-
1
-
-
0043009767
-
Differential expression in SAGE: Accounting for normal between-library variation
-
doi: 10.1093/bioinformatics/btg173
-
Baggerly KA, Deng L, Morris JS, Aldaz CM. 2003. Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics 19:1477-1483. doi: 10.1093/bioinformatics/btg173.
-
(2003)
Bioinformatics
, vol.19
, pp. 1477-1483
-
-
Baggerly, K.A.1
Deng, L.2
Morris, J.S.3
Aldaz, C.M.4
-
2
-
-
33751228400
-
ATP-dependent proteases of bacteria: Recognition logic and operating principles
-
doi: 10.1016/j.tibs.2006.10.006
-
Baker TA, Sauer RT. 2006. ATP-dependent proteases of bacteria: recognition logic and operating principles. Trends in Biochemical Sciences 31:647-653. doi: 10.1016/j.tibs.2006.10.006.
-
(2006)
Trends in Biochemical Sciences
, vol.31
, pp. 647-653
-
-
Baker, T.A.1
Sauer, R.T.2
-
3
-
-
70350641005
-
Genome evolution and adaptation in a long-term experiment with Escherichia coli
-
doi: 10.1038/nature08480
-
Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461:1243-1247. doi: 10.1038/nature08480.
-
(2009)
Nature
, vol.461
, pp. 1243-1247
-
-
Barrick, J.E.1
Yu, D.S.2
Yoon, S.H.3
Jeong, H.4
Oh, T.K.5
Schneider, D.6
Lenski, R.E.7
Kim, J.F.8
-
5
-
-
34748815654
-
The number of colonies allowable on satisfactory agar plates
-
Breed RS, Dotterrer WD. 1916. The number of colonies allowable on satisfactory agar plates. Journal of Bacteriology 1:321-331.
-
(1916)
Journal of Bacteriology
, vol.1
, pp. 321-331
-
-
Breed, R.S.1
Dotterrer, W.D.2
-
6
-
-
28144449309
-
Deinococcus radiodurans-the consummate survivor
-
doi: 10.1038/nrmicro1264
-
Cox MM, Battista JR. 2005. Deinococcus radiodurans-the consummate survivor. Nature Reviews Microbiology 3:882-892. doi: 10.1038/nrmicro1264.
-
(2005)
Nature Reviews Microbiology
, vol.3
, pp. 882-892
-
-
Cox, M.M.1
Battista, J.R.2
-
7
-
-
0034595010
-
The importance of repairing stalled replication forks
-
doi: 10.1038/35003501
-
Cox MM, Goodman MF, Kreuzer KN, Sherratt DJ, Sandler SJ, Marians KJ. 2000. The importance of repairing stalled replication forks. Nature 404:37-41. doi: 10.1038/35003501.
-
(2000)
Nature
, vol.404
, pp. 37-41
-
-
Cox, M.M.1
Goodman, M.F.2
Kreuzer, K.N.3
Sherratt, D.J.4
Sandler, S.J.5
Marians, K.J.6
-
8
-
-
77957802374
-
Studying bacterial transcriptomes using RNA-seq
-
doi: 10.1016/j.mib.2010.09.009
-
Croucher NJ, Thomson NR. 2010. Studying bacterial transcriptomes using RNA-seq. Current Opinion in Microbiology 13:619-624. doi: 10.1016/j.mib.2010.09.009.
-
(2010)
Current Opinion in Microbiology
, vol.13
, pp. 619-624
-
-
Croucher, N.J.1
Thomson, N.R.2
-
9
-
-
60749095652
-
OPINION A new perspective on radiation resistance based on Deinococcus radiodurans
-
doi: 10.1038/nrmicro2073
-
Daly MJ. 2009. OPINION A new perspective on radiation resistance based on Deinococcus radiodurans. Nature Reviews Microbiology 7:237-245. doi: 10.1038/nrmicro2073.
-
(2009)
Nature Reviews Microbiology
, vol.7
, pp. 237-245
-
-
Daly, M.J.1
-
10
-
-
84855352363
-
Death by protein damage in irradiated cells
-
doi: 10.1016/j.dnarep.2011.10.024
-
Daly MJ. 2012. Death by protein damage in irradiated cells. DNA Repair 11:12-21. doi: 10.1016/j.dnarep.2011.10.024.
-
(2012)
DNA Repair
, vol.11
, pp. 12-21
-
-
Daly, M.J.1
-
11
-
-
8344278843
-
Accumulation of Mn(II) in, Deinococcus radiodurans facilitates gamma-radiation resistance
-
doi: 10.1126/science.1103185
-
Daly MJ, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Venkateswaran A, Hess M, Omelchenko MV, Kostandarithes HM, Makarova KS, Wackett LP, Fredrickson JK, Ghosal D. 2004. Accumulation of Mn(II) in, Deinococcus radiodurans facilitates gamma-radiation resistance. Science 306:1025-1028. doi: 10.1126/science.1103185.
-
(2004)
Science
, vol.306
, pp. 1025-1028
-
-
Daly, M.J.1
Gaidamakova, E.K.2
Matrosova, V.Y.3
Vasilenko, A.4
Zhai, M.5
Venkateswaran, A.6
Hess, M.7
Omelchenko, M.V.8
Kostandarithes, H.M.9
Makarova, K.S.10
Wackett, L.P.11
Fredrickson, J.K.12
Ghosal, D.13
-
13
-
-
0030574274
-
Redox signaling and gene control in the Escherichia coli soxRS oxidative stress regulon-A review
-
doi: 10.1016/S0378-1119(96)00329-0
-
Demple B. 1996. Redox signaling and gene control in the Escherichia coli soxRS oxidative stress regulon-A review. Gene 179:53-57. doi: 10.1016/S0378-1119(96)00329-0.
-
(1996)
Gene
, vol.179
, pp. 53-57
-
-
Demple, B.1
-
14
-
-
38649092391
-
Transcription profiling of the stringent response in Escherichia coli
-
doi: 10.1128/JB.01092-07
-
Durfee T, Hansen AM, Zhi H, Blattner FR, Jin DJ. 2008. Transcription profiling of the stringent response in Escherichia coli. Journal of Bacteriology 190:1084-1096. doi: 10.1128/JB.01092-07.
-
(2008)
Journal of Bacteriology
, vol.190
, pp. 1084-1096
-
-
Durfee, T.1
Hansen, A.M.2
Zhi, H.3
Blattner, F.R.4
Jin, D.J.5
-
15
-
-
0038441327
-
Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation
-
doi: 10.1038/nrg1088
-
Elena SF, Lenski RE. 2003. Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation. Nature Reviews Genetics 4:457-469. doi: 10.1038/nrg1088.
-
(2003)
Nature Reviews Genetics
, vol.4
, pp. 457-469
-
-
Elena, S.F.1
Lenski, R.E.2
-
16
-
-
0004039907
-
-
2nd ed. Sunderland, Massachusetts: Sinauer
-
Futuyama DJ. 1986. Evolutionary Biology, 2nd ed. Sunderland, Massachusetts: Sinauer.
-
(1986)
Evolutionary Biology
-
-
Futuyama, D.J.1
-
17
-
-
2542583245
-
The fate of competing beneficial mutations in an asexual population
-
doi: 10.1023/A:1017067816551
-
Gerrish PJ, Lenski RE. 1998. The fate of competing beneficial mutations in an asexual population. Genetica 103:127-144. doi: 10.1023/A:1017067816551.
-
(1998)
Genetica
, vol.103
, pp. 127-144
-
-
Gerrish, P.J.1
Lenski, R.E.2
-
18
-
-
67749132534
-
Directed evolution of radiation resistance in Escherichia coli
-
doi: 10.1128/JB.00502-09
-
Harris DR, Pollock SV, Wood EA, Goiffon RJ, Klingele AJ, Cabot EL, Schackwitz W, Martin J, Eggington J, Durfee TJ, Middle CM, Norton JE, Popelars MC, Li H, Klugman SA, Hamilton LL, Bane LB, Pennacchio LA, Albert TJ, Perna NT, Cox MM, Battista JR. 2009. Directed evolution of radiation resistance in Escherichia coli. Journal of Bacteriology 191:5240-5252. doi: 10.1128/JB.00502-09.
-
(2009)
Journal of Bacteriology
, vol.191
, pp. 5240-5252
-
-
Harris, D.R.1
Pollock, S.V.2
Wood, E.A.3
Goiffon, R.J.4
Klingele, A.J.5
Cabot, E.L.6
Schackwitz, W.7
Martin, J.8
Eggington, J.9
Durfee, T.J.10
Middle, C.M.11
Norton, J.E.12
Popelars, M.C.13
Li, H.14
Klugman, S.A.15
Hamilton, L.L.16
Bane, L.B.17
Pennacchio, L.A.18
Albert, T.J.19
Perna, N.T.20
Cox, M.M.21
Battista, J.R.22
more..
-
19
-
-
84859899271
-
New insights into bacterial adaptation through in vivo and in silico experimental evolution
-
doi: 10.1038/nrmicro2750
-
Hindre T, Knibbe C, Beslon G, Schneider D. 2012. New insights into bacterial adaptation through in vivo and in silico experimental evolution. Nature Reviews Microbiology 10:352-365. doi: 10.1038/nrmicro2750.
-
(2012)
Nature Reviews Microbiology
, vol.10
, pp. 352-365
-
-
Hindre, T.1
Knibbe, C.2
Beslon, G.3
Schneider, D.4
-
20
-
-
0032457906
-
Oxygen sensing by the global regulator, FNR: The role of the iron-sulfur cluster
-
doi: 10.1111/j.1574-6976.1998.tb00375.x
-
Kiley PJ, Beinert H. 1998. Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster. FEMS Microbiology Reviews 22:341-352. doi: 10.1111/j.1574-6976.1998.tb00375.x.
-
(1998)
FEMS Microbiology Reviews
, vol.22
, pp. 341-352
-
-
Kiley, P.J.1
Beinert, H.2
-
21
-
-
77956269639
-
Protein damage and death by radiation in Escherichia coli and Deinococcus radiodurans
-
doi: 10.1073/pnas.1009312107
-
Krisko A, Radman M. 2010. Protein damage and death by radiation in Escherichia coli and Deinococcus radiodurans. Proceedings of the National Academy of Sciences of the United States of America 107:14373-14377. doi: 10.1073/pnas.1009312107.
-
(2010)
Proceedings of the National Academy of Sciences of the United States of America
, vol.107
, pp. 14373-14377
-
-
Krisko, A.1
Radman, M.2
-
22
-
-
0026279651
-
Long-term experimental evolution in Escherichia-coli.1. Adaptation and divergence during 2,000 generations
-
doi: 10.1086/285289
-
Lenski RE, Rose MR, Simpson SC, Tadler SC. 1991. Long-term experimental evolution in Escherichia-coli.1. Adaptation and divergence during 2,000 generations. American Naturalist 138:1315-1341. doi: 10.1086/285289.
-
(1991)
American Naturalist
, vol.138
, pp. 1315-1341
-
-
Lenski, R.E.1
Rose, M.R.2
Simpson, S.C.3
Tadler, S.C.4
-
23
-
-
0037428220
-
Ringlike structure of the Deinococcus radiodurans genome: A key to radioresistance?
-
doi: 10.1126/science.1077865
-
Levin-Zaidman S, Englander J, Shimoni E, Sharma AK, Minton KW, Minsky A. 2003. Ringlike structure of the Deinococcus radiodurans genome: A key to radioresistance? Science 299:254-256. doi: 10.1126/science.1077865.
-
(2003)
Science
, vol.299
, pp. 254-256
-
-
Levin-Zaidman, S.1
Englander, J.2
Shimoni, E.3
Sharma, A.K.4
Minton, K.W.5
Minsky, A.6
-
24
-
-
72249113406
-
rNMR: Open source software for identifying and quantifying metabolites in NMR spectra
-
doi: 10.1002/mrc.2526, S123-S1S6
-
Lewis IA, Schommer SC, Markley JL. 2009. rNMR: open source software for identifying and quantifying metabolites in NMR spectra. Magnetic Resonance in Chemistry 47:S123-S1S6. doi: 10.1002/mrc.2526.
-
(2009)
Magnetic Resonance in Chemistry
, vol.47
-
-
Lewis, I.A.1
Schommer, S.C.2
Markley, J.L.3
-
25
-
-
0034986869
-
Insertion mutagenesis of wca reduces acid and heat tolerance of enterohemorrhagic Escherichia coli O157: H7
-
doi: 10.1128/JB.183.12.3811-3815.2001
-
Mao Y, Doyle MP, Chen JR. 2001. Insertion mutagenesis of wca reduces acid and heat tolerance of enterohemorrhagic Escherichia coli O157: H7. Journal of Bacteriology 183:3811-3815. doi: 10.1128/JB.183.12.3811-3815.2001.
-
(2001)
Journal of Bacteriology
, vol.183
, pp. 3811-3815
-
-
Mao, Y.1
Doyle, M.P.2
Chen, J.R.3
-
26
-
-
38849201038
-
Understanding how the replisome works
-
doi: 10.1038/nsmb0208-125
-
Marians KJ. 2008. Understanding how the replisome works. Nature Structural & Molecular Biology 15:125-127. doi: 10.1038/nsmb0208-125.
-
(2008)
Nature Structural & Molecular Biology
, vol.15
, pp. 125-127
-
-
Marians, K.J.1
-
27
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
doi: 10.1101/gr.079558.108
-
Marioni JC, Mason CE, Mane SM, Stephens MGilad Y. 2008. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research 18:1509-1517. doi: 10.1101/gr.079558.108.
-
(2008)
Genome Research
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens MGilad, Y.4
-
29
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
doi: 10.1038/nmeth.1226
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5:621-628. doi: 10.1038/nmeth.1226.
-
(2008)
Nature Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
30
-
-
80052226692
-
Sequence-specific error profile of Illumina sequencers
-
doi: 10.1093/nar/gkr344
-
Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S. 2011. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Research 39:e90. doi: 10.1093/nar/gkr344.
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Nakamura, K.1
Oshima, T.2
Morimoto, T.3
Ikeda, S.4
Yoshikawa, H.5
Shiwa, Y.6
Ishikawa, S.7
Linak, M.C.8
Hirai, A.9
Takahashi, H.10
Altaf-Ul-Amin, M.11
Ogasawara, N.12
Kanaya, S.13
-
31
-
-
84863279154
-
Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations
-
doi: 10.1098/rspb.2011.1933
-
Perron GG, Lee AEG, Wang Y, Huang WE, Barraclough TG. 2012. Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations. Proceedings Biological sciences/The Royal Society 279:1477-1484. doi: 10.1098/rspb.2011.1933.
-
(2012)
Proceedings Biological sciences/The Royal Society
, vol.279
, pp. 1477-1484
-
-
Perron, G.G.1
Lee, A.E.G.2
Wang, Y.3
Huang, W.E.4
Barraclough, T.G.5
-
32
-
-
0032929297
-
Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuraminic acid by Escherichia coli
-
Plumbridge J, Vimr E. 1999. Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuraminic acid by Escherichia coli. Journal of Bacteriology 181:47-54.
-
(1999)
Journal of Bacteriology
, vol.181
, pp. 47-54
-
-
Plumbridge, J.1
Vimr, E.2
-
33
-
-
0036267593
-
Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins
-
doi: 10.1046/j.1365-2958.2002.02747.x
-
Rangarajan S, Woodgate R, Goodman MF. 2002. Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins. Molecular Microbiology 43:617-628. doi: 10.1046/j.1365-2958.2002.02747.x.
-
(2002)
Molecular Microbiology
, vol.43
, pp. 617-628
-
-
Rangarajan, S.1
Woodgate, R.2
Goodman, M.F.3
-
34
-
-
0037172667
-
Fitness effects of fixed beneficial mutations in microbial populations
-
doi: 10.1016/S0960-9822(02)00896-5
-
Rozen DE, de Visser J, Gerrish PJ. 2002. Fitness effects of fixed beneficial mutations in microbial populations. Current Biology 12:1040-1045. doi: 10.1016/S0960-9822(02)00896-5.
-
(2002)
Current Biology
, vol.12
, pp. 1040-1045
-
-
Rozen, D.E.1
de Visser, J.2
Gerrish, P.J.3
-
35
-
-
62549084295
-
Recombination and Replication in DNA Repair of Heavily Irradiated Deinococcus radiodurans
-
doi: 10.1016/j.cell.2009.01.018
-
Slade D, Lindner AB, Paul Gradman M. 2009. Recombination and Replication in DNA Repair of Heavily Irradiated Deinococcus radiodurans. Cell 136:1044-1055. doi: 10.1016/j.cell.2009.01.018.
-
(2009)
Cell
, vol.136
, pp. 1044-1055
-
-
Slade, D.1
Lindner, A.B.2
Paul Gradman, M.3
-
36
-
-
79952424488
-
Oxidative stress resistance in Deinococcus radiodurans
-
doi: 10.1128/MMBR.00015-10
-
Slade D, Radman M. 2011. Oxidative stress resistance in Deinococcus radiodurans. Microbiology and Molecular Biology Reviews 75:133-191. doi: 10.1128/MMBR.00015-10.
-
(2011)
Microbiology and Molecular Biology Reviews
, vol.75
, pp. 133-191
-
-
Slade, D.1
Radman, M.2
-
38
-
-
33749533999
-
Reassembly of shattered chromosomes in Deinococcus radiodurans
-
doi: 10.1038/nature05160
-
Zahradka K, Slade D, Bailone A, Sommer S, Averbeck D, Petranovic M, Lindner AB, Radman M. 2006. Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature 443:569-573. doi: 10.1038/nature05160.
-
(2006)
Nature
, vol.443
, pp. 569-573
-
-
Zahradka, K.1
Slade, D.2
Bailone, A.3
Sommer, S.4
Averbeck, D.5
Petranovic, M.6
Lindner, A.B.7
Radman, M.8
-
39
-
-
17844364459
-
A ring-like nucleoid is not necessary for radioresistance in the Deinococcaceae
-
doi: 10.1186/1471-2180-5-17
-
Zimmerman JM, Battista JR. 2005. A ring-like nucleoid is not necessary for radioresistance in the Deinococcaceae. BMC Microbiology 5:17. doi: 10.1186/1471-2180-5-17.
-
(2005)
BMC Microbiology
, vol.5
, pp. 17
-
-
Zimmerman, J.M.1
Battista, J.R.2
|