-
1
-
-
84876035030
-
Deciphering post-translational modification codes
-
Lothrop A. P., Torres M. P., Fuchs S. M., Deciphering post-translational modification codes. FEBS Letters 2013 587 1247 1257
-
(2013)
FEBS Letters
, vol.587
, pp. 1247-1257
-
-
Lothrop, A.P.1
Torres, M.P.2
Fuchs, S.M.3
-
2
-
-
0019376492
-
In vivo chemical modification of proteins (post-translational modification)
-
2-s2.0-0019376492
-
Wold F., In vivo chemical modification of proteins (post-translational modification). Annual Review of Biochemistry 1981 50 783 814 2-s2.0-0019376492
-
(1981)
Annual Review of Biochemistry
, vol.50
, pp. 783-814
-
-
Wold, F.1
-
3
-
-
0023716772
-
Selenocysteine, a highly specific component of certain enzymes, is incorporated by a UGA-directed co-translational mechanism
-
2-s2.0-0023716772
-
Bock A., Stadtman T. C., Selenocysteine, a highly specific component of certain enzymes, is incorporated by a UGA-directed co-translational mechanism. BioFactors 1988 1 3 245 250 2-s2.0-0023716772
-
(1988)
BioFactors
, vol.1
, Issue.3
, pp. 245-250
-
-
Bock, A.1
Stadtman, T.C.2
-
5
-
-
0037046864
-
Genetic code: Introducing pyrrolysine
-
DOI 10.1016/S0960-9822(02)00947-8, PII S0960982202009478
-
Ibba M., Söll D., Genetic code: introducing pyrrolysine. Current Biology 2002 12 13 R464 R466 2-s2.0-0037046864 10.1016/S0960-9822(02)00947-8 (Pubitemid 34766924)
-
(2002)
Current Biology
, vol.12
, Issue.13
-
-
Ibba, M.1
Soll, D.2
-
6
-
-
0037166006
-
Pyrrolysine encoded by UAG in archaea: Charging of a UAG-decoding specialized tRNA
-
DOI 10.1126/science.1069588
-
Srinivasan G., James C. M., Krzycki J. A., Pyrrolysine encoded by UAG in archaea: charging of a UAG-decoding specialized tRNA. Science 2002 296 5572 1459 1462 2-s2.0-0037166006 10.1126/science.1069588 (Pubitemid 34553089)
-
(2002)
Science
, vol.296
, Issue.5572
, pp. 1459-1462
-
-
Srinivasan, G.1
James, C.M.2
Krzycki, J.A.3
-
7
-
-
0025963803
-
Selenocysteine: The 21st amino acid
-
Bock A., Forchhammer K., Heider J., Leinfelder W., Sawers G., Veprek B., Zinoni F., Selenocysteine: the 21st amino acid. Molecular Microbiology 1991 5 3 515 520 2-s2.0-0025963803 (Pubitemid 21896072)
-
(1991)
Molecular Microbiology
, vol.5
, Issue.3
, pp. 515-520
-
-
Bock, A.1
Forchhammer, K.2
Heider, J.3
Leinfelder, W.4
Sawers, G.5
Veprek, B.6
Zinoni, F.7
-
8
-
-
33845406199
-
Dynamic evolution of selenocysteine utilization in bacteria: A balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues
-
DOI 10.1186/gb-2006-7-10-r94
-
Zhang Y., Romero H., Salinas G., Gladyshev V. N., Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues. Genome Biology 2006 7 10, article R94 2-s2.0-33845406199 10.1186/gb-2006-7-10-r94 (Pubitemid 44895934)
-
(2006)
Genome Biology
, vol.7
, Issue.10
-
-
Zhang, Y.1
Romero, H.2
Salinas, G.3
Gladyshev, V.N.4
-
9
-
-
0034846198
-
Selenoprotein synthesis in archaea
-
Rother M., Resch A., Wilting R., Böck A., Selenoprotein synthesis in archaea. BioFactors 2001 14 1-4 75 83 2-s2.0-0034846198 (Pubitemid 32848301)
-
(2001)
BioFactors
, vol.14
, Issue.1-4
, pp. 75-83
-
-
Rother, M.1
Resch, A.2
Wilting, R.3
Bock, A.4
-
10
-
-
72649093146
-
Selenoproteins in Archaea and Gram-positive bacteria
-
2-s2.0-72649093146 10.1016/j.bbagen.2009.03.022
-
Stock T., Rother M., Selenoproteins in Archaea and Gram-positive bacteria. Biochimica et Biophysica Acta 2009 1790 11 1520 1532 2-s2.0-72649093146 10.1016/j.bbagen.2009.03.022
-
(2009)
Biochimica et Biophysica Acta
, vol.1790
, Issue.11
, pp. 1520-1532
-
-
Stock, T.1
Rother, M.2
-
11
-
-
79959314842
-
Functional context, biosynthesis, and genetic encoding of pyrrolysine
-
2-s2.0-79959314842 10.1016/j.mib.2011.04.001
-
Gaston M. A., Jiang R., Krzycki J. A., Functional context, biosynthesis, and genetic encoding of pyrrolysine. Current Opinion in Microbiology 2011 14 3 342 349 2-s2.0-79959314842 10.1016/j.mib.2011.04.001
-
(2011)
Current Opinion in Microbiology
, vol.14
, Issue.3
, pp. 342-349
-
-
Gaston, M.A.1
Jiang, R.2
Krzycki, J.A.3
-
12
-
-
77956800914
-
Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea
-
2-s2.0-77956800914 10.1155/2010/453642 453642
-
Rother M., Krzycki J. A., Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea. Archaea 2010 2010 14 2-s2.0-77956800914 10.1155/2010/453642 453642
-
(2010)
Archaea
, vol.2010
, pp. 14
-
-
Rother, M.1
Krzycki, J.A.2
-
13
-
-
79953249251
-
The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine
-
2-s2.0-79953249251 10.1038/nature09918
-
Gaston M. A., Zhang L., Green-Church K. B., Krzycki J. A., The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine. Nature 2011 471 7340 647 650 2-s2.0-79953249251 10.1038/nature09918
-
(2011)
Nature
, vol.471
, Issue.7340
, pp. 647-650
-
-
Gaston, M.A.1
Zhang, L.2
Green-Church, K.B.3
Krzycki, J.A.4
-
14
-
-
33846520754
-
A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine
-
DOI 10.1073/pnas.0610294104
-
Longstaff D. G., Larue R. C., Faust J. E., Mahapatra A., Zhang L., Green-Church K. B., Krzycki J. A., A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine. Proceedings of the National Academy of Sciences of the United States of America 2007 104 3 1021 1026 2-s2.0-33846520754 10.1073/pnas.0610294104 (Pubitemid 46154729)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.3
, pp. 1021-1026
-
-
Longstaff, D.G.1
Larue, R.C.2
Faust, J.E.3
Mahapatra, A.4
Zhang, L.5
Green-Church, K.B.6
Krzycki, J.A.7
-
16
-
-
84879399790
-
Structure and reaction mechanism of pyrrolysine synthase (PylD)
-
Quitterer F., Beck P., Bacher A., Groll M., Structure and reaction mechanism of pyrrolysine synthase (PylD). Angewandte Chemie International Edition 2013 52 27 7033 7037
-
(2013)
Angewandte Chemie International Edition
, vol.52
, Issue.27
, pp. 7033-7037
-
-
Quitterer, F.1
Beck, P.2
Bacher, A.3
Groll, M.4
-
17
-
-
61349139930
-
Pyrrolysyl-tRNA synthetase-tRNAPyl structure reveals the molecular basis of orthogonality
-
2-s2.0-61349139930 10.1038/nature07611
-
Nozawa K., O'Donoghue P., Gundllapalli S., Araiso Y., Ishitani R., Umehara T., Söll D., Nureki O., Pyrrolysyl-tRNA synthetase-tRNAPyl structure reveals the molecular basis of orthogonality. Nature 2009 457 7233 1163 1167 2-s2.0-61349139930 10.1038/nature07611
-
(2009)
Nature
, vol.457
, Issue.7233
, pp. 1163-1167
-
-
Nozawa, K.1
O'Donoghue, P.2
Gundllapalli, S.3
Araiso, Y.4
Ishitani, R.5
Umehara, T.6
Söll, D.7
Nureki, O.8
-
18
-
-
4344643959
-
An aminoacyl-tRNA synthetase that specifically activates pyrrolysine
-
DOI 10.1073/pnas.0405362101
-
Polycarpo C., Ambrogelly A., Bérubé A., Winbush S. M., McCloskey J. A., Crain P. F., Wood J. L., Söll D., An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proceedings of the National Academy of Sciences of the United States of America 2004 101 34 12450 12454 2-s2.0-4344643959 10.1073/pnas.0405362101 (Pubitemid 39122044)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.34
, pp. 12450-12454
-
-
Polycarpo, C.1
Ambrogelly, A.2
Berube, A.3
Winbush, S.M.4
McCloskey, J.A.5
Crain, P.F.6
Wood, J.L.7
Soll, D.8
-
19
-
-
1842743704
-
Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA
-
DOI 10.1093/nar/gkh266
-
Théobald-Dietrich A., Frugier M., Giegé R., Rudinger-Thirion J., Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA. Nucleic Acids Research 2004 32 3 1091 1096 2-s2.0-1842743704 10.1093/nar/gkh266 (Pubitemid 38854710)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.3
, pp. 1091-1096
-
-
Theobald-Dietrich, A.1
Frugier, M.2
Giege, R.3
Rudinger-Thirion, J.4
-
20
-
-
34047120199
-
Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase
-
DOI 10.1093/nar/gkl1151
-
Herring S., Ambrogelly A., Polycarpo C. R., Söll D., Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase. Nucleic Acids Research 2007 35 4 1270 1278 2-s2.0-34047120199 10.1093/nar/gkl1151 (Pubitemid 46522978)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.4
, pp. 1270-1278
-
-
Herring, S.1
Ambrogelly, A.2
Polycarpo, C.R.3
Soll, D.4
-
21
-
-
34547470915
-
Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation
-
DOI 10.1073/pnas.0704769104
-
Kavran J. M., Gundllapalli S., O'Donoghue P., Englert M., Söll D., Steitz T. A., Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. Proceedings of the National Academy of Sciences of the United States of America 2007 104 27 11268 11273 2-s2.0-34547470915 10.1073/pnas.0704769104 (Pubitemid 47175130)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.27
, pp. 11268-11273
-
-
Kavran, J.M.1
Gundllapalli, S.2
O'Donoghue, P.3
Englert, M.4
Soll, D.5
Steitz, T.A.6
-
22
-
-
48849085808
-
Structure of Desulfitobacterium hafniense PylSc, a pyrrolysyl-tRNA synthetase
-
2-s2.0-48849085808 10.1016/j.bbrc.2008.07.074
-
Lee M. M., Jiang R., Jain R., Larue R. C., Krzycki J., Chan M. K., Structure of Desulfitobacterium hafniense PylSc, a pyrrolysyl-tRNA synthetase. Biochemical and Biophysical Research Communications 2008 374 3 470 474 2-s2.0-48849085808 10.1016/j.bbrc.2008.07.074
-
(2008)
Biochemical and Biophysical Research Communications
, vol.374
, Issue.3
, pp. 470-474
-
-
Lee, M.M.1
Jiang, R.2
Jain, R.3
Larue, R.C.4
Krzycki, J.5
Chan, M.K.6
-
23
-
-
42249114824
-
Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase
-
2-s2.0-42249114824 10.1016/j.jmb.2008.02.045
-
Yanagisawa T., Ishii R., Fukunaga R., Kobayashi T., Sakamoto K., Yokoyama S., Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase. Journal of Molecular Biology 2008 378 3 634 652 2-s2.0-42249114824 10.1016/j.jmb.2008.02.045
-
(2008)
Journal of Molecular Biology
, vol.378
, Issue.3
, pp. 634-652
-
-
Yanagisawa, T.1
Ishii, R.2
Fukunaga, R.3
Kobayashi, T.4
Sakamoto, K.5
Yokoyama, S.6
-
24
-
-
84871872269
-
A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site
-
Yanagisawa T., Sumida T., Ishii R., Yokoyama S., A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site. Acta Crystallographica D 2013 69 5 15
-
(2013)
Acta Crystallographica D
, vol.69
, pp. 5-15
-
-
Yanagisawa, T.1
Sumida, T.2
Ishii, R.3
Yokoyama, S.4
-
25
-
-
84871364293
-
Carbon source-dependent expansion of the genetic code in bacteria
-
Prat L., Heinemann I. U., Aerni H. R., Rinehart J., O'Donoghue P., Söll D., Carbon source-dependent expansion of the genetic code in bacteria. Proceedings of the National Academy of Sciences 2012 109 21070 21075
-
(2012)
Proceedings of the National Academy of Sciences
, vol.109
, pp. 21070-21075
-
-
Prat, L.1
Heinemann, I.U.2
Aerni, H.R.3
Rinehart, J.4
O'Donoghue, P.5
Söll, D.6
-
26
-
-
0034005319
-
The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain in-frame and read- through amber codons
-
DOI 10.1128/JB.182.9.2520-2529.2000
-
Paul L., Ferguson D. J. Jr., Krzycki J. A., The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain in-frame and read- through amber codons. Journal of Bacteriology 2000 182 9 2520 2529 2-s2.0-0034005319 10.1128/JB.182.9.2520- 2529.2000 (Pubitemid 30212911)
-
(2000)
Journal of Bacteriology
, vol.182
, Issue.9
, pp. 2520-2529
-
-
Paul, L.1
Ferguson Jr., D.J.2
Krzycki, J.A.3
-
27
-
-
27744558238
-
The residue mass of L-pyrrolysine in three distinct methylamine methyltransferases
-
DOI 10.1074/jbc.M506402200
-
Soares J. A., Zhang L., Pitsch R. L., Kleinholz N. M., Jones R. B., Wolff J. J., Amster J., Green-Church K. B., Krzyck J. A., The residue mass of L-pyrrolysine in three distinct methylamine methyltransferases. The Journal of Biological Chemistry 2005 280 44 36962 36969 2-s2.0-27744558238 10.1074/jbc.M506402200 (Pubitemid 41587779)
-
(2005)
Journal of Biological Chemistry
, vol.280
, Issue.44
, pp. 36962-36969
-
-
Soares, J.A.1
Zhang, L.2
Pitsch, R.L.3
Kleinholz, N.M.4
Jones, R.B.5
Wolff, J.J.6
Amster, J.7
Green-Church, K.B.8
Krzyck, J.A.9
-
28
-
-
52349091138
-
A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene
-
2-s2.0-52349091138 10.1016/j.resmic.2008.06.007
-
Mihajlovski A., Alric M., Brugère J.-F., A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene. Research in Microbiology 2008 159 7-8 516 521 2-s2.0-52349091138 10.1016/j.resmic.2008.06.007
-
(2008)
Research in Microbiology
, vol.159
, Issue.7-8
, pp. 516-521
-
-
Mihajlovski, A.1
Alric, M.2
Brugère, J.-F.3
-
29
-
-
78649715888
-
Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity
-
2-s2.0-78649715888 10.1111/j.1758-2229.2009.00116.x
-
Mihajlovski A., Doré J., Levenez F., Alric M., Brugère J.-F., Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity. Environmental Microbiology Reports 2010 2 2 272 280 2-s2.0-78649715888 10.1111/j.1758-2229.2009.00116.x
-
(2010)
Environmental Microbiology Reports
, vol.2
, Issue.2
, pp. 272-280
-
-
Mihajlovski, A.1
Doré, J.2
Levenez, F.3
Alric, M.4
Brugère, J.-F.5
-
30
-
-
84878500513
-
Candidatus Methanogranum caenicola: A novel methanogen from the anaerobic digested sludge and proposal of Methanomassiliicoccaceae fam.Nov and .Methanomassiliicoccales ord. Nov for a methanogenic lineage of the class Thermoplasmata
-
Iino T., Tamaki H., Tamazawa S., Ueno Y., Ohkuma M., Suzuki K., Igarashi Y., Haruta S., Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata. Microbes and Environments 2013 28 244 250
-
(2013)
Microbes and Environments
, vol.28
, pp. 244-250
-
-
Iino, T.1
Tamaki, H.2
Tamazawa, S.3
Ueno, Y.4
Ohkuma, M.5
Suzuki, K.6
Igarashi, Y.7
Haruta, S.8
-
31
-
-
84870794077
-
'Methanoplasmatales,' Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens
-
Paul K., Nonoh J. O., Mikulski L., Brune A., 'Methanoplasmatales,' Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens. Applied and Environmental Microbiology 2012 78 8245 8253
-
(2012)
Applied and Environmental Microbiology
, vol.78
, pp. 8245-8253
-
-
Paul, K.1
Nonoh, J.O.2
Mikulski, L.3
Brune, A.4
-
32
-
-
84890110026
-
Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis
-
Borrel G., O'Toole P. W., Peyret P., Brugère J. F., Gribaldo S., Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biology and Evolution 2013 5 1769 1780
-
(2013)
Genome Biology and Evolution
, vol.5
, pp. 1769-1780
-
-
Borrel, G.1
O'Toole, P.W.2
Peyret, P.3
Brugère, J.F.4
Gribaldo, S.5
-
33
-
-
84870675165
-
Genome sequence of, "candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens
-
Borrel G., Harris H. M., Tottey W., Genome sequence of, "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. Journal of Bacteriology 2012 194 6944 6945
-
(2012)
Journal of Bacteriology
, vol.194
, pp. 6944-6945
-
-
Borrel, G.1
Harris, H.M.2
Tottey, W.3
-
34
-
-
84866338044
-
Complete genome sequence of Methanomassiliicoccus luminyensis, the largest genome of a human-associated Archaea species
-
Gorlas A., Robert C., Gimenez G., Drancourt M., Raoult D., Complete genome sequence of Methanomassiliicoccus luminyensis, the largest genome of a human-associated Archaea species. Journal of Bacteriology 2012 194 17 4745
-
(2012)
Journal of Bacteriology
, vol.194
, Issue.17
, pp. 4745
-
-
Gorlas, A.1
Robert, C.2
Gimenez, G.3
Drancourt, M.4
Raoult, D.5
-
35
-
-
84864677092
-
Methanomassiliicoccus luminyensis gen.Nov sp.Nov.A methanogenic archaeon isolated from human faeces
-
Dridi B., Fardeau M. L., Ollivier B., Raoult D., Drancourt M., Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. International Journal of Systematic and Evolutionary Microbiology 2012 62 1902 1907
-
(2012)
International Journal of Systematic and Evolutionary Microbiology
, vol.62
, pp. 1902-1907
-
-
Dridi, B.1
Fardeau, M.L.2
Ollivier, B.3
Raoult, D.4
Drancourt, M.5
-
36
-
-
84997703582
-
Genome sequence of " Candidatus methanomassiliicoccus intestinalis" Issoire-Mx1, a third Thermoplasmatales -related methanogenic archaeon from human feces
-
e00453 10.1128/genomeA.00453-13
-
Borrel G., Harris H. M., Parisot N., Genome sequence of " Candidatus methanomassiliicoccus intestinalis" Issoire-Mx1, a third Thermoplasmatales -related methanogenic archaeon from human feces. Genome Announcements 2013 1 4 13 e00453 10.1128/genomeA.00453-13
-
(2013)
Genome Announcements
, vol.1
, Issue.4
, pp. 13
-
-
Borrel, G.1
Harris, H.M.2
Parisot, N.3
-
37
-
-
85052274144
-
Archaebiotics: Proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease
-
Brugère J. F., Borrel G., Gaci N., Tottey W., 'Toole P. W. O., Malpuech-Brugère C., Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease. Gut Microbes 2013 5 1
-
(2013)
Gut Microbes
, vol.5
, Issue.1
-
-
Brugère, J.F.1
Borrel, G.2
Gaci, N.3
Tottey, W.4
'Toole, P.W.O.5
Malpuech-Brugère, C.6
-
38
-
-
84874628087
-
Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen
-
Poulsen M., Schwab C., Jensen B. B., Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nature Communications 2013 4, article 1428
-
(2013)
Nature Communications
-
-
Poulsen, M.1
Schwab, C.2
Jensen, B.B.3
-
39
-
-
40549120596
-
The RAST Server: Rapid annotations using subsystems technology
-
DOI 10.1186/1471-2164-9-75
-
Aziz R. K., Bartels D., Best A., DeJongh M., Disz T., Edwards R. A., Formsma K., Gerdes S., Glass E. M., Kubal M., Meyer F., Olsen G. J., Olson R., Osterman A. L., Overbeek R. A., McNeil L. K., Paarmann D., Paczian T., Parrello B., Pusch G. D., Reich C., Stevens R., Vassieva O., Vonstein V., Wilke A., Zagnitko O., The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008 9, article 75 2-s2.0-40549120596 10.1186/1471-2164-9-75 (Pubitemid 351356785)
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.3
DeJongh, M.4
Disz, T.5
Edwards, R.A.6
Formsma, K.7
Gerdes, S.8
Glass, E.M.9
Kubal, M.10
Meyer, F.11
Olsen, G.J.12
Olson, R.13
Osterman, A.L.14
Overbeek, R.A.15
McNeil, L.K.16
Paarmann, D.17
Paczian, T.18
Parrello, B.19
Pusch, G.D.20
Reich, C.21
Stevens, R.22
Vassieva, O.23
Vonstein, V.24
Wilke, A.25
Zagnitko, O.26
more..
-
40
-
-
0033635022
-
Artemis: Sequence visualization and annotation
-
2-s2.0-0033635022
-
Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.-A., Barrell B., Artemis: sequence visualization and annotation. Bioinformatics 2000 16 10 944 945 2-s2.0-0033635022
-
(2000)
Bioinformatics
, vol.16
, Issue.10
, pp. 944-945
-
-
Rutherford, K.1
Parkhill, J.2
Crook, J.3
Horsnell, T.4
Rice, P.5
Rajandream, M.-A.6
Barrell, B.7
-
41
-
-
0025183708
-
Basic local alignment search tool
-
DOI 10.1006/jmbi.1990.9999
-
Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J., Basic local alignment search tool. Journal of Molecular Biology 1990 215 3 403 410 2-s2.0-0025183708 10.1006/jmbi.1990.9999 (Pubitemid 20364473)
-
(1990)
Journal of Molecular Biology
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
42
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
DOI 10.1093/bioinformatics/btm404
-
Larkin M. A., Blackshields G., Brown N. P., Chenna R., Mcgettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A., Lopez R., Thompson J. D., Gibson T. J., Higgins D. G., Clustal W and clustal X version 2.0. Bioinformatics 2007 23 21 2947 2948 2-s2.0-36448991500 10.1093/bioinformatics/btm404 (Pubitemid 350162903)
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
Mcgettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
43
-
-
0034623005
-
T-coffee: A novel method for fast and accurate multiple sequence alignment
-
2-s2.0-0034623005 10.1006/jmbi.2000.4042
-
Notredame C., Higgins D. G., Heringa J., T-coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 2000 302 1 205 217 2-s2.0-0034623005 10.1006/jmbi.2000.4042
-
(2000)
Journal of Molecular Biology
, vol.302
, Issue.1
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
44
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
DOI 10.1093/nar/gkh340
-
Edgar R. C., MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 2004 32 5 1792 1797 2-s2.0-3042666256 10.1093/nar/gkh340 (Pubitemid 38832724)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
45
-
-
44349140636
-
R-Coffee: A method for multiple alignment of non-coding RNA
-
DOI 10.1093/nar/gkn174
-
Wilm A., Higgins D. G., Notredame C., R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Research 2008 36 9, article e52 2-s2.0-44349140636 10.1093/nar/gkn174 (Pubitemid 351737210)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.9
-
-
Wilm, A.1
Higgins, D.G.2
Notredame, C.3
-
46
-
-
48449095385
-
The Vienna RNA websuite
-
2-s2.0-48449095385 10.1093/nar/gkn188
-
Gruber A. R., Lorenz R., Bernhart S. H., Neuböck R., Hofacker I. L., The Vienna RNA websuite. Nucleic Acids Research 2008 36 W70 W74 2-s2.0-48449095385 10.1093/nar/gkn188
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Gruber, A.R.1
Lorenz, R.2
Bernhart, S.H.3
Neuböck, R.4
Hofacker, I.L.5
-
47
-
-
77949447172
-
RNAstructure: Software for RNA secondary structure prediction and analysis
-
2-s2.0-77949447172 10.1186/1471-2105-11-129
-
Reuter J. S., Mathews D. H., RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 2010 11, article 129 2-s2.0-77949447172 10.1186/1471-2105-11-129
-
(2010)
BMC Bioinformatics
-
-
Reuter, J.S.1
Mathews, D.H.2
-
48
-
-
77954403053
-
BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments
-
2-s2.0-77954403053 10.1186/1471-2148-10-210
-
Criscuolo A., Gribaldo S., BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology 2010 10 1, article 210 2-s2.0-77954403053 10.1186/1471-2148-10-210
-
(2010)
BMC Evolutionary Biology
, vol.10
-
-
Criscuolo, A.1
Gribaldo, S.2
-
49
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
2-s2.0-77950806408 10.1093/sysbio/syq010
-
Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 2010 59 3 307 321 2-s2.0-77950806408 10.1093/sysbio/syq010
-
(2010)
Systematic Biology
, vol.59
, Issue.3
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.-F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
50
-
-
45849154166
-
An improved general amino acid replacement matrix
-
DOI 10.1093/molbev/msn067
-
Le S. Q., Gascuel O., An improved general amino acid replacement matrix. Molecular Biology and Evolution 2008 25 7 1307 1320 2-s2.0-45849154166 10.1093/molbev/msn067 (Pubitemid 351882003)
-
(2008)
Molecular Biology and Evolution
, vol.25
, Issue.7
, pp. 1307-1320
-
-
Le, S.Q.1
Gascuel, O.2
-
51
-
-
13444259388
-
TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics
-
DOI 10.1186/1471-2148-4-18
-
Jobb G., von Haeseler A., Strimmer K., TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evolutionary Biology 2004 4, article 18 2-s2.0-13444259388 10.1186/1471-2148-4-18 (Pubitemid 40205271)
-
(2004)
BMC Evolutionary Biology
, vol.4
, pp. 18
-
-
Jobb, G.1
Von Haeseler, A.2
Strimmer, K.3
-
52
-
-
69949126557
-
PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
-
2-s2.0-69949126557 10.1093/bioinformatics/btp368
-
Lartillot N., Lepage T., Blanquart S., PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009 25 17 2286 2288 2-s2.0-69949126557 10.1093/bioinformatics/btp368
-
(2009)
Bioinformatics
, vol.25
, Issue.17
, pp. 2286-2288
-
-
Lartillot, N.1
Lepage, T.2
Blanquart, S.3
-
53
-
-
71549118507
-
Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl-tRNA formation systems
-
2-s2.0-71549118507 10.1016/j.febslet.2009.11.005
-
Yuan J., O'Donoghue P., Ambrogelly A., Gundllapalli S., Lynn Sherrer R., Palioura S., Simonović M., Söll D., Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl-tRNA formation systems. FEBS Letters 2010 584 2 342 349 2-s2.0-71549118507 10.1016/j.febslet.2009.11.005
-
(2010)
FEBS Letters
, vol.584
, Issue.2
, pp. 342-349
-
-
Yuan, J.1
O'Donoghue, P.2
Ambrogelly, A.3
Gundllapalli, S.4
Lynn Sherrer, R.5
Palioura, S.6
Simonović, M.7
Söll, D.8
-
54
-
-
70849110294
-
RNA secondary structure analysis using the Vienna RNA package
-
Chapter 12, Unit 12.2 2-s2.0-43349093418
-
Hofacker I. L., RNA secondary structure analysis using the Vienna RNA package. Current Protocols in Bioinformatics 2004. Chapter 12, Unit 12.2 2-s2.0-43349093418
-
(2004)
Current Protocols in Bioinformatics
-
-
Hofacker, I.L.1
-
55
-
-
84866548719
-
PylSn and the homologous N-terminal domain of pyrrolysyl-tRNA synthetase bind the tRNA that is essential for the genetic encoding of pyrrolysine
-
Jiang R., Krzycki J. A., PylSn and the homologous N-terminal domain of pyrrolysyl-tRNA synthetase bind the tRNA that is essential for the genetic encoding of pyrrolysine. The Journal of Biological Chemistry 2012 287 32738 32746
-
(2012)
The Journal of Biological Chemistry
, vol.287
, pp. 32738-32746
-
-
Jiang, R.1
Krzycki, J.A.2
-
56
-
-
0034800374
-
InterProScan - An integration platform for the signature-recognition methods in InterPro
-
Zdobnov E. M., Apweiler R., InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001 17 9 847 848 2-s2.0-0034800374 (Pubitemid 32970486)
-
(2001)
Bioinformatics
, vol.17
, Issue.9
, pp. 847-848
-
-
Zdobnov, E.M.1
Apweiler, R.2
-
57
-
-
33845328427
-
Emergence of the universal genetic code imprinted in an RNA record
-
DOI 10.1073/pnas.0608762103
-
Hohn M. J., Park H.-S., O'Donoghue P., Schnitzbauer M., Söll D., Emergence of the universal genetic code imprinted in an RNA record. Proceedings of the National Academy of Sciences of the United States of America 2006 103 48 18095 18100 2-s2.0-33845328427 10.1073/pnas.0608762103 (Pubitemid 44871618)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.48
, pp. 18095-18100
-
-
Hohn, M.J.1
Park, H.-S.2
O'Donoghue, P.3
Schnitzbauer, M.4
Soll, D.5
-
58
-
-
65549127700
-
Horizontal gene transfer and the evolution of methanogenic pathways
-
2-s2.0-65549127700 10.1007/978-1-60327-853-9-9
-
Fournier G., Horizontal gene transfer and the evolution of methanogenic pathways. Methods in Molecular Biology 2009 532 163 179 2-s2.0-65549127700 10.1007/978-1-60327-853-9-9
-
(2009)
Methods in Molecular Biology
, vol.532
, pp. 163-179
-
-
Fournier, G.1
-
59
-
-
67651064681
-
Horizontal gene transfer from extinct and extant lineages: Biological innovation and the coral of life
-
2-s2.0-67651064681 10.1098/rstb.2009.0033
-
Fournier G. P., Huang J., Peter Gogarten J., Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Philosophical Transactions of the Royal Society B 2009 364 1527 2229 2239 2-s2.0-67651064681 10.1098/rstb.2009.0033
-
(2009)
Philosophical Transactions of the Royal Society B
, vol.364
, Issue.1527
, pp. 2229-2239
-
-
Fournier, G.P.1
Huang, J.2
Peter Gogarten, J.3
-
60
-
-
77954574436
-
Dual functions of codons in the genetic code
-
2-s2.0-77954574436 10.3109/10409231003786094
-
Lobanov A. V., Turanov A. A., Hatfield D. L., Gladyshev V. N., Dual functions of codons in the genetic code. Critical Reviews in Biochemistry and Molecular Biology 2010 45 4 257 265 2-s2.0-77954574436 10.3109/10409231003786094
-
(2010)
Critical Reviews in Biochemistry and Molecular Biology
, vol.45
, Issue.4
, pp. 257-265
-
-
Lobanov, A.V.1
Turanov, A.A.2
Hatfield, D.L.3
Gladyshev, V.N.4
-
61
-
-
20144364162
-
Higher-level classification of the Archaea: Evolution of methanogenesis and methanogens
-
Bapteste É., Brochier C., Boucher Y., Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 2005 1 5 353 363 2-s2.0-20144364162 (Pubitemid 40801843)
-
(2005)
Archaea
, vol.1
, Issue.5
, pp. 353-363
-
-
Bapteste, E.1
Brochier, C.2
Boucher, Y.3
-
63
-
-
17844405021
-
Coevolutlon theory of genetic code at age thirty
-
DOI 10.1002/bies.20208
-
Wong J. T.-F., Coevolutlon theory of genetic code at age thirty. BioEssays 2005 27 4 416 425 2-s2.0-17844405021 10.1002/bies.20208 (Pubitemid 40592598)
-
(2005)
BioEssays
, vol.27
, Issue.4
, pp. 416-425
-
-
Wong, J.T.-F.1
-
64
-
-
33845691072
-
In vivo contextual requirements for UAG translation as pyrrolysine
-
DOI 10.1111/j.1365-2958.2006.05500.x
-
Longstaff D. G., Blight S. K., Zhang L., Green-Church K. B., Krzycki J. A., In vivo contextual requirements for UAG translation as pyrrolysine. Molecular Microbiology 2007 63 1 229 241 2-s2.0-33845691072 10.1111/j.1365-2958. 2006.05500.x (Pubitemid 44968121)
-
(2007)
Molecular Microbiology
, vol.63
, Issue.1
, pp. 229-241
-
-
Longstaff, D.G.1
Blight, S.K.2
Zhang, L.3
Green-Church, K.B.4
Krzycki, J.A.5
|