-
1
-
-
70449723389
-
Establishing legitimacy and function in the new transcriptome
-
van Bakel H, Hughes TR (2009) Establishing legitimacy and function in the new transcriptome. Brief Funct Genomic Proteomic 8: 424-436.
-
(2009)
Brief Funct Genomic Proteomic
, vol.8
, pp. 424-436
-
-
van Bakel, H.1
Hughes, T.R.2
-
4
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
-
(2008)
Nat Genet
, vol.40
, pp. 1413-1415
-
-
Pan, Q.1
Shai, O.2
Lee, L.J.3
Frey, B.J.4
Blencowe, B.J.5
-
5
-
-
0016669094
-
Evolution at two levels in humans and chimpanzees
-
King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
-
(1975)
Science
, vol.188
, pp. 107-116
-
-
King, M.C.1
Wilson, A.C.2
-
6
-
-
0037066542
-
Intra- and interspecific variation in primate gene expression patterns
-
Enard W, Khaitovich P, Klose J, Zöllner S, Heissig F, et al. (2002) Intra- and interspecific variation in primate gene expression patterns. Science 296: 340-343.
-
(2002)
Science
, vol.296
, pp. 340-343
-
-
Enard, W.1
Khaitovich, P.2
Klose, J.3
Zöllner, S.4
Heissig, F.5
-
7
-
-
0242268390
-
Elevated gene expression levels distinguish human from non-human primate brains
-
Cáceres M, Lachuer J, Zapala MA, Redmond JC, Kudo L, et al. (2003) Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci USA 100: 13030-13035.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13030-13035
-
-
Cáceres, M.1
Lachuer, J.2
Zapala, M.A.3
Redmond, J.C.4
Kudo, L.5
-
8
-
-
0037303824
-
Induced gene expression in human brain after the split from chimpanzee
-
Gu J, Gu X (2003) Induced gene expression in human brain after the split from chimpanzee. Trends Genet 19: 63-65.
-
(2003)
Trends Genet
, vol.19
, pp. 63-65
-
-
Gu, J.1
Gu, X.2
-
9
-
-
33750482555
-
Functionality of intergenic transcription: An evolutionary comparison
-
Khaitovich P, Kelso J, Franz H, Visagie J, Giger T, et al. (2006) Functionality of intergenic transcription: an evolutionary comparison. PLoS Genet 2: e171.
-
(2006)
PLoS Genet
, vol.2
-
-
Khaitovich, P.1
Kelso, J.2
Franz, H.3
Visagie, J.4
Giger, T.5
-
10
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
11
-
-
47949084846
-
Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing
-
Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, et al. (2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45: 81-94.
-
(2008)
Biotechniques
, vol.45
, pp. 81-94
-
-
Morin, R.1
Bainbridge, M.2
Fejes, A.3
Hirst, M.4
Krzywinski, M.5
-
12
-
-
50949090496
-
Poly A- transcripts expressed in HeLa cells
-
Wu Q, Kim YC, Lu J, Xuan Z, Chen J, et al. (2008) Poly A- transcripts expressed in HeLa cells. PLoS One 3: e2803.
-
(2008)
PLoS One
, vol.3
-
-
Wu, Q.1
Kim, Y.C.2
Lu, J.3
Xuan, Z.4
Chen, J.5
-
13
-
-
67349173665
-
The regulated retrotransposon transcriptome of mammalian cells
-
Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, et al. (2009) The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41: 563-571.
-
(2009)
Nat Genet
, vol.41
, pp. 563-571
-
-
Faulkner, G.J.1
Kimura, Y.2
Daub, C.O.3
Wani, S.4
Plessy, C.5
-
14
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A, Bejerano G, Pedersen J, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research 15: 1034-1050.
-
(2005)
Genome Research
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.3
Hinrichs, A.S.4
Hou, M.5
-
15
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
-
16
-
-
0033982936
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
17
-
-
38849101777
-
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
-
Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, et al. (2007) Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Research 17: 1823-1836.
-
(2007)
Genome Research
, vol.17
, pp. 1823-1836
-
-
Lin, M.F.1
Carlson, J.W.2
Crosby, M.A.3
Matthews, B.B.4
Yu, C.5
-
18
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman M, Amit I, Garber M, French C, Lin MF, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
Amit, I.2
Garber, M.3
French, C.4
Lin, M.F.5
-
19
-
-
67650921949
-
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
-
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106: 11667-11672.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
Guttman, M.2
Huarte, M.3
Garber, M.4
Raj, A.5
-
20
-
-
33646272409
-
Identification and classification of conserved RNA secondary structures in the human genome
-
Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, et al. (2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2: e33.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Pedersen, J.S.1
Bejerano, G.2
Siepel, A.3
Rosenbloom, K.4
Lindblad-Toh, K.5
-
21
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
-
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
22
-
-
4444287699
-
Regional patterns of gene expression in human and chimpanzee brains
-
Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, et al. (2004) Regional patterns of gene expression in human and chimpanzee brains. Genome Research 14: 1462-1473.
-
(2004)
Genome Research
, vol.14
, pp. 1462-1473
-
-
Khaitovich, P.1
Muetzel, B.2
She, X.3
Lachmann, M.4
Hellmann, I.5
-
23
-
-
76049088399
-
Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain
-
Nowick K, Gernat T, Almaas E, Stubbs L (2009) Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proc Natl Acad Sci U S A 106: 22358-22363.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 22358-22363
-
-
Nowick, K.1
Gernat, T.2
Almaas, E.3
Stubbs, L.4
-
24
-
-
34548346860
-
Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
-
Haygood R, Fedrigo O, Hanson B, Yokoyama KD, 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
-
25
-
-
33644855479
-
Expression profiling in primates reveals a rapid evolution of human transcription factors
-
Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440: 242-245.
-
(2006)
Nature
, vol.440
, pp. 242-245
-
-
Gilad, Y.1
Oshlack, A.2
Smyth, G.K.3
Speed, T.P.4
White, K.P.5
-
26
-
-
56649102089
-
Genomic convergence analysis of schizophrenia: MRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum
-
Mudge J, Miller NA, Khrebtukova I, Lindquist IE, May GD, et al. (2008) Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS One 3: e3625.
-
(2008)
PLoS One
, vol.3
-
-
Mudge, J.1
Miller, N.A.2
Khrebtukova, I.3
Lindquist, I.E.4
May, G.D.5
-
27
-
-
67749132423
-
Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
-
Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486.
-
(2009)
Nature
, vol.460
, pp. 479-486
-
-
Chi, S.W.1
Zang, J.B.2
Mele, A.3
Darnell, R.B.4
-
28
-
-
46249092601
-
Proliferating cells express mRNAs with shortened 39 untranslated regions and fewer microRNA target sites
-
Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB (2008) Proliferating cells express mRNAs with shortened 39 untranslated regions and fewer microRNA target sites. Science 320: 1643-1647.
-
(2008)
Science
, vol.320
, pp. 1643-1647
-
-
Sandberg, R.1
Neilson, J.R.2
Sarma, A.3
Sharp, P.A.4
Burge, C.B.5
-
29
-
-
66049104920
-
Progressive lengthening of 39 untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development
-
Ji Z, Lee JY, Pan Z, Jiang B, Tian B (2009) Progressive lengthening of 39 untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci USA 106: 7028-7033.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 7028-7033
-
-
Ji, Z.1
Lee, J.Y.2
Pan, Z.3
Jiang, B.4
Tian, B.5
-
31
-
-
18444402182
-
The Ensembl genome database project
-
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, et al. (2002) The Ensembl genome database project. Nucleic Acids Res 30: 38-41.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 38-41
-
-
Hubbard, T.1
Barker, D.2
Birney, E.3
Cameron, G.4
Chen, Y.5
-
32
-
-
0347755531
-
The UCSC Table Browser data retrieval tool
-
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, et al. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32: D493-496.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Karolchik, D.1
Hinrichs, A.S.2
Furey, T.S.3
Roskin, K.M.4
Sugnet, C.W.5
-
33
-
-
1542748076
-
Aligning multiple genomic sequences with the threaded blockset aligner
-
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14: 708-715.
-
(2004)
Genome Res
, vol.14
, pp. 708-715
-
-
Blanchette, M.1
Kent, W.J.2
Riemer, C.3
Elnitski, L.4
Smit, A.F.5
-
34
-
-
38549131376
-
The UCSC Genome Browser Database: 2008 update
-
Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, et al. (2008) The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 36: D773-779.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Karolchik, D.1
Kuhn, R.M.2
Baertsch, R.3
Barber, G.P.4
Clawson, H.5
-
35
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
36
-
-
33847173733
-
FUNC: A package for detecting significant associations between gene sets and ontological annotations
-
Prufer K, Muetzel B, Do HH, Weiss G, Khaitovich P, et al. (2007) FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8: 41.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 41
-
-
Prufer, K.1
Muetzel, B.2
Do, H.H.3
Weiss, G.4
Khaitovich, P.5
-
37
-
-
24344500211
-
Initial sequence of the chimpanzee genome and comparison with the human genome
-
(2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
-
(2005)
Nature
, vol.437
, pp. 69-87
-
-
-
38
-
-
22144447840
-
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees
-
Khaitovich P, Hellmann I, Enard W, Nowick K, Leinweber M, et al. (2005) Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309: 1850-1854.
-
(2005)
Science
, vol.309
, pp. 1850-1854
-
-
Khaitovich, P.1
Hellmann, I.2
Enard, W.3
Nowick, K.4
Leinweber, M.5
-
39
-
-
34547609849
-
Evolutionary history of mammalian transposons determined by genome-wide defragmentation
-
Giordano J, Ge Y, Gelfand Y, Abrusán G, Benson G, et al. (2007) Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Comput Biol 3: e137.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Giordano, J.1
Ge, Y.2
Gelfand, Y.3
Abrusán, G.4
Benson, G.5
|