-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S., T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schaffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
2
-
-
0036250811
-
Alu repeats and human genomic diversity
-
Batzer, M., and P. L. Deininger. 2001. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3:370-379.
-
(2001)
Nat. Rev. Genet
, vol.3
, pp. 370-379
-
-
Batzer, M.1
Deininger, P.L.2
-
3
-
-
33646928347
-
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
-
Bejerano, G., C. B. Lowe, N. Ahituv, B. King, A. Siepel, S. R. Salama, E. M. Rubin, W. J. Kent, and D. Haussler. 2006. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441:87-90.
-
(2006)
Nature
, vol.441
, pp. 87-90
-
-
Bejerano, G.1
Lowe, C.B.2
Ahituv, N.3
King, B.4
Siepel, A.5
Salama, S.R.6
Rubin, E.M.7
Kent, W.J.8
Haussler, D.9
-
4
-
-
0025864962
-
-
Brosius, J. 1991. Retroposons-Seeds of evolution. Science 251:753. Burt, A., and R. Trivers. 2006. Genes in conflict: The biology of selfish genetic elements. Harvard University Press, Cambridge.
-
Brosius, J. 1991. Retroposons-Seeds of evolution. Science 251:753. Burt, A., and R. Trivers. 2006. Genes in conflict: The biology of selfish genetic elements. Harvard University Press, Cambridge.
-
-
-
-
5
-
-
16344366343
-
A novel abundant family of retroposed elements (DAS-SINEs) in the ninebanded armadillo {Dasypus novemcinctus)
-
Churakov, G., A. F. A. Smit, J. Brosius, and J. Schmitz. 2004. A novel abundant family of retroposed elements (DAS-SINEs) in the ninebanded armadillo {Dasypus novemcinctus). Mol. Biol. Evol. 22:886-893.
-
(2004)
Mol. Biol. Evol
, vol.22
, pp. 886-893
-
-
Churakov, G.1
Smit, A.F.A.2
Brosius, J.3
Schmitz, J.4
-
6
-
-
4444358450
-
Retrotransposition of Alu elements: How many sources?
-
Cordaux, R., D. J. Hedges, and M. A. Batzer. 2004. Retrotransposition of Alu elements: How many sources? Trends Genet. 20:464-467.
-
(2004)
Trends Genet
, vol.20
, pp. 464-467
-
-
Cordaux, R.1
Hedges, D.J.2
Batzer, M.A.3
-
7
-
-
66249084221
-
-
Cracraft, J., F. K. Barker, M. Braun, J. Harshman, G. J. Dyke, J. Feinstein, S. Stanley, A. Cibois, P. Schickler, P. Beresford, J. Garcia-Moreno, M. D. Sorenson, Y. Tamaki, and D. P. Mindell. 2004. Phylogenetic relationships among modern birds (Neornithes): Toward an avian tree of life. Pages 468-489 in Assembling the Tree of Life (C. J., and M. J. Donoghue, eds.). Oxford University Press, New York.
-
Cracraft, J., F. K. Barker, M. Braun, J. Harshman, G. J. Dyke, J. Feinstein, S. Stanley, A. Cibois, P. Schickler, P. Beresford, J. Garcia-Moreno, M. D. Sorenson, Y. Tamaki, and D. P. Mindell. 2004. Phylogenetic relationships among modern birds (Neornithes): Toward an avian tree of life. Pages 468-489 in Assembling the Tree of Life (C. J., and M. J. Donoghue, eds.). Oxford University Press, New York.
-
-
-
-
9
-
-
33646168295
-
Coalescent processes when the distribution of offspring number among individuals is highly skewed
-
Eldon, B., and J. Wakeley. 2006. Coalescent processes when the distribution of offspring number among individuals is highly skewed. Genetics 172:2621-2633.
-
(2006)
Genetics
, vol.172
, pp. 2621-2633
-
-
Eldon, B.1
Wakeley, J.2
-
10
-
-
19844382341
-
Under the genomic radar: The stealth model of Alu amplification
-
Han, K., J. Xing, H. Wang, D. J. Hedges, R. K. Garber, R. Cordaux, and M. A. Batzer. 2005. Under the genomic radar: The stealth model of Alu amplification. Genome Res. 15:655-664.
-
(2005)
Genome Res
, vol.15
, pp. 655-664
-
-
Han, K.1
Xing, J.2
Wang, H.3
Hedges, D.J.4
Garber, R.K.5
Cordaux, R.6
Batzer, M.A.7
-
11
-
-
10644283823
-
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
-
Hillier, L. W., W. Miller, E. Birney, W. Warren, R. C. Hardison, C. P. Ponting, P. Bork, D. W. Burt, M. A. Groenen, M. E. Delaney, and J. B. Dodgson. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.
-
(2004)
Nature
, vol.432
, pp. 695-716
-
-
Hillier, L.W.1
Miller, W.2
Birney, E.3
Warren, W.4
Hardison, R.C.5
Ponting, C.P.6
Bork, P.7
Burt, D.W.8
Groenen, M.A.9
Delaney, M.E.10
Dodgson, J.B.11
-
12
-
-
0037020114
-
The genome sequence of the malaria mosquito Anopheles gambiae
-
Holt, R. A., G. M. Subramanian, A. Halpern, G. G. Sutton, R. Charlab, D. R. Nusskern, P. Wincker, A. G. Clark, J. M. C. Ribeiro, R. Wides, et al. 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298:129-149.
-
(2002)
Science
, vol.298
, pp. 129-149
-
-
Holt, R.A.1
Subramanian, G.M.2
Halpern, A.3
Sutton, G.G.4
Charlab, R.5
Nusskern, D.R.6
Wincker, P.7
Clark, A.G.8
Ribeiro, J.M.C.9
Wides, R.10
-
13
-
-
84907150192
-
The mapbased sequence of the rice genome
-
International Rice Genome Sequencing Consortium
-
International Rice Genome Sequencing Consortium. 2005. The mapbased sequence of the rice genome. Nature 436:793-800.
-
(2005)
Nature
, vol.436
, pp. 793-800
-
-
-
14
-
-
7244259101
-
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
-
Jaillon, O., J.-M. Aury, F. Brunet, J.-L. Petit, N. Stange-Thomann, E. Mauceli, L. Bouneau, C. Fischer, C. Ozouf-Costaz, A. Bernot, et al. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957.
-
(2004)
Nature
, vol.431
, pp. 946-957
-
-
Jaillon, O.1
Aury, J.-M.2
Brunet, F.3
Petit, J.-L.4
Stange-Thomann, N.5
Mauceli, E.6
Bouneau, L.7
Fischer, C.8
Ozouf-Costaz, C.9
Bernot, A.10
-
15
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements (www.girinst.org/repbase/index.html)
-
Jurka, J., V. V. Kapitonov, A. Pavlicek, P. Klownowski, O. Kohany, and J. Walichiewicz. 2005. Repbase Update, a database of eukaryotic repetitive elements (www.girinst.org/repbase/index.html). Cytogenet. Genome Res. 110:462-467.
-
(2005)
Cytogenet. Genome Res
, vol.110
, pp. 462-467
-
-
Jurka, J.1
Kapitonov, V.V.2
Pavlicek, A.3
Klownowski, P.4
Kohany, O.5
Walichiewicz, J.6
-
16
-
-
24944569270
-
The evolutionary dynamics of endogenous retroviruses
-
Katzourakis, A., A. Rambaut, and O. G. Pybus. 2005. The evolutionary dynamics of endogenous retroviruses. Trends Microbiol. 13:463-468.
-
(2005)
Trends Microbiol
, vol.13
, pp. 463-468
-
-
Katzourakis, A.1
Rambaut, A.2
Pybus, O.G.3
-
17
-
-
1542513556
-
Mobile elements: Drivers of genome evolution
-
Kazazian, H. H. J. 2004. Mobile elements: Drivers of genome evolution. Science 303:1626-1632.
-
(2004)
Science
, vol.303
, pp. 1626-1632
-
-
Kazazian, H.H.J.1
-
18
-
-
0002556819
-
On the genealogy of large populations
-
J. Gani and E. Hannan, eds, Applied Probability Trust, London
-
Kingman, J. 1982. On the genealogy of large populations. Pages 27-43 in Essays in statistical science (J. Gani and E. Hannan, eds.). Applied Probability Trust, London.
-
(1982)
Essays in statistical science
, pp. 27-43
-
-
Kingman, J.1
-
19
-
-
0141596080
-
The dog genome: Survey sequencing and comparative analysis
-
Kirkness, E. F., V. Bafna, A. L. Halpern, S. Levy, K. Remington, D. B. Rusch, A. L. Delcher, M. Pop, W. Wang, C. M. Fraser, and J. C. Venter. 2003. The dog genome: Survey sequencing and comparative analysis. Science 301:1898-1903.
-
(2003)
Science
, vol.301
, pp. 1898-1903
-
-
Kirkness, E.F.1
Bafna, V.2
Halpern, A.L.3
Levy, S.4
Remington, K.5
Rusch, D.B.6
Delcher, A.L.7
Pop, M.8
Wang, W.9
Fraser, C.M.10
Venter, J.C.11
-
20
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander, E. S., L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, 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
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
FitzHugh, W.10
-
21
-
-
0030854739
-
tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe, T. M., and S. R. Eddy. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-996.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-996
-
-
Lowe, T.M.1
Eddy, S.R.2
-
22
-
-
0033805215
-
Consistency of SINE insertion topology and flanking sequence tree: Quantifying relationships among Cetartiodactyls
-
Lum, J. K., M. Nikaido, M. Shimamura, H. Shimodaira, A. M. Shedlock, N. Okada, and M. Hasegawa. 2000. Consistency of SINE insertion topology and flanking sequence tree: Quantifying relationships among Cetartiodactyls. Mol. Biol. Evol. 17:1417-1424.
-
(2000)
Mol. Biol. Evol
, vol.17
, pp. 1417-1424
-
-
Lum, J.K.1
Nikaido, M.2
Shimamura, M.3
Shimodaira, H.4
Shedlock, A.M.5
Okada, N.6
Hasegawa, M.7
-
23
-
-
66249121463
-
-
is maintained by the author at the School of Biological Sciences, Queen Mary University of London
-
Malcolm, C. 2006. Retroposon Base is maintained by the author at the School of Biological Sciences, Queen Mary University of London (www.retroposonbase.com).
-
(2006)
Retroposon Base
-
-
Malcolm, C.1
-
24
-
-
0032976398
-
The age and evolution of non-LTR retrotransposable elements
-
Malik, H. S., W. D. Burke, and T. Eickbush. 1999. The age and evolution of non-LTR retrotransposable elements. Mol. Biol. Evol. 16:793-805.
-
(1999)
Mol. Biol. Evol
, vol.16
, pp. 793-805
-
-
Malik, H.S.1
Burke, W.D.2
Eickbush, T.3
-
25
-
-
0035252080
-
Molecular phylogenetics and the origins of placental mammals
-
Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
-
(2001)
Nature
, vol.409
, pp. 614-618
-
-
Murphy, W.J.1
Eizirik, E.2
Johnson, W.E.3
Zhang, Y.P.4
Ryder, O.A.5
O'Brien, S.J.6
-
26
-
-
0035912816
-
Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins
-
Nikaido, M., F. Matsuno, H. Hamilton, R. L. J. Brownell, Y. Cao, W. Ding, Z. Zuoyani, A. M. Shedlock, R. E. Fordyce, H. M., and N. Okada. 2001. Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins. Proc. Natl. Acad. Sci. USA 98:7384-7389.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 7384-7389
-
-
Nikaido, M.F.1
Matsuno, H.2
Hamilton, R.L.J.3
Brownell, Y.4
Cao, W.5
Ding, Z.6
Zuoyani, A.M.7
Shedlock, R.E.8
Fordyce, H.M.9
Okada, N.10
-
27
-
-
33745620751
-
Functional noncoding sequences derived from SINEs in the mammalian genome
-
Nishihara, H., A. F. A. Smit, and N. Okada. 2006. Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res. 16:864-874.
-
(2006)
Genome Res
, vol.16
, pp. 864-874
-
-
Nishihara, H.1
Smit, A.F.A.2
Okada, N.3
-
28
-
-
2542452120
-
Retroposon mapping in molecular systematics
-
W. J. Miller and P. Capy, eds, Humana Press, Totowa, New Jersey
-
Okada, N., A. M. Shedlock, and M. Nikaido. 2004. Retroposon mapping in molecular systematics. Pages 189-226 in Mobile genetic elements (W. J. Miller and P. Capy, eds.). Humana Press, Totowa, New Jersey.
-
(2004)
Mobile genetic elements
, pp. 189-226
-
-
Okada, N.1
Shedlock, A.M.2
Nikaido, M.3
-
29
-
-
66249136455
-
SINEs of progress: Mobile element applications to molecular ecology
-
In press
-
Ray, D. A. 2006. SINEs of progress: Mobile element applications to molecular ecology. Mol. Ecol. In press.
-
(2006)
Mol. Ecol
-
-
Ray, D.A.1
-
30
-
-
0029526909
-
Objections to bootstrapping phylogenies: A critique
-
Sanderson, M. J. 1995. Objections to bootstrapping phylogenies: A critique. Syst. Biol. 44:299-320.
-
(1995)
Syst. Biol
, vol.44
, pp. 299-320
-
-
Sanderson, M.J.1
-
31
-
-
66249145798
-
Amniote phylogenomics: Testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles
-
W. J. Murphy, ed, Humana Press, Totowa, New Jersey
-
Shedlock, A. M., D. Janes, and S. V. Edwards. 2006. Amniote phylogenomics: Testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles. Pages xx-xx in Phylogenomics (W. J. Murphy, ed.) Humana Press, Totowa, New Jersey.
-
(2006)
Pages xx-xx in Phylogenomics
-
-
Shedlock, A.M.1
Janes, D.2
Edwards, S.V.3
-
32
-
-
0033964296
-
SINE insertions: Powerful tools for molecular systematics
-
Shedlock, A. M., and N. Okada. 2000. SINE insertions: Powerful tools for molecular systematics. Bioessays 22:148-160.
-
(2000)
Bioessays
, vol.22
, pp. 148-160
-
-
Shedlock, A.M.1
Okada, N.2
-
33
-
-
4544222472
-
SINEs of speciation: Tracking lineages with retroposons
-
Shedlock, A. M., K. Takahashi, and N. Okada. 2004. SINEs of speciation: Tracking lineages with retroposons. Trends Ecol. Evol. 19:545-553.
-
(2004)
Trends Ecol. Evol
, vol.19
, pp. 545-553
-
-
Shedlock, A.M.1
Takahashi, K.2
Okada, N.3
-
34
-
-
66249126349
-
-
Smit, A. F. A. 2006. RepeatMasker version 3.1.5
-
Smit, A. F. A. 2006. RepeatMasker version 3.1.5 (http://www. repeatmasker.org).
-
-
-
-
35
-
-
0031741182
-
Estimating the rate of evolution of the rate of molecular evolution
-
Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.
-
(1998)
Mol. Biol. Evol
, vol.15
, pp. 1647-1657
-
-
Thorne, J.L.1
Kishino, H.2
Painter, I.S.3
-
36
-
-
0035752767
-
A phylogenetic foundation for comparative mammalian genomics
-
Waddell, P. J., H. Kishino, and R. Ota. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Informat. 12:141-154.
-
(2001)
Genome Informat
, vol.12
, pp. 141-154
-
-
Waddell, P.J.1
Kishino, H.2
Ota, R.3
-
37
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston, R. H., K. Lindblad-Toh, E. Birney, J. Rogers, J. F. Abril, P. Agarwal, R. Agarwala, R. Ainscough, M. Alexandersson, and P. An, 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
Agarwal, P.6
Agarwala, R.7
Ainscough, R.8
Alexandersson, M.9
An, P.10
-
38
-
-
0036591885
-
SINEs and LINEs: The art of biting the hand that feeds you
-
Weiner, A. M. 2002. SINEs and LINEs: The art of biting the hand that feeds you. Curr. Opin. Cell Biol. 14:343-350.
-
(2002)
Curr. Opin. Cell Biol
, vol.14
, pp. 343-350
-
-
Weiner, A.M.1
-
39
-
-
33746801653
-
A family of conserved noncoding elements derived from an ancient transposable lement
-
Xie, X., M. Kamal, and E. S. Lander. 2006. A family of conserved noncoding elements derived from an ancient transposable lement. Proc. Natl. Acad. Sci. USA 103:11659-11664.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 11659-11664
-
-
Xie, X.1
Kamal, M.2
Lander, E.S.3
-
40
-
-
0025006614
-
Origin and evolution of retroelements based upon their reverse transcriptase sequences
-
Xiong, Y., and T. H. Eickbush. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9:3353-3362.
-
(1990)
EMBO J
, vol.9
, pp. 3353-3362
-
-
Xiong, Y.1
Eickbush, T.H.2
|