-
2
-
-
0003604405
-
-
3rd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
-
Gesteland RF, Cech T, Atkins JF. The RNA world: the nature of modern RNA suggests a prebiotic RNAworld. 3rd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2006 xxiii, 768 p
-
(2006)
The RNA world: the nature of modern RNA suggests a prebiotic RNAworld
, vol.23
, pp. 768
-
-
Gesteland, R.F.1
Cech, T.2
Atkins, J.F.3
-
3
-
-
54249116230
-
Genetic regulatory mechanisms in the synthesis of proteins
-
Jacob F, Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol. 1961;3:318-56
-
(1961)
J Mol Biol
, vol.3
, pp. 318-356
-
-
Jacob, F.1
Monod, J.2
-
4
-
-
0036544755
-
Micro RNAs are complementary to 3?. UTR sequence motifs that mediate negative post-transcriptional regulation
-
Lai EC. Micro RNAs are complementary to 3? UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet. 2002;30:363-4
-
(2002)
Nat Genet
, vol.30
, pp. 363-364
-
-
Lai, E.C.1
-
5
-
-
23944514849
-
Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation
-
Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, et al. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell. 2005;122:553-63
-
(2005)
Cell
, vol.122
, pp. 553-563
-
-
Bagga, S.1
Bracht, J.2
Hunter, S.3
Massirer, K.4
Holtz, J.5
Eachus, R.6
-
6
-
-
0347444723
-
MicroRNAs: genomics, biogenesis, mechanism, and function
-
Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116:281-97
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
7
-
-
33644499134
-
Cell-type-specific signatures of microRNAs on target mRNA expression
-
Sood P, Krek A, Zavolan M, Macino G, Rajewsky N. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci USA. 2006;103:2746-51
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 2746-2751
-
-
Sood, P.1
Krek, A.2
Zavolan, M.3
Macino, G.4
Rajewsky, N.5
-
8
-
-
84870599244
-
Small RNA deep sequencing reveals a distinct miRNA signature released in exosomes from prion-infected neuronal cells
-
Bellingham SA, Coleman BM, Hill AF. Small RNA deep sequencing reveals a distinct miRNA signature released in exosomes from prion-infected neuronal cells. Nucleic Acids Res. 2012;40:10937-49
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 10937-10949
-
-
Bellingham, S.A.1
Coleman, B.M.2
Hill, A.F.3
-
9
-
-
85016304525
-
Exosomes provide a protective and enriched source of miRNA for biomarker profiling compared to intracellular and cell-free blood
-
Cheng L, Sharples RA, Scicluna BJ, Hill AF. Exosomes provide a protective and enriched source of miRNA for biomarker profiling compared to intracellular and cell-free blood. J Extracell Vesicles. 2014;3:23743, doi: http://dx.doi.org/10.3402/jev.v3.23743
-
(2014)
J Extracell Vesicles
, vol.3
, pp. 23743
-
-
Cheng, L.1
Sharples, R.A.2
Scicluna, B.J.3
Hill, A.F.4
-
10
-
-
84915814932
-
The emerging role of exosomes in epithelial-mesenchymal-transition in cancer
-
Vella LJ. The emerging role of exosomes in epithelial-mesenchymal-transition in cancer. Front Oncol. 2014;4:361
-
(2014)
Front Oncol
, vol.4
, pp. 361
-
-
Vella, L.J.1
-
11
-
-
84925446437
-
Differentiation of tumour-promoting stromal myofibroblasts by cancer exosomes
-
Webber JP, Spary LK, Sanders AJ, Chowdhury R, Jiang WG, Steadman R, et al. Differentiation of tumour-promoting stromal myofibroblasts by cancer exosomes. Oncogene. 2015; 34:290-302
-
(2015)
Oncogene
, vol.34
, pp. 290-302
-
-
Webber, J.P.1
Spary, L.K.2
Sanders, A.J.3
Chowdhury, R.4
Jiang, W.G.5
Steadman, R.6
-
12
-
-
84903763537
-
Exosomes from bone marrow mesenchymal stem cells contain a microRNA that promotes dormancy in metastatic breast cancer cells
-
Ono M, Kosaka N, Tominaga N, Yoshioka Y, Takeshita F, Takahashi RU, et al. Exosomes from bone marrow mesenchymal stem cells contain a microRNA that promotes dormancy in metastatic breast cancer cells. Sci Signal. 2014;7(332):ra63
-
(2014)
Sci Signal
, vol.7
, Issue.332
-
-
Ono, M.1
Kosaka, N.2
Tominaga, N.3
Yoshioka, Y.4
Takeshita, F.5
Takahashi, R.U.6
-
13
-
-
84942549950
-
Prognostic serum miRNA biomarkers associated with Alzheimer's disease shows concordance with neuropsychological and neuroimaging assessment
-
Cheng L, Doecke JD, Sharples RA, Villemagne VL, Fowler CJ, Rembach A, et al. Prognostic serum miRNA biomarkers associated with Alzheimer's disease shows concordance with neuropsychological and neuroimaging assessment. Mol Psychiatry. 2015;20:1188-96, doi: http://dx.doi.org/10.1038/mp.2014.127
-
(2015)
Mol Psychiatry
, vol.20
, pp. 1188-1196
-
-
Cheng, L.1
Doecke, J.D.2
Sharples, R.A.3
Villemagne, V.L.4
Fowler, C.J.5
Rembach, A.6
-
14
-
-
84902309873
-
Identification of circulating microRNAs for the differential diagnosis of Parkinson's disease and multiple system atrophy
-
Vallelunga A, Ragusa M, Di Mauro S, Iannitti T, Pilleri M, Biundo R, et al. Identification of circulating microRNAs for the differential diagnosis of Parkinson's disease and multiple system atrophy. Front Cell Neurosci. 2014;8:156
-
(2014)
Front Cell Neurosci
, vol.8
, pp. 156
-
-
Vallelunga, A.1
Ragusa, M.2
Di Mauro, S.3
Iannitti, T.4
Pilleri, M.5
Biundo, R.6
-
15
-
-
84924536514
-
Systemic exosomal siRNA delivery reduced alpha-synuclein aggregates in brains of transgenic mice
-
Cooper JM, Wiklander PB, Nordin JZ, Al-Shawi R, Wood MJ, Vithlani M, et al. Systemic exosomal siRNA delivery reduced alpha-synuclein aggregates in brains of transgenic mice. Mov Disord. 2014;29:1476-85
-
(2014)
Mov Disord
, vol.29
, pp. 1476-1485
-
-
Cooper, J.M.1
Wiklander, P.B.2
Nordin, J.Z.3
Al-Shawi, R.4
Wood, M.J.5
Vithlani, M.6
-
16
-
-
67649595548
-
Limitations and possibilities of small RNA digital gene expression profiling
-
Linsen SE, de Wit E, Janssens G, Heater S, Chapman L, Parkin RK, et al. Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods. 2009;6:474-6
-
(2009)
Nat Methods
, vol.6
, pp. 474-476
-
-
Linsen, S.E.1
de Wit, E.2
Janssens, G.3
Heater, S.4
Chapman, L.5
Parkin, R.K.6
-
17
-
-
84875033024
-
Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations
-
Williams Z, Ben-Dov IZ, Elias R, Mihailovic A, Brown M, Rosenwaks Z, et al. Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. Proc Natl Acad Sci USA. 2013;110:4255-60
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 4255-4260
-
-
Williams, Z.1
Ben-Dov, I.Z.2
Elias, R.3
Mihailovic, A.4
Brown, M.5
Rosenwaks, Z.6
-
18
-
-
58149513263
-
Annotating genomes with massive-scale RNA sequencing
-
Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O, Delledonne M, et al. Annotating genomes with massive-scale RNA sequencing. Genome Biol. 2008;9:R175
-
(2008)
Genome Biol
, vol.9
, pp. R175
-
-
Denoeud, F.1
Aury, J.M.2
Da Silva, C.3
Noel, B.4
Rogier, O.5
Delledonne, M.6
-
20
-
-
84883492783
-
Deepsequencing of microRNA associated with Alzheimer's disease in biological fluids: from biomarker discovery to diagnostic practice
-
Cheng L, Quek C, Sun X, Bellingham SA, Hill AF. Deepsequencing of microRNA associated with Alzheimer's disease in biological fluids: from biomarker discovery to diagnostic practice. Front Genet. 2013;4:150
-
(2013)
Front Genet
, vol.4
, pp. 150
-
-
Cheng, L.1
Quek, C.2
Sun, X.3
Bellingham, S.A.4
Hill, A.F.5
-
21
-
-
84880902774
-
mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing
-
Wu J, Liu Q, Wang X, Zheng J, Wang T, You M, et al. mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing. RNA Biol. 2013;10:1087-92
-
(2013)
RNA Biol
, vol.10
, pp. 1087-1092
-
-
Wu, J.1
Liu, Q.2
Wang, X.3
Zheng, J.4
Wang, T.5
You, M.6
-
22
-
-
77954330416
-
mirTools: microRNA profiling and discovery based on high-throughput sequencing
-
Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, et al. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res. 2010;38:W392-7
-
(2010)
Nucleic Acids Res
, vol.38
, pp. W392-W397
-
-
Zhu, E.1
Zhao, F.2
Xu, G.3
Hou, H.4
Zhou, L.5
Li, X.6
-
23
-
-
77957779549
-
miRNAkey: a software for microRNA deep sequencing analysis
-
Ronen R, Gan I, Modai S, Sukacheov A, Dror G, Halperin E, et al. miRNAkey: a software for microRNA deep sequencing analysis. Bioinformatics. 2010;26:2615-6
-
(2010)
Bioinformatics
, vol.26
, pp. 2615-2616
-
-
Ronen, R.1
Gan, I.2
Modai, S.3
Sukacheov, A.4
Dror, G.5
Halperin, E.6
-
24
-
-
41849084855
-
Discovering microRNAs from deep sequencing data using miRDeep
-
Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, et al. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol. 2008;26: 407-15
-
(2008)
Nat Biotechnol
, vol.26
, pp. 407-415
-
-
Friedlander, M.R.1
Chen, W.2
Adamidi, C.3
Maaskola, J.4
Einspanier, R.5
Knespel, S.6
-
25
-
-
84875476368
-
miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data
-
An JY, Lai J, Lehman ML, Nelson CC. miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res. 2013;41:727-37
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 727-737
-
-
An, J.Y.1
Lai, J.2
Lehman, M.L.3
Nelson, C.C.4
-
26
-
-
77954304695
-
DSAP: deep-sequencing small RNA analysis pipeline
-
Huang PJ, Liu YC, Lee CC, Lin WC, Gan RR, Lyu PC, et al. DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res. 2010;38:W385-91
-
(2010)
Nucleic Acids Res
, vol.38
, pp. W385-W391
-
-
Huang, P.J.1
Liu, Y.C.2
Lee, C.C.3
Lin, W.C.4
Gan, R.R.5
Lyu, P.C.6
-
27
-
-
78650281342
-
New methods for next generation sequencing based microRNA expression profiling
-
Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, t Hoen PA. New methods for next generation sequencing based microRNA expression profiling. BMC Genom. 2010;11:716
-
(2010)
BMC Genom
, vol.11
, pp. 716
-
-
Buermans, H.P.1
Ariyurek, Y.2
van Ommen, G.3
den Dunnen, J.T.4
t Hoen, P.A.5
-
28
-
-
67849114241
-
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments
-
Hackenberg M, Sturm M, Langenberger D, Falcon-Perez JM, Aransay AM. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 2009;37:W68-76
-
(2009)
Nucleic Acids Res
, vol.37
, pp. W68-W76
-
-
Hackenberg, M.1
Sturm, M.2
Langenberger, D.3
Falcon-Perez, J.M.4
Aransay, A.M.5
-
29
-
-
77956508095
-
MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data
-
Mathelier A, Carbone A. MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics. 2010;26:2226-34
-
(2010)
Bioinformatics
, vol.26
, pp. 2226-2234
-
-
Mathelier, A.1
Carbone, A.2
-
30
-
-
70449639806
-
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression
-
Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS. miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics. 2009; 10:328
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 328
-
-
Wang, W.C.1
Lin, F.M.2
Chang, W.C.3
Lin, K.Y.4
Huang, H.D.5
Lin, N.S.6
-
31
-
-
84883480053
-
miRspring: a compact standalone research tool for analyzing miRNA-seq data
-
Humphreys DT, Suter CM. miRspring: a compact standalone research tool for analyzing miRNA-seq data. Nucleic Acids Res. 2013;41:e147
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Humphreys, D.T.1
Suter, C.M.2
-
32
-
-
84889954757
-
iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNASeq
-
Giurato G, De Filippo MR, Rinaldi A, Hashim A, Nassa G, Ravo M, et al. iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNASeq. BMC Bioinformatics. 2013;14:362
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 362
-
-
Giurato, G.1
De Filippo, M.R.2
Rinaldi, A.3
Hashim, A.4
Nassa, G.5
Ravo, M.6
-
33
-
-
84902553235
-
CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data
-
Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, et al. CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. BMC Genom. 2014;15:423
-
(2014)
BMC Genom
, vol.15
, pp. 423
-
-
Sun, Z.1
Evans, J.2
Bhagwate, A.3
Middha, S.4
Bockol, M.5
Yan, H.6
-
34
-
-
84861537341
-
Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis
-
Li Y, Zhang Z, Liu F, Vongsangnak W, Jing Q, Shen B. Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic Acids Res. 2012;40:4298-305
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 4298-4305
-
-
Li, Y.1
Zhang, Z.2
Liu, F.3
Vongsangnak, W.4
Jing, Q.5
Shen, B.6
-
35
-
-
84878213539
-
Where we stand, where we are moving: surveying computational techniques for identifying miRNA genes and uncovering their regulatory role
-
Kleftogiannis D, Korfiati A, Theofilatos K, Likothanassis S, Tsakalidis A, Mavroudi S. Where we stand, where we are moving: surveying computational techniques for identifying miRNA genes and uncovering their regulatory role. J Biomed Inform. 2013;46:563-73
-
(2013)
J Biomed Inform
, vol.46
, pp. 563-573
-
-
Kleftogiannis, D.1
Korfiati, A.2
Theofilatos, K.3
Likothanassis, S.4
Tsakalidis, A.5
Mavroudi, S.6
-
36
-
-
0043026713
-
Biopipe: a flexible framework for protocolbased bioinformatics analysis
-
Hoon S, Ratnapu KK, Chia JM, Kumarasamy B, Juguang X, Clamp M, et al. Biopipe: a flexible framework for protocolbased bioinformatics analysis. Genome Res. 2003;13:1904-15
-
(2003)
Genome Res
, vol.13
, pp. 1904-1915
-
-
Hoon, S.1
Ratnapu, K.K.2
Chia, J.M.3
Kumarasamy, B.4
Juguang, X.5
Clamp, M.6
-
37
-
-
34547763724
-
Bioinformatics software for biologists in the genomics era
-
Kumar S, Dudley J. Bioinformatics software for biologists in the genomics era. Bioinformatics. 2007;23:1713-7
-
(2007)
Bioinformatics
, vol.23
, pp. 1713-1717
-
-
Kumar, S.1
Dudley, J.2
-
38
-
-
78650539308
-
From RNA-seq reads to differential expression results
-
Oshlack A, Robinson MD, Young MD. From RNA-seq reads to differential expression results. Genome Biol. 2010;11(12):220
-
(2010)
Genome Biol
, vol.11
, Issue.12
, pp. 220
-
-
Oshlack, A.1
Robinson, M.D.2
Young, M.D.3
-
39
-
-
84878893666
-
A user-friendly computational workflow for the analysis of microRNA deep sequencing data
-
Ying S-Y, editors, Methods in molecular biology. Totowa,NJ: Humana Press;
-
Majer A, Caligiuri K, Booth S. A user-friendly computational workflow for the analysis of microRNA deep sequencing data. In: Ying S-Y, editor. MicroRNA protocols. Methods in molecular biology. Vol. 936. Totowa,NJ: Humana Press; 2013. p. 35-45
-
(2013)
MicroRNA protocols
, vol.936
, pp. 35-45
-
-
Majer, A.1
Caligiuri, K.2
Booth, S.3
-
40
-
-
70449701942
-
Sense from sequence reads: methods for alignment and assembly
-
Flicek P, Birney E. Sense from sequence reads: methods for alignment and assembly. Nat Methods. 2009;6(11 Suppl): S6-12
-
(2009)
Nat Methods
, vol.6
, Issue.11
, pp. S6-S12
-
-
Flicek, P.1
Birney, E.2
-
41
-
-
84897960349
-
Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data
-
Caboche S, Audebert C, Lemoine Y, Hot D. Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data. BMC Genom. 2014;15:264
-
(2014)
BMC Genom
, vol.15
, pp. 264
-
-
Caboche, S.1
Audebert, C.2
Lemoine, Y.3
Hot, D.4
-
42
-
-
84870495569
-
Progress in ion torrent semiconductor chip based sequencing
-
Merriman B, Rothberg JM. Progress in ion torrent semiconductor chip based sequencing. Electrophoresis. 2012;33: 3397-417
-
(2012)
Electrophoresis
, vol.33
, pp. 3397-3417
-
-
Merriman, B.1
Rothberg, J.M.2
-
43
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25
-
(2010)
Genome Biol
, vol.11
, pp. R25
-
-
Robinson, M.D.1
Oshlack, A.2
-
44
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
-
Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics. 2010; 11:94
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 94
-
-
Bullard, J.H.1
Purdom, E.2
Hansen, K.D.3
Dudoit, S.4
-
45
-
-
78149407836
-
Normalization strategies for microRNA profiling experiments: a ''normal'' way to a hidden layer of complexity?
-
Meyer SU, Pfaffl MW, Ulbrich SE. Normalization strategies for microRNA profiling experiments: a ''normal'' way to a hidden layer of complexity? Biotechnol Lett. 2010;32:1777-88
-
(2010)
Biotechnol Lett
, vol.32
, pp. 1777-1788
-
-
Meyer, S.U.1
Pfaffl, M.W.2
Ulbrich, S.E.3
-
46
-
-
79957578583
-
Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments
-
McCormick KP, Willmann MR, Meyers BC. Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence. 2011;2:2
-
(2011)
Silence
, vol.2
, pp. 2
-
-
McCormick, K.P.1
Willmann, M.R.2
Meyers, B.C.3
-
47
-
-
84859892863
-
MicroRNA profiling: approaches and considerations
-
Pritchard CC, Cheng HH, Tewari M. MicroRNA profiling: approaches and considerations. Nat Rev Genet. 2012;13: 358-69
-
(2012)
Nat Rev Genet
, vol.13
, pp. 358-369
-
-
Pritchard, C.C.1
Cheng, H.H.2
Tewari, M.3
-
48
-
-
84887791432
-
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
-
Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform. 2013;14:671-83
-
(2013)
Brief Bioinform
, 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
-
49
-
-
84938380221
-
Optimization of miRNA-seq data preprocessing
-
Tam S, Tsao MS, McPherson JD. Optimization of miRNA-seq data preprocessing. Brief Bioinform. 2015, doi: http://dx.doi. org/10.1093/bib/bbv019
-
(2015)
Brief Bioinform
-
-
Tam, S.1
Tsao, M.S.2
McPherson, J.D.3
-
50
-
-
84861370963
-
Evaluation of normalization methods in mammalian microRNA-seq data
-
Garmire LX, Subramaniam S. Evaluation of normalization methods in mammalian microRNA-seq data. RNA. 2012;18: 1279-88
-
(2012)
RNA
, vol.18
, pp. 1279-1288
-
-
Garmire, L.X.1
Subramaniam, S.2
-
51
-
-
84878079625
-
miRNA-Seq normalization comparisons need improvement
-
Zhou X, Oshlack A, Robinson MD. miRNA-Seq normalization comparisons need improvement. RNA. 2013;19:733-4
-
(2013)
RNA
, vol.19
, pp. 733-734
-
-
Zhou, X.1
Oshlack, A.2
Robinson, M.D.3
-
52
-
-
84901741983
-
MicroRNAs located in the Hox gene clusters are implicated in Huntington's disease pathogenesis
-
Hoss AG, Kartha VK, Dong XJ, Latourelle JC, Dumitriu A, Hadzi TC, et al. MicroRNAs located in the Hox gene clusters are implicated in Huntington's disease pathogenesis. PLoS Genet. 2014;10:e1004188
-
(2014)
PLoS Genet
, vol.10
-
-
Hoss, A.G.1
Kartha, V.K.2
Dong, X.J.3
Latourelle, J.C.4
Dumitriu, A.5
Hadzi, T.C.6
-
53
-
-
84868149990
-
Prion-infected cells regulate the release of exosomes with distinct ultrastructural features
-
Coleman BM, Hanssen E, Lawson VA, Hill AF. Prion-infected cells regulate the release of exosomes with distinct ultrastructural features. FASEB J. 2012;26:4160-73
-
(2012)
FASEB J
, vol.26
, pp. 4160-4173
-
-
Coleman, B.M.1
Hanssen, E.2
Lawson, V.A.3
Hill, A.F.4
-
54
-
-
84877298502
-
Characterization of human plasma-derived exosomal RNAs by deep sequencing
-
Huang X, Yuan T, Tschannen M, Sun Z, Jacob H, Du M, et al. Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genom. 2013;14:319
-
(2013)
BMC Genom
, vol.14
, pp. 319
-
-
Huang, X.1
Yuan, T.2
Tschannen, M.3
Sun, Z.4
Jacob, H.5
Du, M.6
-
55
-
-
84897493652
-
eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing
-
Yuan T, Huang X, Dittmar RL, Du M, Kohli M, Boardman L, et al. eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. BMC Genom. 2014;15:176
-
(2014)
BMC Genom
, vol.15
, pp. 176
-
-
Yuan, T.1
Huang, X.2
Dittmar, R.L.3
Du, M.4
Kohli, M.5
Boardman, L.6
-
56
-
-
33644750115
-
miRBase: microRNA sequences, targets and gene nomenclature
-
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006;34:D140-4
-
(2006)
Nucleic Acids Res
, vol.34
, pp. D140-D144
-
-
Griffiths-Jones, S.1
Grocock, R.J.2
van Dongen, S.3
Bateman, A.4
Enright, A.J.5
-
57
-
-
58149189877
-
GtRNAdb: a database of transfer RNA genes detected in genomic sequence
-
Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009; 37:D93-7
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D93-D97
-
-
Chan, P.P.1
Lowe, T.M.2
-
58
-
-
38549141630
-
piRNABank: a web resource on classified and clustered Piwi-interacting RNAs
-
Sai Lakshmi S, Agrawal S. piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Nucleic Acids Res. 2008;36:D173-7
-
(2008)
Nucleic Acids Res
, vol.36
, pp. D173-D177
-
-
Sai Lakshmi, S.1
Agrawal, S.2
-
59
-
-
84875391572
-
Ensembl 2013
-
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, et al. Ensembl 2013. Nucleic Acids Res. 2013;41:D48-55
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D48-D55
-
-
Flicek, P.1
Ahmed, I.2
Amode, M.R.3
Barrell, D.4
Beal, K.5
Brent, S.6
-
60
-
-
77958489718
-
Ruffus: a lightweight Python library for computational pipelines
-
Goodstadt L. Ruffus: a lightweight Python library for computational pipelines. Bioinformatics. 2010;26:2778-9
-
(2010)
Bioinformatics
, vol.26
, pp. 2778-2779
-
-
Goodstadt, L.1
-
61
-
-
84905049901
-
Trimmomatic: a flexible trimmer for Illumina sequence data
-
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30: 2114-20
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
62
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357-9
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
63
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078-9
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
65
-
-
84861743958
-
RNA-SeQC: RNA-seq metrics for quality control and process optimization
-
DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012;28: 1530-2
-
(2012)
Bioinformatics
, vol.28
, pp. 1530-1532
-
-
DeLuca, D.S.1
Levin, J.Z.2
Sivachenko, A.3
Fennell, T.4
Nazaire, M.D.5
Williams, C.6
-
66
-
-
77951770756
-
BEDTools: a flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26: 841-2
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
67
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550
-
(2014)
Genome Biol
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
68
-
-
75249087100
-
edgeR: a bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139-40
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
69
-
-
84896735766
-
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
-
Law CW, Chen Y, Shi W, Smyth GK. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014;15:R29
-
(2014)
Genome Biol
, vol.15
, pp. R29
-
-
Law, C.W.1
Chen, Y.2
Shi, W.3
Smyth, G.K.4
-
70
-
-
84926507971
-
limma powers differential expression analyses for RNAsequencing and microarray studies
-
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNAsequencing and microarray studies. Nucleic Acids Res. 2015; 43:e47
-
(2015)
Nucleic Acids Res
, vol.43
-
-
Ritchie, M.E.1
Phipson, B.2
Wu, D.3
Hu, Y.4
Law, C.W.5
Shi, W.6
-
71
-
-
57749195712
-
RNA-Seq: a revolutionary tool for transcriptomics
-
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57-63
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
72
-
-
75949108066
-
Galaxy: a web-based genome analysis tool for experimentalists
-
Chapter 19, Unit 19.10.1-21
-
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010;Chapter 19:Unit 19.10.1-21
-
(2010)
Curr Protoc Mol Biol
-
-
Blankenberg, D.1
Von Kuster, G.2
Coraor, N.3
Ananda, G.4
Lazarus, R.5
Mangan, M.6
-
73
-
-
25844449770
-
Galaxy: a platform for interactive large-scale genome analysis
-
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005;15:1451-5
-
(2005)
Genome Res
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
-
74
-
-
77953142134
-
Hypoxic tumor cell modulates its microenvironment to enhance angiogenic and metastatic potential by secretion of proteins and exosomes
-
Park JE, Tan HS, Datta A, Lai RC, Zhang H, Meng W, et al. Hypoxic tumor cell modulates its microenvironment to enhance angiogenic and metastatic potential by secretion of proteins and exosomes. Mol Cell Proteomics. 2010;9:1085-99
-
(2010)
Mol Cell Proteomics
, vol.9
, pp. 1085-1099
-
-
Park, J.E.1
Tan, H.S.2
Datta, A.3
Lai, R.C.4
Zhang, H.5
Meng, W.6
-
75
-
-
34249302620
-
Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells
-
Valadi H, Ekstrom K, Bossios A, Sjostrand M, Lee JJ, Lotvall JO. Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol. 2007;9:654-9
-
(2007)
Nat Cell Biol
, vol.9
, pp. 654-659
-
-
Valadi, H.1
Ekstrom, K.2
Bossios, A.3
Sjostrand, M.4
Lee, J.J.5
Lotvall, J.O.6
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