-
1
-
-
30744432134
-
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
-
Chamary J., Hurst L.D. Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol. 2005, 6:R75.
-
(2005)
Genome Biol.
, vol.6
-
-
Chamary, J.1
Hurst, L.D.2
-
2
-
-
58149189877
-
GtRNAdb: a database of transfer RNA genes detected in genomic sequence
-
Chan P.P., Lowe T.M. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009, 37:D93.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Chan, P.P.1
Lowe, T.M.2
-
3
-
-
77949456534
-
Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function
-
Clarke T., Clark P. Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. BMC Genomics 2010, 11:118.
-
(2010)
BMC Genomics
, vol.11
, pp. 118
-
-
Clarke, T.1
Clark, P.2
-
4
-
-
55249096894
-
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
-
de Godoy L.M.F., et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455:1251-1254.
-
(2008)
Nature
, vol.455
, pp. 1251-1254
-
-
de Godoy, L.M.F.1
-
5
-
-
77950645440
-
Directionality in protein fold prediction
-
Ellis J., Huard F., Deane C., Srivastava S., Wood G. Directionality in protein fold prediction. BMC Bioinformatics 2010, 11:172.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 172
-
-
Ellis, J.1
Huard, F.2
Deane, C.3
Srivastava, S.4
Wood, G.5
-
6
-
-
0030595344
-
The "+70 pause": hypothesis of a translational control of membrane protein assembly
-
François K. The "+70 pause": hypothesis of a translational control of membrane protein assembly. J. Mol. Biol. 1996, 262:77-86.
-
(1996)
J. Mol. Biol.
, vol.262
, pp. 77-86
-
-
François, K.1
-
7
-
-
0030068269
-
Translation of Sindbis virus mRNA: analysis of sequences downstream of the initiating AUG codon that enhance translation
-
Frolov I., Schlesinger S. Translation of Sindbis virus mRNA: analysis of sequences downstream of the initiating AUG codon that enhance translation. J. Virol. 1996, 70:1182.
-
(1996)
J. Virol.
, vol.70
, pp. 1182
-
-
Frolov, I.1
Schlesinger, S.2
-
8
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami S., et al. Global analysis of protein expression in yeast. Nature 2003, 425:737-741.
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
-
9
-
-
48449095385
-
The Vienna RNA Websuite
-
Gruber A.R., Lorenz R., Bernhart S.H., Neuböck R., Hofacker I.L. The Vienna RNA Websuite. Nucleic Acids Res. 2008, 36:W70-W74.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Gruber, A.R.1
Lorenz, R.2
Bernhart, S.H.3
Neuböck, R.4
Hofacker, I.L.5
-
10
-
-
77649198142
-
A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
-
Gu W., Zhou T., Wilke C.O. A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput. Biol. 2010, 6:e1000664.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Gu, W.1
Zhou, T.2
Wilke, C.O.3
-
11
-
-
67849095416
-
BioMart Central Portal-unified access to biological data
-
Haider S., Ballester B., Smedley D., Zhang J., Rice P., Kasprzyk A. BioMart Central Portal-unified access to biological data. Nucleic Acids Res. 2009, 37:W23-W27.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Haider, S.1
Ballester, B.2
Smedley, D.3
Zhang, J.4
Rice, P.5
Kasprzyk, A.6
-
12
-
-
66849143696
-
Converging concepts of protein folding in vitro and in vivo
-
Hartl F.U., Hayer-Hartl M. Converging concepts of protein folding in vitro and in vivo. Nat. Struct. Mol. Biol. 2009, 16:574-581.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 574-581
-
-
Hartl, F.U.1
Hayer-Hartl, M.2
-
13
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
Ingolia N.T., Ghaemmaghami S., Newman J.R.S., Weissman J.S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 2009, 324:218-223.
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.S.3
Weissman, J.S.4
-
14
-
-
0347133536
-
Statistical correlation between protein secondary structure and messenger RNA stem-loop structure
-
Jia M., Luo L., Liu C. Statistical correlation between protein secondary structure and messenger RNA stem-loop structure. Biopolymers 2004, 73:16-26.
-
(2004)
Biopolymers
, vol.73
, pp. 16-26
-
-
Jia, M.1
Luo, L.2
Liu, C.3
-
15
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
Kanehisa M., et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008, 36:D480-D484.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Kanehisa, M.1
-
16
-
-
84865808846
-
Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes
-
Keller T.E., Mis S.D., Jia K.E., Wilke C.O. Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biol. Evol. 2012, 4:80-88.
-
(2012)
Genome Biol. Evol.
, vol.4
, pp. 80-88
-
-
Keller, T.E.1
Mis, S.D.2
Jia, K.E.3
Wilke, C.O.4
-
17
-
-
75549090948
-
Ensembl genomes: extending Ensembl across the taxonomic space
-
Kersey P.J., et al. Ensembl genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res. 2010, 38:D563-D569.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Kersey, P.J.1
-
18
-
-
46049107404
-
Alternative translation start sites and hidden coding potential of eukaryotic mRNAs
-
Kochetov A.V. Alternative translation start sites and hidden coding potential of eukaryotic mRNAs. Bioessays 2008, 30:683-691.
-
(2008)
Bioessays
, vol.30
, pp. 683-691
-
-
Kochetov, A.V.1
-
19
-
-
35548935529
-
AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site
-
Kochetov A.V., Palyanov A., Titov I.I., Grigorovich D., Sarai A., Kolchanov N.A. AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site. BMC Bioinformatics 2007, 8:318.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 318
-
-
Kochetov, A.V.1
Palyanov, A.2
Titov, I.I.3
Grigorovich, D.4
Sarai, A.5
Kolchanov, N.A.6
-
20
-
-
0025107694
-
Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes
-
Kozak M. Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes. Proc. Natl. Acad. Sci. U. S. A. 1990, 87:8301-8305.
-
(1990)
Proc. Natl. Acad. Sci. U. S. A.
, vol.87
, pp. 8301-8305
-
-
Kozak, M.1
-
21
-
-
27144555357
-
Regulation of translation via mRNA structure in prokaryotes and eukaryotes
-
Kozak M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 2005, 361:13-37.
-
(2005)
Gene
, vol.361
, pp. 13-37
-
-
Kozak, M.1
-
22
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
Kudla G., Murray A.W., Tollervey D., Plotkin J.B. Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324:255-258.
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
Murray, A.W.2
Tollervey, D.3
Plotkin, J.B.4
-
23
-
-
4344616800
-
Protein structure preference, tRNA copy number, and mRNA stem/loop content
-
Luo L., Jia M., Li X. Protein structure preference, tRNA copy number, and mRNA stem/loop content. Biopolymers 2004, 74:432-447.
-
(2004)
Biopolymers
, vol.74
, pp. 432-447
-
-
Luo, L.1
Jia, M.2
Li, X.3
-
24
-
-
0034254190
-
Elongation arrest is a physiologically important function of signal recognition particle
-
Mason N., Ciufo L.F., Brown J.D. Elongation arrest is a physiologically important function of signal recognition particle. EMBO J. 2000, 19:4164-4174.
-
(2000)
EMBO J.
, vol.19
, pp. 4164-4174
-
-
Mason, N.1
Ciufo, L.F.2
Brown, J.D.3
-
25
-
-
40549132858
-
Tools for analyzing and predicting N terminal protein modifications
-
Meinnel T., Giglione C. Tools for analyzing and predicting N terminal protein modifications. Proteomics 2008, 8:626-649.
-
(2008)
Proteomics
, vol.8
, pp. 626-649
-
-
Meinnel, T.1
Giglione, C.2
-
26
-
-
28544440092
-
Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs
-
Meyer I.M., Miklós I. Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs. Nucleic Acids Res. 2005, 33:6338-6348.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 6338-6348
-
-
Meyer, I.M.1
Miklós, I.2
-
27
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman J.R.S., et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006, 441:840-846.
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.S.1
-
28
-
-
33646272409
-
Identification and classification of conserved RNA secondary structures in the human genome
-
Pedersen J.S., et al. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput. Biol. 2006, 2:e33.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Pedersen, J.S.1
-
29
-
-
80053345905
-
SignalP 4.0: discriminating signal peptides from transmembrane regions
-
Petersen T.N., Brunak S., von Heijne G., Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 2011, 8:785-786.
-
(2011)
Nat. Methods
, vol.8
, pp. 785-786
-
-
Petersen, T.N.1
Brunak, S.2
von Heijne, G.3
Nielsen, H.4
-
30
-
-
4644280499
-
Solving the riddle of codon usage preferences: a test for translational selection
-
Reis M., Savva R., Wernisch L. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 2004, 32:5036.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5036
-
-
Reis, M.1
Savva, R.2
Wernisch, L.3
-
31
-
-
77951221728
-
Protein structure prediction begins well but ends badly
-
Saunders R., Deane C.M. Protein structure prediction begins well but ends badly. Proteins Struct. Funct. Bioinform. 2010, 78:1282-1290.
-
(2010)
Proteins Struct. Funct. Bioinform.
, vol.78
, pp. 1282-1290
-
-
Saunders, R.1
Deane, C.M.2
-
34
-
-
0027494569
-
Ribosomal pausing during translation of an RNA pseudoknot
-
Somogyi P., Jenner A., Brierley I., Inglis S. Ribosomal pausing during translation of an RNA pseudoknot. Mol. Cell. Biol. 1993, 13:6931.
-
(1993)
Mol. Cell. Biol.
, vol.13
, pp. 6931
-
-
Somogyi, P.1
Jenner, A.2
Brierley, I.3
Inglis, S.4
-
35
-
-
38549141104
-
LOCATE: a mammalian protein subcellular localization database
-
Sprenger J., Fink J.L., Karunaratne S., Hanson K., Hamilton N.A., Teasdale R.D. LOCATE: a mammalian protein subcellular localization database. Nucleic Acids Res. 2008, 36:D230-D233.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Sprenger, J.1
Fink, J.L.2
Karunaratne, S.3
Hanson, K.4
Hamilton, N.A.5
Teasdale, R.D.6
-
36
-
-
51649116095
-
Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures
-
Stoletzki N. Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures. BMC Evol. Biol. 2008, 8:224.
-
(2008)
BMC Evol. Biol.
, vol.8
, pp. 224
-
-
Stoletzki, N.1
-
37
-
-
0029908504
-
Protein secondary structural types are differentially coded on messenger RNA
-
Thanaraj T.A., Argos P. Protein secondary structural types are differentially coded on messenger RNA. Protein Sci. 1996, 5:1973-1983.
-
(1996)
Protein Sci.
, vol.5
, pp. 1973-1983
-
-
Thanaraj, T.A.1
Argos, P.2
-
38
-
-
77951715627
-
An evolutionarily conserved mechanism for controlling the efficiency of protein translation
-
Tuller T., et al. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 2010, 141:344-354.
-
(2010)
Cell
, vol.141
, pp. 344-354
-
-
Tuller, T.1
-
39
-
-
77649245858
-
Translation efficiency is determined by both codon bias and folding energy
-
Tuller T., Waldman Y.Y., Kupiec M., Ruppin E. Translation efficiency is determined by both codon bias and folding energy. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:3645-3650.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 3645-3650
-
-
Tuller, T.1
Waldman, Y.Y.2
Kupiec, M.3
Ruppin, E.4
-
40
-
-
80155213999
-
Composite effects of gene determinants on the translation speed and density of ribosomes
-
Tuller T., Veksler-Lublinsky I., Gazit N., Kupiec M., Ruppin E., Ziv-Ukelson M. Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol. 2011, 12:R110.
-
(2011)
Genome Biol.
, vol.12
-
-
Tuller, T.1
Veksler-Lublinsky, I.2
Gazit, N.3
Kupiec, M.4
Ruppin, E.5
Ziv-Ukelson, M.6
-
41
-
-
80051989609
-
Understanding the transcriptome through RNA structure
-
Wan Y., Kertesz M., Spitale R.C., Segal E., Chang H.Y. Understanding the transcriptome through RNA structure. Nat. Rev. Genet. 2011, 12:641-655.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 641-655
-
-
Wan, Y.1
Kertesz, M.2
Spitale, R.C.3
Segal, E.4
Chang, H.Y.5
-
42
-
-
68449092202
-
Architecture and secondary structure of an entire HIV-1 RNA genome
-
Watts J.M., et al. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 2009, 460:711-716.
-
(2009)
Nature
, vol.460
, pp. 711-716
-
-
Watts, J.M.1
-
43
-
-
41149155366
-
Following translation by single ribosomes one codon at a time
-
Wen J.-D., et al. Following translation by single ribosomes one codon at a time. Nature 2008, 452:598-603.
-
(2008)
Nature
, vol.452
, pp. 598-603
-
-
Wen, J.-D.1
-
44
-
-
0033572893
-
No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
-
Workman C., Krogh A. No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res. 1999, 27:4816.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4816
-
-
Workman, C.1
Krogh, A.2
-
45
-
-
0033289080
-
Correlation between mRNA structure of the coding region and translational pauses
-
Zama M. Correlation between mRNA structure of the coding region and translational pauses. Nucleic Acids Symp. Ser. 1999, 42:81-82.
-
(1999)
Nucleic Acids Symp. Ser.
, vol.42
, pp. 81-82
-
-
Zama, M.1
-
46
-
-
0141447335
-
Discontinuous translation and mRNA structure of the coding region
-
Zama M. Discontinuous translation and mRNA structure of the coding region. Nucleic Acids Symp. Ser. 2000, 44:91-92.
-
(2000)
Nucleic Acids Symp. Ser.
, vol.44
, pp. 91-92
-
-
Zama, M.1
-
47
-
-
79551690253
-
Folding at the birth of the nascent chain: coordinating translation with co-translational folding
-
Zhang G., Ignatova Z. Folding at the birth of the nascent chain: coordinating translation with co-translational folding. Curr. Opin. Struct. Biol. 2010, 21(1):25-31.
-
(2010)
Curr. Opin. Struct. Biol.
, vol.21
, Issue.1
, pp. 25-31
-
-
Zhang, G.1
Ignatova, Z.2
-
48
-
-
79952350113
-
Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses
-
Zhou T., Wilke C. Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses. BMC Evol. Biol. 2011, 11:59.
-
(2011)
BMC Evol. Biol.
, vol.11
, pp. 59
-
-
Zhou, T.1
Wilke, C.2
|