-
1
-
-
0030801002
-
Gapped blast and psi-blast: A new generation of protein database search programs
-
Altschul SF, et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
2
-
-
0036673472
-
Automated de novo identification of repeat sequence families in sequenced genomes
-
Bao Z, Eddy SR (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12: 1269-1276.
-
(2002)
Genome Res.
, vol.12
, pp. 1269-1276
-
-
Bao, Z.1
Eddy, S.R.2
-
3
-
-
77954790368
-
Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of sodalis glossinidius, the secondary endosymbiont of tsetse flies
-
Belda E, Moya A, Bentley S, Silva FJ (2010) Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies. BMC Genomics 11: 449.
-
(2010)
BMC Genomics
, vol.11
, pp. 449
-
-
Belda, E.1
Moya, A.2
Bentley, S.3
Silva, F.J.4
-
4
-
-
79951530130
-
Scaffolding pre-assembled contigs using sspace
-
Boetzer M, Henkel CV, Jansen HJ, Butler D, PirovanoW (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27: 578-579.
-
(2011)
Bioinformatics
, vol.27
, pp. 578-579
-
-
Boetzer, M.1
Henkel, C.V.2
Jansen, H.J.3
Butler, D.4
Pirovano, W.5
-
5
-
-
84862591603
-
Toward almost closed genomes with gapfiller
-
Boetzer M, Pirovano W (2012) Toward almost closed genomes with GapFiller. Genome Biol. 13: R56.
-
(2012)
Genome Biol.
, vol.13
-
-
Boetzer, M.1
Pirovano, W.2
-
6
-
-
84859739224
-
Domain enhanced lookup time accelerated blast
-
Boratyn GM, et al (2012) Domain enhanced lookup time accelerated BLAST. Biol Direct. 7: 12.Brady A, Salzberg S (2011) PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nat Methods. 8: 367.
-
(2012)
Biol Direct.
, vol.7
, pp. 12
-
-
Boratyn, G.M.1
-
7
-
-
79955611184
-
Phymmbl expanded: Confidence scores, custom databases, parallelization and more
-
Brady A, Salzberg S (2011) PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nat Methods. 8: 367.
-
(2011)
Nat Methods.
, vol.8
, pp. 367
-
-
Brady, A.1
Salzberg, S.2
-
8
-
-
0242276633
-
Developmental origin and evolution of bacteriocytes in the aphid-buchnera symbiosis
-
Braendle C, et al (2003) Developmental origin and evolution of bacteriocytes in the aphid-Buchnera symbiosis. PLoS Biol. 1: E21.
-
(2003)
PLoS Biol.
, vol.1
-
-
Braendle, C.1
-
9
-
-
84874266637
-
Rfam 11.0: 10 years of rna families
-
Burge SW, et al (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 41: D226-D232.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Burge, S.W.1
-
10
-
-
76349093143
-
Effects of facultative symbionts and heat stress on the metabolome of pea aphids
-
Burke GR, Fiehn O, Moran NA (2010) Effects of facultative symbionts and heat stress on the metabolome of pea aphids. ISME J. 4: 242-252.
-
(2010)
ISME J.
, vol.4
, pp. 242-252
-
-
Burke, G.R.1
Fiehn, O.2
Moran, N.A.3
-
11
-
-
79958280684
-
Massive genomic decay in serratia symbiotica, a recently evolved symbiont of aphids
-
Burke GR,Moran NA (2011) Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. Genome Biol Evol. 3: 195-208.
-
(2011)
Genome Biol Evol.
, vol.3
, pp. 195-208
-
-
Burke, G.R.1
Moran, N.A.2
-
12
-
-
84860490976
-
The metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases
-
Caspi R, et al (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 40: D742-D753.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Caspi, R.1
-
13
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17: 540-552.
-
(2000)
Mol Biol Evol.
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
14
-
-
37849023306
-
Assessing performance of orthology detection strategies applied to eukaryotic genomes
-
Chen F, Mackey AJ, Vermunt JK, Roos DS (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One 2: e383.
-
(2007)
PLoS One
, vol.2
-
-
Chen, F.1
Mackey, A.J.2
Vermunt, J.K.3
Roos, D.S.4
-
15
-
-
3042631307
-
Genome sequence assembly using trace signals and additional sequence information. Computer science and biology
-
Available from
-
Chevreux B, Wetter T, Suhai S (1999) Genome sequence assembly using trace signals and additional sequence information. Computer science and biology: Proceedings of the German Conference on Bioinformatics (GCB). p. 45-46) Available from: http: //www.bioinfo. de/isb/gcb99/talks/chevreux/.
-
(1999)
Proceedings of the German Conference on Bioinformatics (GCB
, pp. 45-46
-
-
Chevreux, B.1
Wetter, T.2
Suhai, S.3
-
16
-
-
80053458871
-
Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont buchnera
-
Degnan PH, Ochman H, Moran NA (2011) Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera. PLoS Genet. 7: e1002252.
-
(2011)
PLoS Genet.
, vol.7
-
-
Degnan, P.H.1
Ochman, H.2
Moran, N.A.3
-
17
-
-
67049146381
-
Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors
-
Degnan PH, Yu Y, Sisneros N, Wing RA, Moran NA (2009) Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors. Proc Natl Acad Sci U S A (106: 9063-9068.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 9063-9068
-
-
Degnan, P.H.1
Yu, Y.2
Sisneros, N.3
Wing, R.A.4
Moran, N.A.5
-
18
-
-
77955254855
-
Dynamics of genome evolution in facultative symbionts of aphids
-
Degnan PH, et al (2009) Dynamics of genome evolution in facultative symbionts of aphids. Environ Microbiol. 12: 2060-2069.
-
(2009)
Environ Microbiol.
, vol.12
, pp. 2060-2069
-
-
Degnan, P.H.1
-
19
-
-
84873334559
-
Proteomic analysis of an unculturable bacterial endosymbiont (blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes
-
Fan Y, Thompson JW, Dubois LG, Moseley MA, Wernegreen JJ (2013) Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes. J Proteome Res. 12: 704-718.
-
(2013)
J Proteome Res.
, vol.12
, pp. 704-718
-
-
Fan, Y.1
Thompson, J.W.2
Dubois, L.G.3
Moseley, M.A.4
Wernegreen, J.J.5
-
20
-
-
84891782659
-
Pfam: The protein families database
-
Finn RD, et al (2014) Pfam: The protein families database. Nucleic Acids Res. 42: D222-D230.
-
(2014)
Nucleic Acids Res.
, vol.42
-
-
Finn, R.D.1
-
21
-
-
0033933787
-
The secondary endosymbiotic bacterium of the pea aphid acyrthosiphon pisum (insecta: Homoptera
-
Fukatsu T, Nikoh N, Kawai R, Koga R (2000) The secondary endosymbiotic bacterium of the pea aphid Acyrthosiphon pisum (Insecta: Homoptera). Appl Environ Microbiol. 66: 2748-2758.
-
(2000)
Appl Environ Microbiol.
, vol.66
, pp. 2748-2758
-
-
Fukatsu, T.1
Nikoh, N.2
Kawai, R.3
Koga, R.4
-
22
-
-
33644859474
-
Plasmids in the aphid endosymbiont buchnera aphidicola with the smallest genomes
-
Gil R, Sabater-Muñoz B, Perez-Brocal V, Silva FJ, Latorre A (2006) Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story. Gene 370: 17-25.
-
(2006)
A puzzling evolutionary story. Gene
, vol.370
, pp. 17-25
-
-
Gil, R.1
Sabater-Muñoz, B.2
Perez-Brocal, V.3
Silva, F.J.4
Latorre, A.5
-
23
-
-
0041422250
-
The genome sequence of blochmannia floridanus: Comparative analysis of reduced genomes
-
Gil R, et al (2003) The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc Natl Acad Sci U S A (100: 9388-9393.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 9388-9393
-
-
Gil, R.1
-
24
-
-
4544379926
-
Coexistence of wolbachia with buchnera aphidicola and a secondary symbiont in the aphid cinara cedri
-
Gómez-Valero L, et al (2004) Coexistence of Wolbachia with Buchnera aphidicola and a secondary symbiont in the aphid Cinara cedri. J Bacteriol. 186: 6626-6633.
-
(2004)
J Bacteriol.
, vol.186
, pp. 6626-6633
-
-
Gómez-Valero, L.1
-
25
-
-
50249183451
-
The striking case of tryptophan provision in the cedar aphid cinara cedri
-
Gosalbes MJ, Lamelas A, Moya A, Latorre A (2008) The striking case of tryptophan provision in the cedar aphid Cinara cedri. J Bacteriol. 190: 6026-6029.
-
(2008)
J Bacteriol.
, vol.190
, pp. 6026-6029
-
-
Gosalbes, M.J.1
Lamelas, A.2
Moya, A.3
Latorre, A.4
-
26
-
-
64049084455
-
The genus serratia
-
In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, editors.New York: Springer
-
Grimont F, Grimont PAD (2006) The genus Serratia. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, editors. The prokaryotes. Volume 6: proteobacteria: gamma subclass, Vol. 2) New York: Springer. p. 219-244.
-
(2006)
The Prokaryotes. Volume 6: Proteobacteria: Gamma Subclass
, vol.2
, pp. 219-244
-
-
Grimont, F.1
Grimont, P.A.D.2
-
27
-
-
77956519355
-
Genoplotr: Comparative gene and genome visualization in r
-
Guy L, Kultima JR, Andersson SGE (2010) genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26: 2334-2335.
-
(2010)
Bioinformatics
, vol.26
, pp. 2334-2335
-
-
Guy, L.1
Kultima, J.R.2
Andersson, S.G.E.3
-
28
-
-
79952612931
-
Aphid genome expression reveals hostsymbiont cooperation in the production of amino acids
-
Hansen AK, Moran NA (2011) Aphid genome expression reveals hostsymbiont cooperation in the production of amino acids. Proc Natl Acad Sci U S A (108: 2849-2854.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 2849-2854
-
-
Hansen, A.K.1
Moran, N.A.2
-
29
-
-
84855297482
-
Genomic basis of endosymbiont-conferred protection against an insect parasitoid
-
Hansen AK, Vorburger C, Moran NA (2012) Genomic basis of endosymbiont-conferred protection against an insect parasitoid. Genome Res. 22: 106-114.
-
(2012)
Genome Res.
, vol.22
, pp. 106-114
-
-
Hansen, A.K.1
Vorburger, C.2
Moran, N.A.3
-
30
-
-
84883782152
-
Horizontally transmitted symbionts and host colonization of ecological niches
-
Henry LM, et al (2013) Horizontally transmitted symbionts and host colonization of ecological niches. Curr Biol. 23: 1713-1717.
-
(2013)
Curr Biol.
, vol.23
, pp. 1713-1717
-
-
Henry, L.M.1
-
31
-
-
84858602406
-
Interpro in 2011: New developments in the family and domain prediction database
-
Hunter S, et al (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 40: D306-D312.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Hunter, S.1
-
32
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
Hyatt D, et al (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
-
33
-
-
79959341239
-
Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool
-
Jérôme M, Noirot C, Klopp C (2011) Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool. BMC Res Notes. 4: 149.
-
(2011)
BMC Res Notes.
, vol.4
, pp. 149
-
-
Jérôme, M.1
Noirot, C.2
Klopp, C.3
-
34
-
-
75849133666
-
Pathway tools version 13.0: Integrated software for pathway/genome informatics and systems biology
-
Karp PD, et al (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform. 11: 40-79.
-
(2010)
Brief Bioinform.
, vol.11
, pp. 40-79
-
-
Karp, P.D.1
-
35
-
-
84875619226
-
Mafft multiple sequence alignment software version 7: Improvements in performance and usability
-
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30: 772-780.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
36
-
-
70349898249
-
Endosymbiotic bacteria in insects: Their diversity and culturability
-
Kikuchi Y (2009) Endosymbiotic bacteria in insects: Their diversity and culturability. Microbes Environ. 24: 195-204.
-
(2009)
Microbes Environ.
, vol.24
, pp. 195-204
-
-
Kikuchi, Y.1
-
37
-
-
77955459130
-
Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle
-
Kirkness EF, et al (2010) Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci U S A (107: 12168-12173.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 12168-12173
-
-
Kirkness, E.F.1
-
38
-
-
0347091990
-
Changing partners in an obligate symbiosis: A facultative endosymbiont can compensate for loss of the essential endosymbiont buchnera in an aphid
-
Koga R, Tsuchida T, Fukatsu T (2003) Changing partners in an obligate symbiosis: a facultative endosymbiont can compensate for loss of the essential endosymbiont Buchnera in an aphid. Proc Biol Sci. 270: 2543-2550.
-
(2003)
Proc Biol Sci.
, vol.270
, pp. 2543-2550
-
-
Koga, R.1
Tsuchida, T.2
Fukatsu, T.3
-
39
-
-
0020390455
-
Attenuation in amino acid biosynthetic operons
-
Kolter R, Yanofsky C (1982) Attenuation in amino acid biosynthetic operons. Annu Rev Genet. 16: 113-134.
-
(1982)
Annu Rev Genet.
, vol.16
, pp. 113-134
-
-
Kolter, R.1
Yanofsky, C.2
-
40
-
-
69649109364
-
Circos: An information aesthetic for comparative genomics
-
Krzywinski M, et al (2009) Circos: an information aesthetic for comparative genomics. Genome Res. 19: 1639-1645.
-
(2009)
Genome Res.
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
-
41
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
Kurtz S, et al (2004) Versatile and open software for comparing large genomes. Genome Biol. 5: R12.
-
(2004)
Genome Biol.
, vol.5
-
-
Kurtz, S.1
-
42
-
-
0028217395
-
Amplification of trpeg: Adaptation of buchnera aphidicola to an endosymbiotic association with aphids
-
Lai C-YY, Baumann L, Baumann P (1994) Amplification of trpEG: adaptation of Buchnera aphidicola to an endosymbiotic association with aphids. Proc Natl Acad Sci U S A. 91: 3819-3823.
-
(1994)
Proc Natl Acad Sci U S A.
, vol.91
, pp. 3819-3823
-
-
Lai, C.-Y.Y.1
Baumann, L.2
Baumann, P.3
-
43
-
-
46949093528
-
Evolution of the secondary symbiont "candidatus serratia symbiotica" in aphid species of the subfamily lachninae
-
Lamelas A, et al (2008) Evolution of the secondary symbiont "Candidatus Serratia symbiotica" in aphid species of the subfamily lachninae. Appl Environ Microbiol. 74: 4236-4240.
-
(2008)
Appl Environ Microbiol.
, vol.74
, pp. 4236-4240
-
-
Lamelas, A.1
-
44
-
-
81755163088
-
Serratia symbiotica from the aphid cinara cedri: A missing link from facultative to obligate insect endosymbiont
-
Lamelas A, et al (2011) Serratia symbiotica from the aphid cinara cedri: a missing link from facultative to obligate insect endosymbiont. PLoS Genet. 7: e1002357.Lamelas A, Gosalbes MJ, Moya A, Latorre A (2011) New clues about the evolutionary history of metabolic losses in bacterial endosymbionts, provided by the genome of Buchnera aphidicola from the aphid Cinara tujafilina. Appl Environ Microbiol. 77: 4446-4454.
-
(2011)
PLoS Genet.
, vol.7
-
-
Lamelas, A.1
-
45
-
-
79960080098
-
New clues about the evolutionary history of metabolic losses in bacterial endosymbionts, provided by the genome of buchnera aphidicola from the aphid cinara tujafilina
-
Lamelas A, Gosalbes MJ, Moya A, Latorre A (2011) New clues about the evolutionary history of metabolic losses in bacterial endosymbionts, provided by the genome of Buchnera aphidicola from the aphid Cinara tujafilina. Appl Environ Microbiol. 77: 4446-4454.
-
(2011)
Appl Environ Microbiol.
, vol.77
, pp. 4446-4454
-
-
Lamelas, A.1
Gosalbes, M.J.2
Moya, A.3
Latorre, A.4
-
46
-
-
84859210032
-
Fast gapped-read alignment with bowtie 2
-
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2) Nat Methods. 9: 357-359.
-
(2012)
Nat Methods.
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
47
-
-
1342271382
-
From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-proteobacteria
-
Lerat E, Daubin V, Moran NA (2003) From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-proteobacteria. PLoS Biol. 1: E19.
-
(2003)
PLoS Biol.
, vol.1
-
-
Lerat, E.1
Daubin, V.2
Moran, N.A.3
-
48
-
-
77949512908
-
Webmgr: An online tool for the multiple genome rearrangement problem
-
Lin CH, Zhao H, Lowcay SH, Shahab A, Bourque G (2010) webMGR: an online tool for the multiple genome rearrangement problem. Bioinformatics 26: 408-410.
-
(2010)
Bioinformatics
, vol.26
, pp. 408-410
-
-
Lin, C.H.1
Zhao, H.2
Lowcay, S.H.3
Shahab, A.4
Bourque, G.5
-
49
-
-
0030854739
-
Trnascan-se: A program for improved detection of transfer rna genes in genomic sequence
-
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
50
-
-
79955580332
-
Genetic and metabolic determinants of nutritional phenotype in an insect-bacterial symbiosis
-
MacDonald SJ, Thomas GH, Douglas AE (2011) Genetic and metabolic determinants of nutritional phenotype in an insect-bacterial symbiosis. Mol Ecol. 20: 2073-2084.
-
(2011)
Mol Ecol.
, vol.20
, pp. 2073-2084
-
-
MacDonald, S.J.1
Thomas, G.H.2
Douglas, A.E.3
-
51
-
-
84867550229
-
Comparative genomics of serratia spp.: Two paths towards endosymbiotic life
-
Manzano-Marín A, Lamelas A, Moya A, Latorre A (2012) Comparative genomics of Serratia spp.: Two paths towards endosymbiotic life. PLoS One 7: e47274.
-
(2012)
PLoS One
, vol.7
-
-
Manzano-Marín, A.1
Lamelas, A.2
Moya, A.3
Latorre, A.4
-
52
-
-
37649023694
-
Parallel genomic evolution and metabolic interdependence in an ancient symbiosis
-
McCutcheon JP, Moran NA (2007) Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. Proc Natl Acad Sci U S A (104: 19392-19397.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 19392-19397
-
-
McCutcheon, J.P.1
Moran, N.A.2
-
53
-
-
83855165692
-
Extreme genome reduction in symbiotic bacteria
-
McCutcheon JP, Moran NA (2012) Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol. 10: 13-26.
-
(2012)
Nat Rev Microbiol.
, vol.10
, pp. 13-26
-
-
McCutcheon, J.P.1
Moran, N.A.2
-
54
-
-
84875578097
-
Using tablet for visual exploration of second-generation sequencing data
-
Milne I, et al (2013) Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinform. 14: 193-202.
-
(2013)
Brief Bioinform.
, vol.14
, pp. 193-202
-
-
Milne, I.1
-
55
-
-
0036222272
-
Facultative bacterial endosymbionts benefit pea aphids acyrthosiphon pisum under heat stress
-
Montllor CB, et al (2002) Facultative bacterial endosymbionts benefit pea aphids Acyrthosiphon pisum under heat stress. Ecol Entomol. 27: 189-195.
-
(2002)
Ecol Entomol.
, vol.27
, pp. 189-195
-
-
Montllor, C.B.1
-
56
-
-
20444492834
-
Regulation of transcription in a reduced bacterial genome: Nutrient-provisioning genes of the obligate symbiont buchnera aphidicola
-
Moran NA, Dunbar HE, Wilcox JL (2005) Regulation of transcription in a reduced bacterial genome: nutrient-provisioning genes of the obligate symbiont Buchnera aphidicola. J Bacteriol. 187: 4229-4237.
-
(2005)
J Bacteriol.
, vol.187
, pp. 4229-4237
-
-
Moran, N.A.1
Dunbar, H.E.2
Wilcox, J.L.3
-
57
-
-
58449126084
-
The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria
-
Moran NA, McLaughlin HJ, Sorek R (2009) The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323: 379-382.
-
(2009)
Science
, vol.323
, pp. 379-382
-
-
Moran, N.A.1
McLaughlin, H.J.2
Sorek, R.3
-
58
-
-
0027254254
-
Amolecular clock in endosymbiotic bacteria is calibrated using the insect hosts
-
Moran NA, Munson MA, Baumann P, Ishikawa H (1993) Amolecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proc R Soc B Biol Sci. 253: 167-171.
-
(1993)
Proc R Soc B Biol Sci.
, vol.253
, pp. 167-171
-
-
Moran, N.A.1
Munson, M.A.2
Baumann, P.3
Ishikawa, H.4
-
59
-
-
20444415226
-
Evolutionary relationships of three new species of enterobacteriaceae living as symbionts of aphids and other insects
-
Moran NA, Russell JA, Koga R, Fukatsu T (2005) Evolutionary relationships of three new species of Enterobacteriaceae living as symbionts of aphids and other insects. Appl Environ Microbiol. 71: 3302-3310.
-
(2005)
Appl Environ Microbiol.
, vol.71
, pp. 3302-3310
-
-
Moran, N.A.1
Russell, J.A.2
Koga, R.3
Fukatsu, T.4
-
60
-
-
39449118068
-
Learning how to live together: Genomic insights into prokaryote-animal symbioses
-
Moya A, PeretóJ, Gil R, Latorre A (2008) Learning how to live together: genomic insights into prokaryote-animal symbioses. Nat Rev Genet. 9: 218-229.
-
(2008)
Nat Rev Genet.
, vol.9
, pp. 218-229
-
-
Moya, A.1
Pereto, J.2
Gil, R.3
Latorre, A.4
-
61
-
-
0034708758
-
A whole-genome assembly of drosophila
-
Myers EW, et al (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
-
(2000)
Science
, vol.287
, pp. 2196-2204
-
-
Myers, E.W.1
-
62
-
-
0032924695
-
Provision of riboflavin to the host aphid, acyrthosiphon pisum, by endosymbiotic bacteria, buchnera
-
Nakabachi A, Ishikawa H (1999) Provision of riboflavin to the host aphid, Acyrthosiphon pisum, by endosymbiotic bacteria, Buchnera. J Insect Physiol. 45: 1-6.
-
(1999)
J Insect Physiol.
, vol.45
, pp. 1-6
-
-
Nakabachi, A.1
Ishikawa, H.2
-
63
-
-
84890037468
-
Infernal 1.1: 100-fold faster rna homology searches
-
Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29: 2933-2935.
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
64
-
-
79151472877
-
Correlations between bacterial ecology and mobile dna
-
Newton ILG, Bordenstein SR (2011) Correlations between bacterial ecology and mobile DNA. Curr Microbiol. 62: 198-208.
-
(2011)
Curr Microbiol.
, vol.62
, pp. 198-208
-
-
Newton, I.L.G.1
Bordenstein, S.R.2
-
65
-
-
84892496453
-
Genome degeneration and adaptation in a nascent stage of symbiosis
-
Oakeson KF, et al (2014) Genome degeneration and adaptation in a nascent stage of symbiosis. Genome Biol Evol. 6: 76-93.
-
(2014)
Genome Biol Evol.
, vol.6
, pp. 76-93
-
-
Oakeson, K.F.1
-
69
-
-
79251523486
-
The genome of the amoeba symbiont "candidatus amoebophilus asiaticus" encodes an afplike prophage possibly used for protein secretion
-
Penz T, Horn M, Schmitz-Esser S (2010) The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" encodes an afplike prophage possibly used for protein secretion. Virulence 1: 541-545.
-
(2010)
Virulence
, vol.1
, pp. 541-545
-
-
Penz, T.1
Horn, M.2
Schmitz-Esser, S.3
-
70
-
-
33750009568
-
A small microbial genome: The end of a long symbiotic relationship?
-
Perez-Brocal V, et al (2006) A small microbial genome: The end of a long symbiotic relationship? Science 314: 312-313.
-
(2006)
Science
, vol.314
, pp. 312-313
-
-
Perez-Brocal, V.1
-
71
-
-
79958008118
-
Large-scale label-free quantitative proteomics of the pea aphid-buchnera symbiosis
-
10M110.007039
-
Poliakov A, et al (2011) Large-scale label-free quantitative proteomics of the pea aphid-Buchnera symbiosis. Mol Cell Proteomics. 10M110.007039.
-
(2011)
Mol Cell Proteomics
-
-
Poliakov, A.1
-
72
-
-
84864134721
-
Sina: Accurate high-throughput multiple sequence alignment of ribosomal rna genes
-
Pruesse E, Peplies J, Glöckner FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28: 1823-1829.
-
(2012)
Bioinformatics
, vol.28
, pp. 1823-1829
-
-
Pruesse, E.1
Peplies, J.2
Glöckner, F.O.3
-
73
-
-
84873739311
-
The silva ribosomal rna gene database project: Improved data processing and web-based tools
-
Quast C, et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41: D590-D596.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Quast, C.1
-
74
-
-
0034201441
-
Emboss: The european molecular biology open software suite
-
Rice P, Longden I, Bleasby A (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16: 276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
76
-
-
0038477097
-
Sidestepping secondary symbionts: Widespread horizontal transfer across and beyond the aphidoidea
-
Russell JA, Latorre A, Sabater-Munoz B, Moya A, Moran N A (2003) Sidestepping secondary symbionts: widespread horizontal transfer across and beyond the Aphidoidea. Mol Ecol. 12: 1061-1075.
-
(2003)
Mol Ecol.
, vol.12
, pp. 1061-1075
-
-
Russell, J.A.1
Latorre, A.2
Sabater-Munoz, B.3
Moya, A.4
Moran N, A.5
-
77
-
-
22144435947
-
Rickettsia symbiont in the pea aphid acyrthosiphon pisum: Novel cellular tropism, effect on host fitness, and interaction with the essential symbiont buchnera
-
Sakurai M, Koga R, Tsuchida T, Meng XY, Fukatsu T (2005) Rickettsia symbiont in the pea aphid Acyrthosiphon pisum: novel cellular tropism, effect on host fitness, and interaction with the essential symbiont Buchnera. Appl Environ Microbiol. 71: 4069-4075.
-
(2005)
Appl Environ Microbiol.
, vol.71
, pp. 4069-4075
-
-
Sakurai, M.1
Koga, R.2
Tsuchida, T.3
Meng, X.Y.4
Fukatsu, T.5
-
79
-
-
79952422304
-
Quality control and preprocessing ofmetagenomic datasets
-
Schmieder R, Edwards R (2011) Quality control and preprocessing ofmetagenomic datasets. Bioinformatics 27: 863-864.
-
(2011)
Bioinformatics
, vol.27
, pp. 863-864
-
-
Schmieder, R.1
Edwards, R.2
-
80
-
-
0034618559
-
Genome sequence of the endocellular bacterial symbiont of aphids buchnera sp
-
Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H (2000) Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407: 81-86.
-
(2000)
APS. Nature
, vol.407
, pp. 81-86
-
-
Shigenobu, S.1
Watanabe, H.2
Hattori, M.3
Sakaki, Y.4
Ishikawa, H.5
-
81
-
-
79953681013
-
Genomic revelations of amutualism: The pea aphid and its obligate bacterial symbiont
-
Shigenobu S, Wilson ACC (2011) Genomic revelations of amutualism: The pea aphid and its obligate bacterial symbiont. Cell Mol Life Sci. 68: 1297-1309.
-
(2011)
Cell Mol Life Sci.
, vol.68
, pp. 1297-1309
-
-
Shigenobu, S.1
Wilson, A.C.C.2
-
82
-
-
33644873699
-
Isfinder: The reference centre for bacterial insertion sequences
-
Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M (2006) ISfinder: The reference centre for bacterial insertion sequences. Nucleic Acids Res. 34: D32-D36.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Siguier, P.1
Perochon, J.2
Lestrade, L.3
Mahillon, J.4
Chandler, M.5
-
83
-
-
84869840246
-
Endosymbiotic bacteria as a source of carotenoids in whiteflies
-
Sloan DB, Moran NA (2012) Endosymbiotic bacteria as a source of carotenoids in whiteflies. Biol Lett. 8: 986-989.
-
(2012)
Biol Lett.
, vol.8
, pp. 986-989
-
-
Sloan, D.B.1
Moran, N.A.2
-
84
-
-
0033990060
-
The staden package, 1998
-
In: Misener S, Krawetz SA, editors. Totowa (NJ): Springer
-
Staden R, Beal KF, Bonfield JK (1999) The Staden package, 1998) In: Misener S, Krawetz SA, editors. Bioinformaticsmethods and protocols, Vol. 132) Totowa (NJ): Springer. p. 115-130.
-
(1999)
Bioinformatics Methods and Protocols
, vol.132
, pp. 115-130
-
-
Staden, R.1
Beal, K.F.2
Bonfield, J.K.3
-
85
-
-
33750403801
-
Raxml-vi-hpc: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
87
-
-
0037189373
-
50 Million years of genomic stasis in endosymbiotic bacteria
-
Tamas I, et al (2002) 50 Million years of genomic stasis in endosymbiotic bacteria. Science 296: 2376-2379.
-
(2002)
Science
, vol.296
, pp. 2376-2379
-
-
Tamas, I.1
-
89
-
-
84878206137
-
Maintenance of essential amino acid synthesis pathways in the blattabacterium cuenoti symbiont of a wood-feeding cockroach
-
Tokuda G, et al (2013) Maintenance of essential amino acid synthesis pathways in the Blattabacterium cuenoti symbiont of a wood-feeding cockroach. Biol Lett. 9: 20121153.Tsuchida T, Koga R, Fujiwara A, Fukatsu T (2014) Phenotypic effect of "Candidatus Rickettsiella viridis," a facultative symbiont of the pea aphid (Acyrthosiphon pisum), and its interaction with a coexisting symbiont. Appl Environ Microbiol. 80: 525-533.
-
(2013)
Biol Lett.
, vol.9
, pp. 20121153
-
-
Tokuda, G.1
-
90
-
-
84892450981
-
Phenotypic effect of "candidatus rickettsiella viridis," a facultative symbiont of the pea aphid (acyrthosiphon pisum), and its interaction with a coexisting symbiont
-
Tsuchida T, Koga R, Fujiwara A, Fukatsu T (2014) Phenotypic effect of "Candidatus Rickettsiella viridis," a facultative symbiont of the pea aphid (Acyrthosiphon pisum), and its interaction with a coexisting symbiont. Appl Environ Microbiol. 80: 525-533.
-
(2014)
Appl Environ Microbiol.
, vol.80
, pp. 525-533
-
-
Tsuchida, T.1
Koga, R.2
Fujiwara, A.3
Fukatsu, T.4
-
91
-
-
84865022311
-
Primer3-new capabilities and interfaces
-
Untergasser A, et al (2012) Primer3-new capabilities and interfaces. Nucleic Acids Res. 40: e115.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Untergasser, A.1
-
92
-
-
23144467676
-
Basys: A web server for automated bacterial genome annotation
-
Van Domselaar GH, et al (2005) BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res. 33: W455-W459.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Van Domselaar, G.H.1
-
93
-
-
0037457901
-
Reductive genome evolution in buchnera aphidicola
-
van Ham RCHJ, et al (2003) Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A (100: 581-586.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 581-586
-
-
Van Ham, R.C.H.J.1
-
94
-
-
32444450157
-
A mobile quorum-sensing system in serratia marcescens
-
Wei J-R, et al (2006a. A mobile quorum-sensing system in Serratia marcescens. J Bacteriol. 188: 1518-1525.
-
(2006)
J Bacteriol
, vol.188
, pp. 1518-1525
-
-
Wei, J.-R.1
-
95
-
-
33747200892
-
Regulatory roles of spnt, a novel gene located within transposon tntir
-
Wei J-R, et al (2006b. Regulatory roles of spnT, a novel gene located within transposon TnTIR. Biochem Biophys Res Commun. 348: 1038-1046.
-
(2006)
Biochem Biophys Res Commun
, vol.348
, pp. 1038-1046
-
-
Wei, J.-R.1
-
96
-
-
0001279038
-
Preparation of genomic dna from bacteria
-
In: Ausbel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K, editors New York: John Wiley & Sons Inc. Section I, Unit 2.4) Available from
-
Wilson K (2002) Preparation of genomic DNA from bacteria. In: Ausbel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K, editors. Short protocols in molecular biology. New York: John Wiley & Sons Inc. Section I, Unit 2.4) Available from: http: //www.wiley.com/WileyCDA/WileyTitle/productCd- 0471250929.html.
-
(2002)
Short Protocols in Molecular Biology
-
-
Wilson, K.1
-
97
-
-
33745208719
-
Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters
-
Wu D, et al (2006) Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol. 4: e188.
-
(2006)
PLoS Biol.
, vol.4
-
-
Wu, D.1
|