-
1
-
-
77953203584
-
Global and unbiased detection of splice junctions from RNA-seq data
-
Ameur A, Wetterbom A, Feuk L, Gyllensten U (2010) Global and unbiased detection of splice junctions from RNA-seq data. Genome Biol 11(3): R34.
-
(2010)
Genome Biol
, vol.11
, Issue.3
-
-
Ameur, A.1
Wetterbom, A.2
Feuk, L.3
Gyllensten, U.4
-
2
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11(10): R106.
-
(2010)
Genome Biol
, vol.11
, Issue.10
-
-
Anders, S.1
Huber, W.2
-
3
-
-
77955443472
-
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
-
Au K, Jiang H, Lin L, Xing Y, Wong W (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res 38(14): 4570-4578.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.14
, pp. 4570-4578
-
-
Au, K.1
Jiang, H.2
Lin, L.3
Xing, Y.4
Wong, W.5
-
4
-
-
79958115654
-
A two-stage Poisson model for testing RNA-seq data
-
Auer P, Doerge R (2011) A two-stage Poisson model for testing RNA-seq data. Stat Appl Genet Mol Biol 10(1): 26.
-
(2011)
Stat Appl Genet Mol Biol
, vol.10
, Issue.1
, pp. 26
-
-
Auer, P.1
Doerge, R.2
-
5
-
-
70350664649
-
De novo transcriptome assembly with ABySS
-
Birol I, Jackman S, Nielsen C, Qian J, Varhol R, Stazyk G, Morin R, Zhao Y, Hirst M, Schein J et al. (2009) De novo transcriptome assembly with ABySS. Bioinformatics 25(21): 2872.
-
(2009)
Bioinformatics
, vol.25
, Issue.21
, pp. 2872
-
-
Birol, I.1
Jackman, S.2
Nielsen, C.3
Qian, J.4
Varhol, R.5
Stazyk, G.6
Morin, R.7
Zhao, Y.8
Hirst, M.9
Schein, J.10
-
6
-
-
77954302477
-
rQuant. web: a tool for RNA-seq-based transcript quantitation
-
Bohnert R, Rätsch G (2010) rQuant. web: a tool for RNA-seq-based transcript quantitation. Nucleic Acids Res 38(Suppl 2): W348-W351.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.SUPPL. 2
-
-
Bohnert, R.1
Rätsch, G.2
-
7
-
-
0037177625
-
Genetic dissection of transcriptional regulation in budding yeast
-
Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296(5568): 752-755.
-
(2002)
Science
, vol.296
, Issue.5568
, pp. 752-755
-
-
Brem, R.B.1
Yvert, G.2
Clinton, R.3
Kruglyak, L.4
-
8
-
-
35348817330
-
Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
-
Browning S, Browning B (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81(5): 1084-1097.
-
(2007)
Am J Hum Genet
, vol.81
, Issue.5
, pp. 1084-1097
-
-
Browning, S.1
Browning, B.2
-
9
-
-
20144386111
-
Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function
-
Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu HC, Mountz JD, Baldwin NE, Langston MA, Threadgill DW, Manly KF, Williams RW (2005) Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 37(3): 233-242.
-
(2005)
Nat Genet
, vol.37
, Issue.3
, pp. 233-242
-
-
Chesler, E.J.1
Lu, L.2
Shou, S.3
Qu, Y.4
Gu, J.5
Wang, J.6
Hsu, H.C.7
Mountz, J.D.8
Baldwin, N.E.9
Langston, M.A.10
Threadgill, D.W.11
Manly, K.F.12
Williams, R.W.13
-
10
-
-
46249103973
-
Stem cell transcriptome profiling via massive-scale mRNA sequencing
-
Cloonan N, Forrest A, Kolle G, Gardiner B, Faulkner G, Brown M, Taylor D, Steptoe A, Wani S, Bethel G et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5(7): 613-619.
-
(2008)
Nat Methods
, vol.5
, Issue.7
, pp. 613-619
-
-
Cloonan, N.1
Forrest, A.2
Kolle, G.3
Gardiner, B.4
Faulkner, G.5
Brown, M.6
Taylor, D.7
Steptoe, A.8
Wani, S.9
Bethel, G.10
-
11
-
-
60349092402
-
Mapping complex disease traits with global gene expression
-
Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M (2009) Mapping complex disease traits with global gene expression. Nat Rev Genet 10(3): 184-194.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.3
, pp. 184-194
-
-
Cookson, W.1
Liang, L.2
Abecasis, G.3
Moffatt, M.4
Lathrop, M.5
-
12
-
-
0036843938
-
Detection of regulatory variation in mouse genes
-
Cowles CR, Hirschhorn JN, Altshuler D, Lander ES (2002) Detection of regulatory variation in mouse genes. Nat Genet 32(3): 432-437.
-
(2002)
Nat Genet
, vol.32
, Issue.3
, pp. 432-437
-
-
Cowles, C.R.1
Hirschhorn, J.N.2
Altshuler, D.3
Lander, E.S.4
-
14
-
-
70349910898
-
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
-
Degner J, Marioni J, Pai A, Pickrell J, Nkadori E, Gilad Y, Pritchard J (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 25(24): 3207.
-
(2009)
Bioinformatics
, vol.25
, Issue.24
, pp. 3207
-
-
Degner, J.1
Marioni, J.2
Pai, A.3
Pickrell, J.4
Nkadori, E.5
Gilad, Y.6
Pritchard, J.7
-
15
-
-
58149513263
-
Annotating genomes with massive-scale RNA sequencing
-
Denoeud F, Aury J, Da Silva C, Noel B, Rogier O, Delledonne M, Morgante M, Valle G, Wincker P Scarpelli C et al. (2008) Annotating genomes with massive-scale RNA sequencing. Genome Biol 9(12): R175.
-
(2008)
Genome Biol
, vol.9
, Issue.12
-
-
Denoeud, F.1
Aury, J.2
Da Silva, C.3
Noel, B.4
Rogier, O.5
Delledonne, M.6
Morgante, M.7
Valle, G.8
Wincker, P.9
Scarpelli, C.10
-
16
-
-
19844366096
-
Cis-acting expression quantitative trait loci in mice
-
Doss S, Schadt E, Drake T, Lusis A (2005) Cis-acting expression quantitative trait loci in mice. Genome Res 15(5): 681.
-
(2005)
Genome Res
, vol.15
, Issue.5
, pp. 681
-
-
Doss, S.1
Schadt, E.2
Drake, T.3
Lusis, A.4
-
17
-
-
84975742565
-
A map of human genome variation from population-scale sequencing
-
Durbin R, Altshuler D, Abecasis G, Bentley D, Chakravarti A, Clark A, Collins F, De La Vega F, Donnelly P, Egholm M et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467(7319): 1061-1073.
-
(2010)
Nature
, vol.467
, Issue.7319
, pp. 1061-1073
-
-
Durbin, R.1
Altshuler, D.2
Abecasis, G.3
Bentley, D.4
Chakravarti, A.5
Clark, A.6
Collins, F.7
de la Vega, F.8
Donnelly, P.9
Egholm, M.10
-
18
-
-
41349095280
-
Genetics of gene expression and its effect on disease
-
Emilsson V, Thorleifsson G, Zhang B, Leonardson A, Zink F, Zhu J, Carlson S, Helgason A, Walters G, Gunnarsdottir S et al. (2008) Genetics of gene expression and its effect on disease. Nature 452(7186): 423-428.
-
(2008)
Nature
, vol.452
, Issue.7186
, pp. 423-428
-
-
Emilsson, V.1
Thorleifsson, G.2
Zhang, B.3
Leonardson, A.4
Zink, F.5
Zhu, J.6
Carlson, S.7
Helgason, A.8
Walters, G.9
Gunnarsdottir, S.10
-
19
-
-
78651304279
-
Whole-genome molecular haplotyping of single cells
-
Fan H, Wang J, Potanina A, Quake S (2010) Whole-genome molecular haplotyping of single cells. Nat Biotechnol 29(1): 51-57.
-
(2010)
Nat Biotechnol
, vol.29
, Issue.1
, pp. 51-57
-
-
Fan, H.1
Wang, J.2
Potanina, A.3
Quake, S.4
-
20
-
-
78651289449
-
Ensembl 2011
-
Flicek P, Amode M, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S et al. (2011) Ensembl 2011. Nucleic Acids Res 39(Suppl 1): D800.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.SUPPL. 1
-
-
Flicek, P.1
Amode, M.2
Barrell, D.3
Beal, K.4
Brent, S.5
Chen, Y.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
-
21
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber M, Grabherr M, Guttman M, Trapnell C (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8(6): 469-477.
-
(2011)
Nat Methods
, vol.8
, Issue.6
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.2
Guttman, M.3
Trapnell, C.4
-
23
-
-
70350651269
-
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis
-
Ge B, Pokholok DK, Kwan T, Grundberg E, Morcos L, Verlaan DJ, Le J, Koka V, Lam KC, Gagn V, Dias J, Hoberman R, Montpetit A, Joly MM, Harvey EJ, Sinnett D, Beaulieu P, Hamon R, Graziani A, Dewar K, Harmsen E, Majewski J, Güring HH, Naumova AK, Blanchette M, Gunderson KL, Pastinen T (2009) Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet 41(11): 1216-1222.
-
(2009)
Nat Genet
, vol.41
, Issue.11
, pp. 1216-1222
-
-
Ge, B.1
Pokholok, D.K.2
Kwan, T.3
Grundberg, E.4
Morcos, L.5
Verlaan, D.J.6
Le, J.7
Koka, V.8
Lam, K.C.9
Gagn, V.10
Dias, J.11
Hoberman, R.12
Montpetit, A.13
Joly, M.M.14
Harvey, E.J.15
Sinnett, D.16
Beaulieu, P.17
Hamon, R.18
Graziani, A.19
Dewar, K.20
Harmsen, E.21
Majewski, J.22
Güring, H.H.23
Naumova, A.K.24
Blanchette, M.25
Gunderson, K.L.26
Pastinen, T.27
more..
-
24
-
-
36249017308
-
Widespread monoallelic expression on human autosomes
-
Gimelbrant A, Hutchinson JN, Thompson BR, Chess A (2007) Widespread monoallelic expression on human autosomes. Science 318(5853): 1136-1140.
-
(2007)
Science
, vol.318
, Issue.5853
, pp. 1136-1140
-
-
Gimelbrant, A.1
Hutchinson, J.N.2
Thompson, B.R.3
Chess, A.4
-
25
-
-
77955299096
-
High-resolution analysis of parent-of-origin allelic expression in the mouse brain
-
Gregg C, Zhang J, Weissbourd B, Luo S, Schroth G, Haig D, Dulac C (2010) High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329(5992): 643.
-
(2010)
Science
, vol.329
, Issue.5992
, pp. 643
-
-
Gregg, C.1
Zhang, J.2
Weissbourd, B.3
Luo, S.4
Schroth, G.5
Haig, D.6
Dulac, C.7
-
26
-
-
77957663917
-
Alternative expression analysis by RNA sequencing
-
Griffith M, Griffith O, Mwenifumbo J, Goya R, Morrissy A, Morin R, Corbett R, Tang M, Hou Y, Pugh T et al. (2010) Alternative expression analysis by RNA sequencing. Nat Methods 7(10): 843-847.
-
(2010)
Nat Methods
, vol.7
, Issue.10
, pp. 843-847
-
-
Griffith, M.1
Griffith, O.2
Mwenifumbo, J.3
Goya, R.4
Morrissy, A.5
Morin, R.6
Corbett, R.7
Tang, M.8
Hou, Y.9
Pugh, T.10
-
27
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman M, Garber M, Levin J, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol M, Gnirke A, Nusbaum C et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28(5): 503-510.
-
(2010)
Nat Biotechnol
, vol.28
, Issue.5
, pp. 503-510
-
-
Guttman, M.1
Garber, M.2
Levin, J.3
Donaghey, J.4
Robinson, J.5
Adiconis, X.6
Fan, L.7
Koziol, M.8
Gnirke, A.9
Nusbaum, C.10
-
28
-
-
77955883388
-
Biases in illumina transcriptome sequencing caused by random hexamer priming
-
Hansen K, Brenner S, Dudoit S (2010) Biases in illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38(12): e131.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.12
-
-
Hansen, K.1
Brenner, S.2
Dudoit, S.3
-
29
-
-
77955298482
-
baySeq: empirical Bayesian methods for identifying differential expression in sequence count data
-
Hardcastle T, Kelly K (2010) baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinform 11(1): 422.
-
(2010)
BMC Bioinform
, vol.11
, Issue.1
, pp. 422
-
-
Hardcastle, T.1
Kelly, K.2
-
30
-
-
0031977436
-
Mechanism of cyclin d1 (ccnd1, prad1) overexpression in human cancer cells: analysis of allele-specific expression
-
Hosokawa Y, Arnold A (1998) Mechanism of cyclin d1 (ccnd1, prad1) overexpression in human cancer cells: analysis of allele-specific expression. Genes Chromosomes Cancer 22(1): 66-71.
-
(1998)
Genes Chromosomes Cancer
, vol.22
, Issue.1
, pp. 66-71
-
-
Hosokawa, Y.1
Arnold, A.2
-
31
-
-
34547438105
-
A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity
-
Huang R, Duan S, Bleibel W, Kistner E, Zhang W, Clark T, Chen T, Schweitzer A, Blume J, Cox N et al. (2007) A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. Proc Natl Acad Sci 104(23): 9758.
-
(2007)
Proc Natl Acad Sci
, vol.104
, Issue.23
, pp. 9758
-
-
Huang, R.1
Duan, S.2
Bleibel, W.3
Kistner, E.4
Zhang, W.5
Clark, T.6
Chen, T.7
Schweitzer, A.8
Blume, J.9
Cox, N.10
-
32
-
-
64549119707
-
Statistical inferences for isoform expression in RNA-Seq
-
Jiang H, Wong W (2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25(8): 1026.
-
(2009)
Bioinformatics
, vol.25
, Issue.8
, pp. 1026
-
-
Jiang, H.1
Wong, W.2
-
33
-
-
0347623371
-
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays
-
Johnson J, Castle J, Garrett-Engele P, Kan Z, Loerch P, Armour C, Santos R, Schadt E, Stoughton R, Shoemaker D (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302(5653): 2141.
-
(2003)
Science
, vol.302
, Issue.5653
, pp. 2141
-
-
Johnson, J.1
Castle, J.2
Garrett-Engele, P.3
Kan, Z.4
Loerch, P.5
Armour, C.6
Santos, R.7
Schadt, E.8
Stoughton, R.9
Shoemaker, D.10
-
34
-
-
78649714014
-
Analysis and design of RNA sequencing experiments for identifying isoform regulation
-
Katz Y, Wang E, Airoldi E, Burge C (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7(12): 1009-1015.
-
(2010)
Nat Methods
, vol.7
, Issue.12
, pp. 1009-1015
-
-
Katz, Y.1
Wang, E.2
Airoldi, E.3
Burge, C.4
-
35
-
-
78651333227
-
Haplotype-resolved genome sequencing of a Gujarati Indian individual
-
Kitzman J, MacKenzie A, Adey A, Hiatt J, Patwardhan R, Sudmant P, Ng S, Alkan C, Qiu R, Eichler E et al. (2010) Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol 29(1): 59-63.
-
(2010)
Nat Biotechnol
, vol.29
, Issue.1
, pp. 59-63
-
-
Kitzman, J.1
MacKenzie, A.2
Adey, A.3
Hiatt, J.4
Patwardhan, R.5
Sudmant, P.6
Ng, S.7
Alkan, C.8
Qiu, R.9
Eichler, E.10
-
36
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al. (2001) Initial sequencing and analysis of the human genome. Nature 409(6822): 860-921.
-
(2001)
Nature
, vol.409
, Issue.6822
, pp. 860-921
-
-
Lander, E.1
Linton, L.2
Birren, B.3
Nusbaum, C.4
Zody, M.5
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
FitzHugh, W.10
-
37
-
-
0000568233
-
On the comparison of multinomial and Poisson log-linear models
-
(Methodological)
-
Lang J (1996) On the comparison of multinomial and Poisson log-linear models. Journal of the Royal Statistical Society Series B (Methodological), 253-266.
-
(1996)
Journal of the Royal Statistical Society Series B
, pp. 253-266
-
-
Lang, J.1
-
38
-
-
79551494866
-
Accurate quantification of transcriptome from RNA-seq data by effective length normalization
-
Lee S, Seo C, Lim B, Yang J, Oh J, Kim M, Lee S, Lee B, Kang C, Lee S (2011) Accurate quantification of transcriptome from RNA-seq data by effective length normalization. Nucleic Acids Res 39(2): e9.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.2
-
-
Lee, S.1
Seo, C.2
Lim, B.3
Yang, J.4
Oh, J.5
Kim, M.6
Lee, S.7
Lee, B.8
Kang, C.9
Lee, S.10
-
39
-
-
77949507153
-
RNA-seq gene expression estimation with read mapping uncertainty
-
Li B, Ruotti V, Stewart R, Thomson J, Dewey C (2010) RNA-seq gene expression estimation with read mapping uncertainty. Bioinformatics 26(4): 493-500.
-
(2010)
Bioinformatics
, vol.26
, Issue.4
, pp. 493-500
-
-
Li, B.1
Ruotti, V.2
Stewart, R.3
Thomson, J.4
Dewey, C.5
-
40
-
-
84877074491
-
Sparse linear modeling of RNA-seq data for isoform discovery and abundance estimation
-
in press
-
Li J, Jiang C, Hu Y, Brown B, Huang H, Bickel P (2011, in press) Sparse linear modeling of RNA-seq data for isoform discovery and abundance estimation. Proc Natl Acad Sci USA.
-
(2011)
Proc Natl Acad Sci USA
-
-
Li, J.1
Jiang, C.2
Hu, Y.3
Brown, B.4
Huang, H.5
Bickel, P.6
-
41
-
-
77951940273
-
Modeling non-uniformity in short-read rates in RNA-seq data
-
Li J, Jiang H, Wong W (2010) Modeling non-uniformity in short-read rates in RNA-seq data. Genome Biol 11(5): R25.
-
(2010)
Genome Biol
, vol.11
, Issue.5
-
-
Li, J.1
Jiang, H.2
Wong, W.3
-
42
-
-
79953186446
-
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. Research in Computational Molecular Biology, 168-188.
-
(2011)
Research in Computational Molecular Biology
, pp. 168-188
-
-
Li, W.1
Feng, J.2
Jiang, T.3
-
43
-
-
33845976693
-
Mapping determinants of gene expression plasticity by genetical genomics in C elegans
-
Li Y, Alvarez OA, Gutteling EW, Tijsterman M, Fu J, Riksen JAG, Hazendonk E, Prins P, Plasterk RHA, Jansen RC, Breitling R, Kammenga JE (2006) Mapping determinants of gene expression plasticity by genetical genomics in C elegans. PLoS Genet 2(12): e222.
-
(2006)
PLoS Genet
, vol.2
, Issue.12
-
-
Li, Y.1
Alvarez, O.A.2
Gutteling, E.W.3
Tijsterman, M.4
Fu, J.5
Riksen, J.A.G.6
Hazendonk, E.7
Prins, P.8
Plasterk, R.H.A.9
Jansen, R.C.10
Breitling, R.11
Kammenga, J.E.12
-
44
-
-
78649508578
-
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
-
Li Y, Willer C, Ding J, Scheet P, Abecasis G (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34(8): 816-834.
-
(2010)
Genet Epidemiol
, vol.34
, Issue.8
, pp. 816-834
-
-
Li, Y.1
Willer, C.2
Ding, J.3
Scheet, P.4
Abecasis, G.5
-
45
-
-
0012789869
-
Allelic variation in gene expression is common in the human genome
-
Lo HS, Wang Z, Hu Y, Yang HH, Gere S, Buetow KH, Lee MP (2003) Allelic variation in gene expression is common in the human genome. Genome Res 13(8): 1855-1862.
-
(2003)
Genome Res
, vol.13
, Issue.8
, pp. 1855-1862
-
-
Lo, H.S.1
Wang, Z.2
Hu, Y.3
Yang, H.H.4
Gere, S.5
Buetow, K.H.6
Lee, M.P.7
-
46
-
-
33344458848
-
A comparison of phasing algorithms for trios and unrelated individuals
-
Marchini J, Cutler D, Patterson N, Stephens M, Eskin E, Halperin E, Lin S, Qin Z, Munro H, Abecasis G et al. (2006) A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 78(3): 437-450.
-
(2006)
Am J Hum Genet
, vol.78
, Issue.3
, pp. 437-450
-
-
Marchini, J.1
Cutler, D.2
Patterson, N.3
Stephens, M.4
Eskin, E.5
Halperin, E.6
Lin, S.7
Qin, Z.8
Munro, H.9
Abecasis, G.10
-
47
-
-
50649089207
-
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni J, Mason C, Mane S, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18(9): 1509-1517.
-
(2008)
Genome Res
, vol.18
, Issue.9
, pp. 1509-1517
-
-
Marioni, J.1
Mason, C.2
Mane, S.3
Stephens, M.4
Gilad, Y.5
-
48
-
-
77953010033
-
Regulatory divergence in drosophila revealed by mRNA-seq
-
McManus C, Coolon J, Duff M, Eipper-Mains J, Graveley B, Wittkopp P (2010) Regulatory divergence in drosophila revealed by mRNA-seq. Genome Res 20(6): 816-825.
-
(2010)
Genome Res
, vol.20
, Issue.6
, pp. 816-825
-
-
McManus, C.1
Coolon, J.2
Duff, M.3
Eipper-Mains, J.4
Graveley, B.5
Wittkopp, P.6
-
49
-
-
45149099137
-
Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer
-
Meyer K, Maia A, O'Reilly M, Teschendorff A, Chin S, Caldas C, Ponder B (2008) Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer. PLoS Biol 6(5): e108.
-
(2008)
PLoS Biol
, vol.6
, Issue.5
-
-
Meyer, K.1
Maia, A.2
O'Reilly, M.3
Teschendorff, A.4
Chin, S.5
Caldas, C.6
Ponder, B.7
-
50
-
-
77950458649
-
Transcriptome genetics using second generation sequencing in a Caucasian population
-
Montgomery S, Sammeth M, Gutierrez-Arcelus M, Lach R, Ingle C, Nisbett J, Guigo R, Dermitzakis E (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464(7289): 773-777.
-
(2010)
Nature
, vol.464
, Issue.7289
, pp. 773-777
-
-
Montgomery, S.1
Sammeth, M.2
Gutierrez-Arcelus, M.3
Lach, R.4
Ingle, C.5
Nisbett, J.6
Guigo, R.7
Dermitzakis, E.8
-
51
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, Williams B, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7): 621-628.
-
(2008)
Nat Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
52
-
-
78751570979
-
RNA sequencing: advances, challenges and opportunities
-
Ozsolak F, Milos P (2010) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12(2): 87-98.
-
(2010)
Nat Rev Genet
, vol.12
, Issue.2
, pp. 87-98
-
-
Ozsolak, F.1
Milos, P.2
-
54
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Pan Q, Shai O, Lee L, Frey B, Blencowe B (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40(12): 1413-1415.
-
(2008)
Nat Genet
, vol.40
, Issue.12
, pp. 1413-1415
-
-
Pan, Q.1
Shai, O.2
Lee, L.3
Frey, B.4
Blencowe, B.5
-
55
-
-
77954763156
-
Genome-wide allele-specific analysis: insights into regulatory variation
-
Pastinen T (2010) Genome-wide allele-specific analysis: insights into regulatory variation. Nat Rev Genet 11(8): 533-538.
-
(2010)
Nat Rev Genet
, vol.11
, Issue.8
, pp. 533-538
-
-
Pastinen, T.1
-
56
-
-
84870267097
-
Regularized multivariate regression for identifying master predictors with application to integrative genomics study of breast cancer
-
Peng J, Zhu J, Bergamaschi A, Han W, Noh DY, Pollack J, Wang P (2010) Regularized multivariate regression for identifying master predictors with application to integrative genomics study of breast cancer. Ann Appl Stat 4(1): 53-77.
-
(2010)
Ann Appl Stat
, vol.4
, Issue.1
, pp. 53-77
-
-
Peng, J.1
Zhu, J.2
Bergamaschi, A.3
Han, W.4
Noh, D.Y.5
Pollack, J.6
Wang, P.7
-
57
-
-
33750481513
-
Heritability and tissue specificity of expression quantitative trait loci
-
Petretto E, Mangion J, Dickens NJ, Cook SA, Kumaran MK, Lu H, Fischer J, Maatz H, Kren V, Pravenec M, Hubner N, Aitman TJ (2006) Heritability and tissue specificity of expression quantitative trait loci. PLoS Genet 2(10): e172.
-
(2006)
PLoS Genet
, vol.2
, Issue.10
-
-
Petretto, E.1
Mangion, J.2
Dickens, N.J.3
Cook, S.A.4
Kumaran, M.K.5
Lu, H.6
Fischer, J.7
Maatz, H.8
Kren, V.9
Pravenec, M.10
Hubner, N.11
Aitman, T.J.12
-
58
-
-
77950460661
-
Understanding mechanisms underlying human gene expression variation with RNA sequencing
-
Pickrell J, Marioni J, Pai A, Degner J, Engelhardt B, Nkadori E, Veyrieras J, Stephens M, Gilad Y, Pritchard J (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464(7289): 768-772.
-
(2010)
Nature
, vol.464
, Issue.7289
, pp. 768-772
-
-
Pickrell, J.1
Marioni, J.2
Pai, A.3
Degner, J.4
Engelhardt, B.5
Nkadori, E.6
Veyrieras, J.7
Stephens, M.8
Gilad, Y.9
Pritchard, J.10
-
59
-
-
77954127002
-
Prediction of alternative isoforms from exon expression levels in RNA-seq experiments
-
Richard H, Schulz M, Sultan M, Nürnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M et al. (2010) Prediction of alternative isoforms from exon expression levels in RNA-seq experiments. Nucleic Acids Res 38(10): e112.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.10
-
-
Richard, H.1
Schulz, M.2
Sultan, M.3
Nürnberger, A.4
Schrinner, S.5
Balzereit, D.6
Dagand, E.7
Rasche, A.8
Lehrach, H.9
Vingron, M.10
-
60
-
-
79952709611
-
Improving RNA-seq expression estimates by correcting for fragment bias
-
Roberts A, Trapnell C, Donaghey J, Rinn J, Pachter L et al. (2011) Improving RNA-seq expression estimates by correcting for fragment bias. Genome Biol 12(3): R22.
-
(2011)
Genome Biol
, vol.12
, Issue.3
-
-
Roberts, A.1
Trapnell, C.2
Donaghey, J.3
Rinn, J.4
Pachter, L.5
-
61
-
-
78049346632
-
De novo assembly and analysis of RNA-seq data
-
Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman S, Mungall K, Lee S, Okada H, Qian J et al. (2010) De novo assembly and analysis of RNA-seq data. Nat Methods 7(11): 909-912.
-
(2010)
Nat Methods
, vol.7
, Issue.11
, pp. 909-912
-
-
Robertson, G.1
Schein, J.2
Chiu, R.3
Corbett, R.4
Field, M.5
Jackman, S.6
Mungall, K.7
Lee, S.8
Okada, H.9
Qian, J.10
-
62
-
-
75249087100
-
edgeR: a bioconductor package for differential expression analysis of digital gene expression data
-
Robinson M, McCarthy D, Smyth G (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1): 139-140.
-
(2010)
Bioinformatics
, vol.26
, Issue.1
, pp. 139-140
-
-
Robinson, M.1
McCarthy, D.2
Smyth, G.3
-
63
-
-
33750204290
-
Genetics of global gene expression
-
Rockman M, Kruglyak L (2006) Genetics of global gene expression. Nat Rev Genet 7(11): 862-872.
-
(2006)
Nat Rev Genet
, vol.7
, Issue.11
, pp. 862-872
-
-
Rockman, M.1
Kruglyak, L.2
-
64
-
-
48949094754
-
Local regulatory variation in Saccharomyces cerevisiae
-
Ronald J, Brem R, Whittle J, Kruglyak L (2005) Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet 1(2): e25.
-
(2005)
PLoS Genet
, vol.1
, Issue.2
-
-
Ronald, J.1
Brem, R.2
Whittle, J.3
Kruglyak, L.4
-
65
-
-
80053314092
-
Statistical modeling of RNA-seq data
-
Salzman J, Jiang H, Wong W (2011) Statistical modeling of RNA-seq data. Stat Sci 26(1): 62-83.
-
(2011)
Stat Sci
, vol.26
, Issue.1
, pp. 62-83
-
-
Salzman, J.1
Jiang, H.2
Wong, W.3
-
66
-
-
45149108420
-
Mapping the genetic architecture of gene expression in human liver
-
Schadt E, Molony C, Chudin E, Hao K, Yang X, Lum P, Kasarskis A, Zhang B, Wang S, Suver C et al. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6(5): e107.
-
(2008)
PLoS Biol
, vol.6
, Issue.5
-
-
Schadt, E.1
Molony, C.2
Chudin, E.3
Hao, K.4
Yang, X.5
Lum, P.6
Kasarskis, A.7
Zhang, B.8
Wang, S.9
Suver, C.10
-
67
-
-
0037456823
-
Genetics of gene expression surveyed in maize, mouse and man
-
Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422(6929): 297-302.
-
(2003)
Nature
, vol.422
, Issue.6929
, pp. 297-302
-
-
Schadt, E.E.1
Monks, S.A.2
Drake, T.A.3
Lusis, A.J.4
Che, N.5
Colinayo, V.6
Ruff, T.G.7
Milligan, S.B.8
Lamb, J.R.9
Cavet, G.10
Linsley, P.S.11
Mao, M.12
Stoughton, R.B.13
Friend, S.H.14
-
68
-
-
77950490438
-
MADS+: discovery of differential splicing events from Affymetrix exon junction array data
-
Shen S, Warzecha C, Carstens R, Xing Y (2010) MADS+: discovery of differential splicing events from Affymetrix exon junction array data. Bioinformatics 26(2): 268.
-
(2010)
Bioinformatics
, vol.26
, Issue.2
, pp. 268
-
-
Shen, S.1
Warzecha, C.2
Carstens, R.3
Xing, Y.4
-
69
-
-
66449136667
-
ABySS: a parallel assembler for short read sequence data
-
Simpson J, Wong K, Jackman S, Schein J, Jones S, Birol İ (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19(6): 1117.
-
(2009)
Genome Res
, vol.19
, Issue.6
, pp. 1117
-
-
Simpson, J.1
Wong, K.2
Jackman, S.3
Schein, J.4
Jones, S.5
Birol, I.6
-
70
-
-
80053435328
-
FDM: a graph-based statistical method to detect differential transcription using RNA-seq data
-
Singh D, Orellana C, Hu Y, Jones C, Liu Y, Chiang D, Liu J, Prins J (2011) FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics 27(19): 2633-2640.
-
(2011)
Bioinformatics
, vol.27
, Issue.19
, pp. 2633-2640
-
-
Singh, D.1
Orellana, C.2
Hu, Y.3
Jones, C.4
Liu, Y.5
Chiang, D.6
Liu, J.7
Prins, J.8
-
71
-
-
80053522581
-
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
-
Skelly DA, Johansson M, Madeoy J, Wakefield J, Akey JM (2011) A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome Res 21(10): 1728-1737.
-
(2011)
Genome Res
, vol.21
, Issue.10
, pp. 1728-1737
-
-
Skelly, D.A.1
Johansson, M.2
Madeoy, J.3
Wakefield, J.4
Akey, J.M.5
-
72
-
-
33846631884
-
Common genetic variants account for differences in gene expression among ethnic groups
-
Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG (2007) Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 39(2): 226-231.
-
(2007)
Nat Genet
, vol.39
, Issue.2
, pp. 226-231
-
-
Spielman, R.S.1
Bastone, L.A.2
Burdick, J.T.3
Morley, M.4
Ewens, W.J.5
Cheung, V.G.6
-
73
-
-
85052549687
-
A two-parameter generalized Poisson model to improve the analysis of RNA-seq data
-
Srivastava S, Chen L (2010) A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Res 38(17): e170.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.17
-
-
Srivastava, S.1
Chen, L.2
-
74
-
-
33846978695
-
Relative impact of nucleotide and copy number variation on gene expression phenotypes
-
Stranger B, Forrest M, Dunning M, Ingle C, Beazley C, Thorne N, Redon R, Bird C, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer S, Tavare S, Deloukas P, Hurles M, Dermitzakis E (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853.
-
(2007)
Science
, vol.315
, pp. 848-853
-
-
Stranger, B.1
Forrest, M.2
Dunning, M.3
Ingle, C.4
Beazley, C.5
Thorne, N.6
Redon, R.7
Bird, C.8
de Grassi, A.9
Lee, C.10
Tyler-Smith, C.11
Carter, N.12
Scherer, S.13
Tavare, S.14
Deloukas, P.15
Hurles, M.16
Dermitzakis, E.17
-
75
-
-
34548738566
-
Population genomics of human gene expression
-
Stranger B, Nica A, Forrest M, Dimas A, Bird C, Beazley C, Ingle C, Dunning M, Flicek P, Koller D et al. (2007) Population genomics of human gene expression. Nat Genet 39(10): 1217-1224.
-
(2007)
Nat Genet
, vol.39
, Issue.10
, pp. 1217-1224
-
-
Stranger, B.1
Nica, A.2
Forrest, M.3
Dimas, A.4
Bird, C.5
Beazley, C.6
Ingle, C.7
Dunning, M.8
Flicek, P.9
Koller, D.10
-
76
-
-
47649124124
-
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
-
Sultan M, Schulz M, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321(5891): 956.
-
(2008)
Science
, vol.321
, Issue.5891
, pp. 956
-
-
Sultan, M.1
Schulz, M.2
Richard, H.3
Magen, A.4
Klingenhoff, A.5
Scherf, M.6
Seifert, M.7
Borodina, T.8
Soldatov, A.9
Parkhomchuk, D.10
-
77
-
-
84877031236
-
A statistical framework for EQTL mapping using RNA-seq data
-
in press
-
Sun W (2011, in press) A statistical framework for EQTL mapping using RNA-seq data. Biometrics.
-
(2011)
Biometrics
-
-
Sun, W.1
-
78
-
-
85194972808
-
Regression shrinkage and selection via the Lasso
-
Tibshirani R (1996) Regression shrinkage and selection via the Lasso. J R Stat Soc B 58(1): 267-288.
-
(1996)
J R Stat Soc B
, vol.58
, Issue.1
, pp. 267-288
-
-
Tibshirani, R.1
-
79
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-seq
-
Trapnell C, Pachter L, Salzberg S (2009) TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25(9): 1105.
-
(2009)
Bioinformatics
, vol.25
, Issue.9
, pp. 1105
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.3
-
80
-
-
77952123055
-
Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M, Salzberg S, Wold B, Pachter L (2010) Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5): 511-515.
-
(2010)
Nat Biotechnol
, vol.28
, Issue.5
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
van Baren, M.6
Salzberg, S.7
Wold, B.8
Pachter, L.9
-
81
-
-
79751531332
-
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
-
Turro E, Su S, Gonçalves Â, Coin L, Richardson S, Lewin A (2011) Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol 12(2): R13.
-
(2011)
Genome Biol
, vol.12
, Issue.2
-
-
Turro, E.1
Su, S.2
Gonçalves, Â.3
Coin, L.4
Richardson, S.5
Lewin, A.6
-
82
-
-
51149099981
-
Germline allele-specific expression of tgfbr1 confers an increased risk of colorectal cancer
-
Valle L, Serena-Acedo T, Liyanarachchi S, Hampel H, Comeras I, Li Z, Zeng Q, Zhang H, Pennison M, Sadim M et al. (2008) Germline allele-specific expression of tgfbr1 confers an increased risk of colorectal cancer. Science 321(5894): 1361.
-
(2008)
Science
, vol.321
, Issue.5894
, pp. 1361
-
-
Valle, L.1
Serena-Acedo, T.2
Liyanarachchi, S.3
Hampel, H.4
Comeras, I.5
Li, Z.6
Zeng, Q.7
Zhang, H.8
Pennison, M.9
Sadim, M.10
-
83
-
-
7444220147
-
Aberrant and alternative splicing in cancer
-
Venables J (2004) Aberrant and alternative splicing in cancer. Cancer Res 64(21): 7647.
-
(2004)
Cancer Res
, vol.64
, Issue.21
, pp. 7647
-
-
Venables, J.1
-
84
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang E, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore S, Schroth G, Burge C (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456(7221): 470-476.
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 470-476
-
-
Wang, E.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
Kingsmore, S.7
Schroth, G.8
Burge, C.9
-
85
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang E, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore S, Schroth G, Burge C (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456(7221): 470-476.
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 470-476
-
-
Wang, E.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
Kingsmore, S.7
Schroth, G.8
Burge, C.9
-
86
-
-
34548758543
-
Splicing in disease: disruption of the splicing code and the decoding machinery
-
Wang G, Cooper T (2007) Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 8(10): 749-761.
-
(2007)
Nat Rev Genet
, vol.8
, Issue.10
, pp. 749-761
-
-
Wang, G.1
Cooper, T.2
-
87
-
-
78649345104
-
Mapsplice: accurate mapping of RNA-seq reads for splice junction discovery
-
Wang K, Singh D, Zeng Z, Coleman S, Huang Y, Savich G, He X, Mieczkowski P, Grimm S, Perou C et al. (2010) Mapsplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 38(18): e178.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.18
-
-
Wang, K.1
Singh, D.2
Zeng, Z.3
Coleman, S.4
Huang, Y.5
Savich, G.6
He, X.7
Mieczkowski, P.8
Grimm, S.9
Perou, C.10
-
88
-
-
75249095274
-
Degseq: an r package for identifying differentially expressed genes from RNA-seq data
-
Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) Degseq: an r package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26(1): 136-138.
-
(2010)
Bioinformatics
, vol.26
, Issue.1
, pp. 136-138
-
-
Wang, L.1
Feng, Z.2
Wang, X.3
Wang, X.4
Zhang, X.5
-
89
-
-
33645770040
-
Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity
-
Wang S, Yehya N, Schadt EE, Wang H, Drake TA, Lusis AJ (2006) Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet 2(2): e15.
-
(2006)
PLoS Genet
, vol.2
, Issue.2
-
-
Wang, S.1
Yehya, N.2
Schadt, E.E.3
Wang, H.4
Drake, T.A.5
Lusis, A.J.6
-
90
-
-
57749195712
-
RNA-Seq: a revolutionary tool for transcriptomics
-
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1): 57-63.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.1
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
91
-
-
3042722019
-
Evolutionary changes in cis and trans gene regulation
-
Wittkopp P, Haerum B, Clark A (2004) Evolutionary changes in cis and trans gene regulation. Nature 430(6995): 85-88.
-
(2004)
Nature
, vol.430
, Issue.6995
, pp. 85-88
-
-
Wittkopp, P.1
Haerum, B.2
Clark, A.3
-
92
-
-
79951522882
-
Using non-uniform read distribution models to improve isoform expression inference in RNA-seq
-
Wu Z, Wang X, Zhang X (2011) Using non-uniform read distribution models to improve isoform expression inference in RNA-seq. Bioinformatics 27(4): 502.
-
(2011)
Bioinformatics
, vol.27
, Issue.4
, pp. 502
-
-
Wu, Z.1
Wang, X.2
Zhang, X.3
-
93
-
-
79955914959
-
NSMAP: a method for spliced isoforms identification and quantification from RNA-seq
-
Xia Z, Wen J, Chang C, Zhou X (2011) NSMAP: a method for spliced isoforms identification and quantification from RNA-seq. BMC Bioinform 12(1): 162.
-
(2011)
BMC Bioinform
, vol.12
, Issue.1
, pp. 162
-
-
Xia, Z.1
Wen, J.2
Chang, C.3
Zhou, X.4
-
94
-
-
80051803605
-
Detection of cis-acting regulatory SNPs using allelic expression data
-
Xiao R, Scott L (2011) Detection of cis-acting regulatory SNPs using allelic expression data. Genet Epidemiol 35: 515-525.
-
(2011)
Genet Epidemiol
, vol.35
, pp. 515-525
-
-
Xiao, R.1
Scott, L.2
-
95
-
-
48149096726
-
MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays
-
Xing Y, Stoilov P, Kapur K, Han A, Jiang H, Shen S, Black D, Wong W (2008) MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA 14(8): 1470-1479.
-
(2008)
Rna
, vol.14
, Issue.8
, pp. 1470-1479
-
-
Xing, Y.1
Stoilov, P.2
Kapur, K.3
Han, A.4
Jiang, H.5
Shen, S.6
Black, D.7
Wong, W.8
-
96
-
-
33745156134
-
An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs
-
Xing Y, Yu T, Wu Y, Roy M, Kim J, Lee C (2006) An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res 34(10): 3150.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.10
, pp. 3150
-
-
Xing, Y.1
Yu, T.2
Wu, Y.3
Roy, M.4
Kim, J.5
Lee, C.6
-
97
-
-
78651109312
-
Completely phased genome sequencing through chromosome sorting
-
Yang H, Chen X, Wong W (2011) Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci 108(1): 12.
-
(2011)
Proc Natl Acad Sci
, vol.108
, Issue.1
, pp. 12
-
-
Yang, H.1
Chen, X.2
Wong, W.3
-
98
-
-
84860352230
-
A sparse conditional Gaussian graphical model for analysis of genetical genomics data
-
Yin J, Li H (2011) A sparse conditional Gaussian graphical model for analysis of genetical genomics data. Ann Appl Stat 5(4): 2630-2650.
-
(2011)
Ann Appl Stat
, vol.5
, Issue.4
, pp. 2630-2650
-
-
Yin, J.1
Li, H.2
-
99
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino D, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5): 821-829.
-
(2008)
Genome Res
, vol.18
, Issue.5
, pp. 821-829
-
-
Zerbino, D.1
Birney, E.2
-
100
-
-
68349089152
-
Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human
-
Zhang K, Li JB, Gao Y, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, Leproust EM, Eggan K, Church GM (2009) Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods 6(8): 613-618.
-
(2009)
Nat Methods
, vol.6
, Issue.8
, pp. 613-618
-
-
Zhang, K.1
Li, J.B.2
Gao, Y.3
Egli, D.4
Xie, B.5
Deng, J.6
Li, Z.7
Lee, J.H.8
Aach, J.9
Leproust, E.M.10
Eggan, K.11
Church, G.M.12
-
101
-
-
78649329196
-
Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing
-
Zhao Q, Kirkness E, Caballero O, Galante P, Parmigiani R, Edsall L, Kuan S, Ye Z, Levy S, Vasconcelos A et al. (2010) Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing. Genome Biol 11(11): R114.
-
(2010)
Genome Biol
, vol.11
, Issue.11
-
-
Zhao, Q.1
Kirkness, E.2
Caballero, O.3
Galante, P.4
Parmigiani, R.5
Edsall, L.6
Kuan, S.7
Ye, Z.8
Levy, S.9
Vasconcelos, A.10
-
102
-
-
67249136028
-
A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level
-
Zheng S, Chen L (2009) A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res 37(10): e75.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.10
-
-
Zheng, S.1
Chen, L.2
-
103
-
-
77950339092
-
Integrating pathway analysis and genetics of gene expression for genome-wide association studies
-
Zhong H, Yang X, Kaplan L, Molony C, Schadt E (2010) Integrating pathway analysis and genetics of gene expression for genome-wide association studies. Am J Hum Genet 86(4): 581-591.
-
(2010)
Am J Hum Genet
, vol.86
, Issue.4
, pp. 581-591
-
-
Zhong, H.1
Yang, X.2
Kaplan, L.3
Molony, C.4
Schadt, E.5
|