-
1
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816 (2007).
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
-
2
-
-
37749047490
-
Sequence census methods for functional genomics
-
Wold, B. & Myers, R.M. Sequence census methods for functional genomics. Nat. Methods 5, 19-21 (2008).
-
(2008)
Nat. Methods
, vol.5
, pp. 19-21
-
-
Wold, B.1
Myers, R.M.2
-
3
-
-
66149192669
-
How to map billions of short reads onto genomes
-
Trapnell, C. & Salzberg, S.L. How to map billions of short reads onto genomes. Nat. Biotechnol. 27, 455-457 (2009).
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 455-457
-
-
Trapnell, C.1
Salzberg, S.L.2
-
4
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007).
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
5
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
-
Rozowsky, J. et al. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol. 27, 66-75 (2009).
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
-
6
-
-
64249139132
-
RNA Pol II accumulates at promoters of growth genes during developmental arrest
-
Baugh, L.R., Demodena, J. & Sternberg, P.W. RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science 324, 92-94 (2009).
-
(2009)
Science
, vol.324
, pp. 92-94
-
-
Baugh, L.R.1
Demodena, J.2
Sternberg, P.W.3
-
7
-
-
34249026300
-
High-resolution profiling on histone methylations in the human genome
-
Barski, A. et al. High-resolution profiling on histone methylations in the human genome. Cell 129, 823-837 (2007).
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
-
8
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and linearge-committed cells
-
Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and linearge-committed cells. Nature 448, 553-560 (2007).
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
-
9
-
-
50849090969
-
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
-
Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5, 829-834 (2008).
-
(2008)
Nat. Methods
, vol.5
, pp. 829-834
-
-
Valouev, A.1
-
10
-
-
55749094855
-
An integrated software system for analyzing ChIP-chip and ChIP-seq data
-
Ji, H. et al. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol. 26, 1293-1300 (2008).
-
(2008)
Nat. Biotechnol
, vol.26
, pp. 1293-1300
-
-
Ji, H.1
-
11
-
-
52649132425
-
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-seq data
-
Jothi, R., Cuddapah, S., Barski, A., Cui, K. & Zhao, K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-seq data. Nucleic Acids Res. 36, 5221-5231 (2008).
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
Cui, K.4
Zhao, K.5
-
12
-
-
57449100870
-
Design and anlysis of ChIP-seq experiments for DNA-binding proteins
-
Kharchenko, P.V., Tolstorukov, M.Y. & Park, P.J. Design and anlysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol. 26, 1351-1359 (2008).
-
(2008)
Nat. Biotechnol
, vol.26
, pp. 1351-1359
-
-
Kharchenko, P.V.1
Tolstorukov, M.Y.2
Park, P.J.3
-
13
-
-
53849146020
-
Model-based analysis of ChIP-seq (MACS)
-
Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137.1- R137.9 (2008).
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
-
14
-
-
54949147307
-
F-Seq: A feature density estimator for high-throughput sequence tags
-
Boyle, A.P., Guinney, J., Crawford, G.E. & Furey, T.S. F-Seq: A feature density estimator for high-throughput sequence tags. Bioinformatics 24, 2537-2538 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 2537-2538
-
-
Boyle, A.P.1
Guinney, J.2
Crawford, G.E.3
Furey, T.S.4
-
15
-
-
67650711619
-
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
-
Zang, C. et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25, 1952-1958 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1952-1958
-
-
Zang, C.1
-
16
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651-657 (2007).
-
(2007)
Nat. Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.1
-
17
-
-
73049112582
-
Extracting transcription factor targets from ChIP-Seq data
-
(24 June
-
Tuteja, G., White, P., Schug, J. & Kaestner, K.H. Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res. advance online publication doi:10.1093/nar/gkp536 (24 June 2009).
-
(2009)
Nucleic Acids Res. Advance Online Publication Doi:10.1093/Nar/Gkp536
-
-
Tuteja, G.1
White, P.2
Schug, J.3
Kaestner, K.H.4
-
18
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-seq
-
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5, 621-628 (2008).
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
19
-
-
48249140621
-
FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology
-
Fejes, A.P. et al. FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24, 1729-1730 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 1729-1730
-
-
Fejes, A.P.1
-
20
-
-
60849117520
-
Empirical methods for controlling false positives and estimating confidence in ChIP-seq peaks
-
Nix, D.A., Courdy, S.J. & Boucher, K.M. Empirical methods for controlling false positives and estimating confidence in ChIP-seq peaks. BMC Bioinformatics 9, 523 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 523
-
-
Nix, D.A.1
Courdy, S.J.2
Boucher, K.M.3
-
21
-
-
53749092745
-
An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
-
Xu, H., Wei, C., Lin, F. & Sung, W.K. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics 24, 2344-2349 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 2344-2349
-
-
Xu, H.1
Wei, C.2
Lin, F.3
Sung, W.K.4
-
22
-
-
55549118625
-
ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome
-
Hon, G., Ren, B. & Wang, W. ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome. PLOS Comput. Biol. 4, e1000201 (2008).
-
(2008)
PLOS Comput. Biol
, vol.e10
, pp. 4
-
-
Hon, G.1
Ren, B.2
Wang, W.3
-
23
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344-1349 (2008).
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
-
24
-
-
46249096804
-
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
-
Wihelm, B.T. et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239-1243 (2008).
-
(2008)
Nature
, vol.453
, pp. 1239-1243
-
-
Wihelm, B.T.1
-
25
-
-
46249103973
-
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat
-
Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613-619 (2008).
-
(2008)
Methods
, vol.5
, pp. 613-619
-
-
Cloonan, N.1
-
26
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M. & Gilad, Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509-1517 (2008).
-
(2008)
Genome Res
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
27
-
-
47649124124
-
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
-
Sultan, M. et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956-960 (2008).
-
(2008)
Science
, vol.321
, pp. 956-960
-
-
Sultan, M.1
-
28
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476 (2008).
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.T.1
-
29
-
-
65649126066
-
Transcript length bias in RNA-seq data confounds systems
-
Oshlack, A. & Wakefield, M.J. Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct 4, 14 (2009).
-
(2009)
Biology. Biol. Direct
, vol.4
, pp. 14
-
-
Oshlack, A.1
Wakefield, M.J.2
-
30
-
-
77949582444
-
Statistical inference in mRNA-seq: Exploratory data analysis and differential expression
-
Bullard, J.H., Purdom, E.A., Hansen, K.D, Durinck, S. & Dudoit, S. Statistical inference in mRNA-seq: Exploratory data analysis and differential expression. UC Berkeley Division of Biostatistics Working Paper Series 247 (2009).
-
(2009)
UC Berkeley Division of Biostatistics Working Paper Series
, pp. 247
-
-
Bullard, J.H.1
Purdom, E.A.2
Hansen, K.D.3
Durinck, S.4
Dudoit, S.5
-
31
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino, D.R. & Birney, E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008).
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
32
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-seq
-
Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: Discovering splice junctions with RNA-seq. Bioinformatics 25, 1105-1111 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
34
-
-
62349130698
-
Ultrafast and memory- efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory- efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
35
-
-
40049104732
-
SOAP: Short oligonucleotide alignment program
-
Li, R., Li, Y., Kristiansen, K. & Wang, J. SOAP: Short oligonucleotide alignment program. Bioinformatics 24, 713-714 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 713-714
-
-
Li, R.1
Li, Y.2
Kristiansen, K.3
Wang, J.4
-
36
-
-
70349884341
-
RNA-MATE: A recursive mapping strategy for high- throughput RNA-sequencing data
-
Online Blication, Oi:10.1093/Bioinformatics/Btp459, 30 July
-
Cloonan, N. et al. RNA-MATE: A recursive mapping strategy for high- throughput RNA-sequencing data. Bioinformatics advance online blication, oi:10.1093/bioinformatics/btp459 (30 July 2009).
-
(2009)
Bioinformatics Advance
-
-
Cloonan, N.1
-
37
-
-
58149513263
-
Annotating genomes with massive-scale RNA sequencing
-
Denoeud, F. et al. Annotating genomes with massive-scale RNA sequencing. Genome Biol. 9, R175 (2009).
-
(2009)
Genome Biol
, vol.9
, pp. R175
-
-
Denoeud, F.1
-
38
-
-
49549102475
-
Optimal spliced alignments of short sequence reads
-
De Bona, F., Ossowski, S., Schneeberger, K. & Rätsch, G. Optimal spliced alignments of short sequence reads. Bioinformatics 24, i175-i180 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. i175-i180
-
-
de Bona, F.1
Ossowski, S.2
Schneeberger, K.3
Rätsch, G.4
-
39
-
-
1642473033
-
Comparative analysis of processed pseudogenes in the mouse and human genomes
-
Zhang, Z., Carriero, N. & Gerstein, M. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet. 20, 62-67 (2004).
-
(2004)
Trends Genet
, vol.20
, pp. 62-67
-
-
Zhang, Z.1
Carriero, N.2
Gerstein, M.3
-
40
-
-
64549119707
-
Statistical inferences for isoform expression in RNA- seq
-
Jiang, H. & Wong, W.H. Statistical inferences for isoform expression in RNA- seq. Bioinformatics 25, 1026-1032 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1026-1032
-
-
Jiang, H.1
Wong, W.H.2
-
41
-
-
67249136028
-
A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level
-
Zheng, S. & Chen, L. A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res. 37, e75 (2009).
-
(2009)
Nucleic Acids Res
, vol.e75
, pp. 37
-
-
Zheng, S.1
Chen, L.2
-
42
-
-
11244346557
-
Variance stabilization applied to microarray data calibration and to the quantification of differential gene expression
-
Huber, W., von Heydebreck, A., Sültmann, H., Poustka, A. & Vingron, M. Variance stabilization applied to microarray data calibration and to the quantification of differential gene expression. Bioinformatics 18 Suppl 1, S96-S104 (2002).
-
(2002)
Bioinformatics 18 Suppl
, vol.1
, pp. SS96-S104
-
-
Huber, W.1
Von Heydebreck, A.2
Sültmann, H.3
Poustka, A.4
Vingron, M.5
-
43
-
-
77249117360
-
Detection of single nucleotide variations in expressed exons of the human genome using RNA-seq
-
15 June
-
Chepelev, I., Wei, G., Tang, Q. & Zhao, K. Detection of single nucleotide variations in expressed exons of the human genome using RNA-seq. Nucleic Acids Res. advance online publication, doi:10.1093/nar/gkp507 (15 June 2009).
-
(2009)
Nucleic Acids Res. Advance Online Publication, Doi:10.1093/Nar/Gkp507
-
-
Chepelev, I.1
Wei, G.2
Tang, Q.3
Zhao, K.4
-
44
-
-
66349122954
-
Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
-
Li, J.B. et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324, 1210-1213 (2009).
-
(2009)
Science
, vol.324
, pp. 1210-1213
-
-
Li, J.B.1
-
45
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
-
46
-
-
33749400168
-
Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements
-
Dostie, J. et al. Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Res. 16, 1299-1309 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 1299-1309
-
-
Dostie, J.1
-
47
-
-
63849091245
-
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genomes analyses
-
Fullwood, M.J., Wei, C.L., Liu, E.T. & Ruan, Y. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genomes analyses. Genome Res. 19, 521-532 (2009).
-
(2009)
Genome Res
, vol.19
, pp. 521-532
-
-
Fullwood, M.J.1
Wei, C.L.2
Liu, E.T.3
Ruan, Y.4
-
48
-
-
69549112743
-
Digital transcriptome profiling using selective priming for cDNA synthesis
-
Armour, C.D. et al. Digital transcriptome profiling using selective priming for cDNA synthesis. Nat. Methods 6, 647-649 (2009).
-
(2009)
Nat. Methods
, vol.6
, pp. 647-649
-
-
Armour, C.D.1
|