-
1
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
ENCODE Project Consortium; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute PMID:17571346
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, et al.; ENCODE Project Consortium; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799-816; PMID:17571346; http://dx.doi. org/10.1038/nature05874.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigó, R.4
Gingeras, T.R.5
Margulies, E.H.6
-
2
-
-
34250160256
-
RNA maps reveal new RNA classes and a possible function for pervasive transcription
-
PMID:17510325
-
Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007; 316:1484-8; PMID:17510325; http://dx.doi.org/10. 1126/science.1138341.
-
(2007)
Science
, vol.316
, pp. 1484-1488
-
-
Kapranov, P.1
Cheng, J.2
Dike, S.3
Nix, D.A.4
Duttagupta, R.5
Willingham, A.T.6
-
3
-
-
47649124124
-
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
-
PMID:18599741
-
Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008; 321:956-60; PMID:18599741; http://dx.doi.org/10.1126/science.1160342.
-
(2008)
Science
, vol.321
, pp. 956-960
-
-
Sultan, M.1
Schulz, M.H.2
Richard, H.3
Magen, A.4
Klingenhoff, A.5
Scherf, M.6
-
4
-
-
68249102779
-
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi
-
PMID:19609351
-
Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, et al. A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet 2009; 5:1000569; PMID:19609351; http://dx.doi.org/10.1371/journal. pgen.1000569.
-
(2009)
PLoS Genet
, vol.5
, pp. 1000569
-
-
Perkins, T.T.1
Kingsley, R.A.2
Fookes, M.C.3
Gardner, P.P.4
James, K.D.5
Yu, L.6
-
5
-
-
84874758856
-
-
http://www.ebi.ac.uk/~zerbino/oases/
-
-
-
-
6
-
-
67649464356
-
Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis
-
PMID:19454017
-
Hahn DA, Ragland GJ, Shoemaker DD, Denlinger DL. Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis. BMC Genomics 2009; 10:234; PMID:19454017; http://dx.doi.org/10. 1186/1471-2164-10-234.
-
(2009)
BMC Genomics
, vol.10
, pp. 234
-
-
Hahn, D.A.1
Ragland, G.J.2
Shoemaker, D.D.3
Denlinger, D.L.4
-
7
-
-
41149167170
-
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
-
PMID:18266620
-
Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, et al. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 2008; 17:1636-47; http:// dx.doi.org/10.1111/j.1365- 294X.2008.03666.x; PMID:18266620.
-
(2008)
Mol Ecol
, vol.17
, pp. 1636-1647
-
-
Vera, J.C.1
Wheat, C.W.2
Fescemyer, H.W.3
Frilander, M.J.4
Crawford, D.L.5
Hanski, I.6
-
8
-
-
78649294100
-
Optimization of de novo transcriptome assembly from next-generation sequencing data
-
PMID:20693479
-
Surget-Groba Y, Montoya-Burgos JI. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res 2010; 20:1432- 40; PMID:20693479; http://dx.doi.org/10.1101/gr.103846.109.
-
(2010)
Genome Res
, vol.20
, pp. 1432-1440
-
-
Surget-Groba, Y.1
Montoya-Burgos, J.I.2
-
9
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
PMID:19015660
-
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009; 10:57-63; PMID:19015660; http://dx.doi. org/10.1038/nrg2484.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
10
-
-
69249217649
-
Regulatory roles of natural antisense transcripts
-
PMID:19638999
-
Faghihi MA, Wahlestedt C. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 2009; 10:637-43; PMID:19638999; http://dx.doi. org/10.1038/nrm2738.
-
(2009)
Nat Rev Mol Cell Biol
, vol.10
, pp. 637-643
-
-
Faghihi, M.A.1
Wahlestedt, C.2
-
11
-
-
74949084336
-
Genome-wide mapping of alternative splicing in Arabidopsis thaliana
-
PMID:19858364
-
Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 2010; 20:45-58; PMID:19858364; http://dx.doi. org/10.1101/gr.093302.109.
-
(2010)
Genome Res
, vol.20
, pp. 45-58
-
-
Filichkin, S.A.1
Priest, H.D.2
Givan, S.A.3
Shen, R.4
Bryant, D.W.5
Fox, S.E.6
-
12
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
PMID:18978789
-
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; 40:1413-5; PMID:18978789; http:// dx.doi.org/10.1038/ng.259.
-
(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
-
13
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
PMID:18978772
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008; 456:470-6; PMID:18978772; http://dx.doi.org/10.1038/nature07509.
-
(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
-
14
-
-
0034625260
-
Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity
-
PMID:10892653
-
Schmucker D, Clemens JC, Shu H, Worby CA, Xiao J, Muda M, et al. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 2000; 101:671-84; PMID:10892653; http:// dx.doi.org/10.1016/ S0092-8674(00)80878-8.
-
(2000)
Cell
, vol.101
, pp. 671-684
-
-
Schmucker, D.1
Clemens, J.C.2
Shu, H.3
Worby, C.A.4
Xiao, J.5
Muda, M.6
-
15
-
-
70350653808
-
Transcriptome analysis by strand-specific sequencing of complementary DNA
-
PMID:19620212
-
Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 2009; 37:123; PMID:19620212; http://dx.doi.org/10.1093/ nar/gkp596.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 123
-
-
Parkhomchuk, D.1
Borodina, T.2
Amstislavskiy, V.3
Banaru, M.4
Hallen, L.5
Krobitsch, S.6
-
16
-
-
77954222910
-
Strand-specific deep sequencing of the transcriptome
-
PMID:20519413
-
Vivancos AP, Güell M, Dohm JC, Serrano L, Himmelbauer H. Strand-specific deep sequencing of the transcriptome. Genome Res 2010; 20:989- 99; PMID:20519413; http://dx.doi.org/10.1101/gr.094318.109.
-
(2010)
Genome Res
, vol.20
, pp. 989-999
-
-
Vivancos, A.P.1
Güell, M.2
Dohm, J.C.3
Serrano, L.4
Himmelbauer, H.5
-
17
-
-
42749087226
-
Highly integrated singlebase resolution maps of the epigenome in Arabidopsis
-
PMID:18423832
-
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, et al. Highly integrated singlebase resolution maps of the epigenome in Arabidopsis. Cell 2008; 133:523-36; PMID:18423832; http:// dx.doi.org/10.1016/j. cell.2008.03.029.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
Gregory, B.D.4
Berry, C.C.5
Millar, A.H.6
-
18
-
-
77956340995
-
Comprehensive comparative analysis of strand-specific RNA sequencing methods
-
PMID:20711195
-
Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 2010; 7:709- 15; PMID:20711195; http://dx.doi.org/10.1038/ nmeth.1491.
-
(2010)
Nat Methods
, vol.7
, pp. 709-715
-
-
Levin, J.Z.1
Yassour, M.2
Adiconis, X.3
Nusbaum, C.4
Thompson, D.A.5
Friedman, N.6
-
19
-
-
77951041162
-
Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs and antisense activity
-
PMID:20190049
-
Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, Lindeberg M, Grills G, et al. Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs and antisense activity. J Bacteriol 2010; 192:2359-72; PMID:20190049; http://dx.doi. org/10.1128/JB.01445-09.
-
(2010)
J Bacteriol
, vol.192
, pp. 2359-2372
-
-
Filiatrault, M.J.1
Stodghill, P.V.2
Bronstein, P.A.3
Moll, S.4
Lindeberg, M.5
Grills, G.6
-
20
-
-
84860389888
-
RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries
-
PMID:21775473
-
Hafner M, Renwick N, Brown M, Mihailović A, Holoch D, Lin C, et al. RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA 2011; 17:1697- 712; PMID:21775473; http://dx.doi.org/10. 1261/ rna.2799511.
-
(2011)
RNA
, vol.17
, pp. 1697-1712
-
-
Hafner, M.1
Renwick, N.2
Brown, M.3
Mihailović, A.4
Holoch, D.5
Lin, C.6
-
21
-
-
56649100471
-
Exact Transcriptome Reconstruction from Short Sequence Reads
-
Lacroix V, Sammeth M, Guigo R, Bergeron A. Exact Transcriptome Reconstruction from Short Sequence Reads. Algorithms in Bioinformatics 2008; 5251:50-63; http://dx.doi.org/10.1007/978-3-540-87361-7-5.
-
(2008)
Algorithms in Bioinformatics
, vol.5251
, pp. 50-63
-
-
Lacroix, V.1
Sammeth, M.2
Guigo, R.3
Bergeron, A.4
-
22
-
-
79951554574
-
Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays
-
PMID:21324185
-
Eichner J, Zeller G, Laubinger S, Rätsch G. Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays. BMC Bioinformatics 2011; 12:55; PMID:21324185; http://dx.doi.org/10.1186/1471-2105-12-55.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 55
-
-
Eichner, J.1
Zeller, G.2
Laubinger, S.3
Rätsch, G.4
-
23
-
-
79551610956
-
Genome-wide analysis of alternative splicing in Caenorhabditis elegans
-
PMID:21177968
-
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; 21:342-8; PMID:21177968; http://dx.doi. org/10.1101/gr.114645.110.
-
(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
-
24
-
-
50849100742
-
Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation
-
PMID:19160512
-
Vigneault F, Sismour AM, Church GM. Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation. Nat Methods 2008; 5:777-9; PMID:19160512; http://dx.doi.org/10.1038/nmeth.1244.
-
(2008)
Nat Methods
, vol.5
, pp. 777-779
-
-
Vigneault, F.1
Sismour, A.M.2
Church, G.M.3
-
25
-
-
67651089508
-
Improved protocols for the illumina genome analyzer sequencing system
-
PMID: 19582764
-
Quail MA, Swerdlow H, Turner DJ. Improved protocols for the illumina genome analyzer sequencing system. Curr Protoc Hum Genet 2009; 18:2; PMID: 19582764; http://dx.doi.org/10.1002/0471142905.hg1802s62.
-
(2009)
Curr Protoc Hum Genet
, vol.18
, pp. 2
-
-
Quail, M.A.1
Swerdlow, H.2
Turner, D.J.3
-
26
-
-
55549089660
-
Accurate whole human genome sequencing using reversible terminator chemistry
-
PMID:18987734
-
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008; 456:53-9; PMID:18987734; http:// dx.doi.org/10.1038/ nature07517.
-
(2008)
Nature
, vol.456
, pp. 53-59
-
-
Bentley, D.R.1
Balasubramanian, S.2
Swerdlow, H.P.3
Smith, G.P.4
Milton, J.5
Brown, C.G.6
-
27
-
-
80053132716
-
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
-
PMID:21874022
-
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 2011; 477:419-23; PMID:21874022; http://dx.doi. org/10.1038/nature10414.
-
(2011)
Nature
, vol.477
, pp. 419-423
-
-
Gan, X.1
Stegle, O.2
Behr, J.3
Steffen, J.G.4
Drewe, P.5
Hildebrand, K.L.6
-
28
-
-
78650689920
-
Noisy splicing drives mRNA isoform diversity in human cells
-
PMID:21151575
-
Pickrell JK, Pai AA, Gilad Y, Pritchard JK. Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet 2010; 6:1001236; PMID:21151575; http://dx.doi.org/10.1371/journal.pgen.1001236.
-
(2010)
PLoS Genet
, vol.6
, pp. 1001236
-
-
Pickrell, J.K.1
Pai, A.A.2
Gilad, Y.3
Pritchard, J.K.4
-
29
-
-
79551602797
-
Multimodal RNA-seq using single-strand, doublestrand and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome
-
PMID:21177965
-
Lamm AT, Stadler MR, Zhang H, Gent JI, Fire AZ. Multimodal RNA-seq using single-strand, doublestrand and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. Genome Res 2011; 21:265-75; PMID:21177965; http://dx.doi.org/10.1101/gr.108845.110.
-
(2011)
Genome Res
, vol.21
, pp. 265-275
-
-
Lamm, A.T.1
Stadler, M.R.2
Zhang, H.3
Gent, J.I.4
Fire, A.Z.5
-
30
-
-
78650410139
-
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
-
modENCODE Consortium. PMID:21177976
-
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, et al.; modENCODE Consortium. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010; 330:1775-87; PMID:21177976; http://dx.doi. org/10.1126/science.1196914.
-
(2010)
Science
, vol.330
, pp. 1775-1787
-
-
Gerstein, M.B.1
Lu, Z.J.2
Van Nostrand, E.L.3
Cheng, C.4
Arshinoff, B.I.5
Liu, T.6
-
31
-
-
26944454054
-
Evidence for a preferential targeting of 3′-UTRs by cis-encoded natural antisense transcripts
-
PMID:16204454
-
Sun M, Hurst LD, Carmichael GG, Chen J. Evidence for a preferential targeting of 3′-UTRs by cis-encoded natural antisense transcripts. Nucleic Acids Res 2005; 33:5533-43; PMID:16204454; http://dx.doi. org/10.1093/nar/ gki852.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5533-5543
-
-
Sun, M.1
Hurst, L.D.2
Carmichael, G.G.3
Chen, J.4
-
32
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
PMID:19056941
-
Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008; 322:1845-8; PMID:19056941; http://dx.doi.org/10.1126/science.1162228.
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
33
-
-
57849140661
-
Divergent transcription from active promoters
-
PMID:19056940
-
Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, et al. Divergent transcription from active promoters. Science 2008; 322:1849-51; PMID:19056940; http://dx.doi.org/10.1126/science.1162253.
-
(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
Flynn, R.A.6
-
34
-
-
33745607884
-
Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity
-
PMID:16769979
-
Sun M, Hurst LD, Carmichael GG, Chen J. Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. Genome Res 2006; 16:922-33; PMID:16769979; http://dx.doi. org/10.1101/gr.5210006.
-
(2006)
Genome Res
, vol.16
, pp. 922-933
-
-
Sun, M.1
Hurst, L.D.2
Carmichael, G.G.3
Chen, J.4
-
35
-
-
77955975125
-
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
-
PMID:20796282
-
Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, et al. Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol 2010; 11:87; PMID:20796282; http://dx.doi. org/10.1186/gb-2010-11-8-r87.
-
(2010)
Genome Biol
, vol.11
, pp. 87
-
-
Yassour, M.1
Pfiffner, J.2
Levin, J.Z.3
Adiconis, X.4
Gnirke, A.5
Nusbaum, C.6
-
36
-
-
33947604744
-
Comparative analysis of cis-encoded antisense RNAs in eukaryotes
-
PMID:17250976
-
Numata K, Okada Y, Saito R, Kiyosawa H, Kanai A, Tomita M. Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene 2007; 392:134-41; PMID:17250976; http://dx.doi.org/10.1016/j. gene.2006.12.005.
-
(2007)
Gene
, vol.392
, pp. 134-141
-
-
Numata, K.1
Okada, Y.2
Saito, R.3
Kiyosawa, H.4
Kanai, A.5
Tomita, M.6
-
37
-
-
33645785104
-
A high-resolution map of transcription in the yeast genome
-
PMID:16569694
-
David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, et al. A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA 2006; 103:5320-5; PMID:16569694; http://dx.doi. org/10.1073/pnas.0601091103.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 5320-5325
-
-
David, L.1
Huber, W.2
Granovskaia, M.3
Toedling, J.4
Palm, C.J.5
Bofkin, L.6
-
38
-
-
70350708134
-
mGene: Accurate SVM-based gene finding with an application to nematode genomes
-
PMID:19564452
-
Schweikert G, Zien A, Zeller G, Behr J, Dieterich C, Ong CS, et al. mGene: accurate SVM-based gene finding with an application to nematode genomes. Genome Res 2009; 19:2133-43; PMID:19564452; http://dx.doi.org/10.1101/gr.090597. 108.
-
(2009)
Genome Res
, vol.19
, pp. 2133-2143
-
-
Schweikert, G.1
Zien, A.2
Zeller, G.3
Behr, J.4
Dieterich, C.5
Ong, C.S.6
-
39
-
-
79551613376
-
A spatial and temporal map of C. elegans gene expression
-
PMID:21177967
-
Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, et al. A spatial and temporal map of C. elegans gene expression. Genome Res 2011; 21:325-41; PMID:21177967; http://dx.doi. org/10.1101/gr.114595.110.
-
(2011)
Genome Res
, vol.21
, pp. 325-341
-
-
Spencer, W.C.1
Zeller, G.2
Watson, J.D.3
Henz, S.R.4
Watkins, K.L.5
McWhirter, R.D.6
-
40
-
-
55449131096
-
Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes
-
PMID:19013275
-
Wierzbicki AT, Haag JR, Pikaard CS. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 2008; 135:635-48; PMID:19013275; http://dx.doi.org/10.1016/ j.cell.2008.09.035.
-
(2008)
Cell
, vol.135
, pp. 635-648
-
-
Wierzbicki, A.T.1
Haag, J.R.2
Pikaard, C.S.3
-
41
-
-
77953699256
-
Deep SAGE analysis of the Caenorhabditis elegans transcriptome
-
PMID:20129939
-
Ruzanov P, Riddle DL. Deep SAGE analysis of the Caenorhabditis elegans transcriptome. Nucleic Acids Res 2010; 38:3252-62; PMID:20129939; http://dx.doi. org/10.1093/nar/gkq035.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 3252-3262
-
-
Ruzanov, P.1
Riddle, D.L.2
-
42
-
-
0034892172
-
Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans
-
PMID:11483575
-
Jones SJ, Riddle DL, Pouzyrev AT, Velculescu VE, Hillier L, Eddy SR, et al. Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res 2001; 11:1346-52; PMID:11483575; http://dx.doi.org/10.1101/ gr.184401.
-
(2001)
Genome Res
, vol.11
, pp. 1346-1352
-
-
Jones, S.J.1
Riddle, D.L.2
Pouzyrev, A.T.3
Velculescu, V.E.4
Hillier, L.5
Eddy, S.R.6
-
43
-
-
84874758446
-
-
http://www.sanger.ac.uk/research/projects/vertebrategenome/havana
-
ftp://ftp.ensembl.org/pub/release-59/gtf/homo-sapiens/ 44. http://www.sanger.ac.uk/research/projects/vertebrategenome/havana/
-
-
-
-
44
-
-
84874758704
-
-
ftp://ftp.wormbase.org/pub/wormbase/genomes/c-elegans/sequences/dna/ c-elegans.WS200.dna.fa.gz
-
-
-
-
45
-
-
79952360093
-
RNA-Seq read alignments with PALMapper
-
PMID:21154708
-
Jean G, Kahles A, Sreedharan VT, De Bona F, Rätsch G. RNA-Seq read alignments with PALMapper. Curr Protoc Bioinformatics 2010; 11:6; PMID:21154708.
-
(2010)
Curr Protoc Bioinformatics
, vol.11
, pp. 6
-
-
Jean, G.1
Kahles, A.2
Sreedharan, V.T.3
De Bona, F.4
Rätsch, G.5
-
46
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
1,000 Genome Project Data Processing Subgroup. PMID:19505943
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al.; 1,000 Genome Project Data Processing Subgroup. The sequence alignment/map format and SAMtools. Bioinformatics 2009; 25:2078- 9; PMID:19505943; http://dx.doi.org/10. 1093/bioinformatics/btp352.
-
(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
-
47
-
-
75549084124
-
WormBase: A comprehensive resource for nematode research
-
PMID:19910365
-
Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, et al. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res 2010; 38:463-7; PMID:19910365; http://dx.doi. org/10.1093/nar/gkp952.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 463-467
-
-
Harris, T.W.1
Antoshechkin, I.2
Bieri, T.3
Blasiar, D.4
Chan, J.5
Chen, W.J.6
-
48
-
-
0142121516
-
Exploration, normalization and summaries of high density oligonucleotide array probe level data
-
PMID:12925520
-
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, et al. Exploration, normalization and summaries of high density oligonucleotide array probe level data. Biostatistics 2003; 4:249-64; PMID:12925520; http://dx.doi.org/10.1093/biostatistics/4.2.249.
-
(2003)
Biostatistics
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.D.4
Antonellis, K.J.5
Scherf, U.6
-
49
-
-
0013159620
-
Splicing graphs and EST assembly problem
-
PMID:12169546
-
Heber S, Alekseyev M, Sze SH, Tang H, Pevzner PA. Splicing graphs and EST assembly problem. Bioinformatics 2002; 18:181-8; PMID:12169546; http://dx.doi.org/10.1093/bioinformatics/18.suppl-1.S181.
-
(2002)
Bioinformatics
, vol.18
, pp. 181-188
-
-
Heber, S.1
Alekseyev, M.2
Sze, S.H.3
Tang, H.4
Pevzner, P.A.5
-
50
-
-
60849139395
-
GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists
-
PMID:19192299
-
Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 2009; 10:48; PMID:19192299; http:// dx.doi.org/10.1186/1471-2105- 10-48.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 48
-
-
Eden, E.1
Navon, R.2
Steinfeld, I.3
Lipson, D.4
Yakhini, Z.5
|