-
1
-
-
52449130150
-
Multi-break rearrangements and breakpoint reuses: From circular to linear genomes
-
Alekseyev, M.A. 2008. Multi-break rearrangements and breakpoint reuses: From circular to linear genomes. J. Comput. Biol. 15: 1117-1131.
-
(2008)
J. Comput. Biol.
, vol.15
, pp. 1117-1131
-
-
Alekseyev, M.A.1
-
2
-
-
84969256270
-
Whole genome duplications, multibreak rearrangements, and genome halving theorem
-
SIAM, Philadelphia.
-
Alekseyev, M.A. and Pevzner, P.A. 2007. Whole genome duplications, multibreak rearrangements, and genome halving theorem. In Proceedings of the 18th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 665-679. SIAM, Philadelphia.
-
(2007)
Proceedings of the 18th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)
, pp. 665-679
-
-
Alekseyev, M.A.1
Pevzner, P.A.2
-
3
-
-
45849108363
-
Multi-break rearrangements and chromosomal evolution
-
Alekseyev, M.A. and Pevzner, P.A. 2008. Multi-break rearrangements and chromosomal evolution. Theor. Comput. Sci. 395: 193-202.
-
(2008)
Theor. Comput. Sci.
, vol.395
, pp. 193-202
-
-
Alekseyev, M.A.1
Pevzner, P.A.2
-
4
-
-
0141609704
-
A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships
-
Amrine-Madsen, H., Koepfli, K.-P., Wayne, R.K., and Springer, M.S. 2003. A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships. Mol. Phylogenet. Evol. 28: 225-240.
-
(2003)
Mol. Phylogenet. Evol.
, vol.28
, pp. 225-240
-
-
Amrine-Madsen, H.1
Koepfli, K.-P.2
Wayne, R.K.3
Springer, M.S.4
-
5
-
-
0037062433
-
Mammalian mitogenomic relationships and the root of the eutherian tree
-
Arnason, U., Adegoke, J.A., Bodin, K., Born, E.W., Esa, Y.B., Gullberg, A., Nilsson, M., Short, R.V., Xu, X., Janke, A., et al. 2002. Mammalian mitogenomic relationships and the root of the eutherian tree. Proc. Natl. Acad. Sci. 99: 8151-8156.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 8151-8156
-
-
Arnason, U.1
Adegoke, J.A.2
Bodin, K.3
Born, E.W.4
Esa, Y.B.5
Gullberg, A.6
Nilsson, M.7
Short, R.V.8
Xu, X.9
Janke, A.10
-
6
-
-
0030130366
-
Genome rearrangement and sorting by reversals
-
Bafna, V. and Pevzner, P.A. 1996. Genome rearrangement and sorting by reversals. SIAM J. Comput. 25: 272-289.
-
(1996)
SIAM J. Comput.
, vol.25
, pp. 272-289
-
-
Bafna, V.1
Pevzner, P.A.2
-
7
-
-
10244270170
-
Sorting permutations by transpositions
-
Bafna, V. and Pevzner, P.A. 1998. Sorting permutations by transpositions. SIAM J. Discrete Math. 11: 224-240.
-
(1998)
SIAM J. Discrete Math.
, vol.11
, pp. 224-240
-
-
Bafna, V.1
Pevzner, P.A.2
-
8
-
-
4444264564
-
Hotspots of mammalian chromosomal evolution
-
doi: 10.1186/gb-2004-5-4-r23.
-
Bailey, J., Baertsch, R., Kent, W., Haussler, D., and Eichler, E. 2004. Hotspots of mammalian chromosomal evolution. Genome Biol. 5: R23. doi: 10.1186/gb-2004-5-4-r23.
-
(2004)
Genome Biol.
, vol.5
-
-
Bailey, J.1
Baertsch, R.2
Kent, W.3
Haussler, D.4
Eichler, E.5
-
9
-
-
33750264868
-
A unifying view of genome rearrangements
-
Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings
-
Bergeron, A., Mixtacki, J., and Stoye, J. 2006. A unifying view of genome rearrangements. Lect. Notes Comput. Sci. 4175: 163-173. (Pubitemid 44609667)
-
(2006)
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
, vol.4175 LNBI
, pp. 163-173
-
-
Bergeron, A.1
Mixtacki, J.2
Stoye, J.3
-
10
-
-
0036107903
-
Discovery of regulatory elements by a computational method for phylogenetic footprinting
-
DOI 10.1101/gr.6902
-
Blanchette, M. and Tompa, M. 2002. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12: 739-748. (Pubitemid 34546461)
-
(2002)
Genome Research
, vol.12
, Issue.5
, pp. 739-748
-
-
Blanchette, M.1
Tompa, M.2
-
11
-
-
0002163159
-
Breakpoint phylogenies
-
Blanchette, M., Bourque, G., and Sankoff, D. 1997. Breakpoint phylogenies. Genome Inform. Ser. Workshop Genome Inform. 8: 25-34.
-
(1997)
Genome Inform. Ser. Workshop Genome Inform.
, vol.8
, pp. 25-34
-
-
Blanchette, M.1
Bourque, G.2
Sankoff, D.3
-
12
-
-
0036143403
-
Genome-scale evolution: Reconstructing gene orders in the ancestral species
-
Bourque, G. and Pevzner, P.A. 2002. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res. 12: 26-36.
-
(2002)
Genome Res.
, vol.12
, pp. 26-36
-
-
Bourque, G.1
Pevzner, P.A.2
-
13
-
-
1842768393
-
Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes
-
Bourque, G., Pevzner, P.A., and Tesler, G. 2004. Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes. Genome Res. 14: 507-516.
-
(2004)
Genome Res.
, vol.14
, pp. 507-516
-
-
Bourque, G.1
Pevzner, P.A.2
Tesler, G.3
-
14
-
-
12744263078
-
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
-
Bourque, G., Zdobnov, E.M., Bork, P., Pevzner, P.A., and Tesler, G. 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15: 98-110.
-
(2005)
Genome Res.
, vol.15
, pp. 98-110
-
-
Bourque, G.1
Zdobnov, E.M.2
Bork, P.3
Pevzner, P.A.4
Tesler, G.5
-
15
-
-
33644640712
-
The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
-
DOI 10.1101/gr.4631806
-
Bourque, G., Tesler, G., and Pevzner, P.A. 2006. The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res. 16: 311-313. (Pubitemid 43327499)
-
(2006)
Genome Research
, vol.16
, Issue.3
, pp. 311-313
-
-
Bourque, G.1
Tesler, G.2
Pevzner, P.A.3
-
16
-
-
37249084343
-
Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages
-
doi: 10.1186/gb-2007-8-8-r170.
-
Bulazel, K., Ferreri, G., Eldridge, M., and O'Neill, R. 2007. Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages. Genome Biol. 8: R170. doi: 10.1186/gb-2007-8-8-r170.
-
(2007)
Genome Biol.
, vol.8
-
-
Bulazel, K.1
Ferreri, G.2
Eldridge, M.3
O'Neill, R.4
-
17
-
-
36749059019
-
A recurrent inversion on the eutherian X chromosome
-
DOI 10.1073/pnas.0706604104
-
Caceres, M., Sullivan, R.T., and Thomas, J.W. 2007. A recurrent inversion on the eutherian X chromosome. Proc. Natl. Acad. Sci. 104: 18571-18576. (Pubitemid 350210738)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.47
, pp. 18571-18576
-
-
Caceres, M.1
McDowell, J.C.2
Gupta, J.3
Brooks, S.4
Bouffard, G.G.5
Blakesley, R.W.6
Green, E.D.7
Sullivan, R.T.8
Thomas, J.W.9
-
18
-
-
33846491679
-
A phylogenomic study of human, dog, and mouse
-
doi: 10.1371/journal.pcbi.0030002.
-
Cannarozzi, G., Schneider, A., and Gonnet, G. 2007. A phylogenomic study of human, dog, and mouse. PLoS Comput. Biol. 3: e2. doi: 10.1371/journal.pcbi. 0030002.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Cannarozzi, G.1
Schneider, A.2
Gonnet, G.3
-
20
-
-
0008507968
-
On the Tightness of the Alternating-Cycle Lower Bound for Sorting by Reversals
-
Caprara, A. 1999b. On the tightness of the alternating-cycle lower bound for sorting by reversals. J. Comb. Optim. 3: 149-182. (Pubitemid 129575312)
-
(1999)
Journal of Combinatorial Optimization
, vol.3
, Issue.2-3
, pp. 149-182
-
-
Caprara, A.1
-
21
-
-
43549099991
-
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication
-
doi: 10.1186/gb-2008-9-2-r28.
-
Cardone, M., Jiang, Z., D'Addabbo, P., Archidiacono, N., Rocchi, M., Eichler, E., and Ventura, M. 2008. Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication. Genome Biol. 9: R28. doi: 10.1186/gb-2008-9-2-r28.
-
(2008)
Genome Biol.
, vol.9
-
-
Cardone, M.1
Jiang, Z.2
D'Addabbo, P.3
Archidiacono, N.4
Rocchi, M.5
Eichler, E.6
Ventura, M.7
-
22
-
-
33845945178
-
Microinversions in mammalian evolution
-
DOI 10.1073/pnas.0603984103
-
Chaisson, M.J., Raphael, B.J., and Pevzner, P.A. 2006. Microinversions in mammalian evolution. Proc. Natl. Acad. Sci. 103: 19824-19829. (Pubitemid 46037515)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.52
, pp. 19824-19829
-
-
Chaisson, M.J.1
Raphael, B.J.2
Pevzner, F.A.3
-
23
-
-
57149085266
-
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes
-
doi: 10.1371/journal.pcbi.1000234.
-
Chauve, C. and Tannier, E. 2008. A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput. Biol. 4: e1000234. doi: 10.1371/journal.pcbi. 1000234.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Chauve, C.1
Tannier, E.2
-
24
-
-
39749114419
-
Chromosomal phylogeny and evolution of the African mole-rats (Bathyergidae)
-
Deuve, J., Bennett, N., Britton-Davidian, J., and Robinson, T. 2008. Chromosomal phylogeny and evolution of the African mole-rats (Bathyergidae). Chromosome Res. 16: 57-74.
-
(2008)
Chromosome Res.
, vol.16
, pp. 57-74
-
-
Deuve, J.1
Bennett, N.2
Britton-Davidian, J.3
Robinson, T.4
-
25
-
-
33644655538
-
Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?
-
Froenicke, L., Caldes, M.G., Graphodatsky, A., Muller, S., Lyons, L.A., Robinson, T.J., Volleth, M., Yang, F., and Wienberg, J. 2006. Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes? Genome Res. 16: 306-310.
-
(2006)
Genome Res.
, vol.16
, pp. 306-310
-
-
Froenicke, L.1
Caldes, M.G.2
Graphodatsky, A.3
Muller, S.4
Lyons, L.A.5
Robinson, T.J.6
Volleth, M.7
Yang, F.8
Wienberg, J.9
-
26
-
-
35948969243
-
Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions
-
Gordon, L., Yang, S., Tran-Gyamfi, M., Baggott, D., Christensen, M., Hamilton, A., Crooijmans, R., Groenen, M., Lucas, S., Ovcharenko, I., et al. 2007. Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. Genome Res. 17: 1603-1613.
-
(2007)
Genome Res.
, vol.17
, pp. 1603-1613
-
-
Gordon, L.1
Yang, S.2
Tran-Gyamfi, M.3
Baggott, D.4
Christensen, M.5
Hamilton, A.6
Crooijmans, R.7
Groenen, M.8
Lucas, S.9
Ovcharenko, I.10
-
27
-
-
0027176992
-
Towards a molecular resolution of the ordinal phylogeny of the eutherian mammals
-
Graur, D. 1993. Towards a molecular resolution of the ordinal phylogeny of the eutherian mammals. FEBS Lett. 325: 152-159. (Pubitemid 223028304)
-
(1993)
FEBS Letters
, vol.325
, Issue.1-2
, pp. 152-159
-
-
Graur, D.1
-
29
-
-
0002856077
-
Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals)
-
Hannenhalli, S. and Pevzner, P. 1999. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). JACM 46: 1-27.
-
(1999)
JACM
, vol.46
, pp. 1-27
-
-
Hannenhalli, S.1
Pevzner, P.2
-
30
-
-
33751193501
-
Recurring genomic breaks in independent lineages support genomic fragility
-
doi: 10.1186/1471-2148-6-90.
-
Hinsch, H. and Hannenhalli, S. 2006. Recurring genomic breaks in independent lineages support genomic fragility. BMC Evol. Biol. 6: 90. doi: 10.1186/1471-2148-6-90.
-
(2006)
BMC Evol. Biol.
, vol.6
, pp. 90
-
-
Hinsch, H.1
Hannenhalli, S.2
-
31
-
-
36448938389
-
The human phylome
-
doi: 10.1186/gb-2007-8-6-r109.
-
Huerta-Cepas, J., Dopazo, H., Dopazo, J., and Gabaldon, T. 2007. The human phylome. Genome Biol. 8: R109. doi: 10.1186/gb-2007-8-6-r109.
-
(2007)
Genome Biol.
, vol.8
-
-
Huerta-Cepas, J.1
Dopazo, H.2
Dopazo, J.3
Gabaldon, T.4
-
32
-
-
34547753508
-
Rates of genome evolution and branching order from whole genome analysis
-
DOI 10.1093/molbev/msm094
-
Huttley, G.A., Wakefield, M.J., and Easteal, S. 2007. Rates of genome evolution and branching order from whole genome analysis. Mol. Biol. Evol. 24: 1722-1730. (Pubitemid 47236694)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1722-1730
-
-
Huttley, G.A.1
Wakefield, M.J.2
Easteal, S.3
-
33
-
-
0028270434
-
The marsupial mitochondrial genome and the evolution of placental mammals
-
Janke, A., Feldmaier-Fuchs, G., Thomas, W.K., von Haeseler, A., and Paabo, S. 1994. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137: 243-256.
-
(1994)
Genetics
, vol.137
, pp. 243-256
-
-
Janke, A.1
Feldmaier-Fuchs, G.2
Thomas, W.K.3
Von Haeseler, A.4
Paabo, S.5
-
34
-
-
13844281341
-
Comparative analysis of protein coding sequences from human, mouse and the domesticated pig
-
doi: 10.1186/1741-7007-3-12
-
Jorgensen, F., Hobolth, A., Hornshoj, H., Bendixen, C., Fredholm, M., and Schierup, M. 2005. Comparative analysis of protein coding sequences from human, mouse and the domesticated pig. BMC Biol. 3: 2. doi: 10.1186/1741-7007-3-12
-
(2005)
BMC Biol.
, vol.3
, pp. 2
-
-
Jorgensen, F.1
Hobolth, A.2
Hornshoj, H.3
Bendixen, C.4
Fredholm, M.5
Schierup, M.6
-
35
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
36
-
-
33846460751
-
Reconstruction of the ancestral ferungulate karyotype by electronic chromosome painting (E-painting)
-
DOI 10.1007/s10577-006-1097-7
-
Kemkemer, C., Kohn, M., Kehrer-Sawatzki, H., Minich, P., Högel, J., Froenicke, L., and Hameister, H. 2006. Reconstruction of the ancestral ferungulate karyotype by electronic chromosome painting (E-painting). Chromosome Res. 14: 899-907. (Pubitemid 46144232)
-
(2006)
Chromosome Research
, vol.14
, Issue.8
, pp. 899-907
-
-
Kemkemer, C.1
Kohn, M.2
Kehrer-Sawatzki, H.3
Minich, P.4
Hogel, J.5
Froenicke, L.6
Hameister, H.7
-
37
-
-
34248153777
-
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
-
Kikuta, H., Laplante, M., Navratilova, P., Komisarczuk, A.Z., Engstrom, P.G., Fredman, D., Akalin, A., Caccamo, M., Sealy, I., Howe, K., et al. 2007. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 17: 545-555.
-
(2007)
Genome Res.
, vol.17
, pp. 545-555
-
-
Kikuta, H.1
Laplante, M.2
Navratilova, P.3
Komisarczuk, A.Z.4
Engstrom, P.G.5
Fredman, D.6
Akalin, A.7
Caccamo, M.8
Sealy, I.9
Howe, K.10
-
38
-
-
0032580152
-
A molecular timescale for vertebrate evolution
-
Kumar, S. and Hedges, S.B. 1998. A molecular timescale for vertebrate evolution. Nature 392: 917-920.
-
(1998)
Nature
, vol.392
, pp. 917-920
-
-
Kumar, S.1
Hedges, S.B.2
-
39
-
-
46249101804
-
Estimating true evolutionary distances under the DCJ model
-
Lin, Y. and Moret, B.M. 2008. Estimating true evolutionary distances under the DCJ model. Bioinformatics 24: i114-i122.
-
(2008)
Bioinformatics
, vol.24
-
-
Lin, Y.1
Moret, B.M.2
-
40
-
-
34247626400
-
Dog as an outgroup to human and mouse
-
doi: 10.1371/journal.pcbi.0030074.
-
Lunter, G. 2007. Dog as an outgroup to human and mouse. PLoS Comput. Biol. 3: e74. doi: 10.1371/journal.pcbi.0030074.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Lunter, G.1
-
41
-
-
33750386912
-
Reconstructing contiguous regions of an ancestral genome
-
Ma, J., Zhang, L., Suh, B.B., Raney, B.J., Burhans, R.C., Kent, J.W., Blanchette, M., Haussler, D., and Miller, W. 2006. Reconstructing contiguous regions of an ancestral genome. Genome Res. 16: 1557-1565.
-
(2006)
Genome Res.
, vol.16
, pp. 1557-1565
-
-
Ma, J.1
Zhang, L.2
Suh, B.B.3
Raney, B.J.4
Burhans, R.C.5
Kent, J.W.6
Blanchette, M.7
Haussler, D.8
Miller, W.9
-
42
-
-
55549136564
-
The infinite sites model of genome evolution
-
Ma, J., Ratan, A., Raney, B.J., Suh, B.B., Miller, W., and Haussler, D. 2008. The infinite sites model of genome evolution. Proc. Natl. Acad. Sci. 105: 14254-14261.
-
(2008)
Proc. Natl. Acad. Sci.
, vol.105
, pp. 14254-14261
-
-
Ma, J.1
Ratan, A.2
Raney, B.J.3
Suh, B.B.4
Miller, W.5
Haussler, D.6
-
43
-
-
0035252569
-
Parallel adaptive radiations in two major clades of placental mammals
-
Madsen, O., Scally, M., Douady, C.J., Kao, D.J., DeBry, R.W., Adkins, R., Amrine, H.M., Stanhope, M.J., de Jong,W.W., Springer, M.S., et al. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409: 610-614.
-
(2001)
Nature
, vol.409
, pp. 610-614
-
-
Madsen, O.1
Scally, M.2
Douady, C.J.3
Kao, D.J.4
DeBry, R.W.5
Adkins, R.6
Amrine, H.M.7
Stanhope, M.J.8
De Jong, W.W.9
Springer, M.S.10
-
44
-
-
33947201571
-
Analysis of segmental duplications reveals a distinct pattern of continuation-of-synteny between human and mouse genomes
-
DOI 10.1007/s00439-006-0277-z
-
Mehan, M.R., Almonte, M., Slaten, E., Freimer, N.B., Rao, P.N., and Ophoff, R.A. 2007. Analysis of segmental duplications reveals a distinct pattern of continuation-of-synteny between human and mouse genomes. Hum. Genet. 121: 93-100. (Pubitemid 46421145)
-
(2007)
Human Genetics
, vol.121
, Issue.1
, pp. 93-100
-
-
Mehan, M.R.1
Almonte, M.2
Slaten, E.3
Freimer, N.B.4
Rao, P.N.5
Ophoff, R.A.6
-
45
-
-
34248576291
-
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
-
Mikkelsen, T.S.,Wakefield, M.J., Aken, B., Amemiya, C.T., Chang, J.L., Duke, S., Garber, M., Gentles, A.J., Goodstadt, L., Heger, A., et al. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167-177.
-
(2007)
Nature
, vol.447
, pp. 167-177
-
-
Mikkelsen, T.S.1
Wakefield, M.J.2
Aken, B.3
Amemiya, C.T.4
Chang, J.L.5
Duke, S.6
Garber, M.7
Gentles, A.J.8
Goodstadt, L.9
Heger, A.10
-
46
-
-
0141832717
-
Revisiting the Glires concept - Phylogenetic analysis of nuclear sequences
-
DOI 10.1016/S1055-7903(03)00079-4
-
Misawa, K. and Janke, A. 2003. Revisiting the Glires concept-Phylogenetic analysis of nuclear sequences. Mol. Phylogenet. Evol. 28: 320-327. (Pubitemid 37435997)
-
(2003)
Molecular Phylogenetics and Evolution
, vol.28
, Issue.2
, pp. 320-327
-
-
Misawa, K.1
Janke, A.2
-
47
-
-
0035234694
-
A new implementation and detailed study of breakpoint analysis
-
Hawaii.
-
Moret, B., Wyman, S., Bader, D.A., Warnow, T., and Yan, M. 2001. A new implementation and detailed study of breakpoint analysis. In Pacific Symposium on Biocomputing, pp. 583-594. Hawaii.
-
(2001)
Pacific Symposium on Biocomputing
, pp. 583-594
-
-
Moret, B.1
Wyman, S.2
Bader, D.A.3
Warnow, T.4
Yan, M.5
-
48
-
-
84957042462
-
Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data
-
Moret, B.M.E., Siepel, A.C., Tang, J., and Liu, T. 2002. Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. Lect. Notes Comput. Sci. 2452: 521-536.
-
(2002)
Lect. Notes Comput. Sci.
, vol.2452
, pp. 521-536
-
-
Moret, B.M.E.1
Siepel, A.C.2
Tang, J.3
Liu, T.4
-
49
-
-
0035252080
-
Molecular phylogenetics and the origins of placental mammals
-
Murphy, W.J., Eizirik, E., Johnson, W.E., Zhang, Y.P., Ryder, O.A., and O'Brien, S.J. 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
-
50
-
-
22744440499
-
Dynamics of mammalian chromosome evolution inferred from multispecies comparative map
-
Murphy, W.J., Larkin, D.M., van der Wind, A.E., Bourque, G., Tesler, G., Auvil, L., Beever, J.E., Chowdhary, B.P., Galibert, F., Gatzke, L., et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative map. Science 309: 613-617.
-
(2005)
Science
, vol.309
, pp. 613-617
-
-
Murphy, W.J.1
Larkin, D.M.2
Van Der Wind, A.E.3
Bourque, G.4
Tesler, G.5
Auvil, L.6
Beever, J.E.7
Chowdhary, B.P.8
Galibert, F.9
Gatzke, L.10
-
51
-
-
40249098860
-
Extensive gains and losses of olfactory receptor genes in mammalian evolution
-
doi: 10.1371/journal.pone.0000708.
-
Niimura, Y. and Nei, M. 2007. Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One 2: e708. doi: 10.1371/journal.pone.0000708.
-
(2007)
PLoS One
, vol.2
-
-
Niimura, Y.1
Nei, M.2
-
55
-
-
36048982458
-
Initial sequence and comparative analysis of the cat genome
-
Pontius, J.U., Mullikin, J.C., Smith, D.R., Lindblad-Toh, K., Gnerre, S., Clamp, M., Chang, J., Stephens, R., Neelam, B., Volfovsky, N., et al. 2007. Initial sequence and comparative analysis of the cat genome. Genome Res. 17: 1675-1689.
-
(2007)
Genome Res.
, vol.17
, pp. 1675-1689
-
-
Pontius, J.U.1
Mullikin, J.C.2
Smith, D.R.3
Lindblad-Toh, K.4
Gnerre, S.5
Clamp, M.6
Chang, J.7
Stephens, R.8
Neelam, B.9
Volfovsky, N.10
-
56
-
-
0036853613
-
Sequence gaps join mice and men: Phylogenetic evidence from deletions in two proteins
-
Poux, C., van Rheede, T., Madsen, O., and de Jong, W.W. 2002. Sequence gaps join mice and men: Phylogenetic evidence from deletions in two proteins. Mol. Biol. Evol. 19: 2035-2037.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 2035-2037
-
-
Poux, C.1
Van Rheede, T.2
Madsen, O.3
De Jong, W.W.4
-
57
-
-
0034117084
-
Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris [2]
-
Reyes, A., Gissi, C., Pesole, G., Catzeflis, F.M., and Saccone, C. 2000. Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris. Mol. Biol. Evol. 17: 979-983. (Pubitemid 30346558)
-
(2000)
Molecular Biology and Evolution
, vol.17
, Issue.6
, pp. 979-983
-
-
Reyes, A.1
Gissi, C.2
Pesole, G.3
Catzeflis, F.M.4
Saccone, C.5
-
58
-
-
1542376765
-
Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods
-
DOI 10.1093/molbev/msh033
-
Reyes, A., Gissi, C., Catzeflis, F., Nevo, E., Pesole, G., and Saccone, C. 2004. Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods. Mol. Biol. Evol. 21: 397-403. (Pubitemid 38314627)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.2
, pp. 397-403
-
-
Reyes, A.1
Gissi, C.2
Catzeflis, F.3
Nevo, E.4
Pesole, G.5
Saccone, C.6
-
59
-
-
33845292242
-
Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed
-
Rocchi, M., Archidiacono, N., and Stanyon, R. 2006. Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed. Genome Res. 16: 1441-1444.
-
(2006)
Genome Res.
, vol.16
, pp. 1441-1444
-
-
Rocchi, M.1
Archidiacono, N.2
Stanyon, R.3
-
60
-
-
34249697132
-
Is mammalian chromosomal evolution driven by regions of genome fragility?
-
doi: 10.1186/gb-2006-7-12-r115.
-
Ruiz-Herrera, A., Castresana, J., and Robinson, T.J. 2006. Is mammalian chromosomal evolution driven by regions of genome fragility? Genome Biol. 7: R115. doi: 10.1186/gb-2006-7-12-r115.
-
(2006)
Genome Biol.
, vol.7
-
-
Ruiz-Herrera, A.1
Castresana, J.2
Robinson, T.J.3
-
61
-
-
0031721577
-
Multiple genome rearrangement and breakpoint phylogeny
-
Sankoff, D. and Blanchette, M. 1998. Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol. 5: 555-570. (Pubitemid 28436301)
-
(1998)
Journal of Computational Biology
, vol.5
, Issue.3
, pp. 555-570
-
-
Sankoff, D.1
Blanchette, M.2
-
62
-
-
0026680446
-
Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome
-
Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B.F., and Cedergren, R. 1992. Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. 89: 6575-6579.
-
(1992)
Proc. Natl. Acad. Sci.
, vol.89
, pp. 6575-6579
-
-
Sankoff, D.1
Leduc, G.2
Antoine, N.3
Paquin, B.4
Lang, B.F.5
Cedergren, R.6
-
63
-
-
0032085453
-
Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data
-
Shoshani, J. and McKenna, M.C. 1998. Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data. Mol. Phylogenet. Evol. 9: 572-584.
-
(1998)
Mol. Phylogenet. Evol.
, vol.9
, pp. 572-584
-
-
Shoshani, J.1
McKenna, M.C.2
-
64
-
-
0345225320
-
Scaling up accurate phylogenetic reconstruction from gene-order data
-
Tang, J. and Moret, B.M. 2003. Scaling up accurate phylogenetic reconstruction from gene-order data. Bioinformatics 19: i305-i312.
-
(2003)
Bioinformatics
, vol.19
-
-
Tang, J.1
Moret, B.M.2
-
65
-
-
35048862957
-
Sorting by Reversals in Subquadratic Time
-
Combinatorial Pattern Matching 15th Annual Symposium, CPM 2004 Istanbul, Turkey, July 5-7, 2004 Proceedings
-
Tannier, E. and Sagot, M.-F. 2004. Sorting by reversals in subquadratic time. Lect. Notes Comput. Sci. 3109: 1-13. (Pubitemid 38945531)
-
(2004)
LECTURE NOTES in COMPUTER SCIENCE.
, Issue.3109
, pp. 1-13
-
-
Tannier, E.1
Sagot, M.-F.2
-
66
-
-
56649103607
-
Multichromosomal genome median and halving problems
-
Tannier, E., Zheng, C., and Sankoff, D. 2008. Multichromosomal genome median and halving problems. Lect. Notes Bioinformatics 5251: 1-13.
-
(2008)
Lect. Notes Bioinformatics
, vol.5251
, pp. 1-13
-
-
Tannier, E.1
Zheng, C.2
Sankoff, D.3
-
67
-
-
0038658640
-
Efficient algorithms for multichromosomal genome rearrangements
-
Tesler, G. 2002a. Efficient algorithms for multichromosomal genome rearrangements. J. Comput. Syst. Sci. 65: 587-609.
-
(2002)
J. Comput. Syst. Sci.
, vol.65
, pp. 587-609
-
-
Tesler, G.1
-
68
-
-
0036211065
-
GRIMM: Genome rearrangements web server
-
Tesler, G. 2002b. GRIMM: Genome rearrangements web server. Bioinformatics 18: 492-493.
-
(2002)
Bioinformatics
, vol.18
, pp. 492-493
-
-
Tesler, G.1
-
69
-
-
0041465867
-
Comparative analyses of multispecies sequences from targeted genomic regions
-
Thomas, J.W., Touchman, J.W., Blakesley, R.W., Bouffard, G.G., Beckstrom-Sternberg, S.M., Margulies, E.H., Blanchette, M., Siepel, A.C., Thomas, P.J., McDowell, J.C., et al. 2003. Comparative analyses of multispecies sequences from targeted genomic regions. Nature 424: 788-793.
-
(2003)
Nature
, vol.424
, pp. 788-793
-
-
Thomas, J.W.1
Touchman, J.W.2
Blakesley, R.W.3
Bouffard, G.G.4
Beckstrom-Sternberg, S.M.5
Margulies, E.H.6
Blanchette, M.7
Siepel, A.C.8
Thomas, P.J.9
McDowell, J.C.10
-
70
-
-
3543102097
-
A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates
-
van der Wind, A.E., Kata, S.R., Band, M.R., Rebeiz, M., Larkin, D.M., Everts, R.E., Green, C.A., Liu, L., Natarajan, S., Goldammer, T., et al. 2004. A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Res. 14: 1424-1437.
-
(2004)
Genome Res.
, vol.14
, pp. 1424-1437
-
-
Van Der Wind, A.E.1
Kata, S.R.2
Band, M.R.3
Rebeiz, M.4
Larkin, D.M.5
Everts, R.E.6
Green, C.A.7
Liu, L.8
Natarajan, S.9
Goldammer, T.10
-
71
-
-
28844452823
-
Hotspots of mutation and breakage in dog and human chromosomes
-
DOI 10.1101/gr.3896805
-
Webber, C. and Ponting, C.P. 2005. Hotspots of mutation and breakage in dog and human chromosomes. Genome Res. 15: 1787-1797. (Pubitemid 41780409)
-
(2005)
Genome Research
, vol.15
, Issue.12
, pp. 1787-1797
-
-
Webber, C.1
Ponting, C.P.2
-
73
-
-
38349018959
-
Reconstructing an inversion history in the Anopheles gambiae complex
-
Xia, A., Sharakhova, M., and Sharakhov, I. 2007. Reconstructing an inversion history in the Anopheles gambiae complex. Lect. Notes Bioinformatics 4751: 136-148.
-
(2007)
Lect. Notes Bioinformatics
, vol.4751
, pp. 136-148
-
-
Xia, A.1
Sharakhova, M.2
Sharakhov, I.3
-
74
-
-
24044535485
-
Efficient sorting of genomic permutations by translocation, inversion and block interchange
-
Yancopoulos, S., Attie, O., and Friedberg, R. 2005. Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21: 3340-3346.
-
(2005)
Bioinformatics
, vol.21
, pp. 3340-3346
-
-
Yancopoulos, S.1
Attie, O.2
Friedberg, R.3
-
75
-
-
27644571041
-
7E olfactory receptor gene clusters and evolutionary chromosome rearrangements
-
DOI 10.1159/000087507
-
Yue, Y. and Haaf, T. 2006. 7E olfactory receptor gene clusters and evolutionary chromosome rearrangements. Cytogenet. Genome Res. 112: 6-10. (Pubitemid 41579449)
-
(2006)
Cytogenetic and Genome Research
, vol.112
, Issue.1-2
, pp. 6-10
-
-
Yue, Y.1
Haaf, T.2
-
76
-
-
38349105423
-
Recovering true rearrangement events on phylogenetic trees
-
Zhao, H. and Bourque, G. 2007. Recovering true rearrangement events on phylogenetic trees. Lect. Notes Bioinformatics 4751: 149-161.
-
(2007)
Lect. Notes Bioinformatics
, vol.4751
, pp. 149-161
-
-
Zhao, H.1
Bourque, G.2
-
77
-
-
66049098213
-
Recovering genome rearrangements in the mammalian phylogeny
-
doi: 10.1101/gr.086009.108.
-
Zhao, H. and Bourque, G. 2009. Recovering genome rearrangements in the mammalian phylogeny. Genome Res. (this issue). doi: 10.1101/gr.086009.108.
-
(2009)
Genome Res.
, Issue.THIS ISSUE
-
-
Zhao, H.1
Bourque, G.2
-
78
-
-
6344222248
-
Human, mouse, and rat genome large-scale rearrangements: Stability versus speciation
-
Zhao, S., Shetty, J., Hou, L., Delcher, A., Zhu, B., Osoegawa, K., de Jong, P., Nierman, W.C., Strausberg, R.L., Fraser, C.M., et al. 2004. Human, mouse, and rat genome large-scale rearrangements: Stability versus speciation. Genome Res. 14: 1851-1860.
-
(2004)
Genome Res.
, vol.14
, pp. 1851-1860
-
-
Zhao, S.1
Shetty, J.2
Hou, L.3
Delcher, A.4
Zhu, B.5
Osoegawa, K.6
De Jong, P.7
Nierman, W.C.8
Strausberg, R.L.9
Fraser, C.M.10
|