-
1
-
-
0043269205
-
The RNA polymerase II core promoter
-
Smale ST, Kadonaga JT, (2003) The RNA polymerase II core promoter. Annu Rev Biochem 72: 449-479.
-
(2003)
Annu Rev Biochem
, vol.72
, pp. 449-479
-
-
Smale, S.T.1
Kadonaga, J.T.2
-
2
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. (2005) The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
-
3
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (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
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
-
4
-
-
0028213438
-
Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides
-
Maruyama K, Sugano S, (1994) Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138: 171-174.
-
(1994)
Gene
, vol.138
, pp. 171-174
-
-
Maruyama, K.1
Sugano, S.2
-
5
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, et al. (2003) Human-mouse alignments with BLASTZ. Genome Research 13: 103-107.
-
(2003)
Genome Research
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
-
6
-
-
59949103704
-
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
-
Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, et al. (2009) Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Research 19: 255-265.
-
(2009)
Genome Research
, vol.19
, pp. 255-265
-
-
Valen, E.1
Pascarella, G.2
Chalk, A.3
Maeda, N.4
Kojima, M.5
-
7
-
-
33646473694
-
Complex loci in human and mouse genomes
-
Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, et al. (2006) Complex loci in human and mouse genomes. Plos Genetics 2: 564-577.
-
(2006)
Plos Genetics
, vol.2
, pp. 564-577
-
-
Engstrom, P.G.1
Suzuki, H.2
Ninomiya, N.3
Akalin, A.4
Sessa, L.5
-
8
-
-
65149092197
-
Transcriptional features of genomic regulatory blocks
-
Akalin A, Fredman D, Arner E, Dong XJ, Bryne JC, et al. (2009) Transcriptional features of genomic regulatory blocks. Genome Biology 10:-.
-
(2009)
Genome Biology
, vol.10
-
-
Akalin, A.1
Fredman, D.2
Arner, E.3
Dong, X.J.4
Bryne, J.C.5
-
9
-
-
33646472425
-
Mice and men: Their promoter properties
-
Bajic VB, Tan SL, Christoffels A, Schonbach C, Lipovich L, et al. (2006) Mice and men: Their promoter properties. Plos Genetics 2: 614-626.
-
(2006)
Plos Genetics
, vol.2
, pp. 614-626
-
-
Bajic, V.B.1
Tan, S.L.2
Christoffels, A.3
Schonbach, C.4
Lipovich, L.5
-
10
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genetics 38: 626-635.
-
(2006)
Nature Genetics
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
-
11
-
-
33749128065
-
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters
-
Ponjavic J, Lenhard B, Kai C, Kawai J, Carninci P, et al. (2006) Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. Genome Biology 7:-.
-
(2006)
Genome Biology
, vol.7
-
-
Ponjavic, J.1
Lenhard, B.2
Kai, C.3
Kawai, J.4
Carninci, P.5
-
12
-
-
80052458531
-
Small RNA profiles from human genic regions suggest biogenic mechanisms and identify new Argonaute-associated species
-
DOI:10.1038/nsmb.2091 Available:
-
Valen E, Preker P, Andersen P, Zhao X, Chen Y, et al. (2011) Small RNA profiles from human genic regions suggest biogenic mechanisms and identify new Argonaute-associated species. Nat Struct Mol Biol DOI:10.1038/nsmb.2091 Available:http://www.nature.com/nsmb/.
-
(2011)
Nat Struct Mol Biol
-
-
Valen, E.1
Preker, P.2
Andersen, P.3
Zhao, X.4
Chen, Y.5
-
13
-
-
34249063835
-
Dynamic usage of transcription start sites within core promoters
-
Kawaji H, Frith MC, Katayama S, Sandelin A, Kai C, et al. (2006) Dynamic usage of transcription start sites within core promoters. Genome Biology 7:-.
-
(2006)
Genome Biology
, vol.7
-
-
Kawaji, H.1
Frith, M.C.2
Katayama, S.3
Sandelin, A.4
Kai, C.5
-
14
-
-
30044442791
-
Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes
-
Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, et al. (2006) Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes. Genome Research 16: 55-65.
-
(2006)
Genome Research
, vol.16
, pp. 55-65
-
-
Kimura, K.1
Wakamatsu, A.2
Suzuki, Y.3
Ota, T.4
Nishikawa, T.5
-
15
-
-
0034991911
-
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
-
Suzuki Y, Taira H, Tsunoda T, Mizushima-Sugano J, Sese J, et al. (2001) Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. Embo Reports 2: 388-393.
-
(2001)
Embo Reports
, vol.2
, pp. 388-393
-
-
Suzuki, Y.1
Taira, H.2
Tsunoda, T.3
Mizushima-Sugano, J.4
Sese, J.5
-
16
-
-
77954716355
-
A paired-end sequencing strategy to map the complex landscape of transcription initiation
-
Ni T, Corcoran DL, Rach EA, Song S, Spana EP, et al. (2010) A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nature Methods 7: 521-U557.
-
(2010)
Nature Methods
, vol.7
, pp. 521-557
-
-
Ni, T.1
Corcoran, D.L.2
Rach, E.A.3
Song, S.4
Spana, E.P.5
-
17
-
-
33646484899
-
Transcriptional network dynamics in macrophage activation
-
Nilsson R, Bajic VB, Suzuki H, di Bernardo D, Bjorkegren J, et al. (2006) Transcriptional network dynamics in macrophage activation. Genomics 88: 133-142.
-
(2006)
Genomics
, vol.88
, pp. 133-142
-
-
Nilsson, R.1
Bajic, V.B.2
Suzuki, H.3
di Bernardo, D.4
Bjorkegren, J.5
-
18
-
-
65149083962
-
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
-
Suzuki H, Forrest ARR, van Nimwegen E, Daub CO, Balwierz PJ, et al. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics 41: 553-562.
-
(2009)
Nature Genetics
, vol.41
, pp. 553-562
-
-
Suzuki, H.1
Forrest, A.R.R.2
van Nimwegen, E.3
Daub, C.O.4
Balwierz, P.J.5
-
19
-
-
33744824906
-
Evolutionary turnover of mammalian transcription start sites
-
Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, et al. (2006) Evolutionary turnover of mammalian transcription start sites. Genome Research 16: 713-722.
-
(2006)
Genome Research
, vol.16
, pp. 713-722
-
-
Frith, M.C.1
Ponjavic, J.2
Fredman, D.3
Kai, C.4
Kawai, J.5
-
20
-
-
33646489947
-
Heterotachy in mammalian promoter evolution
-
Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, et al. (2006) Heterotachy in mammalian promoter evolution. Plos Genetics 2: e30.
-
(2006)
Plos Genetics
, vol.2
-
-
Taylor, M.S.1
Kai, C.2
Kawai, J.3
Carninci, P.4
Hayashizaki, Y.5
-
21
-
-
38049020974
-
A code for transcription initiation in mammalian genomes
-
Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, et al. (2008) A code for transcription initiation in mammalian genomes. Genome Research 18: 1-12.
-
(2008)
Genome Research
, vol.18
, pp. 1-12
-
-
Frith, M.C.1
Valen, E.2
Krogh, A.3
Hayashizaki, Y.4
Carninci, P.5
-
22
-
-
34249098071
-
Mammalian RNA polymerase II core promoters: insights from genome-wide studies
-
Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, et al. (2007) Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nature Reviews Genetics 8: 424-436.
-
(2007)
Nature Reviews Genetics
, vol.8
, pp. 424-436
-
-
Sandelin, A.1
Carninci, P.2
Lenhard, B.3
Ponjavic, J.4
Hayashizaki, Y.5
-
23
-
-
77954918638
-
Structure and basal transcription complex of RNA polymerase II core promoters in the mammalian genome: an overview
-
Baumann M, Pontiller J, Ernst W, (2010) Structure and basal transcription complex of RNA polymerase II core promoters in the mammalian genome: an overview. Molecular Biotechnology 45: 241-247.
-
(2010)
Molecular Biotechnology
, vol.45
, pp. 241-247
-
-
Baumann, M.1
Pontiller, J.2
Ernst, W.3
-
24
-
-
79851485916
-
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level
-
Rach EA, Winter DR, Benjamin AM, Corcoran DL, Ni T, et al. (2011) Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. Plos Genetics 7: e1001274.
-
(2011)
Plos Genetics
, vol.7
-
-
Rach, E.A.1
Winter, D.R.2
Benjamin, A.M.3
Corcoran, D.L.4
Ni, T.5
-
25
-
-
31944432339
-
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
-
Saxonov S, Berg P, Brutlag DL, (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 103: 1412-1417.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 1412-1417
-
-
Saxonov, S.1
Berg, P.2
Brutlag, D.L.3
-
26
-
-
77951073899
-
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns
-
Kratz A, Arner E, Saito R, Kubosaki A, Kawai J, et al. (2010) Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. Bmc Genomics 11: 257.
-
(2010)
Bmc Genomics
, vol.11
, pp. 257
-
-
Kratz, A.1
Arner, E.2
Saito, R.3
Kubosaki, A.4
Kawai, J.5
-
27
-
-
0036604863
-
On measuring the distance between histograms
-
Cha S-H, Srihari SN, (2002) On measuring the distance between histograms. Pattern Recognition 35: 1355-1370.
-
(2002)
Pattern Recognition
, vol.35
, pp. 1355-1370
-
-
Cha, S.-H.1
Srihari, S.N.2
-
28
-
-
0032319998
-
-
A metric for distributions with applications to image databases; 1998
-
Rubner Y, Tomasi C, Guibas LJ, (1998) pp. 59-66 A metric for distributions with applications to image databases; 1998.
-
(1998)
, pp. 59-66
-
-
Rubner, Y.1
Tomasi, C.2
Guibas, L.J.3
-
29
-
-
80051994139
-
-
Cluster Analysis (Quantitative Applications in the Social Sciences)
-
Mark S, Aldenderfer RKKB, (1984) Cluster Analysis (Quantitative Applications in the Social Sciences).
-
(1984)
-
-
Mark, S.1
Aldenderfer, R.K.K.B.2
-
31
-
-
32044442759
-
Promoter features related to tissue specificity as measured by Shannon entropy
-
Schug J, Schuller WP, Kappen C, Salbaum JM, Bucan M, et al. (2005) Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biology 6:-.
-
(2005)
Genome Biology
, vol.6
-
-
Schug, J.1
Schuller, W.P.2
Kappen, C.3
Salbaum, J.M.4
Bucan, M.5
-
32
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635.
-
(2006)
Nat Genet
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
-
33
-
-
78649291183
-
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
-
Chavez L, Jozefczuk J, Grimm C, Dietrich J, Timmermann B, et al. (2010) Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res 20: 1441-1450.
-
(2010)
Genome Res
, vol.20
, pp. 1441-1450
-
-
Chavez, L.1
Jozefczuk, J.2
Grimm, C.3
Dietrich, J.4
Timmermann, B.5
-
34
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.Y.4
Schones, D.E.5
-
35
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560.
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
-
36
-
-
46249112085
-
Combinatorial patterns of histone acetylations and methylations in the human genome
-
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics 40: 897-903.
-
(2008)
Nature Genetics
, vol.40
, pp. 897-903
-
-
Wang, Z.1
Zang, C.2
Rosenfeld, J.A.3
Schones, D.E.4
Barski, A.5
-
37
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, et al. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898.
-
(2008)
Cell
, vol.132
, pp. 887-898
-
-
Schones, D.E.1
Cui, K.2
Cuddapah, S.3
Roh, T.Y.4
Barski, A.5
-
38
-
-
0033822364
-
Large-scale human promoter mapping using CpG islands
-
Ioshikhes IP, Zhang MQ, (2000) Large-scale human promoter mapping using CpG islands. Nature Genetics 26: 61-63.
-
(2000)
Nature Genetics
, vol.26
, pp. 61-63
-
-
Ioshikhes, I.P.1
Zhang, M.Q.2
-
39
-
-
63549108475
-
H2A.Z and DNA methylation: irreconcilable differences
-
Kobor MS, Lorincz MC, (2009) H2A.Z and DNA methylation: irreconcilable differences. Trends Biochem Sci 34: 158-161.
-
(2009)
Trends Biochem Sci
, vol.34
, pp. 158-161
-
-
Kobor, M.S.1
Lorincz, M.C.2
-
40
-
-
2642542643
-
A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin
-
Schotta G, Lachner M, Sarma K, Ebert A, Sengupta R, et al. (2004) A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev 18: 1251-1262.
-
(2004)
Genes Dev
, vol.18
, pp. 1251-1262
-
-
Schotta, G.1
Lachner, M.2
Sarma, K.3
Ebert, A.4
Sengupta, R.5
-
42
-
-
38049020974
-
A code for transcription initiation in mammalian genomes
-
Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, et al. (2008) A code for transcription initiation in mammalian genomes. Genome Res 18: 1-12.
-
(2008)
Genome Res
, vol.18
, pp. 1-12
-
-
Frith, M.C.1
Valen, E.2
Krogh, A.3
Hayashizaki, Y.4
Carninci, P.5
-
43
-
-
0345865009
-
GenBank: update
-
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL, (2004) GenBank: update. Nucleic Acids Res 32: D23-26.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
44
-
-
17544380551
-
The architecture of mammalian ribosomal protein promoters
-
Perry RP, (2005) The architecture of mammalian ribosomal protein promoters. BMC Evol Biol 5: 15.
-
(2005)
BMC Evol Biol
, vol.5
, pp. 15
-
-
Perry, R.P.1
-
45
-
-
0036796620
-
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome
-
Zhang Z, Harrison P, Gerstein M, (2002) Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res 12: 1466-1482.
-
(2002)
Genome Res
, vol.12
, pp. 1466-1482
-
-
Zhang, Z.1
Harrison, P.2
Gerstein, M.3
-
46
-
-
33646468946
-
Pseudo-messenger RNA: phantoms of the transcriptome
-
Frith MC, Wilming LG, Forrest A, Kawaji H, Tan SL, et al. (2006) Pseudo-messenger RNA: phantoms of the transcriptome. Plos Genetics 2: e23.
-
(2006)
Plos Genetics
, vol.2
-
-
Frith, M.C.1
Wilming, L.G.2
Forrest, A.3
Kawaji, H.4
Tan, S.L.5
-
47
-
-
23644460630
-
Tag-based approaches for transcriptome research and genome annotation
-
Harbers M, Carninci P, (2005) Tag-based approaches for transcriptome research and genome annotation. Nat Methods 2: 495-502.
-
(2005)
Nat Methods
, vol.2
, pp. 495-502
-
-
Harbers, M.1
Carninci, P.2
-
48
-
-
84881837496
-
-
Cap-Analysis Gene Expression (CAGE): The Science of Decoding Gene Transcription: Pan Stanford Publishing
-
Carninci P, (2009) Cap-Analysis Gene Expression (CAGE): The Science of Decoding Gene Transcription: Pan Stanford Publishing.
-
(2009)
-
-
Carninci, P.1
-
49
-
-
77954738647
-
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
-
Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, et al. (2010) Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods 7: 528-534.
-
(2010)
Nat Methods
, vol.7
, pp. 528-534
-
-
Plessy, C.1
Bertin, N.2
Takahashi, H.3
Simone, R.4
Salimullah, M.5
-
50
-
-
79959403670
-
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
-
Islam S, Kjallquist U, Moliner A, Zajac P, Fan JB, et al. (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res.
-
(2011)
Genome Res
-
-
Islam, S.1
Kjallquist, U.2
Moliner, A.3
Zajac, P.4
Fan, J.B.5
-
51
-
-
76749141381
-
Ancient human genome sequence of an extinct Palaeo-Eskimo
-
Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, et al. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463: 757-762.
-
(2010)
Nature
, vol.463
, pp. 757-762
-
-
Rasmussen, M.1
Li, Y.2
Lindgreen, S.3
Pedersen, J.S.4
Albrechtsen, A.5
-
52
-
-
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. Nature Genetics 41: 563-571.
-
(2009)
Nature Genetics
, vol.41
, pp. 563-571
-
-
Faulkner, G.J.1
Kimura, Y.2
Daub, C.O.3
Wani, S.4
Plessy, C.5
-
53
-
-
79551610291
-
Genome-wide analysis of promoter architecture in Drosophila melanogaster
-
Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, et al. (2010) Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res 21: 182-192.
-
(2010)
Genome Res
, vol.21
, pp. 182-192
-
-
Hoskins, R.A.1
Landolin, J.M.2
Brown, J.B.3
Sandler, J.E.4
Takahashi, H.5
-
55
-
-
77649299348
-
An atlas of combinatorial transcriptional regulation in mouse and man
-
Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, et al. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140: 744-752.
-
(2010)
Cell
, vol.140
, pp. 744-752
-
-
Ravasi, T.1
Suzuki, H.2
Cannistraci, C.V.3
Katayama, S.4
Bajic, V.B.5
-
56
-
-
0036604863
-
On measuring the distance between histograms
-
Cha SH, Srihari SN, (2002) On measuring the distance between histograms. Pattern Recognition 35: 1355-1370.
-
(2002)
Pattern Recognition
, vol.35
, pp. 1355-1370
-
-
Cha, S.H.1
Srihari, S.N.2
-
57
-
-
75549083247
-
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
-
Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, et al. (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 38: D105-110.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Portales-Casamar, E.1
Thongjuea, S.2
Kwon, A.T.3
Arenillas, D.4
Zhao, X.5
-
58
-
-
3242891274
-
ConSite: web-based prediction of regulatory elements using cross-species comparison
-
Sandelin A, Wasserman WW, Lenhard B, (2004) ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res 32: W249-252.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Sandelin, A.1
Wasserman, W.W.2
Lenhard, B.3
-
59
-
-
0023216891
-
CpG islands in vertebrate genomes
-
Gardiner-Garden M, Frommer M, (1987) CpG islands in vertebrate genomes. J Mol Biol 196: 261-282.
-
(1987)
J Mol Biol
, vol.196
, pp. 261-282
-
-
Gardiner-Garden, M.1
Frommer, M.2
-
60
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, 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
-
61
-
-
1542537849
-
Combining phylogenetic and hidden Markov models in biosequence analysis
-
Siepel A, Haussler D, (2004) Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol 11: 413-428.
-
(2004)
J Comput Biol
, vol.11
, pp. 413-428
-
-
Siepel, A.1
Haussler, D.2
-
62
-
-
33644874573
-
The UCSC Genome Browser Database: update 2006
-
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, et al. (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 34: D590-598.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Hinrichs, A.S.1
Karolchik, D.2
Baertsch, R.3
Barber, G.P.4
Bejerano, G.5
-
63
-
-
49649125042
-
Genome-scale DNA methylation maps of pluripotent and differentiated cells
-
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766-770.
-
(2008)
Nature
, vol.454
, pp. 766-770
-
-
Meissner, A.1
Mikkelsen, T.S.2
Gu, H.3
Wernig, M.4
Hanna, J.5
-
65
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10: R25.
-
(2009)
Genome Biology
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
66
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biology 9: R137.
-
(2008)
Genome Biology
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
-
67
-
-
70350013550
-
Biased chromatin signatures around polyadenylation sites and exons
-
Spies N, Nielsen CB, Padgett RA, Burge CB, (2009) Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 36: 245-254.
-
(2009)
Mol Cell
, vol.36
, pp. 245-254
-
-
Spies, N.1
Nielsen, C.B.2
Padgett, R.A.3
Burge, C.B.4
-
68
-
-
0025008168
-
Sequence logos: a new way to display consensus sequences
-
Schneider TD, Stephens RM, (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100.
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
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