-
1
-
-
77953676254
-
GeneTack: Frameshift identification in protein-coding sequences by the viterbi algorithm
-
Antonov,I. and Borodovsky,M. (2010) GeneTack: frameshift identification in protein-coding sequences by the Viterbi algorithm. J. Bioinformatics Comput. Biol., 8, 535.
-
(2010)
J. Bioinformatics Comput. Biol.
, Issue.8
, pp. 535
-
-
Antonov, I.1
Borodovsky, M.2
-
2
-
-
0345685440
-
Detecting and analyzing dna sequencing errors: Toward a higher quality of the bacillus subtilis genome sequence
-
Medigue,C., Rose,M., Viari,A. and Danchin,A. (1999) Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence. Genome Res., 9, 1116-1127.
-
(1999)
Genome Res.
, vol.9
, pp. 1116-1127
-
-
Medigue, C.1
Rose, M.2
Viari, A.3
Danchin, A.4
-
3
-
-
34447525635
-
Interrupted coding sequences in mycobacterium smegmatis: Authentic mutations or sequencing errors?
-
Deshayes,C., Perrodou,E., Gallien,S., Euphrasie,D., Schaeffer,C., Van-Dorsselaer,A., Poch,O., Lecompte,O. and Reyrat,J.M. (2007) Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors? Genome Biol., 8, R20.
-
(2007)
Genome Biol.
, vol.8
-
-
Deshayes, C.1
Perrodou, E.2
Gallien, S.3
Euphrasie, D.4
Schaeffer, C.5
Van-Dorsselaer, A.6
Poch, O.7
Lecompte, O.8
Reyrat, J.M.9
-
4
-
-
0037139583
-
Recoding: Translational bifurcations in gene expression
-
Baranov,P.V., Gesteland,R.F. and Atkins,J.F. (2002) Recoding: translational bifurcations in gene expression. Gene, 286, 187-201.
-
(2002)
Gene
, vol.286
, pp. 187-201
-
-
Baranov, P.V.1
Gesteland, R.F.2
Atkins, J.F.3
-
5
-
-
0842267214
-
Reprogrammed genetic decoding in cellular gene expression
-
Namy,O., Rousset,J.P., Napthine,S. and Brierley,I. (2004) Reprogrammed genetic decoding in cellular gene expression. Mol. Cell, 13, 157-168.
-
(2004)
Mol. Cell
, vol.13
, pp. 157-168
-
-
Namy, O.1
Rousset, J.P.2
Napthine, S.3
Brierley, I.4
-
7
-
-
33644849698
-
Re-examining the role and random nature of phase variation
-
van der Woude,M.W. (2006) Re-examining the role and random nature of phase variation. FEMS Microbiol. Lett., 254, 190-197.
-
(2006)
FEMS Microbiol. Lett.
, vol.254
, pp. 190-197
-
-
Van Der, WoudeM.W.1
-
8
-
-
58149110766
-
Translational coupling controls expression and function of the drrab drug efflux pump
-
Pradhan,P., Li,W. and Kaur,P. (2009) Translational coupling controls expression and function of the DrrAB drug efflux pump. J. Mol. Biol., 385, 831-842.
-
(2009)
J. Mol. Biol.
, vol.385
, pp. 831-842
-
-
Pradhan, P.1
Li, W.2
Kaur, P.3
-
9
-
-
0035898609
-
Two overlapping reading frames in a single exon encode interacting proteins-A novel way of gene usage
-
Klemke,M., Kehlenbach,R.H. and Huttner,W.B. (2001) Two overlapping reading frames in a single exon encode interacting proteins-a novel way of gene usage. EMBO J., 20, 3849-3860.
-
(2001)
EMBO J.
, vol.20
, pp. 3849-3860
-
-
Klemke, M.1
Kehlenbach, R.H.2
Huttner, W.B.3
-
10
-
-
34848893914
-
Evolutionary impact of limited splicing fidelity in mammalian genes
-
Zhang,C., Krainer,A.R. and Zhang,M.Q. (2007) Evolutionary impact of limited splicing fidelity in mammalian genes. Trends Genet., 23, 484-488.
-
(2007)
Trends Genet.
, vol.23
, pp. 484-488
-
-
Zhang, C.1
Krainer, A.R.2
Zhang, M.Q.3
-
11
-
-
70349741137
-
Assessing the genomic evidence for conserved transcribed pseudogenes under selection
-
Khachane,A. and Harrison,P. (2009) Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics, 10, 435.
-
(2009)
BMC Genomics
, vol.10
, pp. 435
-
-
Khachane, A.1
Harrison, P.2
-
13
-
-
0022547355
-
Expression of peptide chain release factor 2 requires high-efficiency frameshift
-
Craigen,W.J. and Caskey,C.T. (1986) Expression of peptide chain release factor 2 requires high-efficiency frameshift. Nature, 322, 273-275.
-
(1986)
Nature
, vol.322
, pp. 273-275
-
-
Craigen, W.J.1
Caskey, C.T.2
-
14
-
-
34247876224
-
Ribosomal frameshifting in decoding antizyme mrnas from yeast and protists to humans: Close to 300 cases reveal remarkable diversity despite underlying conservation
-
Ivanov,I.P. and Atkins,J.F. (2007) Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation. Nucleic Acids Res., 35, 1842-1858.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 1842-1858
-
-
Ivanov, I.P.1
Atkins, J.F.2
-
15
-
-
84862642115
-
Non-canonical translation in rna viruses
-
Firth,A. and Brierley,I. (2012) Non-canonical translation in RNA viruses. J. Gen. Virol., 93(Pt 7), 1385-1409.
-
(2012)
J. Gen. Virol.
, Issue.93 PART 7
, pp. 1385-1409
-
-
Firth, A.1
Brierley, I.2
-
16
-
-
33344468695
-
Recoding in bacteriophages and bacterial is elements
-
Baranov,P., Fayet,O., Hendrix,R. and Atkins,J. (2006) Recoding in bacteriophages and bacterial IS elements. Trends Genet., 22, 174-181.
-
(2006)
Trends Genet.
, vol.22
, pp. 174-181
-
-
Baranov, P.1
Fayet, O.2
Hendrix, R.3
Atkins, J.4
-
17
-
-
80155192426
-
A pilot study of bacterial genes with disrupted orfs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment
-
Sharma,V., Firth,A., Antonov,I., Fayet,O., Atkins,J., Borodovsky,M. and Baranov,P. (2011) A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. Mol. Biol. Evol., 28, 3195-3211.
-
(2011)
Mol. Biol. Evol.
, Issue.28
, pp. 3195-3211
-
-
Sharma, V.1
Firth, A.2
Antonov, I.3
Fayet, O.4
Atkins, J.5
Borodovsky, M.6
Baranov, P.7
-
18
-
-
75549087350
-
Recode-2: New design, new search tools, and many more genes
-
Bekaert,M., Firth,A.E., Zhang,Y., Gladyshev,V.N., Atkins,J.F. and Baranov,P.V. (2010) Recode-2: new design, new search tools, and many more genes. Nucleic Acids Res., 38, D69-D74.
-
(2010)
Nucleic Acids Res.
, Issue.38
-
-
Bekaert, M.1
Firth, A.E.2
Zhang, Y.3
Gladyshev, V.N.4
Atkins, J.F.5
Baranov, P.V.6
-
19
-
-
48149095822
-
Alternative splicing resulting in nonsense-mediated mrna decay: What is the meaning of nonsense?
-
McGlincy,N. and Smith,C. (2008) Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense? Trends Biochem. Sci., 33, 385-393.
-
(2008)
Trends Biochem. Sci.
, vol.33
, pp. 385-393
-
-
McGlincy, N.1
Smith, C.2
-
20
-
-
0037422575
-
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mrna decay in humans
-
Lewis,B.P., Green,R.E. and Brenner,S.E. (2003) Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl Acad. Sci. USA, 100, 189-192.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 189-192
-
-
Lewis, B.P.1
Green, R.E.2
Brenner, S.E.3
-
21
-
-
30944449484
-
Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mrna decay to control gene expression
-
Pan,Q., Saltzman,A., Kim,Y., Misquitta,C., Shai,O., Maquat,L., Frey,B. and Blencowe,B. (2006) Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev., 20, 153.
-
(2006)
Genes Dev.
, vol.20
, pp. 153
-
-
Pan, Q.1
Saltzman, A.2
Kim, Y.3
Misquitta, C.4
Shai, O.5
Maquat, L.6
Frey, B.7
Blencowe, B.8
-
22
-
-
34249719998
-
A first look at arfome: Dual-coding genes in mammalian genomes
-
Chung,W., Wadhawan,S., Szklarczyk,R., Pond,S. and Nekrutenko,A. (2007) A first look at ARFome: dual-coding genes in mammalian genomes. PLoS Comput. Biol., 3, e91.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Chung, W.1
Wadhawan, S.2
Szklarczyk, R.3
Pond, S.4
Nekrutenko, A.5
-
23
-
-
84868324214
-
Observation of dually decoded regions of the human genome using ribosome profiling data
-
Michel,A.M., Roy Choudhury,K., Firth,A.E., Ingolia,N.T., Atkins,J.F. and Baranov,P.V. (2012) Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res., 22, 2219-2229.
-
(2012)
Genome Res.
, Issue.22
, pp. 2219-2229
-
-
Michel, A.M.1
Roy Choudhury, K.2
Firth, A.E.3
Ingolia, N.T.4
Atkins, J.F.5
Baranov, P.V.6
-
24
-
-
79551629027
-
Translational pausing ensures membrane targeting and cytoplasmic splicing of xbp1u mrna
-
Yanagitani,K., Kimata,Y., Kadokura,H. and Kohno,K. (2011) Translational pausing ensures membrane targeting and cytoplasmic splicing of XBP1u mRNA. Science, 331, 586.
-
(2011)
Science
, Issue.331
, pp. 586
-
-
Yanagitani, K.1
Kimata, Y.2
Kadokura, H.3
Kohno, K.4
-
25
-
-
0029587551
-
Alternative reading frames of the ink4a tumor suppressor gene encode two unrelated proteins capable of inducing cell cycle arrest
-
Ouelle,D., Zindy,F., Ashmun,R. and Sherr,C. (1995) Alternative reading frames of the INK4a tumor suppressor gene encode two unrelated proteins capable of inducing cell cycle arrest. Cell, 83, 993-1000.
-
(1995)
Cell
, vol.83
, pp. 993-1000
-
-
Ouelle, D.1
Zindy, F.2
Ashmun, R.3
Sherr, C.4
-
26
-
-
55449135271
-
Oscillating evolution of a mammalian locus with overlapping reading frames: An xlas/alex relay
-
Nekrutenko,A., Wadhawan,S., Goetting-Minesky,P. and Makova,K. (2005) Oscillating evolution of a mammalian locus with overlapping reading frames: an XLas/ALEX relay. PLoS Genet., 1, e18.
-
(2005)
PLoS Genet.
, vol.1
-
-
Nekrutenko, A.1
Wadhawan, S.2
Goetting-Minesky, P.3
Makova, K.4
-
27
-
-
0025008168
-
Sequence logos: A new way to display consensus sequences
-
Schneider,T. and Stephens,R. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 6097-6100
-
-
Schneider, T.1
Stephens, R.2
-
28
-
-
0035875343
-
Genemarks: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
-
Besemer,J., Lomsadze,A. and Borodovsky,M. (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29, 2607-2618.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2607-2618
-
-
Besemer, J.1
Lomsadze, A.2
Borodovsky, M.3
-
29
-
-
67849122320
-
Meme suite: Tools for motif discovery and searching
-
Bailey,T.L., Boden,M., Buske,F.A., Frith,M., Grant,C.E., Clementi,L., Ren,J., Li,W.W. and Noble,W.S. (2009) MEME Suite: tools for motif discovery and searching. Nucleic Acids Res., 37, W202-W208.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Bailey, T.L.1
Boden, M.2
Buske, F.A.3
Frith, M.4
Grant, C.E.5
Clementi, L.6
Ren, J.7
Li, W.W.8
Noble, W.S.9
-
30
-
-
77955902981
-
Ab initio gene identification in metagenomic sequences
-
Zhu,W., Lomsadze,A. and Borodovsky,M. (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res., 38, e132.
-
(2010)
Nucleic Acids Res.
, Issue.38
-
-
Zhu, W.1
Lomsadze, A.2
Borodovsky, M.3
|