-
2
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57: 289-300.
-
(1995)
J R Stat Soc Ser B Methodol
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
3
-
-
39049157173
-
Fast-evolving noncoding sequences in the human genome
-
doi: 10.1186/gb-2007-8-6-r118
-
Bird CP, Stranger BE, Liu M, Thomas DJ, Ingle CE, Beazley C, Miller W, Hurles ME, Dermitzakis ET. 2007. Fast-evolving noncoding sequences in the human genome. Genome Biol 8: R118. doi: 10.1186/gb-2007-8-6-r118.
-
(2007)
Genome Biol
, vol.8
-
-
Bird, C.P.1
Stranger, B.E.2
Liu, M.3
Thomas, D.J.4
Ingle, C.E.5
Beazley, C.6
Miller, W.7
Hurles, M.E.8
Dermitzakis, E.T.9
-
4
-
-
1542748076
-
-
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14: 708-715.
-
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14: 708-715.
-
-
-
-
5
-
-
0242418246
-
Phylogenetic shadowing of primate sequences to find functional regions of the human genome
-
Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM. 2003. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299: 1391-1394.
-
(2003)
Science
, vol.299
, pp. 1391-1394
-
-
Boffelli, D.1
McAuliffe, J.2
Ovcharenko, D.3
Lewis, K.D.4
Ovcharenko, I.5
Pachter, L.6
Rubin, E.M.7
-
6
-
-
67049158348
-
-
Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. 2009. Fast statistical alignment. PLoS Comput Biol 5: e1000392. doi: 10.1371/journal.pcbi.1000392.
-
Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. 2009. Fast statistical alignment. PLoS Comput Biol 5: e1000392. doi: 10.1371/journal.pcbi.1000392.
-
-
-
-
8
-
-
2442555497
-
The share of human genomic DNA under selection estimated from human-mouse genomic alignments
-
Chiaromonte F, Weber RJ, Roskin KM, Diekhans M, Kent WJ, Haussler D. 2003. The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harb Symp Quant Biol 68: 245-254.
-
(2003)
Cold Spring Harb Symp Quant Biol
, vol.68
, pp. 245-254
-
-
Chiaromonte, F.1
Weber, R.J.2
Roskin, K.M.3
Diekhans, M.4
Kent, W.J.5
Haussler, D.6
-
9
-
-
0038781885
-
-
Cooper GM, Brudno M, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. 2003. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res 13: 813-820.
-
Cooper GM, Brudno M, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. 2003. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res 13: 813-820.
-
-
-
-
10
-
-
1842667855
-
Characterization of evolutionary rates and constraints in three mammalian genomes
-
Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A. 2004. Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Res 14: 539-548.
-
(2004)
Genome Res
, vol.14
, pp. 539-548
-
-
Cooper, G.M.1
Brudno, M.2
Stone, E.A.3
Dubchak, I.4
Batzoglou, S.5
Sidow, A.6
-
11
-
-
22244452677
-
Distribution and intensity of constraint in mammalian genomic sequence
-
Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. 2005. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15: 901-913.
-
(2005)
Genome Res
, vol.15
, pp. 901-913
-
-
Cooper, G.M.1
Stone, E.A.2
Asimenos, G.3
Green, E.D.4
Batzoglou, S.5
Sidow, A.6
-
12
-
-
34948890647
-
Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion
-
Dreszer TR, Wall GD, Haussler D, Pollard KS. 2007. Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion. Genome Res 17: 1420-1430.
-
(2007)
Genome Res
, vol.17
, pp. 1420-1430
-
-
Dreszer, T.R.1
Wall, G.D.2
Haussler, D.3
Pollard, K.S.4
-
13
-
-
14644390333
-
A model of the statistical power of comparative genome sequence analysis
-
doi: 10.1371/journal.pbio. 0030010
-
Eddy SR. 2005. A model of the statistical power of comparative genome sequence analysis. PLoS Biol 3: e10. doi: 10.1371/journal.pbio. 0030010.
-
(2005)
PLoS Biol
, vol.3
-
-
Eddy, S.R.1
-
14
-
-
0019884371
-
5-Methylcytosine in eukaryotic DNA
-
Ehrlich M, Wang RY. 1981. 5-Methylcytosine in eukaryotic DNA. Science 212: 1350-1357.
-
(1981)
Science
, vol.212
, pp. 1350-1357
-
-
Ehrlich, M.1
Wang, R.Y.2
-
15
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
-
16
-
-
72649102150
-
Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes
-
in press, doi: 10.1093/molbev/msp219
-
Eöry L, Halligan DL, Keightley PD. 2009. Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Mol Biol Evol (in press). doi: 10.1093/molbev/msp219.
-
(2009)
Mol Biol Evol
-
-
Eöry, L.1
Halligan, D.L.2
Keightley, P.D.3
-
17
-
-
66349086264
-
Identifying novel constrained elements by exploiting biased substitution patterns
-
Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. 2009. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics 25: 54-62.
-
(2009)
Bioinformatics
, vol.25
, pp. 54-62
-
-
Garber, M.1
Guttman, M.2
Clamp, M.3
Zody, M.C.4
Friedman, N.5
Xie, X.6
-
18
-
-
0037380022
-
-
Green P, Ewing B, Miller W, Thomas PJ, NISC Comparative Sequencing Program, Green ED. 2003. Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 33: 514-517.
-
Green P, Ewing B, Miller W, Thomas PJ, NISC Comparative Sequencing Program, Green ED. 2003. Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 33: 514-517.
-
-
-
-
19
-
-
40449115745
-
CONTRAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction
-
doi: 10.1186/gb-2007-8-12-r269
-
Gross SS, Do CB, Sirota M, Batzoglou S. 2007. CONTRAST: A discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol 8: R269. doi: 10.1186/gb-2007-8-12-r269.
-
(2007)
Genome Biol
, vol.8
-
-
Gross, S.S.1
Do, C.B.2
Sirota, M.3
Batzoglou, S.4
-
20
-
-
0037417884
-
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
-
Guigó R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C, et al. 2003. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci 100: 1140-1145.
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 1140-1145
-
-
Guigó, R.1
Dermitzakis, E.T.2
Agarwal, P.3
Ponting, C.P.4
Parra, G.5
Reymond, A.6
Abril, J.F.7
Keibler, E.8
Lyle, R.9
Ucla, C.10
-
21
-
-
18544404720
-
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution
-
Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, et al. 2003. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res 13: 13-26.
-
(2003)
Genome Res
, vol.13
, pp. 13-26
-
-
Hardison, R.C.1
Roskin, K.M.2
Yang, S.3
Diekhans, M.4
Kent, W.J.5
Weber, R.6
Elnitski, L.7
Li, J.8
O'Connor, M.9
Kolbe, D.10
-
22
-
-
33748645500
-
GENCODE: Producing a reference annotation for ENCODE
-
doi: 10.1186/gb-2006-7-s1-s4
-
Harrow J, Denoeud F, Frankish A, Reymond A, Chen C-K, Chrast J, Lagarde J, Gilbert JGR, Storey R, Swarbreck D, et al. 2006. GENCODE: Producing a reference annotation for ENCODE. Genome Biol 7: S4. doi: 10.1186/gb-2006-7-s1-s4.
-
(2006)
Genome Biol
, vol.7
-
-
Harrow, J.1
Denoeud, F.2
Frankish, A.3
Reymond, A.4
Chen, C.-K.5
Chrast, J.6
Lagarde, J.7
Gilbert, J.G.R.8
Storey, R.9
Swarbreck, D.10
-
23
-
-
34548346860
-
Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
-
Haygood R, Fedrigo O, Hanson B, Yokoyama K-D, Wray GA. 2007. Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nat Genet 39: 1140-1144.
-
(2007)
Nat Genet
, vol.39
, pp. 1140-1144
-
-
Haygood, R.1
Fedrigo, O.2
Hanson, B.3
Yokoyama, K.-D.4
Wray, G.A.5
-
24
-
-
0030902563
-
Phylogenetic methods come of age: Testing hypotheses in an evolutionary context
-
Huelsenbeck J, Rannala B. 1997. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276: 227-232.
-
(1997)
Science
, vol.276
, pp. 227-232
-
-
Huelsenbeck, J.1
Rannala, B.2
-
25
-
-
4644300141
-
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
-
Hwang D, Green P. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci 101: 13994-14001.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 13994-14001
-
-
Hwang, D.1
Green, P.2
-
26
-
-
15744388330
-
Evidence for widespread degradation of gene control regions in hominid genomes
-
doi: 10.1371/journal.pbio.0030042
-
Keightley PD, Lercher MJ, Eyre-Walker A. 2005. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol 3: e42. doi: 10.1371/journal.pbio.0030042.
-
(2005)
PLoS Biol
, vol.3
-
-
Keightley, P.D.1
Lercher, M.J.2
Eyre-Walker, A.3
-
27
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
28
-
-
34848901059
-
Adaptive evolution of conserved noncoding elements in mammals
-
Kim SY, Pritchard JK. 2007. Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet 3: 1572-1586.
-
(2007)
PLoS Genet
, vol.3
, pp. 1572-1586
-
-
Kim, S.Y.1
Pritchard, J.K.2
-
29
-
-
0017368336
-
Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution
-
Kimura M. 1977. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267: 275-276.
-
(1977)
Nature
, vol.267
, pp. 275-276
-
-
Kimura, M.1
-
30
-
-
0027200764
-
A molecular approach to estimating the human deleterious mutation rate
-
Kondrashov AS, Crow JF. 1993. A molecular approach to estimating the human deleterious mutation rate. Hum Mutat 2: 229-234.
-
(1993)
Hum Mutat
, vol.2
, pp. 229-234
-
-
Kondrashov, A.S.1
Crow, J.F.2
-
31
-
-
50849122974
-
-
Kosiol C, Vinar T, da Fonseca R, Hubisz M, Bustamante C, Nielsen R, Siepel A. 2008. Patterns of positive selection in six mammalian genomes. PLoS Genet 4: e1000144. doi: 10.1371/journal.pgen.1000144.
-
Kosiol C, Vinar T, da Fonseca R, Hubisz M, Bustamante C, Nielsen R, Siepel A. 2008. Patterns of positive selection in six mammalian genomes. PLoS Genet 4: e1000144. doi: 10.1371/journal.pgen.1000144.
-
-
-
-
32
-
-
58149178565
-
The UCSC Genome Browser Database: Update 2009
-
Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, et al. 2009. The UCSC Genome Browser Database: Update 2009. Nucleic Acids Res 37: D755-D761.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Kuhn, R.M.1
Karolchik, D.2
Zweig, A.S.3
Wang, T.4
Smith, K.E.5
Rosenbloom, K.R.6
Rhead, B.7
Raney, B.J.8
Pohl, A.9
Pheasant, M.10
-
33
-
-
33645798112
-
Genome-wide identification of human functional DNA using a neutral indel model
-
doi: 10.1371/journal.pcbi.0020005
-
Lunter G, Ponting CP, Hein J. 2006. Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol 2: e5. doi: 10.1371/journal.pcbi.0020005.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Lunter, G.1
Ponting, C.P.2
Hein, J.3
-
34
-
-
39049145326
-
Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
-
Lunter G, Rocco A, Mimouni N, Heger A, Caldeira A, Hein J. 2008. Uncertainty in homology inferences: Assessing and improving genomic sequence alignment. Genome Res 18: 298-309.
-
(2008)
Genome Res
, vol.18
, pp. 298-309
-
-
Lunter, G.1
Rocco, A.2
Mimouni, N.3
Heger, A.4
Caldeira, A.5
Hein, J.6
-
35
-
-
0038543069
-
Biased gene conversion: Implications for genome and sex evolution
-
Marais G. 2003. Biased gene conversion: Implications for genome and sex evolution. Trends Genet 19: 330-338.
-
(2003)
Trends Genet
, vol.19
, pp. 330-338
-
-
Marais, G.1
-
36
-
-
10744222156
-
Identification and characterization of multi-species conserved sequences
-
NISC Comparative Sequencing Program, Haussler D, Green ED
-
Margulies EH, Blanchette M. NISC Comparative Sequencing Program, Haussler D, Green ED. 2003. Identification and characterization of multi-species conserved sequences. Genome Res 13: 2507-2518.
-
(2003)
Genome Res
, vol.13
, pp. 2507-2518
-
-
Margulies, E.H.1
Blanchette, M.2
-
37
-
-
34250365369
-
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
-
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, et al. 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 17: 760-774.
-
(2007)
Genome Res
, vol.17
, pp. 760-774
-
-
Margulies, E.H.1
Cooper, G.M.2
Asimenos, G.3
Thomas, D.J.4
Dewey, C.N.5
Siepel, A.6
Birney, E.7
Keefe, D.8
Schwartz, A.S.9
Hou, M.10
-
38
-
-
20344379192
-
Subtree power analysis and species selection for comparative genomics
-
McAuliffe JD, Jordan MI, Pachter L. 2005. Subtree power analysis and species selection for comparative genomics. Proc Natl Acad Sci 102: 7900-7905.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 7900-7905
-
-
McAuliffe, J.D.1
Jordan, M.I.2
Pachter, L.3
-
39
-
-
38849149795
-
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
-
Miller W, Rosenbloom K, Hardison R, Hou M, Taylor J, Raney B, Burhans R, King D, Baertsch R, Blankenberg D, et al. 2007. 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res 17: 1797-1808.
-
(2007)
Genome Res
, vol.17
, pp. 1797-1808
-
-
Miller, W.1
Rosenbloom, K.2
Hardison, R.3
Hou, M.4
Taylor, J.5
Raney, B.6
Burhans, R.7
King, D.8
Baertsch, R.9
Blankenberg, D.10
-
40
-
-
0007663470
-
Nucleotide sequence divergence and functional constraint in mRNA evolution
-
Miyata T, Yasunaga T, Nishida T. 1980. Nucleotide sequence divergence and functional constraint in mRNA evolution. Proc Natl Acad Sci 77: 7328-7332.
-
(1980)
Proc Natl Acad Sci
, vol.77
, pp. 7328-7332
-
-
Miyata, T.1
Yasunaga, T.2
Nishida, T.3
-
41
-
-
0642368358
-
Position specific variation in the rate of evolution in transcription factor binding sites
-
doi: 10.1186/1471-2148-3-19
-
Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB. 2003. Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol 3: 19. doi: 10.1186/1471-2148-3-19.
-
(2003)
BMC Evol Biol
, vol.3
, pp. 19
-
-
Moses, A.M.1
Chiang, D.Y.2
Kellis, M.3
Lander, E.S.4
Eisen, M.B.5
-
42
-
-
22144491990
-
MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
-
doi: 10.1186/gb-2004-5-12-r98
-
Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB. 2004. MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol 5: R98. doi: 10.1186/gb-2004-5-12-r98.
-
(2004)
Genome Biol
, vol.5
-
-
Moses, A.M.1
Chiang, D.Y.2
Pollard, D.A.3
Iyer, V.N.4
Eisen, M.B.5
-
43
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Mouse Genome Sequencing Consortium
-
Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
-
44
-
-
0142084743
-
Scanning human gene deserts for long-range enhancers
-
doi: 10.1126/science.1088328
-
Nobrega MA, Ovcharenko I, Afzal V, Rubin EM. 2003. Scanning human gene deserts for long-range enhancers. Science 302: 413. doi: 10.1126/science.1088328.
-
(2003)
Science
, vol.302
, pp. 413
-
-
Nobrega, M.A.1
Ovcharenko, I.2
Afzal, V.3
Rubin, E.M.4
-
45
-
-
59549102237
-
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
-
Paten B, Herrero J, Beal K, Birney E. 2009. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics 25: 295-301.
-
(2009)
Bioinformatics
, vol.25
, pp. 295-301
-
-
Paten, B.1
Herrero, J.2
Beal, K.3
Birney, E.4
-
46
-
-
33646272409
-
Identification and classification of conserved RNA secondary structures in the human genome
-
doi: 10.1371/journal.pcbi.0020033
-
Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. 2006. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2: e33. doi: 10.1371/journal.pcbi.0020033.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Pedersen, J.S.1
Bejerano, G.2
Siepel, A.3
Rosenbloom, K.4
Lindblad-Toh, K.5
Lander, E.S.6
Kent, J.7
Miller, W.8
Haussler, D.9
-
47
-
-
33750428182
-
Forces shaping the fastest evolving regions in the human genome
-
doi: 10.1371/journal.pgen.0020168
-
Pollard K, Salama S, King B, Kern A, Dreszer T, Katzman S, Siepel A, Pedersen J, Bejerano G, Baertsch R, et al. 2006a. Forces shaping the fastest evolving regions in the human genome. PLoS Genet 2: e168. doi: 10.1371/journal.pgen.0020168.
-
(2006)
PLoS Genet
, vol.2
-
-
Pollard, K.1
Salama, S.2
King, B.3
Kern, A.4
Dreszer, T.5
Katzman, S.6
Siepel, A.7
Pedersen, J.8
Bejerano, G.9
Baertsch, R.10
-
48
-
-
33748675254
-
An RNA gene expressed during cortical development evolved rapidly in humans
-
Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, et al. 2006b. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443: 167-172.
-
(2006)
Nature
, vol.443
, pp. 167-172
-
-
Pollard, K.S.1
Salama, S.R.2
Lambert, N.3
Lambot, M.-A.4
Coppens, S.5
Pedersen, J.S.6
Katzman, S.7
King, B.8
Onodera, C.9
Siepel, A.10
-
49
-
-
33750737061
-
Accelerated evolution of conserved noncoding sequences in humans
-
doi: 10.1126/science.1130738
-
Prabhakar S, Noonan JP, Paabo S, Rubin EM. 2006. Accelerated evolution of conserved noncoding sequences in humans. Science 314: 786. doi: 10.1126/science.1130738.
-
(2006)
Science
, vol.314
, pp. 786
-
-
Prabhakar, S.1
Noonan, J.P.2
Paabo, S.3
Rubin, E.M.4
-
50
-
-
0002394561
-
Large sample tests of statistical hypotheses concerning several parameters with applications to problems of estimation
-
Rao CR. 1948. Large sample tests of statistical hypotheses concerning several parameters with applications to problems of estimation. Proc Camb Philol Soc 44: 50-57.
-
(1948)
Proc Camb Philol Soc
, vol.44
, pp. 50-57
-
-
Rao, C.R.1
-
51
-
-
74949088616
-
Score test: Historical review and recent developments
-
eds. N Balakrishnan et al, pp, Birkhäuser, Boston, MA
-
Rao CR. 2005. Score test: Historical review and recent developments. In Advances in ranking and selection, multiple comparisons, and reliability (eds. N Balakrishnan et al.), pp. 3-20. Birkhäuser, Boston, MA.
-
(2005)
Advances in ranking and selection, multiple comparisons, and reliability
, pp. 3-20
-
-
Rao, C.R.1
-
52
-
-
70349205853
-
BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC
-
doi: 10.1186/1471-2148-9-217
-
Satija R, Novak A, Miklos I, Lyngso R, Hein J. 2009. BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. BMC Evol Biol 9: 217. doi: 10.1186/1471-2148-9-217.
-
(2009)
BMC Evol Biol
, vol.9
, pp. 217
-
-
Satija, R.1
Novak, A.2
Miklos, I.3
Lyngso, R.4
Hein, J.5
-
53
-
-
84907319426
-
Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions
-
Self S, Liang K. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J Am Stat Assoc 82: 605-610.
-
(1987)
J Am Stat Assoc
, vol.82
, pp. 605-610
-
-
Self, S.1
Liang, K.2
-
55
-
-
1542510106
-
Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
-
Siepel A, Haussler D. 2004b. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol 21: 468-488.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 468-488
-
-
Siepel, A.1
Haussler, D.2
-
56
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
-
57
-
-
33745772571
-
New methods for detecting lineage-specific selection
-
Springer-Verlag, Berlin, Germany
-
Siepel A, Pollard K, Haussler D. 2006. New methods for detecting lineage-specific selection. In Proc. 10th Int'l Conf. on Research in Computational Molecular Biology, pp. 190-205. Springer-Verlag, Berlin, Germany.
-
(2006)
Proc. 10th Int'l Conf. on Research in Computational Molecular Biology
, pp. 190-205
-
-
Siepel, A.1
Pollard, K.2
Haussler, D.3
-
58
-
-
38849145798
-
Targeted discovery of novel human exons by comparative genomics
-
Siepel A, Diekhans M, Brejova B, Langton L, Stevens M, Comstock C, Davis C, Ewing B, Oommen S, Lau C, et al. 2007. Targeted discovery of novel human exons by comparative genomics. Genome Res 17: 1763-1773.
-
(2007)
Genome Res
, vol.17
, pp. 1763-1773
-
-
Siepel, A.1
Diekhans, M.2
Brejova, B.3
Langton, L.4
Stevens, M.5
Comstock, C.6
Davis, C.7
Ewing, B.8
Oommen, S.9
Lau, C.10
-
59
-
-
25844498846
-
Trade-offs in detecting evolutionarily constrained sequence by comparative genomics
-
Stone EA, Cooper GM, Sidow A. 2005. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annu Rev Genomics Hum Genet 6: 143-164.
-
(2005)
Annu Rev Genomics Hum Genet
, vol.6
, pp. 143-164
-
-
Stone, E.A.1
Cooper, G.M.2
Sidow, A.3
-
60
-
-
0024497416
-
Mutation rates differ among regions of the mammalian genome
-
Wolfe KH, Sharp PM, Li W-H. 1989. Mutation rates differ among regions of the mammalian genome. Nature 337: 283-285.
-
(1989)
Nature
, vol.337
, pp. 283-285
-
-
Wolfe, K.H.1
Sharp, P.M.2
Li, W.-H.3
-
61
-
-
3142739466
-
Detecting selection in noncoding regions of nucleotide sequences
-
Wong WSW, Nielsen R. 2004. Detecting selection in noncoding regions of nucleotide sequences. Genetics 167: 949-958.
-
(2004)
Genetics
, vol.167
, pp. 949-958
-
-
Wong, W.S.W.1
Nielsen, R.2
-
62
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 39 UTRs by comparison of several mammals
-
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. 2005. Systematic discovery of regulatory motifs in human promoters and 39 UTRs by comparison of several mammals. Nature 434: 338-345.
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
Golub, T.R.4
Mootha, V.5
Lindblad-Toh, K.6
Lander, E.S.7
Kellis, M.8
-
63
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
-
Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 39: 306-314.
-
(1994)
J Mol Evol
, vol.39
, pp. 306-314
-
-
Yang, Z.1
|