-
1
-
-
8844227502
-
Population history and natural selection shape patterns of genetic variation in 132 genes
-
doi: 10.1371/journal.pbio.0020286
-
Akey, J.M., Eberle, M.A., Rieder, M.J., Carlson, C.S., Shriver, M.D., Nickerson, D.A., and Kruglyak, L. 2004. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol. 2: e286. doi: 10.1371/journal.pbio.0020286.
-
(2004)
PLoS Biol
, vol.2
-
-
Akey, J.M.1
Eberle, M.A.2
Rieder, M.J.3
Carlson, C.S.4
Shriver, M.D.5
Nickerson, D.A.6
Kruglyak, L.7
-
2
-
-
0013394889
-
Mechanisms of alternative pre-messenger RNA splicing
-
Black, D.L. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72: 291-336.
-
(2003)
Annu. Rev. Biochem
, vol.72
, pp. 291-336
-
-
Black, D.L.1
-
3
-
-
1242325944
-
Alternative pre-mRNA splicing and neuronal function
-
Black, D.L. and Grabowski, P.J. 2003. Alternative pre-mRNA splicing and neuronal function. Prog. Mol. Subcell. Biol. 31: 187-216.
-
(2003)
Prog. Mol. Subcell. Biol
, vol.31
, pp. 187-216
-
-
Black, D.L.1
Grabowski, P.J.2
-
4
-
-
0242636197
-
Alternative splicing and evolution
-
Boue, S., Letunic, I., and Bork, P. 2003. Alternative splicing and evolution. BioEssays 25: 1031-1034.
-
(2003)
BioEssays
, vol.25
, pp. 1031-1034
-
-
Boue, S.1
Letunic, I.2
Bork, P.3
-
5
-
-
0142134358
-
The relevance of alternative RNA splicing to pharmacogenomics
-
Bracco, L. and Kearsey, J. 2003. The relevance of alternative RNA splicing to pharmacogenomics. Trends Biotechnol. 21: 346-353.
-
(2003)
Trends Biotechnol
, vol.21
, pp. 346-353
-
-
Bracco, L.1
Kearsey, J.2
-
6
-
-
0034716987
-
EST comparison indicates 38% of human mRNAs contain possible alternative splice forms
-
Brett, D., Hanke, J., Lehmann, G., Haase, S., Delbruck, S., Krueger, S., Reich, J., and Bork, P. 2000. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett. 474: 83-86.
-
(2000)
FEBS Lett
, vol.474
, pp. 83-86
-
-
Brett, D.1
Hanke, J.2
Lehmann, G.3
Haase, S.4
Delbruck, S.5
Krueger, S.6
Reich, J.7
Bork, P.8
-
7
-
-
33746855164
-
Defective splicing, disease and therapy: Searching for master checkpoints in exon definition
-
Buratti, E., Baralle, M., and Baralle, F.E. 2006. Defective splicing, disease and therapy: Searching for master checkpoints in exon definition. Nucleic Acids Res. 34: 3494-3510.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3494-3510
-
-
Buratti, E.1
Baralle, M.2
Baralle, F.E.3
-
8
-
-
0036534129
-
Alternative splicing: Multiple control mechanisms and involvement in human disease
-
Caceres, J.F. and Kornblihtt, A.R. 2002. Alternative splicing: Multiple control mechanisms and involvement in human disease. Trends Genet. 18: 186-193.
-
(2002)
Trends Genet
, vol.18
, pp. 186-193
-
-
Caceres, J.F.1
Kornblihtt, A.R.2
-
9
-
-
0029240368
-
Generation of a pseudogene during retroviral infection
-
Carlton, M.B., Colledge, W.H., and Evans, M.J. 1995. Generation of a pseudogene during retroviral infection. Mamm. Genome 6: 90-95.
-
(1995)
Mamm. Genome
, vol.6
, pp. 90-95
-
-
Carlton, M.B.1
Colledge, W.H.2
Evans, M.J.3
-
10
-
-
19544378363
-
ESTviewer: A web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variants
-
Chen, F.C. and Chuang, T.J. 2005. ESTviewer: A web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variants. Bioinformatics 21: 2510-2513.
-
(2005)
Bioinformatics
, vol.21
, pp. 2510-2513
-
-
Chen, F.C.1
Chuang, T.J.2
-
11
-
-
35948982990
-
Different alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation
-
doi: 10.1186/1471-2148-7- 179
-
Chen, F.C. and Chuang, T.J. 2007. Different alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation. BMC Evol. Biol. 7: 179. doi: 10.1186/1471-2148-7- 179.
-
(2007)
BMC Evol. Biol
, vol.7
, pp. 179
-
-
Chen, F.C.1
Chuang, T.J.2
-
12
-
-
33745106263
-
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat
-
doi: 10.1186/1471-2105-7-136
-
Chen, F.C., Chen, C.J., Ho, J.Y., and Chuang, T.J. 2006. Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat. BMC Bioinformatics 7: 136. doi: 10.1186/1471-2105-7-136.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 136
-
-
Chen, F.C.1
Chen, C.J.2
Ho, J.Y.3
Chuang, T.J.4
-
13
-
-
34547657299
-
Opposite evolutionary effects between different alternative splicing patterns
-
Chen, F.C., Chaw, S.M., Tzeng, Y.H., Wang, S.S., and Chuang, T.J. 2007a. Opposite evolutionary effects between different alternative splicing patterns. Mol. Biol. Evol. 24: 1443-1446.
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 1443-1446
-
-
Chen, F.C.1
Chaw, S.M.2
Tzeng, Y.H.3
Wang, S.S.4
Chuang, T.J.5
-
14
-
-
34547565560
-
INDELSCAN: A web server for comparative identification of species-specific and non-species-specific insertion/deletion events
-
Chen, F.C., Chen, C.J., and Chuang, T.J. 2007b. INDELSCAN: A web server for comparative identification of species-specific and non-species-specific insertion/deletion events. Nucleic Acids Res. 35: W633-W638.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Chen, F.C.1
Chen, C.J.2
Chuang, T.J.3
-
15
-
-
33846027485
-
Human-specific insertions and deletions inferred from mammalian genome sequences
-
Chen, F.C., Chen, C.J., Li, W.H., and Chuang, T.J. 2007c. Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Res. 17: 16-22.
-
(2007)
Genome Res
, vol.17
, pp. 16-22
-
-
Chen, F.C.1
Chen, C.J.2
Li, W.H.3
Chuang, T.J.4
-
16
-
-
34250666605
-
Plant gene and alternatively spliced variant annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species
-
Chen, F.C., Wang, S.S., Chaw, S.M., Huang, Y.T., and Chuang, T.J. 2007d. Plant gene and alternatively spliced variant annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species. Plant Physiol. 143: 1086-1095.
-
(2007)
Plant Physiol
, vol.143
, pp. 1086-1095
-
-
Chen, F.C.1
Wang, S.S.2
Chaw, S.M.3
Huang, Y.T.4
Chuang, T.J.5
-
17
-
-
24344500211
-
Initial sequence of the chimpanzee genome and comparison with the human genome
-
Chimpanzee Sequencing and Analysis Consortium
-
Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
-
(2005)
Nature
, vol.437
, pp. 69-87
-
-
-
18
-
-
10244261633
-
A comparative method for identification of gene structures and alternatively spliced variants
-
Chuang, T.J., Chen, F.C., and Chou, M.Y. 2004. A comparative method for identification of gene structures and alternatively spliced variants. Bioinformatics 20: 3064-3079.
-
(2004)
Bioinformatics
, vol.20
, pp. 3064-3079
-
-
Chuang, T.J.1
Chen, F.C.2
Chou, M.Y.3
-
19
-
-
0030772379
-
The regulation of splice-site selection, and its role in human disease
-
Cooper, T.A. and Mattox, W. 1997. The regulation of splice-site selection, and its role in human disease. Am. J. Hum. Genet. 61: 259-266.
-
(1997)
Am. J. Hum. Genet
, vol.61
, pp. 259-266
-
-
Cooper, T.A.1
Mattox, W.2
-
20
-
-
33751000477
-
Multiple glucocorticoid receptor isoforms and mechanisms of post-translational modification
-
Duma, D., Jewell, C.M., and Cidlowski, J.A. 2006. Multiple glucocorticoid receptor isoforms and mechanisms of post-translational modification. J. Steroid Biochem. Mol. Biol. 102: 11-21.
-
(2006)
J. Steroid Biochem. Mol. Biol
, vol.102
, pp. 11-21
-
-
Duma, D.1
Jewell, C.M.2
Cidlowski, J.A.3
-
21
-
-
0034079713
-
Human LINE retrotransposons generate processed pseudogenes
-
Esnault, C., Maestre, J., and Heidmann, T. 2000. Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 24: 363-367.
-
(2000)
Nat. Genet
, vol.24
, pp. 363-367
-
-
Esnault, C.1
Maestre, J.2
Heidmann, T.3
-
22
-
-
0037443035
-
Pre-mRNA splicing and human disease
-
Faustino, N.A. and Cooper, T.A. 2003. Pre-mRNA splicing and human disease. Genes & Dev. 17: 419-437.
-
(2003)
Genes & Dev
, vol.17
, pp. 419-437
-
-
Faustino, N.A.1
Cooper, T.A.2
-
23
-
-
0031732094
-
A computer program for aligning a cDNA sequence with a genomic DNA sequence
-
Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., and Miller, W. 1998. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8: 967-974.
-
(1998)
Genome Res
, vol.8
, pp. 967-974
-
-
Florea, L.1
Hartzell, G.2
Zhang, Z.3
Rubin, G.M.4
Miller, W.5
-
24
-
-
1942533477
-
Detection and evaluation of intron retention events in the human transcriptome
-
Galante, P.A., Sakabe, N.J., Kirschbaum-Slager, N., and de Souza, S.J. 2004. Detection and evaluation of intron retention events in the human transcriptome. RNA 10: 757-765.
-
(2004)
RNA
, vol.10
, pp. 757-765
-
-
Galante, P.A.1
Sakabe, N.J.2
Kirschbaum-Slager, N.3
de Souza, S.J.4
-
25
-
-
2342450548
-
Alternative splicing in disease and therapy
-
Garcia-Blanco, M.A., Baraniak, A.P., and Lasda, E.L. 2004. Alternative splicing in disease and therapy. Nat. Biotechnol. 22: 535-546.
-
(2004)
Nat. Biotechnol
, vol.22
, pp. 535-546
-
-
Garcia-Blanco, M.A.1
Baraniak, A.P.2
Lasda, E.L.3
-
26
-
-
0034887203
-
Creating the gene ontology resource: Design and implementation
-
Gene Ontology Consortium
-
Gene Ontology Consortium. 2001. Creating the gene ontology resource: Design and implementation. Genome Res. 11: 1425-1433.
-
(2001)
Genome Res
, vol.11
, pp. 1425-1433
-
-
-
27
-
-
0342858851
-
Nature and structure of human genes that generate retropseudogenes
-
Goncalves, I., Duret, L., and Mouchiroud, D. 2000. Nature and structure of human genes that generate retropseudogenes. Genome Res. 10: 672-678.
-
(2000)
Genome Res
, vol.10
, pp. 672-678
-
-
Goncalves, I.1
Duret, L.2
Mouchiroud, D.3
-
28
-
-
0042009406
-
Alternative splicing affecting a novel domain in the C. elegans EGL-15 FGF receptor confers functional specificity
-
Goodman, S.J., Branda, C.S., Robinson, M.K., Burdine, R.D., and Stern, M.J. 2003. Alternative splicing affecting a novel domain in the C. elegans EGL-15 FGF receptor confers functional specificity. Development 130: 3757-3766.
-
(2003)
Development
, vol.130
, pp. 3757-3766
-
-
Goodman, S.J.1
Branda, C.S.2
Robinson, M.K.3
Burdine, R.D.4
Stern, M.J.5
-
30
-
-
0035252410
-
Alternative splicing: Increasing diversity in the proteomic world
-
Graveley, B.R. 2001. Alternative splicing: Increasing diversity in the proteomic world. Trends Genet. 17: 100-107.
-
(2001)
Trends Genet
, vol.17
, pp. 100-107
-
-
Graveley, B.R.1
-
31
-
-
0347623371
-
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays
-
Johnson, J.M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P.M., Armour, C.D., Santos, R., Schadt, E.E., Stoughton, R., and Shoemaker, D.D. 2003. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302: 2141-2144.
-
(2003)
Science
, vol.302
, pp. 2141-2144
-
-
Johnson, J.M.1
Castle, J.2
Garrett-Engele, P.3
Kan, Z.4
Loerch, P.M.5
Armour, C.D.6
Santos, R.7
Schadt, E.E.8
Stoughton, R.9
Shoemaker, D.D.10
-
32
-
-
0035036534
-
Gene structure prediction and alternative splicing analysis using genomically aligned ESTs
-
Kan, Z., Rouchka, E.C., Gish, W.R., and States, D.J. 2001. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 11: 889-900.
-
(2001)
Genome Res
, vol.11
, pp. 889-900
-
-
Kan, Z.1
Rouchka, E.C.2
Gish, W.R.3
States, D.J.4
-
33
-
-
2442655665
-
Detection of novel splice forms in human and mouse using cross-species approach
-
Kan, Z., Castle, J., Johnson, J.M., and Tsinoremas, N.F. 2004. Detection of novel splice forms in human and mouse using cross-species approach. Pac. Symp. Biocomput. 2004: 42-53.
-
(2004)
Pac. Symp. Biocomput
, vol.2004
, pp. 42-53
-
-
Kan, Z.1
Castle, J.2
Johnson, J.M.3
Tsinoremas, N.F.4
-
34
-
-
33846074757
-
Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation
-
Karro, J.E., Yan, Y., Zheng, D., Zhang, Z., Carriero, N., Cayting, P., Harrrison, P., and Gerstein, M. 2007. Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res. 35: D55-D60.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Karro, J.E.1
Yan, Y.2
Zheng, D.3
Zhang, Z.4
Carriero, N.5
Cayting, P.6
Harrrison, P.7
Gerstein, M.8
-
35
-
-
35148861084
-
Beta-catenin regulates multiple steps of RNA metabolism as revealed by the RNA aptamer in colon cancer cells
-
Lee, H.K., Kwak, H.Y., Hur, J., Kim, I.A., Yang, J.S., Park, M.W., Yu, J., and Jeong, S. 2007. Beta-catenin regulates multiple steps of RNA metabolism as revealed by the RNA aptamer in colon cancer cells. Cancer Res. 67: 9315-9321.
-
(2007)
Cancer Res
, vol.67
, pp. 9315-9321
-
-
Lee, H.K.1
Kwak, H.Y.2
Hur, J.3
Kim, I.A.4
Yang, J.S.5
Park, M.W.6
Yu, J.7
Jeong, S.8
-
36
-
-
33745146904
-
Alternative splicing and control of apoptotic DNA fragmentation
-
Li, X. and Manley, J.L. 2006. Alternative splicing and control of apoptotic DNA fragmentation. Cell Cycle 5: 1286-1288.
-
(2006)
Cell Cycle
, vol.5
, pp. 1286-1288
-
-
Li, X.1
Manley, J.L.2
-
37
-
-
33750040230
-
Structure, function, and regulation of STAT proteins
-
Lim, C.P. and Cao, X. 2006. Structure, function, and regulation of STAT proteins. Mol. Biosyst. 2: 536-550.
-
(2006)
Mol. Biosyst
, vol.2
, pp. 536-550
-
-
Lim, C.P.1
Cao, X.2
-
38
-
-
0037062982
-
Alternative pre-mRNA splicing and proteome expansion in metazoans
-
Maniatis, T. and Tasic, B. 2002. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418: 236-243.
-
(2002)
Nature
, vol.418
, pp. 236-243
-
-
Maniatis, T.1
Tasic, B.2
-
39
-
-
0033955368
-
Vertebrate pseudogenes
-
Mighell, A.J., Smith, N.R., Robinson, P.A., and Markham, A.F. 2000. Vertebrate pseudogenes. FEBS Lett. 468: 109-114.
-
(2000)
FEBS Lett
, vol.468
, pp. 109-114
-
-
Mighell, A.J.1
Smith, N.R.2
Robinson, P.A.3
Markham, A.F.4
-
40
-
-
0035393343
-
Genome-wide detection of alternative splicing in expressed sequences of human genes
-
Modrek, B., Resch, A., Grasso, C., and Lee, C. 2001. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 29: 2850-2859.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2850-2859
-
-
Modrek, B.1
Resch, A.2
Grasso, C.3
Lee, C.4
-
41
-
-
0037678415
-
Cell-specific RNA-binding proteins in human disease
-
Musunuru, K. 2003. Cell-specific RNA-binding proteins in human disease. Trends Cardiovasc. Med. 13: 188-195.
-
(2003)
Trends Cardiovasc. Med
, vol.13
, pp. 188-195
-
-
Musunuru, K.1
-
42
-
-
0036144777
-
S ratio test for assessing the protein-coding potential of genomic regions: An empirical and simulation study
-
S ratio test for assessing the protein-coding potential of genomic regions: An empirical and simulation study. Genome Res. 12: 198-202.
-
(2002)
Genome Res
, vol.12
, pp. 198-202
-
-
Nekrutenko, A.1
Makova, K.D.2
Li, W.H.3
-
43
-
-
35348839507
-
CD99 isoforms dictate opposite functions in tumour malignancy and metastases by activating or repressing c-Src kinase activity
-
Scotlandi, K., Zuntini, M., Manara, M.C., Sciandra, M., Rocchi, A., Benini, S., Nicoletti, G., Bernard, G., Nanni, P., Lollini, P.L., et al. 2007. CD99 isoforms dictate opposite functions in tumour malignancy and metastases by activating or repressing c-Src kinase activity. Oncogene 26: 6604-6618.
-
(2007)
Oncogene
, vol.26
, pp. 6604-6618
-
-
Scotlandi, K.1
Zuntini, M.2
Manara, M.C.3
Sciandra, M.4
Rocchi, A.5
Benini, S.6
Nicoletti, G.7
Bernard, G.8
Nanni, P.9
Lollini, P.L.10
-
44
-
-
31944431889
-
Genomic fossils as a snapshot of the human transcriptome
-
Shemesh, R., Novik, A., Edelheit, S., and Sorek, R. 2006. Genomic fossils as a snapshot of the human transcriptome. Proc. Natl. Acad. Sci. 103: 1364-1369.
-
(2006)
Proc. Natl. Acad. Sci
, vol.103
, pp. 1364-1369
-
-
Shemesh, R.1
Novik, A.2
Edelheit, S.3
Sorek, R.4
-
45
-
-
33644878582
-
ASD: A bioinformatics resource on alternative splicing
-
Stamm, S., Riethoven, J.J., Le Texier, V., Gopalakrishnan, C., Kumanduri, V., Tang, Y., Barbosa-Morais, N.L., and Thanaraj, T.A. 2006. ASD: A bioinformatics resource on alternative splicing. Nucleic Acids Res. 34: D46-D55.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Stamm, S.1
Riethoven, J.J.2
Le Texier, V.3
Gopalakrishnan, C.4
Kumanduri, V.5
Tang, Y.6
Barbosa-Morais, N.L.7
Thanaraj, T.A.8
-
46
-
-
0022293979
-
Processed pseudogenes: Characteristics and evolution
-
Vanin, E.F. 1985. Processed pseudogenes: Characteristics and evolution. Annu. Rev. Genet. 19: 253-272.
-
(1985)
Annu. Rev. Genet
, vol.19
, pp. 253-272
-
-
Vanin, E.F.1
-
47
-
-
7444220147
-
Aberrant and alternative splicing in cancer
-
Venables, J.P. 2004. Aberrant and alternative splicing in cancer. Cancer Res. 64: 7647-7654.
-
(2004)
Cancer Res
, vol.64
, pp. 7647-7654
-
-
Venables, J.P.1
-
48
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
-
(1997)
Comput. Appl. Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
49
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
Yang, Z. and Nielsen, R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17: 32-43.
-
(2000)
Mol. Biol. Evol
, vol.17
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
-
50
-
-
0346752110
-
Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome
-
Zhang, Z., Harrison, P.M., Liu, Y., and Gerstein, M. 2003. Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome. Genome Res. 13: 2541-2558.
-
(2003)
Genome Res
, vol.13
, pp. 2541-2558
-
-
Zhang, Z.1
Harrison, P.M.2
Liu, Y.3
Gerstein, M.4
-
51
-
-
33745614319
-
PseudoPipe: An automated pseudogene identification pipeline
-
Zhang, Z., Carriero, N., Zheng, D., Karro, J., Harrison, P.M., and Gerstein, M. 2006. PseudoPipe: An automated pseudogene identification pipeline. Bioinformatics 22: 1437-1439.
-
(2006)
Bioinformatics
, vol.22
, pp. 1437-1439
-
-
Zhang, Z.1
Carriero, N.2
Zheng, D.3
Karro, J.4
Harrison, P.M.5
Gerstein, M.6
|