-
1
-
-
1842527099
-
Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae iso-lated from a microbial mat in Lake Fryxell, Ant-arctica
-
PubMed
-
Van Trappen S, Vandecandelaere I, Mergaert J, Swings J. Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae iso-lated from a microbial mat in Lake Fryxell, Ant-arctica. Int J Syst Evol Microbiol 2004; 54:445-448. PubMed http://dx.doi.org/10.1099/ijs.0.02922-0
-
(2004)
Int J Syst Evol Microbiol
, vol.54
, pp. 445-448
-
-
van Trappen, S.1
Vandecandelaere, I.2
Mergaert, J.3
Swings, J.4
-
2
-
-
0036962276
-
Diversity of 746 heterotrophic bacteria isolated from microbi-al mats from ten Antarctic lakes
-
PubMed
-
Van Trappen S, Mergaert J, Van Eygen S, Dawyndt P, Cnockaert MC, Swings J. Diversity of 746 heterotrophic bacteria isolated from microbi-al mats from ten Antarctic lakes. Syst Appl Microbiol 2002; 25:603-610. PubMed http://dx.doi.org/10.1078/07232020260517742
-
(2002)
Syst Appl Microbiol
, vol.25
, pp. 603-610
-
-
van Trappen, S.1
Mergaert, J.2
van Eygen, S.3
Dawyndt, P.4
Cnockaert, M.C.5
Swings, J.6
-
3
-
-
0025183708
-
Basic local alignment search tool
-
PubMed
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
4
-
-
10044259013
-
-
Korf I, Yandell M, Bedell J. BLAST, O'Reilly, Se-bastopol, 2003.
-
(2003)
BLAST, O'Reilly, Se-bastopol
-
-
Korf, I.1
Yandell, M.2
Bedell, J.3
-
5
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compat-ible with ARB
-
PubMed
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compat-ible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed http://dx.doi.org/10.1128/AEM.03006-05
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
7
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
PubMed
-
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformat-ics 2002; 18:452-464. PubMed http://dx.doi.org/10.1093/bioinformatics/18.3.452
-
(2002)
Bioinformat-ics
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
8
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Pub-Med
-
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. Pub-Med http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
-
(2000)
Mol Biol Evol
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
9
-
-
50249100595
-
A rapid bootstrap algorithm for the RAxML web servers
-
PubMed
-
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008; 57:758-771. PubMed http://dx.doi.org/10.1080/10635150802429642
-
(2008)
Syst Biol
, vol.57
, pp. 758-771
-
-
Stamatakis, A.1
Hoover, P.2
Rougemont, J.3
-
10
-
-
36849014457
-
An empirical test of the midpoint rooting method
-
Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. http://dx.doi.org/10.1111/j.1095-8312.2007.00864.x
-
(2007)
Biol J Linn Soc Lond
, vol.92
, pp. 669-674
-
-
Hess, P.N.1
de Moraes Russo, C.A.2
-
11
-
-
67650340717
-
How many bootstrap replicates are necessary?
-
Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184-200. http://dx.doi.org/10.1007/978-3-642-02008-7_13
-
(2009)
Lect Notes Comput Sci
, vol.5541
, pp. 184-200
-
-
Pattengale, N.D.1
Alipour, M.2
Bininda-Emonds, O.R.P.3
Moret, B.M.E.4
Stamatakis, A.5
-
13
-
-
84859165788
-
The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their as-sociated metadata
-
PubMed
-
Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their as-sociated metadata. Nucleic Acids Res 2012; 40:D571-D579. PubMed http://dx.doi.org/10.1093/nar/gkr1100
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Pagani, I.1
Liolios, K.2
Jansson, J.3
Chen, I.M.4
Smirnova, T.5
Nosrat, B.6
Markowitz, V.M.7
Kyrpides, N.C.8
-
14
-
-
77950888128
-
The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea en-vironment and ecological role in sedimentary or-ganic degradation
-
PubMed
-
Qin QL, Zhang XY, Wang XM, Liu GM, Chen XL, Xie BB, Dang HY, Zhou BC, Yu J, Zhang YZ. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea en-vironment and ecological role in sedimentary or-ganic degradation. BMC Genomics 2010; 11:247. PubMed http://dx.doi.org/10.1186/1471-2164-11-247
-
(2010)
BMC Genomics
, vol.11
, pp. 247
-
-
Qin, Q.L.1
Zhang, X.Y.2
Wang, X.M.3
Liu, G.M.4
Chen, X.L.5
Xie, B.B.6
Dang, H.Y.7
Zhou, B.C.8
Yu, J.9
Zhang, Y.Z.10
-
15
-
-
80053517168
-
T)
-
PubMed
-
T). Stand Genomic Sci 2011; 4:221-232. PubMed http://dx.doi.org/10.4056/sigs.1774329
-
(2011)
Stand Genomic Sci
, vol.4
, pp. 221-232
-
-
Pati, A.1
Abt, B.2
Teshima, H.3
Nolan, M.4
Lapidus, A.5
Lucas, S.6
Hammon, N.7
Deshpande, S.8
Cheng, J.F.9
Tapia, R.10
-
16
-
-
80052320683
-
T)
-
PubMed
-
T). Stand Genomic Sci 2009; 1:101-109. PubMed http://dx.doi.org/10.4056/sigs.15195
-
(2009)
Stand Genomic Sci
, vol.1
, pp. 101-109
-
-
Mavrommatis, K.1
Gronow, S.2
Saunders, E.3
Land, M.4
Lapidus, A.5
Copeland, A.6
Glavina del Rio, T.7
Nolan, M.8
Lucas, S.9
Chen, F.10
-
17
-
-
43449108562
-
The minimum information about a genome sequence (MIGS) specification
-
PubMed
-
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed http://dx.doi.org/10.1038/nbt1360
-
(2008)
Nat Biotechnol
, vol.26
, pp. 541-547
-
-
Field, D.1
Garrity, G.2
Gray, T.3
Morrison, N.4
Selengut, J.5
Sterk, P.6
Tatusova, T.7
Thomson, N.8
Allen, M.J.9
Angiuoli, S.V.10
-
18
-
-
77955908592
-
NamesforLife. BrowserTool takes ex-pertise out of the database and puts it right in the browser
-
Garrity G. NamesforLife. BrowserTool takes ex-pertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
-
(2010)
Microbiol Today
, vol.37
, pp. 9
-
-
Garrity, G.1
-
19
-
-
0025300402
-
Towards a natural system of organisms. Proposal for the do-mains Archaea and
-
PubMed
-
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms. Proposal for the do-mains Archaea and Bacteria. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
-
(1990)
Bacteria. Proc Natl Acad Sci USA
, vol.87
, pp. 4576-4579
-
-
Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
-
20
-
-
84855665878
-
Phylum XIV
-
phyl. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Se-cond Edition, Volume 4, Springer, New York
-
Krieg NR, Ludwig W, Euzéby J, Whitman WB. Phylum XIV. Bacteroidetes phyl. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Se-cond Edition, Volume 4, Springer, New York, 2011, p. 25.
-
(2011)
Bacteroidetes
, pp. 25
-
-
Krieg, N.R.1
Ludwig, W.2
Euzéby, J.3
Whitman, W.B.4
-
21
-
-
84863628521
-
-
Editor L., Validation List No. 143. [PubMed]
-
Editor L. Validation List No. 143. [PubMed]. Int J Syst Evol Microbiol 2012; 62:1-4.
-
(2012)
Int J Syst Evol Microbiol
, vol.62
, pp. 1-4
-
-
-
22
-
-
84860756312
-
Class II
-
class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Pas-ter BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Se-cond Edition, Volume 4, Springer, New York
-
Bernardet JF. Class II. Flavobacteriia class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Pas-ter BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Se-cond Edition, Volume 4, Springer, New York, 2011, p. 105.
-
(2011)
Flavobacteriia
, pp. 105
-
-
Bernardet, J.F.1
-
23
-
-
70350704116
-
Draft taxo-nomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes
-
Ludwig W, Euzeby J, Whitman WG. Draft taxo-nomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes.
-
-
-
Ludwig, W.1
Euzeby, J.2
Whitman, W.G.3
-
24
-
-
13244252390
-
-
PubMed, Judicial Commission of the International Commit-tee on Systematics of Prokaryotes, The nomencla-tural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion
-
Judicial Commission of the International Commit-tee on Systematics of Prokaryotes. The nomencla-tural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int J Syst Evol Microbiol 2005; 55:517-518. PubMed http://dx.doi.org/10.1099/ijs.0.63548-0 79
-
(2005)
Int J Syst Evol Microbiol
, vol.55
, pp. 517-518
-
-
-
25
-
-
84860756312
-
Order I
-
ord. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriolo-gy, Second Edition, Volume 4, Springer, New York
-
Bernardet JF. Order I. Flavobacteriales ord. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriolo-gy, Second Edition, Volume 4, Springer, New York, 2011, p. 105.
-
(2011)
Flavobacteriales
, pp. 105
-
-
Bernardet, J.F.1
-
26
-
-
0001702209
-
Order 1
-
Leadbetter 1974, 99AL. In: Holt JG (ed), Bergey's Manual of Systematic Bacteriology, First Edition, Volume 3, The Williams and Wilkins Co., Balti-more
-
Reichenbach H. Order 1. Cytophagales Leadbetter 1974, 99AL. In: Holt JG (ed), Bergey's Manual of Systematic Bacteriology, First Edition, Volume 3, The Williams and Wilkins Co., Balti-more, 1989, p. 2011-2013.
-
(1989)
Cytophagales
, pp. 2011-2013
-
-
Reichenbach, H.1
-
27
-
-
0030052649
-
Cutting a Gordian knot: Emended classification and description of the ge-nus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978)
-
Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P. Cutting a Gordian knot: emended classification and description of the ge-nus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128-148. http://dx.doi.org/10.1099/00207713-46-1-128
-
(1996)
Int J Syst Bacteriol
, vol.46
, pp. 128-148
-
-
Bernardet, J.F.1
Segers, P.2
Vancanneyt, M.3
Berthe, F.4
Kersters, K.5
Vandamme, P.6
-
28
-
-
0035989637
-
Proposed minimal standards for describing new taxa of the family Flavobacteriaceae, and emended descrip-tion of the family. [PubMed]
-
PubMed
-
Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae, and emended descrip-tion of the family. [PubMed]. Int J Syst Evol Microbiol 2002; 52:1049-1070. PubMed http://dx.doi.org/10.1099/ijs.0.02136-0
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 1049-1070
-
-
Bernardet, J.F.1
Nakagawa, Y.2
Holmes, B.3
-
29
-
-
0042032933
-
Validation of the publication of new names and new combinations previously effectively pub-lished outside the IJSB. List No. 41
-
Validation of the publication of new names and new combinations previously effectively pub-lished outside the IJSB. List No. 41. Int J Syst Bacteriol 1992; 42:327-328. http://dx.doi.org/10.1099/00207713-42-2-327
-
(1992)
Int J Syst Bacteriol
, vol.42
, pp. 327-328
-
-
-
30
-
-
84879100871
-
2010, Classification of Bacteria and
-
BAuA, in risk groups, TRBA 466
-
BAuA. 2010, Classification of Bacteria and Archaea in risk groups. http://www.baua.de TRBA 466, p. 93.
-
Archaea
, pp. 93
-
-
-
31
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Con-sortium
-
PubMed
-
Ashburner M, Ball CA, Blake JA, Botstein D, But-ler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Con-sortium. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
But-ler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
32
-
-
33747873466
-
Gillisia myxillae sp. nov., a novel member of the family Flavobacteriaceae, isolated from the marine sponge
-
PubMed
-
Lee OO, Lau SC, Tsoi MM, Li X, Plakhotnikova I, Dobretsov S, Wu MC, Wong PK, Qian PY. Gillisia myxillae sp. nov., a novel member of the family Flavobacteriaceae, isolated from the marine sponge Myxilla incrustans. Int J Syst Evol Microbiol 2006; 56:1795-1799. PubMed http://dx.doi.org/10.1099/ijs.0.64345-0
-
(2006)
Myxilla incrustans. Int J Syst Evol Microbiol
, vol.56
, pp. 1795-1799
-
-
Lee, O.O.1
Lau, S.C.2
Tsoi, M.M.3
Li, X.4
Plakhotnikova, I.5
Dobretsov, S.6
Wu, M.C.7
Wong, P.K.8
Qian, P.Y.9
-
33
-
-
22544462274
-
Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and
-
PubMed
-
Bowman JP, Nichols DS. Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia. Int J Syst Evol Microbiol 2005; 55:1471-1486. PubMed http://dx.doi.org/10.1099/ijs.0.63527-0
-
(2005)
Gillisia. Int J Syst Evol Microbiol
, vol.55
, pp. 1471-1486
-
-
Bowman, J.P.1
Nichols, D.S.2
-
34
-
-
13244279691
-
Gillisia mitskevichiae sp. nov., a nov-el bacterium of the family Flavobacteriaceae, iso-lated from sea water
-
PubMed
-
Nedashkovskaya OI, Kim SB, Lee KH, Mikhailov VV, Bae KS. Gillisia mitskevichiae sp. nov., a nov-el bacterium of the family Flavobacteriaceae, iso-lated from sea water. Int J Syst Evol Microbiol 2005; 55:321-323. PubMed http://dx.doi.org/10.1099/ijs.0.63256-0
-
(2005)
Int J Syst Evol Microbiol
, vol.55
, pp. 321-323
-
-
Nedashkovskaya, O.I.1
Kim, S.B.2
Lee, K.H.3
Mikhailov, V.V.4
Bae, K.S.5
-
35
-
-
77952889628
-
En route to a genome-based classification of Archaea and
-
PubMed
-
Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed http://dx.doi.org/10.1016/j.syapm.2010.03.003
-
(2010)
Bacteria? Syst Appl Microbiol
, vol.33
, pp. 175-182
-
-
Klenk, H.P.1
Göker, M.2
-
36
-
-
72949101201
-
A phylogeny-driven Genomic Encyclopaedia of Bacteria and
-
PubMed
-
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven Genomic Encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. PubMed http://dx.doi.org/10.1038/nature08656
-
(2009)
Archaea. Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
Hugenholtz, P.2
Mavromatis, K.3
Pukall, R.4
Dalin, E.5
Ivanova, N.N.6
Kunin, V.7
Goodwin, L.8
Wu, M.9
Tindall, B.J.10
-
37
-
-
84872027115
-
-
List of growth media used at DSMZ: http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technolog y/list-of-media-for-microorganisms.html.
-
List of growth media used at DSMZ
-
-
-
38
-
-
79953824958
-
The DNA Bank Network: The start from a German initiative
-
Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreserv Biobank 2011; 9:51-55. http://dx.doi.org/10.1089/bio.2010.0029
-
(2011)
Biopreserv Biobank
, vol.9
, pp. 51-55
-
-
Gemeinholzer, B.1
Dröge, G.2
Zetzsche, H.3
Haszprunar, G.4
Klenk, H.P.5
Güntsch, A.6
Berendsohn, W.G.7
Wägele, J.W.8
-
39
-
-
84879124252
-
-
The DOE Joint Genome Institute
-
The DOE Joint Genome Institute. www.jgi.doe.gov
-
-
-
-
41
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
PubMed
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed http://dx.doi.org/10.1101/gr.074492.107
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
43
-
-
80053373249
-
-
AGBT, Marco Island, FL
-
Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for us-ing ultra short reads in microbial genome assem-bly and finishing. AGBT, Marco Island, FL, 2008.
-
(2008)
POLISHER: An effective tool for us-ing ultra short reads in microbial genome assem-bly and finishing
-
-
Lapidus, A.1
LaButti, K.2
Foster, B.3
Lowry, S.4
Trong, S.5
Goltsman, E.6
-
44
-
-
77952299957
-
Prodigal Prokaryotic Dynam-ic Programming Genefinding Algorithm
-
PubMed
-
Hyatt D, Chen GL, Locascio PF, Land ML, Lar-imer FW, Hauser LJ. Prodigal Prokaryotic Dynam-ic Programming Genefinding Algorithm. BMC Bi-oinformatics 2010; 11:119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119
-
(2010)
BMC Bi-oinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
Chen, G.L.2
Locascio, P.F.3
Land, M.L.4
Lar-imer, F.W.5
Hauser, L.J.6
-
45
-
-
77953023066
-
GenePRIMP: A Gene Prediction Improvement Pipeline for mi-crobial genomes
-
PubMed
-
Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for mi-crobial genomes. Nat Methods 2010; 7:455-457. PubMed http://dx.doi.org/10.1038/nmeth.1457
-
(2010)
Nat Methods
, vol.7
, pp. 455-457
-
-
Pati, A.1
Ivanova, N.2
Mikhailova, N.3
Ovchinikova, G.4
Hooper, S.D.5
Lykidis, A.6
Kyrpides, N.C.7
-
46
-
-
69949116874
-
IMG ER: A system for microbial ge-nome annotation expert review and curation
-
PubMed
-
Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial ge-nome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393
-
(2009)
Bio-informatics
, vol.25
, pp. 2271-2278
-
-
Markowitz, V.M.1
Ivanova, N.N.2
Chen, I.M.A.3
Chu, K.4
Kyrpides, N.C.5
-
47
-
-
0034519206
-
Retinylidene proteins: Structures and functions from archaea to humans
-
PubMed
-
Spudich JL, Yang CS, Jung KH, Spudich EN. Retinylidene proteins: structures and functions from archaea to humans. Annu Rev Cell Dev Biol 2000; 16:365-392. PubMed http://dx.doi.org/10.1146/annurev.cellbio.16.1.365
-
(2000)
Annu Rev Cell Dev Biol
, vol.16
, pp. 365-392
-
-
Spudich, J.L.1
Yang, C.S.2
Jung, K.H.3
Spudich, E.N.4
-
49
-
-
34248151050
-
Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host
-
PubMed
-
Martinez A, Bradley AS, Waldbauer JR, Summons RE, DeLong EF. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc Natl Acad Sci USA 2007; 104:5590-5595. PubMed http://dx.doi.org/10.1073/pnas.0611470104
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 5590-5595
-
-
Martinez, A.1
Bradley, A.S.2
Waldbauer, J.R.3
Summons, R.E.4
DeLong, E.F.5
-
50
-
-
33847770775
-
Liphardt. Light-powering Escherichia coli with proteorhodopsin
-
PubMed
-
Walter JM, Greenfield D, Bustamante C. Liphardt. Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci USA 2007; 104:2408-2412. PubMed http://dx.doi.org/10.1073/pnas.0611035104
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 2408-2412
-
-
Walter, J.M.1
Greenfield, D.2
Bustamante, C.3
-
51
-
-
25444463058
-
Xanthorhodopsin. A proton pump with a light-harvesting carotenoid antenna
-
PubMed
-
Balashov SP, Imasheva ES, Boichenko VA, Anton J, Wang JM, Lanyi JK. Xanthorhodopsin. A proton pump with a light-harvesting carotenoid antenna. Science 2005; 309:2061-2064. PubMed http://dx.doi.org/10.1126/science.1118046
-
(2005)
Science
, vol.309
, pp. 2061-2064
-
-
Balashov, S.P.1
Imasheva, E.S.2
Boichenko, V.A.3
Anton, J.4
Wang, J.M.5
Lanyi, J.K.6
-
52
-
-
34548652250
-
Xanthorhodopsin: Proton pump with a carotenoid antenna
-
PubMed
-
Balashov SP, Lanyi JK. Xanthorhodopsin: Proton pump with a carotenoid antenna. Cell Mol Life Sci 2007; 64:2323-2328. PubMed http://dx.doi.org/10.1007/s00018-007-7167-y
-
(2007)
Cell Mol Life Sci
, vol.64
, pp. 2323-2328
-
-
Balashov, S.P.1
Lanyi, J.K.2
-
53
-
-
0036200510
-
Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds
-
PubMed
-
Antón J, Oren A, Benlloch S, Rodriguez-Valera F, Amann R, Rossello-Mora R. Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds. Int J Syst Evol Microbiol 2002; 52:485-491. PubMed
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 485-491
-
-
Antón, J.1
Oren, A.2
Benlloch, S.3
Rodriguez-Valera, F.4
Amann, R.5
Rossello-Mora, R.6
-
54
-
-
29144485325
-
The genome of Salinibacter ruber: Convergence and gene ex-change among hyperhalophilic bacteria and archaea
-
PubMed
-
Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez PG, et al. The genome of Salinibacter ruber: convergence and gene ex-change among hyperhalophilic bacteria and archaea. Proc Natl Acad Sci USA 2005; 102:18147-18152. PubMed http://dx.doi.org/10.1073/pnas.0509073102
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, 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
Sanchez, P.G.10
-
55
-
-
51649103856
-
Excitation energy-transfer and the relative orienta-tion of retinal and carotenoid in xanthorhodopsin
-
PubMed
-
Balashov SP, Imasheva ES, Wang JM, Lanyi JK. Excitation energy-transfer and the relative orienta-tion of retinal and carotenoid in xanthorhodopsin. Biophys J 2008; 95:2402-2414. PubMed http://dx.doi.org/10.1529/biophysj.108.132175
-
(2008)
Biophys J
, vol.95
, pp. 2402-2414
-
-
Balashov, S.P.1
Imasheva, E.S.2
Wang, J.M.3
Lanyi, J.K.4
-
56
-
-
0034665853
-
Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea
-
PubMed
-
Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feld-man RA, Spudich JL, et al. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 2000; 289:1902-1906. PubMed http://dx.doi.org/10.1126/science.289.5486.1902
-
(2000)
Science
, vol.289
, pp. 1902-1906
-
-
Béjà, O.1
Aravind, L.2
Koonin, E.V.3
Suzuki, M.T.4
Hadd, A.5
Nguyen, L.P.6
Jovanovich, S.B.7
Gates, C.M.8
Feld-man, R.A.9
Spudich, J.L.10
-
57
-
-
0035859080
-
Proteorhodopsin phototrophy in the ocean
-
PubMed
-
Béjà O, Spudich EN, Spudich JL, Leclerc M, DeLong EF. Proteorhodopsin phototrophy in the ocean. Nature 2001; 411:786-789. PubMed http://dx.doi.org/10.1038/35081051
-
(2001)
Nature
, vol.411
, pp. 786-789
-
-
Béjà, O.1
Spudich, E.N.2
Spudich, J.L.3
Leclerc, M.4
DeLong, E.F.5
-
59
-
-
45849154166
-
An improved general amino acid replacement matrix
-
PubMed
-
Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008; 25:1307-1320. PubMed http://dx.doi.org/10.1093/molbev/msn067
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1307-1320
-
-
le, S.Q.1
Gascuel, O.2
-
60
-
-
0037197668
-
Proton transfers in the pho-tochemical reaction cycle of proteorhodopsin
-
PubMed
-
Dioumaev AK, Brown LS, Shih J, Spudich EN, Spudich JL, Lanyi JK. Proton transfers in the pho-tochemical reaction cycle of proteorhodopsin. Bi-ochemistry 2002; 41:5348-5358. PubMed http://dx.doi.org/10.1021/bi025563x
-
(2002)
Bi-ochemistry
, vol.41
, pp. 5348-5358
-
-
Dioumaev, A.K.1
Brown, L.S.2
Shih, J.3
Spudich, E.N.4
Spudich, J.L.5
Lanyi, J.K.6
-
61
-
-
0141817991
-
Spectroscopic and photochemical characterization of a deep ocean proteorhodopsin
-
PubMed
-
Wang WW, Sineshchekov A, Spudich EN, Spudich JL. Spectroscopic and photochemical characterization of a deep ocean proteorhodopsin. J Biol Chem 2003; 278:33985-33991. PubMed http://dx.doi.org/10.1074/jbc.M305716200
-
(2003)
J Biol Chem
, vol.278
, pp. 33985-33991
-
-
Wang, W.W.1
Sineshchekov, A.2
Spudich, E.N.3
Spudich, J.L.4
-
62
-
-
0038391981
-
Di-versification and spectral tuning in marine proteorhodopsins
-
PubMed
-
Man D, Wang W, Sabehi G, Aravind L, Post AF, Massana R, Spudich EN, Spudich JL, Beja O. Di-versification and spectral tuning in marine proteorhodopsins. EMBO J 2003; 22:1725-1731. PubMed http://dx.doi.org/10.1093/emboj/cdg183
-
(2003)
EMBO J
, vol.22
, pp. 1725-1731
-
-
Man, D.1
Wang, W.2
Sabehi, G.3
Aravind, L.4
Post, A.F.5
Massana, R.6
Spudich, E.N.7
Spudich, J.L.8
Beja, O.9
-
63
-
-
77952279613
-
Constitutive ex-pression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea
-
PubMed
-
Riedel T, Tomasch J, Buchholz I, Jacobs J, Kollenberg M, Gerdts G, Wichels A, Brinkhoff T, Cypionka H, Wagner-Döbler I. Constitutive ex-pression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl Environ Microbiol 2010; 76:3187-3197. PubMed http://dx.doi.org/10.1128/AEM.02971-09
-
(2010)
Appl Environ Microbiol
, vol.76
, pp. 3187-3197
-
-
Riedel, T.1
Tomasch, J.2
Buchholz, I.3
Jacobs, J.4
Kollenberg, M.5
Gerdts, G.6
Wichels, A.7
Brinkhoff, T.8
Cypionka, H.9
Wagner-Döbler, I.10
-
64
-
-
80052340733
-
Complete Genome Sequences of Krokinobacter sp. Strain 4H-3-7-5 and Lacinutrix sp. Strain 5H-3-7-4, Polysaccharide-Degrading Members of the Family
-
PubMed
-
Klippel B, Lochner A, Bruce DC, Walston DK, Detter C, Goodwin LA, Han J, Han S, Hauser L, Land ML, et al. Complete Genome Sequences of Krokinobacter sp. Strain 4H-3-7-5 and Lacinutrix sp. Strain 5H-3-7-4, Polysaccharide-Degrading Members of the Family Flavobacteriaceae. J Bacteriol 2011; 193:4545-4546. PubMed http://dx.doi.org/10.1128/JB.05518-11
-
(2011)
Flavobacteriaceae. J Bacteriol
, vol.193
, pp. 4545-4546
-
-
Klippel, B.1
Lochner, A.2
Bruce, D.C.3
Walston, D.K.4
Detter, C.5
Goodwin, L.A.6
Han, J.7
Han, S.8
Hauser, L.9
Land, M.L.10
-
65
-
-
27844540777
-
Dokdonia donghaensis gen. nov., sp. nov., isolated from sea water
-
PubMed
-
Yoon JH, Kang SJ, Lee CH, Oh TK. Dokdonia donghaensis gen. nov., sp. nov., isolated from sea water. Int J Syst Evol Microbiol 2005; 55:2323-2328. PubMed http://dx.doi.org/10.1099/ijs.0.63817-0
-
(2005)
Int J Syst Evol Microbiol
, vol.55
, pp. 2323-2328
-
-
Yoon, J.H.1
Kang, S.J.2
Lee, C.H.3
Oh, T.K.4
-
66
-
-
84879101233
-
Reclassification of the three Krokinobacter species into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphora comb. nov. and Dokdonia eikasta comb. nov. and emended description of the genus
-
Yoon et al. 2005. Int J Syst Evol Microbiol 2011; [Epup ahead of print]
-
Yoon JH, Kang SJ, Park S, Oh TK. Reclassification of the three Krokinobacter species into the genus Dokdonia as Dokdonia genika comb. nov., Dokdonia diaphora comb. nov. and Dokdonia eikasta comb. nov. and emended description of the genus Dokdonia Yoon et al. 2005. Int J Syst Evol Microbiol 2011; [Epup ahead of print].
-
Dokdonia
-
-
Yoon, J.H.1
Kang, S.J.2
Park, S.3
Oh, T.K.4
-
67
-
-
84863998953
-
Draft Genome Sequence of Gillisia sp strain CBA3202, a novel member of the genus Gillisia, which belongs to the family
-
PubMed
-
Nam YD, Lee HW, Lee M, Yim KJ, Kim KN, Roh SW, Kim D. Draft Genome Sequence of Gillisia sp strain CBA3202, a novel member of the genus Gillisia, which belongs to the family Flavobacteriaceae. J Bacteriol 2012; 194:3739. PubMed http://dx.doi.org/10.1128/JB.00631-12
-
(2012)
Flavobacteriaceae. J Bacteriol
, vol.194
, pp. 3739
-
-
Nam, Y.D.1
Lee, H.W.2
Lee, M.3
Yim, K.J.4
Kim, K.N.5
Roh, S.W.6
Kim, D.7
-
68
-
-
77952891045
-
Standard operat-ing procedure for calculating genome-to-genome distances based on high-scoring segment pairs
-
PubMed
-
Auch AF, Klenk HP. Göker, M. Standard operat-ing procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142-148. PubMed http://dx.doi.org/10.4056/sigs.541628
-
(2010)
Stand Genomic Sci
, vol.2
, pp. 142-148
-
-
Auch, A.F.1
Klenk, H.P.2
Göker, M.3
-
69
-
-
0027801562
-
Phyloge-netic diversity of aggregate-attached versus free-living marine bacterial assemblages
-
DeLong EF, Franks DG, Alldredge AL. Phyloge-netic diversity of aggregate-attached versus free-living marine bacterial assemblages. Limnol Oceanogr 1993; 38:924-934. http://dx.doi.org/10.4319/lo.1993.38.5.0924
-
(1993)
Limnol Oceanogr
, vol.38
, pp. 924-934
-
-
DeLong, E.F.1
Franks, D.G.2
Alldredge, A.L.3
-
70
-
-
8744282719
-
Changes in bacterioplancton composition under different phytoplankton regimes
-
PubMed
-
Pinhassi J, Sala MM, Havskum H, Peters F, Guadayol O, Malits A, Marrasé C. Changes in bacterioplancton composition under different phytoplankton regimes. Appl Environ Microbiol 2004; 70:6753-6766. PubMed http://dx.doi.org/10.1128/AEM.70.11.6753-6766.2004
-
(2004)
Appl Environ Microbiol
, vol.70
, pp. 6753-6766
-
-
Pinhassi, J.1
Sala, M.M.2
Havskum, H.3
Peters, F.4
Guadayol, O.5
Malits, A.6
Marrasé, C.7
-
71
-
-
0033951021
-
Dynamics of bacterial community composition and activity during a mesocosm diatom bloom
-
PubMed
-
Riemann L, Steward GF, Azam F. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl Environ Microbiol 2000; 66:578-587. PubMed http://dx.doi.org/10.1128/AEM.66.2.578-587.2000
-
(2000)
Appl Environ Microbiol
, vol.66
, pp. 578-587
-
-
Riemann, L.1
Steward, G.F.2
Azam, F.3
-
72
-
-
0034769801
-
Bacterial gliding motility: Multiple mechanisms for cell movement over surfaces
-
PubMed
-
McBride MJ. Bacterial gliding motility: multiple mechanisms for cell movement over surfaces. Annu Rev Microbiol 2001; 55:49-75. PubMed http://dx.doi.org/10.1146/annurev.micro.55.1.49
-
(2001)
Annu Rev Microbiol
, vol.55
, pp. 49-75
-
-
McBride, M.J.1
-
73
-
-
2642529310
-
Cytophaga-Flavobacterium gliding motility
-
PubMed
-
McBride MJ. Cytophaga-Flavobacterium gliding motility. J Mol Microbiol Biotechnol 2004; 7:63-71. PubMed http://dx.doi.org/10.1159/000077870
-
(2004)
J Mol Microbiol Biotechnol
, vol.7
, pp. 63-71
-
-
McBride, M.J.1
|