-
1
-
-
2942534292
-
LGL: creating a map of protein function with an algorithm for visualizing very large biological networks
-
Adai AT, Date SV, Wieland S, Marcotte EM (2004) LGL: creating a map of protein function with an algorithm for visualizing very large biological networks. J Mol Biol 340(1): 179-190.
-
(2004)
J Mol Biol
, vol.340
, Issue.1
, pp. 179-190
-
-
Adai, A.T.1
Date, S.V.2
Wieland, S.3
Marcotte, E.M.4
-
2
-
-
78650789727
-
Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets
-
Alperovitch-Lavy A, Sharon I, Rohwer F, Aro EM, Glaser F, Milo R, Nelson N, Beja O (2011) Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets. Environ Microbiol 13(1): 24-32.
-
(2011)
Environ Microbiol
, vol.13
, Issue.1
, pp. 24-32
-
-
Alperovitch-Lavy, A.1
Sharon, I.2
Rohwer, F.3
Aro, E.M.4
Glaser, F.5
Milo, R.6
Nelson, N.7
Beja, O.8
-
3
-
-
77956011404
-
On the need for integrative Phylogenomics, and some steps toward its creation
-
Bapteste E, Burian RM (2010) On the need for integrative Phylogenomics, and some steps toward its creation. Biol Philos 25: 711-736.
-
(2010)
Biol Philos
, vol.25
, pp. 711-736
-
-
Bapteste, E.1
Burian, R.M.2
-
4
-
-
38349128272
-
Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny
-
Bapteste E, Susko E, Leigh J, Ruiz-Trillo I, Bucknam J, Doolittle WF (2008) Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol Biol Evol 25(1): 83-91.
-
(2008)
Mol Biol Evol
, vol.25
, Issue.1
, pp. 83-91
-
-
Bapteste, E.1
Susko, E.2
Leigh, J.3
Ruiz-Trillo, I.4
Bucknam, J.5
Doolittle, W.F.6
-
5
-
-
70449515444
-
Prokaryotic evolution and the tree of life are two different things
-
Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct 4: 34.
-
(2009)
Biol Direct
, vol.4
, pp. 34
-
-
Bapteste, E.1
O'Malley, M.A.2
Beiko, R.G.3
Ereshefsky, M.4
Gogarten, J.P.5
Franklin-Hall, L.6
Lapointe, F.J.7
Dupré, J.8
Dagan, T.9
Boucher, Y.10
Martin, W.11
-
6
-
-
84860155555
-
Philosophy and evolution: minding the gap between evolutionary patterns and tree-like patterns
-
In: Anisimova M (ed), Humana Press, New York
-
Bapteste E, Burian RM, Bouchard F (2012) Philosophy and evolution: minding the gap between evolutionary patterns and tree-like patterns. In: Anisimova M (ed) Evolutionary genomics: statistical and computational methods, vol 2. Humana Press, New York, pp 81-110.
-
(2012)
Evolutionary genomics: Statistical and computational methods
, vol.2
, pp. 81-110
-
-
Bapteste, E.1
Burian, R.M.2
Bouchard, F.3
-
7
-
-
84868599126
-
Evolutionary analyses of non-genealogical bonds produced by introgressive descent
-
doi: 10. 1073/pnas. 1206541109
-
Bapteste E, Lopez P, Bouchard F, Baquero F, McInerney JO, Burian RM (2012) Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proc Natl Acad Sci USA. doi: 10. 1073/pnas. 1206541109.
-
(2012)
Proc Natl Acad Sci USA
-
-
Bapteste, E.1
Lopez, P.2
Bouchard, F.3
Baquero, F.4
McInerney, J.O.5
Burian, R.M.6
-
8
-
-
79960445478
-
The 2010 Garrod Lecture: the dimensions of evolution in antibiotic resistance: ex unibus plurum et ex pluribus unum
-
Baquero F (2011) The 2010 Garrod Lecture: the dimensions of evolution in antibiotic resistance: ex unibus plurum et ex pluribus unum. J Antimicrob Chemother 66(8): 1659-1672.
-
(2011)
J Antimicrob Chemother
, vol.66
, Issue.8
, pp. 1659-1672
-
-
Baquero, F.1
-
9
-
-
79960563690
-
Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli
-
Beauregard-Racine J, Bicep C, Schliep K, Lopez P, Lapointe FJ, Bapteste E (2011) Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli. Biol Direct 6(1): 39.
-
(2011)
Biol Direct
, vol.6
, Issue.1
, pp. 39
-
-
Beauregard-Racine, J.1
Bicep, C.2
Schliep, K.3
Lopez, P.4
Lapointe, F.J.5
Bapteste, E.6
-
10
-
-
80054090399
-
Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011
-
Bezuidt O, Pierneef R, Mncube K, Lima-Mendez G, Reva ON (2011) Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104: H4 in Germany in 2011. PLoS ONE 6(10): e25702.
-
(2011)
PLoS ONE
, vol.6
, Issue.10
-
-
Bezuidt, O.1
Pierneef, R.2
Mncube, K.3
Lima-Mendez, G.4
Reva, O.N.5
-
11
-
-
84859510055
-
Roles for intrinsic disorder and fuzziness in generating context-specific function in Ultrabithorax, a Hox transcription factor
-
Bondos SE, Hsiao HC (2012) Roles for intrinsic disorder and fuzziness in generating context-specific function in Ultrabithorax, a Hox transcription factor. Adv Exp Med Biol 725: 86-105.
-
(2012)
Adv Exp Med Biol
, vol.725
, pp. 86-105
-
-
Bondos, S.E.1
Hsiao, H.C.2
-
12
-
-
77956013078
-
Symbiosis, lateral function transfer and the (many) saplings of life
-
Bouchard F (2010) Symbiosis, lateral function transfer and the (many) saplings of life. Biol Philos 25(4): 623-641.
-
(2010)
Biol Philos
, vol.25
, Issue.4
, pp. 623-641
-
-
Bouchard, F.1
-
15
-
-
10944248427
-
Computing prokaryotic gene ubiquity: rescuing the core from extinction
-
Charlebois RL, Doolittle WF (2004) Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res 14(12): 2469-2477.
-
(2004)
Genome Res
, vol.14
, Issue.12
, pp. 2469-2477
-
-
Charlebois, R.L.1
Doolittle, W.F.2
-
17
-
-
33750810896
-
The tree of one percent
-
Dagan T, Martin W (2006) The tree of one percent. Genome Biol 7(10): 118.
-
(2006)
Genome Biol
, vol.7
, Issue.10
, pp. 118
-
-
Dagan, T.1
Martin, W.2
-
18
-
-
48249151749
-
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution
-
Dagan T, Artzy-Randrup Y, Martin W (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci USA 105(29): 10039-10044.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.29
, pp. 10039-10044
-
-
Dagan, T.1
Artzy-Randrup, Y.2
Martin, W.3
-
19
-
-
84879295485
-
The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new killer bugs are created because of a sympatric lifestyle
-
doi: 10. 1093/molbev/mss236
-
Diene SM, Merhej V, Henry M, El Filali A, Roux V, Robert C, Azza S, Gavory F, Barbe V, La Scola B, Raoult D, Rolain JM (2012) The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new killer bugs are created because of a sympatric lifestyle. Mol Biol Evol. doi: 10. 1093/molbev/mss236.
-
(2012)
Mol Biol Evol
-
-
Diene, S.M.1
Merhej, V.2
Henry, M.3
El Filali, A.4
Roux, V.5
Robert, C.6
Azza, S.7
Gavory, F.8
Barbe, V.9
La Scola, B.10
Raoult, D.11
Rolain, J.M.12
-
20
-
-
41649109613
-
Functional metagenomic profiling of nine biomes
-
Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F (2008) Functional metagenomic profiling of nine biomes. Nature 452(7187): 629-632.
-
(2008)
Nature
, vol.452
, Issue.7187
, pp. 629-632
-
-
Dinsdale, E.A.1
Edwards, R.A.2
Hall, D.3
Angly, F.4
Breitbart, M.5
Brulc, J.M.6
Furlan, M.7
Desnues, C.8
Haynes, M.9
Li, L.10
McDaniel, L.11
Moran, M.A.12
Nelson, K.E.13
Nilsson, C.14
Olson, R.15
Paul, J.16
Brito, B.R.17
Ruan, Y.18
Swan, B.K.19
Stevens, R.20
Valentine, D.L.21
Thurber, R.V.22
Wegley, L.23
White, B.A.24
Rohwer, F.25
more..
-
21
-
-
66049089612
-
On the origin of prokaryotic species
-
Doolittle WF, Zhaxybayeva O (2009) On the origin of prokaryotic species. Genome Res 19(5): 744-756.
-
(2009)
Genome Res
, vol.19
, Issue.5
, pp. 744-756
-
-
Doolittle, W.F.1
Zhaxybayeva, O.2
-
22
-
-
33645961876
-
DNA mimicry by proteins
-
Dryden DT, Tock MR (2006) DNA mimicry by proteins. Biochem Soc Trans 34(Pt 2): 317-319.
-
(2006)
Biochem Soc Trans
, vol.34
, Issue.Pt 2
, pp. 317-319
-
-
Dryden, D.T.1
Tock, M.R.2
-
23
-
-
79958763366
-
50 ways to build a spindle: the complexity of microtubule generation during mitosis
-
Duncan T, Wakefield JG (2011) 50 ways to build a spindle: the complexity of microtubule generation during mitosis. Chromosome Res 19(3): 321-333.
-
(2011)
Chromosome Res
, vol.19
, Issue.3
, pp. 321-333
-
-
Duncan, T.1
Wakefield, J.G.2
-
25
-
-
77951765145
-
Varieties of living things: life at the intersection of lineage and metabolism
-
Dupré J, O'Malley MA (2009) Varieties of living things: life at the intersection of lineage and metabolism. Philosophy and Theory in Biology 1: e003.
-
(2009)
Philosophy and Theory in Biology
, vol.1
-
-
Dupré, J.1
O'Malley, M.A.2
-
27
-
-
84874555810
-
Biological individuality: the case of biofilms
-
doi: 10. 1007/s10539-012-9340-4
-
Ereshefsky M, Pedroso M (2012) Biological individuality: the case of biofilms. Biol Philos. doi: 10. 1007/s10539-012-9340-4.
-
(2012)
Biol Philos
-
-
Ereshefsky, M.1
Pedroso, M.2
-
28
-
-
44449137093
-
The microbial engines that drive earth's biogeochemical cycles
-
Falkowski PG, Fenchel T, Delong EF (2008) The microbial engines that drive earth's biogeochemical cycles. Science 320(5879): 1034-1039.
-
(2008)
Science
, vol.320
, Issue.5879
, pp. 1034-1039
-
-
Falkowski, P.G.1
Fenchel, T.2
Delong, E.F.3
-
29
-
-
78650051417
-
The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks
-
Fondi M, Fani R (2010) The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks. Environ Microbiol 12(12): 3228-3242.
-
(2010)
Environ Microbiol
, vol.12
, Issue.12
, pp. 3228-3242
-
-
Fondi, M.1
Fani, R.2
-
30
-
-
77951767484
-
Defining life: the virus viewpoint
-
Forterre P (2010) Defining life: the virus viewpoint. Orig Life Evol Biosph 40(2): 151-160.
-
(2010)
Orig Life Evol Biosph
, vol.40
, Issue.2
, pp. 151-160
-
-
Forterre, P.1
-
31
-
-
23944437942
-
Opinion: re-evaluating prokaryotic species
-
Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, van de Peer Y, Vandamme P, Thompson FL, Swings J (2005) Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3(9): 733-739.
-
(2005)
Nat Rev Microbiol
, vol.3
, Issue.9
, pp. 733-739
-
-
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
Swings, J.11
-
32
-
-
0035954733
-
Natural conjugative plasmids induce bacterial biofilm development
-
Ghigo JM (2001) Natural conjugative plasmids induce bacterial biofilm development. Nature 412(6845): 442-445.
-
(2001)
Nature
, vol.412
, Issue.6845
, pp. 442-445
-
-
Ghigo, J.M.1
-
34
-
-
84856011484
-
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
-
Greenblum S, Turnbaugh PJ, Borenstein E (2012) Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci USA 109(2): 594-599.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.2
, pp. 594-599
-
-
Greenblum, S.1
Turnbaugh, P.J.2
Borenstein, E.3
-
35
-
-
77955795400
-
Uniting sex and eukaryote origins in an emerging oxygenic world
-
Gross J, Bhattacharya D (2010) Uniting sex and eukaryote origins in an emerging oxygenic world. Biol Direct 5: 53.
-
(2010)
Biol Direct
, vol.5
, pp. 53
-
-
Gross, J.1
Bhattacharya, D.2
-
36
-
-
36148972811
-
Trouble with lichen: the re-evaluation and re-interpretation of thallus form and fruit body types in the molecular era
-
Grube M, Hawksworth DL (2007) Trouble with lichen: the re-evaluation and re-interpretation of thallus form and fruit body types in the molecular era. Mycol Res 111(Pt 9): 1116-1132.
-
(2007)
Mycol Res
, vol.111
, Issue.Pt 9
, pp. 1116-1132
-
-
Grube, M.1
Hawksworth, D.L.2
-
37
-
-
34547754024
-
Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates
-
Hackett JD, Yoon HS, Li S, Reyes-Prieto A, Rummele SE, Bhattacharya D (2007) Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol Biol Evol 24(8): 1702-1713.
-
(2007)
Mol Biol Evol
, vol.24
, Issue.8
, pp. 1702-1713
-
-
Hackett, J.D.1
Yoon, H.S.2
Li, S.3
Reyes-Prieto, A.4
Rummele, S.E.5
Bhattacharya, D.6
-
38
-
-
1842612577
-
Bacterial biofilms: from the natural environment to infectious diseases
-
Hall-Stoodley L, Costerton JW, Stoodley P (2004) Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol 2(2): 95-108.
-
(2004)
Nat Rev Microbiol
, vol.2
, Issue.2
, pp. 95-108
-
-
Hall-Stoodley, L.1
Costerton, J.W.2
Stoodley, P.3
-
39
-
-
49149113206
-
Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution
-
Hatfull GF, Cresawn SG, Hendrix RW (2008) Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution. Res Microbiol 159(5): 332-339.
-
(2008)
Res Microbiol
, vol.159
, Issue.5
, pp. 332-339
-
-
Hatfull, G.F.1
Cresawn, S.G.2
Hendrix, R.W.3
-
40
-
-
66649092982
-
Carrying photosynthesis genes increases ecological fitness of cyanophage in silico
-
Hellweger FL (2009) Carrying photosynthesis genes increases ecological fitness of cyanophage in silico. Environ Microbiol 11(6): 1386-1394.
-
(2009)
Environ Microbiol
, vol.11
, Issue.6
, pp. 1386-1394
-
-
Hellweger, F.L.1
-
41
-
-
84880153102
-
Bacterial moonlighting proteins and bacterial virulence
-
doi:10.1007/82_2011_188
-
Henderson B, Martin A (2011) Bacterial moonlighting proteins and bacterial virulence. Curr Top Microbiol Immunol. doi: 10. 1007/82_2011_188.
-
(2011)
Curr Top Microbiol Immunol
-
-
Henderson, B.1
Martin, A.2
-
42
-
-
78049425463
-
Evidence of selection upon genomic GC-content in bacteria
-
Hildebrand F, Meyer A, Eyre-Walker A (2010) Evidence of selection upon genomic GC-content in bacteria. PLoS Genet 6(9): e1001107.
-
(2010)
PLoS Genet
, vol.6
, Issue.9
-
-
Hildebrand, F.1
Meyer, A.2
Eyre-Walker, A.3
-
43
-
-
77950369259
-
Moonlighting proteins: an intriguing mode of multitasking
-
Huberts DH, van der Klei IJ (2010) Moonlighting proteins: an intriguing mode of multitasking. Biochim Biophys Acta 1803(4): 520-525.
-
(2010)
Biochim Biophys Acta
, vol.1803
, Issue.4
, pp. 520-525
-
-
Huberts, D.H.1
van der Klei, I.J.2
-
45
-
-
84859474080
-
Insights into the bovine rumen plasmidome
-
Kav AB, Sasson G, Jami E, Doron-Faigenboim A, Benhar I, Mizrahi I (2012) Insights into the bovine rumen plasmidome. Proc Natl Acad Sci USA 109(14): 5452-5457.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.14
, pp. 5452-5457
-
-
Kav, A.B.1
Sasson, G.2
Jami, E.3
Doron-Faigenboim, A.4
Benhar, I.5
Mizrahi, I.6
-
46
-
-
78751527447
-
Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths
-
Kloesges T, Popa O, Martin W, Dagan T (2011) Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol 28(2): 1057-1074.
-
(2011)
Mol Biol Evol
, vol.28
, Issue.2
, pp. 1057-1074
-
-
Kloesges, T.1
Popa, O.2
Martin, W.3
Dagan, T.4
-
47
-
-
66249130020
-
A unified hydrophobicity scale for multispan membrane proteins
-
Koehler J, Woetzel N, Staritzbichler R, Sanders CR, Meiler J (2009) A unified hydrophobicity scale for multispan membrane proteins. Proteins 76(1): 13-29.
-
(2009)
Proteins
, vol.76
, Issue.1
, pp. 13-29
-
-
Koehler, J.1
Woetzel, N.2
Staritzbichler, R.3
Sanders, C.R.4
Meiler, J.5
-
48
-
-
27744591844
-
On the origin of genomes and cells within inorganic compartments
-
Koonin EV, Martin W (2005) On the origin of genomes and cells within inorganic compartments. Trends Genet 21(12): 647-654.
-
(2005)
Trends Genet
, vol.21
, Issue.12
, pp. 647-654
-
-
Koonin, E.V.1
Martin, W.2
-
49
-
-
43049085945
-
The eukaryotic tree of life: endosymbiosis takes its TOL
-
Lane CE, Archibald JM (2008) The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol Evol 23(5): 268-275.
-
(2008)
Trends Ecol Evol
, vol.23
, Issue.5
, pp. 268-275
-
-
Lane, C.E.1
Archibald, J.M.2
-
50
-
-
77955410887
-
The myth of bacterial species and speciation
-
Lawrence JG, Retchless AC (2010) The myth of bacterial species and speciation. Biol Philos 25: 569-588.
-
(2010)
Biol Philos
, vol.25
, pp. 569-588
-
-
Lawrence, J.G.1
Retchless, A.C.2
-
51
-
-
3042581065
-
The strategy of model-building in population biology
-
1st edn., E. Sober (Ed.), Cambridge: MIT Press
-
Levins R (1984) The strategy of model-building in population biology. In: Sober E (ed) Conceptual issues in evolutionary biology, 1st edn. MIT Press, Cambridge, pp 18-27.
-
(1984)
Conceptual Issues in Evolutionary Biology
, pp. 18-27
-
-
Levins, R.1
-
52
-
-
40849126681
-
Reticulate representation of evolutionary and functional relationships between phage genomes
-
Lima-Mendez G, van Helden J, Toussaint A, Leplae R (2008) Reticulate representation of evolutionary and functional relationships between phage genomes. Mol Biol Evol 25(4): 762-777.
-
(2008)
Mol Biol Evol
, vol.25
, Issue.4
, pp. 762-777
-
-
Lima-Mendez, G.1
van Helden, J.2
Toussaint, A.3
Leplae, R.4
-
53
-
-
61849126837
-
Molecular phylogeny: reconstructing the forest
-
Lopez P, Bapteste E (2009) Molecular phylogeny: reconstructing the forest. C R Biol 332(2-3): 171-182.
-
(2009)
C R Biol
, vol.332
, Issue.2-3
, pp. 171-182
-
-
Lopez, P.1
Bapteste, E.2
-
54
-
-
54449097150
-
The convergence of carbohydrate active gene repertoires in human gut microbes
-
Lozupone CA, Hamady M, Cantarel BL, Coutinho PM, Henrissat B, Gordon JI, Knight R (2008) The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci USA 105(39): 15076-15081.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.39
, pp. 15076-15081
-
-
Lozupone, C.A.1
Hamady, M.2
Cantarel, B.L.3
Coutinho, P.M.4
Henrissat, B.5
Gordon, J.I.6
Knight, R.7
-
55
-
-
78149470831
-
Comparison of 61 sequenced Escherichia coli genomes
-
Lukjancenko O, Wassenaar TM, Ussery DW (2010) Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol 60(4): 708-720.
-
(2010)
Microb Ecol
, vol.60
, Issue.4
, pp. 708-720
-
-
Lukjancenko, O.1
Wassenaar, T.M.2
Ussery, D.W.3
-
56
-
-
84863496231
-
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
-
The Heliconius Genome Consortium, (published online) doi: 10. 1038/nature11041
-
Mallet J, The Heliconius Genome Consortium (2012). Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature (published online) doi: 10. 1038/nature11041.
-
(2012)
Nature
-
-
Mallet, J.1
-
57
-
-
84862777909
-
Suppression of the antiviral response by an influenza histone mimic
-
Marazzi I, Ho JS, Kim J, Manicassamy B, Dewell S, Albrecht RA, Seibert CW, Schaefer U, Jeffrey KL, Prinjha RK, Lee K, Garcia-Sastre A, Roeder RG, Tarakhovsky A (2012) Suppression of the antiviral response by an influenza histone mimic. Nature 483(7390): 428-433.
-
(2012)
Nature
, vol.483
, Issue.7390
, pp. 428-433
-
-
Marazzi, I.1
Ho, J.S.2
Kim, J.3
Manicassamy, B.4
Dewell, S.5
Albrecht, R.A.6
Seibert, C.W.7
Schaefer, U.8
Jeffrey, K.L.9
Prinjha, R.K.10
Lee, K.11
Garcia-Sastre, A.12
Roeder, R.G.13
Tarakhovsky, A.14
-
58
-
-
33645456207
-
Eukaryotic evolution, changes and challenges
-
Martin W, Embley TM (2006) Eukaryotic evolution, changes and challenges. Nature 430: 623-630.
-
(2006)
Nature
, vol.430
, pp. 623-630
-
-
Martin, W.1
Embley, T.M.2
-
59
-
-
2642689666
-
The hydrogen hypothesis for the first eukaryote
-
Martin W, Müller M (1998) The hydrogen hypothesis for the first eukaryote. Nature 392(6671): 37-41.
-
(1998)
Nature
, vol.392
, Issue.6671
, pp. 37-41
-
-
Martin, W.1
Müller, M.2
-
61
-
-
69849087746
-
Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance
-
McMahon SA, Roberts GA, Johnson KA, Cooper LP, Liu H, White JH, Carter LG, Sanghvi B, Oke M, Walkinshaw MD, Blakely GW, Naismith JH, Dryden DT (2009) Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance. Nucleic Acids Res 37(15): 4887-4897.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.15
, pp. 4887-4897
-
-
McMahon, S.A.1
Roberts, G.A.2
Johnson, K.A.3
Cooper, L.P.4
Liu, H.5
White, J.H.6
Carter, L.G.7
Sanghvi, B.8
Oke, M.9
Walkinshaw, M.D.10
Blakely, G.W.11
Naismith, J.H.12
Dryden, D.T.13
-
62
-
-
27444438599
-
The microbial pan-genome
-
Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15(6): 589-594.
-
(2005)
Curr Opin Genet Dev
, vol.15
, Issue.6
, pp. 589-594
-
-
Medini, D.1
Donati, C.2
Tettelin, H.3
Masignani, V.4
Rappuoli, R.5
-
64
-
-
80052310753
-
How many species are there on Earth and in the ocean?
-
Mora C, Tittensor DP, Adl S, Simpson AG, Worm B (2011) How many species are there on Earth and in the ocean? PLoS Biol 9(8): e1001127.
-
(2011)
PLoS Biol
, vol.9
, Issue.8
-
-
Mora, C.1
Tittensor, D.P.2
Adl, S.3
Simpson, A.G.4
Worm, B.5
-
65
-
-
0031735879
-
Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis
-
Moreira D, Lopez-Garcia P (1998) Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J Mol Evol 47(5): 517-530.
-
(1998)
J Mol Evol
, vol.47
, Issue.5
, pp. 517-530
-
-
Moreira, D.1
Lopez-Garcia, P.2
-
66
-
-
67649998350
-
Genomic footprints of a cryptic plastid endosymbiosis in diatoms
-
Moustafa A, Beszteri B, Maier UG, Bowler C, Valentin K, Bhattacharya D (2009) Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 324(5935): 1724-1726.
-
(2009)
Science
, vol.324
, Issue.5935
, pp. 1724-1726
-
-
Moustafa, A.1
Beszteri, B.2
Maier, U.G.3
Bowler, C.4
Valentin, K.5
Bhattacharya, D.6
-
68
-
-
50149083715
-
Everything is everywhere: but the environment selects': ubiquitous distribution and ecological determinism in microbial biogeography
-
O'Malley MA (2008) 'Everything is everywhere: but the environment selects': ubiquitous distribution and ecological determinism in microbial biogeography. Stud Hist Philos Biol Biomed Sci 39(3): 314-325.
-
(2008)
Stud Hist Philos Biol Biomed Sci
, vol.39
, Issue.3
, pp. 314-325
-
-
O'Malley, M.A.1
-
69
-
-
34047190388
-
Size doesn't matter: towards a more inclusive philosophy of biology
-
O'Malley MA, Dupré J (2007) Size doesn't matter: towards a more inclusive philosophy of biology. Biol Philos 22: 155-191.
-
(2007)
Biol Philos
, vol.22
, pp. 155-191
-
-
O'Malley, M.A.1
Dupré, J.2
-
70
-
-
77955504696
-
The phototrophic consortium "Chlorochromatium aggregatum"-a model for bacterial heterologous multicellularity
-
Overmann J (2010) The phototrophic consortium "Chlorochromatium aggregatum"-a model for bacterial heterologous multicellularity. Adv Exp Med Biol 675: 15-29.
-
(2010)
Adv Exp Med Biol
, vol.675
, pp. 15-29
-
-
Overmann, J.1
-
71
-
-
79953315166
-
Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes
-
Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T (2011) Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21(4): 599-609.
-
(2011)
Genome Res
, vol.21
, Issue.4
, pp. 599-609
-
-
Popa, O.1
Hazkani-Covo, E.2
Landan, G.3
Martin, W.4
Dagan, T.5
-
72
-
-
79952201675
-
The tree and net components of prokaryote evolution
-
Puigbo 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
-
-
Puigbo, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
73
-
-
51449108782
-
Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome
-
Qu A, Brulc JM, Wilson MK, Law BF, Theoret JR, Joens LA, Konkel ME, Angly F, Dinsdale EA, Edwards RA, Nelson KE, White BA (2008) Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS ONE 3(8): e2945.
-
(2008)
PLoS ONE
, vol.3
, Issue.8
-
-
Qu, A.1
Brulc, J.M.2
Wilson, M.K.3
Law, B.F.4
Theoret, J.R.5
Joens, L.A.6
Konkel, M.E.7
Angly, F.8
Dinsdale, E.A.9
Edwards, R.A.10
Nelson, K.E.11
White, B.A.12
-
74
-
-
33646539782
-
Synergistic effects in mixed Escherichia coli biofilms: conjugative plasmid transfer drives biofilm expansion
-
Reisner A, Holler BM, Molin S, Zechner EL (2006) Synergistic effects in mixed Escherichia coli biofilms: conjugative plasmid transfer drives biofilm expansion. J Bacteriol 188(10): 3582-3588.
-
(2006)
J Bacteriol
, vol.188
, Issue.10
, pp. 3582-3588
-
-
Reisner, A.1
Holler, B.M.2
Molin, S.3
Zechner, E.L.4
-
75
-
-
35348890199
-
Bacterial DNA repair by non-homologous end joining
-
Shuman S, Glickman MS (2007) Bacterial DNA repair by non-homologous end joining. Nat Rev Microbiol 5(11): 852-861.
-
(2007)
Nat Rev Microbiol
, vol.5
, Issue.11
, pp. 852-861
-
-
Shuman, S.1
Glickman, M.S.2
-
76
-
-
79960313230
-
Lateral genetic transfer and the construction of genetic exchange communities
-
Skippington E, Ragan MA (2011a) Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol Rev 35(5): 707-735.
-
(2011)
FEMS Microbiol Rev
, vol.35
, Issue.5
, pp. 707-735
-
-
Skippington, E.1
Ragan, M.A.2
-
77
-
-
80054976329
-
Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella
-
Skippington E, Ragan MA (2011b) Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella. BMC Genomics 29(12): 532.
-
(2011)
BMC Genomics
, vol.29
, Issue.12
, pp. 532
-
-
Skippington, E.1
Ragan, M.A.2
-
78
-
-
84863227681
-
Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella a genomes
-
Skippington E, Ragan MA (2012) Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella a genomes. Genome Biol Evol. 4(3): 330-345.
-
(2012)
Genome Biol Evol.
, vol.4
, Issue.3
, pp. 330-345
-
-
Skippington, E.1
Ragan, M.A.2
-
79
-
-
83055186603
-
Ecology drives a global network of gene exchange connecting the human microbiome
-
Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480: 241-244.
-
(2011)
Nature
, vol.480
, pp. 241-244
-
-
Smillie, C.S.1
Smith, M.B.2
Friedman, J.3
Cordero, O.X.4
David, L.A.5
Alm, E.J.6
-
80
-
-
36249021315
-
Genome-wide experimental determination of barriers to horizontal gene transfer
-
Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318(5855): 1449-1452.
-
(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
-
81
-
-
0036097343
-
Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A
-
Sullivan JT, Trzebiatowski JR, Cruickshank RW, Gouzy J, Brown SD, Elliot RM, Fleetwood DJ, McCallum NG, Rossbach U, Stuart GS, Weaver JE, Webby RJ, De Bruijn FJ, Ronson CW (2002) Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J Bacteriol 184(11): 3086-3095.
-
(2002)
J Bacteriol
, vol.184
, Issue.11
, pp. 3086-3095
-
-
Sullivan, J.T.1
Trzebiatowski, J.R.2
Cruickshank, R.W.3
Gouzy, J.4
Brown, S.D.5
Elliot, R.M.6
Fleetwood, D.J.7
McCallum, N.G.8
Rossbach, U.9
Stuart, G.S.10
Weaver, J.E.11
Webby, R.J.12
de Bruijn, F.J.13
Ronson, C.W.14
-
82
-
-
33747369803
-
Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts
-
Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW (2006) Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol 4(8): e234.
-
(2006)
PLoS Biol
, vol.4
, Issue.8
-
-
Sullivan, M.B.1
Lindell, D.2
Lee, J.A.3
Thompson, L.R.4
Bielawski, J.P.5
Chisholm, S.W.6
-
84
-
-
0035162592
-
The COG database: new developments in phylogenetic classification of proteins from complete genomes
-
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29(1): 22-28.
-
(2001)
Nucleic 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
-
85
-
-
33845895973
-
Self-splicing of a group IIC intron: 5′ exon recognition and alternative 5′ splicing events implicate the stem-loop motif of a transcriptional terminator
-
Toor N, Robart AR, Christianson J, Zimmerly S (2006) Self-splicing of a group IIC intron: 5′ exon recognition and alternative 5′ splicing events implicate the stem-loop motif of a transcriptional terminator. Nucleic Acids Res 34(22): 6461-6471.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.22
, pp. 6461-6471
-
-
Toor, N.1
Robart, A.R.2
Christianson, J.3
Zimmerly, S.4
-
86
-
-
68049117072
-
Persistence pays: how viruses promote host group survival
-
Villarreal LP (2009) Persistence pays: how viruses promote host group survival. Curr Opin Microbiol 12(4): 467-472.
-
(2009)
Curr Opin Microbiol
, vol.12
, Issue.4
, pp. 467-472
-
-
Villarreal, L.P.1
-
87
-
-
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, Devine KM, Bowater RP, Jeggo PA, Jackson SP, Doherty AJ (2002) Identification of a DNA nonhomologous end-joining complex in bacteria. Science 297(5587): 1686-1689.
-
(2002)
Science
, vol.297
, Issue.5587
, 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
Devine, K.M.11
Bowater, R.P.12
Jeggo, P.A.13
Jackson, S.P.14
Doherty, A.J.15
-
89
-
-
0025019643
-
Evolutionary questions: the "progenote"
-
Woese CR (1990) Evolutionary questions: the "progenote". Science 247(4944): 789.
-
(1990)
Science
, vol.247
, Issue.4944
, pp. 789
-
-
Woese, C.R.1
-
91
-
-
0032028624
-
On the best evolutionary rate for phylogenetic analysis
-
Yang Z (1998) On the best evolutionary rate for phylogenetic analysis. Syst Biol 47(1): 125-133.
-
(1998)
Syst Biol
, vol.47
, Issue.1
, pp. 125-133
-
-
Yang, Z.1
-
92
-
-
0028797990
-
DNA mimics a self-protein that may be a target for some anti-DNA antibodies in systemic lupus erythematosus
-
Zack DJ, Yamamoto K, Wong AL, Stempniak M, French C, Weisbart RH (1995) DNA mimics a self-protein that may be a target for some anti-DNA antibodies in systemic lupus erythematosus. J Immunol 154(4): 1987-1994.
-
(1995)
J Immunol
, vol.154
, Issue.4
, pp. 1987-1994
-
-
Zack, D.J.1
Yamamoto, K.2
Wong, A.L.3
Stempniak, M.4
French, C.5
Weisbart, R.H.6
-
93
-
-
65249126970
-
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales
-
Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbo CL, Doolittle WF, Gogarten JP, Noll KM (2009) On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci USA 106(14): 5865-5870.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.14
, pp. 5865-5870
-
-
Zhaxybayeva, O.1
Swithers, K.S.2
Lapierre, P.3
Fournier, G.P.4
Bickhart, D.M.5
DeBoy, R.T.6
Nelson, K.E.7
Nesbo, C.L.8
Doolittle, W.F.9
Gogarten, J.P.10
Noll, K.M.11
|