-
1
-
-
50849122974
-
Patterns of positive selection in six mammalian genomes
-
Kosiol, C. et al. Patterns of positive selection in six mammalian genomes. PLoS Genet. 4, e1000144 (2008).
-
(2008)
PLoS Genet
, vol.4
-
-
Kosiol, C.1
-
2
-
-
80054976678
-
The evolution of gene expression levels in mammalian organs
-
Brawand, D. et al. The evolution of gene expression levels in mammalian organs. Nature 478, 343-348 (2011).
-
(2011)
Nature
, vol.478
, pp. 343-348
-
-
Brawand, D.1
-
3
-
-
67650921949
-
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
-
Khalil, A. M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl Acad. Sci. USA 106, 11667-11672 (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
-
4
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
-
5
-
-
84865727393
-
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
-
Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775-1789 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1775-1789
-
-
Derrien, T.1
-
6
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227 (2009).
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
-
7
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnol. 28, 503-510 (2010).
-
(2010)
Nature Biotechnol
, vol.28
, pp. 503-510
-
-
Guttman, M.1
-
8
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559-1563 (2005).
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
-
9
-
-
38649114329
-
Specific expression of long noncoding RNAs in the mouse brain
-
Mercer, T. R., Dinger, M. E., Sunkin, S. M., Mehler, M. F. & Mattick, J. S. Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl Acad. Sci. USA 105, 716-721 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 716-721
-
-
Mercer, T.R.1
Dinger, M.E.2
Sunkin, S.M.3
Mehler, M.F.4
Mattick, J.S.5
-
10
-
-
84864098110
-
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome
-
Young, R. S. et al. Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol. Evol. 4, 427-442 (2012).
-
(2012)
Genome Biol. Evol.
, vol.4
, pp. 427-442
-
-
Young, R.S.1
-
11
-
-
84870566023
-
Long non-coding RNAs in C. Elegans
-
Nam, J. W. & Bartel, D. Long non-coding RNAs in C. elegans. Genome Res. (2012).
-
(2012)
Genome Res.
-
-
Nam, J.W.1
Bartel, D.2
-
12
-
-
84455206362
-
Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
-
Ulitsky, I., Shkumatava, A., Jan, C. H., Sive, H. & Bartel, D. P. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147, 1537-1550 (2011).
-
(2011)
Cell
, vol.147
, pp. 1537-1550
-
-
Ulitsky, I.1
Shkumatava, A.2
Jan, C.H.3
Sive, H.4
Bartel, D.P.5
-
13
-
-
25844492496
-
Silencing of the mammalian X chromosome
-
Chow, J. C., Yen, Z., Ziesche, S. M. & Brown, C. J. Silencing of the mammalian X chromosome. Annu. Rev. Genomics Hum. Genet. 6, 69-92 (2005).
-
(2005)
Annu. Rev. Genomics Hum. Genet.
, vol.6
, pp. 69-92
-
-
Chow, J.C.1
Yen, Z.2
Ziesche, S.M.3
Brown, C.J.4
-
14
-
-
0037075032
-
The non-coding Air RNA is required for silencing autosomal imprinted genes
-
Sleutels, F., Zwart, R. & Barlow, D. P. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810-813 (2002).
-
(2002)
Nature
, vol.415
, pp. 810-813
-
-
Sleutels, F.1
Zwart, R.2
Barlow, D.P.3
-
15
-
-
50649118350
-
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
-
Dinger, M. E. et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 18, 1433-1445 (2008).
-
(2008)
Genome Res.
, vol.18
, pp. 1433-1445
-
-
Dinger, M.E.1
-
16
-
-
34250729138
-
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
-
Rinn, J. L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311-1323 (2007).
-
(2007)
Cell
, vol.129
, pp. 1311-1323
-
-
Rinn, J.L.1
-
17
-
-
77957243921
-
Long noncodingRNAs with enhancer-like function inhumancells
-
Ørom, U.A. et al. Long noncodingRNAs with enhancer-like function inhumancells. Cell 143, 46-58 (2010).
-
(2010)
Cell
, vol.143
, pp. 46-58
-
-
Ørom, U.A.1
-
18
-
-
80054715378
-
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA
-
Cesana, M. et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147, 358-369 (2011).
-
(2011)
Cell
, vol.147
, pp. 358-369
-
-
Cesana, M.1
-
19
-
-
77954399763
-
Long noncoding RNA genes: Conservation of sequence and brain expression among diverse amniotes
-
Chodroff, R. A. et al. Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol. 11, R72 (2010).
-
(2010)
Genome Biol.
, vol.11
-
-
Chodroff, R.A.1
-
20
-
-
76249108851
-
Catalogues of mammalian long noncoding RNAs: Modest conservation and incompleteness
-
Marques, A. C. & Ponting, C. P. Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol. 10, R124 (2009).
-
(2009)
Genome Biol.
, vol.10
-
-
Marques, A.C.1
Ponting, C.P.2
-
21
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
-
22
-
-
84864629645
-
Rapid turnover of long noncoding RNAs and the evolution of gene expression
-
Kutter, C. et al. Rapid turnover of long noncoding RNAs and the evolution of gene expression. PLoS Genet. 8, e1002841 (2012).
-
(2012)
PLoS Genet.
, vol.8
-
-
Kutter, C.1
-
23
-
-
33751381461
-
TimeTree: A public knowledge-base of divergence times among organisms
-
Hedges, S. B., Dudley, J. & Kumar, S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22, 2971-2972 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 2971-2972
-
-
Hedges, S.B.1
Dudley, J.2
Kumar, S.3
-
24
-
-
38849101777
-
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
-
Lin, M. F. et al. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res. 17, 1823-1836 (2007).
-
(2007)
Genome Res.
, vol.17
, pp. 1823-1836
-
-
Lin, M.F.1
-
25
-
-
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
-
26
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
The 1000 Genomes Project Consortium
-
The 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 135, 56-65 (2012).
-
(2012)
Nature
, vol.135
, pp. 56-65
-
-
-
27
-
-
84866775366
-
Evidence of abundant purifying selection in humans for recently-acquired regulatory functions
-
Ward, L. D. & Kellis, M. Evidence of abundant purifying selection in humans for recently-acquired regulatory functions. Science 337, 1675-1678 (2012).
-
(2012)
Science
, vol.337
, pp. 1675-1678
-
-
Ward, L.D.1
Kellis, M.2
-
28
-
-
34248641119
-
Adaptation or biased gene conversion Extending the null hypothesis of molecular evolution
-
Galtier, N. & Duret, L. Adaptation or biased gene conversion Extending the null hypothesis of molecular evolution. Trends Genet. 23, 273-277 (2007).
-
(2007)
Trends Genet.
, vol.23
, pp. 273-277
-
-
Galtier, N.1
Duret, L.2
-
29
-
-
84879795456
-
Cellular source and mechanisms of high transcriptome complexity in the mammalian testis
-
Soumillon, M. et al. Cellular source and mechanisms of high transcriptome complexity in the mammalian testis. Cell Rep. 3, 2179-2190 (2013).
-
(2013)
Cell Rep.
, vol.3
, pp. 2179-2190
-
-
Soumillon, M.1
-
30
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
Lindblad-Toh, K. et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478, 476-482 (2011).
-
(2011)
Nature
, vol.478
, pp. 476-482
-
-
Lindblad-Toh, K.1
-
31
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The Encode Project Consortium
-
The Encode Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
32
-
-
77953062527
-
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
Schmidt, D. et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328, 1036-1040 (2010).
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
-
33
-
-
78650821207
-
PCL2 modulates gene regulatory networks controlling self-renewal and commitment in embryonic stem cells
-
Walker, E., Manias, J. L., Chang, W. Y. & Stanford, W. L. PCL2 modulates gene regulatory networks controlling self-renewal and commitment in embryonic stem cells. Cell Cycle 10, 45-51 (2011).
-
(2011)
Cell Cycle
, vol.10
, pp. 45-51
-
-
Walker, E.1
Manias, J.L.2
Chang, W.Y.3
Stanford, W.L.4
-
34
-
-
69649084228
-
The transcriptional foundation of pluripotency
-
Chambers, I. & Tomlinson, S. R. The transcriptional foundation of pluripotency. Development 136, 2311-2322 (2009).
-
(2009)
Development
, vol.136
, pp. 2311-2322
-
-
Chambers, I.1
Tomlinson, S.R.2
-
35
-
-
0141993704
-
Gene-coexpression network for global discovery of conserved genetic modules
-
Stuart, J. M., Segal, E., Koller, D., Kim, S. K. & A. Gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249-255 (2003).
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.A.4
-
36
-
-
61449224546
-
Coherent but overlapping expression of microRNAs and their targets during vertebrate development
-
Shkumatava, A., Stark, A., Sive, H. & Bartel, D. P. Coherent but overlapping expression of microRNAs and their targets during vertebrate development. Genes Dev. 23, 466-481 (2009).
-
(2009)
Genes Dev.
, vol.23
, pp. 466-481
-
-
Shkumatava, A.1
Stark, A.2
Sive, H.3
Bartel, D.P.4
-
37
-
-
84876515907
-
STRING v9.1: Protein-protein interaction networks, with increased coverage and integration
-
Franceschini, A. et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41, D808-D815 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Franceschini, A.1
-
38
-
-
84863219731
-
The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r
-
Keniry, A. et al. The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. Nature Cell Biol. 14, 659-665 (2012).
-
(2012)
Nature Cell Biol.
, vol.14
, pp. 659-665
-
-
Keniry, A.1
-
39
-
-
84855896819
-
Using MCL to extract clusters from networks
-
Van Dongen, S. & Abreu-Goodger, C. Using MCL to extract clusters from networks. Methods Mol. Biol. 804, 281-295 (2012).
-
(2012)
Methods Mol. Biol.
, vol.804
, pp. 281-295
-
-
Van Dongen, S.1
Abreu-Goodger, C.2
-
40
-
-
84863723258
-
Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation
-
Grant, J. et al. Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation. Nature 487, 254-258 (2012).
-
(2012)
Nature
, vol.487
, pp. 254-258
-
-
Grant, J.1
-
41
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
42
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol. 28, 511-515 (2010).
-
(2010)
Nature Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
-
43
-
-
84860833500
-
Reorganizing the protein space at the Universal Protein Resource (UniProt)
-
Uni Prot
-
UniProt. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 40, D71-D75 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
-
44
-
-
84858077472
-
The Pfam protein families database
-
Punta, M. et al. The Pfam protein families database. Nucleic Acids Res. 40, D290-D301 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Punta, M.1
-
46
-
-
20144376345
-
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
-
Yanai, I. et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21, 650-659 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 650-659
-
-
Yanai, I.1
-
47
-
-
79551587720
-
Cytoscape 2.8: New features for data integration and network visualization
-
Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P.-L. & Ideker, T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431-432 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 431-432
-
-
Smoot, M.E.1
Ono, K.2
Ruscheinski, J.3
Wang, P.-L.4
Ideker, T.5
-
48
-
-
84858341887
-
-
R Development Core Team. R: A language and environment for statistical computing
-
R Development Core Team. R: A language and environment for statistical computing http://www.r-project.org (R Foundation for Statistical Computing, 2011).
-
(2011)
R Foundation for Statistical Computing
-
-
-
49
-
-
62349130698
-
Ultrafast andmemory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M.&Salzberg, S. L. Ultrafast andmemory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
50
-
-
75549089967
-
The UCSC Genome Browser database: Update 2010
-
Rhead, B. et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 38, D613-D619 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Rhead, B.1
-
51
-
-
3142592324
-
Methods in comparative genomics: Genome correspondence, gene identification and regulatory motif discovery
-
Kellis, M., Patterson, N., Birren, B., Berger, B. & Lander, E. S. Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery. J. Comput. Biol. 11, 319-355 (2004).
-
(2004)
J. Comput. Biol.
, vol.11
, pp. 319-355
-
-
Kellis, M.1
Patterson, N.2
Birren, B.3
Berger, B.4
Lander, E.S.5
-
52
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. & Lipman, D. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.4
Lipman, D.5
-
53
-
-
59949096873
-
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
-
Vilella, A. J. et al. EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res. 19, 327-335 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 327-335
-
-
Vilella, A.J.1
-
54
-
-
1542748076
-
Aligning multiple genomic sequences with the threaded blockset aligner
-
Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715 (2004).
-
(2004)
Genome Res.
, vol.14
, pp. 708-715
-
-
Blanchette, M.1
-
55
-
-
78049354879
-
Fine-scale recombination rate differences between sexes, populations and individuals
-
Kong, A. et al. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467, 1099-1103 (2010).
-
(2010)
Nature
, vol.467
, pp. 1099-1103
-
-
Kong, A.1
-
56
-
-
84865739425
-
Architecture of the human regulatory network derived from ENCODE data
-
Gerstein, M. B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100 (2012).
-
(2012)
Nature
, vol.489
, pp. 91-100
-
-
Gerstein, M.B.1
-
57
-
-
33744805985
-
Genome-wide analysis ofmammalian promoter architecture and evolution
-
Carninci, P. et al. Genome-wide analysis ofmammalian promoter architecture and evolution. Nature Genet. 38, 626-635 (2006).
-
(2006)
Nature Genet.
, vol.38
, pp. 626-635
-
-
Carninci, P.1
-
58
-
-
78651293534
-
MiRBase: Integrating microRNAannotation and deep-sequencing data
-
Kozomara, A.& Griffiths-Jones, S. miRBase: integrating microRNAannotation and deep-sequencing data. Nucleic Acids Res. 39, D152-D157 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Kozomara, A.1
Griffiths-Jones, S.2
|