-
1
-
-
5444257222
-
Comparative genomics
-
Miller, W., Makova, K. D., Nekrutenko, A. & Hardison, R. C. Comparative genomics. Annu. Rev. Genomics Hum. Genet. 5, 15-56 (2004).
-
(2004)
Annu. Rev. Genomics Hum. Genet
, vol.5
, pp. 15-56
-
-
Miller, W.1
Makova, K.D.2
Nekrutenko, A.3
Hardison, R.C.4
-
2
-
-
3142740663
-
Comparative genomics
-
Hardison, R. C. Comparative genomics. PLoS Biol. 1, E58 (2003).
-
(2003)
PLoS Biol
, vol.1
-
-
Hardison, R.C.1
-
3
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
-
Xie, X. et al. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434, 338-345 (2005).
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
-
4
-
-
0033972132
-
Analysis of vertebrate SCL loci identifies conserved enhancers
-
Göttgens, B. et al. Analysis of vertebrate SCL loci identifies conserved enhancers. Nature Biotechnol. 18, 181-186 (2000).
-
(2000)
Nature Biotechnol
, vol.18
, pp. 181-186
-
-
Göttgens, B.1
-
5
-
-
0034616398
-
Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons
-
Loots, G. G. et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288, 136-140 (2000).
-
(2000)
Science
, vol.288
, pp. 136-140
-
-
Loots, G.G.1
-
6
-
-
0016087667
-
On some principles governing molecular evolution
-
Kimura, M. & Ohta, T. On some principles governing molecular evolution. Proc. Natl Acad. Sci. USA 71, 2848-2852 (1974).
-
(1974)
Proc. Natl Acad. Sci. USA
, vol.71
, pp. 2848-2852
-
-
Kimura, M.1
Ohta, T.2
-
7
-
-
39049156079
-
Confidence in comparative genomics
-
Margulies, E. H. Confidence in comparative genomics. Genome Res. 18, 199-200 (2008).
-
(2008)
Genome Res
, vol.18
, pp. 199-200
-
-
Margulies, E.H.1
-
8
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
International Human Genome Sequencing Consortium
-
International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
-
9
-
-
1542563409
-
-
International Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002). The first vertebrate genome-wide comparative sequence analysis. The many seminal findings include initial estimates of the extent of evolutionary constraint among mammalian genomes and the fact that there is more than twice as much non-coding constrained sequence compared with protein-coding regions.
-
International Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002). The first vertebrate genome-wide comparative sequence analysis. The many seminal findings include initial estimates of the extent of evolutionary constraint among mammalian genomes and the fact that there is more than twice as much non-coding constrained sequence compared with protein-coding regions.
-
-
-
-
10
-
-
3242694931
-
-
Margulies, E. H., NISC Comparative Sequencing Program & Green, E. D. Detecting highly conserved regions of the human genome by multispecies sequence comparisons. Cold Spring Harb. Symp. Quant. Biol. 68, 255-263 (2003).
-
Margulies, E. H., NISC Comparative Sequencing Program & Green, E. D. Detecting highly conserved regions of the human genome by multispecies sequence comparisons. Cold Spring Harb. Symp. Quant. Biol. 68, 255-263 (2003).
-
-
-
-
11
-
-
0041465867
-
-
Thomas, J. W. et al. Comparative analyses of multispecies sequences from targeted genomic regions. Nature 424, 788-793 (2003). This landmark manuscript was one of the first to highlight the power of sequencing and analysing the genomes of many species and provided intellectual support for sequencing many vertebrate genomes.
-
Thomas, J. W. et al. Comparative analyses of multispecies sequences from targeted genomic regions. Nature 424, 788-793 (2003). This landmark manuscript was one of the first to highlight the power of sequencing and analysing the genomes of many species and provided intellectual support for sequencing many vertebrate genomes.
-
-
-
-
12
-
-
14644390333
-
A model of the statistical power of comparative genome sequence analysis
-
The 'go-to' manuscript outlining the theoretical basis for choosing the amount and diversity of genomes to sequence in order to obtain a certain level of resolution for constrained sequences
-
Eddy, S. R. A model of the statistical power of comparative genome sequence analysis. PLoS Biol. 3, e10 (2005). The 'go-to' manuscript outlining the theoretical basis for choosing the amount and diversity of genomes to sequence in order to obtain a certain level of resolution for constrained sequences.
-
(2005)
PLoS Biol
, vol.3
-
-
Eddy, S.R.1
-
13
-
-
0035432364
-
Strategies for the systematic sequencing of complex genomes
-
An excellent review outlining the approaches used for sequencing genomes
-
Green, E. D. Strategies for the systematic sequencing of complex genomes. Nature Rev. Genet. 2, 573-583 (2001). An excellent review outlining the approaches used for sequencing genomes.
-
(2001)
Nature Rev. Genet
, vol.2
, pp. 573-583
-
-
Green, E.D.1
-
14
-
-
7244245762
-
Finishing the euchromatic sequence of the human genome
-
International Human Genome Sequencing Consortium
-
International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).
-
(2004)
Nature
, vol.431
, pp. 931-945
-
-
-
15
-
-
7444259980
-
An intermediate grade of finished genomic sequence suitable for comparative analyses
-
Blakesley, R. W. et al. An intermediate grade of finished genomic sequence suitable for comparative analyses. Genome Res. 14, 2235-2244 (2004).
-
(2004)
Genome Res
, vol.14
, pp. 2235-2244
-
-
Blakesley, R.W.1
-
16
-
-
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
-
17
-
-
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
-
18
-
-
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
-
19
-
-
40849131751
-
-
ENCODE Project Consortium. The ENCODE pilot project: functional annotation of 1% of the human genome. Nature 447, 799-816 (2007). This manuscript, along with Reference 20 and the entire April 2007 issue of Genome Research, highlights the first systematic identification and analysis of functional elements in the human genome. Of particular interest here is the section describing the extent of evolutionary sequence constraint that was observed in functional elements.
-
ENCODE Project Consortium. The ENCODE pilot project: functional annotation of 1% of the human genome. Nature 447, 799-816 (2007). This manuscript, along with Reference 20 and the entire April 2007 issue of Genome Research, highlights the first systematic identification and analysis of functional elements in the human genome. Of particular interest here is the section describing the extent of evolutionary sequence constraint that was observed in functional elements.
-
-
-
-
20
-
-
34250365369
-
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
-
Margulies, E. H. et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17, 760-774 (2007).
-
(2007)
Genome Res
, vol.17
, pp. 760-774
-
-
Margulies, E.H.1
-
21
-
-
33750953227
-
Whole-genome re-sequencing
-
Bentley, D. R. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16, 545-552 (2006).
-
(2006)
Curr. Opin. Genet. Dev
, vol.16
, pp. 545-552
-
-
Bentley, D.R.1
-
22
-
-
47149117454
-
-
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218 (2007). This manuscript, along with Reference 56, highlights seminal multi-species sequence comparisons on a genome-wide scale. Furthermore, Reference 56 presents new approaches for computationally identifying and classifying the functions of constrained sequences.
-
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218 (2007). This manuscript, along with Reference 56, highlights seminal multi-species sequence comparisons on a genome-wide scale. Furthermore, Reference 56 presents new approaches for computationally identifying and classifying the functions of constrained sequences.
-
-
-
-
23
-
-
4243088097
-
The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics
-
Stein, L. D. et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 1, E45 (2003).
-
(2003)
PLoS Biol
, vol.1
-
-
Stein, L.D.1
-
24
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254 (2003).
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
25
-
-
36549051577
-
Aligning multiple whole genomes with Mercator and MAVID
-
Dewey, C. N. Aligning multiple whole genomes with Mercator and MAVID. Methods Mol. Biol. 395, 221-236 (2007).
-
(2007)
Methods Mol. Biol
, vol.395
, pp. 221-236
-
-
Dewey, C.N.1
-
26
-
-
0036211065
-
GRIMM: Genome rearrangements web server
-
Tesler, G. GRIMM: genome rearrangements web server. Bioinformatics 18, 492-493 (2002).
-
(2002)
Bioinformatics
, vol.18
, pp. 492-493
-
-
Tesler, G.1
-
27
-
-
0141815478
-
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
-
Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W. & Haussler, D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA 100, 11484-11489 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 11484-11489
-
-
Kent, W.J.1
Baertsch, R.2
Hinrichs, A.3
Miller, W.4
Haussler, D.5
-
28
-
-
33750386912
-
Reconstructing contiguous regions of an ancestral genome
-
Ma, J. et al. Reconstructing contiguous regions of an ancestral genome. Genome Res. 16, 1557-1565 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 1557-1565
-
-
Ma, J.1
-
29
-
-
39049145326
-
Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
-
Lunter, G. et al. Uncertainty in homology inferences: assessing and improving genomic sequence alignment. Genome Res. 18, 298-309 (2008).
-
(2008)
Genome Res
, vol.18
, pp. 298-309
-
-
Lunter, G.1
-
30
-
-
0031721576
-
Dynamic programming alignment accuracy
-
Holmes, I. & Durbin, R. Dynamic programming alignment accuracy. J. Comput. Biol. 5, 493-504 (1998).
-
(1998)
J. Comput. Biol
, vol.5
, pp. 493-504
-
-
Holmes, I.1
Durbin, R.2
-
31
-
-
38549135938
-
Alignment uncertainty and genomic analysis
-
Wong, K. M., Suchard, M. A. & Huelsenbeck, J. P. Alignment uncertainty and genomic analysis. Science 319, 473-476 (2008).
-
(2008)
Science
, vol.319
, pp. 473-476
-
-
Wong, K.M.1
Suchard, M.A.2
Huelsenbeck, J.P.3
-
32
-
-
0036606576
-
Fast algorithms for large-scale genome alignment and comparison
-
Delcher, A. L., Phillippy, A., Carlton, J. & Salzberg, S. L. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30, 2478-2483 (2002).
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 2478-2483
-
-
Delcher, A.L.1
Phillippy, A.2
Carlton, J.3
Salzberg, S.L.4
-
33
-
-
0024234855
-
CLUSTAL: A package for performing multiple sequence alignment on a microcomputer
-
Higgins, D. G. & Sharp, P. M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237-244 (1988).
-
(1988)
Gene
, vol.73
, pp. 237-244
-
-
Higgins, D.G.1
Sharp, P.M.2
-
34
-
-
0037398368
-
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
-
Brudno, M. et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721-731 (2003).
-
(2003)
Genome Res
, vol.13
, pp. 721-731
-
-
Brudno, M.1
-
35
-
-
1542748076
-
-
Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715 (2004).
-
Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715 (2004).
-
-
-
-
36
-
-
33645875606
-
Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons
-
Margulies, E. H., Chen, C. W. & Green, E. D. Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons. Trends Genet. 22, 187-193 (2006).
-
(2006)
Trends Genet
, vol.22
, pp. 187-193
-
-
Margulies, E.H.1
Chen, C.W.2
Green, E.D.3
-
37
-
-
0034623005
-
-
Notredame, C., Higgins, D. G. & Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217 (2000).
-
Notredame, C., Higgins, D. G. & Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217 (2000).
-
-
-
-
38
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
Do, C. B., Mahabhashyam, M. S. P., Brudno, M. & Batzoglou, S. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res. 15, 330-340 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.P.2
Brudno, M.3
Batzoglou, S.4
-
39
-
-
1842667852
-
MAVID: Constrained ancestral alignment of multiple sequences
-
Bray, N. & Pachter, L. MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14, 693-699 (2004).
-
(2004)
Genome Res
, vol.14
, pp. 693-699
-
-
Bray, N.1
Pachter, L.2
-
40
-
-
2942516151
-
Benchmarking tools for the alignment of functional noncoding DNA
-
Pollard, D. A., Bergman, C. M., Stoye, J., Celniker, S. E. & Eisen, M. B. Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 5, 6 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 6
-
-
Pollard, D.A.1
Bergman, C.M.2
Stoye, J.3
Celniker, S.E.4
Eisen, M.B.5
-
41
-
-
25844498846
-
Trade-offs in detecting evolutionarily constrained sequence by comparative genomics
-
An excellent review outlining how various comparative sequence analysis methods combined with different sequence data sets affect the sensitivity, specificity and phylogenetic scope for detecting constrained sequences
-
Stone, E. A., Cooper, G. M. & Sidow, A. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annu. Rev. Genomics Hum. Genet. 6, 143-164 (2005). An excellent review outlining how various comparative sequence analysis methods combined with different sequence data sets affect the sensitivity, specificity and phylogenetic scope for detecting constrained sequences.
-
(2005)
Annu. Rev. Genomics Hum. Genet
, vol.6
, pp. 143-164
-
-
Stone, E.A.1
Cooper, G.M.2
Sidow, A.3
-
42
-
-
10744222156
-
-
Margulies, E. H., Blanchette, M., NISC Comparative Sequencing Program, Haussler, D. & Green, E. D. Identification and characterization of multi-species conserved sequences. Genome Res. 13, 2507-2518 (2003). This was the first report of a computational approach for logically combining the conservation information from many species' sequences for the identification of constrained elements. Also see References 43 and 45 for subsequent methods.
-
Margulies, E. H., Blanchette, M., NISC Comparative Sequencing Program, Haussler, D. & Green, E. D. Identification and characterization of multi-species conserved sequences. Genome Res. 13, 2507-2518 (2003). This was the first report of a computational approach for logically combining the conservation information from many species' sequences for the identification of constrained elements. Also see References 43 and 45 for subsequent methods.
-
-
-
-
43
-
-
22244452677
-
Distribution and intensity of constraint in mammalian genomic sequence
-
Cooper, G. M. et al. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 15, 901-913 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 901-913
-
-
Cooper, G.M.1
-
44
-
-
0003516147
-
-
Cambridge Univ. Press, Cambridge, UK
-
Durbin, R., Eddy, S., Krogh, A. & Mitchison, G. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (Cambridge Univ. Press, Cambridge, UK, 1998).
-
(1998)
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
-
-
Durbin, R.1
Eddy, S.2
Krogh, A.3
Mitchison, G.4
-
45
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
-
46
-
-
33644503176
-
A large family of ancient repeat elements in the human genome is under strong selection
-
Kamal, M., Xie, X. & Lander, E. S. A large family of ancient repeat elements in the human genome is under strong selection. Proc. Natl Acad. Sci. USA 103, 2740-2745 (2006).
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 2740-2745
-
-
Kamal, M.1
Xie, X.2
Lander, E.S.3
-
47
-
-
33745772571
-
-
eds Apostolico, A, Guerra, C, Istrail, S, Pevzner, P. & Waterman, M, Springer, Berlin
-
Siepel, A., Pollard, K. S. & Haussler, D. in Proc. 10th Int. Conf. Res. Comput. Mol. Biol. (eds Apostolico, A., Guerra, C., Istrail, S., Pevzner, P. & Waterman, M.) 190-205 (Springer, Berlin, 2006).
-
(2006)
Proc. 10th Int. Conf. Res. Comput. Mol. Biol
, pp. 190-205
-
-
Siepel, A.1
Pollard, K.S.2
Haussler, D.3
-
48
-
-
34247352040
-
Evolutionary and biomedical insights from the Rhesus macaque genome
-
Rhesus Macaque Genome Sequencing and Analysis Consortium
-
Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and biomedical insights from the Rhesus macaque genome. Science 316, 222-234 (2007).
-
(2007)
Science
, vol.316
, pp. 222-234
-
-
-
49
-
-
0242418246
-
Phylogenetic shadowing of primate sequences to find functional regions of the human genome
-
Boffelli, D. et al. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299, 1391-1394 (2003).
-
(2003)
Science
, vol.299
, pp. 1391-1394
-
-
Boffelli, D.1
-
50
-
-
33745628791
-
Close sequence comparisons are sufficient to identify human cis-regulatory elements
-
Prabhakar, S. et al. Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res. 16, 855-863 (2006).
-
(2006)
Genome Res
, vol.16
, pp. 855-863
-
-
Prabhakar, S.1
-
51
-
-
34147170895
-
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons
-
Wang, Q.-f. et al. Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. Genome Biol. 8, R1 (2007).
-
(2007)
Genome Biol
, vol.8
-
-
Wang, Q.-F.1
-
52
-
-
33748756610
-
Primate-specific evolution of an LDLR enhancer
-
Wang, Q.-f. et al. Primate-specific evolution of an LDLR enhancer. Genome Biol. 7, R68 (2006).
-
(2006)
Genome Biol
, vol.7
-
-
Wang, Q.-F.1
-
53
-
-
33750442876
-
Large-scale turnover of functional transcription factor binding sites in Drosophila
-
Moses, A. M. et al. Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput. Biol. 2, e130 (2006).
-
(2006)
PLoS Comput. Biol
, vol.2
-
-
Moses, A.M.1
-
54
-
-
0036107903
-
Discovery of regulatory elements by a computational method for phylogenetic footprinting
-
Blanchette, M. & Tompa, M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12, 739-748 (2002).
-
(2002)
Genome Res
, vol.12
, pp. 739-748
-
-
Blanchette, M.1
Tompa, M.2
-
55
-
-
0344906814
-
Combining phylogenetic data with co-regulated genes to identify regulatory motifs
-
Wang, T. & Stormo, G. D. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 19, 2369-2380 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 2369-2380
-
-
Wang, T.1
Stormo, G.D.2
-
56
-
-
36049018312
-
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
-
Stark, A. et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219-232 (2007).
-
(2007)
Nature
, vol.450
, pp. 219-232
-
-
Stark, A.1
-
57
-
-
0141519291
-
A general approach for identifying distant regulatory elements applied to the Gdf6 gene
-
Mortlock, D. P., Guenther, C. & Kingsley, D. M. A general approach for identifying distant regulatory elements applied to the Gdf6 gene. Genome Res. 13, 2069-2081 (2003).
-
(2003)
Genome Res
, vol.13
, pp. 2069-2081
-
-
Mortlock, D.P.1
Guenther, C.2
Kingsley, D.M.3
-
58
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio, L. A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499-502 (2006).
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
-
59
-
-
33645833857
-
Conservation of RET regulatory function from human to zebrafish without sequence similarity
-
Fisher, S., Grice, E. A., Vinton, R. M., Bessling, S. L. & McCallion, A. S. Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312, 276-279 (2006).
-
(2006)
Science
, vol.312
, pp. 276-279
-
-
Fisher, S.1
Grice, E.A.2
Vinton, R.M.3
Bessling, S.L.4
McCallion, A.S.5
-
60
-
-
33846078622
-
The UCSC genome browser database: Update 2007
-
Kuhn, R. M. et al. The UCSC genome browser database: update 2007. Nucleic Acids Res. 35, D668-D673 (2007).
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Kuhn, R.M.1
-
62
-
-
40849090414
-
Genome browsing with Ensembl: A practical overview
-
Spudich, G., Fernández-Suárez, X. M. & Birney, E. Genome browsing with Ensembl: a practical overview. Brief. Funct. Genomic. Proteomic. 6, 202-219 (2007).
-
(2007)
Brief. Funct. Genomic. Proteomic
, vol.6
, pp. 202-219
-
-
Spudich, G.1
Fernández-Suárez, X.M.2
Birney, E.3
-
63
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
Giardine, B. et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451-1455 (2005).
-
(2005)
Genome Res
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
-
64
-
-
34250376884
-
A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
-
Blankenberg, D. et al. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 17, 960-964 (2007).
-
(2007)
Genome Res
, vol.17
, pp. 960-964
-
-
Blankenberg, D.1
-
65
-
-
33846112470
-
VISTA Enhancer Browser - a database of tissue-specific human enhancers
-
Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L. A. VISTA Enhancer Browser - a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88-D92 (2007).
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Visel, A.1
Minovitsky, S.2
Dubchak, I.3
Pennacchio, L.A.4
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