-
1
-
-
83755163021
-
Molecular biology. Translation goes global
-
Weiss, R.B. and Atkins, J.F. (2011) Molecular biology. Translation goes global. Science, 334, 1509-1510.
-
(2011)
Science
, vol.334
, pp. 1509-1510
-
-
Weiss, R.B.1
Atkins, J.F.2
-
2
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
Ingolia, N.T., Ghaemmaghami, S., Newman, J.R. and Weissman, J.S. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 218-223.
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
Ghaemmaghami, S.2
Newman, J.R.3
Weissman, J.S.4
-
3
-
-
77955644289
-
Mammalian microRNAs predominantly act to decrease target mRNA levels
-
Guo, H., Ingolia, N.T., Weissman, J.S. and Bartel, D.P. (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466, 835-840.
-
(2010)
Nature
, vol.466
, pp. 835-840
-
-
Guo, H.1
Ingolia, N.T.2
Weissman, J.S.3
Bartel, D.P.4
-
4
-
-
81755184408
-
Wobble base-pairing slows in vivo translation elongation in metazoans
-
Stadler, M. and Fire, A. (2011) Wobble base-pairing slows in vivo translation elongation in metazoans. RNA, 17, 2063-2073.
-
(2011)
RNA
, vol.17
, pp. 2063-2073
-
-
Stadler, M.1
Fire, A.2
-
5
-
-
84857253794
-
Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling
-
Reid, D.W. and Nicchitta, C.V. (2012) Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling. J. Biol. Chem., 287, 5518-5527.
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 5518-5527
-
-
Reid, D.W.1
Nicchitta, C.V.2
-
6
-
-
84862777192
-
The translational landscape of mTOR signalling steers cancer initiation and metastasis
-
Hsieh, A.C., Liu, Y., Edlind, M.P., Ingolia, N.T., Janes, M.R., Sher, A., Shi, E.Y., Stumpf, C.R., Christensen, C., Bonham, M.J. et al. (2012) The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature, 485, 55-61.
-
(2012)
Nature
, vol.485
, pp. 55-61
-
-
Hsieh, A.C.1
Liu, Y.2
Edlind, M.P.3
Ingolia, N.T.4
Janes, M.R.5
Sher, A.6
Shi, E.Y.7
Stumpf, C.R.8
Christensen, C.9
Bonham, M.J.10
-
7
-
-
84866267681
-
Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution
-
Lee, S., Liu, B., Huang, S.X., Shen, B. and Qian, S.B. (2012) Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc. Natl Acad. Sci. USA, 109, E2424-E2432.
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
-
-
Lee, S.1
Liu, B.2
Huang, S.X.3
Shen, B.4
Qian, S.B.5
-
8
-
-
84868315457
-
Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
-
Fritsch, C., Herrmann, A., Nothnagel, M., Szafranski, K., Huse, K., Schumann, F., Schreiber, S., Platzer, M., Krawczak, M., Hampe, J. et al. (2012) Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res., 22, 2208-2218.
-
(2012)
Genome Res.
, vol.22
, pp. 2208-2218
-
-
Fritsch, C.1
Herrmann, A.2
Nothnagel, M.3
Szafranski, K.4
Huse, K.5
Schumann, F.6
Schreiber, S.7
Platzer, M.8
Krawczak, M.9
Hampe, J.10
-
9
-
-
84873442839
-
Widespread regulation of translation by elongation pausing in heat shock
-
Shalgi, R., Hurt, J.A., Krykbaeva, I., Taipale, M., Lindquist, S. and Burge, C.B. (2013) Widespread regulation of translation by elongation pausing in heat shock. Mol. Cell, 49, 439-452.
-
(2013)
Mol. Cell
, vol.49
, pp. 439-452
-
-
Shalgi, R.1
Hurt, J.A.2
Krykbaeva, I.3
Taipale, M.4
Lindquist, S.5
Burge, C.B.6
-
10
-
-
84873467908
-
Cotranslational response to proteotoxic stress by elongation pausing of ribosomes
-
Liu, B., Han, Y. and Qian, S.B. (2013) Cotranslational response to proteotoxic stress by elongation pausing of ribosomes. Mol. Cell, 49, 453-463.
-
(2013)
Mol. Cell
, vol.49
, pp. 453-463
-
-
Liu, B.1
Han, Y.2
Qian, S.B.3
-
11
-
-
84876093209
-
P53 induces transcriptional and translational programs to suppress cell proliferation and growth
-
Loayza-Puch, F., Drost, J., Rooijers, K., Lopes, R., Elkon, R. and Agami, R. (2013) p53 induces transcriptional and translational programs to suppress cell proliferation and growth. Genome Biol., 14, R32.
-
(2013)
Genome Biol.
, vol.14
-
-
Loayza-Puch, F.1
Drost, J.2
Rooijers, K.3
Lopes, R.4
Elkon, R.5
Agami, R.6
-
12
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
-
Ingolia, N.T., Lareau, L.F. and Weissman, J.S. (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147, 789-802.
-
(2011)
Cell
, vol.147
, pp. 789-802
-
-
Ingolia, N.T.1
Lareau, L.F.2
Weissman, J.S.3
-
13
-
-
84860527756
-
A unifying model for mTORC1-mediated regulation of mRNA translation
-
Thoreen, C.C., Chantranupong, L., Keys, H.R., Wang, T., Gray, N.S. and Sabatini, D.M. (2012) A unifying model for mTORC1-mediated regulation of mRNA translation. Nature, 485, 109-113.
-
(2012)
Nature
, vol.485
, pp. 109-113
-
-
Thoreen, C.C.1
Chantranupong, L.2
Keys, H.R.3
Wang, T.4
Gray, N.S.5
Sabatini, D.M.6
-
14
-
-
84862778053
-
Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish
-
Bazzini, A.A., Lee, M.T. and Giraldez, A.J. (2012) Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science, 336, 233-237.
-
(2012)
Science
, vol.336
, pp. 233-237
-
-
Bazzini, A.A.1
Lee, M.T.2
Giraldez, A.J.3
-
15
-
-
84870527178
-
Contributions of mRNA abundance, ribosome loading, and post-or peri-translational effects to temporal repression of C. Elegans heterochronic miRNA targets
-
Stadler, M., Artiles, K., Pak, J. and Fire, A. (2012) Contributions of mRNA abundance, ribosome loading, and post-or peri-translational effects to temporal repression of C. Elegans heterochronic miRNA targets. Genome Res., 22, 2418-2426.
-
(2012)
Genome Res.
, vol.22
, pp. 2418-2426
-
-
Stadler, M.1
Artiles, K.2
Pak, J.3
Fire, A.4
-
16
-
-
84856625798
-
High-resolution view of the yeast meiotic program revealed by ribosome profiling
-
Brar, G.A., Yassour, M., Friedman, N., Regev, A., Ingolia, N.T. and Weissman, J.S. (2012) High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science, 335, 552-557.
-
(2012)
Science
, vol.335
, pp. 552-557
-
-
Brar, G.A.1
Yassour, M.2
Friedman, N.3
Regev, A.4
Ingolia, N.T.5
Weissman, J.S.6
-
17
-
-
84867919856
-
Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress
-
Gerashchenko, M.V., Lobanov, A.V. and Gladyshev, V.N. (2012) Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress. Proc. Natl Acad. Sci. USA, 109, 17394-17399.
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 17394-17399
-
-
Gerashchenko, M.V.1
Lobanov, A.V.2
Gladyshev, V.N.3
-
18
-
-
83255164895
-
Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo
-
Oh, E., Becker, A.H., Sandikci, A., Huber, D., Chaba, R., Gloge, F., Nichols, R.J., Typas, A., Gross, C.A., Kramer, G. et al. (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell, 147, 1295-1308.
-
(2011)
Cell
, vol.147
, pp. 1295-1308
-
-
Oh, E.1
Becker, A.H.2
Sandikci, A.3
Huber, D.4
Chaba, R.5
Gloge, F.6
Nichols, R.J.7
Typas, A.8
Gross, C.A.9
Kramer, G.10
-
19
-
-
84860231100
-
The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
-
Li, G.W., Oh, E. and Weissman, J.S. (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature, 484, 538-541.
-
(2012)
Nature
, vol.484
, pp. 538-541
-
-
Li, G.W.1
Oh, E.2
Weissman, J.S.3
-
20
-
-
84869806462
-
Decoding human cytomegalovirus
-
Stern-Ginossar, N., Weisburd, B., Michalski, A., Le, V.T., Hein, M.Y., Huang, S.X., Ma, M., Shen, B., Qian, S.B., Hengel, H. et al. (2012) Decoding human cytomegalovirus. Science, 338, 1088-1093.
-
(2012)
Science
, vol.338
, pp. 1088-1093
-
-
Stern-Ginossar, N.1
Weisburd, B.2
Michalski, A.3
Le, V.T.4
Hein, M.Y.5
Huang, S.X.6
Ma, M.7
Shen, B.8
Qian, S.B.9
Hengel, H.10
-
21
-
-
84880372200
-
Highresolution view of bacteriophage lambda gene expression by ribosome profiling
-
Liu, X., Jiang, H., Gu, Z. and Roberts, J.W. (2013) Highresolution view of bacteriophage lambda gene expression by ribosome profiling. Proc. Natl Acad. Sci. USA, 110, 11928-11933.
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 11928-11933
-
-
Liu, X.1
Jiang, H.2
Gu, Z.3
Roberts, J.W.4
-
22
-
-
84882258295
-
Ribosome profiling: A Hi-Def monitor for protein synthesis at the genome-wide scale
-
Michel, A.M. and Baranov, P.V. (2013) Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale. Wiley Interdiscip. Rev. RNA, 4, 473-490.
-
(2013)
Wiley Interdiscip. Rev. RNA
, vol.4
, pp. 473-490
-
-
Michel, A.M.1
Baranov, P.V.2
-
23
-
-
75549084998
-
Archiving next generation sequencing data
-
Shumway, M., Cochrane, G. and Sugawara, H. (2010) Archiving next generation sequencing data. Nucleic Acids Res., 38, D870-D871.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Shumway, M.1
Cochrane, G.2
Sugawara, H.3
-
24
-
-
84865226981
-
Next-generation sequencing data interpretation: Enhancing reproducibility and accessibility
-
Nekrutenko, A. and Taylor, J. (2012) Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nat. Rev. Genet., 13, 667-672.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 667-672
-
-
Nekrutenko, A.1
Taylor, J.2
-
25
-
-
75949108066
-
Galaxy: A web-based genome analysis tool for experimentalists
-
Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol., Chapter 19, Unit 19 10 11-21.
-
(2010)
Curr. Protoc. Mol. Biol., Chapter 19, Unit 19
, vol.10
, pp. 11-21
-
-
Blankenberg, D.1
Von Kuster, G.2
Coraor, N.3
Ananda, G.4
Lazarus, R.5
Mangan, M.6
Nekrutenko, A.7
Taylor, J.8
-
26
-
-
84875404794
-
The UCSC Genome Browser database: Extensions and updates 2013
-
Meyer, L.R., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Kuhn, R.M., Wong, M., Sloan, C.A., Rosenbloom, K.R., Roe, G., Rhead, B. et al. (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
Karolchik, D.4
Kuhn, R.M.5
Wong, M.6
Sloan, C.A.7
Rosenbloom, K.R.8
Roe, G.9
Rhead, B.10
-
27
-
-
84868324214
-
Observation of dually decoded regions of the human genome using ribosome profiling data
-
Michel, A.M., Choudhury, K.R., 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.
, vol.22
, pp. 2219-2229
-
-
Michel, A.M.1
Choudhury, K.R.2
Firth, A.E.3
Ingolia, N.T.4
Atkins, J.F.5
Baranov, P.V.6
-
28
-
-
0031559590
-
Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: Programmed efficiency of 50%
-
Larsen, B., Gesteland, R.F. and Atkins, J.F. (1997) Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of 50%. J. Mol. Biol., 271, 47-60.
-
(1997)
J. Mol. Biol.
, vol.271
, pp. 47-60
-
-
Larsen, B.1
Gesteland, R.F.2
Atkins, J.F.3
-
29
-
-
0025355475
-
Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme
-
Tsuchihashi, Z. and Kornberg, A. (1990) Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme. Proc. Natl Acad. Sci. USA, 87, 2516-2520.
-
(1990)
Proc. Natl Acad. Sci. USA
, vol.87
, pp. 2516-2520
-
-
Tsuchihashi, Z.1
Kornberg, A.2
-
30
-
-
84859436530
-
NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy
-
Pruitt, K.D., Tatusova, T., Brown, G.R. and Maglott, D.R. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Pruitt, K.D.1
Tatusova, T.2
Brown, G.R.3
Maglott, D.R.4
-
31
-
-
84875391572
-
Ensembl 2013
-
Flicek, P., Ahmed, I., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S. et al. (2013) Ensembl 2013. Nucleic Acids Res., 41, D48-D55.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Flicek, P.1
Ahmed, I.2
Amode, M.R.3
Barrell, D.4
Beal, K.5
Brent, S.6
Carvalho-Silva, D.7
Clapham, P.8
Coates, G.9
Fairley, S.10
-
32
-
-
84862258061
-
Tracking and coordinating an international curation effort for the CCDS Project
-
Oxford
-
Harte, RA., Farrell, C.M., Loveland, J.E., Suner, M.M., Wilming, L., Aken, B., Barrell, D., Frankish, A., Wallin, C, Searle, S. et al. (2012) Tracking and coordinating an international curation effort for the CCDS Project. Database (Oxford), 2012, bas008.
-
(2012)
Database
, vol.2012
-
-
Harte, R.A.1
Farrell, C.M.2
Loveland, J.E.3
Suner, M.M.4
Wilming, L.5
Aken, B.6
Barrell, D.7
Frankish, A.8
Wallin, C.9
Searle, S.10
-
33
-
-
74949092081
-
Detection of nonneutral substitution rates on mammalian phylogenies
-
Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R. and Siepel, A. (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res., 20, 110-121.
-
(2010)
Genome Res.
, vol.20
, pp. 110-121
-
-
Pollard, K.S.1
Hubisz, M.J.2
Rosenbloom, K.R.3
Siepel, A.4
-
34
-
-
0345865009
-
GenBank: Update
-
Benson, DA., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Wheeler, D.L. (2004) GenBank: update. Nucleic Acids Res., 32, D23-D26.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
35
-
-
84858588614
-
Saccharomyces Genome Database: The genomics resource of budding yeast
-
Cherry, J.M., Hong, E.L., Amundsen, C, Balakrishnan, R., Binkley, G, Chan, E.T., Christie, K.R., Costanzo, M.C, Dwight, S.S., Engel, S.R. et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res., 40, D700-D705.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Cherry, J.M.1
Hong, E.L.2
Amundsen, C.3
Balakrishnan, R.4
Binkley, G.5
Chan, E.T.6
Christie, K.R.7
Costanzo, M.C.8
Dwight, S.S.9
Engel, S.R.10
-
36
-
-
58149189877
-
GtRNAdb: A database of transfer RNA genes detected in genomic sequence
-
Chan, P.P. and Lowe, T.M. (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
-
37
-
-
80052745094
-
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
-
Grant, GR., Farkas, M.H., Pizarro, A.D., Lahens, N.F., Schug, J., Brunk, B.P., Stoeckert, C.J., Hogenesch, J.B. and Pierce, EA. (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics, 27, 2518-2528.
-
(2011)
Bioinformatics
, vol.27
, pp. 2518-2528
-
-
Grant, G.R.1
Farkas, M.H.2
Pizarro, A.D.3
Lahens, N.F.4
Schug, J.5
Brunk, B.P.6
Stoeckert, C.J.7
Hogenesch, J.B.8
Pierce, E.A.9
-
38
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J., 17, 10-12.
-
(2011)
EMBnet J.
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
39
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C, Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
40
-
-
0036226603
-
BLAT the blast-like alignment tool
-
Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
41
-
-
77955895425
-
BigWig and BigBed: Enabling browsing of large distributed datasets
-
Kent, W.J., Zweig, A.S., Barber, G, Hinrichs, A.S. and Karolchik, D. (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics, 26, 2204-2207.
-
(2010)
Bioinformatics
, vol.26
, pp. 2204-2207
-
-
Kent, W.J.1
Zweig, A.S.2
Barber, G.3
Hinrichs, A.S.4
Karolchik, D.5
|