-
1
-
-
45449118785
-
Recognition of nonsense mRNA: Towards a unified model
-
Mühlemann,O. (2008) Recognition of nonsense mRNA: towards a unified model. Biochem. Soc. Trans., 36, 497-501.
-
(2008)
Biochem. Soc. Trans.
, vol.36
, pp. 497-501
-
-
Mühlemann, O.1
-
2
-
-
0347416978
-
Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5 to 3 mRNA decay pathways in yeast
-
He,F., Li,X., Spatrick,P., Casillo,R., Dong,S. and Jacobson,A. (2003) Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5 to 3 mRNA decay pathways in yeast. Mol. Cell, 12, 1439-1452.
-
(2003)
Mol. Cell
, vol.12
, pp. 1439-1452
-
-
He, F.1
Li, X.2
Spatrick, P.3
Casillo, R.4
Dong, S.5
Jacobson, A.6
-
3
-
-
6944256813
-
Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise
-
Mendell,J.T., Sharifi,N.A., Meyers,J.L., Martinez-Murillo,F. and Dietz,H.C. (2004) Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet., 36, 1073-1078.
-
(2004)
Nat. Genet.
, vol.36
, pp. 1073-1078
-
-
Mendell, J.T.1
Sharifi, N.A.2
Meyers, J.L.3
Martinez-Murillo, F.4
Dietz, H.C.5
-
4
-
-
25844435702
-
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets
-
Rehwinkel,J., Letunic,I., Raes,J., Bork,P. and Izaurralde,E. (2005) Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA, 11, 1530-1544.
-
(2005)
RNA
, vol.11
, pp. 1530-1544
-
-
Rehwinkel, J.1
Letunic, I.2
Raes, J.3
Bork, P.4
Izaurralde, E.5
-
5
-
-
33751375141
-
Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast
-
Guan,Q., Zheng,W., Tang,S., Liu,X., Zinkel,R.A., Tsui,K.-W., Yandell,B.S. and Culbertson,M.R. (2006) Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genet., 2, e203.
-
(2006)
PLoS Genet
, vol.2
, pp. e203
-
-
Guan, Q.1
Zheng, W.2
Tang, S.3
Liu, X.4
Zinkel, R.A.5
Tsui, K.-W.6
Yandell, B.S.7
Culbertson, M.R.8
-
6
-
-
60549106018
-
Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis
-
Kurihara,Y., Matsui,A., Hanada,K., Kawashima,M., Ishida,J., Morosawa,T., Tanaka,M., Kaminuma,E., Mochizuki,Y., Matsushima,A. et al. (2009) Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 106, 2453-2458.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 2453-2458
-
-
Kurihara, Y.1
Matsui, A.2
Hanada, K.3
Kawashima, M.4
Ishida, J.5
Morosawa, T.6
Tanaka, M.7
Kaminuma, E.8
Mochizuki, Y.9
Matsushima, A.10
-
7
-
-
84857478172
-
A role for nonsense-mediated mRNA decay in plants: Pathogen responses are induced in Arabidopsis thaliana NMD mutants
-
Rayson,S., Arciga-Reyes,L., Wootton,L., De Torres Zabala,M., Truman,W., Graham,N., Grant,M. and Davies,B. (2012) A role for nonsense-mediated mRNA decay in plants: pathogen responses are induced in Arabidopsis thaliana NMD mutants. PLoS One, 7, e31917.
-
(2012)
PLoS One
, vol.7
, pp. e31917
-
-
Rayson, S.1
Arciga-Reyes, L.2
Wootton, L.3
De Torres Zabala, M.4
Truman, W.5
Graham, N.6
Grant, M.7
Davies, B.8
-
8
-
-
34247330971
-
Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
-
Lareau,L.F., Inada,M., Green,R.E., Wengrod,J.C. and Brenner,S.E. (2007) Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature, 446, 926-929.
-
(2007)
Nature
, vol.446
, pp. 926-929
-
-
Lareau, L.F.1
Inada, M.2
Green, R.E.3
Wengrod, J.C.4
Brenner, S.E.5
-
9
-
-
84979220633
-
Nonsense-mediated mRNA decay modulates FLM-dependent thermosensory flowering response in Arabidopsis
-
Sureshkumar,S., Dent,C., Seleznev,A., Tasset,C. and Balasubramanian,S. (2016) Nonsense-mediated mRNA decay modulates FLM-dependent thermosensory flowering response in Arabidopsis. Nature Plants, 2, 16055.
-
(2016)
Nature Plants
, vol.2
, pp. 16055
-
-
Sureshkumar, S.1
Dent, C.2
Seleznev, A.3
Tasset, C.4
Balasubramanian, S.5
-
10
-
-
84867850145
-
NMD: A multifaceted response to premature translational termination
-
Kervestin,S. and Jacobson,A. (2012) NMD: a multifaceted response to premature translational termination. Nat. Rev. Mol. Cell Biol., 13, 700-712.
-
(2012)
Nat. Rev. Mol. Cell Biol.
, vol.13
, pp. 700-712
-
-
Kervestin, S.1
Jacobson, A.2
-
11
-
-
77949904260
-
Nonsense-mediated mRNA decay in human cells: Mechanistic insights, functions beyond quality control and the double-life of NMD factors
-
Nicholson,P., Yepiskoposyan,H., Metze,S., Zamudio Orozco,R., Kleinschmidt,N. and Mühlemann,O. (2010) Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors. Cell. Mol. Life Sci., 67, 677-700.
-
(2010)
Cell. Mol. Life Sci.
, vol.67
, pp. 677-700
-
-
Nicholson, P.1
Yepiskoposyan, H.2
Metze, S.3
Zamudio Orozco, R.4
Kleinschmidt, N.5
Mühlemann, O.6
-
12
-
-
44649127573
-
Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay
-
Kerényi,Z., Mérai,Z., Hiripi,L., Benkovics,A., Gyula,P., Lacomme,C., Barta,E., Nagy,F. and Silhavy,D. (2008) Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay. EMBO J., 27, 1585-1595.
-
(2008)
EMBO J
, vol.27
, pp. 1585-1595
-
-
Kerényi, Z.1
Mérai, Z.2
Hiripi, L.3
Benkovics, A.4
Gyula, P.5
Lacomme, C.6
Barta, E.7
Nagy, F.8
Silhavy, D.9
-
13
-
-
84880534583
-
Plant nonsense-mediated mRNA decay is controlled by different autoregulatory circuits and can be induced by an EJC-like complex
-
Nyiko,T., Kerenyi,F., Szabadkai,L., Benkovics,A.H., Major,P., Sonkoly,B., Merai,Z., Barta,E., Niemiec,E., Kufel,J. et al. (2013) Plant nonsense-mediated mRNA decay is controlled by different autoregulatory circuits and can be induced by an EJC-like complex. Nucleic Acids Res., 41, 6715-6728.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 6715-6728
-
-
Nyiko, T.1
Kerenyi, F.2
Szabadkai, L.3
Benkovics, A.H.4
Major, P.5
Sonkoly, B.6
Merai, Z.7
Barta, E.8
Niemiec, E.9
Kufel, J.10
-
14
-
-
0032104190
-
A rule for termination-codon position within intron-containing genes: When nonsense affects RNA abundance
-
Nagy,E. and Maquat,L.E. (1998) A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. Trends Biochem. Sci., 23, 198-199.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 198-199
-
-
Nagy, E.1
Maquat, L.E.2
-
15
-
-
43249084802
-
A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay
-
Singh,G., Rebbapragada,I. and Lykke-Andersen,J. (2008) A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay. PLoS Biol., 6, e111.
-
(2008)
PLoS Biol
, vol.6
, pp. e111
-
-
Singh, G.1
Rebbapragada, I.2
Lykke-Andersen, J.3
-
16
-
-
66249097064
-
Long 3-UTRs target wild-type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae
-
Kebaara,B.W. and Atkin,A.L. (2009) Long 3-UTRs target wild-type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae. Nucleic acids Res., 37, 2771-2778.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 2771-2778
-
-
Kebaara, B.W.1
Atkin, A.L.2
-
17
-
-
33845622065
-
Both introns and long 3-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants
-
Kertész,S., Kerényi,Z., Mérai,Z., Bartos,I., Pálfy,T., Barta,E. and Silhavy,D. (2006) Both introns and long 3-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants. Nucleic Acids Res., 34, 6147-6157.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 6147-6157
-
-
Kertész, S.1
Kerényi, Z.2
Mérai, Z.3
Bartos, I.4
Pálfy, T.5
Barta, E.6
Silhavy, D.7
-
18
-
-
70350216071
-
Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner
-
Nyikó,T., Sonkoly,B., Mérai,Z., Benkovics,A.H. and Silhavy,D. (2009) Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner. Plant Mol. Biol., 71, 367-378.
-
(2009)
Plant Mol. Biol.
, vol.71
, pp. 367-378
-
-
Nyikó, T.1
Sonkoly, B.2
Mérai, Z.3
Benkovics, A.H.4
Silhavy, D.5
-
19
-
-
44349167189
-
Hypoxic inhibition of nonsense-mediated RNA decay regulates gene expression and the integrated stress response
-
Gardner,L.B. (2008) Hypoxic inhibition of nonsense-mediated RNA decay regulates gene expression and the integrated stress response. Mol. Cell. Biol., 28, 3729-3741.
-
(2008)
Mol. Cell. Biol.
, vol.28
, pp. 3729-3741
-
-
Gardner, L.B.1
-
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. U.S.A., 100, 189-192.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 189-192
-
-
Lewis, B.P.1
Green, R.E.2
Brenner, S.E.3
-
21
-
-
84861333042
-
Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns
-
Weischenfeldt,J., Waage,J., Tian,G., Zhao,J., Damgaard,I., Jakobsen,J.S., Kristiansen,K., Krogh,A., Wang,J. and Porse,B.T. (2012) Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns. Genome Biol., 13, R35.
-
(2012)
Genome Biol
, vol.13
, pp. R35
-
-
Weischenfeldt, J.1
Waage, J.2
Tian, G.3
Zhao, J.4
Damgaard, I.5
Jakobsen, J.S.6
Kristiansen, K.7
Krogh, A.8
Wang, J.9
Porse, B.T.10
-
22
-
-
84859293997
-
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis
-
Kalyna,M., Simpson,C.G., Syed,N.H., Lewandowska,D., Marquez,Y., Kusenda,B., Marshall,J., Fuller,J., Cardle,L., McNicol,J. et al. (2012) Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res., 40, 2454-2469.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 2454-2469
-
-
Kalyna, M.1
Simpson, C.G.2
Syed, N.H.3
Lewandowska, D.4
Marquez, Y.5
Kusenda, B.6
Marshall, J.7
Fuller, J.8
Cardle, L.9
McNicol, J.10
-
23
-
-
84888407848
-
Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome
-
Drechsel,G., Kahles,A., Kesarwani,A.K., Stauffer,E., Behr,J., Drewe,P., Rätsch,G. and Wachter,A. (2013) Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome. Plant Cell, 25, 3726-3742.
-
(2013)
Plant Cell
, vol.25
, pp. 3726-3742
-
-
Drechsel, G.1
Kahles, A.2
Kesarwani, A.K.3
Stauffer, E.4
Behr, J.5
Drewe, P.6
Rätsch, G.7
Wachter, A.8
-
24
-
-
84988288865
-
Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible
-
Lareau,L.F. and Brenner,S.E. (2015) Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. Mol. Biol. Evol., 32, 1072-1079.
-
(2015)
Mol. Biol. Evol.
, vol.32
, pp. 1072-1079
-
-
Lareau, L.F.1
Brenner, S.E.2
-
25
-
-
33745817833
-
UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis
-
Arciga-Reyes,L., Wootton,L., Kieffer,M. and Davies,B. (2006) UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis. Plant J., 47, 480-489.
-
(2006)
Plant J
, vol.47
, pp. 480-489
-
-
Arciga-Reyes, L.1
Wootton, L.2
Kieffer, M.3
Davies, B.4
-
26
-
-
84871949409
-
The late steps of plant nonsense-mediated mRNA decay
-
Mérai,Z., Benkovics,A.H., Nyikó,T., Debreczeny,M., Hiripi,L., Kerényi,Z., Kondorosi,E. and Silhavy,D. (2012) The late steps of plant nonsense-mediated mRNA decay. Plant J., 73, 50-62.
-
(2012)
Plant J
, vol.73
, pp. 50-62
-
-
Mérai, Z.1
Benkovics, A.H.2
Nyikó, T.3
Debreczeny, M.4
Hiripi, L.5
Kerényi, Z.6
Kondorosi, E.7
Silhavy, D.8
-
27
-
-
84889099630
-
Phosphorylation of the N- And C-terminal UPF1 domains plays a critical role in plant nonsense-mediated mRNA decay
-
Kerényi,F., Wawer,I., Sikorski,P.J., Kufel,J. and Silhavy,D. (2013) Phosphorylation of the N- and C-terminal UPF1 domains plays a critical role in plant nonsense-mediated mRNA decay. Plant J., 76, 836-848.
-
(2013)
Plant J
, vol.76
, pp. 836-848
-
-
Kerényi, F.1
Wawer, I.2
Sikorski, P.J.3
Kufel, J.4
Silhavy, D.5
-
28
-
-
4344570947
-
SMG-1 is a phosphatidylinositol kinase-related protein kinase required for nonsense-mediated mRNA Decay in Caenorhabditis elegans
-
Grimson,A., O'Connor,S., Newman,C.L. and Anderson,P. (2004) SMG-1 is a phosphatidylinositol kinase-related protein kinase required for nonsense-mediated mRNA Decay in Caenorhabditis elegans. Mol. Cell. Biol., 24, 7483-7490.
-
(2004)
Mol. Cell. Biol.
, vol.24
, pp. 7483-7490
-
-
Grimson, A.1
O'Connor, S.2
Newman, C.L.3
Anderson, P.4
-
29
-
-
84889096702
-
SMG1 is an ancient nonsense-mediated mRNA decay effector
-
Lloyd,J.P.B. and Davies,B. (2013) SMG1 is an ancient nonsense-mediated mRNA decay effector. Plant J., 76, 800-810.
-
(2013)
Plant J
, vol.76
, pp. 800-810
-
-
Lloyd, J.P.B.1
Davies, B.2
-
30
-
-
85036614133
-
Conservation of nonsense-mediated mRNA decay complex components throughout eukaryotic evolution
-
Causier,B., Li,Z., De Smet,R., Lloyd,J.P.B., Van de Peer,Y. and Davies,B. (2017) Conservation of nonsense-mediated mRNA decay complex components throughout eukaryotic evolution. Scientific Rep., 7, 16692.
-
(2017)
Scientific Rep
, vol.7
, pp. 16692
-
-
Causier, B.1
Li, Z.2
De Smet, R.3
Lloyd, J.P.B.4
Van De Peer, Y.5
Davies, B.6
-
31
-
-
0017404566
-
The isolation and preliminary characterisation of auxotrophic and analogue resistant mutants of the moss, Physcomitrella patens
-
Ashton,N. and Cove,D. (1977) The isolation and preliminary characterisation of auxotrophic and analogue resistant mutants of the moss, Physcomitrella patens. Mol. Gen. Genet. MGG, 154, 87-95.
-
(1977)
Mol. Gen. Genet. MGG
, vol.154
, pp. 87-95
-
-
Ashton, N.1
Cove, D.2
-
32
-
-
37849032457
-
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
-
Rensing,S.A., Lang,D., Zimmer,A.D., Terry,A., Salamov,A., Shapiro,H., Nishiyama,T., Perroud,P.-F., Lindquist,E.A., Kamisugi,Y. et al. (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science, 319, 64-69.
-
(2008)
Science
, vol.319
, pp. 64-69
-
-
Rensing, S.A.1
Lang, D.2
Zimmer, A.D.3
Terry, A.4
Salamov, A.5
Shapiro, H.6
Nishiyama, T.7
Perroud, P.-F.8
Lindquist, E.A.9
Kamisugi, Y.10
-
33
-
-
0034723470
-
Tagged mutagenesis and gene-trap in the moss, Physcomitrella patens by shuttle mutagenesis
-
Nishiyama,T., Hiwatashi,Y., Sakakibara,I., Kato,M. and Hasebe,M. (2000) Tagged mutagenesis and gene-trap in the moss, Physcomitrella patens by shuttle mutagenesis. DNA Res., 7, 9-17.
-
(2000)
DNA Res
, vol.7
, pp. 9-17
-
-
Nishiyama, T.1
Hiwatashi, Y.2
Sakakibara, I.3
Kato, M.4
Hasebe, M.5
-
34
-
-
84860379038
-
MRE11 and RAD50, but not NBS1, are essential for gene targeting in the moss Physcomitrella patens
-
Kamisugi,Y., Schaefer,D.G., Kozak,J., Charlot,F., Vrielynck,N., Holá,M., Angelis,K.J., Cuming,A.C. and Nogué,F. (2011) MRE11 and RAD50, but not NBS1, are essential for gene targeting in the moss Physcomitrella patens. Nucleic Acids Res., 40, 3496-3510.
-
(2011)
Nucleic Acids Res
, vol.40
, pp. 3496-3510
-
-
Kamisugi, Y.1
Schaefer, D.G.2
Kozak, J.3
Charlot, F.4
Vrielynck, N.5
Holá, M.6
Angelis, K.J.7
Cuming, A.C.8
Nogué, F.9
-
35
-
-
79958126664
-
-
ACM, Vancouver
-
Wobbrock,J.O., Findlater,L., Gergle,D. and Higgins,J.J. (2011) Proceedings of the SIGCHI Conference on Human Factors in Computing Systems. ACM, Vancouver, pp. 143-146.
-
(2011)
Proceedings of The SIGCHI Conference on Human Factors in Computing Systems
, pp. 143-146
-
-
Wobbrock, J.O.1
Findlater, L.2
Gergle, D.3
Higgins, J.J.4
-
36
-
-
65449136284
-
Tophat: Discovering splice junctions with RNA-Seq
-
Trapnell,C., Pachter,L. and Salzberg,S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
37
-
-
84880334849
-
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions
-
Zimmer,A.D., Lang,D., Buchta,K., Rombauts,S., Nishiyama,T., Hasebe,M., Van de Peer,Y., Rensing,S.A. and Reski,R. (2013) Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. BMC Genomics, 14, 498.
-
(2013)
BMC Genomics
, vol.14
, pp. 498
-
-
Zimmer, A.D.1
Lang, D.2
Buchta, K.3
Rombauts, S.4
Nishiyama, T.5
Hasebe, M.6
Van De Peer, Y.7
Rensing, S.A.8
Reski, R.9
-
38
-
-
84928987900
-
HTSeq-a Python framework to work with high-throughput sequencing data
-
Anders,S., Pyl,P.T. and Huber,W. (2015) HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166-169.
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
39
-
-
84858041341
-
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
-
McCarthy,D.J., Chen,Y. and Smyth,G.K. (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res., 40, 4288-4297.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 4288-4297
-
-
McCarthy, D.J.1
Chen, Y.2
Smyth, G.K.3
-
40
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders,S. and Huber,W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
-
(2010)
Genome Biol
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
41
-
-
83055192078
-
Differential expression in RNA-seq: A matter of depth
-
Tarazona,S., Garcia-Alcalde,F., Dopazo,J., Ferrer,A. and Conesa,A. (2011) Differential expression in RNA-seq: a matter of depth. Genome Res., 21, 2213-2223.
-
(2011)
Genome Res
, vol.21
, pp. 2213-2223
-
-
Tarazona, S.1
Garcia-Alcalde, F.2
Dopazo, J.3
Ferrer, A.4
Conesa, A.5
-
42
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell,C., Williams,B.A., Pertea,G., Mortazavi,A., Kwan,G., van Baren,M.J., Salzberg,S.L., Wold,B.J. and Pachter,L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
43
-
-
77952355762
-
Genome-wide evolutionary analysis of eukaryotic DNA methylation
-
Zemach,A., McDaniel,I.E., Silva,P. and Zilberman,D. (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science, 328, 916-919.
-
(2010)
Science
, vol.328
, pp. 916-919
-
-
Zemach, A.1
McDaniel, I.E.2
Silva, P.3
Zilberman, D.4
-
44
-
-
56249113343
-
Building predictive models in R using the caret package
-
Kuhn,M. (2008) Building predictive models in R using the caret package. J. Stat. Softw., 28, 26.
-
(2008)
J. Stat. Softw.
, vol.28
, pp. 26
-
-
Kuhn, M.1
-
45
-
-
75249087100
-
Edger: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson,M.D., McCarthy,D.J. and Smyth,G.K. (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
46
-
-
0037064145
-
Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts
-
Mendell,J.T., ap Rhys,C.M.J. and Dietz,H.C. (2002) Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts. Science, 298, 419-422.
-
(2002)
Science
, vol.298
, pp. 419-422
-
-
Mendell, J.T.1
Ap Rhys, C.M.J.2
Dietz, H.C.3
-
47
-
-
84868545662
-
The salicylic acid dependent and independent effects of NMD in plants
-
Rayson,S., Ashworth,M., de Torres Zabala,M., Grant,M. and Davies,B. (2012) The salicylic acid dependent and independent effects of NMD in plants. Plant Signal. Behav., 7, 1434-1437.
-
(2012)
Plant Signal. Behav.
, vol.7
, pp. 1434-1437
-
-
Rayson, S.1
Ashworth, M.2
De Torres Zabala, M.3
Grant, M.4
Davies, B.5
-
48
-
-
76349096255
-
High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans
-
Ramani,A.K., Nelson,A.C., Kapranov,P., Bell,I., Gingeras,T.R. and Fraser,A.G. (2009) High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biol., 10, R101.
-
(2009)
Genome Biol
, vol.10
, pp. R101
-
-
Ramani, A.K.1
Nelson, A.C.2
Kapranov, P.3
Bell, I.4
Gingeras, T.R.5
Fraser, A.G.6
-
49
-
-
84938949945
-
Cell-specific transcriptomic analyses of three-dimensional shoot development in the moss Physcomitrella patens
-
Frank,M.H. and Scanlon,M.J. (2015) Cell-specific transcriptomic analyses of three-dimensional shoot development in the moss Physcomitrella patens. Plant J., 83, 743-751.
-
(2015)
Plant J
, vol.83
, pp. 743-751
-
-
Frank, M.H.1
Scanlon, M.J.2
-
50
-
-
0345359349
-
Identification of Physcomitrella patens genes specific of bud and gametophore formation
-
Brun,F., Gonneau,M., Laloue,M. and Nogué,F. (2003) Identification of Physcomitrella patens genes specific of bud and gametophore formation. Plant Sci., 165, 1267-1274.
-
(2003)
Plant Sci
, vol.165
, pp. 1267-1274
-
-
Brun, F.1
Gonneau, M.2
Laloue, M.3
Nogué, F.4
-
51
-
-
12144291195
-
Mapman: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
-
Thimm,O., Blasing,O., Gibon,Y., Nagel,A., Meyer,S., Kruger,P., Selbig,J., Muller,L.A., Rhee,S.Y. and Stitt,M. (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J., 37, 914-939.
-
(2004)
Plant J
, vol.37
, pp. 914-939
-
-
Thimm, O.1
Blasing, O.2
Gibon, Y.3
Nagel, A.4
Meyer, S.5
Kruger, P.6
Selbig, J.7
Muller, L.A.8
Rhee, S.Y.9
Stitt, M.10
-
52
-
-
2942572923
-
The mRNA surveillance protein hSMG-1 functions in genotoxic stress response pathways in mammalian cells
-
Brumbaugh,K.M., Otterness,D.M., Geisen,C., Oliveira,V., Brognard,J., Li,X., Lejeune,F., Tibbetts,R.S., Maquat,L.E. and Abraham,R.T. (2004) The mRNA surveillance protein hSMG-1 functions in genotoxic stress response pathways in mammalian cells. Mol. Cell, 14, 585-598.
-
(2004)
Mol. Cell
, vol.14
, pp. 585-598
-
-
Brumbaugh, K.M.1
Otterness, D.M.2
Geisen, C.3
Oliveira, V.4
Brognard, J.5
Li, X.6
Lejeune, F.7
Tibbetts, R.S.8
Maquat, L.E.9
Abraham, R.T.10
-
53
-
-
84870293462
-
Plant transducers of the endoplasmic reticulum unfolded protein response
-
Iwata,Y. and Koizumi,N. (2012) Plant transducers of the endoplasmic reticulum unfolded protein response. Trends Plant Sci., 17, 720-727
-
(2012)
Trends Plant Sci
, vol.17
, pp. 720-727
-
-
Iwata, Y.1
Koizumi, N.2
-
54
-
-
84861434815
-
RNA surveillance is required for endoplasmic reticulum homeostasis
-
Sakaki,K., Yoshina,S., Shen,X., Han,J., Desantis,M.R., Xiong,M., Mitani,S. and Kaufman,R.J. (2012) RNA surveillance is required for endoplasmic reticulum homeostasis. Proc. Natl. Acad. Sci. U.S.A., 109, 8079-8084
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 8079-8084
-
-
Sakaki, K.1
Yoshina, S.2
Shen, X.3
Han, J.4
Desantis, M.R.5
Xiong, M.6
Mitani, S.7
Kaufman, R.J.8
-
55
-
-
84862224647
-
Alteration of the bZIP60/IRE1 pathway affects plant response to ER Stress in Arabidopsis thaliana
-
Humbert,S., Zhong,S., Deng,Y., Howell,S.H. and Rothstein,S.J. (2012) Alteration of the bZIP60/IRE1 pathway affects plant response to ER Stress in Arabidopsis thaliana. PLoS One, 7, e39023.
-
(2012)
PLoS One
, vol.7
, pp. e39023
-
-
Humbert, S.1
Zhong, S.2
Deng, Y.3
Howell, S.H.4
Rothstein, S.J.5
-
56
-
-
34247210084
-
Heterotrimeric G protein signaling in the Arabidopsis unfolded protein response
-
Wang,S., Narendra,S. and Fedoroff,N. (2007) Heterotrimeric G protein signaling in the Arabidopsis unfolded protein response. Proc. Natl. Acad. Sci. U.S.A., 104, 3817-3822.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 3817-3822
-
-
Wang, S.1
Narendra, S.2
Fedoroff, N.3
-
57
-
-
64749086697
-
The cytosolic protein response as a subcomponent of the wider heat shock response in Arabidopsis
-
Sugio,A., Dreos,R., Aparicio,F. and Maule,A.J. (2009) The cytosolic protein response as a subcomponent of the wider heat shock response in Arabidopsis. Plant Cell, 21, 642-654.
-
(2009)
Plant Cell
, vol.21
, pp. 642-654
-
-
Sugio, A.1
Dreos, R.2
Aparicio, F.3
Maule, A.J.4
-
58
-
-
58549108606
-
Arabidopsis bZIP60 is a proteolysis-activated transcription factor involved in the endoplasmic reticulum stress response
-
Iwata,Y., Fedoroff,N.V. and Koizumi,N. (2008) Arabidopsis bZIP60 is a proteolysis-activated transcription factor involved in the endoplasmic reticulum stress response. Plant Cell, 20, 3107-3121.
-
(2008)
Plant Cell
, vol.20
, pp. 3107-3121
-
-
Iwata, Y.1
Fedoroff, N.V.2
Koizumi, N.3
-
59
-
-
22144447152
-
Gene expression in response to endoplasmic reticulum stress in Arabidopsis thaliana
-
Kamauchi,S., Nakatani,H., Nakano,C. and Urade,R. (2005) Gene expression in response to endoplasmic reticulum stress in Arabidopsis thaliana. FEBS J., 272, 3461-3476.
-
(2005)
FEBS J
, vol.272
, pp. 3461-3476
-
-
Kamauchi, S.1
Nakatani, H.2
Nakano, C.3
Urade, R.4
-
60
-
-
80052331341
-
Inhibition of nonsense-mediated RNA decay by the tumor microenvironment promotes tumorigenesis
-
Wang,D., Zavadil,J., Martin,L., Parisi,F., Friedman,E., Levy,D., Harding,H., Ron,D. and Gardner,L.B. (2011) Inhibition of nonsense-mediated RNA decay by the tumor microenvironment promotes tumorigenesis. Mol. Cell. Biol., 31, 3670-3680.
-
(2011)
Mol. Cell. Biol.
, vol.31
, pp. 3670-3680
-
-
Wang, D.1
Zavadil, J.2
Martin, L.3
Parisi, F.4
Friedman, E.5
Levy, D.6
Harding, H.7
Ron, D.8
Gardner, L.B.9
-
61
-
-
84899952675
-
The unfolded protein response affects readthrough of premature termination codons
-
Oren,Y.S., McClure,M.L., Rowe,S.M., Sorscher,E.J., Bester,A.C., Manor,M., Kerem,E., Rivlin,J., Zahdeh,F., Mann,M. et al. (2014) The unfolded protein response affects readthrough of premature termination codons. EMBO Mol. Med., 6, 685-701.
-
(2014)
EMBO Mol. Med.
, vol.6
, pp. 685-701
-
-
Oren, Y.S.1
McClure, M.L.2
Rowe, S.M.3
Sorscher, E.J.4
Bester, A.C.5
Manor, M.6
Kerem, E.7
Rivlin, J.8
Zahdeh, F.9
Mann, M.10
-
62
-
-
84928925194
-
The unfolded protein response is shaped by the NMD pathway
-
Karam,R., Lou,C.H., Kroeger,H., Huang,L., Lin,J.H. and Wilkinson,M.F. (2015) The unfolded protein response is shaped by the NMD pathway. EMBO Rep., 16, 599-609.
-
(2015)
EMBO Rep
, vol.16
, pp. 599-609
-
-
Karam, R.1
Lou, C.H.2
Kroeger, H.3
Huang, L.4
Lin, J.H.5
Wilkinson, M.F.6
-
63
-
-
33746261445
-
The double life of UPF1 in RNA and DNA stability pathways
-
Azzalin,C.M. and Lingner,J. (2006) The double life of UPF1 in RNA and DNA stability pathways. Cell Cycle, 5, 1496-1498.
-
(2006)
Cell Cycle
, vol.5
, pp. 1496-1498
-
-
Azzalin, C.M.1
Lingner, J.2
-
64
-
-
84984829468
-
The transcriptional response to DNA-double-strand breaks in Physcomitrella patens
-
Kamisugi,Y., Whitaker,J.W. and Cuming,A.C. (2016) The transcriptional response to DNA-double-strand breaks in Physcomitrella patens. PLoS One, 11, e0161204.
-
(2016)
PLoS One
, vol.11
, pp. e0161204
-
-
Kamisugi, Y.1
Whitaker, J.W.2
Cuming, A.C.3
-
65
-
-
85046054974
-
RecQ helicases function in development, DNA repair, and gene targeting in Physcomitrella patens
-
Wiedemann,G., van Gessel,N., Kochl,F., Hunn,L., Schulze,K., Maloukh,L., Nogue,F., Decker,E.L., Hartung,F. and Reski,R. (2018) RecQ helicases function in development, DNA repair, and gene targeting in Physcomitrella patens. Plant Cell, doi:10.1105/tpc.17.00632.
-
(2018)
Plant Cell
-
-
Wiedemann, G.1
Van Gessel, N.2
Kochl, F.3
Hunn, L.4
Schulze, K.5
Maloukh, L.6
Nogue, F.7
Decker, E.L.8
Hartung, F.9
Reski, R.10
-
66
-
-
0141905891
-
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
-
Haas,B.J., Delcher,A.L., Mount,S.M., Wortman,J.R., Smith,R.K. Jr., Hannick,L.I., Maiti,R., Ronning,C.M., Rusch,D.B., Town,C.D. et al. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res., 31, 5654-5666.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 5654-5666
-
-
Haas, B.J.1
Delcher, A.L.2
Mount, S.M.3
Wortman, J.R.4
Smith, R.K.5
Hannick, L.I.6
Maiti, R.7
Ronning, C.M.8
Rusch, D.B.9
Town, C.D.10
-
67
-
-
0035801373
-
The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay
-
Le Hir,H., Gatfield,D., Izaurralde,E. and Moore,M.J. (2001) The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J., 20, 4987-4997.
-
(2001)
EMBO J
, vol.20
, pp. 4987-4997
-
-
Le Hir, H.1
Gatfield, D.2
Izaurralde, E.3
Moore, M.J.4
-
68
-
-
84937031603
-
Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
-
Marquez,Y., Hopfler,M., Ayatollahi,Z., Barta,A. and Kalyna,M. (2015) Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. Genome Res., 25, 995-1007.
-
(2015)
Genome Res
, vol.25
, pp. 995-1007
-
-
Marquez, Y.1
Hopfler, M.2
Ayatollahi, Z.3
Barta, A.4
Kalyna, M.5
-
69
-
-
37849047501
-
Erwinia carotovora elicitors and Botrytis cinerea activate defense responses in Physcomitrella patens
-
Ponce de León,I., Oliver,J.P., Castro,A., Gaggero,C., Bentancor,M. and Vidal,S. (2007) Erwinia carotovora elicitors and Botrytis cinerea activate defense responses in Physcomitrella patens. BMC Plant Biol., 7, 52.
-
(2007)
BMC Plant Biol
, vol.7
, pp. 52
-
-
Ponce De León, I.1
Oliver, J.P.2
Castro, A.3
Gaggero, C.4
Bentancor, M.5
Vidal, S.6
-
70
-
-
48349096177
-
Widespread impact of nonsense-mediated mRNA decay on the yeast intronome
-
Sayani,S., Janis,M., Lee,C.Y., Toesca,I. and Chanfreau,G.F. (2008) Widespread impact of nonsense-mediated mRNA decay on the yeast intronome. Mol. Cell, 31, 360-370.
-
(2008)
Mol. Cell
, vol.31
, pp. 360-370
-
-
Sayani, S.1
Janis, M.2
Lee, C.Y.3
Toesca, I.4
Chanfreau, G.F.5
-
71
-
-
84920460444
-
Detained introns are a novel, widespread class of post-transcriptionally spliced introns
-
Boutz,P.L., Bhutkar,A. and Sharp,P.A. (2015) Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Genes Dev., 29, 63-80.
-
(2015)
Genes Dev
, vol.29
, pp. 63-80
-
-
Boutz, P.L.1
Bhutkar, A.2
Sharp, P.A.3
-
72
-
-
84863218026
-
Aberrant growth and lethality of Arabidopsis deficient in nonsense-mediated RNA decay factors is caused by autoimmune-like response
-
Riehs-Kearnan,N., Gloggnitzer,J., Dekrout,B., Jonak,C. and Riha,K. (2012) Aberrant growth and lethality of Arabidopsis deficient in nonsense-mediated RNA decay factors is caused by autoimmune-like response. Nucleic Acids Res., 40, 5615-5624.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 5615-5624
-
-
Riehs-Kearnan, N.1
Gloggnitzer, J.2
Dekrout, B.3
Jonak, C.4
Riha, K.5
-
73
-
-
84907703051
-
Nonsense-mediated mRNA decay modulates immune receptor levels to regulate plant antibacterial defense
-
Gloggnitzer,J., Akimcheva,S., Srinivasan,A., Kusenda,B., Riehs,N., Stampfl,H., Bautor,J., Dekrout,B., Jonak,C., Jimenez-Gomez,J.M. et al. (2014) Nonsense-mediated mRNA decay modulates immune receptor levels to regulate plant antibacterial defense. Cell Host Microbe, 16, 376-390.
-
(2014)
Cell Host Microbe
, vol.16
, pp. 376-390
-
-
Gloggnitzer, J.1
Akimcheva, S.2
Srinivasan, A.3
Kusenda, B.4
Riehs, N.5
Stampfl, H.6
Bautor, J.7
Dekrout, B.8
Jonak, C.9
Jimenez-Gomez, J.M.10
-
74
-
-
85027016791
-
A role for the nonsense-mediated mRNA decay pathway in maintaining genome stability in Caenorhabditis elegans
-
Gonzalez-Huici,V., Wang,B. and Gartner,A. (2017) A role for the nonsense-mediated mRNA decay pathway in maintaining genome stability in Caenorhabditis elegans. Genetics, 206, 1853-1864.
-
(2017)
Genetics
, vol.206
, pp. 1853-1864
-
-
Gonzalez-Huici, V.1
Wang, B.2
Gartner, A.3
-
75
-
-
46449097470
-
HSMG-1 and ATM sequentially and independently regulate the G1 checkpoint during oxidative stress
-
Gehen,S.C., Staversky,R.J., Bambara,R.A., Keng,P.C. and O'Reilly,M.A. (2008) hSMG-1 and ATM sequentially and independently regulate the G1 checkpoint during oxidative stress. Oncogene, 27, 4065-4074.
-
(2008)
Oncogene
, vol.27
, pp. 4065-4074
-
-
Gehen, S.C.1
Staversky, R.J.2
Bambara, R.A.3
Keng, P.C.4
O'Reilly, M.A.5
-
76
-
-
69149101216
-
Suppressor of gamma response 1 (SOG1) encodes a putative transcription factor governing multiple responses to DNA damage
-
Yoshiyama,K., Conklin,P.A., Huefner,N.D. and Britt,A.B. (2009) Suppressor of gamma response 1 (SOG1) encodes a putative transcription factor governing multiple responses to DNA damage. Proc. Natl. Acad. Sci. U.S.A., 106, 12843-12848.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 12843-12848
-
-
Yoshiyama, K.1
Conklin, P.A.2
Huefner, N.D.3
Britt, A.B.4
-
77
-
-
84883486972
-
ATM-mediated phosphorylation of SOG1 is essential for the DNA damage response in Arabidopsis
-
Yoshiyama,K.O., Kobayashi,J., Ogita,N., Ueda,M., Kimura,S., Maki,H. and Umeda,M. (2013) ATM-mediated phosphorylation of SOG1 is essential for the DNA damage response in Arabidopsis. EMBO Rep., 14, 817-822.
-
(2013)
EMBO Rep
, vol.14
, pp. 817-822
-
-
Yoshiyama, K.O.1
Kobayashi, J.2
Ogita, N.3
Ueda, M.4
Kimura, S.5
Maki, H.6
Umeda, M.7
-
78
-
-
81055157688
-
Repairing breaks in the plant genome: The importance of keeping it together
-
Waterworth,W.M., Drury,G.E., Bray,C.M. and West,C.E. (2011) Repairing breaks in the plant genome: the importance of keeping it together. New Phytologist, 192, 805-822.
-
(2011)
New Phytologist
, vol.192
, pp. 805-822
-
-
Waterworth, W.M.1
Drury, G.E.2
Bray, C.M.3
West, C.E.4
-
79
-
-
0035449691
-
Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay
-
Yamashita,A., Ohnishi,T., Kashima,I., Taya,Y. and Ohno,S. (2001) Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. Genes Dev., 15, 2215-2228.
-
(2001)
Genes Dev
, vol.15
, pp. 2215-2228
-
-
Yamashita, A.1
Ohnishi, T.2
Kashima, I.3
Taya, Y.4
Ohno, S.5
-
80
-
-
84856858152
-
N- And C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD
-
Okada-Katsuhata,Y., Yamashita,A., Kutsuzawa,K., Izumi,N., Hirahara,F. and Ohno,S. (2012) N- and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD. Nucleic Acids Res., 40, 1251-1266.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 1251-1266
-
-
Okada-Katsuhata, Y.1
Yamashita, A.2
Kutsuzawa, K.3
Izumi, N.4
Hirahara, F.5
Ohno, S.6
-
81
-
-
85022093326
-
Identification of a DNA damage-Induced alternative splicing pathway that regulates p53 and cellular senescence markers
-
Chen,J., Crutchley,J., Zhang,D., Owzar,K. and Kastan,M.B. (2017) Identification of a DNA damage-Induced alternative splicing pathway that regulates p53 and cellular senescence markers. Cancer Discov., 7, 766-781.
-
(2017)
Cancer Discov
, vol.7
, pp. 766-781
-
-
Chen, J.1
Crutchley, J.2
Zhang, D.3
Owzar, K.4
Kastan, M.B.5
-
82
-
-
84902187810
-
Human RecQ helicases in DNA repair, recombination, and replication
-
Croteau,D.L., Popuri,V., Opresko,P.L. and Bohr,V.A. (2014) Human RecQ helicases in DNA repair, recombination, and replication. Annu. Rev. Biochem., 83, 519-552.
-
(2014)
Annu. Rev. Biochem.
, vol.83
, pp. 519-552
-
-
Croteau, D.L.1
Popuri, V.2
Opresko, P.L.3
Bohr, V.A.4
-
83
-
-
77958459763
-
Upf1 senses 3UTR length to potentiate mRNA decay
-
Hogg,J.R. and Goff,S.P. (2010) Upf1 senses 3UTR length to potentiate mRNA decay. Cell, 143, 379-389.
-
(2010)
Cell
, vol.143
, pp. 379-389
-
-
Hogg, J.R.1
Goff, S.P.2
-
84
-
-
85027061624
-
Nonsense-mediated mRNA decay in Tetrahymena is EJC independent and requires a protozoa-specific nuclease
-
Tian,M., Yang,W., Zhang,J., Dang,H., Lu,X., Fu,C. and Miao,W. (2017) Nonsense-mediated mRNA decay in Tetrahymena is EJC independent and requires a protozoa-specific nuclease. Nucleic Acids Res., 45, 6848-6863.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. 6848-6863
-
-
Tian, M.1
Yang, W.2
Zhang, J.3
Dang, H.4
Lu, X.5
Fu, C.6
Miao, W.7
-
85
-
-
77951976646
-
Splicing-dependent NMD does not require the EJC in Schizosaccharomyces pombe
-
Wen,J. and Brogna,S. (2010) Splicing-dependent NMD does not require the EJC in Schizosaccharomyces pombe. EMBO J., 29, 1537-1551.
-
(2010)
EMBO J
, vol.29
, pp. 1537-1551
-
-
Wen, J.1
Brogna, S.2
-
86
-
-
84987641578
-
The rules and impact of nonsense-mediated mRNA decay in human cancers
-
Lindeboom,R.G., Supek,F. and Lehner,B. (2016) The rules and impact of nonsense-mediated mRNA decay in human cancers. Nat. Genet., 48, 1112-1118.
-
(2016)
Nat. Genet.
, vol.48
, pp. 1112-1118
-
-
Lindeboom, R.G.1
Supek, F.2
Lehner, B.3
-
87
-
-
85011092575
-
Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- And SMG7-mediated degradation pathways
-
Colombo,M., Karousis,E.D., Bourquin,J., Bruggmann,R. and Muhlemann,O. (2017) Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways. RNA, 23, 189-201.
-
(2017)
RNA
, vol.23
, pp. 189-201
-
-
Colombo, M.1
Karousis, E.D.2
Bourquin, J.3
Bruggmann, R.4
Muhlemann, O.5
-
88
-
-
84928042455
-
Identification of elements in human long 3 UTRs that inhibit nonsense-mediated decay
-
Toma,K.G., Rebbapragada,I., Durand,S. and Lykke-Andersen,J. (2015) Identification of elements in human long 3 UTRs that inhibit nonsense-mediated decay. RNA, 21, 887-897
-
(2015)
RNA
, vol.21
, pp. 887-897
-
-
Toma, K.G.1
Rebbapragada, I.2
Durand, S.3
Lykke-Andersen, J.4
-
89
-
-
84958580914
-
Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway
-
Ge,Z., Quek,B.L., Beemon,K.L. and Hogg,J.R. (2016) Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway. Elife, 5, e11155.
-
(2016)
Elife
, vol.5
, pp. e11155
-
-
Ge, Z.1
Quek, B.L.2
Beemon, K.L.3
Hogg, J.R.4
-
90
-
-
0038814325
-
Y14 and hUpf3b form an NMD-activating complex
-
Gehring,N.H., Neu-Yilik,G., Schell,T., Hentze,M.W. and Kulozik,A.E. (2003) Y14 and hUpf3b form an NMD-activating complex. Mol. Cell, 11, 939-949.
-
(2003)
Mol. Cell
, vol.11
, pp. 939-949
-
-
Gehring, N.H.1
Neu-Yilik, G.2
Schell, T.3
Hentze, M.W.4
Kulozik, A.E.5
-
91
-
-
25844512736
-
Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements
-
Gehring,N.H., Kunz,J.B., Neu-Yilik,G., Breit,S., Viegas,M.H., Hentze,M.W. and Kulozik,A.E. (2005) Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. Mol. Cell, 20, 65-75.
-
(2005)
Mol. Cell
, vol.20
, pp. 65-75
-
-
Gehring, N.H.1
Kunz, J.B.2
Neu-Yilik, G.3
Breit, S.4
Viegas, M.H.5
Hentze, M.W.6
Kulozik, A.E.7
-
92
-
-
38349125022
-
Translational control of intron splicing in eukaryotes
-
Jaillon,O., Bouhouche,K., Gout,J.-F., Aury,J.-M., Noel,B., Saudemont,B., Nowacki,M., Serrano,V., Porcel,B.M., Ségurens,B. et al. (2008) Translational control of intron splicing in eukaryotes. Nature, 451, 359-362.
-
(2008)
Nature
, vol.451
, pp. 359-362
-
-
Jaillon, O.1
Bouhouche, K.2
Gout, J.-F.3
Aury, J.-M.4
Noel, B.5
Saudemont, B.6
Nowacki, M.7
Serrano, V.8
Porcel, B.M.9
Ségurens, B.10
-
93
-
-
33646484347
-
Genomewide comparative analysis of alternative splicing in plants
-
Wang,B.-B. and Brendel,V. (2006) Genomewide comparative analysis of alternative splicing in plants. Proc. Natl. Acad. Sci. U.S.A., 103, 7175-7180.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 7175-7180
-
-
Wang, B.-B.1
Brendel, V.2
-
94
-
-
84897039206
-
Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis
-
Gohring,J., Jacak,J. and Barta,A. (2014) Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis. Plant Cell, 26, 754-764.
-
(2014)
Plant Cell
, vol.26
, pp. 754-764
-
-
Gohring, J.1
Jacak, J.2
Barta, A.3
-
95
-
-
84923356695
-
Polyribosomal RNA-Seq reveals the decreased complexity and diversity of the Arabidopsis translatome
-
Zhang,X., Rosen,B.D., Tang,H., Krishnakumar,V. and Town,C.D. (2015) Polyribosomal RNA-Seq reveals the decreased complexity and diversity of the Arabidopsis translatome. PLoS One, 10, e0117699.
-
(2015)
PLoS One
, vol.10
, pp. e0117699
-
-
Zhang, X.1
Rosen, B.D.2
Tang, H.3
Krishnakumar, V.4
Town, C.D.5
-
96
-
-
4944241489
-
Intron retention is a major phenomenon in alternative splicing in Arabidopsis
-
Ner-Gaon,H., Halachmi,R., Savaldi-Goldstein,S., Rubin,E., Ophir,R. and Fluhr,R. (2004) Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J., 39, 877-885.
-
(2004)
Plant J
, vol.39
, pp. 877-885
-
-
Ner-Gaon, H.1
Halachmi, R.2
Savaldi-Goldstein, S.3
Rubin, E.4
Ophir, R.5
Fluhr, R.6
-
97
-
-
77957799907
-
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
-
Jiao,Y. and Meyerowitz,E.M. (2010) Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol. Syst. Biol., 6, 419.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 419
-
-
Jiao, Y.1
Meyerowitz, E.M.2
-
98
-
-
85019973466
-
Genome annotation for clinical genomic diagnostics: Strengths and weaknesses
-
Steward,C.A., Parker,A.P.J., Minassian,B.A., Sisodiya,S.M., Frankish,A. and Harrow,J. (2017) Genome annotation for clinical genomic diagnostics: strengths and weaknesses. Genome Med., 9, 49.
-
(2017)
Genome Med
, vol.9
, pp. 49
-
-
Steward, C.A.1
Parker, A.P.J.2
Minassian, B.A.3
Sisodiya, S.M.4
Frankish, A.5
Harrow, J.6
-
99
-
-
84941272877
-
Lost in translation: Pitfalls in deciphering plant alternative splicing transcripts
-
Brown,J.W., Simpson,C.G., Marquez,Y., Gadd,G.M., Barta,A. and Kalyna,M. (2015) Lost in translation: pitfalls in deciphering plant alternative splicing transcripts. Plant Cell, 27, 2083-2087.
-
(2015)
Plant Cell
, vol.27
, pp. 2083-2087
-
-
Brown, J.W.1
Simpson, C.G.2
Marquez, Y.3
Gadd, G.M.4
Barta, A.5
Kalyna, M.6
-
100
-
-
84876020023
-
CPAT: Coding-potential assessment tool using an alignment-free logistic regression model
-
Wang,L., Park,H.J., Dasari,S., Wang,S., Kocher,J.P. and Li,W. (2013) CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res., 41, e74.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. e74
-
-
Wang, L.1
Park, H.J.2
Dasari, S.3
Wang, S.4
Kocher, J.P.5
Li, W.6
-
101
-
-
85028799493
-
The landscape of isoform switches in human cancers
-
Vitting-Seerup,K. and Sandelin,A. (2017) The landscape of isoform switches in human cancers. Mol. Cancer Res., 15, 1206-1220.
-
(2017)
Mol. Cancer Res.
, vol.15
, pp. 1206-1220
-
-
Vitting-Seerup, K.1
Sandelin, A.2
-
102
-
-
85017018481
-
NMD classifier: A reliable and systematic classification tool for nonsense-mediated decay events
-
Hsu,M.K., Lin,H.Y. and Chen,F.C. (2017) NMD Classifier: a reliable and systematic classification tool for nonsense-mediated decay events. PLoS One, 12, e0174798.
-
(2017)
PLoS One
, vol.12
, pp. e0174798
-
-
Hsu, M.K.1
Lin, H.Y.2
Chen, F.C.3
-
103
-
-
67650096774
-
Nonsense-mediated mRNA decay effectors are essential for zebrafish embryonic development and survival
-
Wittkopp,N., Huntzinger,E., Weiler,C., Saulière,J., Schmidt,S., Sonawane,M. and Izaurralde,E. (2009) Nonsense-mediated mRNA decay effectors are essential for zebrafish embryonic development and survival. Mol. Cell. Biol., 29, 3517-3528.
-
(2009)
Mol. Cell. Biol.
, vol.29
, pp. 3517-3528
-
-
Wittkopp, N.1
Huntzinger, E.2
Weiler, C.3
Saulière, J.4
Schmidt, S.5
Sonawane, M.6
Izaurralde, E.7
-
104
-
-
33846015866
-
Functions of the nonsense-mediated mRNA decay pathway in Drosophila development
-
Metzstein,M.M. and Krasnow,M.A. (2006) Functions of the nonsense-mediated mRNA decay pathway in Drosophila development. PLoS Genet., 2, e180.
-
(2006)
PLoS Genet
, vol.2
, pp. e180
-
-
Metzstein, M.M.1
Krasnow, M.A.2
-
105
-
-
25844454826
-
Smg1 nonsense mutations do not abolish nonsense-mediated mRNA decay in Drosophila melanogaster
-
Chen,Z., Smith,K.R., Batterham,P. and Robin,C. (2005) Smg1 nonsense mutations do not abolish nonsense-mediated mRNA decay in Drosophila melanogaster. Genetics, 171, 403-406.
-
(2005)
Genetics
, vol.171
, pp. 403-406
-
-
Chen, Z.1
Smith, K.R.2
Batterham, P.3
Robin, C.4
-
106
-
-
84967225586
-
The meaning of NMD: Translate or perish
-
Brogna,S., McLeod,T. and Petric,M. (2016) The meaning of NMD: translate or perish. Trends Genet., 32, 395-407.
-
(2016)
Trends Genet
, vol.32
, pp. 395-407
-
-
Brogna, S.1
McLeod, T.2
Petric, M.3
-
107
-
-
84871949409
-
The late steps of plant nonsense-mediated mRNA decay
-
Merai,Z., Benkovics,A.H., Nyiko,T., Debreczeny,M., Hiripi,L., Kerenyi,Z., Kondorosi,E. and Silhavy,D. (2013) The late steps of plant nonsense-mediated mRNA decay. Plant J., 73, 50-62.
-
(2013)
Plant J
, vol.73
, pp. 50-62
-
-
Merai, Z.1
Benkovics, A.H.2
Nyiko, T.3
Debreczeny, M.4
Hiripi, L.5
Kerenyi, Z.6
Kondorosi, E.7
Silhavy, D.8
-
108
-
-
57049126216
-
SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan
-
Huntzinger,E., Kashima,I., Fauser,M., Sauliere,J. and Izaurralde,E. (2008) SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan. RNA, 14, 2609-2617.
-
(2008)
RNA
, vol.14
, pp. 2609-2617
-
-
Huntzinger, E.1
Kashima, I.2
Fauser, M.3
Sauliere, J.4
Izaurralde, E.5
|