-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
doi: 10.1093/nar/25.17.3389
-
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402. doi: 10.1093/nar/25.17.3389.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
-
2
-
-
33646739111
-
The NYN domains: novel predicted RNAses with a PIN domain-like fold
-
doi: 10.4161/rna.3.1.2548
-
Anantharaman, V., and Aravind, L. (2006). The NYN domains: novel predicted RNAses with a PIN domain-like fold. RNA Biol. 3, 18-27. doi: 10.4161/rna.3.1.2548.
-
(2006)
RNA Biol.
, vol.3
, pp. 18-27
-
-
Anantharaman, V.1
Aravind, L.2
-
3
-
-
84868092588
-
Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing
-
doi: 10.1039/c2mb25239b
-
Anantharaman, V., Iyer, L. M., and Aravind, L. (2012). Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. Mol. Biosyst. 8, 3142-3165. doi: 10.1039/c2mb25239b.
-
(2012)
Mol. Biosyst.
, vol.8
, pp. 3142-3165
-
-
Anantharaman, V.1
Iyer, L.M.2
Aravind, L.3
-
4
-
-
84878893667
-
Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing
-
doi: 10.1186/1745-6150-8-15
-
Anantharaman, V., Makarova, K. S., Burroughs, A. M., Koonin, E. V., and Aravind, L. (2013). Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol. Direct 8, 15. doi: 10.1186/1745-6150-8-15.
-
(2013)
Biol. Direct
, vol.8
, pp. 15
-
-
Anantharaman, V.1
Makarova, K.S.2
Burroughs, A.M.3
Koonin, E.V.4
Aravind, L.5
-
5
-
-
84883019152
-
Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems
-
doi: 10.1186/1745-6150-8-20
-
Aravind, L., Anand, S., and Iyer, L. M. (2013). Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems. Biol. Direct 8, 20. doi: 10.1186/1745-6150-8-20.
-
(2013)
Biol. Direct
, vol.8
, pp. 20
-
-
Aravind, L.1
Anand, S.2
Iyer, L.M.3
-
6
-
-
77954385632
-
'Natural history of sensor domains in bacterial signaling systems,'
-
eds S. Spiro and R. Dixon (Norfolk: Caister Academic Press)
-
Aravind, L., Iyer, L. M., and Anantharaman, V. (2010). "Natural history of sensor domains in bacterial signaling systems," in Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition, eds S. Spiro and R. Dixon (Norfolk: Caister Academic Press), 1-38.
-
(2010)
Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition
, pp. 1-38
-
-
Aravind, L.1
Iyer, L.M.2
Anantharaman, V.3
-
7
-
-
0027324744
-
Biology of DNA restriction
-
Bickle, T. A., and Kruger, D. H. (1993). Biology of DNA restriction. Microbiol. Rev. 57, 434-450.
-
(1993)
Microbiol. Rev.
, vol.57
, pp. 434-450
-
-
Bickle, T.A.1
Kruger, D.H.2
-
8
-
-
33746922036
-
Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes
-
doi: 10.1016/j.jmb.2006.06.049
-
Burroughs, A. M., Allen, K. N., Dunaway-Mariano, D., and Aravind, L. (2006). Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J. Mol. Biol. 361, 1003-1034. doi: 10.1016/j.jmb.2006.06.049.
-
(2006)
J. Mol. Biol.
, vol.361
, pp. 1003-1034
-
-
Burroughs, A.M.1
Allen, K.N.2
Dunaway-Mariano, D.3
Aravind, L.4
-
9
-
-
84893804492
-
New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing
-
doi: 10.1002/wrna.1210
-
Burroughs, A. M., Ando, Y., and Aravind, L. (2013a). New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. Wiley Interdiscip. Rev. RNA 5, 141-182. doi: 10.1002/wrna.1210.
-
(2013)
Wiley Interdiscip. Rev. RNA
, vol.5
, pp. 141-182
-
-
Burroughs, A.M.1
Ando, Y.2
Aravind, L.3
-
10
-
-
66149175454
-
Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation
-
doi: 10.1002/prot.22298
-
Burroughs, A. M., Iyer, L. M., and Aravind, L. (2009). Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation. Proteins 75, 895-910. doi: 10.1002/prot.22298.
-
(2009)
Proteins
, vol.75
, pp. 895-910
-
-
Burroughs, A.M.1
Iyer, L.M.2
Aravind, L.3
-
11
-
-
84878660353
-
Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes
-
doi: 10.1186/1745-6150-8-13
-
Burroughs, A. M., Iyer, L. M., and Aravind, L. (2013b). Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes. Biol. Direct 8:13. doi: 10.1186/1745-6150-8-13.
-
(2013)
Biol. Direct
, vol.8
, pp. 13
-
-
Burroughs, A.M.1
Iyer, L.M.2
Aravind, L.3
-
12
-
-
84859983403
-
RNA ligase RtcB splices 3'-phosphate and 5'-OH ends via covalent RtcB-(histidinyl)-GMP and polynucleotide-(3')pp(5')G intermediates
-
doi: 10.1073/pnas.1201207109
-
Chakravarty, A. K., Subbotin, R., Chait, B. T., and Shuman, S. (2012). RNA ligase RtcB splices 3'-phosphate and 5'-OH ends via covalent RtcB-(histidinyl)-GMP and polynucleotide-(3')pp(5')G intermediates. Proc. Natl. Acad. Sci. U.S.A. 109, 6072-6077. doi: 10.1073/pnas.1201207109.
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 6072-6077
-
-
Chakravarty, A.K.1
Subbotin, R.2
Chait, B.T.3
Shuman, S.4
-
13
-
-
0032420333
-
JPred: a consensus secondary structure prediction server
-
doi: 10.1093/bioinformatics/14.10.892
-
Cuff, J. A., Clamp, M. E., Siddiqui, A. S., Finlay, M., and Barton, G. J. (1998). JPred: a consensus secondary structure prediction server. Bioinformatics 14, 892-893. doi: 10.1093/bioinformatics/14.10.892.
-
(1998)
Bioinformatics
, vol.14
, pp. 892-893
-
-
Cuff, J.A.1
Clamp, M.E.2
Siddiqui, A.S.3
Finlay, M.4
Barton, G.J.5
-
14
-
-
84874195392
-
A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus
-
doi: 10.1111/mmi.12152
-
Deng, L., Garrett, R. A., Shah, S. A., Peng, X., and She, Q. (2013). A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol. Microbiol. 87, 1088-1099. doi: 10.1111/mmi.12152.
-
(2013)
Mol. Microbiol.
, vol.87
, pp. 1088-1099
-
-
Deng, L.1
Garrett, R.A.2
Shah, S.A.3
Peng, X.4
She, Q.5
-
15
-
-
84861134293
-
Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions
-
doi: 10.1039/c2mb05487f
-
de Souza, R. F., and Aravind, L. (2012). Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions. Mol. Biosyst. 8, 1661-1677. doi: 10.1039/c2mb05487f.
-
(2012)
Mol. Biosyst.
, vol.8
, pp. 1661-1677
-
-
de Souza, R.F.1
Aravind, L.2
-
16
-
-
84901070543
-
Chromosomal targeting by CRISPR-Cas systems can contribute to genome plasticity in bacteria
-
doi: 10.4161/mge.26831
-
Dy, R. L., Pitman, A. R., and Fineran, P. C. (2013). Chromosomal targeting by CRISPR-Cas systems can contribute to genome plasticity in bacteria. Mob. Genet. Elements 3, e26831. doi: 10.4161/mge.26831.
-
(2013)
Mob. Genet. Elements
, vol.3
-
-
Dy, R.L.1
Pitman, A.R.2
Fineran, P.C.3
-
17
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
doi: 10.1093/nar/gkh340
-
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. doi: 10.1093/nar/gkh340.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
18
-
-
84891782659
-
Pfam: the protein families database
-
doi: 10.1093/nar/gkt1223
-
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., et al. (2014). Pfam: the protein families database. Nucleic Acids Res. 42, D222-D230. doi: 10.1093/nar/gkt1223.
-
(2014)
Nucleic Acids Res.
, vol.42
-
-
Finn, R.D.1
Bateman, A.2
Clements, J.3
Coggill, P.4
Eberhardt, R.Y.5
Eddy, S.R.6
-
19
-
-
0032566718
-
Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon
-
doi: 10.1074/jbc.273.39.25516
-
Genschik, P., Drabikowski, K., and Filipowicz, W. (1998). Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon. J. Biol. Chem. 273, 25516-25526. doi: 10.1074/jbc.273.39.25516.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 25516-25526
-
-
Genschik, P.1
Drabikowski, K.2
Filipowicz, W.3
-
20
-
-
0029145415
-
Hypermodified bases in DNA
-
Gommers-Ampt, J. H., and Borst, P. (1995). Hypermodified bases in DNA. FASEB J. 9, 1034-1042.
-
(1995)
FASEB J.
, vol.9
, pp. 1034-1042
-
-
Gommers-Ampt, J.H.1
Borst, P.2
-
21
-
-
34548179003
-
Solution structure of YaeO, a Rho-specific inhibitor of transcription termination
-
doi: 10.1074/jbc.M702010200
-
Gutierrez, P., Kozlov, G., Gabrielli, L., Elias, D., Osborne, M. J., Gallouzi, I. E., et al. (2007). Solution structure of YaeO, a Rho-specific inhibitor of transcription termination. J. Biol. Chem. 282, 23348-23353. doi: 10.1074/jbc.M702010200.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 23348-23353
-
-
Gutierrez, P.1
Kozlov, G.2
Gabrielli, L.3
Elias, D.4
Osborne, M.J.5
Gallouzi, I.E.6
-
22
-
-
84890935599
-
Genetic characterization of anti-plasmid immunity by a Type III-A CRISPR-Cas system
-
doi: 10.1128/JB.01130-13
-
Hatoum-Aslan, A., Maniv, I., Samai, P., and Marraffini, L. A. (2013). Genetic characterization of anti-plasmid immunity by a Type III-A CRISPR-Cas system. J. Bacteriol. 196, 310-317. doi: 10.1128/JB.01130-13.
-
(2013)
J. Bacteriol.
, vol.196
, pp. 310-317
-
-
Hatoum-Aslan, A.1
Maniv, I.2
Samai, P.3
Marraffini, L.A.4
-
23
-
-
84874161995
-
Adaptation and modification of three CRISPR loci in two closely related cyanobacteria
-
doi: 10.4161/rna.24160
-
Hein, S., Scholz, I., Voss, B., and Hess, W. R. (2013). Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. RNA Biol. 10, 852-864. doi: 10.4161/rna.24160.
-
(2013)
RNA Biol.
, vol.10
, pp. 852-864
-
-
Hein, S.1
Scholz, I.2
Voss, B.3
Hess, W.R.4
-
24
-
-
77954288774
-
Dali server: conservation mapping in 3D
-
doi: 10.1093/nar/gkq366
-
Holm, L., and Rosenstrom, P. (2010). Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545-W549. doi: 10.1093/nar/gkq366.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Holm, L.1
Rosenstrom, P.2
-
25
-
-
0031000649
-
An evolutionary treasure: unification of a broad set of amidohydrolases related to urease
-
doi: 10.1002/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L
-
Holm, L., and Sander, C. (1997). An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins 28, 72-82. doi: 10.1002/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L.
-
(1997)
Proteins
, vol.28
, pp. 72-82
-
-
Holm, L.1
Sander, C.2
-
26
-
-
84886810542
-
Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA
-
doi: 10.1093/nar/gkt573
-
Iyer, L. M., Zhang, D., Burroughs, A. M., and Aravind, L. (2013). Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Nucleic Acids Res. 41, 7635-7655. doi: 10.1093/nar/gkt573.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 7635-7655
-
-
Iyer, L.M.1
Zhang, D.2
Burroughs, A.M.3
Aravind, L.4
-
27
-
-
84884696268
-
Dealing with the Evolutionary Downside of CRISPR Immunity: bacteria and beneficial Plasmids
-
doi: 10.1371/journal.pgen.1003844
-
Jiang, W., Maniv, I., Arain, F., Wang, Y., Levin, B. R., and Marraffini, L. A. (2013). Dealing with the Evolutionary Downside of CRISPR Immunity: bacteria and beneficial Plasmids. PLoS Genet. 9:e1003844. doi: 10.1371/journal.pgen.1003844.
-
(2013)
PLoS Genet.
, vol.9
-
-
Jiang, W.1
Maniv, I.2
Arain, F.3
Wang, Y.4
Levin, B.R.5
Marraffini, L.A.6
-
28
-
-
84876567971
-
RNA-programmed genome editing in human cells
-
doi: 10.7554/eLife.00471
-
Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., and Doudna, J. (2013). RNA-programmed genome editing in human cells. Elife 2:e00471. doi: 10.7554/eLife.00471.
-
(2013)
Elife
, vol.2
-
-
Jinek, M.1
East, A.2
Cheng, A.3
Lin, S.4
Ma, E.5
Doudna, J.6
-
29
-
-
70449521979
-
A lower-order oligomer form of phage shock protein A (PspA) stably associates with the hexameric AAA(+) transcription activator protein PspF for negative regulation
-
doi: 10.1016/j.jmb.2009.09.055
-
Joly, N., Burrows, P. C., Engl, C., Jovanovic, G., and Buck, M. (2009). A lower-order oligomer form of phage shock protein A (PspA) stably associates with the hexameric AAA(+) transcription activator protein PspF for negative regulation. J. Mol. Biol. 394, 764-775. doi: 10.1016/j.jmb.2009.09.055.
-
(2009)
J. Mol. Biol.
, vol.394
, pp. 764-775
-
-
Joly, N.1
Burrows, P.C.2
Engl, C.3
Jovanovic, G.4
Buck, M.5
-
30
-
-
77955127606
-
Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology
-
doi: 10.1111/j.1574-6976.2010.00240.x
-
Joly, N., Engl, C., Jovanovic, G., Huvet, M., Toni, T., Sheng, X., et al. (2010). Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology. FEMS Microbiol. Rev. 34, 797-827. doi: 10.1111/j.1574-6976.2010.00240.x.
-
(2010)
FEMS Microbiol. Rev.
, vol.34
, pp. 797-827
-
-
Joly, N.1
Engl, C.2
Jovanovic, G.3
Huvet, M.4
Toni, T.5
Sheng, X.6
-
31
-
-
84872594608
-
Crystal structure and nucleic acid-binding activity of the CRISPR-associated protein Csx1 of Pyrococcus furiosus
-
doi: 10.1002/prot.24183
-
Kim, Y. K., Kim, Y. G., and Oh, B. H. (2013). Crystal structure and nucleic acid-binding activity of the CRISPR-associated protein Csx1 of Pyrococcus furiosus. Proteins 81, 261-270. doi: 10.1002/prot.24183.
-
(2013)
Proteins
, vol.81
, pp. 261-270
-
-
Kim, Y.K.1
Kim, Y.G.2
Oh, B.H.3
-
32
-
-
84895172125
-
The double-edged sword of Lamarck: comment on diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems by Edwin L. Cooper and Nicola Overstreet
-
doi: 10.1016/j.plrev.2013.12.002
-
Koonin, E. V. (2014). The double-edged sword of Lamarck: comment on diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems by Edwin L. Cooper and Nicola Overstreet. Phys. Life Rev. 11, 141-143. doi: 10.1016/j.plrev.2013.12.002.
-
(2014)
Phys. Life Rev.
, vol.11
, pp. 141-143
-
-
Koonin, E.V.1
-
33
-
-
84878168552
-
CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes
-
doi: 10.4161/rna.24022
-
Koonin, E. V., and Makarova, K. S. (2013). CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes. RNA Biol. 10, 679-686. doi: 10.4161/rna.24022.
-
(2013)
RNA Biol.
, vol.10
, pp. 679-686
-
-
Koonin, E.V.1
Makarova, K.S.2
-
34
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
-
doi: 10.1006/jmbi.2000.4315
-
Krogh, A., Larsson, B., Von Heijne, G., and Sonnhammer, E. L. (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580. doi: 10.1006/jmbi.2000.4315.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
Von Heijne, G.3
Sonnhammer, E.L.4
-
35
-
-
79251598240
-
The structure of the CRISPR-Associated Protein Csa3 provides insight into the regulation of the CRISPR/Cas system
-
doi: 10.1016/j.jmb.2010.11.019
-
Lintner, N. G., Frankel, K. A., Tsutakawa, S. E., Alsbury, D. L., Copie, V., Young, M. J., et al. (2010). The structure of the CRISPR-Associated Protein Csa3 provides insight into the regulation of the CRISPR/Cas system. J. Mol. Biol. 405, 939-955. doi: 10.1016/j.jmb.2010.11.019.
-
(2010)
J. Mol. Biol.
, vol.405
, pp. 939-955
-
-
Lintner, N.G.1
Frankel, K.A.2
Tsutakawa, S.E.3
Alsbury, D.L.4
Copie, V.5
Young, M.J.6
-
36
-
-
84868685897
-
Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes
-
doi: 10.1186/1745-6150-7-40
-
Makarova, K. S., Anantharaman, V., Aravind, L., and Koonin, E. V. (2012). Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes. Biol. Direct 7, 40. doi: 10.1186/1745-6150-7-40.
-
(2012)
Biol. Direct
, vol.7
, pp. 40
-
-
Makarova, K.S.1
Anantharaman, V.2
Aravind, L.3
Koonin, E.V.4
-
37
-
-
79960554003
-
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems
-
doi: 10.1186/1745-6150-6-38
-
Makarova, K. S., Aravind, L., Wolf, Y. I., and Koonin, E. V. (2011a). Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol. Direct 6, 38. doi: 10.1186/1745-6150-6-38.
-
(2011)
Biol. Direct
, vol.6
, pp. 38
-
-
Makarova, K.S.1
Aravind, L.2
Wolf, Y.I.3
Koonin, E.V.4
-
38
-
-
34248374277
-
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
-
doi: 10.1186/1745-6150-1-7
-
Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., and Koonin, E. V. (2006). A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1:7. doi: 10.1186/1745-6150-1-7.
-
(2006)
Biol. Direct
, vol.1
, pp. 7
-
-
Makarova, K.S.1
Grishin, N.V.2
Shabalina, S.A.3
Wolf, Y.I.4
Koonin, E.V.5
-
39
-
-
79956157571
-
Evolution and classification of the CRISPR-Cas systems
-
doi: 10.1038/nrmicro2577
-
Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J., Charpentier, E., Horvath, P., et al. (2011b). Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467-477. doi: 10.1038/nrmicro2577.
-
(2011)
Nat. Rev. Microbiol.
, vol.9
, pp. 467-477
-
-
Makarova, K.S.1
Haft, D.H.2
Barrangou, R.3
Brouns, S.J.4
Charpentier, E.5
Horvath, P.6
-
40
-
-
84877304698
-
Comparative genomics of defense systems in archaea and bacteria
-
doi: 10.1093/nar/gkt157
-
Makarova, K. S., Wolf, Y. I., and Koonin, E. V. (2013). Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res. 41, 4360-4377. doi: 10.1093/nar/gkt157.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 4360-4377
-
-
Makarova, K.S.1
Wolf, Y.I.2
Koonin, E.V.3
-
41
-
-
70849123800
-
Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements
-
doi: 10.1186/1745-6150-4-29
-
Makarova, K. S., Wolf, Y. I., Van der Oost, J., and Koonin, E. V. (2009). Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol. Direct 4, 29. doi: 10.1186/1745-6150-4-29.
-
(2009)
Biol. Direct
, vol.4
, pp. 29
-
-
Makarova, K.S.1
Wolf, Y.I.2
Van der Oost, J.3
Koonin, E.V.4
-
42
-
-
84873734105
-
RNA-guided human genome engineering via Cas9
-
doi: 10.1126/science.1232033
-
Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., Dicarlo, J. E., et al. (2013). RNA-guided human genome engineering via Cas9. Science 339, 823-826. doi: 10.1126/science.1232033.
-
(2013)
Science
, vol.339
, pp. 823-826
-
-
Mali, P.1
Yang, L.2
Esvelt, K.M.3
Aach, J.4
Guell, M.5
Dicarlo, J.E.6
-
43
-
-
0021723865
-
DNA synthesis in Pseudomonas acidovorans infected with mutants of bacteriophage phi W-14 defective in the synthesis of alpha-putrescinylthymine
-
Miller, P. B., and Warren, R. A. (1984). DNA synthesis in Pseudomonas acidovorans infected with mutants of bacteriophage phi W-14 defective in the synthesis of alpha-putrescinylthymine. J. Virol. 52, 1036-1038.
-
(1984)
J. Virol.
, vol.52
, pp. 1036-1038
-
-
Miller, P.B.1
Warren, R.A.2
-
44
-
-
0030907620
-
The Escherichia coli phage-shock-protein (psp) operon
-
doi: 10.1046/j.1365-2958.1997.3481712.x
-
Model, P., Jovanovic, G., and Dworkin, J. (1997). The Escherichia coli phage-shock-protein (psp) operon. Mol. Microbiol. 24, 255-261. doi: 10.1046/j.1365-2958.1997.3481712.x.
-
(1997)
Mol. Microbiol.
, vol.24
, pp. 255-261
-
-
Model, P.1
Jovanovic, G.2
Dworkin, J.3
-
45
-
-
84894081986
-
Generation of gene-modified cynomolgus monkey via Cas9/RNA-Mediated gene targeting in one-cell embryos
-
doi: 10.1016/j.cell.2014.01.027
-
Niu, Y., Shen, B., Cui, Y., Chen, Y., Wang, J., Wang, L., et al. (2014). Generation of gene-modified cynomolgus monkey via Cas9/RNA-Mediated gene targeting in one-cell embryos. Cell 156, 836-843. doi: 10.1016/j.cell.2014.01.027.
-
(2014)
Cell
, vol.156
, pp. 836-843
-
-
Niu, Y.1
Shen, B.2
Cui, Y.3
Chen, Y.4
Wang, J.5
Wang, L.6
-
46
-
-
0017441019
-
Functioning of purine salvage pathways in Escherichia coli K-12
-
Nygaard, P. (1977). Functioning of purine salvage pathways in Escherichia coli K-12. Adv. Exp. Med. Biol. 76A, 186-195.
-
(1977)
Adv. Exp. Med. Biol.
, vol.76 A
, pp. 186-195
-
-
Nygaard, P.1
-
47
-
-
0029807312
-
AbiG, a genotypically novel abortive infection mechanism encoded by plasmid pCI750 of Lactococcus lactis subsp. cremoris UC653
-
O'Connor, L., Coffey, A., Daly, C., and Fitzgerald, G. F. (1996). AbiG, a genotypically novel abortive infection mechanism encoded by plasmid pCI750 of Lactococcus lactis subsp. cremoris UC653. Appl. Environ. Microbiol. 62, 3075-3082.
-
(1996)
Appl. Environ. Microbiol.
, vol.62
, pp. 3075-3082
-
-
O'Connor, L.1
Coffey, A.2
Daly, C.3
Fitzgerald, G.F.4
-
48
-
-
84883752794
-
Bacterial argonaute samples the transcriptome to identify foreign DNA
-
doi: 10.1016/j.molcel.2013.08.014
-
Olovnikov, I., Chan, K., Sachidanandam, R., Newman, D. K., and Aravin, A. A. (2013). Bacterial argonaute samples the transcriptome to identify foreign DNA. Mol. Cell 51, 594-605. doi: 10.1016/j.molcel.2013.08.014.
-
(2013)
Mol. Cell
, vol.51
, pp. 594-605
-
-
Olovnikov, I.1
Chan, K.2
Sachidanandam, R.3
Newman, D.K.4
Aravin, A.A.5
-
49
-
-
0037178275
-
Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements
-
doi: 10.1016/S0378-1119(02)00701-1
-
Permina, E. A., Mironov, A. A., and Gelfand, M. S. (2002). Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements. Gene 293, 133-140. doi: 10.1016/S0378-1119(02)00701-1.
-
(2002)
Gene
, vol.293
, pp. 133-140
-
-
Permina, E.A.1
Mironov, A.A.2
Gelfand, M.S.3
-
50
-
-
33846078626
-
REBASE-enzymes and genes for DNA restriction and modification
-
doi: 10.1093/nar/gkl891
-
Roberts, R. J., Vincze, T., Posfai, J., and Macelis, D. (2007). REBASE-enzymes and genes for DNA restriction and modification. Nucleic Acids Res. 35, D269-D270. doi: 10.1093/nar/gkl891.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Roberts, R.J.1
Vincze, T.2
Posfai, J.3
Macelis, D.4
-
51
-
-
0036645689
-
Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein
-
doi: 10.1093/emboj/cdf322
-
Schumacher, M. A., Pearson, R. F., Moller, T., Valentin-Hansen, P., and Brennan, R. G. (2002). Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. EMBO J. 21, 3546-3556. doi: 10.1093/emboj/cdf322.
-
(2002)
EMBO J.
, vol.21
, pp. 3546-3556
-
-
Schumacher, M.A.1
Pearson, R.F.2
Moller, T.3
Valentin-Hansen, P.4
Brennan, R.G.5
-
52
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
doi: 10.1093/nar/gki408
-
Soding, J., Biegert, A., and Lupas, A. N. (2005). The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244-W248. doi: 10.1093/nar/gki408.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Soding, J.1
Biegert, A.2
Lupas, A.N.3
-
53
-
-
84878936806
-
CRISPR-mediated adaptive immune systems in bacteria and archaea
-
doi: 10.1146/annurev-biochem-072911-172315
-
Sorek, R., Lawrence, C. M., and Wiedenheft, B. (2013). CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu. Rev. Biochem. 82, 237-266. doi: 10.1146/annurev-biochem-072911-172315.
-
(2013)
Annu. Rev. Biochem.
, vol.82
, pp. 237-266
-
-
Sorek, R.1
Lawrence, C.M.2
Wiedenheft, B.3
-
54
-
-
77955085897
-
Self-targeting by CRISPR: gene regulation or autoimmunity?
-
doi: 10.1016/j.tig.2010.05.008
-
Stern, A., Keren, L., Wurtzel, O., Amitai, G., and Sorek, R. (2010). Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet. 26, 335-340. doi: 10.1016/j.tig.2010.05.008.
-
(2010)
Trends Genet.
, vol.26
, pp. 335-340
-
-
Stern, A.1
Keren, L.2
Wurtzel, O.3
Amitai, G.4
Sorek, R.5
-
55
-
-
83355174071
-
Novel mechanism of RNA repair by RtcB via sequential 2',3'-cyclic phosphodiesterase and 3'-Phosphate/5'-hydroxyl ligation reactions
-
doi: 10.1074/jbc.M111.302133
-
Tanaka, N., Chakravarty, A. K., Maughan, B., and Shuman, S. (2011). Novel mechanism of RNA repair by RtcB via sequential 2',3'-cyclic phosphodiesterase and 3'-Phosphate/5'-hydroxyl ligation reactions. J. Biol. Chem. 286, 43134-43143. doi: 10.1074/jbc.M111.302133.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 43134-43143
-
-
Tanaka, N.1
Chakravarty, A.K.2
Maughan, B.3
Shuman, S.4
-
56
-
-
36549075971
-
BLAST QuickStart: example-driven web-based BLAST tutorial
-
doi: 10.1007/978-1-59745-514-5_9
-
Wheeler, D., and Bhagwat, M. (2007). BLAST QuickStart: example-driven web-based BLAST tutorial. Methods Mol. Biol. 395, 149-176. doi: 10.1007/978-1-59745-514-5_9.
-
(2007)
Methods Mol. Biol.
, vol.395
, pp. 149-176
-
-
Wheeler, D.1
Bhagwat, M.2
-
57
-
-
0021188608
-
Selective protection of 5'... GGCC... 3' and 5'... GCNGC... 3' sequences by the hypermodified oxopyrimidine in Bacillus subtilis bacteriophage SP10 DNA
-
Wiatr, C. L., and Witmer, H. J. (1984). Selective protection of 5'... GGCC... 3' and 5'... GCNGC... 3' sequences by the hypermodified oxopyrimidine in Bacillus subtilis bacteriophage SP10 DNA. J. Virol. 52, 47-54.
-
(1984)
J. Virol.
, vol.52
, pp. 47-54
-
-
Wiatr, C.L.1
Witmer, H.J.2
-
58
-
-
84857097177
-
RNA-guided genetic silencing systems in bacteria and archaea
-
doi: 10.1038/nature10886
-
Wiedenheft, B., Sternberg, S. H., and Doudna, J. A. (2012). RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331-338. doi: 10.1038/nature10886.
-
(2012)
Nature
, vol.482
, pp. 331-338
-
-
Wiedenheft, B.1
Sternberg, S.H.2
Doudna, J.A.3
-
59
-
-
0030958319
-
ADP-ribosylation and early transcription regulation by bacteriophage T4
-
doi: 10.1007/978-1-4419-8632-0_8
-
Wilkens, K., Tiemann, B., Bazan, F., and Ruger, W. (1997). ADP-ribosylation and early transcription regulation by bacteriophage T4. Adv. Exp. Med. Biol. 419, 71-82. doi: 10.1007/978-1-4419-8632-0_8.
-
(1997)
Adv. Exp. Med. Biol.
, vol.419
, pp. 71-82
-
-
Wilkens, K.1
Tiemann, B.2
Bazan, F.3
Ruger, W.4
-
60
-
-
0021960028
-
Polymer-level synthesis of oxopyrimidine deoxynucleotides by Bacillus subtilis phage SP10: characterization of modification-defective mutants
-
Witmer, H., and Wiatr, C. (1985). Polymer-level synthesis of oxopyrimidine deoxynucleotides by Bacillus subtilis phage SP10: characterization of modification-defective mutants. J. Virol. 53, 522-527.
-
(1985)
J. Virol.
, vol.53
, pp. 522-527
-
-
Witmer, H.1
Wiatr, C.2
-
61
-
-
80054759036
-
Regulation of growth and death in Escherichia coli by toxin-antitoxin systems
-
doi: 10.1038/nrmicro2651
-
Yamaguchi, Y., and Inouye, M. (2011). Regulation of growth and death in Escherichia coli by toxin-antitoxin systems. Nat. Rev. Microbiol. 9, 779-790. doi: 10.1038/nrmicro2651.
-
(2011)
Nat. Rev. Microbiol.
, vol.9
, pp. 779-790
-
-
Yamaguchi, Y.1
Inouye, M.2
-
62
-
-
84862602464
-
Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics
-
doi: 10.1186/1745-6150-7-18
-
Zhang, D., de Souza, R. F., Anantharaman, V., Iyer, L. M., and Aravind, L. (2012). Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol. Direct 7, 18. doi: 10.1186/1745-6150-7-18.
-
(2012)
Biol. Direct
, vol.7
, pp. 18
-
-
Zhang, D.1
de Souza, R.F.2
Anantharaman, V.3
Iyer, L.M.4
Aravind, L.5
|