-
1
-
-
25144485401
-
Nanoarchaea: Representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?
-
Brochier C, Gribaldo S, Zivanovic Y, Confalonieri F, Forterre P. 2005. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol. 6:R42.
-
(2005)
Genome Biol
, vol.6
-
-
Brochier, C.1
Gribaldo, S.2
Zivanovic, Y.3
Confalonieri, F.4
Forterre, P.5
-
2
-
-
79953861250
-
Discovery of permuted and recently split transfer RNAs in Archaea
-
Chan PP, Cozen AE, Lowe TM. 2011. Discovery of permuted and recently split transfer RNAs in Archaea. Genome Biol. 12:R38.
-
(2011)
Genome Biol
, vol.12
-
-
Chan, P.P.1
Cozen, A.E.2
Lowe, T.M.3
-
3
-
-
58149189877
-
GtRNAdb: A database of transfer RNA genes detected in genomic sequence
-
Chan PP, Lowe TM. 2009. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37:D93-D97.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Chan, P.P.1
Lowe, T.M.2
-
4
-
-
0027067096
-
On the origin of the transfer RNA molecule
-
Di Giulio M. 1992. On the origin of the transfer RNA molecule. J Theor Biol. 159:199-214.
-
(1992)
J Theor Biol
, vol.159
, pp. 199-214
-
-
Di Giulio, M.1
-
5
-
-
0033531780
-
The non-monophyletic origin of the tRNA molecule
-
Di Giulio M. 1999. The non-monophyletic origin of the tRNA molecule. J Theor Biol. 197:403-414.
-
(1999)
J Theor Biol
, vol.197
, pp. 403-414
-
-
Di Giulio, M.1
-
6
-
-
33646248891
-
The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA)
-
Di Giulio M. 2006. The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA). J Theor Biol. 240:343-352.
-
(2006)
J Theor Biol
, vol.240
, pp. 343-352
-
-
Di Giulio, M.1
-
7
-
-
48349144848
-
The split genes of Nanoarchaeum equitans are an ancestral character
-
Di Giulio M. 2008a. The split genes of Nanoarchaeum equitans are an ancestral character. Gene 421:20-26.
-
(2008)
Gene
, vol.421
, pp. 20-26
-
-
Di Giulio, M.1
-
8
-
-
51049124543
-
Transfer RNA genes in pieces are an ancestral character
-
author reply 820-821
-
Di Giulio M. 2008b. Transfer RNA genes in pieces are an ancestral character. EMBO Rep. 9:820; author reply 820-821.
-
(2008)
EMBO Rep
, vol.9
, pp. 820
-
-
Di Giulio, M.1
-
9
-
-
84863439668
-
The recently split transfer RNA genes may be close to merging the two halves of the tRNA rather than having just separated them
-
Di Giulio M. 2012. The "recently" split transfer RNA genes may be close to merging the two halves of the tRNA rather than having just separated them. J Theor Biol. 310:1-2.
-
(2012)
J Theor Biol
, vol.310
, pp. 1-2
-
-
Di Giulio, M.1
-
10
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
11
-
-
77951213498
-
Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly
-
Emara MM, Ivanov P, Hickman T, Dawra N, Tisdale S, Kedersha N, Hu GF, Anderson P. 2010. Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J Biol Chem. 285:10959-10968.
-
(2010)
J Biol Chem
, vol.285
, pp. 10959-10968
-
-
Emara, M.M.1
Ivanov, P.2
Hickman, T.3
Dawra, N.4
Tisdale, S.5
Kedersha, N.6
Hu, G.F.7
Anderson, P.8
-
12
-
-
67349173665
-
The regulated retrotransposon transcriptome of mammalian cells
-
(22 co-authors)
-
Faulkner GJ, Kimura Y, Daub CO, et al. (22 co-authors). 2009. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet. 41:563-571.
-
(2009)
Nat Genet
, vol.41
, pp. 563-571
-
-
Faulkner, G.J.1
Kimura, Y.2
Daub, C.O.3
-
13
-
-
58149498297
-
Stress induces tRNA cleavage by angiogenin in mammalian cells
-
Fu H, Feng J, Liu Q, Sun F, Tie Y, Zhu J, Xing R, Sun Z, Zheng X. 2009. Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett. 583:437-442.
-
(2009)
FEBS Lett
, vol.583
, pp. 437-442
-
-
Fu, H.1
Feng, J.2
Liu, Q.3
Sun, F.4
Tie, Y.5
Zhu, J.6
Xing, R.7
Sun, Z.8
Zheng, X.9
-
14
-
-
62449123460
-
Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea
-
Fujishima K, Sugahara J, Kikuta K, Hirano R, Sato A, Tomita M, Kanai A. 2009. Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. Proc Natl Acad Sci USA. 106:2683-2687.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 2683-2687
-
-
Fujishima, K.1
Sugahara, J.2
Kikuta, K.3
Hirano, R.4
Sato, A.5
Tomita, M.6
Kanai, A.7
-
15
-
-
45449093194
-
Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 50 and 30 tRNA halves
-
Fujishima K, Sugahara J, Tomita M, Kanai A. 2008. Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 50 and 30 tRNA halves. PLoS One 3:e1622.
-
(2008)
PLoS One
, vol.3
-
-
Fujishima, K.1
Sugahara, J.2
Tomita, M.3
Kanai, A.4
-
16
-
-
36849148382
-
Origin of life: The RNA world
-
Gilbert W. 1986. Origin of life: the RNA world. Nature 319:618.
-
(1986)
Nature
, vol.319
, pp. 618
-
-
Gilbert, W.1
-
17
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12: 656-664.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
18
-
-
0024978663
-
A unique tRNA intron in the variable loop of the extreme thermophile Thermofilum pendens and its possible evolutionary implications
-
Kjems J, Leffers H, Olesen T, Garrett RA. 1989. A unique tRNA intron in the variable loop of the extreme thermophile Thermofilum pendens and its possible evolutionary implications. J Biol Chem. 264: 17834-17837.
-
(1989)
J Biol Chem
, vol.264
, pp. 17834-17837
-
-
Kjems, J.1
Leffers, H.2
Olesen, T.3
Garrett, R.A.4
-
19
-
-
0035955361
-
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
-
Lau NC, Lim LP, Weinstein EG, Bartel DP. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858-862.
-
(2001)
Science
, vol.294
, pp. 858-862
-
-
Lau, N.C.1
Lim, L.P.2
Weinstein, E.G.3
Bartel, D.P.4
-
20
-
-
0030854739
-
TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
21
-
-
0028338701
-
Phylogeny from function: Evidence from the molecular fossil record that tRNA originated in replication, not translation
-
Maizels N, Weiner AM. 1994. Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc Natl Acad Sci USA. 91:6729-6734.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 6729-6734
-
-
Maizels, N.1
Weiner, A.M.2
-
22
-
-
0344874260
-
Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: Evolutionary implications
-
Marck C, Grosjean H. 2003. Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA 9:1516-1531.
-
(2003)
RNA
, vol.9
, pp. 1516-1531
-
-
Marck, C.1
Grosjean, H.2
-
24
-
-
84875404794
-
The UCSC Genome Browser database: Extensions and updates 2013
-
(32 co-authors)
-
Meyer LR, Zweig AS, Hinrichs AS, et al. (32 co-authors). 2013. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 41:D64-D69.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Meyer, L.R.1
Zweig, A.S.2
Hinrichs, A.S.3
-
26
-
-
13444251251
-
Nanoarchaeum equitans creates functional tRNAs from separate genes for their 50-and 30-halves
-
Randau L, Munch R, Hohn MJ, Jahn D, Soll D. 2005. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 50-and 30-halves. Nature 433:537-541.
-
(2005)
Nature
, vol.433
, pp. 537-541
-
-
Randau, L.1
Munch, R.2
Hohn, M.J.3
Jahn, D.4
Soll, D.5
-
27
-
-
46449136416
-
Transfer RNA genes in pieces
-
Randau L, Soll D. 2008. Transfer RNA genes in pieces. EMBO Rep. 9: 623-628.
-
(2008)
EMBO Rep
, vol.9
, pp. 623-628
-
-
Randau, L.1
Soll, D.2
-
28
-
-
0024967060
-
Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements
-
Reiter WD, Palm P, Yeats S. 1989. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 17:1907-1914.
-
(1989)
Nucleic Acids Res
, vol.17
, pp. 1907-1914
-
-
Reiter, W.D.1
Palm, P.2
Yeats, S.3
-
29
-
-
84871107922
-
Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress
-
Saikia M, Krokowski D, Guan BJ, Ivanov P, Parisien M, Hu GF, Anderson P, Pan T, Hatzoglou M. 2012. Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J Biol Chem. 287:42708-42725.
-
(2012)
J Biol Chem
, vol.287
, pp. 42708-42725
-
-
Saikia, M.1
Krokowski, D.2
Guan, B.J.3
Ivanov, P.4
Parisien, M.5
Hu, G.F.6
Anderson, P.7
Pan, T.8
Hatzoglou, M.9
-
30
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, MillerW. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13:103-107.
-
(2003)
Genome Res
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
Hardison, R.C.6
Haussler, D.7
Miller, W.8
-
31
-
-
0026696161
-
RNA tetraloops as minimalist substrates for aminoacylation
-
Shi JP, Martinis SA, Schimmel P. 1992. RNA tetraloops as minimalist substrates for aminoacylation. Biochemistry 31:4931-4936.
-
(1992)
Biochemistry
, vol.31
, pp. 4931-4936
-
-
Shi, J.P.1
Martinis, S.A.2
Schimmel, P.3
-
32
-
-
0031883924
-
A top-half tDNA minihelix is a good substrate for the eubacterial CCA-adding enzyme
-
Shi PY, Weiner AM, Maizels N. 1998. A top-half tDNA minihelix is a good substrate for the eubacterial CCA-adding enzyme. RNA 4: 276-284.
-
(1998)
RNA
, vol.4
, pp. 276-284
-
-
Shi, P.Y.1
Weiner, A.M.2
Maizels, N.3
-
33
-
-
35348946378
-
Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae
-
Soma A, Onodera A, Sugahara J, Kanai A, Yachie N, Tomita M, Kawamura F, Sekine Y. 2007. Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science 318:450-453.
-
(2007)
Science
, vol.318
, pp. 450-453
-
-
Soma, A.1
Onodera, A.2
Sugahara, J.3
Kanai, A.4
Yachie, N.5
Tomita, M.6
Kawamura, F.7
Sekine, Y.8
-
34
-
-
56449099760
-
Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales
-
Sugahara J, Kikuta K, Fujishima K, Yachie N, Tomita M, Kanai A. 2008. Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Mol Biol Evol. 25:2709-2716.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 2709-2716
-
-
Sugahara, J.1
Kikuta, K.2
Fujishima, K.3
Yachie, N.4
Tomita, M.5
Kanai, A.6
-
35
-
-
38649093627
-
The origin and evolution of tRNA inferred from phylogenetic analysis of structure
-
Sun FJ, Caetano-Anolles G. 2008. The origin and evolution of tRNA inferred from phylogenetic analysis of structure. JMol Evol. 66:21-35.
-
(2008)
JMol Evol
, vol.66
, pp. 21-35
-
-
Sun, F.J.1
Caetano-Anolles, G.2
-
36
-
-
79957613599
-
MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
Kumar, S.6
-
37
-
-
52949145277
-
TRNA cleavage is a conserved response to oxidative stress in eukaryotes
-
Thompson DM, Lu C, Green PJ, Parker R. 2008. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14: 2095-2103.
-
(2008)
RNA
, vol.14
, pp. 2095-2103
-
-
Thompson, D.M.1
Lu, C.2
Green, P.J.3
Parker, R.4
-
38
-
-
51349155028
-
Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
-
Tian D, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J, Chen JQ. 2008. Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature 455: 105-108.
-
(2008)
Nature
, vol.455
, pp. 105-108
-
-
Tian, D.1
Wang, Q.2
Zhang, P.3
Araki, H.4
Yang, S.5
Kreitman, M.6
Nagylaki, T.7
Hudson, R.8
Bergelson, J.9
Chen, J.Q.10
-
39
-
-
33747465505
-
High rate of chimeric gene origination by retroposition in plant genomes
-
(14 co-authors)
-
Wang W, Zheng H, Fan C, et al. (14 co-authors). 2006. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18:1791-1802.
-
(2006)
Plant Cell
, vol.18
, pp. 1791-1802
-
-
Wang, W.1
Zheng, H.2
Fan, C.3
-
40
-
-
0023449816
-
TRNA-like structures tag the 30 ends of genomic RNA molecules for replication: Implications for the origin of protein synthesis
-
Weiner AM, Maizels N. 1987. tRNA-like structures tag the 30 ends of genomic RNA molecules for replication: implications for the origin of protein synthesis. Proc Natl Acad Sci USA. 84: 7383-7387.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 7383-7387
-
-
Weiner, A.M.1
Maizels, N.2
-
41
-
-
0033152855
-
The genomic tag hypo thesis modern viruses as molecular fossils of ancient strategies for genomic replication, and clues regarding the origin of protein synthesis
-
discussion 329-330
-
Weiner AM, Maizels N. 1999. The genomic tag hypothesis: modern viruses as molecular fossils of ancient strategies for genomic replication, and clues regarding the origin of protein synthesis. Biol Bull. 196:327-328; discussion 329-330.
-
(1999)
Biol Bull
, vol.196
, pp. 327-328
-
-
Weiner, A.M.1
Maizels, N.2
-
42
-
-
0001580909
-
Genes for stable RNA in the extreme thermophile Thermoproteus tenax: Introns and transcription signals
-
Wich G, Leinfelder W, Bock A. 1987. Genes for stable RNA in the extreme thermophile Thermoproteus tenax: introns and transcription signals. EMBO J. 6:523-528.
-
(1987)
EMBO J
, vol.6
, pp. 523-528
-
-
Wich, G.1
Leinfelder, W.2
Bock, A.3
-
44
-
-
23844530544
-
Transfer RNA gene-targeted integration: An adaptation of retrotransposable elements to survive in the compact Dictyostelium discoideum genome
-
Winckler T, Szafranski K, Glockner G. 2005. Transfer RNA gene-targeted integration: an adaptation of retrotransposable elements to survive in the compact Dictyostelium discoideum genome. Cytogenet Genome Res. 110:288-298.
-
(2005)
Cytogenet Genome Res
, vol.110
, pp. 288-298
-
-
Winckler, T.1
Szafranski, K.2
Glockner, G.3
-
45
-
-
84866443937
-
Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo
-
Yadav VP, Mandal PK, Bhattacharya A, Bhattacharya S. 2012. Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo. Nature Commun. 3:854.
-
(2012)
Nature Commun
, vol.3
, pp. 854
-
-
Yadav, V.P.1
Mandal, P.K.2
Bhattacharya, A.3
Bhattacharya, S.4
-
46
-
-
0028249154
-
Prediction of RNA secondary structure by energy minimization
-
Zuker M. 1994. Prediction of RNA secondary structure by energy minimization. Methods Mol Biol. 25:267-294.
-
(1994)
Methods Mol Biol
, vol.25
, pp. 267-294
-
-
Zuker, M.1
|