-
1
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
-
2
-
-
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, (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 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
-
3
-
-
63849342015
-
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans
-
Hillier LW, Reinke V, Green P, Hirst M, Marra MA, et al. (2009) Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res 19: 657-666.
-
(2009)
Genome Res
, vol.19
, pp. 657-666
-
-
Hillier, L.W.1
Reinke, V.2
Green, P.3
Hirst, M.4
Marra, M.A.5
-
4
-
-
79551593972
-
The Drosophila melanogaster transcriptome by paired-end RNA sequencing
-
Daines B, Wang H, Wang L, Li Y, Han Y, et al. (2010) The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res 21: 315-324.
-
(2010)
Genome Res
, vol.21
, pp. 315-324
-
-
Daines, B.1
Wang, H.2
Wang, L.3
Li, Y.4
Han, Y.5
-
5
-
-
77951871117
-
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
-
Zhang G, Guo G, Hu X, Zhang Y, Li Q, et al. (2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res 20: 646-654.
-
(2010)
Genome Res
, vol.20
, pp. 646-654
-
-
Zhang, G.1
Guo, G.2
Hu, X.3
Zhang, Y.4
Li, Q.5
-
6
-
-
74949084336
-
Genome-wide mapping of alternative splicing in Arabidopsis thaliana
-
Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, et al. (2009) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20: 45-58.
-
(2009)
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
-
7
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber M, Grabherr MG, Guttman M, Trapnell C, (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8: 469-477.
-
(2011)
Nat Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
8
-
-
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
-
9
-
-
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. 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
-
10
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28: 503-510.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 503-510
-
-
Guttman, M.1
Garber, M.2
Levin, J.Z.3
Donaghey, J.4
Robinson, J.5
-
11
-
-
77951820899
-
Fast and SNP-tolerant detection of complex variants and splicing in short reads
-
Wu TD, Nacu S, (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
-
(2010)
Bioinformatics
, vol.26
, pp. 873-881
-
-
Wu, T.D.1
Nacu, S.2
-
12
-
-
80052745094
-
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
-
Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, et al. (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics 27: 2518-2528.
-
(2011)
Bioinformatics
, vol.27
, pp. 2518-2528
-
-
Grant, G.R.1
Farkas, M.H.2
Pizarro, A.D.3
Lahens, N.F.4
Schug, J.5
-
13
-
-
84255194654
-
Effects of inversions on within- and between-species recombination and divergence
-
Stevison LS, Hoehn KB, Noor MA, (2011) Effects of inversions on within- and between-species recombination and divergence. Genome Biol Evol 3: 830-841.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 830-841
-
-
Stevison, L.S.1
Hoehn, K.B.2
Noor, M.A.3
-
14
-
-
0029911389
-
The speciation history of Drosophila pseudoobscura and close relatives: inferences from DNA sequence variation at the period locus
-
Wang RL, Hey J, (1996) The speciation history of Drosophila pseudoobscura and close relatives: inferences from DNA sequence variation at the period locus. Genetics 144: 1113-1126.
-
(1996)
Genetics
, vol.144
, pp. 1113-1126
-
-
Wang, R.L.1
Hey, J.2
-
15
-
-
77955003456
-
Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome
-
Meisel RP, Hilldorfer BB, Koch JL, Lockton S, Schaeffer SW, (2010) Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome. Mol Biol Evol 27: 1963-1978.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 1963-1978
-
-
Meisel, R.P.1
Hilldorfer, B.B.2
Koch, J.L.3
Lockton, S.4
Schaeffer, S.W.5
-
16
-
-
19944434180
-
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution
-
Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, et al. (2005) Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res 15: 1-18.
-
(2005)
Genome Res
, vol.15
, pp. 1-18
-
-
Richards, S.1
Liu, Y.2
Bettencourt, B.R.3
Hradecky, P.4
Letovsky, S.5
-
17
-
-
79251557454
-
PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals
-
Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, et al. (2011) PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS One 6: e15925.
-
(2011)
PLoS One
, vol.6
-
-
Kofler, R.1
Orozco-terWengel, P.2
De Maio, N.3
Pandey, R.V.4
Nolte, V.5
-
18
-
-
24044447664
-
Automated generation of heuristics for biological sequence comparison
-
Slater GS, Birney E, (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 31
-
-
Slater, G.S.1
Birney, E.2
-
19
-
-
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
-
20
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
21
-
-
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 Res 35: W345-349.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Kong, L.1
Zhang, Y.2
Ye, Z.Q.3
Liu, X.Q.4
Zhao, S.Q.5
-
22
-
-
70449477656
-
Next generation software for functional trend analysis
-
Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP, (2009) Next generation software for functional trend analysis. Bioinformatics 25: 3043-3044.
-
(2009)
Bioinformatics
, vol.25
, pp. 3043-3044
-
-
Berriz, G.F.1
Beaver, J.E.2
Cenik, C.3
Tasan, M.4
Roth, F.P.5
-
23
-
-
58349111875
-
AmiGO: online access to ontology and annotation data
-
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, et al. (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25: 288-289.
-
(2009)
Bioinformatics
, vol.25
, pp. 288-289
-
-
Carbon, S.1
Ireland, A.2
Mungall, C.J.3
Shu, S.4
Marshall, B.5
-
24
-
-
78049346632
-
De novo assembly and analysis of RNA-seq data
-
Robertson G, Schein J, Chiu R, Corbett R, Field M, et al. (2010) De novo assembly and analysis of RNA-seq data. Nat Methods 7: 909-912.
-
(2010)
Nat Methods
, vol.7
, pp. 909-912
-
-
Robertson, G.1
Schein, J.2
Chiu, R.3
Corbett, R.4
Field, M.5
-
25
-
-
84859768479
-
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
-
Schulz MH, Zerbino DR, Vingron M, Birney E, (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28: 1086-1092.
-
(2012)
Bioinformatics
, vol.28
, pp. 1086-1092
-
-
Schulz, M.H.1
Zerbino, D.R.2
Vingron, M.3
Birney, E.4
-
26
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29: 644-652.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
-
27
-
-
84860485003
-
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
-
Zhao QY, Wang Y, Kong YM, Luo D, Li X, et al. (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 12 (Suppl 14):: S2.
-
(2011)
BMC Bioinformatics
, vol.12
, Issue.SUPPL. 14
-
-
Zhao, Q.Y.1
Wang, Y.2
Kong, Y.M.3
Luo, D.4
Li, X.5
-
28
-
-
79551634894
-
PHAST and RPHAST: phylogenetic analysis with space/time models
-
Hubisz MJ, Pollard KS, Siepel A, (2011) PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform 12: 41-51.
-
(2011)
Brief Bioinform
, vol.12
, pp. 41-51
-
-
Hubisz, M.J.1
Pollard, K.S.2
Siepel, A.3
-
29
-
-
77952800173
-
On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila
-
Parsch J, Novozhilov S, Saminadin-Peter SS, Wong KM, Andolfatto P, (2010) On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila. Mol Biol Evol 27: 1226-1234.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 1226-1234
-
-
Parsch, J.1
Novozhilov, S.2
Saminadin-Peter, S.S.3
Wong, K.M.4
Andolfatto, P.5
-
30
-
-
80955139613
-
IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly
-
Li W, Feng J, Jiang T, (2011) IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly. J Comput Biol 18: 1693-1707.
-
(2011)
J Comput Biol
, vol.18
, pp. 1693-1707
-
-
Li, W.1
Feng, J.2
Jiang, T.3
-
31
-
-
0030585734
-
Evaluation of gene structure prediction programs
-
Burset M, Guigo R, (1996) Evaluation of gene structure prediction programs. Genomics 34: 353-367.
-
(1996)
Genomics
, vol.34
, pp. 353-367
-
-
Burset, M.1
Guigo, R.2
-
32
-
-
36049041622
-
Constraint and turnover in sex-biased gene expression in the genus Drosophila
-
Zhang Y, Sturgill D, Parisi M, Kumar S, Oliver B, (2007) Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature 450: 233-237.
-
(2007)
Nature
, vol.450
, pp. 233-237
-
-
Zhang, Y.1
Sturgill, D.2
Parisi, M.3
Kumar, S.4
Oliver, B.5
-
33
-
-
72449139061
-
Evolution of sex-dependent gene expression in three recently diverged species of Drosophila
-
Jiang ZF, Machado CA, (2009) Evolution of sex-dependent gene expression in three recently diverged species of Drosophila. Genetics 183: 1175-1185.
-
(2009)
Genetics
, vol.183
, pp. 1175-1185
-
-
Jiang, Z.F.1
Machado, C.A.2
-
34
-
-
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 Biol Evol 4: 427-442.
-
(2012)
Genome Biol Evol
, vol.4
, pp. 427-442
-
-
Young, R.S.1
Marques, A.C.2
Tibbit, C.3
Haerty, W.4
Bassett, A.R.5
-
35
-
-
79953043801
-
The developmental transcriptome of Drosophila melanogaster
-
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, et al. (2010) The developmental transcriptome of Drosophila melanogaster. Nature 471: 473-379.
-
(2010)
Nature
, vol.471
, pp. 379-473
-
-
Graveley, B.R.1
Brooks, A.N.2
Carlson, J.W.3
Duff, M.O.4
Landolin, J.M.5
-
36
-
-
0030917088
-
Transcriptional termination signals for RNA polymerase II in fission yeast
-
Birse CE, Lee BA, Hansen K, Proudfoot NJ, (1997) Transcriptional termination signals for RNA polymerase II in fission yeast. EMBO J 16: 3633-3643.
-
(1997)
EMBO J
, vol.16
, pp. 3633-3643
-
-
Birse, C.E.1
Lee, B.A.2
Hansen, K.3
Proudfoot, N.J.4
-
37
-
-
0034065724
-
Ab initio gene finding in Drosophila genomic DNA
-
Salamov AA, Solovyev VV, (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10: 516-522.
-
(2000)
Genome Res
, vol.10
, pp. 516-522
-
-
Salamov, A.A.1
Solovyev, V.V.2
-
38
-
-
0002636459
-
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
-
Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, et al. (2002) Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol 3: RESEARCH0083.
-
(2002)
Genome Biol
, vol.3
-
-
Misra, S.1
Crosby, M.A.2
Mungall, C.J.3
Matthews, B.B.4
Campbell, K.S.5
-
39
-
-
76749130220
-
Nonsense-mediated decay enables intron gain in Drosophila
-
Farlow A, Meduri E, Dolezal M, Hua L, Schlotterer C, (2010) Nonsense-mediated decay enables intron gain in Drosophila. PLoS Genet 6: e1000819.
-
(2010)
PLoS Genet
, vol.6
-
-
Farlow, A.1
Meduri, E.2
Dolezal, M.3
Hua, L.4
Schlotterer, C.5
-
40
-
-
51849126044
-
Longer first introns are a general property of eukaryotic gene structure
-
Bradnam KR, Korf I, (2008) Longer first introns are a general property of eukaryotic gene structure. PLoS One 3: e3093.
-
(2008)
PLoS One
, vol.3
-
-
Bradnam, K.R.1
Korf, I.2
-
41
-
-
33750962013
-
Intron size, abundance, and distribution within untranslated regions of genes
-
Hong X, Scofield DG, Lynch M, (2006) Intron size, abundance, and distribution within untranslated regions of genes. Mol Biol Evol 23: 2392-2404.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 2392-2404
-
-
Hong, X.1
Scofield, D.G.2
Lynch, M.3
-
42
-
-
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, et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 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
-
43
-
-
84863419877
-
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data
-
Rogers MF, Thomas J, Reddy AS, Ben-Hur A, (2012) SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol 13: R4.
-
(2012)
Genome Biol
, vol.13
-
-
Rogers, M.F.1
Thomas, J.2
Reddy, A.S.3
Ben-Hur, A.4
-
44
-
-
52949118471
-
Determining the relationship of gene expression and global mRNA stability in Drosophila melanogaster and Escherichia coli using linear models
-
Eck S, Stephan W, (2008) Determining the relationship of gene expression and global mRNA stability in Drosophila melanogaster and Escherichia coli using linear models. Gene 424: 102-107.
-
(2008)
Gene
, vol.424
, pp. 102-107
-
-
Eck, S.1
Stephan, W.2
|