-
1
-
-
0029653518
-
Whole-genome random sequencing and assembly of haemophilus influenzae rd
-
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, et al. (1995) Whole-genome random sequencing and assembly of haemophilus influenzae rd. Science 269: 496-512.
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
Clayton, R.A.4
Kirkness, E.F.5
-
2
-
-
19944408938
-
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
-
DOI 10.1038/nature03170
-
Moran MMA, Buchan A, González JMJ, Heidelberg JJF, Whitman WWB, et al. (2004) Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432: 910-913. (Pubitemid 40037153)
-
(2004)
Nature
, vol.432
, Issue.7019
, pp. 910-913
-
-
Moran, M.A.1
Buchan, A.2
Gonzalez, J.M.3
Heidelberg, J.F.4
Whitman, W.B.5
Klene, R.P.6
Henriksen, J.R.7
King, G.M.8
Belas, R.9
Fuqua, C.10
Brinkac, L.11
Lewis, M.12
Johri, S.13
Weaver, B.14
Pai, G.15
Elsen, J.A.16
Rahe, E.17
Sheldon, W.M.18
Ye, W.19
Miller, T.R.20
Carlton, J.21
Rasko, D.A.22
Paulsen, I.T.23
Ren, Q.24
Daugherty, S.C.25
Deboy, R.T.26
Dodson, R.J.27
Durkin, A.S.28
Madupu, R.29
Nelson, W.C.30
Sullivan, S.A.31
Rosovitz, M.J.32
Haft, D.H.33
Selengut, J.34
Ward, N.35
more..
-
3
-
-
4344713183
-
The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments
-
DOI 10.1111/j.1462-2920.2004.00665.x
-
Rabus R, Ruepp A, Frickey T, Rattei T, Fartmann B, et al. (2004) The genome of Desulfotalea psy-chrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ Microbiol 6: 887-902. (Pubitemid 39123243)
-
(2004)
Environmental Microbiology
, vol.6
, Issue.9
, pp. 887-902
-
-
Rabus, R.1
Ruepp, A.2
Frickey, T.3
Rattei, T.4
Fartmann, B.5
Stark, M.6
Bauer, M.7
Zibat, A.8
Lombardot, T.9
Becker, I.10
Amann, J.11
Gellner, K.12
Teeling, H.13
Leuschner, W.D.14
Glockner, F.-O.15
Lupas, A.N.16
Amann, R.17
Klenk, H.-P.18
-
4
-
-
0042878464
-
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation
-
DOI 10.1038/nature01947
-
Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, et al. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-7. (Pubitemid 37064302)
-
(2003)
Nature
, vol.424
, Issue.6952
, pp. 1042-1047
-
-
Rocap, G.1
Larimer, F.W.2
Lamerdin, J.3
Malfatti, S.4
Chain, P.5
Ahlgren, N.A.6
Arellano, A.7
Coleman, M.8
Hauser, L.9
Hess, W.R.10
Johnson, Z.I.11
Land, M.12
Lindell, D.13
Post, A.F.14
Regala, W.15
Shah, M.16
Shaw, S.L.17
Steglich, C.18
Sullivan, M.B.19
Ting, C.S.20
Tolonen, A.21
Webb, E.A.22
Zinser, E.R.23
Chisholm, S.W.24
more..
-
5
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
DOI 10.1038/nature02340
-
Tyson G, Chapman J, Hugenholtz P, Allen E, Ram R, et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43. (Pubitemid 38332350)
-
(2004)
Nature
, vol.428
, Issue.6978
, pp. 37-43
-
-
Tyson, G.W.1
Chapman, J.2
Hugenholtz, P.3
Allen, E.E.4
Ram, R.J.5
Richardson, P.M.6
Solovyev, V.V.7
Rubin, E.M.8
Rokhsar, D.S.9
Banfield, J.F.10
-
6
-
-
19944399720
-
Distributions of microbial activities in deep subseafloor sediments
-
DOI 10.1126/science.1101155
-
D'Hondt S, Jørgensen BB, Miller DJ, Batzke A, Blake R, et al. (2004) Distributions of microbial activities in deep subseafloor sediments. Science 306: 2216-21. (Pubitemid 40024451)
-
(2004)
Science
, vol.306
, Issue.5705
, pp. 2216-2221
-
-
D'Hondt, S.1
Jorgensen, B.B.2
Miller, D.J.3
Batzke, A.4
Blake, R.5
Cragg, B.A.6
Cypionka, H.7
Dickens, G.R.8
Ferdelman, T.9
Hinrichs, K.-U.10
Holm, N.G.11
Mitterer, R.12
Spivack, A.13
Wang, G.14
Bekins, B.15
Engelen, B.16
Ford, K.17
Gettemy, G.18
Rutherford, S.D.19
Sass, H.20
Skilbeck, C.G.21
Aiello, I.W.22
Guerin, G.23
House, C.H.24
Inagaki, F.25
Meister, P.26
Naehr, T.27
Niitsuma, S.28
Parkes, R.J.29
Schippers, A.30
Smith, D.C.31
Teske, A.32
Wiegel, J.33
Padilla, C.N.34
Acosta, J.L.S.35
more..
-
7
-
-
33750332574
-
Long-term sustainability of a high-energy, low-diversity crustal biome
-
Lin LH, Wang PL, Rumble D, Lippmann-Pipke J, Boice E, et al. (2006) Long-term sustainability of a high-energy, low-diversity crustal biome. Science 314: 479-482.
-
(2006)
Science
, vol.314
, pp. 479-482
-
-
Lin, L.H.1
Wang, P.L.2
Rumble, D.3
Lippmann-Pipke, J.4
Boice, E.5
-
9
-
-
33845965687
-
Synthetic biology projects in vitro
-
DOI 10.1101/gr.5776007
-
Forster AC, Church GM (2007) Synthetic biology projects in vitro. Genome res 17: 1-6. (Pubitemid 46041659)
-
(2007)
Genome Research
, vol.17
, Issue.1
, pp. 1-6
-
-
Forster, A.C.1
Church, G.M.2
-
10
-
-
0028829125
-
The minimal gene complement of Mycoplasma genitalium
-
Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
-
(1995)
Science
, vol.270
, pp. 397-403
-
-
Fraser, C.M.1
Gocayne, J.D.2
White, O.3
Adams, M.D.4
Clayton, R.A.5
-
11
-
-
31044439550
-
Essential genes of a minimal bacterium
-
DOI 10.1073/pnas.0510013103
-
Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, et al. (2006) Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 103: 425-30. (Pubitemid 43122417)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.2
, pp. 425-430
-
-
Glass, J.I.1
Assad-Garcia, N.2
Alperovich, N.3
Yooseph, S.4
Lewis, M.R.5
Maruf, M.6
Hutchison III, C.A.7
Smith, H.O.8
Venter, J.C.9
-
13
-
-
0035843908
-
Genes lost and genes found: Evolution of bacterial pathogenesis and symbiosis
-
Ochman H, Moran NA (2001) Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292: 1096-9.
-
(2001)
Science
, vol.292
, pp. 1096-1099
-
-
Ochman, H.1
Moran, N.A.2
-
14
-
-
0032127258
-
Reductive evolution of resident genomes
-
DOI 10.1016/S0966-842X(98)01312-2, PII S0966842X98013122
-
Andersson SG, Kurland CG (1998) Reductive evolution of resident genomes. Trends microbiol 6: 263-8. (Pubitemid 28343306)
-
(1998)
Trends in Microbiology
, vol.6
, Issue.7
, pp. 263-268
-
-
Andersson, S.G.E.1
Kurland, C.G.2
-
15
-
-
84355161780
-
The significance of nitrogen cost minimization in proteomes of marine microorganisms
-
Grzymski JJ, Dussaq AM (2012) The significance of nitrogen cost minimization in proteomes of marine microorganisms. ISME J 6: 71-80.
-
(2012)
ISME J
, vol.6
, pp. 71-80
-
-
Grzymski, J.J.1
Dussaq, A.M.2
-
16
-
-
84879932140
-
Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean
-
10.1073/pnas.1304246110
-
Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, et al. (2013) Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc Natl Acad Sci USA 10.1073/pnas.1304246110.
-
(2013)
Proc Natl Acad Sci USA
-
-
Swan, B.K.1
Tupper, B.2
Sczyrba, A.3
Lauro, F.M.4
Martinez-Garcia, M.5
-
17
-
-
23844446418
-
Genetics: Genome streamlining in a cosmopolitan oceanic bacterium
-
DOI 10.1126/science.1114057
-
Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science (New York, NY) 309: 1242-5. (Pubitemid 41170917)
-
(2005)
Science
, vol.309
, Issue.5738
, pp. 1242-1245
-
-
Giovannoni, S.J.1
Tripp, H.J.2
Givan, S.3
Podar, M.4
Vergin, K.L.5
Baptista, D.6
Bibbs, L.7
Eads, J.8
Richardson, T.H.9
Noordewier, M.10
Rappe, M.S.11
Short, J.M.12
Carrington, J.C.13
Mathur, E.J.14
-
18
-
-
84860992281
-
The use of information theory in evolutionary biology
-
Adami C (2012) The use of information theory in evolutionary biology. Ann NY Acad Sci 1256: 49-65.
-
(2012)
Ann NY Acad Sci
, vol.1256
, pp. 49-65
-
-
Adami, C.1
-
19
-
-
58549116944
-
Natural selection maximizes fisher information
-
Frank SA (2009) Natural selection maximizes fisher information. J Evol Biol 22: 231-44.
-
(2009)
J Evol Biol
, vol.22
, pp. 231-244
-
-
Frank, S.A.1
-
20
-
-
58649113631
-
Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples
-
Liu Z, Venkatesh SS, Maley CC (2008) Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples. BMC Genomics 9: 509.
-
(2008)
BMC Genomics
, vol.9
, pp. 509
-
-
Liu, Z.1
Venkatesh, S.S.2
Maley, C.C.3
-
21
-
-
0024593127
-
Linguistics of nucleotide sequences II: Stationary words in genetic texts and the zonal structure of DNA
-
Pevzner PA, Borodovsky MYU, Mironov AA (1989) Linguistics of nucleotide sequences. II: Stationary words in genetic texts and the zonal structure of DNA. J Biomol Struct Dyn 6: 1027-38. (Pubitemid 19117704)
-
(1989)
Journal of Biomolecular Structure and Dynamics
, vol.6
, Issue.5
, pp. 1027-1038
-
-
Pevzner, P.A.1
Borodovsky, M.Y.2
Mironov, A.A.3
-
22
-
-
35949004397
-
Reconsidering the significance of genomic word frequencies
-
DOI 10.1016/j.tig.2007.07.008, PII S0168952507002983
-
Csurös M, Noé L, Kucherov G (2007) Reconsidering the significance of genomic word frequencies. Trends Genet 23: 543-6. (Pubitemid 350064533)
-
(2007)
Trends in Genetics
, vol.23
, Issue.11
, pp. 543-546
-
-
Csuros, M.1
Noe, L.2
Kucherov, G.3
-
24
-
-
0029916916
-
The Blocks database - A system for protein classification
-
DOI 10.1093/nar/24.1.197
-
Pietrokovski S, Henikoff JG, Henikoff S (1996) The blocks database-a system for protein classification. Nucleic Acids Res 24: 197-200. (Pubitemid 26085765)
-
(1996)
Nucleic Acids Research
, vol.24
, Issue.1
, pp. 197-200
-
-
Pietrokovski, S.1
Henikoff, J.G.2
Henikoff, S.3
-
26
-
-
70349458100
-
The genomic basis of trophic strategy in marine bacteria
-
Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, et al. (2009) The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci USA 106: 15527-33.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 15527-15533
-
-
Lauro, F.M.1
McDougald, D.2
Thomas, T.3
Williams, T.J.4
Egan, S.5
-
27
-
-
0029866448
-
Accelerated evolution and Muller's rachet in endosymbiotic bacteria
-
Moran N (1996) Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci USA 93: 2873-2878.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 2873-2878
-
-
Moran, N.1
-
28
-
-
0024514063
-
Linguistics of nucleotide sequences I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words
-
Pevzner PA, Borodovsky MYU, Mironov AA (1989) Linguistics of nucleotide sequences. I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words. J Biomol Struct Dyn 6: 1013-26. (Pubitemid 19117703)
-
(1989)
Journal of Biomolecular Structure and Dynamics
, vol.6
, Issue.5
, pp. 1013-1026
-
-
Pevzner, P.A.1
Borodovsky, M.Y.2
Mironov, A.A.3
-
29
-
-
84868365613
-
The spatial architecture of protein function and adaptation
-
McLaughlin RN Jr, Poelwijk FJ, Raman A, Gosal WS, Ranganathan R (2012) The spatial architecture of protein function and adaptation. Nature 491: 138-42.
-
(2012)
Nature
, vol.491
, pp. 138-142
-
-
McLaughlin Jr., R.N.1
Poelwijk, F.J.2
Raman, A.3
Gosal, W.S.4
Ranganathan, R.5
-
30
-
-
0031582635
-
Genetic code synonym quotas and amino acid complexity: Cutting the cost of proteins?
-
Dufton MJ (1997) Genetic code synonym quotas and amino acid complexity: cutting the cost of proteins? J Theor Biol 187: 165-73.
-
(1997)
J Theor Biol
, vol.187
, pp. 165-173
-
-
Dufton, M.J.1
-
31
-
-
0033616712
-
Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species
-
DOI 10.1073/pnas.96.7.3578
-
Haney PJ, Badger JH, Buldak GL, Reich CI, Woese CR, et al. (1999) Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc Natl Acad Sci USA 96: 3578-83. (Pubitemid 29168952)
-
(1999)
Proceedings of the National Academy of Sciences of the United States of America
, vol.96
, Issue.7
, pp. 3578-3583
-
-
Haney, P.J.1
Badger, J.H.2
Buldak, G.L.3
Reich, C.I.4
Woese, C.R.5
Olsen, G.J.6
-
32
-
-
0037308511
-
Cost-minimization of amino acid usage
-
Seligmann H (2003) Cost-minimization of amino acid usage. J Mol Evol 56: 151-61.
-
(2003)
J Mol Evol
, vol.56
, pp. 151-161
-
-
Seligmann, H.1
-
33
-
-
0028958292
-
The usage of oligopeptides in proteins correlates negatively with molecular weight
-
Barrai I, Volinia S, Scapoli C (1995) The usage of oligopeptides in proteins correlates negatively with molecular weight. Int J Prot Res 45: 326-331.
-
(1995)
Int J Prot Res
, vol.45
, pp. 326-331
-
-
Barrai, I.1
Volinia, S.2
Scapoli, C.3
-
34
-
-
84887916087
-
Regularized discriminant analysis
-
Friedman J (1989) Regularized discriminant analysis. J Am Stat Assoc 84: 165-175.
-
(1989)
J Am Stat Assoc
, vol.84
, pp. 165-175
-
-
Friedman, J.1
-
35
-
-
0030670395
-
Structural characterization of an abnormally cross-linked muropeptide dimer that is accumulated in the peptidoglycan of methicillin- and cefotaxime-resistant mutants of Staphylococcus aureus
-
DOI 10.1074/jbc.272.46.29053
-
Boneca IG, Xu N, Gage DA, de Jonge BL, Tomasz A (1997) Structural characterization of an abnormally cross-linked muropeptide dimer that is accumulated in the peptidoglycan of methicillinand cefotaxime-resistant mutants of staphylococcus aureus. J Biol Chem 272: 29053-9. (Pubitemid 27498192)
-
(1997)
Journal of Biological Chemistry
, vol.272
, Issue.46
, pp. 29053-29059
-
-
Boneca, I.G.1
Xu, N.2
Gage, D.A.3
De Jonge, B.L.M.4
Tomaszl, A.5
-
36
-
-
0027394738
-
Abnormal peptidoglycan produced in a methicillin-resistant strain of staphylococcus aureus grown in the presence of methicillin: Functional role for penicillin-binding protein 2a in cell wall synthesis
-
de Jonge BL, Tomasz A (1993) Abnormal peptidoglycan produced in a methicillin-resistant strain of staphylococcus aureus grown in the presence of methicillin: functional role for penicillin-binding protein 2a in cell wall synthesis. Antimicrob Agents Chemother 37: 342-6.
-
(1993)
Antimicrob Agents Chemother
, vol.37
, pp. 342-346
-
-
De Jonge, B.L.1
Tomasz, A.2
-
37
-
-
0035932508
-
Laws of form revisited
-
DOI 10.1038/35068645
-
Denton M, Marshall C (2001) Protein folds: laws of form revisited. Nature 410: 417. (Pubitemid 32240025)
-
(2001)
Nature
, vol.410
, Issue.6827
, pp. 417
-
-
Denton, M.1
Marshall, C.2
-
38
-
-
70349775678
-
Exploration of uncharted regions of the protein universe
-
Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, et al. (2009) Exploration of uncharted regions of the protein universe. PLoS Biol 7: e1000205.
-
(2009)
PLoS Biol
, vol.7
-
-
Jaroszewski, L.1
Li, Z.2
Krishna, S.S.3
Bakolitsa, C.4
Wooley, J.5
-
39
-
-
39449112551
-
Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome
-
DOI 10.1126/science.1151721
-
Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, et al. (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319: 1215-20. (Pubitemid 351323011)
-
(2008)
Science
, vol.319
, Issue.5867
, pp. 1215-1220
-
-
Gibson, D.G.1
Benders, G.A.2
Andrews-Pfannkoch, C.3
Denisova, E.A.4
Baden-Tillson, H.5
Zaveri, J.6
Stockwell, T.B.7
Brownley, A.8
Thomas, D.W.9
Algire, M.A.10
Merryman, C.11
Young, L.12
Noskov, V.N.13
Glass, J.I.14
Venter, J.C.15
Hutchison III, C.A.16
Smith, H.O.17
-
40
-
-
0035905809
-
Synthesizing life
-
DOI 10.1038/35053176
-
Szostak JW, Bartel DP, Luisi PL (2001) Synthesizing life. Nature 409: 387-90. (Pubitemid 32151251)
-
(2001)
Nature
, vol.409
, Issue.6818
, pp. 387-390
-
-
Szostak, J.W.1
Bartel, D.P.2
Luisi, P.L.3
-
43
-
-
0035072551
-
Clustering of highly homologous sequences to reduce the size of large protein databases
-
Li W, Jaroszewski L, Godzik A (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17: 282-283. (Pubitemid 32288218)
-
(2001)
Bioinformatics
, vol.17
, Issue.3
, pp. 282-283
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
44
-
-
0036169928
-
Tolerating some redundancy significantly speeds up clustering of large protein databases
-
Li W, Jaroszewski L, Godzik A (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18: 77-82. (Pubitemid 34145034)
-
(2002)
Bioinformatics
, vol.18
, Issue.1
, pp. 77-82
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
|