-
2
-
-
0037047628
-
Recent segmental duplications in the human genome
-
Bailey, J. A., Gu, Z., Clark, R. A., Reinert, K., Samonte, R. V., Schwartz, S., Adams, M. D., Myers, E. W., Li, P. W. and Eichler, E. E. (2002) Recent segmental duplications in the human genome. Science, 297, 1003-1007.
-
(2002)
Science
, vol.297
, pp. 1003-1007
-
-
Bailey, J.A.1
Gu, Z.2
Clark, R.A.3
Reinert, K.4
Samonte, R.V.5
Schwartz, S.6
Adams, M.D.7
Myers, E.W.8
Li, P.W.9
Eichler, E.E.10
-
3
-
-
0003421005
-
-
Sinauer Associates, MA, USA
-
Li, W. (1997) Molecular Evolution. Sinauer Associates, MA, USA.
-
(1997)
Molecular Evolution
-
-
Li, W.1
-
4
-
-
33745373606
-
Primate segmental duplications: Crucibles of evolution, diversity and disease
-
Bailey, J. A. and Eichler, E. E. (2006) Primate segmental duplications: crucibles of evolution, diversity and disease. Nat. Rev. Genet., 7, 552-564.
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 552-564
-
-
Bailey, J.A.1
Eichler, E.E.2
-
5
-
-
57149099396
-
Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history
-
Kim, P. M., Lam, H. Y., Urban, A. E., Korbel, J. O., Affourtit, J., Grubert, F., Chen, X., Weissman, S., Snyder, M. and Gerstein, M. B. (2008) Analysis of copy number variants and segmental duplications in the human genome: evidence for a change in the process of formation in recent evolutionary history. Genome Res., 18, 1865-1874.
-
(2008)
Genome Res.
, vol.18
, pp. 1865-1874
-
-
Kim, P.M.1
Lam, H.Y.2
Urban, A.E.3
Korbel, J.O.4
Affourtit, J.5
Grubert, F.6
Chen, X.7
Weissman, S.8
Snyder, M.9
Gerstein, M.B.10
-
6
-
-
60149083509
-
A burst of segmental duplications in the genome of the African great ape ancestor
-
Marques-Bonet, T., Kidd, J. M., Ventura, M., Graves, T. A., Cheng, Z., Hillier, L. W., Jiang, Z., Baker, C., Malfavon-Borja, R., Fulton, L. A. et al. (2009) A burst of segmental duplications in the genome of the African great ape ancestor. Nature, 457, 877-881.
-
(2009)
Nature
, vol.457
, pp. 877-881
-
-
Marques-Bonet, T.1
Kidd, J.M.2
Ventura, M.3
Graves, T.A.4
Cheng, Z.5
Hillier, L.W.6
Jiang, Z.7
Baker, C.8
Malfavon-Borja, R.9
Fulton, L.A.10
-
7
-
-
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
-
8
-
-
0036314772
-
Studying genomes through the aeons: Protein families, pseudogenes and proteome evolution
-
Harrison, P. M. and Gerstein, M. (2002) Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J. Mol. Biol., 318, 1155-1174.
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 1155-1174
-
-
Harrison, P.M.1
Gerstein, M.2
-
9
-
-
0024505629
-
Deletions in processed pseudogenes accumulate faster in rodents than in humans
-
Graur, D., Shuali, Y. and Li, W. H. (1989) Deletions in processed pseudogenes accumulate faster in rodents than in humans. J. Mol. Evol., 28, 279-285.
-
(1989)
J. Mol. Evol.
, vol.28
, pp. 279-285
-
-
Graur, D.1
Shuali, Y.2
Li, W.H.3
-
10
-
-
44849127601
-
Genomics: Protein fossils live on as RNA
-
Sasidharan, R. and Gerstein, M. (2008) Genomics: protein fossils live on as RNA. Nature, 453, 729-731.
-
(2008)
Nature
, vol.453
, pp. 729-731
-
-
Sasidharan, R.1
Gerstein, M.2
-
11
-
-
48249143133
-
Asymmetric histone modifications between the original and derived loci of human segmental duplications
-
Zheng, D. (2008) Asymmetric histone modifications between the original and derived loci of human segmental duplications. Genome Biol., 9, R105.
-
(2008)
Genome Biol.
, vol.9
-
-
Zheng, D.1
-
12
-
-
58149177159
-
Pseudofam: The pseudogene families database
-
Lam, H. Y., Khurana, E., Fang, G., Cayting, P., Carriero, N., Cheung, K. H. and Gerstein, M. B. (2009) Pseudofam: the pseudogene families database. Nucleic Acids Res., 37, D738-D743.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Lam, H.Y.1
Khurana, E.2
Fang, G.3
Cayting, P.4
Carriero, N.5
Cheung, K.H.6
Gerstein, M.B.7
-
13
-
-
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
-
14
-
-
0009620624
-
A tool for multiple sequence alignment
-
Lipman, D. J., Altschul, S. F. and Kececioglu, J. D. (1989) A tool for multiple sequence alignment. Proc. Natl Acad. Sci. USA, 86, 4412-4415.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 4412-4415
-
-
Lipman, D.J.1
Altschul, S.F.2
Kececioglu, J.D.3
-
15
-
-
0029366816
-
Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment
-
Gupta, S. K., Kececioglu, J. D. and Schaffer, A. A. (1995) Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J. Comput. Biol., 2, 459-472.
-
(1995)
J. Comput. Biol.
, vol.2
, pp. 459-472
-
-
Gupta, S.K.1
Kececioglu, J.D.2
Schaffer, A.A.3
-
17
-
-
35649007348
-
Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution
-
Jiang, Z., Tang, H., Ventura, M., Cardone, M. F., Marques-Bonet, T., She, X., Pevzner, P. A. and Eichler, E. E. (2007) Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat. Genet., 39, 1361-1368.
-
(2007)
Nat. Genet.
, vol.39
, pp. 1361-1368
-
-
Jiang, Z.1
Tang, H.2
Ventura, M.3
Cardone, M.F.4
Marques-Bonet, T.5
She, X.6
Pevzner, P.A.7
Eichler, E.E.8
-
18
-
-
0348013073
-
A genome-wide survey of human pseudogenes
-
Torrents, D., Suyama, M., Zdobnov, E. and Bork, P. (2003) A genome-wide survey of human pseudogenes. Genome Res., 13, 2559-2567.
-
(2003)
Genome Res.
, vol.13
, pp. 2559-2567
-
-
Torrents, D.1
Suyama, M.2
Zdobnov, E.3
Bork, P.4
-
19
-
-
1542682570
-
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
-
Ohshima, K., Hattori, M., Yada, T., Gojobori, T., Sakaki, Y. and Okada, N. (2003) Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol., 4, R74.
-
(2003)
Genome Biol.
, vol.4
-
-
Ohshima, K.1
Hattori, M.2
Yada, T.3
Gojobori, T.4
Sakaki, Y.5
Okada, N.6
-
20
-
-
0345306317
-
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes
-
Zhang, Z. and Gerstein, M. (2003) Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res., 31, 5338-5348.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5338-5348
-
-
Zhang, Z.1
Gerstein, M.2
-
21
-
-
10344222632
-
Patterns of segmental duplication in the human genome
-
Zhang, L., Lu, H. H., Chung, W. Y., Yang, J. and Li, W. H. (2005) Patterns of segmental duplication in the human genome. Mol. Biol. Evol., 22, 135-141.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 135-141
-
-
Zhang, L.1
Lu, H.H.2
Chung, W.Y.3
Yang, J.4
Li, W.H.5
-
22
-
-
75549087305
-
The evolution of gene duplications: Classifying and distinguishing between models
-
Innan, H. and Kondrashov, F. (2010) The evolution of gene duplications: classifying and distinguishing between models. Nat. Rev. Genet., 11, 97-108.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 97-108
-
-
Innan, H.1
Kondrashov, F.2
-
23
-
-
33745000116
-
Genome-wide identification of pseudogenes capable of disease-causing gene conversion
-
Bischof, J. M., Chiang, A. P., Scheetz, T. E., Stone, E. M., Casavant, T. L., Sheffield, V. C. and Braun, T. A. (2006) Genome-wide identification of pseudogenes capable of disease-causing gene conversion. Hum. Mutat., 27, 545-552.
-
(2006)
Hum. Mutat.
, vol.27
, pp. 545-552
-
-
Bischof, J.M.1
Chiang, A.P.2
Scheetz, T.E.3
Stone, E.M.4
Casavant, T.L.5
Sheffield, V.C.6
Braun, T.A.7
-
24
-
-
38349110922
-
Analysis of nuclear receptor pseudogenes in vertebrates: How the silent tell their stories
-
Zhang, Z. D., Cayting, P., Weinstock, G. and Gerstein, M. (2008) Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories. Mol. Biol. Evol., 25, 131-143.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 131-143
-
-
Zhang, Z.D.1
Cayting, P.2
Weinstock, G.3
Gerstein, M.4
-
25
-
-
70449706229
-
Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: The anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity
-
Liu, Y. J., Zheng, D., Balasubramanian, S., Carriero, N., Khurana, E., Robilotto, R. and Gerstein, M. B. (2009) Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. BMC Genomics, 10, 480.
-
(2009)
BMC Genomics
, vol.10
, pp. 480
-
-
Liu, Y.J.1
Zheng, D.2
Balasubramanian, S.3
Carriero, N.4
Khurana, E.5
Robilotto, R.6
Gerstein, M.B.7
-
26
-
-
0031573415
-
Comparison of DNA sequences with protein sequences
-
Pearson, W. R., Wood, T., Zhang, Z. and Miller, W. (1997) Comparison of DNA sequences with protein sequences. Genomics, 46, 24-36.
-
(1997)
Genomics
, vol.46
, pp. 24-36
-
-
Pearson, W.R.1
Wood, T.2
Zhang, Z.3
Miller, W.4
-
27
-
-
59949096873
-
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
-
Vilella, A. J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R. and Birney, E. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327-335.
-
(2009)
Genome Res.
, vol.19
, pp. 327-335
-
-
Vilella, A.J.1
Severin, J.2
Ureta-Vidal, A.3
Heng, L.4
Durbin, R.5
Birney, E.6
-
28
-
-
35348988679
-
Paired-end mapping reveals extensive structural variation in the human genome
-
Korbel, J. O., Urban, A. E., Affourtit, J. P., Godwin, B., Grubert, F., Simons, J. F., Kim, P. M., Palejev, D., Carriero, N. J., Du, L. et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science, 318, 420-426.
-
(2007)
Science
, vol.318
, pp. 420-426
-
-
Korbel, J.O.1
Urban, A.E.2
Affourtit, J.P.3
Godwin, B.4
Grubert, F.5
Simons, J.F.6
Kim, P.M.7
Palejev, D.8
Carriero, N.J.9
Du, L.10
-
29
-
-
0035001936
-
The complete human olfactory subgenome
-
Glusman, G., Yanai, I., Rubin, I. and Lancet, D. (2001) The complete human olfactory subgenome. Genome Res., 11, 685-702.
-
(2001)
Genome Res.
, vol.11
, pp. 685-702
-
-
Glusman, G.1
Yanai, I.2
Rubin, I.3
Lancet, D.4
-
30
-
-
77952694676
-
Identification and analysis of unitary pseudogenes: Historic and contemporary gene losses in humans and other primates
-
Zhang, Z. D., Frankish, A., Hunt, T., Harrow, J. and Gerstein, M. (2010) Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol., 11, R26.
-
(2010)
Genome Biol.
, vol.11
-
-
Zhang, Z.D.1
Frankish, A.2
Hunt, T.3
Harrow, J.4
Gerstein, M.5
-
31
-
-
58049218775
-
1000 Genomes project promises closer look at variation in human genome
-
Kuehn, B. M. (2008) 1000 Genomes project promises closer look at variation in human genome. JAMA, 300, 2715.
-
(2008)
JAMA
, vol.300
, pp. 2715
-
-
Kuehn, B.M.1
-
32
-
-
0036079158
-
The human genome browser at UCSC
-
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M. and Haussler, D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
-
(2002)
Genome Res.
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
|