-
1
-
-
33646244720
-
Positive selection, relaxation, and acceleration in the evolution of the human and chimpanzee genome
-
Arbiza, L., Dopazo, J., and Dopazo, H. 2006. Positive selection, relaxation, and acceleration in the evolution of the human and chimpanzee genome. PLoS Comput. Biol. 2: 288-300.
-
(2006)
PLoS Comput. Biol.
, vol.2
, pp. 288-300
-
-
Arbiza, L.1
Dopazo, J.2
Dopazo, H.3
-
2
-
-
34250659350
-
More genes underwent positive selection in chimpanzee evolution than in human evolution
-
DOI 10.1073/pnas.0701705104
-
Bakewell, M., Shi, P., and Zhang, J. 2007. More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc. Natl. Acad. Sci. 104: 7489-7494. (Pubitemid 47185933)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.18
, pp. 7489-7494
-
-
Bakewell, M.A.1
Shi, P.2
Zhang, J.3
-
3
-
-
0037398368
-
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
-
Brudno, M., Do, C., Cooper, G., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., and Batzoglou, S. 2003. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13: 721-731.
-
(2003)
Genome Res.
, vol.13
, pp. 721-731
-
-
Brudno, M.1
Do, C.2
Cooper, G.3
Kim, M.F.4
Davydov, E.5
Green, E.D.6
Sidow, A.7
Batzoglou, S.8
-
4
-
-
24344500211
-
Initial sequence of the chimpanzee genome and comparison with the human genome
-
The Chimpanzee Sequencing and Analysis Consortium
-
The 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
-
-
-
5
-
-
0031955518
-
Basecalling of automated sequencer traces using phred. I. Accuracy assessment
-
Ewing, B., Hillier, L., Wendl, M., and Green, P. 1998. Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
-
(1998)
Genome Res.
, vol.8
, pp. 175-185
-
-
Ewing, B.1
Hillier, L.2
Wendl, M.3
Green, P.4
-
6
-
-
33846039019
-
Ensembl 2007
-
Hubbard, T.J.P., Aken, B.L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., et al. 2007. Ensembl 2007. Nucleic Acids Res. 35: 610-617.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 610-617
-
-
Hubbard, T.J.P.1
Aken, B.L.2
Beal, K.3
Ballester, B.4
Caccamo, M.5
Chen, Y.6
Clarke, L.7
Coates, G.8
Cunningham, F.9
Cutts, T.10
-
7
-
-
0023764283
-
Patterns of nucleotide substitution at major histocompatibility class I loci reveals overdominant selection
-
Hughes, A.L. and Nei, M. 1988. Patterns of nucleotide substitution at major histocompatibility class I loci reveals overdominant selection. Nature 335: 167-170.
-
(1988)
Nature
, vol.335
, pp. 167-170
-
-
Hughes, A.L.1
Nei, M.2
-
8
-
-
35348983887
-
A second generation human haplotype map of over 3.1 million SNPs
-
The International HapMap Consortium
-
The International HapMap Consortium. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
-
(2007)
Nature
, vol.449
, pp. 851-861
-
-
-
9
-
-
0037267048
-
Whole-genome sequence assembly for mammalian genomes: ARACHNE 2
-
Jaffe, D.B., Butler, J., Gnerre, S., Mauceli, E., Lindblad-Toh, K., Mesirov, J.P., Zody, M.C., and Lander, E.S. 2003. Whole-genome sequence assembly for mammalian genomes: ARACHNE 2. Genome Res. 13: 91-96.
-
(2003)
Genome Res.
, vol.13
, pp. 91-96
-
-
Jaffe, D.B.1
Butler, J.2
Gnerre, S.3
Mauceli, E.4
Lindblad-Toh, K.5
Mesirov, J.P.6
Zody, M.C.7
Lander, E.S.8
-
10
-
-
50849122974
-
Patterns of positive selection in six mammalian genomes
-
Kosiol, C., Vinar, T., da Fonseca, R.R., Hubisz, M.J., Bustamante, C.D., Nielsen, R., and Siepel, A. 2008. Patterns of positive selection in six mammalian genomes. PLoS Genet. 4: 1-17.
-
(2008)
PLoS Genet.
, vol.4
, pp. 1-17
-
-
Kosiol, C.1
Vinar, T.2
Da Fonseca, R.R.3
Hubisz, M.J.4
Bustamante, C.D.5
Nielsen, R.6
Siepel, A.7
-
11
-
-
36448991500
-
ClustalWand ClustalX version 2
-
Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., et al. 2007. ClustalWand ClustalX version 2. Bioinformatics 23: 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
-
12
-
-
38849135019
-
Choosing BLAST options for better detection of orthologs as reciprocal best hits
-
Moreno-Hagelsieb, G. and Latimer, K. 2008. Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics 24: 319-324.
-
(2008)
Bioinformatics
, vol.24
, pp. 319-324
-
-
Moreno-Hagelsieb, G.1
Latimer, K.2
-
13
-
-
0036737630
-
Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs
-
Nembaware, V., Crum, K., Kelso, J., and Seioghe, C. 2002. Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Genome Res. 12: 1370-1376.
-
(2002)
Genome Res.
, vol.12
, pp. 1370-1376
-
-
Nembaware, V.1
Crum, K.2
Kelso, J.3
Seioghe, C.4
-
14
-
-
0034809334
-
Statistical test of selection neutrality in the age of genomes
-
Nielsen, R. 2001. Statistical test of selection neutrality in the age of genomes. Heredity 86: 641-647.
-
(2001)
Heredity
, vol.86
, pp. 641-647
-
-
Nielsen, R.1
-
15
-
-
20444430245
-
A scan for positively selected genes in the genomes of humans and chimpanzees
-
DOI 10.1371/journal.pbio.0030170, e170
-
Nielsen, R., Bustamante, C., Clark, A.G., Glanowski, S., Sackton, T.B., Hubisz,M.J., Fledel-Alon, A., Tanenbaum, D.M., Civello, D., White, T.J., et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3: 70. doi: 10.1371/journal.pbio.0030170. (Pubitemid 41032208)
-
(2005)
PLoS Biology
, vol.3
, Issue.6
, pp. 976-985
-
-
Nielsen, R.1
Bustamante, C.2
Clark, A.G.3
Glanowski, S.4
Sackton, T.B.5
Hubisz, M.J.6
Fledel-Alon, A.7
Tanenbaum, D.M.8
Civello, D.9
White, T.J.10
Sninsky, J.J.11
Adams, M.D.12
Cargill, M.13
-
16
-
-
34247352040
-
Evolutionary and biomedical insights from the rhesus macaque genome
-
Rhesus Macaque Genome Sequencing and Analysis Consortium
-
Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234.
-
(2007)
Science
, vol.316
, pp. 222-234
-
-
-
17
-
-
0034201441
-
EMBOSS: The European Molecular Biology Open Software Suite
-
Rice, P., Longden, I., and Bleasby, A. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16: 276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
18
-
-
0033990048
-
Primer3 on the WWW for general users and for biologist programmers
-
eds. S. Krawets and S. Misener, Humana, Totowa, NJ
-
Rozen, S. and Skaletsky, H. 2000. Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics methods and protocols: Methods in molecular biology (eds. S. Krawets and S. Misener), pp. 365-386. Humana, Totowa, NJ.
-
(2000)
Bioinformatics Methods and Protocols: Methods in Molecular Biology
, pp. 365-386
-
-
Rozen, S.1
Skaletsky, H.2
-
19
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz, S., Kent, J.W., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.H., Haussler, D., and Miller, W. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13: 103-107.
-
(2003)
Genome Res.
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, J.W.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
Hardison, R.H.6
Haussler, D.7
Miller, W.8
-
20
-
-
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
-
21
-
-
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. (Pubitemid 30056990)
-
(2000)
Molecular Biology and Evolution
, vol.17
, Issue.1
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
-
22
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
Yang, Z. and Nielsen, R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19: 908-917. (Pubitemid 34602960)
-
(2002)
Molecular Biology and Evolution
, vol.19
, Issue.6
, pp. 908-917
-
-
Yang, Z.1
Nielsent, R.2
-
23
-
-
27844439855
-
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
-
DOI 10.1093/molbev/msi237
-
Zhang, J., Nielsen, R., and Yang, Z. 2005. Evaluation of an improved branchsite likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22: 2472-2479. (Pubitemid 41661383)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.12
, pp. 2472-2479
-
-
Zhang, J.1
Nielsen, R.2
Yang, Z.3
|