-
1
-
-
59149102602
-
Phylogenetic and functional assessment of orthologs inference projects and methods
-
doi: 10.1371/journal.pcbi.1000262
-
Altenhoff AM, Dessimoz C. 2009. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 5: e1000262. doi: 10.1371/journal.pcbi.1000262.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Altenhoff, A.M.1
Dessimoz, C.2
-
2
-
-
0034889360
-
Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system
-
DOI 10.1101/gr.181001
-
Aravind L, Koonin EV. 2001. Prokaryotic homologs of the eukaryotic DNA-end- binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Genome Res 11: 1365-1374. (Pubitemid 32771543)
-
(2001)
Genome Research
, vol.11
, Issue.8
, pp. 1365-1374
-
-
Aravind, L.1
Koonin, E.V.2
-
3
-
-
0342521525
-
Scale-free characteristics of random networks: The topology of the World-Wide Web
-
Barabási AL, Albert R, Jeong H. 2000. Scale-free characteristics of random networks: the topology of the World-Wide Web. Physica A 281: 69-77.
-
(2000)
Physica A
, vol.281
, pp. 69-77
-
-
Barabási, A.L.1
Albert, R.2
Jeong, H.3
-
4
-
-
3242881500
-
The cellular response to general and programmed DNA double strand breaks
-
DOI 10.1016/j.dnarep.2004.06.001, PII S1568786404001752
-
Bassing CH, Alt FW. 2004. The cellular response to general and programmed DNA double strand breaks. DNA Repair 3: 781-796. (Pubitemid 38997922)
-
(2004)
DNA Repair
, vol.3
, Issue.8-9
, pp. 781-796
-
-
Bassing, C.H.1
Alt, F.W.2
-
5
-
-
0001677717
-
Controlling the false discovery rate - A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Roy Stat Soc B Met 57: 289-300.
-
(1995)
J Roy Stat Soc B Met
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
6
-
-
77954238817
-
A global network of coexisting microbes from environmental and whole-genome sequence data
-
Chaffron S, Rehrauer H, Pernthaler J, von Mering C. 2010. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res 20: 947-959.
-
(2010)
Genome Res
, vol.20
, pp. 947-959
-
-
Chaffron, S.1
Rehrauer, H.2
Pernthaler, J.3
Von Mering, C.4
-
8
-
-
3042596928
-
DNA uptake during bacterial transformation
-
DOI 10.1038/nrmicro844
-
Chen I, Dubnau D. 2004. DNA uptake during bacterial transformation. Nat Rev Microbiol 2: 241-249. (Pubitemid 39490085)
-
(2004)
Nature Reviews Microbiology
, vol.2
, Issue.3
, pp. 241-249
-
-
Chen, I.1
Dubnau, D.2
-
9
-
-
28544449319
-
The ins and outs of DNA transfer in bacteria
-
DOI 10.1126/science.1114021
-
Chen I, Christie PJ, Dubnau D. 2005. The ins and outs of DNA transfer in bacteria. Science 310: 1456-1460. (Pubitemid 41746335)
-
(2005)
Science
, vol.310
, Issue.5753
, pp. 1456-1460
-
-
Chen, I.1
Christie, P.J.2
Dubnau, D.3
-
10
-
-
34248396432
-
Global extent of horizontal gene transfer
-
Choi IG, Kim SH. 2007. Global extent of horizontal gene transfer. Proc Natl Acad Sci 104: 4489-4494.
-
(2007)
Proc Natl Acad Sci
, vol.104
, pp. 4489-4494
-
-
Choi, I.G.1
Kim, S.H.2
-
11
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al. 2007. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382.
-
(2007)
Nat Protoc
, vol.2
, pp. 2366-2382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
Kuchinsky, A.4
Landys, N.5
Workman, C.6
Christmas, R.7
Avila-Campilo, I.8
Creech, M.9
Gross, B.10
-
13
-
-
40149095640
-
The impact of horizontal gene transfer in shaping operons and protein interaction networks-direct evidence of preferential attachment
-
doi: 10.1186/1471-2148-8-23
-
Davids W, Zhang Z. 2008. The impact of horizontal gene transfer in shaping operons and protein interaction networks-direct evidence of preferential attachment. BMCEvol Biol 8: 23. doi: 10.1186/1471-2148-8-23.
-
(2008)
BMCEvol Biol
, vol.8
, pp. 23
-
-
Davids, W.1
Zhang, Z.2
-
14
-
-
0035988323
-
The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea
-
Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Baumer S, Jacobi C, et al. 2002. The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4: 453-461. (Pubitemid 34784706)
-
(2002)
Journal of Molecular Microbiology and Biotechnology
, vol.4
, Issue.4
, pp. 453-461
-
-
Deppenmeier, U.1
Johann, A.2
Hartsch, T.3
Merkl, R.4
Schmitz, R.A.5
Martinez-Arias, R.6
Henne, A.7
Wiezer, A.8
Baumer, S.9
Jacobi, C.10
Bruggemann, H.11
Lienard, T.12
Christmann, A.13
Bomeke, M.14
Steckel, S.15
Bhattacharyya, A.16
Lykidis, A.17
Overbeek, R.18
Klenk, H.-P.19
Gunsalus, R.P.20
Fritz, H.-J.21
Gottschalk, G.22
more..
-
15
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284: 2124-2129.
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
16
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1584. (Pubitemid 34679732)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
17
-
-
33746531322
-
Genome of Rice Cluster I archaea-the key methane producers in the rice rhizosphere
-
Erkel C, Kube M, Reinhardt R, Liesack W. 2006. Genome of Rice Cluster I archaea-the key methane producers in the rice rhizosphere. Science 313: 370-372.
-
(2006)
Science
, vol.313
, pp. 370-372
-
-
Erkel, C.1
Kube, M.2
Reinhardt, R.3
Liesack, W.4
-
18
-
-
0003437299
-
-
Department of Genome Sciences, University of Washington, Seattle, WA
-
Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package). Department of Genome Sciences, University of Washington, Seattle, WA.
-
(2005)
PHYLIP (Phylogeny Inference Package)
-
-
Felsenstein, J.1
-
20
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
Garcia-Vallve S, Romeu A, Palau J. 2000. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res 10: 1719-1725.
-
(2000)
Genome Res
, vol.10
, pp. 1719-1725
-
-
Garcia-Vallve, S.1
Romeu, A.2
Palau, J.3
-
21
-
-
79953316801
-
-
Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, et al. 2005.
-
(2005)
-
-
Gevers, D.1
Cohan, F.M.2
Lawrence, J.G.3
Spratt, B.G.4
Coenye, T.5
Feil, E.J.6
Stackebrandt, E.7
Van De Peer, Y.8
Vandamme, P.9
Thompson, F.L.10
-
22
-
-
23944437942
-
Opinion: Re-evaluating prokaryotic species
-
Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol 3: 733-739.
-
Nat Rev Microbiol
, vol.3
, pp. 733-739
-
-
-
24
-
-
0030606233
-
Pathogenicity islands: Bacterial evolution in quantum leaps
-
DOI 10.1016/S0092-8674(00)81985-6
-
Groisman EA, Ochman H. 1996. Pathogenicity islands: Bacterial evolution in quantum leaps. Cell 87: 791-794. (Pubitemid 26404277)
-
(1996)
Cell
, vol.87
, Issue.5
, pp. 791-794
-
-
Groisman, E.A.1
Ochman, H.2
-
25
-
-
0242578620
-
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
-
DOI 10.1080/10635150390235520
-
Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704. (Pubitemid 37365050)
-
(2003)
Systematic Biology
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
26
-
-
55449085777
-
Numt-mediated double-strand break repair mitigates deletions during primate genome evolution
-
doi: 10.1371/journal.pgen.1000237
-
Hazkani-Covo E, Covo S. 2008. Numt-mediated double-strand break repair mitigates deletions during primate genome evolution. PLoS Genet 4: e1000237. doi: 10.1371/journal.pgen.1000237.
-
(2008)
PLoS Genet
, vol.4
-
-
Hazkani-Covo, E.1
Covo, S.2
-
27
-
-
5444244948
-
Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov
-
DOI 10.1099/ijs.0.02958-0
-
Holmes DE, Nevin KP, Lovley DR. 2004. Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov. Int J Syst Evol Microbiol 54: 1591-1599. (Pubitemid 39359973)
-
(2004)
International Journal of Systematic and Evolutionary Microbiology
, vol.54
, Issue.5
, pp. 1591-1599
-
-
Holmes, D.E.1
Nevin, K.P.2
Lovley, D.R.3
-
29
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL. 2000. The large-scale organization of metabolic networks. Nature 407: 651-654.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabási, A.L.5
-
30
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
doi: 10.1186/gb-2004-5-2-r12
-
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. 2004. Versatile and open software for comparing large genomes. Genome Biol 5: R12. doi: 10.1186/gb-2004-5-2-r12.
-
(2004)
Genome Biol
, vol.5
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
Salzberg, S.L.7
-
31
-
-
33846659065
-
Importance of widespread gene transfer agent genes in alpha-proteobacteria
-
DOI 10.1016/j.tim.2006.12.001, PII S0966842X06002757
-
Lang AS, Beatty JT. 2007. Importance of widespread gene transfer agent genes in alpha-proteobacteria. Trends Microbiol 15: 54-62. (Pubitemid 46199186)
-
(2007)
Trends in Microbiology
, vol.15
, Issue.2
, pp. 54-62
-
-
Lang, A.S.1
Beatty, J.T.2
-
32
-
-
41449087415
-
Community structure in directed networks
-
doi: 10.1103/PhysRevLett.100.118703
-
Leicht EA, Newman ME. 2008. Community structure in directed networks. Phys Rev Lett 100: 118703. doi: 10.1103/PhysRevLett.100.118703.
-
(2008)
Phys Rev Lett
, vol.100
, pp. 118703
-
-
Leicht, E.A.1
Newman, M.E.2
-
33
-
-
3242879122
-
The mechanism of vertebrate nonhomologous DNA end joining and its role in V(D)J recombination
-
DOI 10.1016/j.dnarep.2004.03.015, PII S1568786404000746
-
Lieber MR, Ma Y, Pannicke U, Schwarz K. 2004. The mechanism of vertebrate nonhomologous DNA end joining and its role in V(D)J recombination. DNA Repair 3: 817-826. (Pubitemid 39004089)
-
(2004)
DNA Repair
, vol.3
, Issue.8-9
, pp. 817-826
-
-
Lieber, M.R.1
Ma, Y.2
Pannicke, U.3
Schwarz, K.4
-
34
-
-
0034856864
-
Capture of DNA sequences at double-strand breaks in mammalian chromosomes
-
Lin Y, Waldman AS. 2001a. Capture of DNA sequences at double-strand breaks in mammalian chromosomes. Genetics 158: 1665-1674. (Pubitemid 32783147)
-
(2001)
Genetics
, vol.158
, Issue.4
, pp. 1665-1674
-
-
Lin, Y.1
Waldman, A.S.2
-
35
-
-
0035476653
-
Promiscuous patching of broken chromosomes in mammalian cells with extrachromosomal DNA
-
Lin Y, Waldman AS. 2001b. Promiscuous patching of broken chromosomes in mammalian cells with extrachromosomal DNA. Nucleic Acids Res 29: 3975-3981. (Pubitemid 32962687)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.19
, pp. 3975-3981
-
-
Lin, Y.1
Waldman, A.S.2
-
36
-
-
0036193882
-
Crossing over between regions of limited homology in Escherichia coli. RecA-dependent and RecA-independent pathways
-
Lovett ST, Hurley RL, Sutera VA Jr, Aubuchon RH, Lebedeva MA. 2002. Crossing over between regions of limited homology in Escherichia coli. RecA-dependent and RecA-independent pathways. Genetics 160: 851-859.
-
(2002)
Genetics
, vol.160
, pp. 851-859
-
-
Lovett, S.T.1
Hurley, R.L.2
Sutera Jr., V.A.3
Aubuchon, R.H.4
Lebedeva, M.A.5
-
37
-
-
0031930791
-
The effect of mismatch repair and heteroduplex formation on sexual isolation in Bacillus
-
Majewski J, Cohan FM. 1998. The effect of mismatch repair and heteroduplex formation on sexual isolation in Bacillus. Genetics 148: 13-18. (Pubitemid 28063472)
-
(1998)
Genetics
, vol.148
, Issue.1
, pp. 13-18
-
-
Majewski, J.1
Cohan, F.M.2
-
38
-
-
0032709783
-
DNA sequence similarity requirements for interspecific recombination in Bacillus
-
Majewski J, Cohan FM. 1999. DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 153: 1525-1533.
-
(1999)
Genetics
, vol.153
, pp. 1525-1533
-
-
Majewski, J.1
Cohan, F.M.2
-
39
-
-
33745112085
-
Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli
-
doi: 10.1186/fb-2006-7-5-r44
-
Mau B, Glasner JD, Darling AE, Perna NT. 2006. Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol 7: R44. doi: 10.1186/fb-2006-7-5-r44.
-
(2006)
Genome Biol
, vol.7
-
-
Mau, B.1
Glasner, J.D.2
Darling, A.E.3
Perna, N.T.4
-
40
-
-
4944262629
-
Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes
-
DOI 10.1093/molbev/msh202
-
Medrano-Soto A, Moreno-Hagelsieb G, Vinuesa P, Christen JA, Collado- Vides J. 2004. Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes. Mol Biol Evol 21: 1884-1894. (Pubitemid 39331635)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.10
, pp. 1884-1894
-
-
Medrano-Soto, A.1
Moreno-Hagelsieb, G.2
Vinuesa, P.3
Christen, J.A.4
Collado-Vides, J.5
-
41
-
-
0025133386
-
Molecular evolution of the Escherichia Coli Chromosome. 3. Clonal frames
-
Milkman R, Bridges MM. 1990. Molecular evolution of the Escherichia Coli Chromosome. 3. Clonal frames. Genetics 126: 505-517.
-
(1990)
Genetics
, vol.126
, pp. 505-517
-
-
Milkman, R.1
Bridges, M.M.2
-
42
-
-
29144485325
-
The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea
-
DOI 10.1073/pnas.0509073102
-
Mongodin EF, Nelson KE, Daugherty S, DeBoy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Perez GS, et al. 2005. The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc Natl Acad Sci 102: 18147-18152. (Pubitemid 41798516)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.50
, pp. 18147-18152
-
-
Mongodin, E.F.1
Nelson, K.E.2
Daugherty, S.3
DeBoy, R.T.4
Wister, J.5
Khouri, H.6
Weidman, J.7
Walsh, D.A.8
Papke, R.T.9
Perez, G.S.10
Sharma, A.K.11
Nesbo, C.L.12
MacLeod, D.13
Bapteste, E.14
Doolittle, W.F.15
Charlebois, R.L.16
Legault, B.17
Rodriguez-Valera, F.18
-
43
-
-
0029970701
-
Capture of retrotransposon DNA at the sites of chromosomal double- Strand breaks
-
DOI 10.1038/383644a0
-
Moore JK, Haber JE. 1996. Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature 383: 644-646. (Pubitemid 26347590)
-
(1996)
Nature
, vol.383
, Issue.6601
, pp. 644-646
-
-
Moore, J.K.1
Haber, J.E.2
-
44
-
-
0037040394
-
Microbial minimalism: Genome reduction in bacterial pathogens
-
DOI 10.1016/S0092-8674(02)00665-7
-
Moran NA. 2002. Microbial minimalism: Genome reduction in bacterial pathogens. Cell 108: 583-586. (Pubitemid 34241418)
-
(2002)
Cell
, vol.108
, Issue.5
, pp. 583-586
-
-
Moran, N.A.1
-
45
-
-
33747876810
-
Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium
-
DOI 10.1099/ijs.0.64308-0
-
Muller D, Simeonova DD, Riegel P, Mangenot S, Koechler S, Lievremont D, Bertin PN, Lett MC. 2006. Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium. Int J Syst Evol Microbiol 56: 1765-1769. (Pubitemid 44288396)
-
(2006)
International Journal of Systematic and Evolutionary Microbiology
, vol.56
, Issue.8
, pp. 1765-1769
-
-
Muller, D.1
Simeonova, D.D.2
Riegel, P.3
Mangenot, S.4
Koechler, S.5
Lievremont, D.6
Bertin, P.N.7
Lett, M.-C.8
-
46
-
-
34247589893
-
A tale of two oxidation states: Bacterial colonization of arsenic-rich environments
-
doi: 10.1371/journal.pgen.0030053
-
Muller D, Medigue C, Koechler S, Barbe V, Barakat M, Talla E, Bonnefoy V, Krin E, Arsene-Ploetze F, Carapito C, et al. 2007. A tale of two oxidation states: Bacterial colonization of arsenic-rich environments. PLoS Genet 3: e53. doi: 10.1371/journal.pgen.0030053.
-
(2007)
PLoS Genet
, vol.3
-
-
Muller, D.1
Medigue, C.2
Koechler, S.3
Barbe, V.4
Barakat, M.5
Talla, E.6
Bonnefoy, V.7
Krin, E.8
Arsene-Ploetze, F.9
Carapito, C.10
-
47
-
-
0038054338
-
AAV serotype 2 vectors preferentially integrate into active genes in mice
-
DOI 10.1038/ng1179
-
Nakai H, Montini E, Fuess S, Storm TA, Grompe M, Kay MA. 2003. AAV serotype 2 vectors preferentially integrate into active genes in mice. Nat Genet 34: 297-302. (Pubitemid 36792862)
-
(2003)
Nature Genetics
, vol.34
, Issue.3
, pp. 297-302
-
-
Nakai, H.1
Montini, E.2
Fuess, S.3
Storm, T.A.4
Grompe, M.5
Kay, M.A.6
-
48
-
-
3042849253
-
Biased biological functions of horizontally-transferred genes in prokaryotic genomes
-
DOI 10.1038/ng1381
-
Nakamura Y, Itoh T, Matsuda H, Gojobori T. 2004. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36: 760-766. (Pubitemid 38886640)
-
(2004)
Nature Genetics
, vol.36
, Issue.7
, pp. 760-766
-
-
Nakamura, Y.1
Itoh, T.2
Matsuda, H.3
Gojobori, T.4
-
49
-
-
0022507362
-
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
-
Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426. (Pubitemid 16010523)
-
(1986)
Molecular Biology and Evolution
, vol.3
, Issue.5
, pp. 418-426
-
-
Nei, M.1
Gojobori, T.2
-
50
-
-
0033609333
-
Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima
-
DOI 10.1038/20601
-
Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson LD, Nelson WC, Ketchum KA, et al. 1999. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399: 323-329. (Pubitemid 29318123)
-
(1999)
Nature
, vol.399
, Issue.6734
, pp. 323-329
-
-
Nelson, K.E.1
Clayton, R.A.2
Gill, S.R.3
Gwinn, M.L.4
Dodson, R.J.5
Haft, D.H.6
Hickey, E.K.7
Peterson, J.D.8
Nelson, W.C.9
Ketchum, K.A.10
McDonald, L.11
Utterback, T.R.12
Malek, J.A.13
Linher, K.D.14
Garrett, M.M.15
Stewart, A.M.16
Cotton, M.D.17
Pratt, M.S.18
Phillips, C.A.19
Richardson, D.20
Heidelberg, J.21
Sutton, G.G.22
Fleischmann, R.D.23
Eisen, J.A.24
White, O.25
Salzberg, S.L.26
Smith, H.O.27
Venter, J.C.28
Fraser, C.M.29
more..
-
51
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
DOI 10.1038/35012500
-
Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304. (Pubitemid 30337055)
-
(2000)
Nature
, vol.405
, Issue.6784
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Grolsman, E.A.3
-
52
-
-
20444504323
-
Uncovering the overlapping community structure of complex networks in nature and society
-
DOI 10.1038/nature03607
-
Palla G, Derenyi I, Farkas I, Vicsek T. 2005. Uncovering the overlapping community structure of complex networks in nature and society. Nature 435: 814-818. (Pubitemid 40839731)
-
(2005)
Nature
, vol.435
, Issue.7043
, pp. 814-818
-
-
Palla, G.1
Derenyi, I.2
Farkas, I.3
Vicsek, T.4
-
53
-
-
34247223815
-
Quantifying social group evolution
-
DOI 10.1038/nature05670, PII NATURE05670
-
Palla G, Barabási AL, Vicsek T. 2007. Quantifying social group evolution. Nature 446: 664-667. (Pubitemid 46606882)
-
(2007)
Nature
, vol.446
, Issue.7136
, pp. 664-667
-
-
Palla, G.1
Barabasi, A.-L.2
Vicsek, T.3
-
54
-
-
67650601963
-
Evolution of transcriptional regulatory circuits in bacteria
-
Perez JC, Groisman EA. 2009. Evolution of transcriptional regulatory circuits in bacteria. Cell 138: 233-244.
-
(2009)
Cell
, vol.138
, pp. 233-244
-
-
Perez, J.C.1
Groisman, E.A.2
-
55
-
-
79952201675
-
The tree and net components of prokaryote evolution
-
Puigbò P, Wolf YI, Koonin EV. 2010. The tree and net components of prokaryote evolution. Genome Biol Evol 2: 745-756.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 745-756
-
-
Puigbò, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
56
-
-
30344471824
-
Do different surrogate methods detect lateral genetic transfer events of different relative ages?
-
Ragan MA, Harlow TJ, Beiko RG. 2006. Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends Microbiol 14: 4-8.
-
(2006)
Trends Microbiol
, vol.14
, pp. 4-8
-
-
Ragan, M.A.1
Harlow, T.J.2
Beiko, R.G.3
-
57
-
-
70350150370
-
Sexual isolation in Acinetobacter baylyi is locus-specific and varies 10,000-fold over the genome
-
Ray JL, Harms K, Wikmark OG, Starikova I, Johnsen PJ, Nielsen KM. 2009. Sexual isolation in Acinetobacter baylyi is locus-specific and varies 10,000-fold over the genome. Genetics 182: 1165-1181.
-
(2009)
Genetics
, vol.182
, pp. 1165-1181
-
-
Ray, J.L.1
Harms, K.2
Wikmark, O.G.3
Starikova, I.4
Johnsen, P.J.5
Nielsen, K.M.6
-
58
-
-
0033523903
-
Mitochondrial DNA repairs doublestrand breaks in yeast chromosomes
-
Ricchetti M, Fairhead C, Dujon B. 1999. Mitochondrial DNA repairs doublestrand breaks in yeast chromosomes. Nature 402: 96-100.
-
(1999)
Nature
, vol.402
, pp. 96-100
-
-
Ricchetti, M.1
Fairhead, C.2
Dujon, B.3
-
59
-
-
73149098333
-
Shifting the genomic gold standard for the prokaryotic species definition
-
Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 106: 19126-19131.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 19126-19131
-
-
Richter, M.1
Rosselló-Móra, R.2
-
60
-
-
0042878464
-
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation
-
DOI 10.1038/nature01947
-
Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, et al. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047. (Pubitemid 37064302)
-
(2003)
Nature
, vol.424
, Issue.6952
, pp. 1042-1047
-
-
Rocap, G.1
Larimer, F.W.2
Lamerdin, J.3
Malfatti, S.4
Chain, P.5
Ahlgren, N.A.6
Arellano, A.7
Coleman, M.8
Hauser, L.9
Hess, W.R.10
Johnson, Z.I.11
Land, M.12
Lindell, D.13
Post, A.F.14
Regala, W.15
Shah, M.16
Shaw, S.L.17
Steglich, C.18
Sullivan, M.B.19
Ting, C.S.20
Tolonen, A.21
Webb, E.A.22
Zinser, E.R.23
Chisholm, S.W.24
more..
-
61
-
-
29144529892
-
Horizontal transfer of bacterial symbionts: Heritability and fitness effects in a novel aphid host
-
DOI 10.1128/AEM.71.12.7987-7994.2005
-
Russell JA, Moran NA. 2005. Horizontal transfer of bacterial symbionts: Heritability and fitness effects in a novel aphid host. Appl Environ Microbiol 71: 7987-7994. (Pubitemid 41803920)
-
(2005)
Applied and Environmental Microbiology
, vol.71
, Issue.12
, pp. 7987-7994
-
-
Russell, J.A.1
Moran, N.A.2
-
62
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
63
-
-
0038220925
-
The ars detoxification system is advantageous but not required for As(V) respiration by the genetically tractable Shewanella species strain ANA-3
-
DOI 10.1128/AEM.69.5.2800-2809.2003
-
Saltikov CW, Cifuentes A, Venkateswaran K, Newman DK. 2003. The ars detoxification system is advantageous but not required for As(V) respiration by the genetically tractable Shewanella species strain ANA-3. Appl Environ Microbiol 69: 2800-2809. (Pubitemid 36560359)
-
(2003)
Applied and Environmental Microbiology
, vol.69
, Issue.5
, pp. 2800-2809
-
-
Saltikov, C.W.1
Cifuentes, A.2
Venkateswaran, K.3
Newman, D.K.4
-
64
-
-
0034059439
-
An alpha-proteobacterium converts linear alkylbenzenesulfonate surfactants into sulfophenylcarboxylates and linear alkyldiphenyletherdisulfonate surfactants into sulfodiphenylethercarboxylates
-
DOI 10.1128/AEM.66.5.1911-1916.2000
-
Schleheck D, Dong WB, Denger K, Heinzle E, Cook AM. 2000. An alpha-proteobacterium converts linear alkylbenzenesulfonate surfactants into sulfophenylcarboxylates and linear alkyldiphenyletherdisulfonate surfactants into sulfodiphenylethercarboxylates. Appl Environ Microbiol 66: 1911-1916. (Pubitemid 30253710)
-
(2000)
Applied and Environmental Microbiology
, vol.66
, Issue.5
, pp. 1911-1916
-
-
Schleheck, D.1
Dong, W.2
Denger, K.3
Heinzle, E.4
Cook, A.M.5
-
65
-
-
35348890199
-
Bacterial DNA repair by non-homologous end joining
-
DOI 10.1038/nrmicro1768, PII NRMICRO1768
-
Shuman S, Glickman MS. 2007. Bacterial DNA repair by non-homologous end joining. Nat Rev Microbiol 5: 852-861. (Pubitemid 47578386)
-
(2007)
Nature Reviews Microbiology
, vol.5
, Issue.11
, pp. 852-861
-
-
Shuman, S.1
Glickman, M.S.2
-
66
-
-
36249021315
-
Genome-wide experimental determination of barriers to horizontal gene transfer
-
DOI 10.1126/science.1147112
-
Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM. 2007. Genomewide experimental determination of barriers to horizontal gene transfer. Science 318: 1449-1452. (Pubitemid 350208955)
-
(2007)
Science
, vol.318
, Issue.5855
, pp. 1449-1452
-
-
Sorek, R.1
Zhu, Y.2
Creevey, C.J.3
Francino, M.P.4
Bork, P.5
Rubin, E.M.6
-
67
-
-
0041375471
-
Cyanophages infecting the oceanic cyanobacterium Prochlorococcus
-
DOI 10.1038/nature01929
-
Sullivan MB, Waterbury JB, Chisholm SW. 2003. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 424: 1047-1051. (Pubitemid 37064303)
-
(2003)
Nature
, vol.424
, Issue.6952
, pp. 1047-1051
-
-
Sullivan, M.B.1
Waterbury, J.B.2
Chisholm, S.W.3
-
68
-
-
34548648702
-
Role of phages in the pathogenesis of Burkholderia, or 'Where are the toxin genes in Burkholderia phages?'
-
Summer EJ, Gill JJ, Upton C, Gonzalez CF, Young R. 2007. Role of phages in the pathogenesis of Burkholderia, or 'Where are the toxin genes in Burkholderia phages?' Curr Opin Microbiol 10: 410-417.
-
(2007)
Curr Opin Microbiol
, vol.10
, pp. 410-417
-
-
Summer, E.J.1
Gill, J.J.2
Upton, C.3
Gonzalez, C.F.4
Young, R.5
-
69
-
-
33747847779
-
PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
-
DOI 10.1093/nar/gkl315
-
Suyama M, Torrents D, Bork P. 2006. PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34: W609-W612. (Pubitemid 44529842)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.WEB. SERV. ISS
-
-
Suyama, M.1
Torrents, D.2
Bork, P.3
-
70
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
doi: 10.1186/1471-2105-4-41
-
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. 2003. The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4: 41. doi: 10.1186/1471-2105-4-41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
Krylov, D.M.7
Mazumder, R.8
Mekhedov, S.L.9
Nikolskaya, A.N.10
-
71
-
-
23944475626
-
Mechanisms of, and barriers to, horizontal gene transfer between bacteria
-
DOI 10.1038/nrmicro1234
-
Thomas CM, Nielsen KM. 2005. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3: 711-721. (Pubitemid 41195087)
-
(2005)
Nature Reviews Microbiology
, vol.3
, Issue.9
, pp. 711-721
-
-
Thomas, C.M.1
Nielsen, K.M.2
-
72
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ. 1994. Clustal-W - Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680. (Pubitemid 24354800)
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
73
-
-
77950348609
-
Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures
-
Tsang JS, Ebert MS, van Oudenaarden A. 2010. Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol Cell 38: 140-153.
-
(2010)
Mol Cell
, vol.38
, pp. 140-153
-
-
Tsang, J.S.1
Ebert, M.S.2
Van Oudenaarden, A.3
-
74
-
-
36549000721
-
Metagenomic and functional analysis of hindgut microbiota of a woodfeeding higher termite
-
Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, et al. 2007. Metagenomic and functional analysis of hindgut microbiota of a woodfeeding higher termite. Nature 450: 560-565.
-
(2007)
Nature
, vol.450
, pp. 560-565
-
-
Warnecke, F.1
Luginbuhl, P.2
Ivanova, N.3
Ghassemian, M.4
Richardson, T.H.5
Stege, J.T.6
Cayouette, M.7
McHardy, A.C.8
Djordjevic, G.9
Aboushadi, N.10
-
75
-
-
0037031655
-
Identification of a DNA nonhomologous end-joining complex in bacteria
-
Weller GR, Kysela B, Roy R, Tonkin LM, Scanlan E, Della M, Devine SK, Day JP, Wilkinson A, d'Adda di Fagagna F, et al. 2002. Identification of a DNA nonhomologous end-joining complex in bacteria. Science 297: 1686-1689.
-
(2002)
Science
, vol.297
, pp. 1686-1689
-
-
Weller, G.R.1
Kysela, B.2
Roy, R.3
Tonkin, L.M.4
Scanlan, E.5
Della, M.6
Devine, S.K.7
Day, J.P.8
Wilkinson, A.9
D'Adda Di Fagagna, F.10
-
76
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
DOI 10.1093/molbev/msm088
-
Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591. (Pubitemid 47236688)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1586-1591
-
-
Yang, Z.1
-
77
-
-
33745972964
-
Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis
-
doi: 10.1186/1471-2180-6-46
-
Yu Y, Kim HS, Chua HH, Lin CH, Sim SH, Lin D, Derr A, Engels R, DeShazer D, Birren B, et al. 2006. Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis. BMC Microbiol 6: 46. doi: 10.1186/1471-2180-6-46.
-
(2006)
BMC Microbiol
, vol.6
, pp. 46
-
-
Yu, Y.1
Kim, H.S.2
Chua, H.H.3
Lin, C.H.4
Sim, S.H.5
Lin, D.6
Derr, A.7
Engels, R.8
DeShazer, D.9
Birren, B.10
|