-
1
-
-
0038518196
-
Phylogenomics: Intersection of evolution and genomics
-
PMID: 12805538
-
Eisen JA, Fraser CM. Phylogenomics: Intersection of evolution and genomics. Science 2003; 300(5626):1706-7; PMID: 12805538; http://dx.doi.org/10.1126/science.1086292
-
(2003)
Science
, vol.300
, Issue.5626
, pp. 1706-1707
-
-
Eisen, J.A.1
Fraser, C.M.2
-
2
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
PMID:15861208
-
Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005; 6(5):361-75; PMID:15861208; http://dx.doi.org/10.1038/nrg1603
-
(2005)
Nat Rev Genet
, vol.6
, Issue.5
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
3
-
-
58149492439
-
It is computation time for bacteriology!
-
PMID:18978045
-
Zhulin IB. It is computation time for bacteriology! J Bacteriol 2009; 191(1):20-22; PMID:18978045; http://dx.doi.org/10.1128/JB.01491-08
-
(2009)
J Bacteriol
, vol.191
, Issue.1
, pp. 20-22
-
-
Zhulin, I.B.1
-
4
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
PMID:10381871
-
Doolittle WF. Phylogenetic classification and the universal tree. Science 1999; 284(5423):2124-9; PMID:10381871; http://dx.doi.org/10.1126/science.284.5423.2124
-
(1999)
Science
, vol.284
, Issue.5423
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
5
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
PMID:10830951
-
Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature 2000; 405(6784):299-304; PMID:10830951; http://dx.doi.org/10.1038/35012500
-
(2000)
Nature
, vol.405
, Issue.6784
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
6
-
-
23944506044
-
Mobile genetic elements: The agents of open source evolution
-
Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Micro 2005; 3(9):722-32; http://dx.doi.org/10.1038/nrmicro1235
-
(2005)
Nat Rev Micro
, vol.3
, Issue.9
, pp. 722-732
-
-
Frost, L.S.1
Leplae, R.2
Summers, A.O.3
Toussaint, A.4
-
7
-
-
57149085868
-
Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world
-
PMID: 18948295
-
Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucl Acids Res 2008; 36(21):6688-6719; PMID: 18948295; http://dx.doi.org/10.1093/nar/gkn668
-
(2008)
Nucl Acids Res
, vol.36
, Issue.21
, pp. 6688-6719
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
8
-
-
0036898759
-
Prokaryotic evolution in light of gene transfer
-
PMID:12446813
-
Gogarten JP, Doolittle WF, Lawrence JG. Prokaryotic evolution in light of gene transfer. Mol Biol Evol 2002; 19 (12):2226-2238; PMID:12446813; http://dx.doi.org/10.1093/oxfordjournals.molbev.a004046
-
(2002)
Mol Biol Evol
, vol.19
, Issue.12
, pp. 2226-2238
-
-
Gogarten, J.P.1
Doolittle, W.F.2
Lawrence, J.G.3
-
9
-
-
1942422301
-
Genome mosaicism and organismal lineages
-
PMID:15109780
-
Zhaxybayeva O, Lapierre P, Gogarten JP. Genome mosaicism and organismal lineages. Trends Genet 2004; 20:254-260; PMID:15109780; http://dx.doi.org/10.1016/j.tig.2004.03.009
-
(2004)
Trends Genet
, vol.20
, pp. 254-260
-
-
Zhaxybayeva, O.1
Lapierre, P.2
Gogarten, J.P.3
-
10
-
-
23944499633
-
Horizontal gene transfer, genome innovation and evolution
-
Peter Gogarten J, Townsend JRP. Horizontal gene transfer, genome innovation and evolution. Nat Rev Micro 2005; 3(9):679-687; http://dx.doi.org/10.1038/nrmicro1204
-
(2005)
Nat Rev Micro
, vol.3
, Issue.9
, pp. 679-687
-
-
Peter Gogarten, J.1
Townsend, J.R.P.2
-
11
-
-
21644441587
-
Do orthologous gene phylogenies really support tree-thinking?
-
PMID: 15913459
-
Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF. Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol 2005; 5:33; PMID: 15913459; http://dx.doi.org/10.1186/1471-2148-5-33
-
(2005)
BMC Evol Biol
, vol.5
, pp. 33
-
-
Bapteste, E.1
Susko, E.2
Leigh, J.3
Macleod, D.4
Charlebois, R.L.5
Doolittle, W.F.6
-
12
-
-
33750810896
-
The tree of one percent
-
PMID:17081279
-
Dagan T, Martin W. The tree of one percent. Genome Biol 2006; 7(10):118; PMID:17081279; http://dx.doi.org/10.1186/gb-2006-7-10-118
-
(2006)
Genome Biol
, vol.7
, Issue.10
, pp. 118
-
-
Dagan, T.1
Martin, W.2
-
13
-
-
57149095052
-
Dealing with incongruence in phylogenomic analyses
-
PMID:18852109
-
Galtier N, Daubin V. Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B Biol Sci 2008; 363:4023-4029; PMID:18852109; http://dx.doi.org/10.1098/rstb.2008.0144
-
(2008)
Philos Trans R Soc Lond B Biol Sci
, vol.363
, pp. 4023-4029
-
-
Galtier, N.1
Daubin, V.2
-
14
-
-
33748277982
-
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
-
PMID: 16899658
-
Olga Zhaxybayeva JPG, Charlebois RL, Ford Doolittle W, Thane Papke R. Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. Genome Res 2006; 16(9):1099-1108; PMID: 16899658; http://dx.doi.org/10.1101/gr.5322306
-
(2006)
Genome Res
, vol.16
, Issue.9
, pp. 1099-1108
-
-
Olga Zhaxybayeva, J.1
Charlebois, R.L.2
Ford Doolittle, W.3
Thane Papke, R.4
-
15
-
-
84859467874
-
Lateral gene transfer as a support for the tree of life
-
PMID:22416123
-
Abby SS, Tannier E, Gouy M, Daubin V. Lateral gene transfer as a support for the tree of life. Proc Natl Acad Sci 2012; 109(13):4962-4967; PMID:22416123; http://dx.doi.org/10.1073/pnas.1116871109
-
(2012)
Proc Natl Acad Sci
, vol.109
, Issue.13
, pp. 4962-4967
-
-
Abby, S.S.1
Tannier, E.2
Gouy, M.3
Daubin, V.4
-
16
-
-
38449096427
-
A model of horizontal gene transfer and the bacterial phylogeny problem
-
Galtier N. A model of horizontal gene transfer and the bacterial phylogeny problem. Systematic Biol 2007; 56(4):633-642; http://dx.doi.org/10.1080/10635150701546231
-
(2007)
Systematic Biol
, vol.56
, Issue.4
, pp. 633-642
-
-
Galtier, N.1
-
17
-
-
26444506791
-
Highways of gene sharing in prokaryotes
-
PMID:16176988
-
Beiko RG, Harlow TJ, Ragan MA. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA 2005; 102:14332-14337; PMID:16176988; http://dx.doi.org/10.1073/pnas.0504068102
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 14332-14337
-
-
Beiko, R.G.1
Harlow, T.J.2
Ragan, M.A.3
-
18
-
-
79952201675
-
The tree and net components of prokaryote evolution
-
Puigbo P, Wolf YI, Koonin EV. The tree and net components of prokaryote evolution. Genome Biol Evolution, 2010; 2:745-756; http://dx.doi.org/10.1093/gbe/evq062
-
(2010)
Genome Biol Evolution
, vol.2
, pp. 745-756
-
-
Puigbo, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
19
-
-
79959849261
-
Comparison of phylogenetic trees and search for a central trend in the forest of life
-
Koonin EV, Puigbo P, Wolf Y. Comparison of phylogenetic trees and search for a central trend in the forest of life. J Computational Biol 2011; 18(7):917-924; http://dx.doi.org/10.1089/cmb.2010.0185
-
(2011)
J Computational Biol
, vol.18
, Issue.7
, pp. 917-924
-
-
Koonin, E.V.1
Puigbo, P.2
Wolf, Y.3
-
20
-
-
0038222576
-
Discordant phylogenies within the rrn loci of rhizobia
-
PMID:12730157
-
van Berkum P, Terefework Z, Paulin L, Suomalainen S, Lindstrom K, Eardly BD. Discordant phylogenies within the rrn loci of rhizobia. J Bacteriol 2003; 185(10):2988-2998; PMID:12730157; http://dx.doi.org/10.1128/JB.185. 10.2988-2998.2003
-
(2003)
J Bacteriol
, vol.185
, Issue.10
, pp. 2988-2998
-
-
Van Berkum, P.1
Terefework, Z.2
Paulin, L.3
Suomalainen, S.4
Lindstrom, K.5
Eardly, B.D.6
-
21
-
-
0344666688
-
Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group
-
PMID:14645285
-
Schouls LM, Schot CS, Jacobs JA. Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. J Bacteriol 2003; 185(24):7241-7246; PMID:14645285; http://dx.doi.org/10.1128/JB.185.24.7241-7246.2003
-
(2003)
J Bacteriol
, vol.185
, Issue.24
, pp. 7241-7246
-
-
Schouls, L.M.1
Schot, C.S.2
Jacobs, J.A.3
-
22
-
-
24344510265
-
Discordant 16S and 23S rRNA gene phylogenies for the Genus Helicobacter: Implications for phylogenetic inference and systematics
-
PMID:16109952
-
Dewhirst FE, Shen Z, Scimeca MS, Stokes LN, Boumenna T, Chen T, Paster BJ, Fox JG. Discordant 16S and 23S rRNA gene phylogenies for the Genus Helicobacter: Implications for phylogenetic inference and systematics. J. Bacteriol 2005; 187(17):6106-6118; PMID:16109952; http://dx.doi.org/10.1128/JB.187.17. 6106-6118.2005
-
(2005)
J. Bacteriol
, vol.187
, Issue.17
, pp. 6106-6118
-
-
Dewhirst, F.E.1
Shen, Z.2
Scimeca, M.S.3
Stokes, L.N.4
Boumenna, T.5
Chen, T.6
Paster, B.J.7
Fox, J.G.8
-
23
-
-
38849112675
-
Genomic regulatory blocks underlie extensive microsynteny conservation in insects
-
PMID:17989259
-
Engstrm PG, Ho Sui SJ, Drivenes Y, Becker TS, Lenhard B. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res 2007; 17 (12):1898-1908; PMID:17989259; http://dx.doi.org/10.1101/gr.6669607
-
(2007)
Genome Res
, vol.17
, Issue.12
, pp. 1898-1908
-
-
Engstrm, P.G.1
Ho Sui, S.J.2
Drivenes, Y.3
Becker, T.S.4
Lenhard, B.5
-
24
-
-
0003307601
-
Genome rearrangement
-
Jiang T, Xu Y, Zhang M, editors, CRC Press 2002
-
Sanko D, El-Mabrouk N. Genome rearrangement. In Jiang T, Xu Y, Zhang M, editors, Current topics in computational molecular biology. CRC Press 2002
-
Current Topics in Computational Molecular Biology
-
-
Sanko, D.1
El-Mabrouk, N.2
-
25
-
-
58149492429
-
Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes
-
PMID:18978059
-
Novichkov PS, Wolf YI, Dubchak I, Koonin EV. Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol 2009; 191(1):65-73; PMID:18978059; http://dx.doi.org/10.1128/JB.01237-08
-
(2009)
J Bacteriol
, vol.191
, Issue.1
, pp. 65-73
-
-
Novichkov, P.S.1
Wolf, Y.I.2
Dubchak, I.3
Koonin, E.V.4
-
26
-
-
35349003200
-
Bacterial pathogenomics
-
PMID:17943120
-
Pallen MJ, Wren BW. Bacterial pathogenomics. Nature 2007; 449(7164):835-842; PMID:17943120; http://dx.doi.org/10.1038/nature06248
-
(2007)
Nature
, vol.449
, Issue.7164
, pp. 835-842
-
-
Pallen, M.J.1
Wren, B.W.2
-
27
-
-
0034680103
-
Pathogenic strategies of enteric bacteria
-
PMID:10963606
-
Donnenberg MS. Pathogenic strategies of enteric bacteria. Nature 2000; 406(6797):768-774; PMID:10963606; http://dx.doi.org/10.1038/35021212
-
(2000)
Nature
, vol.406
, Issue.6797
, pp. 768-774
-
-
Donnenberg, M.S.1
-
28
-
-
3042569657
-
Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli
-
PMID:15173110
-
Daubin V, Ochman H. Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli. Genome Res 2004; 14(6):1036-1042; PMID:15173110; http://dx.doi.org/10.1101/gr.2231904
-
(2004)
Genome Res
, vol.14
, Issue.6
, pp. 1036-1042
-
-
Daubin, V.1
Ochman, H.2
-
30
-
-
84895810887
-
Phylo si: A new genome-wide approach for prokaryotic phylogeny
-
PMID: 24243847
-
Shifman A, Ninyo N, Gophna U, Snir S. Phylo si: a new genome-wide approach for prokaryotic phylogeny. Nucleic Acids Res 2014; 42(4):2391-2404; PMID: 24243847; http://dx.doi.org/10.1093/nar/gkt1138
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.4
, pp. 2391-2404
-
-
Shifman, A.1
Ninyo, N.2
Gophna, U.3
Snir, S.4
-
31
-
-
84946092485
-
Detecting horizontal gene transfer between closely related taxa
-
Adato O, Ninyo N, Gophna U, Snir S. Detecting horizontal gene transfer between closely related taxa. Plos Comp Biol 2015; 11(10): e1004408; http://dx.doi.org/10.1371/journal.pcbi.1004408
-
(2015)
Plos Comp Biol
, vol.11
, Issue.10
-
-
Adato, O.1
Ninyo, N.2
Gophna, U.3
Snir, S.4
-
32
-
-
0026680446
-
Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome
-
PMID:1631158
-
Sanko D, Leduc G, Antoine N, Paquin B, Lang BF, Cedergren R. Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proc Natl Acad Sci 1992; 89(14):6575-6579; PMID:1631158; http://dx.doi.org/10.1073/pnas.89.14.6575
-
(1992)
Proc Natl Acad Sci
, vol.89
, Issue.14
, pp. 6575-6579
-
-
Sanko, D.1
Leduc, G.2
Antoine, N.3
Paquin, B.4
Lang, B.F.5
Cedergren, R.6
-
33
-
-
84957615807
-
Edit distance for genome comparison based on non-local operations
-
Apostolico A, Crochemore M, Galil Z, Manber U, editors, Springer Berlin Heidelberg
-
Sanko D. Edit distance for genome comparison based on non-local operations. In Apostolico A, Crochemore M, Galil Z, Manber U, editors, Combinatorial Pattern Matching, volume 644 of Lecture Notes in Computer Science, pages 121-135. Springer Berlin Heidelberg 1992
-
(1992)
Combinatorial Pattern Matching, Volume 644 of Lecture Notes in Computer Science
, pp. 121-135
-
-
Sanko, D.1
-
34
-
-
0002835359
-
Inversions in the chromosomes of drosophila pseudoobscura
-
PMID:17246876
-
Dobzhansky Th, Sturtevant AH. Inversions in the chromosomes of drosophila pseudoobscura. Genetics 1938; 23(1):28-64; PMID:17246876
-
(1938)
Genetics
, vol.23
, Issue.1
, pp. 28-64
-
-
Dobzhansky, T.1
Sturtevant, A.H.2
-
35
-
-
0000791476
-
Lengths of chromosomal segments conserved since divergence of man and mouse
-
PMID:6583681
-
Nadeau JH, Taylor BA. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc Natl Acad Sci 1984; 81(3):814-818; PMID:6583681; http://dx.doi.org/10.1073/pnas.81.3.814
-
(1984)
Proc Natl Acad Sci
, vol.81
, Issue.3
, pp. 814-818
-
-
Nadeau, J.H.1
Taylor, B.A.2
-
36
-
-
84957634698
-
Fast sorting by reversal
-
Hirschberg D, Myers G, editors, Springer Berlin Heidelberg
-
Piotr Berman and Hannenhalli, Sridhar. Fast sorting by reversal. In Hirschberg D, Myers G, editors, Combinatorial Pattern Matching, volume 1075 of Lecture Notes in Computer Science, pages 168-185. Springer Berlin Heidelberg, 1996
-
(1996)
Combinatorial Pattern Matching, Volume 1075 of Lecture Notes in Computer Science
, pp. 168-185
-
-
Berman, P.1
Hannenhalli, S.2
-
37
-
-
0030130366
-
Genome rearrangements and sorting by reversals
-
Bafnabackgroundand V, Pevzner PA. Genome rearrangements and sorting by reversals. SIAM J. Comput 1996; 25 (2):272-289
-
(1996)
SIAM J. Comput
, vol.25
, Issue.2
, pp. 272-289
-
-
Bafnabackgroundand, V.1
Pevzner, P.A.2
-
39
-
-
0029185212
-
Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement
-
PMID:NOT_FOUND
-
Kececioglu JD, Sanko D. Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. Algorithmica 1995; 13:180-210; PMID:NOT_FOUND; http://dx.doi.org/10.1007/BF01188586
-
(1995)
Algorithmica
, vol.13
, pp. 180-210
-
-
Kececioglu, J.D.1
Sanko, D.2
-
40
-
-
0035229986
-
New approaches for reconstructing phylogenies from gene order data
-
PMID:11473006
-
Moret BME, Wang LS, Warnow T, Wyman SK. New approaches for reconstructing phylogenies from gene order data. Bioinformatics 2001; 17(suppl 1):S165-S173; PMID:11473006; http://dx.doi.org/10.1093/bioinformatics/17.suppl_1.S165
-
(2001)
Bioinformatics
, vol.17
, pp. S165-S173
-
-
Moret, B.1
Wang, L.S.2
Warnow, T.3
Wyman, S.K.4
-
41
-
-
33845886105
-
Inferring phylogenetic networks by the maximum parsimony criterion: A case study
-
PMID: 17068107
-
Jin G, Nakhleh L, Snir S, Tuller T. Inferring phylogenetic networks by the maximum parsimony criterion: a case study. Mol Biol Evol 2007; 24(1):324-37; PMID: 17068107; http://dx.doi.org/10.1093/molbev/msl163
-
(2007)
Mol Biol Evol
, vol.24
, Issue.1
, pp. 324-337
-
-
Jin, G.1
Nakhleh, L.2
Snir, S.3
Tuller, T.4
-
42
-
-
0030994798
-
Amelioration of bacterial genomes: Rates of change and exchange
-
PMID:9089078
-
Lawrence JG, Ochman H. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997; 44(4):383-97; PMID:9089078; http://dx.doi.org/10.1007/PL00006158
-
(1997)
J Mol Evol
, vol.44
, Issue.4
, pp. 383-397
-
-
Lawrence, J.G.1
Ochman, H.2
-
43
-
-
3042849253
-
Biased biological functions of horizontally transferred genes in prokaryotic genomes
-
PMID:15208628
-
Nakamura Y, Itoh T, Matsuda H, Gojobori T. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 2004; 36(7):760-6; PMID:15208628; http://dx.doi.org/10.1038/ng1381
-
(2004)
Nat Genet
, vol.36
, Issue.7
, pp. 760-766
-
-
Nakamura, Y.1
Itoh, T.2
Matsuda, H.3
Gojobori, T.4
-
44
-
-
70349581783
-
On the need for widespread horizontal gene transfers under genome size constraint
-
PMID:19703318
-
Isambert H, Stein R. On the need for widespread horizontal gene transfers under genome size constraint. Biol Direct 2009; 4(1):28; PMID:19703318; http://dx.doi.org/10.1186/1745-6150-4-28
-
(2009)
Biol Direct
, vol.4
, Issue.1
, pp. 28
-
-
Isambert, H.1
Stein, R.2
-
45
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
PMID:3447015
-
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4(4):406-425; PMID:3447015
-
(1987)
Mol Biol Evol
, vol.4
, Issue.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
46
-
-
0000122573
-
PHYLIP-phylogenetic inference package, (Version 3.2)
-
Felsenstein J. PHYLIP-phylogenetic inference package, (version 3.2). Cladistics 1989; 5:164-166
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
48
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson DR, Foulds LR. Comparison of phylogenetic trees. Mathematical Biosci 1981; 53:131-147; http://dx.doi.org/10.1016/0025-5564(81)90043-2
-
(1981)
Mathematical Biosci
, vol.53
, pp. 131-147
-
-
Robinson, D.R.1
Foulds, L.R.2
-
49
-
-
0032900532
-
Genome phylogeny based on gene content
-
PMID:9916801
-
Snel B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nat Genet 1999; 21(1):108-110; PMID:9916801; http://dx.doi.org/10.1038/5052
-
(1999)
Nat Genet
, vol.21
, Issue.1
, pp. 108-110
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
50
-
-
0032568582
-
Measuring genome evolution
-
PMID:9600883
-
Huynen MA, Bork P. Measuring genome evolution. Proc Natl Acad Sci 1998; 95(11):5849-5856; PMID:9600883; http://dx.doi.org/10.1073/pnas.95.11.5849
-
(1998)
Proc Natl Acad Sci
, vol.95
, Issue.11
, pp. 5849-5856
-
-
Huynen, M.A.1
Bork, P.2
-
51
-
-
0036499057
-
Shot: A web server for the construction of genome phylogenies
-
Korbel JO, Snel B, Huynen MA, Bork P. Shot: a web server for the construction of genome phylogenies. Trends Genetics 2002; 18(3):158-62; http://dx.doi.org/10.1016/S0168-9525(01)02597-5
-
(2002)
Trends Genetics
, vol.18
, Issue.3
, pp. 158-162
-
-
Korbel, J.O.1
Snel, B.2
Huynen, M.A.3
Bork, P.4
-
52
-
-
13444306641
-
NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
PMID:15608248
-
Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucl Acids Res 2005; 33(suppl):D501-504; PMID:15608248
-
(2005)
Nucl Acids Res
, vol.33
, pp. D501-D504
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
53
-
-
14544295684
-
Weighted genome trees: Refinements and applications
-
PMID:15687194
-
Uri Gophna W. Ford Doolittle, and Robert L. Charlebois. Weighted genome trees: Refinements and applications. J Bacteriol 2005; 187(4):1305-16; PMID:15687194; http://dx.doi.org/10.1128/JB.187.4.1305-1316.2005
-
J Bacteriol 2005
, vol.187
, Issue.4
, pp. 1305-1316
-
-
Ford Doolittle, U.G.W.1
Charlebois, R.L.2
-
54
-
-
77951062024
-
Phylogeny of gammaproteobacteria
-
Williams KP, Gillespie JJ, Sobral BWS, Nordberg EK, Snyder EE, Shallom JM, Dickerman AW. Phylogeny of gammaproteobacteria. J Acteriol 2010; 192(9):2305-14; http://dx.doi.org/10.1128/JB.01480-09
-
(2010)
J Acteriol
, vol.192
, Issue.9
, pp. 2305-2314
-
-
Williams, K.P.1
Gillespie, J.J.2
Sobral, B.3
Nordberg, E.K.4
Snyder, E.E.5
Shallom, J.M.6
Dickerman, A.W.7
-
55
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
PMID:16513982
-
Ciccarelli FD, Doerks T, Von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 2006; 311(5765):1283-7; PMID:16513982; http://dx.doi.org/10.1126/science.1123061
-
(2006)
Science
, vol.311
, Issue.5765
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
Von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
56
-
-
58149200948
-
The ribosomal database project: Improved alignments and new tools for rrna analysis
-
PMID: 19004872
-
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, et al. The ribosomal database project: improved alignments and new tools for rrna analysis. Nucleic Acids Res 2009; 37(suppl 1):D141; PMID: 19004872
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
Fish, J.4
Chai, B.5
Farris, R.J.6
Kulam-Syed-Mohideen, A.S.7
McGarrell, D.M.8
Marsh, T.9
Garrity, G.M.10
-
57
-
-
84859242353
-
Phylogenomic analysis of bacterial and archaeal sequences with amphora2
-
PMID:22332237
-
Wu M, Alexandra J. Scott. Phylogenomic analysis of bacterial and archaeal sequences with amphora2. Bioinformatics 2012; 28(7):1033-4; PMID:22332237; http://dx.doi.org/10.1093/bioinformatics/bts079
-
(2012)
Bioinformatics
, vol.28
, Issue.7
, pp. 1033-1034
-
-
Wu, M.1
Scott, A.J.2
-
58
-
-
84959752542
-
Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units
-
Jorge FE. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. System Biol 1985; 34(2):193-200
-
(1985)
System Biol
, vol.34
, Issue.2
, pp. 193-200
-
-
Jorge, F.E.1
-
59
-
-
13944273799
-
The complete genome sequence of francisella tularensis, the causative agent of tularemia
-
PMID:15640799
-
Larsson P, Oyston PC, Chain P, Chu MC, Duffield M, Fuxelius HH, Garcia E, Hälltorp G, Johansson D, Isherwood KE, et al. The complete genome sequence of francisella tularensis, the causative agent of tularemia. Nat Genet 2005; 37(2):153-9; PMID:15640799; http://dx.doi.org/10.1038/ng1499
-
(2005)
Nat Genet
, vol.37
, Issue.2
, pp. 153-159
-
-
Larsson, P.1
Oyston, P.C.2
Chain, P.3
Chu, M.C.4
Duffield, M.5
Fuxelius, H.H.6
Garcia, E.7
Hälltorp, G.8
Johansson, D.9
Isherwood, K.E.10
-
60
-
-
34249944112
-
The orientia tsutsugamushi genome reveals massive proliferation of conjugative type iv secretion system and hostcell interaction genes
-
PMID:17483455
-
Cho NH, Kim HR, Lee JH, Kim SY, Kim J, Cha S, Kim SY, Darby AC, Fuxelius HH, Yin J, et al. The orientia tsutsugamushi genome reveals massive proliferation of conjugative type iv secretion system and hostcell interaction genes. Proc Natl Acad Sci 2007; 104 (19):7981-6; PMID:17483455; http://dx.doi.org/10.1073/pnas.0611553-104
-
(2007)
Proc Natl Acad Sci
, vol.104
, Issue.19
, pp. 7981-7986
-
-
Cho, N.H.1
Kim, H.R.2
Lee, J.H.3
Kim, S.Y.4
Kim, J.5
Cha, S.6
Kim, S.Y.7
Darby, A.C.8
Fuxelius, H.H.9
Yin, J.10
-
61
-
-
65249190698
-
Whole-genome-based phylogeny and divergence of the genus brucella
-
PMID:19201792
-
Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom-Sternberg JS, Chain PSG, Roberto FF, Hnath J, Brettin T, Keim P. Whole-genome-based phylogeny and divergence of the genus brucella. J Bacteriol 2009; 191(8):2864-2870; PMID:19201792; http://dx.doi.org/10.1128/JB.01581-08
-
(2009)
J Bacteriol
, vol.191
, Issue.8
, pp. 2864-2870
-
-
Foster, J.T.1
Beckstrom-Sternberg, S.M.2
Pearson, T.3
Beckstrom-Sternberg, J.S.4
Chain, P.5
Roberto, F.F.6
Hnath, J.7
Brettin, T.8
Keim, P.9
-
62
-
-
84870689997
-
Universal pacemaker of genome evolution
-
PMID:23209393
-
Snir S, Wolf YI, Koonin EV. Universal pacemaker of genome evolution. PLoS Comput Biol 2012; 8(11): e1002785; PMID:23209393; http://dx.doi.org/10.1371/journal.pcbi.1002785
-
(2012)
Plos Comput Biol
, vol.8
, Issue.11
-
-
Snir, S.1
Wolf, Y.I.2
Koonin, E.V.3
-
63
-
-
84872619745
-
Evolution: Genomic pacemakers or ticking clocks?
-
PMID:23247404
-
Muers M. Evolution: Genomic pacemakers or ticking clocks?. Nat Rev Genet 2013; 14:81; PMID:23247404; http://dx.doi.org/10.1038/nrg3410
-
(2013)
Nat Rev Genet
, vol.14
, pp. 81
-
-
Muers, M.1
-
64
-
-
84891687862
-
Stability along with extreme variability in core genome evolution
-
PMID:23821522
-
Wolf YI, Snir S, Koonin EV. Stability along with extreme variability in core genome evolution. Genome Biol Evol 2013; 5(7):1393-402; PMID:23821522; http://dx.doi.org/10.1093/gbe/evt098
-
(2013)
Genome Biol Evol
, vol.5
, Issue.7
, pp. 1393-1402
-
-
Wolf, Y.I.1
Snir, S.2
Koonin, E.V.3
-
65
-
-
56949097722
-
Evolution of genome architecture
-
Molecular and Cellular Evolution: A Celebration of the 200th Anniversary of the Birth of Charles Darwin
-
Koonin EV. Evolution of genome architecture. Int J Biochem Cell Biol 2009; 41(2):298-306. Molecular and Cellular Evolution: A Celebration of the 200th Anniversary of the Birth of Charles Darwin
-
(2009)
Int J Biochem Cell Biol
, vol.41
, Issue.2
, pp. 298-306
-
-
Koonin, E.V.1
-
66
-
-
0030038509
-
Majority-rule reduced consensus trees and their use in bootstrapping
-
Wilkinson M. Majority-rule reduced consensus trees and their use in bootstrapping. Mol Biol Evolution 1996; 13 (3):437-44; http://dx.doi.org/10.1093/oxfordjournals.molbev.a025604
-
(1996)
Mol Biol Evolution
, vol.13
, Issue.3
, pp. 437-444
-
-
Wilkinson, M.1
-
67
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
PMID:11125040
-
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucl Acids Res 2001; 29(1):22-8; PMID:11125040; http://dx.doi.org/10.1093/nar/29.1.22
-
(2001)
Nucl Acids Res
, vol.29
, Issue.1
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
68
-
-
38549177928
-
EggNOG: Automated construction and annotation of orthologous groups of genes
-
Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. eggNOG: automated construction and annotation of orthologous groups of genes. Nucl Acids Res 2008; 36(suppl):D250-254
-
(2008)
Nucl Acids Res
, vol.36
, pp. D250-D254
-
-
Jensen, L.J.1
Julien, P.2
Kuhn, M.3
Von Mering, C.4
Muller, J.5
Doerks, T.6
Bork, P.7
|