-
1
-
-
33846197539
-
Settling the intractability of multiple alignment
-
Elias I. Settling the intractability of multiple alignment. J Comput Biol 2006, 13(7):1323-1339.
-
(2006)
J Comput Biol
, vol.13
, Issue.7
, pp. 1323-1339
-
-
Elias, I.1
-
2
-
-
38849149795
-
28-way vertebrate alignment and conservation track in the UCSC Genome browser
-
Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk S, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. 28-way vertebrate alignment and conservation track in the UCSC Genome browser. Genes Dev 2007, 17(12):1797-1808.
-
(2007)
Genes Dev
, vol.17
, Issue.12
, pp. 1797-1808
-
-
Miller, W.1
Rosenbloom, K.2
Hardison, R.C.3
Hou, M.4
Taylor, J.5
Raney, B.6
Burhans, R.7
King, D.C.8
Baertsch, R.9
Blankenberg, D.10
Kosakovsky Pond, S.L.11
Nekrutenko, A.12
Giardine, B.13
Harris, R.S.14
Tyekucheva, S.15
Diekhans, M.16
Pringle, T.H.17
Murphy, W.J.18
Lesk, S.19
Weinstock, G.M.20
Lindblad-Toh, K.21
Gibbs, R.A.22
Lander, E.S.23
Siepel, A.24
Haussler, D.25
Kent, W.J.26
more..
-
3
-
-
77956193448
-
Progressivemauve: multiple genome alignment with gene gain, loss and rearrangement
-
Darling AE, Mau B, Perna NT. Progressivemauve: multiple genome alignment with gene gain, loss and rearrangement. PloS one 2010, 5(6):e11147.
-
(2010)
PloS one
, vol.5
, Issue.6
-
-
Darling, A.E.1
Mau, B.2
Perna, N.T.3
-
4
-
-
80052551536
-
Cactus: algorithms for genome multiple sequence alignment
-
Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: algorithms for genome multiple sequence alignment. Genome Res 2011, 21(9):1512-1528.
-
(2011)
Genome Res
, vol.21
, Issue.9
, pp. 1512-1528
-
-
Paten, B.1
Earl, D.2
Nguyen, N.3
Diekhans, M.4
Zerbino, D.5
Haussler, D.6
-
6
-
-
10944228197
-
Reconstructing large regions of an ancestral mammalian genome in silico
-
Blanchette M, Green ED, Miller W, Haussler D. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res 2004, 14(12):2412-2423.
-
(2004)
Genome Res
, vol.14
, Issue.12
, pp. 2412-2423
-
-
Blanchette, M.1
Green, E.D.2
Miller, W.3
Haussler, D.4
-
7
-
-
33847257936
-
Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
-
Kim J, Sinha S. Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics (Oxford, England) 2007, 23(3):289-297.
-
(2007)
Bioinformatics (Oxford, England)
, vol.23
, Issue.3
, pp. 289-297
-
-
Kim, J.1
Sinha, S.2
-
8
-
-
55549095155
-
Genome-wide nucleotide-level mammalian ancestor reconstruction
-
Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res 2008, 18(11):1829-1843.
-
(2008)
Genome Res
, vol.18
, Issue.11
, pp. 1829-1843
-
-
Paten, B.1
Herrero, J.2
Fitzgerald, S.3
Beal, K.4
Flicek, P.5
Holmes, I.6
Birney, E.7
-
9
-
-
0023079987
-
Computational complexity of inferring phylogenies from dissimilarity matrices
-
Day W. Computational complexity of inferring phylogenies from dissimilarity matrices. Bull Math Biol 1987, 49(4):461-467.
-
(1987)
Bull Math Biol
, vol.49
, Issue.4
, pp. 461-467
-
-
Day, W.1
-
10
-
-
33748516782
-
On the inference of parsimonious indel evolutionary scenarios
-
Chindelevitch L, Li Z, Blais E, Blanchette M. On the inference of parsimonious indel evolutionary scenarios. J Bioinform Comput Biol 2006, 4(3):721-744.
-
(2006)
J Bioinform Comput Biol
, vol.4
, Issue.3
, pp. 721-744
-
-
Chindelevitch, L.1
Li, Z.2
Blais, E.3
Blanchette, M.4
-
11
-
-
15944363058
-
Constructing minimal ancestral recombination graphs
-
Song YS, Hein J. Constructing minimal ancestral recombination graphs. J Comput Biol 2005, 12(2):147-169.
-
(2005)
J Comput Biol
, vol.12
, Issue.2
, pp. 147-169
-
-
Song, Y.S.1
Hein, J.2
-
12
-
-
63549098393
-
Accurate detection of recombinant breakpoints in whole-genome alignments
-
Westesson O, Holmes I. Accurate detection of recombinant breakpoints in whole-genome alignments. PLoS Comput Biol 2009, 5(3):e1000318.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.3
-
-
Westesson, O.1
Holmes, I.2
-
13
-
-
0034913468
-
Perfect phylogenetic networks with recombination
-
Wang LL, Zhang KK, Zhang LL. Perfect phylogenetic networks with recombination. J Comput Biol 2001, 8(1):69-78.
-
(2001)
J Comput Biol
, vol.8
, Issue.1
, pp. 69-78
-
-
Wang, L.L.1
Zhang, K.K.2
Zhang, L.L.3
-
15
-
-
45849108363
-
Multi-break rearrangements and chromosomal evolution
-
Alekseyev M, Pevzner P. Multi-break rearrangements and chromosomal evolution. Theor Comput Sci 2008, 395(2-3):193-202.
-
(2008)
Theor Comput Sci
, vol.395
, Issue.2-3
, pp. 193-202
-
-
Alekseyev, M.1
Pevzner, P.2
-
16
-
-
0002856077
-
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
-
Hannenhalli S, Pevzner PA. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J ACM 1999, 46(1):1-27.
-
(1999)
J ACM
, vol.46
, Issue.1
, pp. 1-27
-
-
Hannenhalli, S.1
Pevzner, P.A.2
-
18
-
-
24044535485
-
Efficient sorting of genomic permutations by translocation, inversion and block interchange
-
Yancopoulos S, Attie O, Friedberg R. Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 2005, 21(16):3340-3346.
-
(2005)
Bioinformatics
, vol.21
, Issue.16
, pp. 3340-3346
-
-
Yancopoulos, S.1
Attie, O.2
Friedberg, R.3
-
20
-
-
70349823655
-
A fast and exact algorithm for the median of three problem: a graph decomposition approach
-
Xu AW. A fast and exact algorithm for the median of three problem: a graph decomposition approach. J Comput Biol 2009, 16(10):1369-1381.
-
(2009)
J Comput Biol
, vol.16
, Issue.10
, pp. 1369-1381
-
-
Xu, A.W.1
-
21
-
-
0036143403
-
Genome-scale evolution: reconstructing gene orders in the ancestral species
-
Bourque G, Pevzner PA. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res 2002, 12(1):26-36.
-
(2002)
Genome Res
, vol.12
, Issue.1
, pp. 26-36
-
-
Bourque, G.1
Pevzner, P.A.2
-
22
-
-
55549136564
-
The infinite sites model of genome evolution
-
Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D. The infinite sites model of genome evolution. Proc Natl Acad Sci USA 2008, 105(38):14254-14261.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.38
, pp. 14254-14261
-
-
Ma, J.1
Ratan, A.2
Raney, B.J.3
Suh, B.B.4
Miller, W.5
Haussler, D.6
-
23
-
-
0344794387
-
Sorting signed permutations by reversals and insertions/deletions of contiguous segments
-
El-Mabrouk N. Sorting signed permutations by reversals and insertions/deletions of contiguous segments. J Discrete Algorithm 2000, 1(1):105-121.
-
(2000)
J Discrete Algorithm
, vol.1
, Issue.1
, pp. 105-121
-
-
El-Mabrouk, N.1
-
24
-
-
70349789709
-
DCJ path formulation for genome transformations which include insertions, deletions, and duplications
-
Yancopoulos S, Friedberg R. DCJ path formulation for genome transformations which include insertions, deletions, and duplications. J Comput Biol 2009, 16(10):1311-1338.
-
(2009)
J Comput Biol
, vol.16
, Issue.10
, pp. 1311-1338
-
-
Yancopoulos, S.1
Friedberg, R.2
-
25
-
-
80052638701
-
Double cut and join with insertions and deletions
-
Braga MD, Willing E, Stoye J. Double cut and join with insertions and deletions. J Comput Biol 2011, 18(9):1167-1184.
-
(2011)
J Comput Biol
, vol.18
, Issue.9
, pp. 1167-1184
-
-
Braga, M.D.1
Willing, E.2
Stoye, J.3
-
26
-
-
84859974254
-
Analysis of gene order evolution beyond single-copy genes
-
El-Mabrouk N, Sankoff D. Analysis of gene order evolution beyond single-copy genes. Methods Mol Biol 2012, 855:397-429.
-
(2012)
Methods Mol Biol
, vol.855
, pp. 397-429
-
-
El-Mabrouk, N.1
Sankoff, D.2
-
27
-
-
84944751009
-
-
London: Springer-Verlag
-
Chauve C, El-Mabrouk N, Gueguen L, Semeria M, Tannier E. Models and Algorithms for Genome Evolution 2013, London: Springer-Verlag.
-
(2013)
Models and Algorithms for Genome Evolution
-
-
Chauve, C.1
El-Mabrouk, N.2
Gueguen, L.3
Semeria, M.4
Tannier, E.5
-
28
-
-
84856832577
-
Genome rearrangements with duplications
-
Bader M. Genome rearrangements with duplications. BMC Bioinformatics 2010, 11(Suppl 1):S27-S27.
-
(2010)
BMC Bioinformatics
, vol.11
, Issue.SUPPL. 1
-
-
Bader, M.1
-
29
-
-
84899032346
-
Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion
-
Shao M, Lin Y. Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion. BMC Bioinformatics 2012, 13(Suppl 19):S13.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.SUPPL. 19
-
-
Shao, M.1
Lin, Y.2
-
30
-
-
8744312854
-
A novel method for multiple alignment of sequences with repeated and shuffled elements
-
Raphael B, Zhi D, Tang H, Pevzner P. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res 2004, 14(11):2336-2346.
-
(2004)
Genome Res
, vol.14
, Issue.11
, pp. 2336-2346
-
-
Raphael, B.1
Zhi, D.2
Tang, H.3
Pevzner, P.4
-
31
-
-
79952380591
-
Cactus graphs for genome comparisons
-
Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D. Cactus graphs for genome comparisons. J Comput Biol 2011, 18(3):469-481.
-
(2011)
J Comput Biol
, vol.18
, Issue.3
, pp. 469-481
-
-
Paten, B.1
Diekhans, M.2
Earl, D.3
John, J.S.4
Ma, J.5
Suh, B.6
Haussler, D.7
-
32
-
-
70349204183
-
Maximum likelihood genome assembly
-
Medvedev P, Brudno M. Maximum likelihood genome assembly. J Comput Biol 2009, 16(8):1101-1116.
-
(2009)
J Comput Biol
, vol.16
, Issue.8
, pp. 1101-1116
-
-
Medvedev, P.1
Brudno, M.2
-
33
-
-
0003348586
-
Matching: A Well-Solved Class of Integer Linear Programs
-
Edmonds J, Johnson EL. Matching: A Well-Solved Class of Integer Linear Programs. 1970, 27-30.
-
(1970)
, pp. 27-30
-
-
Edmonds, J.1
Johnson, E.L.2
-
34
-
-
65849156401
-
Multichromosomal median and halving problems under different genomic distances
-
Tannier E, Zheng C, Sankoff D. Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics 2009, 10:120.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 120
-
-
Tannier, E.1
Zheng, C.2
Sankoff, D.3
|