-
2
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
-
3
-
-
77956279237
-
Assembly of large genomes using second-generation sequencing
-
Schatz, M. C., Delcher, A. L. & Salzberg, S. L. Assembly of large genomes using second-generation sequencing. Genome Res. 20, 1165-1173 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1165-1173
-
-
Schatz, M.C.1
Delcher, A.L.2
Salzberg, S.L.3
-
4
-
-
75149155568
-
The sequence and de novo assembly of the giant panda genome
-
Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317 (2010).
-
(2010)
Nature
, vol.463
, pp. 311-317
-
-
Li, R.1
-
5
-
-
84875898037
-
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
-
Jia, J. et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496, 91-95 (2013).
-
(2013)
Nature
, vol.496
, pp. 91-95
-
-
Jia, J.1
-
6
-
-
84881496498
-
The genome sequence of the colonial chordate, Botryllus schlosseri
-
Voskoboynik, A. et al. The genome sequence of the colonial chordate, Botryllus schlosseri. Elife 2, e00569 (2013).
-
(2013)
Elife
, vol.2
-
-
Voskoboynik, A.1
-
7
-
-
84868327508
-
Finished bacterial genomes from shotgun sequence data
-
Ribeiro, F. J. et al. Finished bacterial genomes from shotgun sequence data. Genome Res. 22, 2270-2277 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 2270-2277
-
-
Ribeiro, F.J.1
-
8
-
-
84860342753
-
Current challenges in de novo plant genome sequencing and assembly
-
Schatz, M. C., Witkowski, J. & McCombie, W. R. Current challenges in de novo plant genome sequencing and assembly. Genome Biol. 13, 243 (2012).
-
(2012)
Genome Biol.
, vol.13
, pp. 243
-
-
Schatz, M.C.1
Witkowski, J.2
McCombie, W.R.3
-
9
-
-
20144388947
-
An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing
-
Margulies, E. H. et al. An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proc. Natl Acad. Sci. USA 102, 4795-4800 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 4795-4800
-
-
Margulies, E.H.1
-
10
-
-
35948966737
-
2x genomes-does depth matter?
-
Green, P. 2x genomes-does depth matter? Genome Res. 17, 1547-1549 (2007).
-
(2007)
Genome Res.
, vol.17
, pp. 1547-1549
-
-
Green, P.1
-
11
-
-
84873700991
-
Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence
-
Rands, C. M. et al. Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 14, 95 (2013).
-
(2013)
BMC Genomics
, vol.14
, pp. 95
-
-
Rands, C.M.1
-
12
-
-
55549089660
-
Accurate whole human genome sequencing using reversible terminator chemistry
-
Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
-
(2008)
Nature
, vol.456
, pp. 53-59
-
-
Bentley, D.R.1
-
13
-
-
69749124820
-
The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group
-
Ahn, S. M. et al. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 19, 1622-1629 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 1622-1629
-
-
Ahn, S.M.1
-
14
-
-
55549097849
-
The diploid genome sequence of an Asian individual
-
Wang, J. et al. The diploid genome sequence of an Asian individual. Nature 456, 60-65 (2008).
-
(2008)
Nature
, vol.456
, pp. 60-65
-
-
Wang, J.1
-
15
-
-
80051732262
-
Accurate and comprehensive sequencing of personal genomes
-
Ajay, S. S., Parker, S. C., Abaan, H. O., Fajardo, K. V. & Margulies, E. H. Accurate and comprehensive sequencing of personal genomes. Genome Res. 21, 1498-1505 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1498-1505
-
-
Ajay, S.S.1
Parker, S.C.2
Abaan, H.O.3
Fajardo, K.V.4
Margulies, E.H.5
-
16
-
-
63949083912
-
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
-
Kozarewa, I. et al. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nature Methods 6, 291-295 (2009).
-
(2009)
Nature Methods
, vol.6
, pp. 291-295
-
-
Kozarewa, I.1
-
17
-
-
79951694175
-
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
-
Aird, D. et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12, R18 (2011).
-
(2011)
Genome Biol.
, vol.12
-
-
Aird, D.1
-
18
-
-
80054757012
-
Performance comparison of exome DNA sequencing technologies
-
Clark, M. J. et al. Performance comparison of exome DNA sequencing technologies. Nature Biotech. 29, 908-914 (2011).
-
(2011)
Nature Biotech.
, vol.29
, pp. 908-914
-
-
Clark, M.J.1
-
19
-
-
80052830541
-
Comparison of solution-based exome capture methods for next generation sequencing
-
Sulonen, A. M. et al. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol. 12, R94 (2011).
-
(2011)
Genome Biol.
, vol.12
-
-
Sulonen, A.M.1
-
20
-
-
84867255789
-
A hypermorphic missense mutation in PLCG2, encoding phospholipase Cγ2, causes a dominantly inherited autoinflammatory disease with immunodeficiency
-
Zhou, Q. et al. A hypermorphic missense mutation in PLCG2, encoding phospholipase Cγ2, causes a dominantly inherited autoinflammatory disease with immunodeficiency. Am. J. Hum. Genet. 91, 713-720 (2012).
-
(2012)
Am. J. Hum. Genet.
, vol.91
, pp. 713-720
-
-
Zhou, Q.1
-
21
-
-
84880275532
-
PIK3R1 mutations cause syndromic insulin resistance with lipoatrophy
-
Thauvin-Robinet, C. et al. PIK3R1 mutations cause syndromic insulin resistance with lipoatrophy. Am. J. Hum. Genet. 93, 141-149 (2013).
-
(2013)
Am. J. Hum. Genet.
, vol.93
, pp. 141-149
-
-
Thauvin-Robinet, C.1
-
22
-
-
84872696957
-
Using whole-exome sequencing to identify inherited causes of autism
-
Yu, T. W. et al. Using whole-exome sequencing to identify inherited causes of autism. Neuron 77, 259-273 (2013).
-
(2013)
Neuron
, vol.77
, pp. 259-273
-
-
Yu, T.W.1
-
23
-
-
57049122389
-
A large genome center's improvements to the Illumina sequencing system
-
Quail, M. A. et al. A large genome center's improvements to the Illumina sequencing system. Nature Methods 5, 1005-1010 (2008).
-
(2008)
Nature Methods
, vol.5
, pp. 1005-1010
-
-
Quail, M.A.1
-
24
-
-
84867280219
-
Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth
-
Fromer, M. et al. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. Am. J. Hum. Genet. 91, 597-607 (2012).
-
(2012)
Am. J. Hum. Genet.
, vol.91
, pp. 597-607
-
-
Fromer, M.1
-
25
-
-
84864609288
-
Copy number variation detection and genotyping from exome sequence data
-
Krumm, N. et al. Copy number variation detection and genotyping from exome sequence data. Genome Res. 22, 1525-1532 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1525-1532
-
-
Krumm, N.1
-
26
-
-
64849083125
-
CNV-seq, a new method to detect copy number variation using high-throughput sequencing
-
Xie, C. & Tammi, M. T. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10, 80 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 80
-
-
Xie, C.1
Tammi, M.T.2
-
27
-
-
78649309503
-
Detecting copy number variation with mated short reads
-
Medvedev, P., Fiume, M., Dzamba, M., Smith, T. & Brudno, M. Detecting copy number variation with mated short reads. Genome Res. 20, 1613-1622 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1613-1622
-
-
Medvedev, P.1
Fiume, M.2
Dzamba, M.3
Smith, T.4
Brudno, M.5
-
28
-
-
84861400043
-
Cn.MOPS: Mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
-
Klambauer, G. et al. cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res. 40, e69 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Klambauer, G.1
-
29
-
-
79957950801
-
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
-
Le, S. Q. & Durbin, R. SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res. 21, 952-960 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 952-960
-
-
Le, S.Q.1
Durbin, R.2
-
30
-
-
79957951017
-
Low-coverage sequencing: Implications for design of complex trait association studies
-
Li, Y., Sidore, C., Kang, H. M., Boehnke, M. & Abecasis, G. R. Low-coverage sequencing: implications for design of complex trait association studies. Genome Res. 21, 940-951 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 940-951
-
-
Li, Y.1
Sidore, C.2
Kang, H.M.3
Boehnke, M.4
Abecasis, G.R.5
-
31
-
-
84975795680
-
An integrated map of genetic variation from 1, 092 human genomes
-
Abecasis, G. R. et al. An integrated map of genetic variation from 1, 092 human genomes. Nature 491, 56-65 (2012).
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
Abecasis, G.R.1
-
32
-
-
84861598099
-
Extremely low-coverage sequencing and imputation increases power for genome-wide association studies
-
Pasaniuc, B. et al. Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nature Genet. 44, 631-635 (2012).
-
(2012)
Nature Genet.
, vol.44
, pp. 631-635
-
-
Pasaniuc, B.1
-
33
-
-
77953006634
-
The mutation spectrum revealed by paired genome sequences from a lung cancer patient
-
Lee, W. et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465, 473-477 (2010).
-
(2010)
Nature
, vol.465
, pp. 473-477
-
-
Lee, W.1
-
34
-
-
84869753284
-
Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns
-
Schuh, A. et al. Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. Blood 120, 4191-4196 (2012).
-
(2012)
Blood
, vol.120
, pp. 4191-4196
-
-
Schuh, A.1
-
35
-
-
84868138663
-
A likelihood-based framework for variant calling and de novo mutation detection in families
-
Li, B. et al. A likelihood-based framework for variant calling and de novo mutation detection in families. PLoS Genet. 8, e1002944 (2012).
-
(2012)
PLoS Genet.
, vol.8
-
-
Li, B.1
-
36
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491-498 (2011).
-
(2011)
Nature Genet.
, vol.43
, pp. 491-498
-
-
Depristo, M.A.1
-
37
-
-
84874194145
-
Sequence assembly demystified
-
Nagarajan, N. & Pop, M. Sequence assembly demystified. Nature Rev. Genet. 14, 157-167 (2013).
-
(2013)
Nature Rev. Genet.
, vol.14
, pp. 157-167
-
-
Nagarajan, N.1
Pop, M.2
-
38
-
-
84991528460
-
Assemblathon 2: Evaluating de novo methods of genome assembly in three vertebrate species
-
Bradnam, K. R. et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2, 10 (2013).
-
(2013)
GigaScience
, vol.2
, pp. 10
-
-
Bradnam, K.R.1
-
39
-
-
84857893016
-
GAGE: A critical evaluation of genome assemblies and assembly algorithms
-
Salzberg, S. L. et al. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res. 22, 557-567 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 557-567
-
-
Salzberg, S.L.1
-
40
-
-
84872519326
-
High-throughput microbial population genomics using the Cortex variation assembler
-
Iqbal, Z., Turner, I. & McVean, G. High-throughput microbial population genomics using the Cortex variation assembler. Bioinformatics 29, 275-276 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 275-276
-
-
Iqbal, Z.1
Turner, I.2
McVean, G.3
-
41
-
-
84869014474
-
A comprehensive comparison of RNA-seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: A case study in Saccharomyces cerevisiae
-
Nookaew, I. et al. A comprehensive comparison of RNA-seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res. 40, 10084-10097 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 10084-10097
-
-
Nookaew, I.1
-
42
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev. Genet. 10, 57-63 (2009).
-
(2009)
Nature Rev. Genet.
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
44
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
-
45
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
-
46
-
-
84865727393
-
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
-
Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775-1789 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1775-1789
-
-
Derrien, T.1
-
47
-
-
27844529344
-
Proposed methods for testing and selecting the ERCC external RNA controls
-
External RNA Controls Consortium
-
External RNA Controls Consortium. Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 6, 150 (2005).
-
(2005)
BMC Genomics
, vol.6
, pp. 150
-
-
-
48
-
-
80052521697
-
Synthetic spike-in standards for RNA-seq experiments
-
Jiang, L. et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21, 1543-1551 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1543-1551
-
-
Jiang, L.1
-
49
-
-
77955883388
-
Biases in Illumina transcriptome sequencing caused by random hexamer priming
-
Hansen, K. D., Brenner, S. E. & Dudoit, S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res. 38, e131 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Hansen, K.D.1
Brenner, S.E.2
Dudoit, S.3
-
50
-
-
83055192078
-
Differential expression in RNA-seq: A matter of depth
-
Tarazona, S., Garcia-Alcalde, F., Dopazo, J., Ferrer, A. & Conesa, A. Differential expression in RNA-seq: a matter of depth. Genome Res. 21, 2213-2223 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 2213-2223
-
-
Tarazona, S.1
Garcia-Alcalde, F.2
Dopazo, J.3
Ferrer, A.4
Conesa, A.5
-
51
-
-
34249088350
-
Genome-wide transcription and the implications for genomic organization
-
Kapranov, P., Willingham, A. T. & Gingeras, T. R. Genome-wide transcription and the implications for genomic organization. Nature Rev. Genet. 8, 413-423 (2007).
-
(2007)
Nature Rev. Genet.
, vol.8
, pp. 413-423
-
-
Kapranov, P.1
Willingham, A.T.2
Gingeras, T.R.3
-
52
-
-
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
-
53
-
-
84871599142
-
How deep is deep enough for RNA-seq profiling of bacterial transcriptomes?
-
Haas, B. J., Chin, M., Nusbaum, C., Birren, B. W. & Livny, J. How deep is deep enough for RNA-seq profiling of bacterial transcriptomes? BMC Genomics 13, 734 (2012).
-
(2012)
BMC Genomics
, vol.13
, pp. 734
-
-
Haas, B.J.1
Chin, M.2
Nusbaum, C.3
Birren, B.W.4
Livny, J.5
-
54
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments
-
Bullard, J. H., Purdom, E., Hansen, K. D. & Dudoit, S. Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments. BMC Bioinformatics 11, 94 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 94
-
-
Bullard, J.H.1
Purdom, E.2
Hansen, K.D.3
Dudoit, S.4
-
55
-
-
7444260846
-
The ENCODE (ENCyclopedia of DNA elements) project
-
ENCODE Project Consortium.
-
ENCODE Project Consortium. The ENCODE (ENCyclopedia of DNA elements) project. Science 306, 636-640 (2004).
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
56
-
-
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
-
57
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
ENCODE Project Consortium.
-
ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9, e1001046 (2011)
-
(2011)
PLoS Biol.
, vol.9
-
-
-
58
-
-
84871806968
-
Exome RNA sequencing reveals rare and novel alternative transcripts
-
Halvardson, J., Zaghlool, A. & Feuk, L. Exome RNA sequencing reveals rare and novel alternative transcripts. Nucleic Acids Res. 41, e6 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Halvardson, J.1
Zaghlool, A.2
Feuk, L.3
-
59
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
-
(2010)
Genome Biol.
, vol.11
-
-
Anders, S.1
Huber, W.2
-
60
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
61
-
-
84872198346
-
Differential analysis of gene regulation at transcript resolution with RNA-seq
-
Trapnell, C. et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotech. 31, 46-53 (2013).
-
(2013)
Nature Biotech.
, vol.31
, pp. 46-53
-
-
Trapnell, C.1
-
62
-
-
80053027909
-
Functional consequences of developmentally regulated alternative splicing
-
Kalsotra, A. & Cooper, T. A. Functional consequences of developmentally regulated alternative splicing. Nature Rev. Genet. 12, 715-729 (2011).
-
(2011)
Nature Rev. Genet.
, vol.12
, pp. 715-729
-
-
Kalsotra, A.1
Cooper, T.A.2
-
63
-
-
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
-
64
-
-
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
-
65
-
-
84875664276
-
MRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex
-
Dillman, A. A. et al. mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex. Nature Neurosci. 16, 499-506 (2013).
-
(2013)
Nature Neurosci.
, vol.16
, pp. 499-506
-
-
Dillman, A.A.1
-
66
-
-
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
-
67
-
-
84873020117
-
ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy
-
Rhee, H. S. & Pugh, B. F. ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Curr. Protoc. Mol. Biol. 100, 21.24.1-21.24.14 (2012).
-
(2012)
Curr. Protoc. Mol. Biol.
, vol.100
, pp. 21241-212414
-
-
Rhee, H.S.1
Pugh, B.F.2
-
68
-
-
61849139645
-
Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
-
Sanford, J. R. et al. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res. 19, 381-394 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 381-394
-
-
Sanford, J.R.1
-
69
-
-
56549105330
-
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
-
Licatalosi, D. D. et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456, 464-469 (2008).
-
(2008)
Nature
, vol.456
, pp. 464-469
-
-
Licatalosi, D.D.1
-
70
-
-
77954387023
-
ICLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
-
Konig, J. et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nature Struct. Mol. Biol. 17, 909-915 (2010).
-
(2010)
Nature Struct. Mol. Biol.
, vol.17
, pp. 909-915
-
-
Konig, J.1
-
71
-
-
77950920903
-
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
-
Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129-141 (2010).
-
(2010)
Cell
, vol.141
, pp. 129-141
-
-
Hafner, M.1
-
72
-
-
84862908875
-
The genomic binding sites of a noncoding RNA
-
Simon, M. D. et al. The genomic binding sites of a noncoding RNA. Proc. Natl Acad. Sci. USA 108, 20497-20502 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 20497-20502
-
-
Simon, M.D.1
-
73
-
-
80054756754
-
Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions
-
Chu, C., Qu, K., Zhong, F. L., Artandi, S. E. & Chang, H. Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 44, 667-678 (2011).
-
(2011)
Mol. Cell
, vol.44
, pp. 667-678
-
-
Chu, C.1
Qu, K.2
Zhong, F.L.3
Artandi, S.E.4
Chang, H.Y.5
-
74
-
-
84870317191
-
3C-based technologies to study the shape of the genome
-
de Laat, W. & Dekker, J. 3C-based technologies to study the shape of the genome. Methods 58, 189-191 (2012).
-
(2012)
Methods
, vol.58
, pp. 189-191
-
-
De Laat, W.1
Dekker, J.2
-
75
-
-
84878011578
-
Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
-
Dekker, J., Marti-Renom, M. A. & Mirny, L. A. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nature Rev. Genet. 14, 390-403 (2013).
-
(2013)
Nature Rev. Genet.
, vol.14
, pp. 390-403
-
-
Dekker, J.1
Marti-Renom, M.A.2
Mirny, L.A.3
-
76
-
-
63849308888
-
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
-
Hesselberth, J. R. et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nature Methods 6, 283-289 (2009).
-
(2009)
Nature Methods
, vol.6
, pp. 283-289
-
-
Hesselberth, J.R.1
-
77
-
-
46949098742
-
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
-
Down, T. A. et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nature Biotech. 26, 779-785 (2008).
-
(2008)
Nature Biotech.
, vol.26
, pp. 779-785
-
-
Down, T.A.1
-
78
-
-
84863256915
-
Bio-CAP: A versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA
-
Blackledge, N. P. et al. Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. Nucleic Acids Res. 40, e32 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Blackledge, N.P.1
-
79
-
-
84865777819
-
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
-
Landt, S. G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813-1831 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1813-1831
-
-
Landt, S.G.1
-
80
-
-
57449100870
-
Design and analysis of ChIP-seq experiments for DNA-binding proteins
-
Kharchenko, P. V., Tolstorukov, M. Y. & Park, P. J. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nature Biotech. 26, 1351-1359 (2008).
-
(2008)
Nature Biotech.
, vol.26
, pp. 1351-1359
-
-
Kharchenko, P.V.1
Tolstorukov, M.Y.2
Park, P.J.3
-
81
-
-
84861964081
-
Systematic evaluation of factors influencing ChIP-seq fidelity
-
Chen, Y. et al. Systematic evaluation of factors influencing ChIP-seq fidelity. Nature Methods 9, 609-614 (2012).
-
(2012)
Nature Methods
, vol.9
, pp. 609-614
-
-
Chen, Y.1
-
82
-
-
79953311672
-
High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation
-
Ozdemir, A. et al. High resolution mapping of Twist to DNA in Drosophila embryos: efficient functional analysis and evolutionary conservation. Genome Res. 21, 566-577 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 566-577
-
-
Ozdemir, A.1
-
83
-
-
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. Nature Biotech. 27, 66-75 (2009)
-
(2009)
Nature Biotech.
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
-
84
-
-
70349312354
-
ChIP-seq: Advantages and challenges of a maturing technology
-
Park, P. J. ChIP-seq: advantages and challenges of a maturing technology. Nature Rev. Genet. 10, 669-680 (2009).
-
(2009)
Nature Rev. Genet.
, vol.10
, pp. 669-680
-
-
Park, P.J.1
-
85
-
-
79955564639
-
Measuring reproducibility of high-throughput experiments
-
Li, Q., Brown, J. B., Huang, H. & Bickel, P. J. Measuring reproducibility of high-throughput experiments. Ann. Appl. Statist. 5, 1752-1779 (2011).
-
(2011)
Ann. Appl. Statist.
, vol.5
, pp. 1752-1779
-
-
Li, Q.1
Brown, J.B.2
Huang, H.3
Bickel, P.J.4
-
86
-
-
83255164884
-
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
-
Rhee, H. S. & Pugh, B. F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419 (2011).
-
(2011)
Cell
, vol.147
, pp. 1408-1419
-
-
Rhee, H.S.1
Pugh, B.F.2
-
87
-
-
84858165145
-
Genome-wide structure and organization of eukaryotic pre-initiation complexes
-
Rhee, H. S. & Pugh, B. F. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 483, 295-301 (2012).
-
(2012)
Nature
, vol.483
, pp. 295-301
-
-
Rhee, H.S.1
Pugh, B.F.2
-
88
-
-
38649099445
-
High-resolution mapping and characterization of open chromatin across the genome
-
Boyle, A. P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311-322 (2008).
-
(2008)
Cell
, vol.132
, pp. 311-322
-
-
Boyle, A.P.1
-
89
-
-
84869086143
-
LIN28A is a suppressor of ER-associated translation in embryonic stem cells
-
Cho, J. et al. LIN28A is a suppressor of ER-associated translation in embryonic stem cells. Cell 151, 765-777 (2012).
-
(2012)
Cell
, vol.151
, pp. 765-777
-
-
Cho, J.1
-
90
-
-
84879048904
-
NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure
-
Eom, T. et al. NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure. Elife 2, e00178 (2013).
-
(2013)
Elife
, vol.2
-
-
Eom, T.1
-
91
-
-
80053355174
-
Comprehensive comparison of three commercial human whole-exome capture platforms
-
Asan et al. Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol. 12, R95 (2011).
-
(2011)
Genome Biol.
, vol.12
-
-
Asan1
-
92
-
-
84867003195
-
Robust 4C-seq data analysis to screen for regulatory DNA interactions
-
van de Werken, H. J. G. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 9, 969-972 (2012).
-
(2012)
Nature Methods
, vol.9
, pp. 969-972
-
-
Van De Werken, H.J.G.1
-
93
-
-
84870310006
-
Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation
-
Splinter, E., de Wit, E., van de Werken, H. J. G., Klous, P. & de Laat, W. Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. Methods 58, 221-230 (2012).
-
(2012)
Methods
, vol.58
, pp. 221-230
-
-
Splinter, E.1
De Wit, E.2
Van De Werken, H.J.G.3
Klous, P.4
De Laat, W.5
-
94
-
-
84870379849
-
Hi-C: A comprehensive technique to capture the conformation of genomes
-
Belton, J.-M. et al. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 58, 268-276 (2012).
-
(2012)
Methods
, vol.58
, pp. 268-276
-
-
Belton, J.-M.1
-
95
-
-
84870310396
-
From cells to chromatin: Capturing snapshots of genome organization with 5C technology
-
Ferraiuolo, M. A., Sanyal, A., Naumova, N., Dekker, J. & Dostie, J. From cells to chromatin: capturing snapshots of genome organization with 5C technology. Methods 58, 255-267 (2012).
-
(2012)
Methods
, vol.58
, pp. 255-267
-
-
Ferraiuolo, M.A.1
Sanyal, A.2
Naumova, N.3
Dekker, J.4
Dostie, J.5
-
96
-
-
0023988195
-
Genomic mapping by fingerprinting random clones: A mathematical analysis
-
Lander, E. S. & Waterman, M. S. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2, 231-239 (1988).
-
(1988)
Genomics
, vol.2
, pp. 231-239
-
-
Lander, E.S.1
Waterman, M.S.2
-
97
-
-
84865614936
-
A mechanistic basis for amplification differences between samples and between genome regions
-
Veal, C. D. et al. A mechanistic basis for amplification differences between samples and between genome regions. BMC Genomics 13, 455 (2012).
-
(2012)
BMC Genomics
, vol.13
, pp. 455
-
-
Veal, C.D.1
-
98
-
-
79959568914
-
Efficient study design for next generation sequencing
-
Sampson, J., Jacobs, K., Yeager, M., Chanock, S. & Chatterjee, N. Efficient study design for next generation sequencing. Genet. Epidemiol. 35, 269-277 (2011).
-
(2011)
Genet. Epidemiol.
, vol.35
, pp. 269-277
-
-
Sampson, J.1
Jacobs, K.2
Yeager, M.3
Chanock, S.4
Chatterjee, N.5
-
99
-
-
84857232194
-
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions
-
Wang, W., Wei, Z., Lam, T. W. & Wang, J. Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. Scientif. Rep. 1, 55 (2011).
-
(2011)
Scientif. Rep.
, vol.1
, pp. 55
-
-
Wang, W.1
Wei, Z.2
Lam, T.W.3
Wang, J.4
-
100
-
-
84878629521
-
Benchmarking short sequence mapping tools
-
Hatem, A., Bozdag, D., Toland, A. E. & Catalyürek, Ü. V. Benchmarking short sequence mapping tools. BMC Bioinformatics 14, 184 (2013).
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 184
-
-
Hatem, A.1
Bozdag, D.2
Toland, A.E.3
Catalyürek, Ü.V.4
-
101
-
-
84868118627
-
A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing
-
Mijuskovic, M. et al. A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing. PLoS ONE 7, e48314 (2012).
-
(2012)
PLoS ONE
, vol.7
-
-
Mijuskovic, M.1
-
102
-
-
84864326252
-
Genomic dark matter: The reliability of short read mapping illustrated by the genome mappability score
-
Lee, H. & Schatz, M. C. Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. Bioinformatics 28, 2097-2105 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 2097-2105
-
-
Lee, H.1
Schatz, M.C.2
-
103
-
-
84855989774
-
Fast computation and applications of genome mappability
-
Derrien, T. et al. Fast computation and applications of genome mappability. PLoS ONE 7, e30377 (2012).
-
(2012)
PLoS ONE
, vol.7
-
-
Derrien, T.1
-
104
-
-
84875700725
-
Predicting the molecular complexity of sequencing libraries
-
Daley, T. & Smith, A. D. Predicting the molecular complexity of sequencing libraries. Nature Methods 10, 325-327 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 325-327
-
-
Daley, T.1
Smith, A.D.2
-
105
-
-
81755161195
-
Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines
-
Gottwein, E. et al. Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host Microbe 10, 515-526 (2011).
-
(2011)
Cell Host Microbe
, vol.10
, pp. 515-526
-
-
Gottwein, E.1
-
106
-
-
84866126892
-
Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain
-
Rogelj, B. et al. Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain. Scientif. Rep. 2, 603 (2012).
-
(2012)
Scientif. Rep.
, vol.2
, pp. 603
-
-
Rogelj, B.1
-
107
-
-
84870367830
-
ChIA-PET analysis of transcriptional chromatin interactions
-
Zhang, J. et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods 58, 289-299 (2012).
-
(2012)
Methods
, vol.58
, pp. 289-299
-
-
Zhang, J.1
-
108
-
-
84865800494
-
The long-range interaction landscape of gene promoters
-
Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109-113 (2012).
-
(2012)
Nature
, vol.489
, pp. 109-113
-
-
Sanyal, A.1
Lajoie, B.R.2
Jain, G.3
Dekker, J.4
-
109
-
-
84858146301
-
Methylome analysis using MeDIP-seq with low DNA concentrations
-
Taiwo, O. et al. Methylome analysis using MeDIP-seq with low DNA concentrations. Nature Protoc. 7, 617-636 (2012).
-
(2012)
Nature Protoc.
, vol.7
, pp. 617-636
-
-
Taiwo, O.1
-
110
-
-
84879049092
-
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates
-
Long, H. K. et al. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife 2, e00348 (2013).
-
(2013)
Elife
, vol.2
-
-
Long, H.K.1
|