, T.77
Reed, J.C.78
Reed, D.J.79
Reid, J.80
Ring, B.Z.81
Ringwald, M.82
Sandelin, A.83
Schneider, C.84
Semple, C.A.M.85
Setou, M.86
Shimada, K.87
Sultana, R.88
Takenaka, Y.89
Taylor, M.S.90
Teasdale, R.D.91
Tomita, M.92
Verardo, R.93
Wagner, L.94
Wahlested, C.95
Wang, Y.96
Watanabe, Y.97
Wells, C.98
Wilming, L.G.99
more..
-
9
-
-
30044434769
-
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
-
DOI 10.1101/gr.4200206
-
Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M, et al. (2006) Experimental validation of the regulated expression of large numbers of noncoding RNAs from the mouse genome. Genome Research 16: 11-19. (Pubitemid 43048929)
-
(2006)
Genome Research
, vol.16
, Issue.1
, pp. 11-19
-
-
Ravasi, T.1
Suzuki, H.2
Pang, K.C.3
Katayama, S.4
Furuno, M.5
Okunishi, R.6
Fukuda, S.7
Ru, K.8
Frith, M.C.9
Gongora, M.M.10
Grimmond, S.M.11
Hume, D.A.12
Hayashizaki, Y.13
Mattick, J.S.14
-
10
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman M, Amit I, Garber M, French C, Lin MF, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
Amit, I.2
Garber, M.3
French, C.4
Lin, M.F.5
-
11
-
-
84856987685
-
Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae
-
McKinlay A, Araya CL, Fields S (2011) Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae. G3 1: 549-558.
-
(2011)
G3
, vol.1
, pp. 549-558
-
-
McKinlay, A.1
Araya, C.L.2
Fields, S.3
-
12
-
-
84879150139
-
Identification and function of long non-coding RNAs
-
Young RS, Ponting CP (2013) Identification and function of long non-coding RNAs. Essays in Biochemistry 54: 113-126.
-
(2013)
Essays in Biochemistry
, vol.54
, pp. 113-126
-
-
Young, R.S.1
Ponting, C.P.2
-
13
-
-
33749066576
-
Overlapping transcripts, double-stranded RNA and antisense regulation: A genomic perspective
-
DOI 10.1007/s00018-006-6070-2
-
Munroe SH, Zhu J (2006) Overlapping transcripts, double-stranded RNA and antisense regulation: a genomic perspective. Cellular and Molecular Life Sciences: CMLS 63: 2102-2118. (Pubitemid 44465685)
-
(2006)
Cellular and Molecular Life Sciences
, vol.63
, Issue.18
, pp. 2102-2118
-
-
Munroe, S.H.1
Zhu, J.2
-
15
-
-
79957523447
-
Natural antisense transcript: A concomitant engagement with protein-coding transcript
-
Li K, Ramchandran R (2010) Natural antisense transcript: a concomitant engagement with protein-coding transcript. Oncotarget 1: 447-452.
-
(2010)
Oncotarget
, vol.1
, pp. 447-452
-
-
Li, K.1
Ramchandran, R.2
-
16
-
-
33646473694
-
Complex Loci in human and mouse genomes
-
Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, et al. (2006) Complex Loci in human and mouse genomes. PLoS Genetics 2: e47.
-
(2006)
PLoS Genetics
, vol.2
-
-
Engstrom, P.G.1
Suzuki, H.2
Ninomiya, N.3
Akalin, A.4
Sessa, L.5
-
17
-
-
24644472515
-
Antisense transcription in the mammalian transcriptome
-
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, et al. (2005) Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566.
-
(2005)
Science
, vol.309
, pp. 1564-1566
-
-
Katayama, S.1
Tomaru, Y.2
Kasukawa, T.3
Waki, K.4
Nakanishi, M.5
-
18
-
-
24644448635
-
Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana
-
Wang XJ, Gaasterland T, Chua NH (2005) Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biology 6: R30.
-
(2005)
Genome Biology
, vol.6
-
-
Wang, X.J.1
Gaasterland, T.2
Chua, N.H.3
-
20
-
-
33645785104
-
A high-resolution map of transcription in the yeast genome
-
David L, Huber W, Granovskaia M, Toedling J, Palm CJ, et al. (2006) A high-resolution map of transcription in the yeast genome. Proceedings of the National Academy of Sciences of the United States of America 103: 5320-5325.
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, pp. 5320-5325
-
-
David, L.1
Huber, W.2
Granovskaia, M.3
Toedling, J.4
Palm, C.J.5
-
21
-
-
77955975125
-
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
-
Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, et al. (2010) Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biology 11: R87.
-
(2010)
Genome Biology
, vol.11
-
-
Yassour, M.1
Pfiffner, J.2
Levin, J.Z.3
Adiconis, X.4
Gnirke, A.5
-
22
-
-
84879283199
-
Pervasive antisense transcription is evolutionarily conserved in budding yeast
-
Goodman AJ, Daugharthy ER, Kim J (2013) Pervasive antisense transcription is evolutionarily conserved in budding yeast. Molecular Biology and Evolution 30: 409-421.
-
(2013)
Molecular Biology and Evolution
, vol.30
, pp. 409-421
-
-
Goodman, A.J.1
Daugharthy, E.R.2
Kim, J.3
-
23
-
-
79956319465
-
Comparative functional genomics of the fission yeasts
-
Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, et al. (2011) Comparative functional genomics of the fission yeasts. Science 332: 930-936.
-
(2011)
Science
, vol.332
, pp. 930-936
-
-
Rhind, N.1
Chen, Z.2
Yassour, M.3
Thompson, D.A.4
Haas, B.J.5
-
24
-
-
78650861843
-
The prevalence and regulation of antisense transcripts in Schizosaccharomyces pombe
-
Ni T, Tu K, Wang Z, Song S, Wu H, et al. (2010) The prevalence and regulation of antisense transcripts in Schizosaccharomyces pombe. PloS One 5: e15271.
-
(2010)
PloS One
, vol.5
-
-
Ni, T.1
Tu, K.2
Wang, Z.3
Song, S.4
Wu, H.5
-
25
-
-
55349096760
-
The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus
-
Smith CA, Robertson D, Yates B, Nielsen DM, Brown D, et al. (2008) The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. Current Genetics 54: 241-269.
-
(2008)
Current Genetics
, vol.54
, pp. 241-269
-
-
Smith, C.A.1
Robertson, D.2
Yates, B.3
Nielsen, D.M.4
Brown, D.5
-
26
-
-
0037464589
-
The genome sequence of the filamentous fungus Neurospora crassa
-
DOI 10.1038/nature01554
-
Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868. (Pubitemid 36520034)
-
(2003)
Nature
, vol.422
, Issue.6934
, pp. 859-868
-
-
Galagan, J.E.1
Calvo, S.E.2
Borkovich, K.A.3
Selker, E.U.4
Read, N.O.5
Jaffe, D.6
FitzHugh, W.7
Ma, L.-J.8
Smirnov, S.9
Purcell, S.10
Rehman, B.11
Elkins, T.12
Engels, R.13
Wang, S.14
Nielsen, C.B.15
Butler, J.16
Endrizzi, M.17
Qui, D.18
Ianakiev, P.19
Bell-Pedersen, D.20
Nelson, M.A.21
Werner-Washburne, M.22
Selitrennikoff, C.P.23
Kinsey, J.A.24
Braun, E.L.25
Zelter, A.26
Schulte, U.27
Kothe, G.O.28
Jedd, G.29
Mewes, W.30
Staben, C.31
Marcotte, E.32
Greenberg, D.33
Roy, A.34
Foley, K.35
Naylor, J.36
Stange-Thomann, N.37
Barrett, R.38
Gnerre, S.39
Kamal, M.40
Kamvysselis, M.41
Mauceli, E.42
Bielke, C.43
Rudd, S.44
Frishman, D.45
Krystofova, S.46
Rasmussen, C.47
Metzenberg, R.L.48
Perkins, D.D.49
Kroken, S.50
Cogoni, C.51
Macino, G.52
Catcheside, D.53
Li, W.54
Pratt, R.J.55
Osmani, S.A.56
DeSouza, C.P.C.57
Glass, L.58
Orbach, M.J.59
Berglund, J.A.60
Voelker, R.61
Yarden, O.62
Plamann, M.63
Seiler, S.64
Dunlap, J.65
Radford, A.66
Aramayo, R.67
Natvig, D.O.68
Alex, L.A.69
Mannhaupt, G.70
Ebbole, D.J.71
Freitag, M.72
Paulsen, I.73
Sachs, M.S.74
Lander, E.S.75
Nusbaum, C.76
Birren, B.77
more..
-
27
-
-
67849083041
-
Tools for fungal proteomics: Multifunctional Neurospora vectors for gene replacement, protein expression and protein purification
-
Honda S, Selker EU (2009) Tools for fungal proteomics: multifunctional Neurospora vectors for gene replacement, protein expression and protein purification. Genetics 182: 11-23.
-
(2009)
Genetics
, vol.182
, pp. 11-23
-
-
Honda, S.1
Selker, E.U.2
-
28
-
-
84884661084
-
Genome wide association identifies novel loci involved in fungal communication
-
Palma-Guerrero J, Hall CR, Kowbel D, Welch J, Taylor JW, et al. (2013) Genome wide association identifies novel loci involved in fungal communication. PLoS Genetics 9: e1003669.
-
(2013)
PLoS Genetics
, vol.9
-
-
Palma-Guerrero, J.1
Hall, C.R.2
Kowbel, D.3
Welch, J.4
Taylor, J.W.5
-
29
-
-
33847665978
-
Enabling a community to dissect an organism: Overview of the Neurospora functional genomics project
-
Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, et al. (2007) Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Advances in Genetics 57: 49-96.
-
(2007)
Advances in Genetics
, vol.57
, pp. 49-96
-
-
Dunlap, J.C.1
Borkovich, K.A.2
Henn, M.R.3
Turner, G.E.4
Sachs, M.S.5
-
31
-
-
0036255812
-
Timeline: Neurospora: A model of model microbes
-
Davis RH, Perkins DD (2002) Timeline: Neurospora: a model of model microbes. Nature Reviews Genetics 3: 397-403.
-
(2002)
Nature Reviews Genetics
, vol.3
, pp. 397-403
-
-
Davis, R.H.1
Perkins, D.D.2
-
32
-
-
0242669950
-
Role for antisense RNA in regulating circadian clock function in Neurospora crassa
-
DOI 10.1038/nature01427
-
Kramer C, Loros JJ, Dunlap JC, Crosthwaite SK (2003) Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature 421: 948-952. (Pubitemid 36288026)
-
(2003)
Nature
, vol.421
, Issue.6926
, pp. 948-952
-
-
Kramer, C.1
Loros, J.J.2
Dunlap, J.C.3
Crosthwaite, S.K.4
-
33
-
-
79960953992
-
CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency
-
Belden WJ, Lewis ZA, Selker EU, Loros JJ, Dunlap JC (2011) CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency. PLoS Genetics 7: e1002166.
-
(2011)
PLoS Genetics
, vol.7
-
-
Belden, W.J.1
Lewis, Z.A.2
Selker, E.U.3
Loros, J.J.4
Dunlap, J.C.5
-
34
-
-
0027994487
-
Circadian clock locus frequency: Protein encoded by a single open reading frame defines period length and temperature compensation
-
DOI 10.1073/pnas.91.16.7683
-
Aronson BD, Johnson KA, Dunlap JC (1994) Circadian clock locus frequency: protein encoded by a single open reading frame defines period length and temperature compensation. Proceedings of the National Academy of Sciences of the United States of America 91: 7683-7687. (Pubitemid 24238249)
-
(1994)
Proceedings of the National Academy of Sciences of the United States of America
, vol.91
, Issue.16
, pp. 7683-7687
-
-
Aronson, B.D.1
Johnson, K.A.2
Dunlap, J.C.3
-
35
-
-
24944528366
-
Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes
-
DOI 10.1093/nar/gki804
-
Steigele S, Nieselt K (2005) Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes. Nucleic Acids Research 33: 5034-5044. (Pubitemid 41487811)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.16
, pp. 5034-5044
-
-
Steigele, S.1
Nieselt, K.2
-
36
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
37
-
-
34547582418
-
CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine
-
Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, et al. (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Research 35: W345-349.
-
(2007)
Nucleic Acids Research
, vol.35
-
-
Kong, L.1
Zhang, Y.2
Ye, Z.Q.3
Liu, X.Q.4
Zhao, S.Q.5
-
38
-
-
84864098110
-
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome
-
Young RS, Marques AC, Tibbit C, Haerty W, Bassett AR, et al. (2012) Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biology and Evolution 4: 427-442.
-
(2012)
Genome Biology and Evolution
, vol.4
, pp. 427-442
-
-
Young, R.S.1
Marques, A.C.2
Tibbit, C.3
Haerty, W.4
Bassett, A.R.5
-
40
-
-
9144257282
-
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
-
DOI 10.1093/nar/gkh894
-
Ruepp A, Zollner A, Maier D, Albermann K, Hani J, et al. (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Research 32: 5539-5545. (Pubitemid 39545671)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.18
, pp. 5539-5545
-
-
Ruepp, A.1
Zollner, A.2
Maier, D.3
Albermann, K.4
Hani, J.5
Mokrejs, M.6
Tetko, I.7
Guldener, U.8
Mannhaupt, G.9
Munsterkotter, M.10
Mewes, H.W.11
-
41
-
-
84859335229
-
A preinitiation complex at the 39-end of genes drives antisense transcription independent of divergent sense transcription
-
Murray SC, Serra Barros A, Brown DA, Dudek P, Ayling J, et al. (2012) A preinitiation complex at the 39-end of genes drives antisense transcription independent of divergent sense transcription. Nucleic Acids Research 40: 2432-2444.
-
(2012)
Nucleic Acids Research
, vol.40
, pp. 2432-2444
-
-
Murray, S.C.1
Serra Barros, A.2
Brown, D.A.3
Dudek, P.4
Ayling, J.5
-
43
-
-
34250743796
-
Transcriptional interferences in cis natural antisense transcripts of humans and mice
-
DOI 10.1534/genetics.106.069484
-
Osato N, Suzuki Y, Ikeo K, Gojobori T (2007) Transcriptional interferences in cis natural antisense transcripts of humans and mice. Genetics 176: 1299-1306. (Pubitemid 46961122)
-
(2007)
Genetics
, vol.176
, Issue.2
, pp. 1299-1306
-
-
Osato, N.1
Suzuki, Y.2
Ikeo, K.3
Gojobori, T.4
-
45
-
-
26944454054
-
Evidence for a preferential targeting of 39-UTRs by cis-encoded natural antisense transcripts
-
DOI 10.1093/nar/gki852
-
Sun M, Hurst LD, Carmichael GG, Chen J (2005) Evidence for a preferential targeting of 39-UTRs by cis-encoded natural antisense transcripts. Nucleic Acids Research 33: 5533-5543. (Pubitemid 41548819)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.17
, pp. 5533-5543
-
-
Sun, M.1
Hurst, L.D.2
Carmichael, G.G.3
Chen, J.4
-
46
-
-
24644488895
-
Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation
-
Jen CH, Michalopoulos I, Westhead DR, Meyer P (2005) Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biology 6: R51.
-
(2005)
Genome Biology
, vol.6
-
-
Jen, C.H.1
Michalopoulos, I.2
Westhead, D.R.3
Meyer, P.4
-
47
-
-
77953757597
-
An exonic splicing enhancer within a bidirectional coding sequence regulates alternative splicing of an antisense mRNA
-
Salato VK, Rediske NW, Zhang C, Hastings ML, Munroe SH (2010) An exonic splicing enhancer within a bidirectional coding sequence regulates alternative splicing of an antisense mRNA. RNA Biology 7: 179-190.
-
(2010)
RNA Biology
, vol.7
, pp. 179-190
-
-
Salato, V.K.1
Rediske, N.W.2
Zhang, C.3
Hastings, M.L.4
Munroe, S.H.5
-
48
-
-
77950929337
-
Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi
-
Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, et al. (2010) Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Molecular Cell 38: 803-814.
-
(2010)
Molecular Cell
, vol.38
, pp. 803-814
-
-
Lee, H.C.1
Li, L.2
Gu, W.3
Xue, Z.4
Crosthwaite, S.K.5
-
49
-
-
84884683575
-
Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci
-
Dang Y, Li L, Guo W, Xue Z, Liu Y (2013) Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci. PLoS genetics 9: e1003761.
-
(2013)
PLoS Genetics
, vol.9
-
-
Dang, Y.1
Li, L.2
Guo, W.3
Xue, Z.4
Liu, Y.5
-
51
-
-
60549114880
-
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
-
Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz LM, et al. (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457: 1038-1042.
-
(2009)
Nature
, vol.457
, pp. 1038-1042
-
-
Neil, H.1
Malabat, C.2
D'Aubenton-Carafa, Y.3
Xu, Z.4
Steinmetz, L.M.5
-
52
-
-
57849140661
-
Divergent transcription from active promoters
-
Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, et al. (2008) Divergent transcription from active promoters. Science 322: 1849-1851.
-
(2008)
Science
, vol.322
, pp. 1849-1851
-
-
Seila, A.C.1
Calabrese, J.M.2
Levine, S.S.3
Yeo, G.W.4
Rahl, P.B.5
-
53
-
-
77951964897
-
Filtering error from SOLiD Output
-
Sasson A, Michael TP (2010) Filtering error from SOLiD Output. Bioinformatics 26: 849-850.
-
(2010)
Bioinformatics
, vol.26
, pp. 849-850
-
-
Sasson, A.1
Michael, T.P.2
-
54
-
-
78651271733
-
Integrative genomics viewer
-
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative genomics viewer. Nature Biotechnology 29: 24-26.
-
(2011)
Nature Biotechnology
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
Thorvaldsdottir, H.2
Winckler, W.3
Guttman, M.4
Lander, E.S.5
-
55
-
-
84874266637
-
Rfam 11.0: 10 Years of RNA families
-
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, et al. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Research 41: D226-232.
-
(2013)
Nucleic Acids Research
, vol.41
-
-
Burge, S.W.1
Daub, J.2
Eberhardt, R.3
Tate, J.4
Barquist, L.5
-
56
-
-
84890037468
-
Infernal 1.1: 100-Fold faster RNA homology searches
-
Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29: 2933-2935.
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
57
-
-
0030854739
-
tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
DOI 10.1093/nar/25.5.955
-
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25: 955-964. (Pubitemid 27298263)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.5
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
58
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
59
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 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
-
60
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biology 11: R106.
-
(2010)
Genome Biology
, vol.11
-
-
Anders, S.1
Huber, W.2
-
61
-
-
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, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28: 511-515.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
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