-
1
-
-
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
-
2
-
-
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
-
3
-
-
84996773946
-
Translation of 5? Leaders is pervasive in genes resistant to eIF2 repression
-
Andreev, D.E., OConnor, P.B., Fahey, C., Kenny, E.M., Terenin, I.M., Dmitriev, S.E., Cormican, P., Morris, D.W., Shatsky, I.N., and Baranov, P.V. (2015). Translation of 5? leaders is pervasive in genes resistant to eIF2 repression. eLife 4, e03971.
-
(2015)
ELife
, vol.4
, pp. e03971
-
-
Andreev, D.E.1
OConnor, P.B.2
Fahey, C.3
Kenny, E.M.4
Terenin, I.M.5
Dmitriev, S.E.6
Cormican, P.7
Morris, D.W.8
Shatsky, I.N.9
Baranov, P.V.10
-
4
-
-
84913573216
-
Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation
-
Artieri, C.G. and Fraser, H.B. (2014). Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation. Genome Res. 24, 2011-2021.
-
(2014)
Genome Res.
, vol.24
, pp. 2011-2021
-
-
Artieri, C.G.1
Fraser, H.B.2
-
5
-
-
84919424223
-
-
Aspden, J.L., Eyre-Walker, Y.C., Phillips, R.J., Amin, U., Mumtaz, M.A., Brocard, M., and Couso, J.P. (2014). Extensive translation of small Open Reading Frames revealed by Poly- Ribo-Seq. eLife 3, e03528.
-
(2014)
Extensive Translation of Small Open Reading Frames Revealed by Poly- Ribo-Seq. ELife
, vol.3
, pp. e03528
-
-
Aspden, J.L.1
Eyre-Walker, Y.C.2
Phillips, R.J.3
Amin, U.4
Mumtaz, M.A.5
Brocard, M.6
Couso, J.P.7
-
6
-
-
84904789437
-
Genomewide translational changes induced by the prion [PSI+]
-
Baudin-Baillieu, A., Legendre, R., Kuchly, C., Hatin, I., Demais, S., Mestdagh, C., Gautheret, D., and Namy, O. (2014). Genomewide translational changes induced by the prion [PSI+]. Cell Rep. 8, 439-448.
-
(2014)
Cell Rep.
, vol.8
, pp. 439-448
-
-
Baudin-Baillieu, A.1
Legendre, R.2
Kuchly, C.3
Hatin, I.4
Demais, S.5
Mestdagh, C.6
Gautheret, D.7
Namy, O.8
-
7
-
-
84899884309
-
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
-
Bazzini, A.A., Johnstone, T.G., Christiano, R., Mackowiak, S.D., Obermayer, B., Fleming, E.S., Vejnar, C.E., Lee, M.T., Rajewsky, N., Walther, T.C., et al. (2014). Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J. 33, 981-993.
-
(2014)
EMBO J.
, vol.33
, pp. 981-993
-
-
Bazzini, A.A.1
Johnstone, T.G.2
Christiano, R.3
Mackowiak, S.D.4
Obermayer, B.5
Fleming, E.S.6
Vejnar, C.E.7
Lee, M.T.8
Rajewsky, N.9
Walther, T.C.10
-
8
-
-
84887009051
-
Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes
-
Becker, A.H., Oh, E., Weissman, J.S., Kramer, G., and Bukau, B. (2013). Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes. Nat. Protocols 8, 2212-2239.
-
(2013)
Nat. Protocols
, vol.8
, pp. 2212-2239
-
-
Becker, A.H.1
Oh, E.2
Weissman, J.S.3
Kramer, G.4
Bukau, B.5
-
9
-
-
4444313551
-
TRNA dynamics on the ribosome during translation
-
Blanchard, S.C., Kim, H.D., Gonzalez, R.L., Jr., Puglisi, J.D., and Chu, S. (2004). tRNA dynamics on the ribosome during translation. Proc. Natl. Acad. Sci. USA 101, 12893-12898.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 12893-12898
-
-
Blanchard, S.C.1
Kim, H.D.2
Gonzalez, Jr.R.L.3
Puglisi, J.D.4
Chu, S.5
-
10
-
-
0015009391
-
Dissociation of mammalian polyribosomes into subunits by puromycin
-
Blobel, G., and Sabatini, D. (1971). Dissociation of mammalian polyribosomes into subunits by puromycin. Proc. Natl. Acad. Sci. USA 68, 390-394.
-
(1971)
Proc. Natl. Acad. Sci. USA
, vol.68
, pp. 390-394
-
-
Blobel, G.1
Sabatini, D.2
-
11
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
12
-
-
85027939461
-
Dynamics of translation by single ribosomes through mRNA secondary structures
-
Chen, C., Zhang, H., Broitman, S.L., Reiche, M., Farrell, I., Cooperman, B.S., and Goldman, Y.E. (2013). Dynamics of translation by single ribosomes through mRNA secondary structures. Nat. Struct. Mol. Biol. 20, 582-588.
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 582-588
-
-
Chen, C.1
Zhang, H.2
Broitman, S.L.3
Reiche, M.4
Farrell, I.5
Cooperman, B.S.6
Goldman, Y.E.7
-
13
-
-
84878865619
-
Ribosome profiling reveals resemblance between long non-coding RNAs and 5? Leaders of coding RNAs
-
Chew, G.L., Pauli, A., Rinn, J.L., Regev, A., Schier, A.F., and Valen, E. (2013). Ribosome profiling reveals resemblance between long non-coding RNAs and 5? leaders of coding RNAs. Development 140, 2828-2834.
-
(2013)
Development
, vol.140
, pp. 2828-2834
-
-
Chew, G.L.1
Pauli, A.2
Rinn, J.L.3
Regev, A.4
Schier, A.F.5
Valen, E.6
-
14
-
-
84946037477
-
Ensembl 2015
-
Cunningham, F., Amode, M.R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., et al. (2015). Ensembl 2015. Nucleic Acids Res. 43, D662-669.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 662-669
-
-
Cunningham, F.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Billis, K.5
Brent, S.6
Carvalho-Silva, D.7
Clapham, P.8
Coates, G.9
Fitzgerald, S.10
-
15
-
-
0015502048
-
Association of ribonuclease i with ribosomes and their subunits
-
Datta, A.K. and Burma, D.P. (1972). Association of ribonuclease I with ribosomes and their subunits. J. Biol. Chem. 247, 6795-6801.
-
(1972)
J. Biol. Chem.
, vol.247
, pp. 6795-6801
-
-
Datta, A.K.1
Burma, D.P.2
-
16
-
-
84887791432
-
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
-
Dillies, M.A., Rau, A., Aubert, J., Hennequet-Antier, C., Jeanmougin, M., Servant, N., Keime, C., Marot, G., Castel, D., Estelle, J., et al. (2013). A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Briefings Bioinformatics 14, 671-683.
-
(2013)
Briefings Bioinformatics
, vol.14
, pp. 671-683
-
-
Dillies, M.A.1
Rau, A.2
Aubert, J.3
Hennequet-Antier, C.4
Jeanmougin, M.5
Servant, N.6
Keime, C.7
Marot, G.8
Castel, D.9
Estelle, J.10
-
17
-
-
0019888109
-
High sequence specificity of micrococcal nuclease
-
Dingwall, C., Lomonossoff, G.P., and Laskey, R.A. (1981). High sequence specificity of micrococcal nuclease. Nucleic Acid Res. 9, 2659-2673.
-
(1981)
Nucleic Acid Res.
, vol.9
, pp. 2659-2673
-
-
Dingwall, C.1
Lomonossoff, G.P.2
Laskey, R.A.3
-
18
-
-
52649157765
-
Substantial biases in ultra-short read data sets from highthroughput DNA sequencing
-
Dohm, J.C., Lottaz, C., Borodina, T., and Himmelbauer, H. (2008). Substantial biases in ultra-short read data sets from highthroughput DNA sequencing. Nucleic Acids Res. 36, e105.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. e105
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
19
-
-
37049237272
-
Polyribosomes from Escherichia coli: Enzymatic method for isolation
-
Dresden, M. and Hoagland, M.B. (1965). Polyribosomes from Escherichia coli: Enzymatic method for isolation. Science 149, 647-649.
-
(1965)
Science
, vol.149
, pp. 647-649
-
-
Dresden, M.1
Hoagland, M.B.2
-
20
-
-
84889593808
-
-
Dunn, J.G., Foo, C.K., Belletier, N.G., Gavis, E.R., and Weissman, J.S. (2013). Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. eLife 2, e01179.
-
(2013)
Ribosome Profiling Reveals Pervasive and Regulated Stop Codon Readthrough in Drosophila Melanogaster. ELife
, vol.2
, pp. e01179
-
-
Dunn, J.G.1
Foo, C.K.2
Belletier, N.G.3
Gavis, E.R.4
Weissman, J.S.5
-
21
-
-
84855878005
-
Newly identified genetic variations in common Escherichia coli MG1655 stock cultures
-
Freddolino, P.L., Amini, S., and Tavazoie, S. (2012). Newly identified genetic variations in common Escherichia coli MG1655 stock cultures. J. Bact. 194, 303-306.
-
(2012)
J. Bact.
, vol.194
, pp. 303-306
-
-
Freddolino, P.L.1
Amini, S.2
Tavazoie, S.3
-
22
-
-
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
-
23
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber, M., Grabherr, M.G., Guttman, M., and Trapnell, C. (2011). Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods 8, 469-477.
-
(2011)
Nat. Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
24
-
-
84964315924
-
Translation inhibitors cause abnormalities in ribosome profiling experiments
-
Gerashchenko, M.V. and Gladyshev, V.N. (2014). Translation inhibitors cause abnormalities in ribosome profiling experiments. Nucleic Acids Res. 42, e134.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. e134
-
-
Gerashchenko, M.V.1
Gladyshev, V.N.2
-
25
-
-
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
-
26
-
-
84961626302
-
Verification and validation of bioinformatics software without a gold standard: A case study of BWA and Bowtie
-
Giannoulatou, E., Park, S.H., Humphreys, D.T., and Ho, J.W. (2014). Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie. BMC Bioinform. 15 (Suppl. 16), S15.
-
(2014)
BMC Bioinform
, vol.15
, pp. S15
-
-
Giannoulatou, E.1
Park, S.H.2
Humphreys, D.T.3
Ho, J.W.4
-
27
-
-
84905836835
-
Ribosome profiling reveals a cell-type-specific translational landscape in brain tumors
-
Gonzalez, C., Sims, J.S., Hornstein, N., Mela, A., Garcia, F., Lei, L., Gass, D.A., Amendolara, B., Bruce, J.N., Canoll, P., et al. (2014). Ribosome profiling reveals a cell-type-specific translational landscape in brain tumors. J. Neurosci. 34, 10924-10936.
-
(2014)
J. Neurosci.
, vol.34
, pp. 10924-10936
-
-
Gonzalez, C.1
Sims, J.S.2
Hornstein, N.3
Mela, A.4
Garcia, F.5
Lei, L.6
Gass, D.A.7
Amendolara, B.8
Bruce, J.N.9
Canoll, P.10
-
28
-
-
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
-
29
-
-
84903858214
-
Evaluation of read count based RNAseq analysis methods
-
Guo, Y., Li, C.I., Ye, F., and Shyr, Y. (2013). Evaluation of read count based RNAseq analysis methods. BMC Genom. 14 (Suppl. 8), S2.
-
(2013)
BMC Genom.
, vol.14
, pp. S2
-
-
Guo, Y.1
Li, C.I.2
Ye, F.3
Shyr, Y.4
-
30
-
-
84879969127
-
Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
-
Guttman, M., Russell, P., Ingolia, N.T., Weissman, J.S., and Lander, E.S. (2013). Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154, 240-251.
-
(2013)
Cell
, vol.154
, pp. 240-251
-
-
Guttman, M.1
Russell, P.2
Ingolia, N.T.3
Weissman, J.S.4
Lander, E.S.5
-
31
-
-
84896863244
-
Dom34 rescues ribosomes in 3? Untranslated regions
-
Guydosh, N.R. and Green, R. (2014). Dom34 rescues ribosomes in 3? untranslated regions. Cell 156, 950-962.
-
(2014)
Cell
, vol.156
, pp. 950-962
-
-
Guydosh, N.R.1
Green, R.2
-
32
-
-
84860389888
-
RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries
-
Hafner, M., Renwick, N., Brown, M., Mihailovic, A., Holoch, D., Lin, C., Pena, J.T., Nusbaum, J.D., Morozov, P., Ludwig, J., et al. (2011). RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA 17, 1697-1712.
-
(2011)
RNA
, vol.17
, pp. 1697-1712
-
-
Hafner, M.1
Renwick, N.2
Brown, M.3
Mihailovic, A.4
Holoch, D.5
Lin, C.6
Pena, J.T.7
Nusbaum, J.D.8
Morozov, P.9
Ludwig, J.10
-
33
-
-
77955298482
-
BaySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
-
Hardcastle, T.J. and Kelly, K.A. (2010). baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11, 422.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 422
-
-
Hardcastle, T.J.1
Kelly, K.A.2
-
34
-
-
70450177746
-
BFAST: An alignment tool for large scale genome resequencing
-
Homer, N., Merriman, B., and Nelson, S.F. (2009). BFAST: an alignment tool for large scale genome resequencing. PloS One 4, e7767.
-
(2009)
PloS One
, vol.4
, pp. e7767
-
-
Homer, N.1
Merriman, B.2
Nelson, S.F.3
-
35
-
-
77956024408
-
Genome-wide translational profiling by ribosome footprinting
-
Ingolia, N.T. (2010). Genome-wide translational profiling by ribosome footprinting. Methods Enzymol. 470, 119-142.
-
(2010)
Methods Enzymol.
, vol.470
, pp. 119-142
-
-
Ingolia, N.T.1
-
36
-
-
84894318608
-
Ribosome profiling: New views of translation, from single codons to genome scale
-
Ingolia, N.T. (2014). Ribosome profiling: new views of translation, from single codons to genome scale. Nat. Rev. Genet. 15, 205-213.
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 205-213
-
-
Ingolia, N.T.1
-
37
-
-
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
-
38
-
-
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
-
39
-
-
84864453787
-
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome- protected mRNA fragments
-
Ingolia, N.T., Brar, G.A., Rouskin, S., McGeachy, A.M., and Weissman, J.S. (2012). The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome- protected mRNA fragments. Nat. Protocols 7, 1534-1550.
-
(2012)
Nat. Protocols
, vol.7
, pp. 1534-1550
-
-
Ingolia, N.T.1
Brar, G.A.2
Rouskin, S.3
McGeachy, A.M.4
Weissman, J.S.5
-
40
-
-
84904806049
-
RNA function Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration
-
Ishimura, R., Nagy, G., Dotu, I., Zhou, H., Yang, X.L., Schimmel, P., Senju, S., Nishimura, Y., Chuang, J.H., and Ackerman, S.L. (2014). RNA function. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration. Science 345, 455-459.
-
(2014)
Science
, vol.345
, pp. 455-459
-
-
Ishimura, R.1
Nagy, G.2
Dotu, I.3
Zhou, H.4
Yang, X.L.5
Schimmel, P.6
Senju, S.7
Nishimura, Y.8
Chuang, J.H.9
Ackerman, S.L.10
-
41
-
-
84924972423
-
The awesome power of ribosome profiling
-
Jackson, R. and Standart, N. (2015). The awesome power of ribosome profiling. RNA 21, 652-654.
-
(2015)
RNA
, vol.21
, pp. 652-654
-
-
Jackson, R.1
Standart, N.2
-
42
-
-
84903685076
-
Evaluating bias-reducing protocols for RNA sequencing library preparation
-
Jackson, T.J., Spriggs, R.V., Burgoyne, N.J., Jones, C., and Willis, A.E. (2014). Evaluating bias-reducing protocols for RNA sequencing library preparation. BMC Genomics 15, 569.
-
(2014)
BMC Genomics
, vol.15
, pp. 569
-
-
Jackson, T.J.1
Spriggs, R.V.2
Burgoyne, N.J.3
Jones, C.4
Willis, A.E.5
-
43
-
-
84909607974
-
Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling
-
Jan, C.H., Williams, C.C., and Weissman, J.S. (2014). Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling. Science 346, 1257521.
-
(2014)
Science
, vol.346
, pp. 1257521
-
-
Jan, C.H.1
Williams, C.C.2
Weissman, J.S.3
-
44
-
-
82255185567
-
Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing
-
Jayaprakash, A.D., Jabado, O., Brown, B.D., and Sachidanandam, R. (2011). Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing. Nucleic Acids Res. 39, e141.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. e141
-
-
Jayaprakash, A.D.1
Jabado, O.2
Brown, B.D.3
Sachidanandam, R.4
-
45
-
-
0036079158
-
The human genome browser at UCSC
-
Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, D. (2002). The human genome browser at UCSC. Genome Res. 12, 996-1006.
-
(2002)
Genome Res.
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
46
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., and Salzberg, S.L. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36.
-
(2013)
Genome Biol.
, vol.14
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
47
-
-
66849109240
-
The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins
-
Kramer, G., Boehringer, D., Ban, N., and Bukau, B. (2009). The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nat. Struct. Mol. Biol. 16, 589-597.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 589-597
-
-
Kramer, G.1
Boehringer, D.2
Ban, N.3
Bukau, B.4
-
48
-
-
84885815730
-
Translation regulation gets its omics moment
-
Kuersten, S., Radek, A., Vogel, C., and Penalva, L.O. (2013). Translation regulation gets its omics moment. Wiley Interdiscipl. Rev. RNA 4, 617-630.
-
(2013)
Wiley Interdiscipl. Rev. RNA
, vol.4
, pp. 617-630
-
-
Kuersten, S.1
Radek, A.2
Vogel, C.3
Penalva, L.O.4
-
49
-
-
79551602797
-
Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. Elegans transcriptome
-
Lamm, A.T., Stadler, M.R., Zhang, H., Gent, J.I., and Fire, A.Z. (2011). Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. Genome Res. 21, 265-275.
-
(2011)
Genome Res.
, vol.21
, pp. 265-275
-
-
Lamm, A.T.1
Stadler, M.R.2
Zhang, H.3
Gent, J.I.4
Fire, A.Z.5
-
50
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359.
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
51
-
-
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
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
52
-
-
84900489620
-
-
Lareau, L.F., Hite, D.H., Hogan, G.J., and Brown, P.O. (2014). Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments. eLife 3, e01257.
-
(2014)
Distinct Stages of the Translation Elongation Cycle Revealed by Sequencing Ribosome-protected mRNA Fragments. ELife
, vol.3
, pp. e01257
-
-
Lareau, L.F.1
Hite, D.H.2
Hogan, G.J.3
Brown, P.O.4
-
53
-
-
84866267681
-
Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution
-
Lee, S., Liu, B., Lee, S., 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, E2424-2432.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 2424-2432
-
-
Lee, S.1
Liu, B.2
Lee, S.3
Huang, S.X.4
Shen, B.5
Qian, S.B.6
-
54
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
55
-
-
77957272611
-
A survey of sequence alignment algorithms for next-generation sequencing
-
Li, H. and Homer, N. (2010). A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform. 11, 473-483.
-
(2010)
Brief. Bioinform.
, vol.11
, pp. 473-483
-
-
Li, H.1
Homer, N.2
-
56
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li, H., Ruan, J., and Durbin, R. (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-1858.
-
(2008)
Genome Res.
, vol.18
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
57
-
-
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
-
58
-
-
84863101693
-
AdapterRemoval: Easy cleaning of next-generation sequencing reads
-
Lindgreen, S. (2012). AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes 5, 337.
-
(2012)
BMC Res. Notes
, vol.5
, pp. 337
-
-
Lindgreen, S.1
-
59
-
-
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
-
60
-
-
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 Interdiscipl. Rev. RNA 4, 473-490.
-
(2013)
Wiley Interdiscipl. Rev. RNA
, vol.4
, pp. 473-490
-
-
Michel, A.M.1
Baranov, P.V.2
-
61
-
-
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
-
62
-
-
84941082092
-
Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3? Untranslated regions
-
Miettinen, T.P. and Bjorklund, M. (2015). Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3? untranslated regions. Nucl. Acids Res. 43, 1019-1034.
-
(2015)
Nucl. Acids Res.
, vol.43
, pp. 1019-1034
-
-
Miettinen, T.P.1
Bjorklund, M.2
-
63
-
-
70349330650
-
Ribosomal footprints on a transcriptome landscape
-
Morris, D.R. (2009). Ribosomal footprints on a transcriptome landscape. Genome Biol. 10, 215.
-
(2009)
Genome Biol.
, vol.10
, pp. 215
-
-
Morris, D.R.1
-
64
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628.
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
65
-
-
84931576485
-
Optimization of codon translation rates via tRNA modifications maintains proteome integrity
-
Nedialkova, D.D. and Leidel, S.A. (2015). Optimization of codon translation rates via tRNA modifications maintains proteome integrity. Cell 161, 1606-1618.
-
(2015)
Cell
, vol.161
, pp. 1606-1618
-
-
Nedialkova, D.D.1
Leidel, S.A.2
-
66
-
-
84878820561
-
RRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments
-
OConnor, P.B., Li, G.W., Weissman, J.S., Atkins, J.F., and Baranov, P.V. (2013). rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments. Bioinformatics 29, 1488-1491.
-
(2013)
Bioinformatics
, vol.29
, pp. 1488-1491
-
-
OConnor, P.B.1
Li, G.W.2
Weissman, J.S.3
Atkins, J.F.4
Baranov, P.V.5
-
67
-
-
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
-
68
-
-
84888198198
-
Assessing gene-level translational control from ribosome profiling
-
Olshen, A.B., Hsieh, A.C., Stumpf, C.R., Olshen, R.A., Ruggero, D., and Taylor, B.S. (2013). Assessing gene-level translational control from ribosome profiling. Bioinformatics 29, 2995-3002.
-
(2013)
Bioinformatics
, vol.29
, pp. 2995-3002
-
-
Olshen, A.B.1
Hsieh, A.C.2
Stumpf, C.R.3
Olshen, R.A.4
Ruggero, D.5
Taylor, B.S.6
-
69
-
-
84887462372
-
Tools for characterizing bacterial protein synthesis inhibitors
-
Orelle, C., Carlson, S., Kaushal, B., Almutairi, M.M., Liu, H., Ochabowicz, A., Quan, S., Pham, V.C., Squires, C.L., Murphy, B.T., et al. (2013). Tools for characterizing bacterial protein synthesis inhibitors. Antimicrob. Agents Chemother. 57, 5994-6004.
-
(2013)
Antimicrob. Agents Chemother.
, vol.57
, pp. 5994-6004
-
-
Orelle, C.1
Carlson, S.2
Kaushal, B.3
Almutairi, M.M.4
Liu, H.5
Ochabowicz, A.6
Quan, S.7
Pham, V.C.8
Squires, C.L.9
Murphy, B.T.10
-
70
-
-
78650539308
-
From RNA-seq reads to differential expression results
-
Oshlack, A., Robinson, M.D., and Young, M.D. (2010). From RNA-seq reads to differential expression results. Genome Biol. 11, 220.
-
(2010)
Genome Biol.
, vol.11
, pp. 220
-
-
Oshlack, A.1
Robinson, M.D.2
Young, M.D.3
-
71
-
-
84925553022
-
Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo
-
Pechmann, S., Chartron, J.W., and Frydman, J. (2014). Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo. Nat. Struct. Mol. Biol. 21, 1100-1105.
-
(2014)
Nat. Struct. Mol. Biol.
, vol.21
, pp. 1100-1105
-
-
Pechmann, S.1
Chartron, J.W.2
Frydman, J.3
-
72
-
-
84930682682
-
Widespread Co- translational RNA decay reveals ribosome dynamics
-
Pelechano, V., Wei, W., and Steinmetz, L.M. (2015). Widespread Co- translational RNA Decay Reveals Ribosome Dynamics. Cell 161, 1400-1412.
-
(2015)
Cell
, vol.161
, pp. 1400-1412
-
-
Pelechano, V.1
Wei, W.2
Steinmetz, L.M.3
-
73
-
-
0037439060
-
Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA
-
Pestova, T.V, and Hellen, C.U. (2003). Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA. Genes Dev. 17, 181-186.
-
(2003)
Genes Dev.
, vol.17
, pp. 181-186
-
-
Pestova, T.V.1
And2
Hellen, C.U.3
-
74
-
-
78650304100
-
Synonymous but not the same: The causes and consequences of codon bias
-
Plotkin, J.B. and Kudla, G. (2011). Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet. 12, 32-42.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 32-42
-
-
Plotkin, J.B.1
Kudla, G.2
-
75
-
-
33846057724
-
NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
Pruitt, K.D., Tatusova, T., and Maglott, D.R. (2007). NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61-65.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 61-65
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
76
-
-
84949227547
-
BEDTools: The swiss-army tool for genome feature analysis
-
Quinlan, A.R. (2014). BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Curr. Prot. Bioinformatics 47, 111211-111234.
-
(2014)
Curr. Prot. Bioinformatics
, vol.47
, pp. 111211-111234
-
-
Quinlan, A.R.1
-
77
-
-
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
-
78
-
-
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
-
79
-
-
0014433087
-
Magnesium ion dependence of free and polysomal ribosomes from
-
Ron, E.Z., Kohler, R.E., and Davis, B.D. (1968). Magnesium ion dependence of free and polysomal ribosomes from Escherichia coli. J. Mol. Biol. 36, 83-89.
-
(1968)
Escherichia coli. J. Mol. Biol.
, vol.36
, pp. 83-89
-
-
Ron, E.Z.1
Kohler, R.E.2
Davis, B.D.3
-
80
-
-
84876543942
-
RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
-
Salgado, H., Peralta-Gil, M., Gama-Castro, S., Santos- Zavaleta, A., Muniz-Rascado, L., Garcia-Sotelo, J.S., Weiss, V., Solano- Lira, H., Martinez-Flores, I., Medina-Rivera, A., et al. (2013). RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 41, D203-213.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 203-213
-
-
Salgado, H.1
Peralta-Gil, M.2
Gama-Castro, S.3
Santos- Zavaleta, A.4
Muniz-Rascado, L.5
Garcia-Sotelo, J.S.6
Weiss, V.7
Solano- Lira, H.8
Martinez-Flores, I.9
Medina-Rivera, A.10
-
81
-
-
77249087063
-
Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin
-
Schneider-Poetsch, T., Ju, J., Eyler, D.E., Dang, Y., Bhat, S., Merrick, W.C., Green, R., Shen, B., and Liu, J.O. (2010). Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin. Nat. Chem. Biol. 6, 209-217.
-
(2010)
Nat. Chem. Biol.
, vol.6
, pp. 209-217
-
-
Schneider-Poetsch, T.1
Ju, J.2
Eyler, D.E.3
Dang, Y.4
Bhat, S.5
Merrick, W.C.6
Green, R.7
Shen, B.8
Liu, J.O.9
-
82
-
-
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
-
83
-
-
84964694840
-
The small molecule ISRIB reverses the effects of eIF2a phosphorylation on translation and stress granule assembly
-
Sidrauski, C., McGeachy, A.M., Ingolia, N.T., and Walter, P. (2015). The small molecule ISRIB reverses the effects of eIF2a phosphorylation on translation and stress granule assembly. eLife 4.
-
(2015)
ELife
, vol.4
-
-
Sidrauski, C.1
McGeachy, A.M.2
Ingolia, N.T.3
Walter, P.4
-
84
-
-
84940645811
-
The theory and practice of genome sequence assembly
-
Simpson, J.T. and Pop, M. (2015). The theory and practice of genome sequence assembly. Ann Rev Genomics Human Genet. 16, 153-172.
-
(2015)
Ann Rev Genomics Human Genet.
, vol.16
, pp. 153-172
-
-
Simpson, J.T.1
Pop, M.2
-
85
-
-
84866979410
-
Reducing ligation bias of small RNAs in libraries for next generation sequencing
-
Sorefan, K., Pais, H., Hall, A.E., Kozomara, A., Griffiths-Jones, S., Moulton, V., and Dalmay, T. (2012). Reducing ligation bias of small RNAs in libraries for next generation sequencing. Silence 3, 4.
-
(2012)
Silence
, vol.3
, pp. 4
-
-
Sorefan, K.1
Pais, H.2
Hall, A.E.3
Kozomara, A.4
Griffiths-Jones, S.5
Moulton, V.6
Dalmay, T.7
-
86
-
-
0014666439
-
Polypeptide chain initiation: Nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA
-
Steitz, J.A. (1969). Polypeptide chain initiation: nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA. Nature 224, 957-964.
-
(1969)
Nature
, vol.224
, pp. 957-964
-
-
Steitz, J.A.1
-
87
-
-
84911468469
-
An integrated approach reveals regulatory controls on bacterial translation elongation
-
Subramaniam, A.R., Zid, B.M., and OShea, E.K. (2014). An integrated approach reveals regulatory controls on bacterial translation elongation. Cell 159, 1200-1211.
-
(2014)
Cell
, vol.159
, pp. 1200-1211
-
-
Subramaniam, A.R.1
Zid, B.M.2
OShea, E.K.3
-
88
-
-
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
-
89
-
-
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
-
90
-
-
84936817583
-
Protein degradation and dynamic tRNA thiolation fine-tune translation at elevated temperatures
-
Tyagi, K. and Pedrioli, P.G. (2015). Protein degradation and dynamic tRNA thiolation fine-tune translation at elevated temperatures. Nucleic Acids Res. 43, 4701-4712.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 4701-4712
-
-
Tyagi, K.1
Pedrioli, P.G.2
-
91
-
-
84893723345
-
Library preparation methods for next-generation sequencing: Tone down the bias
-
van Dijk, E.L., Jaszczyszyn, Y., and Thermes, C. (2014). Library preparation methods for next-generation sequencing: tone down the bias. Exp. Cell Res. 322, 12-20.
-
(2014)
Exp. Cell Res.
, vol.322
, pp. 12-20
-
-
Van Dijk, E.L.1
Jaszczyszyn, Y.2
Thermes, C.3
-
92
-
-
41149155366
-
Following translation by single ribosomes one codon at a time
-
Wen, J.D., Lancaster, L., Hodges, C., Zeri, A.C., Yoshimura, S.H., Noller, H.F., Bustamante, C., and Tinoco, I. (2008). Following translation by single ribosomes one codon at a time. Nature 452, 598-603.
-
(2008)
Nature
, vol.452
, pp. 598-603
-
-
Wen, J.D.1
Lancaster, L.2
Hodges, C.3
Zeri, A.C.4
Yoshimura, S.H.5
Noller, H.F.6
Bustamante, C.7
Tinoco, I.8
-
93
-
-
0001660364
-
Ribosomal aggregate engaged in protein syn thesis characterization of the ergosome
-
Wettstein, F.O., Staehelin, T., and Noll, H. (1963). Ribosomal aggregate engaged in protein synthesis: characterization of the ergosome. Nature 197, 430-435.
-
(1963)
Nature
, vol.197
, pp. 430-435
-
-
Wettstein, F.O.1
Staehelin, T.2
Noll, H.3
-
94
-
-
84927693301
-
High-precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP
-
Woolstenhulme, C.J., Guydosh, N.R., Green, R., and Buskirk, A.R. (2015). High-precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP. Cell Rep. 11, 13-21.
-
(2015)
Cell Rep.
, vol.11
, pp. 13-21
-
-
Woolstenhulme, C.J.1
Guydosh, N.R.2
Green, R.3
Buskirk, A.R.4
-
95
-
-
84899698560
-
Assessing the impact of human genome annotation choice on RNA-seq expression estimates
-
Wu, P.Y., Phan, J.H., and Wang, M.D. (2013). Assessing the impact of human genome annotation choice on RNA-seq expression estimates. BMC Bioinformatics 14 (Suppl. 11), S8.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. S8
-
-
Wu, P.Y.1
Phan, J.H.2
Wang, M.D.3
-
96
-
-
79551690253
-
Folding at the birth of the nascent chain: Coordinating translation with co-translational folding
-
Zhang, G. and Ignatova, Z. (2011). Folding at the birth of the nascent chain: coordinating translation with co-translational folding. Curr. Opin. Struct. Biol. 21, 25-31.
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 25-31
-
-
Zhang, G.1
Ignatova, Z.2
-
97
-
-
84862227622
-
FANSe: An accurate algorithm for quantitative mapping of large scale sequencing reads
-
Zhang, G., Fedyunin, I., Kirchner, S., Xiao, C., Valleriani, A., and Ignatova, Z. (2012). FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads. Nucleic Acids Res. 40, e83.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e83
-
-
Zhang, G.1
Fedyunin, I.2
Kirchner, S.3
Xiao, C.4
Valleriani, A.5
Ignatova, Z.6
-
98
-
-
84885008898
-
High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing
-
Zhang, Z., Lee, J.E., Riemondy, K., Anderson, E.M., and Yi, R. (2013). High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing. Genome Biol. 14, R109.
-
(2013)
Genome Biol.
, vol.14
, pp. R109
-
-
Zhang, Z.1
Lee, J.E.2
Riemondy, K.3
Anderson, E.M.4
Yi, R.5
-
99
-
-
84924333321
-
A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
-
Zhao, S. and Zhang, B. (2015). A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification. BMC Genomics 16, 97.
-
(2015)
BMC Genomics
, vol.16
, pp. 97
-
-
Zhao, S.1
Zhang, B.2
-
100
-
-
84868240119
-
Small RNA expression profiling by high-throughput sequencing: Implications of enzymatic manipulation
-
Zhuang, F., Fuchs, R.T., and Robb, G.B. (2012). Small RNA expression profiling by high-throughput sequencing: implications of enzymatic manipulation. J. Nucleic Acids Res. 40, 360358.
-
(2012)
J. Nucleic Acids Res.
, vol.40
, pp. 360358
-
-
Zhuang, F.1
Fuchs, R.T.2
Robb, G.B.3
|