-
2
-
-
70349414048
-
The gene evolution model and computing its associated probabilities
-
Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM 56:1-44
-
(2009)
J ACM
, vol.56
, pp. 1-44
-
-
Arvestad, L.1
Lagergren, J.2
Sennblad, B.3
-
3
-
-
77955504378
-
Statistical design and analysis of RNA sequencing data
-
Auer PL, Doerge RW. 2010. Statistical design and analysis of RNA sequencing data. Genetics 185:405-16
-
(2010)
Genetics
, vol.185
, pp. 405-416
-
-
Auer, P.L.1
Doerge, R.W.2
-
4
-
-
59049088893
-
Optimization of gene expression by natural selection
-
Bedford T, Hartl DL. 2009. Optimization of gene expression by natural selection. Proc Natl Acad Sci USA 106:1133-8
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 1133-1138
-
-
Bedford, T.1
Hartl, D.L.2
-
5
-
-
62349112885
-
Covariance regularization by thresholding
-
Bickel PJ, Levina E. 2008. Covariance regularization by thresholding. The Annals of Statistics 36:2577-604
-
(2008)
Annals of Statistics
, vol.36
, pp. 2577-2604
-
-
Bickel, P.J.1
Levina, E.2
-
6
-
-
80054976678
-
The evolution of gene expression levels in mammalian organs
-
Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, et al. 2011. The evolution of gene expression levels in mammalian organs. Nature 478:343-8
-
(2011)
Nature
, vol.478
, pp. 343-348
-
-
Brawand, D.1
Soumillon, M.2
Necsulea, A.3
Julien, P.4
Csárdi, G.5
Harrigan, P.6
Weier, M.7
Liechti, A.8
Aximu-Petri, A.9
Kircher, M.10
-
7
-
-
0022203256
-
Phylogenies and the comparative method
-
Felsenstein J. 1985. Phylogenies and the comparative method. Am Nat 125:1-15
-
(1985)
Am Nat
, vol.125
, pp. 1-15
-
-
Felsenstein, J.1
-
8
-
-
43949115169
-
Comparative methods with sampling error and within-species variation: Contrasts revisited and revised
-
Felsenstein J. 2008. Comparative methods with sampling error and within-species variation: Contrasts revisited and revised. Am Nat 171:713-25
-
(2008)
Am Nat
, vol.171
, pp. 713-725
-
-
Felsenstein, J.1
-
9
-
-
0032893932
-
Preservation of duplicate genes by complementary, degenerative mutations
-
Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-45
-
(1999)
Genetics
, vol.151
, pp. 1531-1545
-
-
Force, A.1
Lynch, M.2
Pickett, F.B.3
Amores, A.4
Yan, Y.L.5
Postlethwait, J.6
-
12
-
-
77955883388
-
Biases in Illumina transcriptome sequencing caused by random hexamer priming
-
Hansen KD, Brenner SE, Dudoit S. 2010. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38:e131
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Hansen, K.D.1
Brenner, S.E.2
Dudoit, S.3
-
13
-
-
84858068675
-
Removing technical variability in RNA-seq data using conditional quantile normalization
-
Hansen KD, Irizarry RA, Wu Z. 2012. Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics 13:204-16
-
(2012)
Biostatistics
, vol.13
, pp. 204-216
-
-
Hansen, K.D.1
Irizarry, R.A.2
Wu, Z.3
-
15
-
-
71849116163
-
Evolving gene expression: From G to E to G x E
-
Hodgins-Davis A, Townsend JP. 2009. Evolving gene expression: From G to E to G x E. Trends Ecol Evol 24:649-58
-
(2009)
Trends Ecol Evol
, vol.24
, pp. 649-658
-
-
Hodgins-Davis, A.1
Townsend, J.P.2
-
16
-
-
34447280382
-
Within-species variation and measurement error in phylogenetic comparative methods
-
Ives AR, Midford PE, Garland TJ. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Syst Biol 56:252-70
-
(2007)
Syst Biol
, vol.56
, pp. 252-270
-
-
Ives, A.R.1
Midford, P.E.2
Garland, T.J.3
-
17
-
-
34848914038
-
Capturing heterogeneity in gene expression studies by surrogate variable analysis
-
Leek JT, Storey JD. 2007. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet 3:1724-35
-
(2007)
PLoS Genet
, vol.3
, pp. 1724-1735
-
-
Leek, J.T.1
Storey, J.D.2
-
19
-
-
79959828326
-
Testing the ortholog conjecture with comparative functional genomic data from mammals
-
Nehrt NL, Clark WT, Radivojac P, Hahn MW. 2011. Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS Comput Biol 7:e1002073
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Nehrt, N.L.1
Clark, W.T.2
Radivojac, P.3
Hahn, M.W.4
-
20
-
-
78650481676
-
A Bayesian approach for fast and accurate gene tree reconstruction
-
Rasmussen MD, Kellis M. 2010. A Bayesian approach for fast and accurate gene tree reconstruction. Mol Biol Evol 28:273-90
-
(2010)
Mol Biol Evol
, vol.28
, pp. 273-290
-
-
Rasmussen, M.D.1
Kellis, M.2
-
21
-
-
0037313182
-
Evolution of gene expression in the Drosophila melanogaster subgroup
-
Rifkin SA, Kim J, White KP. 2003. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet 33:138-44
-
(2003)
Nat Genet
, vol.33
, pp. 138-144
-
-
Rifkin, S.A.1
Kim, J.2
White, K.P.3
-
22
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
Robinson MD, Oshlack A. 2010. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11:R25
-
(2010)
Genome Biol
, vol.11
-
-
Robinson, M.D.1
Oshlack, A.2
-
23
-
-
84863885448
-
Comparative studies of gene expression and the evolution of gene regulation
-
Romero IG, Ruvinsky I, Gilad Y. 2012. Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet 13:505-16
-
(2012)
Nat Rev Genet
, vol.13
, pp. 505-516
-
-
Romero, I.G.1
Ruvinsky, I.2
Gilad, Y.3
-
24
-
-
70349413154
-
Probabilistic orthology analysis
-
Sennblad B, Lagergren J. 2009. Probabilistic orthology analysis. Syst Biol 58:411-24
-
(2009)
Syst Biol
, vol.58
, pp. 411-424
-
-
Sennblad, B.1
Lagergren, J.2
-
25
-
-
79960896843
-
Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple nextgeneration sequencing workflows
-
Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SHD, Dunn CW. 2011 Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple nextgeneration sequencing workflows. PLoS One 6:e22953
-
(2011)
PLoS One
, vol.6
-
-
Siebert, S.1
Robinson, M.D.2
Tintori, S.C.3
Goetz, F.4
Helm, R.R.5
Smith, S.A.6
Shaner, N.7
Haddock, S.H.D.8
Dunn, C.W.9
-
26
-
-
57149085481
-
Deep sequencingbased expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
-
't Hoen PAC, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RHAM, de Menezes RX, Boer JM, van Ommen GJB, den Dunnen JT. 2008. Deep sequencingbased expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 36:e141
-
(2008)
Nucleic Acids Res
, vol.36
-
-
'T Hoen, P.A.C.1
Ariyurek, Y.2
Thygesen, H.H.3
Vreugdenhil, E.4
Vossen, R.H.A.M.5
De Menezes, R.X.6
Boer, J.M.7
Van Ommen, G.J.B.8
Den Dunnen, J.T.9
-
27
-
-
84871822882
-
TreeFix: Statistically informed gene tree error correction using species trees
-
Wu YC, Rasmussen MD, Bansal MS, Kellis M. 2012. TreeFix: Statistically informed gene tree error correction using species trees. Syst Biol 62:110-20
-
(2012)
Syst Biol
, vol.62
, pp. 110-120
-
-
Wu, Y.C.1
Rasmussen, M.D.2
Bansal, M.S.3
Kellis, M.4
-
28
-
-
80052725687
-
Regulatory variation within and between species
-
Zheng W, Gianoulis TA, Karczewski KJ, Zhao H, Snyder M. 2011. Regulatory variation within and between species. Ann Rev Genomics Hum Genet 12:327-46
-
(2011)
Ann Rev Genomics Hum Genet
, vol.12
, pp. 327-346
-
-
Zheng, W.1
Gianoulis, T.A.2
Karczewski, K.J.3
Zhao, H.4
Snyder, M.5
|