-
1
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
-
2
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
-
3
-
-
21044431735
-
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
-
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308: 1149-1154.
-
(2005)
Science
, vol.308
, pp. 1149-1154
-
-
Cheng, J.1
Kapranov, P.2
Drenkow, J.3
Dike, S.4
Brubaker, S.5
-
4
-
-
19944376457
-
Global identification of human transcribed sequences with genome tiling arrays
-
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, et al. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306: 2242-2246.
-
(2004)
Science
, vol.306
, pp. 2242-2246
-
-
Bertone, P.1
Stolc, V.2
Royce, T.E.3
Rozowsky, J.S.4
Urban, A.E.5
-
5
-
-
0037012881
-
Large-scale transcriptional activity in chromosomes 21 and 22
-
Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, et al. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science 296: 916-919.
-
(2002)
Science
, vol.296
, pp. 916-919
-
-
Kapranov, P.1
Cawley, S.E.2
Drenkow, J.3
Bekiranov, S.4
Strausberg, R.L.5
-
6
-
-
10744226888
-
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
-
Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.
-
(2004)
Cell
, vol.116
, pp. 499-509
-
-
Cawley, S.1
Bekiranov, S.2
Ng, H.H.3
Kapranov, P.4
Sekinger, E.A.5
-
7
-
-
0037673675
-
Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia
-
Carninci P, Waki K, Shiraki T, Konno H, Shibata K, et al. (2003) Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia. Genome Res 13: 1273-1289.
-
(2003)
Genome Res
, vol.13
, pp. 1273-1289
-
-
Carninci, P.1
Waki, K.2
Shiraki, T.3
Konno, H.4
Shibata, K.5
-
8
-
-
0033791308
-
Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes
-
Carninci P, Shibata Y, Hayatsu N, Sugahara Y, Shibata K, et al. (2000) Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res 10: 1617-1630.
-
(2000)
Genome Res
, vol.10
, pp. 1617-1630
-
-
Carninci, P.1
Shibata, Y.2
Hayatsu, N.3
Sugahara, Y.4
Shibata, K.5
-
9
-
-
0035825662
-
Functional annotation of a full-length mouse cDNA collection
-
Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, et al. (2001) Functional annotation of a full-length mouse cDNA collection. Nature 409: 685-690.
-
(2001)
Nature
, vol.409
, pp. 685-690
-
-
Kawai, J.1
Shinagawa, A.2
Shibata, K.3
Yoshino, M.4
Itoh, M.5
-
10
-
-
0142104045
-
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
-
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573.
-
(2002)
Nature
, vol.420
, pp. 563-573
-
-
Okazaki, Y.1
Furuno, M.2
Kasukawa, T.3
Adachi, J.4
Bono, H.5
-
11
-
-
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
-
12
-
-
24644472515
-
Antisense transcription in the mammalian transcriptome
-
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, et al. (2005) Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566.
-
(2005)
Science
, vol.309
, pp. 1564-1566
-
-
Katayama, S.1
Tomaru, Y.2
Kasukawa, T.3
Waki, K.4
Nakanishi, M.5
-
13
-
-
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
-
14
-
-
9144233601
-
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
-
U S A
-
Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A 100: 15776-15781.
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 15776-15781
-
-
Shiraki, T.1
Kondo, S.2
Katayama, S.3
Waki, K.4
Kasukawa, T.5
-
15
-
-
20844463584
-
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation
-
Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, et al. (2005) Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods 2: 105-111.
-
(2005)
Nat Methods
, vol.2
, pp. 105-111
-
-
Ng, P.1
Wei, C.L.2
Sung, W.K.3
Chiu, K.P.4
Lipovich, L.5
-
16
-
-
0038349624
-
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome
-
Zavolan M, Kondo S, Schonbach C, Adachi J, Hume DA, et al. (2003) Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res 13: 1290-1300.
-
(2003)
Genome Res
, vol.13
, pp. 1290-1300
-
-
Zavolan, M.1
Kondo, S.2
Schonbach, C.3
Adachi, J.4
Hume, D.A.5
-
17
-
-
33646493012
-
SPA: A probabilistic algorithm for spliced alignment
-
DOI: 10.1371/journal.pgen.0020024
-
van Nimwegen E, Paul N, Sheridan R, Zavolan M (2006) SPA: A probabilistic algorithm for spliced alignment. PLoS Genet 2: DOI: 10.1371/journal.pgen. 0020024
-
(2006)
PLoS Genet
, vol.2
-
-
Van Nimwegen, E.1
Paul, N.2
Sheridan, R.3
Zavolan, M.4
-
18
-
-
33646491292
-
A simple physical model predicts small exon length variations
-
DOI: 10.1371/journal.pgen.0020045
-
Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, et al. (2006) A simple physical model predicts small exon length variations. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020045
-
(2006)
PLoS Genet
, vol.2
-
-
Chern, T.M.1
Van Nimwegen, E.2
Kai, C.3
Kawai, J.4
Carninci, P.5
-
19
-
-
33646466927
-
Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units
-
DOI: 10.1371/journal.pgen.0020046
-
Davis MJ, Hanson KA, Clark F, Fink JL, Zhang F, et al. (2006) Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020046
-
(2006)
PLoS Genet
, vol.2
-
-
Davis, M.J.1
Hanson, K.A.2
Clark, F.3
Fink, J.L.4
Zhang, F.5
-
20
-
-
33646480845
-
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases
-
Forrest AR, Taylor DF, Crowe ML, Chalk AM, Waddell NJ, et al. (2006) Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biol 7: R5.
-
(2006)
Genome Biol
, vol.7
-
-
Forrest, A.R.1
Taylor, D.F.2
Crowe, M.L.3
Chalk, A.M.4
Waddell, N.J.5
-
21
-
-
33646483032
-
The abundance of short proteins in the mammalian proteome
-
DOI: 10.1371/journal.pgen.0020052
-
Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, et al. (2006) The abundance of short proteins in the mammalian proteome. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020052
-
(2006)
PLoS Genet
, vol.2
-
-
Frith, M.C.1
Forrest, A.R.2
Nourbakhsh, E.3
Pang, K.C.4
Kai, C.5
-
22
-
-
0034084035
-
Analysis of expressed sequence tags indicates 35,000 human genes
-
Ewing B, Green P (2000) Analysis of expressed sequence tags indicates 35,000 human genes. Nat Genet 25: 232-234.
-
(2000)
Nat Genet
, vol.25
, pp. 232-234
-
-
Ewing, B.1
Green, P.2
-
23
-
-
0000508290
-
Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence
-
Roest Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L, et al. (2000) Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet 25: 235-238.
-
(2000)
Nat Genet
, vol.25
, pp. 235-238
-
-
Roest Crollius, H.1
Jaillon, O.2
Bernot, A.3
Dasilva, C.4
Bouneau, L.5
-
24
-
-
0034204044
-
Gene index analysis of the human genome estimates approximately 120,000 genes
-
Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, et al. (2000) Gene index analysis of the human genome estimates approximately 120,000 genes. Nat Genet 25: 239-240.
-
(2000)
Nat Genet
, vol.25
, pp. 239-240
-
-
Liang, F.1
Holt, I.2
Pertea, G.3
Karamycheva, S.4
Salzberg, S.L.5
-
25
-
-
33646488342
-
Distinguishing protein-coding from non-coding RNAs through support vector machines
-
DOI: 10.1371/journal.pgen.0020029
-
Liu J, Gough J, Rost B (2006) Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020029
-
(2006)
PLoS Genet
, vol.2
-
-
Liu, J.1
Gough, J.2
Rost, B.3
-
26
-
-
33646474262
-
Clusters of internally primed transcripts reveal novel long noncoding RNAs
-
DOI: 10.1371/journal.pgen.0020037
-
Furuno M, Pang KC, Ninomiya N, Fukuda S, Frith MC, et al. (2006) Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020037
-
(2006)
PLoS Genet
, vol.2
-
-
Furuno, M.1
Pang, K.C.2
Ninomiya, N.3
Fukuda, S.4
Frith, M.C.5
-
28
-
-
28844443172
-
Genome annotation past, present, and future: How to define an ORF at each locus
-
Brent MR (2005) Genome annotation past, present, and future: How to define an ORF at each locus. Genome Res 15: 1777-1786.
-
(2005)
Genome Res
, vol.15
, pp. 1777-1786
-
-
Brent, M.R.1
-
29
-
-
1642473033
-
Comparative analysis of processed pseudogenes in the mouse and human genomes
-
Zhang Z, Carriero N, Gerstein M (2004) Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet 20: 62-67.
-
(2004)
Trends Genet
, vol.20
, pp. 62-67
-
-
Zhang, Z.1
Carriero, N.2
Gerstein, M.3
-
30
-
-
3142594265
-
Large-scale analysis of pseudogenes in the human genome
-
Zhang Z, Gerstein M (2004) Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev 14: 328-335.
-
(2004)
Curr Opin Genet Dev
, vol.14
, pp. 328-335
-
-
Zhang, Z.1
Gerstein, M.2
-
31
-
-
0038414560
-
An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene
-
Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, et al. (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423: 91-96.
-
(2003)
Nature
, vol.423
, pp. 91-96
-
-
Hirotsune, S.1
Yoshida, N.2
Chen, A.3
Garrett, L.4
Sugiyama, F.5
-
32
-
-
33646468946
-
Pseudo-messenger RNA: Phantoms of the transcriptome
-
DOI: 10.1371/journal.pgen.0020023
-
Frith MC, Wilming LG, Forrest A, Kawaji H, Tan SL, et al. (2006) Pseudo-messenger RNA: Phantoms of the transcriptome. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020023
-
(2006)
PLoS Genet
, vol.2
-
-
Frith, M.C.1
Wilming, L.G.2
Forrest, A.3
Kawaji, H.4
Tan, S.L.5
-
33
-
-
0346155809
-
Pseudogenes: Are they "junk" or functional DNA?
-
Balakirev ES, Ayala FJ (2003) Pseudogenes: Are they "junk" or functional DNA? Annu Rev Genet 37: 123-151.
-
(2003)
Annu Rev Genet
, vol.37
, pp. 123-151
-
-
Balakirev, E.S.1
Ayala, F.J.2
-
34
-
-
0141867857
-
Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms
-
Mattick JS (2003) Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25: 930-939.
-
(2003)
Bioessays
, vol.25
, pp. 930-939
-
-
Mattick, J.S.1
-
35
-
-
29444455072
-
A mouse atlas of gene expression: Large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells
-
U S A
-
Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, et al. (2005) A mouse atlas of gene expression: Large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A 102: 18485-18490.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 18485-18490
-
-
Siddiqui, A.S.1
Khattra, J.2
Delaney, A.D.3
Zhao, Y.4
Astell, C.5
-
36
-
-
33646484360
-
A method for similarity search of genomic positional expression using CAGE
-
DOI: 10.1371/journal.pgen.0020044
-
Seno S, Takenaka Y, Kai C, Kawai J, Carninci P, et al. (2006) A method for similarity search of genomic positional expression using CAGE. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020044
-
(2006)
PLoS Genet
, vol.2
-
-
Seno, S.1
Takenaka, Y.2
Kai, C.3
Kawai, J.4
Carninci, P.5
-
37
-
-
33646473694
-
Complex loci in human and mouse genomes
-
DOI: 10.1371/journal.pgen.0020047
-
Engström PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, et al. (2006) Complex loci in human and mouse genomes. PLoS Genet 2: DOI: 10.1371/journal. pgen.0020047
-
(2006)
PLoS Genet
, vol.2
-
-
Engström, P.G.1
Suzuki, H.2
Ninomiya, N.3
Akalin, A.4
Sessa, L.5
-
38
-
-
33646493110
-
Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data
-
In press
-
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa S, et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data. Nat Genet: In press.
-
(2006)
Nat Genet
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, S.5
-
39
-
-
20144386500
-
Large-scale collection and characterization of promoters of human and mouse genes
-
Suzuki Y, Yamashita R, Shirota M, Sakakibara Y, Chiba J, et al. (2004) Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biol 4: 429-444.
-
(2004)
Silico Biol
, vol.4
, pp. 429-444
-
-
Suzuki, Y.1
Yamashita, R.2
Shirota, M.3
Sakakibara, Y.4
Chiba, J.5
-
40
-
-
33646484899
-
Transcriptional network dynamics in macrophage activation
-
In press
-
Nilsson R, Katayama S, Suzuki H, Reid JF, Tan SL, et al. (2006) Transcriptional network dynamics in macrophage activation. Genomics. In press.
-
(2006)
Genomics
-
-
Nilsson, R.1
Katayama, S.2
Suzuki, H.3
Reid, J.F.4
Tan, S.L.5
-
41
-
-
33646472425
-
Mice and men: Their promoter properties
-
DOI: 10.1371/journal.pgen.0020054
-
Bajic VB, Tan SL, Christoffels A, Schönbach C, Lipovich L, et al. (2006) Mice and men: Their promoter properties. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020054
-
(2006)
PLoS Genet
, vol.2
-
-
Bajic, V.B.1
Tan, S.L.2
Christoffels, A.3
Schönbach, C.4
Lipovich, L.5
-
42
-
-
33646489947
-
Heterotachy in mammalian promoter evolution
-
DOI: 10.1371/journal.pgen.0020030
-
Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, et al. (2006) Heterotachy in mammalian promoter evolution. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020030
-
(2006)
PLoS Genet
, vol.2
-
-
Taylor, M.S.1
Kai, C.2
Kawai, J.3
Carninci, P.4
Hayashizaki, Y.5
-
43
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
-
44
-
-
7444260846
-
The ENCODE (ENCyclopedia of DNA Elements) Project
-
ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-640.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
45
-
-
33646490270
-
Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs
-
DOI: 10.1371/journal.pgen.0020062
-
Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, et al. (2006) Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020062
-
(2006)
PLoS Genet
, vol.2
-
-
Maeda, N.1
Kasukawa, T.2
Oyama, R.3
Gough, J.4
Frith, M.5
-
46
-
-
33644843329
-
LOCATE: A mouse protein subcellular localization database
-
Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K, et al. (2006) LOCATE: A mouse protein subcellular localization database. Nucleic Acids Res 34: D213-D217.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Fink, J.L.1
Aturaliya, R.N.2
Davis, M.J.3
Zhang, F.4
Hanson, K.5
-
47
-
-
33644874143
-
CAGE Basic/Analysis Databases: The CAGE resource for comprehensive promoter analysis
-
Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, et al. (2006) CAGE Basic/Analysis Databases: The CAGE resource for comprehensive promoter analysis. Nucleic Acids Res 34: D632-D636.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kawaji, H.1
Kasukawa, T.2
Fukuda, S.3
Katayama, S.4
Kai, C.5
|