-
1
-
-
77951164018
-
Differential regulation of microRNA stability
-
Bail S., Swerdel M., Liu H., Jiao X., Goff L.A., Hart R.P., Kiledjian M. Differential regulation of microRNA stability. RNA 2010, 16:1032-1039.
-
(2010)
RNA
, vol.16
, pp. 1032-1039
-
-
Bail, S.1
Swerdel, M.2
Liu, H.3
Jiao, X.4
Goff, L.A.5
Hart, R.P.6
Kiledjian, M.7
-
2
-
-
84886044727
-
4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response
-
Burger K., Mühl B., Kellner M., Rohrmoser M., Gruber-Eber A., Windhager L., Friedel C.C., Dölken L., Eick D. 4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response. RNA Biol. 2013, 10:1623-1630.
-
(2013)
RNA Biol.
, vol.10
, pp. 1623-1630
-
-
Burger, K.1
Mühl, B.2
Kellner, M.3
Rohrmoser, M.4
Gruber-Eber, A.5
Windhager, L.6
Friedel, C.C.7
Dölken, L.8
Eick, D.9
-
4
-
-
13844281888
-
Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay
-
Cleary M.D., Meiering C.D., Jan E., Guymon R., Boothroyd J.C. Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay. Nat. Biotechnol. 2005, 23:232-237.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 232-237
-
-
Cleary, M.D.1
Meiering, C.D.2
Jan, E.3
Guymon, R.4
Boothroyd, J.C.5
-
5
-
-
50649118115
-
High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay
-
Dölken L., Ruzsics Z., Rädle B., Friedel C.C., Zimmer R., Mages J., Hoffmann R., Dickinson P., Forster T., Ghazal P., Koszinowski U.H. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 2008, 14:1959-1972.
-
(2008)
RNA
, vol.14
, pp. 1959-1972
-
-
Dölken, L.1
Ruzsics, Z.2
Rädle, B.3
Friedel, C.C.4
Zimmer, R.5
Mages, J.6
Hoffmann, R.7
Dickinson, P.8
Forster, T.9
Ghazal, P.10
Koszinowski, U.H.11
-
6
-
-
84991566019
-
4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells
-
Fuchs G., Voichek Y., Benjamin S., Gilad S., Amit I., Oren M. 4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells. Genome Biol. 2014, 15:R69.
-
(2014)
Genome Biol.
, vol.15
, pp. R69
-
-
Fuchs, G.1
Voichek, Y.2
Benjamin, S.3
Gilad, S.4
Amit, I.5
Oren, M.6
-
7
-
-
80052213072
-
Analysis of microRNA turnover in mammalian cells following Dicer1 ablation
-
Gantier M.P., McCoy C.E., Rusinova I., Saulep D., Wang D., Xu D., Irving A.T., Behlke M.A., Hertzog P.J., Mackay F., Williams B.R. Analysis of microRNA turnover in mammalian cells following Dicer1 ablation. Nucleic Acids Res. 2011, 39:5692-5703.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 5692-5703
-
-
Gantier, M.P.1
McCoy, C.E.2
Rusinova, I.3
Saulep, D.4
Wang, D.5
Xu, D.6
Irving, A.T.7
Behlke, M.A.8
Hertzog, P.J.9
Mackay, F.10
Williams, B.R.11
-
8
-
-
84901240387
-
MOV10 Is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3' UTRs
-
Gregersen L.H., Schueler M., Munschauer M., Mastrobuoni G., Chen W., Kempa S., Dieterich C., Landthaler M. MOV10 Is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3' UTRs. Mol. Cell 2014, 54:573-585.
-
(2014)
Mol. Cell
, vol.54
, pp. 573-585
-
-
Gregersen, L.H.1
Schueler, M.2
Munschauer, M.3
Mastrobuoni, G.4
Chen, W.5
Kempa, S.6
Dieterich, C.7
Landthaler, M.8
-
9
-
-
84941071754
-
Characterization of the mammalian miRNA turnover landscape
-
Guo Y., Liu J., Elfenbein S.J., Ma Y., Zhong M., Qiu C., Ding Y., Lu J. Characterization of the mammalian miRNA turnover landscape. Nucleic Acids Res. 2015, 43:2326-2341.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 2326-2341
-
-
Guo, Y.1
Liu, J.2
Elfenbein, S.J.3
Ma, Y.4
Zhong, M.5
Qiu, C.6
Ding, Y.7
Lu, J.8
-
10
-
-
77950920903
-
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
-
Hafner M., Landthaler M., Burger L., Khorshid M., Hausser J., Berninger P., Rothballer A., Ascano M., Jungkamp A.-C., Munschauer M., et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141:129-141.
-
(2010)
Cell
, vol.141
, pp. 129-141
-
-
Hafner, M.1
Landthaler, M.2
Burger, L.3
Khorshid, M.4
Hausser, J.5
Berninger, P.6
Rothballer, A.7
Ascano, M.8
Jungkamp, A.-C.9
Munschauer, M.10
-
11
-
-
84865760395
-
GENCODE: the reference human genome annotation for The ENCODE Project
-
Harrow J., Frankish A., Gonzalez J.M., Tapanari E., Diekhans M., Kokocinski F., Aken B.L., Barrell D., Zadissa A., Searle S., et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012, 22:1760-1774.
-
(2012)
Genome Res.
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
Tapanari, E.4
Diekhans, M.5
Kokocinski, F.6
Aken, B.L.7
Barrell, D.8
Zadissa, A.9
Searle, S.10
-
12
-
-
57349121991
-
Exploring RNA transcription and turnover in vivo by using click chemistry
-
Jao C.Y., Salic A. Exploring RNA transcription and turnover in vivo by using click chemistry. Proc. Natl. Acad. Sci. USA 2008, 105:15779-15784.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 15779-15784
-
-
Jao, C.Y.1
Salic, A.2
-
13
-
-
84885587001
-
Conformational dynamics and distribution of nitroxide spin labels
-
Jeschke G. Conformational dynamics and distribution of nitroxide spin labels. Prog. Nucl. Magn. Reson. Spectrosc. 2013, 72:42-60.
-
(2013)
Prog. Nucl. Magn. Reson. Spectrosc.
, vol.72
, pp. 42-60
-
-
Jeschke, G.1
-
15
-
-
84891822189
-
Ensembl Genomes 2013: scaling up access to genome-wide data
-
Kersey P.J., Allen J.E., Christensen M., Davis P., Falin L.J., Grabmueller C., Hughes D.S., Humphrey J., Kerhornou A., Khobova J., et al. Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res. 2014, 42:D546-D552.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D546-D552
-
-
Kersey, P.J.1
Allen, J.E.2
Christensen, M.3
Davis, P.4
Falin, L.J.5
Grabmueller, C.6
Hughes, D.S.7
Humphrey, J.8
Kerhornou, A.9
Khobova, J.10
-
16
-
-
84891818318
-
MiRBase: annotating high confidence microRNAs using deep sequencing data
-
Kozomara A., Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014, 42:D68-D73.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D68-D73
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
17
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9:357-359.
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
18
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:R25.
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
19
-
-
0018063623
-
Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography
-
Melvin W.T., Milne H.B., Slater A.A., Allen H.J., Keir H.M. Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography. Eur. J. Biochem. 1978, 92:373-379.
-
(1978)
Eur. J. Biochem.
, vol.92
, pp. 373-379
-
-
Melvin, W.T.1
Milne, H.B.2
Slater, A.A.3
Allen, H.J.4
Keir, H.M.5
-
20
-
-
67349288523
-
TU-tagging: cell type-specific RNA isolation from intact complex tissues
-
Miller M.R., Robinson K.J., Cleary M.D., Doe C.Q. TU-tagging: cell type-specific RNA isolation from intact complex tissues. Nat. Methods 2009, 6:439-441.
-
(2009)
Nat. Methods
, vol.6
, pp. 439-441
-
-
Miller, M.R.1
Robinson, K.J.2
Cleary, M.D.3
Doe, C.Q.4
-
21
-
-
78650930357
-
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast
-
Miller C., Schwalb B., Maier K., Schulz D., Dümcke S., Zacher B., Mayer A., Sydow J., Marcinowski L., Dölken L., et al. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol. Syst. Biol. 2011, 7:458.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 458
-
-
Miller, C.1
Schwalb, B.2
Maier, K.3
Schulz, D.4
Dümcke, S.5
Zacher, B.6
Mayer, A.7
Sydow, J.8
Marcinowski, L.9
Dölken, L.10
-
22
-
-
0032101892
-
Identification of a gene involved in the generation of 4-thiouridine in tRNA
-
Mueller E.G., Buck C.J., Palenchar P.M., Barnhart L.E., Paulson J.L. Identification of a gene involved in the generation of 4-thiouridine in tRNA. Nucleic Acids Res. 1998, 26:2606-2610.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 2606-2610
-
-
Mueller, E.G.1
Buck, C.J.2
Palenchar, P.M.3
Barnhart, L.E.4
Paulson, J.L.5
-
23
-
-
84907199058
-
Determination of in vivo RNA kinetics using RATE-seq
-
Neymotin B., Athanasiadou R., Gresham D. Determination of in vivo RNA kinetics using RATE-seq. RNA 2014, 20:1645-1652.
-
(2014)
RNA
, vol.20
, pp. 1645-1652
-
-
Neymotin, B.1
Athanasiadou, R.2
Gresham, D.3
-
24
-
-
84930665601
-
MiR-191 regulates primary human fibroblast proliferation and directly targets multiple oncogenes
-
Polioudakis D., Abell N.S., Iyer V.R. MiR-191 regulates primary human fibroblast proliferation and directly targets multiple oncogenes. PLoS ONE 2015, 10:e0126535.
-
(2015)
PLoS ONE
, vol.10
, pp. e0126535
-
-
Polioudakis, D.1
Abell, N.S.2
Iyer, V.R.3
-
25
-
-
79955768436
-
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
-
Rabani M., Levin J.Z., Fan L., Adiconis X., Raychowdhury R., Garber M., Gnirke A., Nusbaum C., Hacohen N., Friedman N., et al. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat. Biotechnol. 2011, 29:436-442.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 436-442
-
-
Rabani, M.1
Levin, J.Z.2
Fan, L.3
Adiconis, X.4
Raychowdhury, R.5
Garber, M.6
Gnirke, A.7
Nusbaum, C.8
Hacohen, N.9
Friedman, N.10
-
26
-
-
36448981743
-
Moderated statistical tests for assessing differences in tag abundance
-
Robinson M.D., Smyth G.K. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 2007, 23:2881-2887.
-
(2007)
Bioinformatics
, vol.23
, pp. 2881-2887
-
-
Robinson, M.D.1
Smyth, G.K.2
-
27
-
-
75249087100
-
EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
28
-
-
84942924912
-
SRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments
-
Rueda A., Barturen G., Lebrón R., Gómez-Martín C., Alganza Á., Oliver J.L., Hackenberg M. sRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments. Methods Next Gen. Seq. 2014, 43:W467-W473.
-
(2014)
Methods Next Gen. Seq.
, vol.43
, pp. W467-W473
-
-
Rueda, A.1
Barturen, G.2
Lebrón, R.3
Gómez-Martín, C.4
Alganza, Á.5
Oliver, J.L.6
Hackenberg, M.7
-
29
-
-
84866626156
-
MicroRNA turnover: when, how, and why
-
Rüegger S., Großhans H. MicroRNA turnover: when, how, and why. Trends Biochem. Sci. 2012, 37:436-446.
-
(2012)
Trends Biochem. Sci.
, vol.37
, pp. 436-446
-
-
Rüegger, S.1
Großhans, H.2
-
30
-
-
84897129376
-
Quantitative analysis of ribonucleoside modifications in tRNA by HPCL-coupled mass spectrometry
-
Su D., Chan C.T.Y., Gu C., Lim K.S., Chionh Y.H., McBee M.E., Russell B.S., Babu I.R., Begley T.J., Dedon P.C. Quantitative analysis of ribonucleoside modifications in tRNA by HPCL-coupled mass spectrometry. Nat. Protoc. 2014, 9:828-841.
-
(2014)
Nat. Protoc.
, vol.9
, pp. 828-841
-
-
Su, D.1
Chan, C.T.Y.2
Gu, C.3
Lim, K.S.4
Chionh, Y.H.5
McBee, M.E.6
Russell, B.S.7
Babu, I.R.8
Begley, T.J.9
Dedon, P.C.10
-
31
-
-
84863540819
-
Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation
-
Sun M., Schwalb B., Schulz D., Pirkl N., Etzold S., Larivière L., Maier K.C., Seizl M., Tresch A., Cramer P. Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation. Genome Res. 2012, 22:1350-1359.
-
(2012)
Genome Res.
, vol.22
, pp. 1350-1359
-
-
Sun, M.1
Schwalb, B.2
Schulz, D.3
Pirkl, N.4
Etzold, S.5
Larivière, L.6
Maier, K.C.7
Seizl, M.8
Tresch, A.9
Cramer, P.10
-
32
-
-
84868252050
-
Genome-wide technology for determining RNA stability in mammalian cells: historical perspective and recent advantages based on modified nucleotide labeling
-
Tani H., Akimitsu N. Genome-wide technology for determining RNA stability in mammalian cells: historical perspective and recent advantages based on modified nucleotide labeling. RNA Biol. 2012, 9:1233-1238.
-
(2012)
RNA Biol.
, vol.9
, pp. 1233-1238
-
-
Tani, H.1
Akimitsu, N.2
-
33
-
-
84860575639
-
Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals
-
Tani H., Mizutani R., Salam K.A., Tano K., Ijiri K., Wakamatsu A., Isogai T., Suzuki Y., Akimitsu N. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res. 2012, 22:947-956.
-
(2012)
Genome Res.
, vol.22
, pp. 947-956
-
-
Tani, H.1
Mizutani, R.2
Salam, K.A.3
Tano, K.4
Ijiri, K.5
Wakamatsu, A.6
Isogai, T.7
Suzuki, Y.8
Akimitsu, N.9
-
34
-
-
84875634162
-
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
-
Thorvaldsdóttir H., Robinson J.T., Mesirov J.P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 2013, 14:178-192.
-
(2013)
Brief. Bioinform.
, vol.14
, pp. 178-192
-
-
Thorvaldsdóttir, H.1
Robinson, J.T.2
Mesirov, J.P.3
-
35
-
-
84872074745
-
Identification of microRNA-98 as a therapeutic target inhibiting prostate cancer growth and a biomarker induced by vitamin D
-
Ting H.-J., Messing J., Yasmin-Karim S., Lee Y.-F. Identification of microRNA-98 as a therapeutic target inhibiting prostate cancer growth and a biomarker induced by vitamin D. J. Biol. Chem. 2013, 288:1-9.
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 1-9
-
-
Ting, H.-J.1
Messing, J.2
Yasmin-Karim, S.3
Lee, Y.-F.4
-
36
-
-
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., Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 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
-
37
-
-
61849137222
-
Many roads to maturity: microRNA biogenesis pathways and their regulation
-
Winter J., Jung S., Keller S., Gregory R.I., Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat. Cell Biol. 2009, 11:228-234.
-
(2009)
Nat. Cell Biol.
, vol.11
, pp. 228-234
-
-
Winter, J.1
Jung, S.2
Keller, S.3
Gregory, R.I.4
Diederichs, S.5
|