-
1
-
-
84864418009
-
The physiological way: Monitoring RNA expression changes as new approach to combat illegal growth promoter application
-
Riedmaier, I., Pfaffl, M.W. and Meyer, H.H. (2012) The physiological way: monitoring RNA expression changes as new approach to combat illegal growth promoter application. Drug Test Anal., 4(Suppl. 1), 70-74.
-
(2012)
Drug Test Anal.
, vol.4
, pp. 70-74
-
-
Riedmaier, I.1
Pfaffl, M.W.2
Meyer, H.H.3
-
2
-
-
84872196097
-
Transcriptional biomarkers
-
Pfaffl, M.W. (2013) Transcriptional biomarkers. Methods, 59, 1-2.
-
(2013)
Methods
, vol.59
, pp. 1-2
-
-
Pfaffl, M.W.1
-
3
-
-
0028827574
-
Induced gene transcription: Implications for biomarkers
-
Sewall, C.H., Bell, D.A., Clark, G.C., Tritscher, A.M., Tully, D.B., Vanden Heuvel, J. and Lucier, G.W. (1995) Induced gene transcription: implications for biomarkers. Clin. Chem., 41, 1829-1834.
-
(1995)
Clin. Chem.
, vol.41
, pp. 1829-1834
-
-
Sewall, C.H.1
Bell, D.A.2
Clark, G.C.3
Tritscher, A.M.4
Tully, D.B.5
Vanden Heuvel, J.6
Lucier, G.W.7
-
4
-
-
84943634314
-
Guest editor's introduction for BDQ special issue: 'Advanced Molecular Diagnostics for Biomarker Discovery'
-
Pfaffl, M.W. (2015) Guest editor's introduction for BDQ special issue: 'Advanced Molecular Diagnostics for Biomarker Discovery'. Biomol. Detect. Quantif., 5, 1-2.
-
(2015)
Biomol. Detect. Quantif.
, vol.5
, pp. 1-2
-
-
Pfaffl, M.W.1
-
5
-
-
85015506112
-
Real-time liquid biopsies become a reality in cancer treatment
-
Karachaliou, N., Mayo-de-Las-Casas, C., Molina-Vila, M.A. and Rosell, R. (2015) Real-time liquid biopsies become a reality in cancer treatment. Ann. Transl. Med., 3, doi:10.3978/j.issn.2305-5839.2015.01.16.
-
(2015)
Ann. Transl. Med.
, vol.3
-
-
Karachaliou, N.1
Mayo-De-Las-Casas, C.2
Molina-Vila, M.A.3
Rosell, R.4
-
6
-
-
84957698834
-
The potential of liquid biopsies
-
Buder, A., Tomuta, C. and Filipits, M. (2016) The potential of liquid biopsies. Curr. Opin. Oncol., 28, 130-134.
-
(2016)
Curr. Opin. Oncol.
, vol.28
, pp. 130-134
-
-
Buder, A.1
Tomuta, C.2
Filipits, M.3
-
7
-
-
84884585784
-
Exosomes: The future of biomarkers in medicine
-
Properzi, F., Logozzi, M. and Fais, S. (2013) Exosomes: the future of biomarkers in medicine. Biomark. Med., 7, 769-778.
-
(2013)
Biomark. Med.
, vol.7
, pp. 769-778
-
-
Properzi, F.1
Logozzi, M.2
Fais, S.3
-
8
-
-
33845476677
-
Circulating nucleic acids (CNAs) and cancer - A survey
-
Fleischhacker, M. and Schmidt, B. (2007) Circulating nucleic acids (CNAs) and cancer-a survey. Biochim. Biophys. Acta, 1775, 181-232.
-
(2007)
Biochim. Biophys. Acta
, vol.1775
, pp. 181-232
-
-
Fleischhacker, M.1
Schmidt, B.2
-
9
-
-
77649234385
-
Circulating nucleic acids in cancer and pregnancy
-
Pinzani, P., Salvianti, F., Pazzagli, M. and Orlando, C. (2010) Circulating nucleic acids in cancer and pregnancy. Methods, 50, 302-307.
-
(2010)
Methods
, vol.50
, pp. 302-307
-
-
Pinzani, P.1
Salvianti, F.2
Pazzagli, M.3
Orlando, C.4
-
10
-
-
27244434788
-
A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia.N
-
Calin, G.A., Ferracin, M., Cimmino, A., Di Leva, G., Shimizu, M., Wojcik, S.E., Iorio, M.V., Visone, R., Sever, N.I., Fabbri, M. et al. (2005) A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia.N. Engl. J. Med., 353, 1793-1801.
-
(2005)
Engl. J. Med.
, vol.353
, pp. 1793-1801
-
-
Calin, G.A.1
Ferracin, M.2
Cimmino, A.3
Di Leva, G.4
Shimizu, M.5
Wojcik, S.E.6
Iorio, M.V.7
Visone, R.8
Sever, N.I.9
Fabbri, M.10
-
11
-
-
80053946666
-
Circulating microRNAs: Association with disease and potential use as biomarkers
-
Reid, G., Kirschner, M.B. and van Zandwijk, N. (2011) Circulating microRNAs: association with disease and potential use as biomarkers. Crit. Rev. Oncol. Hematol., 80, 193-208.
-
(2011)
Crit. Rev. Oncol. Hematol.
, vol.80
, pp. 193-208
-
-
Reid, G.1
Kirschner, M.B.2
Van Zandwijk, N.3
-
12
-
-
84891110357
-
Cell-free microRNAs: Potential biomarkers in need of standardized reporting
-
Kirschner, M.B., van Zandwijk, N. and Reid, G. (2013) Cell-free microRNAs: potential biomarkers in need of standardized reporting. Front. Genet., 4, doi:10.3389/fgene.2013.00056.
-
(2013)
Front. Genet.
, vol.4
-
-
Kirschner, M.B.1
Van Zandwijk, N.2
Reid, G.3
-
13
-
-
84959093704
-
Circulating microRNA biomarkers as liquid biopsy for cancer patients: Pros and cons of current assays
-
Ono, S., Lam, S., Nagahara, M. and Hoon, D.S. (2015) Circulating microRNA biomarkers as liquid biopsy for cancer patients: pros and cons of current assays. J. Clin. Med., 4, 1890-1907.
-
(2015)
J. Clin. Med.
, vol.4
, pp. 1890-1907
-
-
Ono, S.1
Lam, S.2
Nagahara, M.3
Hoon, D.S.4
-
14
-
-
84920509010
-
Circulating microRNA biomarker studies: Pitfalls and potential solutions
-
Witwer, K.W. (2015) Circulating microRNA biomarker studies: pitfalls and potential solutions. Clin. Chem., 61, 56-63.
-
(2015)
Clin. Chem.
, vol.61
, pp. 56-63
-
-
Witwer, K.W.1
-
15
-
-
84931264971
-
Microfluidic droplet-based PCR instrumentation for high-throughput gene expression profiling and biomarker discovery
-
Hayes, C.J. and Dalton, T.M. (2015) Microfluidic droplet-based PCR instrumentation for high-throughput gene expression profiling and biomarker discovery. Biomol. Detect. Quantif., 4, 22-32.
-
(2015)
Biomol. Detect. Quantif.
, vol.4
, pp. 22-32
-
-
Hayes, C.J.1
Dalton, T.M.2
-
16
-
-
84884478678
-
Evaluation of digital PCR for absolute RNA quantification
-
Sanders, R., Mason, D.J., Foy, C.A. and Huggett, J.F. (2013) Evaluation of digital PCR for absolute RNA quantification. PLoS One, 8, e75296.
-
(2013)
PLoS One
, vol.8
-
-
Sanders, R.1
Mason, D.J.2
Foy, C.A.3
Huggett, J.F.4
-
17
-
-
84862489277
-
Profound effect of profiling platform and normalization strategy on detection of differentially expressed microRNAs - A comparative study
-
Meyer, S.U., Kaiser, S., Wagner, C., Thirion, C. and Pfaffl, M.W. (2012) Profound effect of profiling platform and normalization strategy on detection of differentially expressed microRNAs-a comparative study. PLoS One, 7, e38946.
-
(2012)
PLoS One
, vol.7
-
-
Meyer, S.U.1
Kaiser, S.2
Wagner, C.3
Thirion, C.4
Pfaffl, M.W.5
-
18
-
-
78149407836
-
Normalization strategies for microRNA profiling experiments: A 'normal' way to a hidden layer of complexity?
-
Meyer, S.U., Pfaffl, M.W. and Ulbrich, S.E. (2010) Normalization strategies for microRNA profiling experiments: a 'normal' way to a hidden layer of complexity? Biotechnol. Lett., 32, 1777-1788.
-
(2010)
Biotechnol. Lett.
, vol.32
, pp. 1777-1788
-
-
Meyer, S.U.1
Pfaffl, M.W.2
Ulbrich, S.E.3
-
19
-
-
84943662356
-
The potential of circulating extracellular small RNAs (smexRNA) in veterinary diagnostics - Identifying biomarker signatures by multivariate data analysis
-
Spornraft, M., Kirchner, B., Pfaffl, M.W. and Irmgard, R. (2015) The potential of circulating extracellular small RNAs (smexRNA) in veterinary diagnostics-Identifying biomarker signatures by multivariate data analysis. Biomol. Detect. Quantif., 5, 15-22.
-
(2015)
Biomol. Detect. Quantif.
, vol.5
, pp. 15-22
-
-
Spornraft, M.1
Kirchner, B.2
Pfaffl, M.W.3
Irmgard, R.4
-
20
-
-
84927752498
-
The reproducibility of biomedical research: Sleepers awake!
-
Bustin, S.A. (2014) The reproducibility of biomedical research: sleepers awake! Biomol. Detect. Quantif., 2, 35-42.
-
(2014)
Biomol. Detect. Quantif.
, vol.2
, pp. 35-42
-
-
Bustin, S.A.1
-
21
-
-
64149097786
-
The MIQE guidelines: Minimum information for publication of quantitative real-time PCR experiments
-
Bustin, S.A., Benes, V., Garson, J.A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M.W., Shipley, G.L. et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem., 55, 611-622.
-
(2009)
Clin. Chem.
, vol.55
, pp. 611-622
-
-
Bustin, S.A.1
Benes, V.2
Garson, J.A.3
Hellemans, J.4
Huggett, J.5
Kubista, M.6
Mueller, R.7
Nolan, T.8
Pfaffl, M.W.9
Shipley, G.L.10
-
22
-
-
84878431927
-
The digital MIQE guidelines: Minimum information for publication of quantitative digital PCR experiments
-
Huggett, J.F., Foy, C.A., Benes, V., Emslie, K., Garson, J.A., Haynes, R., Hellemans, J., Kubista, M., Mueller, R.D., Nolan, T. et al. (2013) The digital MIQE guidelines: minimum information for publication of quantitative digital PCR experiments. Clin Chem, 59, 892-902.
-
(2013)
Clin Chem
, vol.59
, pp. 892-902
-
-
Huggett, J.F.1
Foy, C.A.2
Benes, V.3
Emslie, K.4
Garson, J.A.5
Haynes, R.6
Hellemans, J.7
Kubista, M.8
Mueller, R.D.9
Nolan, T.10
-
23
-
-
83055192078
-
Differential expression in RNA-seq: A matter of depth
-
Tarazona, S., Garcia-Alcalde, F., Dopazo, J., Ferrer, A. and Conesa, A. (2011) Differential expression in RNA-seq: a matter of depth. Genome Res., 21, 2213-2223.
-
(2011)
Genome Res.
, vol.21
, pp. 2213-2223
-
-
Tarazona, S.1
Garcia-Alcalde, F.2
Dopazo, J.3
Ferrer, A.4
Conesa, A.5
-
24
-
-
84888343631
-
Calculating sample size estimates for RNA sequencing data
-
Hart, S.N., Therneau, T.M., Zhang, Y., Poland, G.A. and Kocher, J.-P. (2013) Calculating sample size estimates for RNA sequencing data. J. Comput. Biol., 20, 970-978.
-
(2013)
J. Comput. Biol.
, vol.20
, pp. 970-978
-
-
Hart, S.N.1
Therneau, T.M.2
Zhang, Y.3
Poland, G.A.4
Kocher, J.-P.5
-
25
-
-
84893242996
-
RNA-seq differential expression studies: More sequence or more replicatioň
-
Liu, Y., Zhou, J. and White, K.P. (2013) RNA-seq differential expression studies: more sequence or more replicatioň Bioinformatics, 30, 301-304.
-
(2013)
Bioinformatics
, vol.30
, pp. 301-304
-
-
Liu, Y.1
Zhou, J.2
White, K.P.3
-
26
-
-
85014040805
-
RNA-seq data: Challenges in and recommendations for experimental design and analysis
-
Williams, A.G., Thomas, S., Wyman, S.K. and Holloway, A.K. (2014) RNA-seq data: challenges in and recommendations for experimental design and analysis. Curr. Protoc. Hum. Genet., 83, 11-20.
-
(2014)
Curr. Protoc. Hum. Genet.
, vol.83
, pp. 11-20
-
-
Williams, A.G.1
Thomas, S.2
Wyman, S.K.3
Holloway, A.K.4
-
27
-
-
84858606519
-
A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data
-
Kvam, V.M., Liu, P. and Si, Y. (2012) A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data. Am. J. Bot., 99, 248-256.
-
(2012)
Am. J. Bot.
, vol.99
, pp. 248-256
-
-
Kvam, V.M.1
Liu, P.2
Si, Y.3
-
28
-
-
84970949920
-
How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you usě
-
Schurch, N.J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G.G., Owen-Hughes, T. et al. (2016) How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you usě RNA, 22, 839-851.
-
(2016)
RNA
, vol.22
, pp. 839-851
-
-
Schurch, N.J.1
Schofield, P.2
Gierliński, M.3
Cole, C.4
Sherstnev, A.5
Singh, V.6
Wrobel, N.7
Gharbi, K.8
Simpson, G.G.9
Owen-Hughes, T.10
-
29
-
-
79955756836
-
Design and validation issues in RNA-seq experiments
-
Fang, Z. and Cui, X. (2011) Design and validation issues in RNA-seq experiments. Brief. Bioinform., 12, 280-287.
-
(2011)
Brief. Bioinform.
, vol.12
, pp. 280-287
-
-
Fang, Z.1
Cui, X.2
-
30
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M. and Gilad, Y. (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res., 18, 1509-1517.
-
(2008)
Genome Res.
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
31
-
-
70349653541
-
Design and optimization of reverse-transcription quantitative PCR experiments
-
Tichopad, A., Kitchen, R., Riedmaier, I., Becker, C., Stahlberg, A. and Kubista, M. (2009) Design and optimization of reverse-transcription quantitative PCR experiments. Clin. Chem., 55, 1816-1823.
-
(2009)
Clin. Chem.
, vol.55
, pp. 1816-1823
-
-
Tichopad, A.1
Kitchen, R.2
Riedmaier, I.3
Becker, C.4
Stahlberg, A.5
Kubista, M.6
-
32
-
-
4344564046
-
Comparison of reverse transcriptases in gene expression analysis
-
Stahlberg, A., Kubista, M. and Pfaffl, M. (2004) Comparison of reverse transcriptases in gene expression analysis. Clin. Chem., 50, 1678-1680.
-
(2004)
Clin. Chem.
, vol.50
, pp. 1678-1680
-
-
Stahlberg, A.1
Kubista, M.2
Pfaffl, M.3
-
33
-
-
33750310042
-
Preliminary comparison of quantity, quality, and microarray performance of RNA extracted from formalin-fixed, paraffin-embedded, and unfixed frozen tissue samples
-
Scicchitano, M.S., Dalmas, D.A., Bertiaux, M.A., Anderson, S.M., Turner, L.R., Thomas, R.A., Mirable, R. and Boyce, R.W. (2006) Preliminary comparison of quantity, quality, and microarray performance of RNA extracted from formalin-fixed, paraffin-embedded, and unfixed frozen tissue samples. J. Histochem. Cytochem., 54, 1229-1237.
-
(2006)
J. Histochem. Cytochem.
, vol.54
, pp. 1229-1237
-
-
Scicchitano, M.S.1
Dalmas, D.A.2
Bertiaux, M.A.3
Anderson, S.M.4
Turner, L.R.5
Thomas, R.A.6
Mirable, R.7
Boyce, R.W.8
-
34
-
-
40049086211
-
Improved RNA quality and TaqManR Pre-amplification method (PreAmp) to enhance expression analysis from formalin fixed paraffin embedded (FFPE) materials
-
Li, J., Smyth, P., Cahill, S., Denning, K., Flavin, R., Aherne, S., Pirotta, M., Guenther, S.M., O'Leary, J.J. and Sheils, O. (2008) Improved RNA quality and TaqManR Pre-amplification method (PreAmp) to enhance expression analysis from formalin fixed paraffin embedded (FFPE) materials. BMC Biotechnol., 8, doi:10.1186/1472-6750-8-10.
-
(2008)
BMC Biotechnol.
, vol.8
-
-
Li, J.1
Smyth, P.2
Cahill, S.3
Denning, K.4
Flavin, R.5
Aherne, S.6
Pirotta, M.7
Guenther, S.M.8
O'Leary, J.J.9
Sheils, O.10
-
35
-
-
30944440066
-
Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens
-
Micke, P., Ohshima, M., Tahmasebpoor, S., Ren, Z.P., Ostman, A., Ponten, F. and Botling, J. (2006) Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens. Lab. Invest., 86, 202-211.
-
(2006)
Lab. Invest.
, vol.86
, pp. 202-211
-
-
Micke, P.1
Ohshima, M.2
Tahmasebpoor, S.3
Ren, Z.P.4
Ostman, A.5
Ponten, F.6
Botling, J.7
-
36
-
-
35048890937
-
Preservation of RNA for functional analysis of separated alleles in yeast: Comparison of snap-frozen and RNALater solid tissue storage methods
-
Dekairelle, A.F., Van der Vorst, S., Tombal, B. and Gala, J.L. (2007) Preservation of RNA for functional analysis of separated alleles in yeast: comparison of snap-frozen and RNALater solid tissue storage methods. Clin. Chem. Lab. Med., 45, 1283-1287.
-
(2007)
Clin. Chem. Lab. Med.
, vol.45
, pp. 1283-1287
-
-
Dekairelle, A.F.1
Van Der Vorst, S.2
Tombal, B.3
Gala, J.L.4
-
37
-
-
33645241407
-
The RIN: An RNA integrity number for assigning integrity values to RNA measurements
-
Schroeder, A., Mueller, O., Stocker, S., Salowsky, R., Leiber, M., Gassmann, M., Lightfoot, S., Menzel, W., Granzow, M. and Ragg, T. (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol. Biol., 7, doi:10.1186/1471-2199-7-3.
-
(2006)
BMC Mol. Biol.
, vol.7
-
-
Schroeder, A.1
Mueller, O.2
Stocker, S.3
Salowsky, R.4
Leiber, M.5
Gassmann, M.6
Lightfoot, S.7
Menzel, W.8
Granzow, M.9
Ragg, T.10
-
38
-
-
50649110928
-
Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation
-
Jahn, C.E., Charkowski, A.O. and Willis, D.K. (2008) Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation. J. Microbiol. Methods, 75, 318-324.
-
(2008)
J. Microbiol. Methods
, vol.75
, pp. 318-324
-
-
Jahn, C.E.1
Charkowski, A.O.2
Willis, D.K.3
-
39
-
-
84868032308
-
RNA quality assessment: A view from plant qPCR studies
-
Die, J.V. and Roman, B. (2012) RNA quality assessment: a view from plant qPCR studies. J. Exp. Bot., 63, 6069-6077.
-
(2012)
J. Exp. Bot.
, vol.63
, pp. 6069-6077
-
-
Die, J.V.1
Roman, B.2
-
40
-
-
84949561791
-
Efficient extraction of small and large RNAs in bacteria for excellent total RNA sequencing and comprehensive transcriptome analysis
-
Heera, R., Sivachandran, P., Chinni, S.V., Mason, J., Croft, L., Ravichandran, M. and Yin, L.S. (2015) Efficient extraction of small and large RNAs in bacteria for excellent total RNA sequencing and comprehensive transcriptome analysis. BMC Res. Notes, 8, doi:10.1186/s13104-015-1726-3.
-
(2015)
BMC Res. Notes
, vol.8
-
-
Heera, R.1
Sivachandran, P.2
Chinni, S.V.3
Mason, J.4
Croft, L.5
Ravichandran, M.6
Yin, L.S.7
-
41
-
-
80054056014
-
Characterization of the 3′:5′ ratio for reliable determination of RNA quality
-
Die, J.V., Obrero, Á., González-Verdejo, C.I. and Román, B. (2011) Characterization of the 3′:5′ ratio for reliable determination of RNA quality. Anal. Biochem., 419, 336-338.
-
(2011)
Anal. Biochem.
, vol.419
, pp. 336-338
-
-
Die, J.V.1
Obrero, Á.2
González-Verdejo, C.I.3
Román, B.4
-
42
-
-
33845600784
-
Impact of RNA degradation on gene expression profiles: Assessment of different methods to reliably determine RNA quality
-
Copois, V., Bibeau, F., Bascoul-Mollevi, C., Salvetat, N., Chalbos, P., Bareil, C., Candeil, L., Fraslon, C., Conseiller, E., Granci, V. et al. (2007) Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality. J. Biotechnol., 127, 549-559.
-
(2007)
J. Biotechnol.
, vol.127
, pp. 549-559
-
-
Copois, V.1
Bibeau, F.2
Bascoul-Mollevi, C.3
Salvetat, N.4
Chalbos, P.5
Bareil, C.6
Candeil, L.7
Fraslon, C.8
Conseiller, E.9
Granci, V.10
-
43
-
-
33644975004
-
RNA integrity and the effect on the real-time qRT-PCR performance
-
Fleige, S. and Pfaffl, M.W. (2006) RNA integrity and the effect on the real-time qRT-PCR performance. Mol. Aspects Med., 27, 126-139.
-
(2006)
Mol. Aspects Med.
, vol.27
, pp. 126-139
-
-
Fleige, S.1
Pfaffl, M.W.2
-
44
-
-
33748095919
-
Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR
-
Fleige, S., Walf, V., Huch, S., Prgomet, C., Sehm, J. and Pfaffl, M.W. (2006) Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR. Biotechnol. Lett., 28, 1601-1613.
-
(2006)
Biotechnol. Lett.
, vol.28
, pp. 1601-1613
-
-
Fleige, S.1
Walf, V.2
Huch, S.3
Prgomet, C.4
Sehm, J.5
Pfaffl, M.W.6
-
45
-
-
84903729955
-
RNA-seq: Impact of RNA degradation on transcript quantification
-
Gallego Romero, I., Pai, A.A., Tung, J. and Gilad, Y. (2014) RNA-seq: impact of RNA degradation on transcript quantification. BMC Biol., 12, doi:10.1186/1741-7007-12-42.
-
(2014)
BMC Biol.
, vol.12
-
-
Gallego Romero, I.1
Pai, A.A.2
Tung, J.3
Gilad, Y.4
-
46
-
-
84938546430
-
MRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data
-
Feng, H., Zhang, X. and Zhang, C. (2015) mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data. Nat. Commun., 6, 7816-7826.
-
(2015)
Nat. Commun.
, vol.6
, pp. 7816-7826
-
-
Feng, H.1
Zhang, X.2
Zhang, C.3
-
47
-
-
77649229497
-
mRNA and microRNA quality control for RT-qPCR analysis
-
Becker, C., Hammerle-Fickinger, A., Riedmaier, I. and Pfaffl, M.W. (2010) mRNA and microRNA quality control for RT-qPCR analysis. Methods, 50, 237-243.
-
(2010)
Methods
, vol.50
, pp. 237-243
-
-
Becker, C.1
Hammerle-Fickinger, A.2
Riedmaier, I.3
Pfaffl, M.W.4
-
48
-
-
84883496495
-
The complexity, function and applications of RNA in circulation
-
Etheridge, A., Gomes, C.P.C., Pereira, R.W., Galas, D. and Wang, K. (2013) The complexity, function and applications of RNA in circulation. Front. Genet., 4, doi:10.3389/fgene.2013.00115.
-
(2013)
Front. Genet.
, vol.4
-
-
Etheridge, A.1
Gomes, C.P.C.2
Pereira, R.W.3
Galas, D.4
Wang, K.5
-
49
-
-
79953301730
-
MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins
-
Vickers, K.C., Palmisano, B.T., Shoucri, B.M., Shamburek, R.D. and Remaley, A.T. (2011) MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins. Nat. Cell Biol., 13, 423-433.
-
(2011)
Nat. Cell Biol.
, vol.13
, pp. 423-433
-
-
Vickers, K.C.1
Palmisano, B.T.2
Shoucri, B.M.3
Shamburek, R.D.4
Remaley, A.T.5
-
50
-
-
79953202200
-
Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma
-
Arroyo, J.D., Chevillet, J.R., Kroh, E.M., Ruf, I.K., Pritchard, C.C., Gibson, D.F., Mitchell, P.S., Bennett, C.F., Pogosova-Agadjanyan, E.L., Stirewalt, D.L. et al. (2011) Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc. Natl. Acad. Sci. U.S.A., 108, 5003-5008.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 5003-5008
-
-
Arroyo, J.D.1
Chevillet, J.R.2
Kroh, E.M.3
Ruf, I.K.4
Pritchard, C.C.5
Gibson, D.F.6
Mitchell, P.S.7
Bennett, C.F.8
Pogosova-Agadjanyan, E.L.9
Stirewalt, D.L.10
-
51
-
-
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, J.J. and Lotvall, J.O. (2007) Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat. Cell Biol., 9, 654-659.
-
(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
-
52
-
-
45449093192
-
MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer
-
Taylor, D.D. and Gercel-Taylor, C. (2008) MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer. Gynecol. Oncol., 110, 13-21.
-
(2008)
Gynecol. Oncol.
, vol.110
, pp. 13-21
-
-
Taylor, D.D.1
Gercel-Taylor, C.2
-
53
-
-
40449127919
-
Detection and characterization of placental microRNAs in maternal plasma
-
Chim, S.S., Shing, T.K., Hung, E.C., Leung, T.Y., Lau, T.K., Chiu, R.W. and Lo, Y.M. (2008) Detection and characterization of placental microRNAs in maternal plasma. Clin. Chem., 54, 482-490.
-
(2008)
Clin. Chem.
, vol.54
, pp. 482-490
-
-
Chim, S.S.1
Shing, T.K.2
Hung, E.C.3
Leung, T.Y.4
Lau, T.K.5
Chiu, R.W.6
Lo, Y.M.7
-
54
-
-
84907220073
-
Optimization of extraction of circulating RNAs from plasma - Enabling small RNA sequencing
-
Spornraft, M., Kirchner, B., Haase, B., Benes, V., Pfaffl, M.W. and Riedmaier, I. (2014) Optimization of extraction of circulating RNAs from plasma-enabling small RNA sequencing. PLoS One, 9, e107259.
-
(2014)
PLoS One
, vol.9
-
-
Spornraft, M.1
Kirchner, B.2
Haase, B.3
Benes, V.4
Pfaffl, M.W.5
Riedmaier, I.6
-
55
-
-
85014619748
-
Biological properties of extracellular vesicles and their physiological functions
-
Yanez-Mo, M., Siljander, P.R., Andreu, Z., Zavec, A.B., Borras, F.E., Buzas, E.I., Buzas, K., Casal, E., Cappello, F., Carvalho, J. et al. (2015) Biological properties of extracellular vesicles and their physiological functions. J. Extracell. Vesicles, 4, doi:10.3402/jev.v4.27066.
-
(2015)
J. Extracell. Vesicles
, vol.4
-
-
Yanez-Mo, M.1
Siljander, P.R.2
Andreu, Z.3
Zavec, A.B.4
Borras, F.E.5
Buzas, E.I.6
Buzas, K.7
Casal, E.8
Cappello, F.9
Carvalho, J.10
-
56
-
-
84949539345
-
Towards the realization of clinical extracellular vesicle diagnostics: Challenges and opportunities
-
Yokoi, A., Yoshioka, Y. and Ochiya, T. (2015) Towards the realization of clinical extracellular vesicle diagnostics: challenges and opportunities. Expert Rev. Mol. Diagn., 12, 1555-1566.
-
(2015)
Expert Rev. Mol. Diagn.
, vol.12
, pp. 1555-1566
-
-
Yokoi, A.1
Yoshioka, Y.2
Ochiya, T.3
-
57
-
-
84949934993
-
As we wait: Coping with an imperfect nomenclature for extracellular vesicles
-
Gould, S.J. and Raposo, G. (2013) As we wait: coping with an imperfect nomenclature for extracellular vesicles. J. Extracell. Vesicles, 2, doi:10.3402/jev.v2i0.20389.
-
(2013)
J. Extracell. Vesicles
, vol.2
-
-
Gould, S.J.1
Raposo, G.2
-
58
-
-
84990304468
-
Optimized exosome isolation protocol for cell culture supernatant and human plasma
-
Lobb, R.J., Becker, M., Wen, S.W., Wong, C.S., Wiegmans, A.P., Leimgruber, A. and Moller, A. (2015) Optimized exosome isolation protocol for cell culture supernatant and human plasma. J. Extracell. Vesicles, 4, doi:10.3402/jev.v4.27031.
-
(2015)
J. Extracell. Vesicles
, vol.4
-
-
Lobb, R.J.1
Becker, M.2
Wen, S.W.3
Wong, C.S.4
Wiegmans, A.P.5
Leimgruber, A.6
Moller, A.7
-
59
-
-
84906700936
-
Integrated immunoisolation and protein analysis of circulating exosomes using microfluidic technology
-
He, M., Crow, J., Roth, M., Zeng, Y. and Godwin, A.K. (2014) Integrated immunoisolation and protein analysis of circulating exosomes using microfluidic technology. Lab. Chip, 14, 3773-3780.
-
(2014)
Lab. Chip
, vol.14
, pp. 3773-3780
-
-
He, M.1
Crow, J.2
Roth, M.3
Zeng, Y.4
Godwin, A.K.5
-
60
-
-
85016457286
-
Ready-made chromatography columns for extracellular vesicle isolation from plasma
-
Welton, J.L., Webber, J.P., Botos, L.A., Jones, M. and Clayton, A. (2015) Ready-made chromatography columns for extracellular vesicle isolation from plasma. J. Extracell. Vesicles, 4, doi:10.3402/jev.v4.27269.
-
(2015)
J. Extracell. Vesicles
, vol.4
-
-
Welton, J.L.1
Webber, J.P.2
Botos, L.A.3
Jones, M.4
Clayton, A.5
-
61
-
-
84958207081
-
Isolation of exosomes from blood plasma: Qualitative and quantitative comparison of ultracentrifugation and size exclusion chromatography methods
-
Baranyai, T., Herczeg, K., Onodi, Z., Voszka, I., Modos, K., Marton, N., Nagy, G., Mager, I., Wood, M.J., El Andaloussi, S. et al. (2015) Isolation of exosomes from blood plasma: qualitative and quantitative comparison of ultracentrifugation and size exclusion chromatography methods. PLoS One, 10, e0145686.
-
(2015)
PLoS One
, vol.10
-
-
Baranyai, T.1
Herczeg, K.2
Onodi, Z.3
Voszka, I.4
Modos, K.5
Marton, N.6
Nagy, G.7
Mager, I.8
Wood, M.J.9
El Andaloussi, S.10
-
62
-
-
84964265534
-
A protocol for exosome isolation and characterization: Evaluation of ultracentrifugation, density-gradient separation, and immunoaffinity capture methods
-
Greening, D.W., Xu, R., Ji, H., Tauro, B.J. and Simpson, R.J. (2015) A protocol for exosome isolation and characterization: evaluation of ultracentrifugation, density-gradient separation, and immunoaffinity capture methods. Methods Mol. Biol., 1295, 179-209.
-
(2015)
Methods Mol. Biol.
, vol.1295
, pp. 179-209
-
-
Greening, D.W.1
Xu, R.2
Ji, H.3
Tauro, B.J.4
Simpson, R.J.5
-
63
-
-
84957583645
-
Focus on extracellular vesicles: Introducing the next small big thing
-
Kalra, H., Drummen, G.P. and Mathivanan, S. (2016) Focus on extracellular vesicles: introducing the next small big thing. Int. J. Mol. Sci., 17, doi:10.3390/ijms17020170.
-
(2016)
Int. J. Mol. Sci.
, vol.17
-
-
Kalra, H.1
Drummen, G.P.2
Mathivanan, S.3
-
64
-
-
84930345994
-
Isolation of extracellular vesicles: Determining the correct approach (Review)
-
Szatanek, R., Baran, J., Siedlar, M. and Baj-Krzyworzeka, M. (2015) Isolation of extracellular vesicles: determining the correct approach (Review). Int. J. Mol. Med., 36, 11-17.
-
(2015)
Int. J. Mol. Med.
, vol.36
, pp. 11-17
-
-
Szatanek, R.1
Baran, J.2
Siedlar, M.3
Baj-Krzyworzeka, M.4
-
65
-
-
84926220052
-
Strategies for isolation of exosomes
-
Zeringer, E., Barta, T., Li, M. and Vlassov, A.V. (2015) Strategies for isolation of exosomes. Cold Spring Harb. Protoc., 2015, 319-323.
-
(2015)
Cold Spring Harb. Protoc.
, vol.2015
, pp. 319-323
-
-
Zeringer, E.1
Barta, T.2
Li, M.3
Vlassov, A.V.4
-
66
-
-
85015684168
-
The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling
-
Van Deun, J., Mestdagh, P., Sormunen, R., Cocquyt, V., Vermaelen, K., Vandesompele, J., Bracke, M., De Wever, O. and Hendrix, A. (2014) The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling. J. Extracell. Vesicles, 3, doi:10.3402/jev.v3.24858.
-
(2014)
J. Extracell. Vesicles
, vol.3
-
-
Van Deun, J.1
Mestdagh, P.2
Sormunen, R.3
Cocquyt, V.4
Vermaelen, K.5
Vandesompele, J.6
Bracke, M.7
De Wever, O.8
Hendrix, A.9
-
67
-
-
84890562207
-
Comparison of serum exosome isolation methods for microRNA profiling
-
Rekker, K., Saare, M., Roost, A.M., Kubo, A.L., Zarovni, N., Chiesi, A., Salumets, A. and Peters, M. (2014) Comparison of serum exosome isolation methods for microRNA profiling. Clin. Biochem., 47, 135-138.
-
(2014)
Clin. Biochem.
, vol.47
, pp. 135-138
-
-
Rekker, K.1
Saare, M.2
Roost, A.M.3
Kubo, A.L.4
Zarovni, N.5
Chiesi, A.6
Salumets, A.7
Peters, M.8
-
68
-
-
84975790728
-
Different EV enrichment methods suitable for clinical settings yield different subpopulations of urinary extracellular vesicles from human samples
-
Royo, F., Zuniga-Garcia, P., Sanchez-Mosquera, P., Egia, A., Perez, A., Loizaga, A., Arceo, R., Lacasa, I., Rabade, A., Arrieta, E. et al. (2016) Different EV enrichment methods suitable for clinical settings yield different subpopulations of urinary extracellular vesicles from human samples. J. Extracell. Vesicles, 5, doi:10.3402/jev.v5.29497.
-
(2016)
J. Extracell. Vesicles
, vol.5
-
-
Royo, F.1
Zuniga-Garcia, P.2
Sanchez-Mosquera, P.3
Egia, A.4
Perez, A.5
Loizaga, A.6
Arceo, R.7
Lacasa, I.8
Rabade, A.9
Arrieta, E.10
-
69
-
-
84959386845
-
Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes
-
Kowal, J., Arras, G., Colombo, M., Jouve, M., Morath, J.P., Primdal-Bengtson, B., Dingli, F., Loew, D., Tkach, M. and Thery, C. (2016) Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes. Proc. Natl. Acad. Sci. U.S.A., 113, E968-E977.
-
(2016)
Proc. Natl. Acad. Sci. U.S.A.
, vol.113
, pp. E968-E977
-
-
Kowal, J.1
Arras, G.2
Colombo, M.3
Jouve, M.4
Morath, J.P.5
Primdal-Bengtson, B.6
Dingli, F.7
Loew, D.8
Tkach, M.9
Thery, C.10
-
70
-
-
84959513695
-
Cells release subpopulations of exosomes with distinct molecular and biological properties
-
Willms, E., Johansson, H.J., Mager, I., Lee, Y., Blomberg, K.E., Sadik, M., Alaarg, A., Smith, C.I., Lehtio, J., El Andaloussi, S. et al. (2016) Cells release subpopulations of exosomes with distinct molecular and biological properties. Sci. Rep., 6, doi:10.1038/srep22519.
-
(2016)
Sci. Rep.
, vol.6
-
-
Willms, E.1
Johansson, H.J.2
Mager, I.3
Lee, Y.4
Blomberg, K.E.5
Sadik, M.6
Alaarg, A.7
Smith, C.I.8
Lehtio, J.9
El Andaloussi, S.10
-
71
-
-
84962227579
-
Residual matrix from different separation techniques impacts exosome biological activity
-
Paolini, L., Zendrini, A., Noto, G.D., Busatto, S., Lottini, E., Radeghieri, A., Dossi, A., Caneschi, A., Ricotta, D. and Bergese, P. (2016) Residual matrix from different separation techniques impacts exosome biological activity. Sci. Rep., 6, doi:10.1038/srep23550.
-
(2016)
Sci. Rep.
, vol.6
-
-
Paolini, L.1
Zendrini, A.2
Noto, G.D.3
Busatto, S.4
Lottini, E.5
Radeghieri, A.6
Dossi, A.7
Caneschi, A.8
Ricotta, D.9
Bergese, P.10
-
72
-
-
84966318628
-
Proteomic analysis of exosomal cargo: The challenge of high purity vesicle isolation
-
Abramowicz, A., Widlak, P. and Pietrowska, M. (2016) Proteomic analysis of exosomal cargo: the challenge of high purity vesicle isolation. Mol. Biosyst., 12, 1407-1419.
-
(2016)
Mol. Biosyst.
, vol.12
, pp. 1407-1419
-
-
Abramowicz, A.1
Widlak, P.2
Pietrowska, M.3
-
73
-
-
84915733870
-
Comparison of whole blood RNA preservation tubes and novel generation RNA extraction kits for analysis of mRNA and MiRNA profiles
-
Müller, R., Häntzsch, M., Tolios, A., Beutner, F., Nagel, D., Thiery, J., Teupser, D. and Holdt, L.M. (2014) Comparison of whole blood RNA preservation tubes and novel generation RNA extraction kits for analysis of mRNA and MiRNA profiles. PLoS One, 9, e113298.
-
(2014)
PLoS One
, vol.9
-
-
Müller, R.1
Häntzsch, M.2
Tolios, A.3
Beutner, F.4
Nagel, D.5
Thiery, J.6
Teupser, D.7
Holdt, L.M.8
-
74
-
-
84873899437
-
Genome-wide comparison of two RNA-stabilizing reagents for transcriptional profiling of peripheral blood
-
Nikula, T., Mykkänen, J., Simell, O. and Lahesmaa, R. (2013) Genome-wide comparison of two RNA-stabilizing reagents for transcriptional profiling of peripheral blood. Transl. Res., 161, 181-188.
-
(2013)
Transl. Res.
, vol.161
, pp. 181-188
-
-
Nikula, T.1
Mykkänen, J.2
Simell, O.3
Lahesmaa, R.4
-
75
-
-
72249098584
-
Validation of extraction methods for total RNA and miRNA from bovine blood prior to quantitative gene expression analyses
-
Hammerle-Fickinger, A., Riedmaier, I., Becker, C., Meyer, H.H., Pfaffl, M.W. and Ulbrich, S.E. (2010) Validation of extraction methods for total RNA and miRNA from bovine blood prior to quantitative gene expression analyses. Biotechnol. Lett., 32, 35-44.
-
(2010)
Biotechnol. Lett.
, vol.32
, pp. 35-44
-
-
Hammerle-Fickinger, A.1
Riedmaier, I.2
Becker, C.3
Meyer, H.H.4
Pfaffl, M.W.5
Ulbrich, S.E.6
-
76
-
-
84887308221
-
Isolation of RNA from equine peripheral blood cells: Comparison of methods
-
Jiang, Z., Uboh, C.E., Chen, J. and Soma, L.R. (2013) Isolation of RNA from equine peripheral blood cells: comparison of methods. Springerplus, 2, 478-484.
-
(2013)
Springerplus
, vol.2
, pp. 478-484
-
-
Jiang, Z.1
Uboh, C.E.2
Chen, J.3
Soma, L.R.4
-
77
-
-
84900298821
-
Comparison of blood RNA extraction methods used for gene expression profiling in amyotrophic lateral sclerosis
-
Bayatti, N., Cooper-Knock, J., Bury, J.J., Wyles, M., Heath, P.R., Kirby, J. and Shaw, P.J. (2014) Comparison of blood RNA extraction methods used for gene expression profiling in amyotrophic lateral sclerosis. PLoS One, 9, e87508.
-
(2014)
PLoS One
, vol.9
-
-
Bayatti, N.1
Cooper-Knock, J.2
Bury, J.J.3
Wyles, M.4
Heath, P.R.5
Kirby, J.6
Shaw, P.J.7
-
79
-
-
84880896577
-
Comparison of methods for miRNA extraction from plasma and quantitative recovery of RNA from cerebrospinal fluid
-
McAlexander, M.A., Phillips, M.J. and Witwer, K.W. (2013) Comparison of methods for miRNA extraction from plasma and quantitative recovery of RNA from cerebrospinal fluid. Front. Genet., 4, 1-8.
-
(2013)
Front. Genet.
, vol.4
, pp. 1-8
-
-
McAlexander, M.A.1
Phillips, M.J.2
Witwer, K.W.3
-
80
-
-
84867237573
-
Method for microRNA isolation from clinical serum samples
-
Li, Y. and Kowdley, K.V. (2012) Method for microRNA isolation from clinical serum samples. Anal. Biochem., 431, 69-75.
-
(2012)
Anal. Biochem.
, vol.431
, pp. 69-75
-
-
Li, Y.1
Kowdley, K.V.2
-
81
-
-
84876581756
-
Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing
-
Burgos, K.L., Javaherian, A., Bomprezzi, R., Ghaffari, L., Rhodes, S., Courtright, A., Tembe, W., Kim, S., Metpally, R. and Van Keuren-Jensen, K. (2013) Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing. RNA, 19, 712-722.
-
(2013)
RNA
, vol.19
, pp. 712-722
-
-
Burgos, K.L.1
Javaherian, A.2
Bomprezzi, R.3
Ghaffari, L.4
Rhodes, S.5
Courtright, A.6
Tembe, W.7
Kim, S.8
Metpally, R.9
Van Keuren-Jensen, K.10
-
82
-
-
84896706999
-
Biases in small RNA deep sequencing data
-
Raabe, C.A., Tang, T.H., Brosius, J. and Rozhdestvensky, T.S. (2014) Biases in small RNA deep sequencing data. Nucleic Acids Res., 42, 1414-1426.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 1414-1426
-
-
Raabe, C.A.1
Tang, T.H.2
Brosius, J.3
Rozhdestvensky, T.S.4
-
83
-
-
67649595548
-
Limitations and possibilities of small RNA digital gene expression profiling
-
Linsen, S.E., de Wit, E., Janssens, G., Heater, S., Chapman, L., Parkin, R.K., Fritz, B., Wyman, S.K., de Bruijn, E., Voest, E.E. et al. (2009) Limitations and possibilities of small RNA digital gene expression profiling. Nat. Methods, 6, 474-476.
-
(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
Fritz, B.7
Wyman, S.K.8
De Bruijn, E.9
Voest, E.E.10
-
84
-
-
84945190366
-
An efficient and sensitive method for preparing cDNA libraries from scarce biological samples
-
Sterling, C.H., Veksler-Lublinsky, I. and Ambros, V. (2015) An efficient and sensitive method for preparing cDNA libraries from scarce biological samples. Nucleic Acids Res., 43, e1.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. e1
-
-
Sterling, C.H.1
Veksler-Lublinsky, I.2
Ambros, V.3
-
85
-
-
84943583637
-
Control for stochastic sampling variation and qualitative sequencing error in next generation sequencing
-
Blomquist, T., Crawford, E.L., Yeo, J., Zhang, X. and Willey, J.C. (2015) Control for stochastic sampling variation and qualitative sequencing error in next generation sequencing. Biomol. Detect. Quantif., 5, 30-37.
-
(2015)
Biomol. Detect. Quantif.
, vol.5
, pp. 30-37
-
-
Blomquist, T.1
Crawford, E.L.2
Yeo, J.3
Zhang, X.4
Willey, J.C.5
-
86
-
-
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
-
87
-
-
84862991525
-
Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells
-
Kim, Y.K., Yeo, J., Kim, B., Ha, M. and Kim, V.N. (2012) Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Mol. Cell, 46, 893-895.
-
(2012)
Mol. Cell
, vol.46
, pp. 893-895
-
-
Kim, Y.K.1
Yeo, J.2
Kim, B.3
Ha, M.4
Kim, V.N.5
-
88
-
-
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, doi:10.1186/1471-2164-15-569.
-
(2014)
BMC Genomics
, vol.15
-
-
Jackson, T.J.1
Spriggs, R.V.2
Burgoyne, N.J.3
Jones, C.4
Willis, A.E.5
-
89
-
-
84860198538
-
Structural bias in T4 RNA ligase-mediated 3′-adapter ligation
-
Zhuang, F., Fuchs, R.T., Sun, Z., Zheng, Y. and Robb, G.B. (2012) Structural bias in T4 RNA ligase-mediated 3′-adapter ligation. Nucleic Acids Res., 40, e54.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e54
-
-
Zhuang, F.1
Fuchs, R.T.2
Sun, Z.3
Zheng, Y.4
Robb, G.B.5
-
90
-
-
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, 2012, doi:10.1155/2012/360358.
-
(2012)
J. Nucleic Acids
, vol.2012
-
-
Zhuang, F.1
Fuchs, R.T.2
Robb, G.B.3
-
91
-
-
81755162782
-
A bias-reducing strategy in profiling small RNAs using Solexa
-
Sun, G., Wu, X., Wang, J., Li, H., Li, X., Gao, H., Rossi, J. and Yen, Y. (2011) A bias-reducing strategy in profiling small RNAs using Solexa. RNA, 17, 2256-2262.
-
(2011)
RNA
, vol.17
, pp. 2256-2262
-
-
Sun, G.1
Wu, X.2
Wang, J.3
Li, H.4
Li, X.5
Gao, H.6
Rossi, J.7
Yen, Y.8
-
92
-
-
80052520350
-
Barcoding bias in high-throughput multiplex sequencing of miRNA
-
Alon, S., Vigneault, F., Eminaga, S., Christodoulou, D.C., Seidman, J.G., Church, G.M. and Eisenberg, E. (2011) Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res., 21, 1506-1511.
-
(2011)
Genome Res.
, vol.21
, pp. 1506-1511
-
-
Alon, S.1
Vigneault, F.2
Eminaga, S.3
Christodoulou, D.C.4
Seidman, J.G.5
Church, G.M.6
Eisenberg, E.7
-
93
-
-
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
-
94
-
-
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
-
95
-
-
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, doi:10.1186/1758-907X-3-4.
-
(2012)
Silence
, vol.3
-
-
Sorefan, K.1
Pais, H.2
Hall, A.E.3
Kozomara, A.4
Griffiths-Jones, S.5
Moulton, V.6
Dalmay, T.7
-
96
-
-
84929095115
-
Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure
-
Fuchs, R.T., Sun, Z., Zhuang, F. and Robb, G.B. (2015) Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure. PLoS One, 10, e0126049.
-
(2015)
PLoS One
, vol.10
-
-
Fuchs, R.T.1
Sun, Z.2
Zhuang, F.3
Robb, G.B.4
-
97
-
-
84954467693
-
Addressing bias in small RNA library preparation for sequencing: A new protocol recovers microRNAs that evade capture by current methods
-
Baran-Gale, J., Kurtz, C.L., Erdos, M.R., Sison, C., Young, A., Fannin, E.E., Chines, P.S. and Sethupathy, P. (2015) Addressing bias in small RNA library preparation for sequencing: a new protocol recovers microRNAs that evade capture by current methods. Front. Genet., 6, doi:10.3389/fgene.2015.00352.
-
(2015)
Front. Genet.
, vol.6
-
-
Baran-Gale, J.1
Kurtz, C.L.2
Erdos, M.R.3
Sison, C.4
Young, A.5
Fannin, E.E.6
Chines, P.S.7
Sethupathy, P.8
-
98
-
-
80055041450
-
Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing
-
Van Nieuwerburgh, F., Soetaert, S., Podshivalova, K., Ay-Lin Wang, E., Schaffer, L., Deforce, D., Salomon, D.R., Head, S.R. and Ordoukhanian, P. (2011) Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS One, 6, e26969.
-
(2011)
PLoS One
, vol.6
-
-
Van Nieuwerburgh, F.1
Soetaert, S.2
Podshivalova, K.3
Ay-Lin Wang, E.4
Schaffer, L.5
Deforce, D.6
Salomon, D.R.7
Head, S.R.8
Ordoukhanian, P.9
-
99
-
-
78951476270
-
Effect of PCR extension temperature on high-throughput sequencing
-
Lopez-Barragan, M.J., Quinones, M., Cui, K., Lemieux, J., Zhao, K. and Su, X.Z. (2011) Effect of PCR extension temperature on high-throughput sequencing. Mol. Biochem. Parasitol., 176, 64-67.
-
(2011)
Mol. Biochem. Parasitol.
, vol.176
, pp. 64-67
-
-
Lopez-Barragan, M.J.1
Quinones, M.2
Cui, K.3
Lemieux, J.4
Zhao, K.5
Su, X.Z.6
-
100
-
-
34247259831
-
Mouse Piwi-interacting RNAs are 2′-O-methylated at their 3′ termini
-
Kirino, Y. and Mourelatos, Z. (2007) Mouse Piwi-interacting RNAs are 2′-O-methylated at their 3′ termini. Nat. Struct. Mol. Biol., 14, 347-348.
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 347-348
-
-
Kirino, Y.1
Mourelatos, Z.2
-
101
-
-
34247199896
-
The 3′ termini of mouse Piwi-interacting RNAs are 2′-O-methylated
-
Ohara, T., Sakaguchi, Y., Suzuki, T., Ueda, H. and Miyauchi, K. (2007) The 3′ termini of mouse Piwi-interacting RNAs are 2′-O-methylated. Nat. Struct. Mol. Biol., 14, 349-350.
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 349-350
-
-
Ohara, T.1
Sakaguchi, Y.2
Suzuki, T.3
Ueda, H.4
Miyauchi, K.5
-
102
-
-
79959757662
-
T4 RNA ligase 2 truncated active site mutants: Improved tools for RNA analysis
-
Viollet, S., Fuchs, R.T., Munafo, D.B., Zhuang, F. and Robb, G.B. (2011) T4 RNA ligase 2 truncated active site mutants: improved tools for RNA analysis. BMC Biotechnol., 11, doi:10.1186/1472-6750-11-72.
-
(2011)
BMC Biotechnol.
, vol.11
-
-
Viollet, S.1
Fuchs, R.T.2
Munafo, D.B.3
Zhuang, F.4
Robb, G.B.5
-
103
-
-
78649668009
-
Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA
-
Munafo, D.B. and Robb, G.B. (2010) Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA. RNA, 16, 2537-2552.
-
(2010)
RNA
, vol.16
, pp. 2537-2552
-
-
Munafo, D.B.1
Robb, G.B.2
-
104
-
-
84927722380
-
How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments
-
Svec, D., Tichopad, A., Novosadova, V., Pfaffl, M.W. and Kubista, M. (2015) How good is a PCR efficiency estimate: recommendations for precise and robust qPCR efficiency assessments. Biomol. Detect. Quantif., 3, 9-16.
-
(2015)
Biomol. Detect. Quantif.
, vol.3
, pp. 9-16
-
-
Svec, D.1
Tichopad, A.2
Novosadova, V.3
Pfaffl, M.W.4
Kubista, M.5
-
105
-
-
84858829830
-
Multiple heat pulses during PCR extension enabling amplification of GC-rich sequences and reducing amplification bias
-
Orpana, A.K., Ho, T.H. and Stenman, J. (2012) Multiple heat pulses during PCR extension enabling amplification of GC-rich sequences and reducing amplification bias. Anal. Chem., 84, 2081-2087.
-
(2012)
Anal. Chem.
, vol.84
, pp. 2081-2087
-
-
Orpana, A.K.1
Ho, T.H.2
Stenman, J.3
-
106
-
-
80054055413
-
Local and global factors affecting RNA sequencing analysis
-
Sendler, E., Johnson, G.D. and Krawetz, S.A. (2011) Local and global factors affecting RNA sequencing analysis. Anal. Biochem., 419, 317-322.
-
(2011)
Anal. Biochem.
, vol.419
, pp. 317-322
-
-
Sendler, E.1
Johnson, G.D.2
Krawetz, S.A.3
-
107
-
-
84857271408
-
Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries
-
Dabney, J. and Meyer, M. (2012) Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques, 52, 87-94.
-
(2012)
Biotechniques
, vol.52
, pp. 87-94
-
-
Dabney, J.1
Meyer, M.2
-
108
-
-
54149094282
-
A fundamental study of the PCR amplification of GC-rich DNA templates
-
Mamedov, T.G., Pienaar, E., Whitney, S.E., TerMaat, J.R., Carvill, G., Goliath, R., Subramanian, A. and Viljoen, H.J. (2008) A fundamental study of the PCR amplification of GC-rich DNA templates. Comput. Biol. Chem., 32, 452-457.
-
(2008)
Comput. Biol. Chem.
, vol.32
, pp. 452-457
-
-
Mamedov, T.G.1
Pienaar, E.2
Whitney, S.E.3
TerMaat, J.R.4
Carvill, G.5
Goliath, R.6
Subramanian, A.7
Viljoen, H.J.8
-
109
-
-
79951694175
-
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
-
Aird, D., Ross, M.G., Chen, W.S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D.B., Nusbaum, C. and Gnirke, A. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol., 12, doi:10.1186/gb-2011-12-2-r18.
-
(2011)
Genome Biol.
, vol.12
-
-
Aird, D.1
Ross, M.G.2
Chen, W.S.3
Danielsson, M.4
Fennell, T.5
Russ, C.6
Jaffe, D.B.7
Nusbaum, C.8
Gnirke, A.9
-
110
-
-
84893522267
-
Library construction for next-generation sequencing: Overviews and challenges
-
Head, S.R., Komori, H.K., LaMere, S.A., Whisenant, T., Van Nieuwerburgh, F., Salomon, D.R. and Ordoukhanian, P. (2014) Library construction for next-generation sequencing: overviews and challenges. Biotechniques, 56, 61-68.
-
(2014)
Biotechniques
, vol.56
, pp. 61-68
-
-
Head, S.R.1
Komori, H.K.2
LaMere, S.A.3
Whisenant, T.4
Van Nieuwerburgh, F.5
Salomon, D.R.6
Ordoukhanian, P.7
-
111
-
-
84954402610
-
Evaluation of bias associated with high-multiplex, target-specific pre-amplification
-
Okino, S.T., Kong, M., Sarras, H. and Wang, Y. (2016) Evaluation of bias associated with high-multiplex, target-specific pre-amplification. Biomol. Detect. Quantif., 6, 13-21.
-
(2016)
Biomol. Detect. Quantif.
, vol.6
, pp. 13-21
-
-
Okino, S.T.1
Kong, M.2
Sarras, H.3
Wang, Y.4
-
112
-
-
84856484968
-
Counting absolute numbers of molecules using unique molecular identifiers
-
Kivioja, T., Vaharautio, A., Karlsson, K., Bonke, M., Enge, M., Linnarsson, S. and Taipale, J. (2012) Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods, 9, 72-74.
-
(2012)
Nat. Methods
, vol.9
, pp. 72-74
-
-
Kivioja, T.1
Vaharautio, A.2
Karlsson, K.3
Bonke, M.4
Enge, M.5
Linnarsson, S.6
Taipale, J.7
-
113
-
-
84895069488
-
Quantitative single-cell RNA-seq with unique molecular identifiers
-
Islam, S., Zeisel, A., Joost, S., La Manno, G., Zajac, P., Kasper, M., Lonnerberg, P. and Linnarsson, S. (2014) Quantitative single-cell RNA-seq with unique molecular identifiers. Nat. Methods, 11, 163-166.
-
(2014)
Nat. Methods
, vol.11
, pp. 163-166
-
-
Islam, S.1
Zeisel, A.2
Joost, S.3
La Manno, G.4
Zajac, P.5
Kasper, M.6
Lonnerberg, P.7
Linnarsson, S.8
-
114
-
-
84940175415
-
Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization
-
Locati, M.D., Terpstra, I., de Leeuw, W.C., Kuzak, M., Rauwerda, H., Ensink, W.A., van Leeuwen, S., Nehrdich, U., Spaink, H.P., Jonker, M.J. et al. (2015) Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization. Nucleic Acids Res., 43, e89.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. e89
-
-
Locati, M.D.1
Terpstra, I.2
De Leeuw, W.C.3
Kuzak, M.4
Rauwerda, H.5
Ensink, W.A.6
Van Leeuwen, S.7
Nehrdich, U.8
Spaink, H.P.9
Jonker, M.J.10
-
115
-
-
0029839535
-
Protection of DNA during preparative agarose gel electrophoresis against damage induced by ultraviolet light
-
Grundemann, D. and Schomig, E. (1996) Protection of DNA during preparative agarose gel electrophoresis against damage induced by ultraviolet light. Biotechniques, 21, 898-903.
-
(1996)
Biotechniques
, vol.21
, pp. 898-903
-
-
Grundemann, D.1
Schomig, E.2
-
116
-
-
0023887406
-
DNA damage produced by ethidium bromide staining and exposure to ultraviolet light
-
Cariello, N.F., Keohavong, P., Sanderson, B.J. and Thilly, W.G. (1988) DNA damage produced by ethidium bromide staining and exposure to ultraviolet light. Nucleic Acids Res., 16, 4157-4157.
-
(1988)
Nucleic Acids Res.
, vol.16
, pp. 4157
-
-
Cariello, N.F.1
Keohavong, P.2
Sanderson, B.J.3
Thilly, W.G.4
-
117
-
-
0035108634
-
Green-light transilluminator for the detection without photodamage of proteins and DNA labeled with different fluorescent dyes
-
Alba, F.J., Bermudez, A. and Daban, J.R. (2001) Green-light transilluminator for the detection without photodamage of proteins and DNA labeled with different fluorescent dyes. Electrophoresis, 22, 399-403.
-
(2001)
Electrophoresis
, vol.22
, pp. 399-403
-
-
Alba, F.J.1
Bermudez, A.2
Daban, J.R.3
-
118
-
-
0035044143
-
A whole new way of looking at things: The use of Dark Reader technology to detect fluorophors
-
Seville, M. (2001) A whole new way of looking at things: the use of Dark Reader technology to detect fluorophors. Electrophoresis, 22, 814-828.
-
(2001)
Electrophoresis
, vol.22
, pp. 814-828
-
-
Seville, M.1
-
119
-
-
57049122389
-
A large genome center's improvements to the Illumina sequencing system
-
Quail, M.A., Kozarewa, I., Smith, F., Scally, A., Stephens, P.J., Durbin, R., Swerdlow, H. and Turner, D.J. (2008) A large genome center's improvements to the Illumina sequencing system. Nat. Methods, 5, 1005-1010.
-
(2008)
Nat. Methods
, vol.5
, pp. 1005-1010
-
-
Quail, M.A.1
Kozarewa, I.2
Smith, F.3
Scally, A.4
Stephens, P.J.5
Durbin, R.6
Swerdlow, H.7
Turner, D.J.8
-
120
-
-
77649224709
-
Rapid quantification of DNA libraries for next-generation sequencing
-
Buehler, B., Hogrefe, H.H., Scott, G., Ravi, H., Pabon-Pena, C., O'Brien, S., Formosa, R. and Happe, S. (2010) Rapid quantification of DNA libraries for next-generation sequencing. Methods, 50, S15-S18.
-
(2010)
Methods
, vol.50
, pp. S15-S18
-
-
Buehler, B.1
Hogrefe, H.H.2
Scott, G.3
Ravi, H.4
Pabon-Pena, C.5
O'Brien, S.6
Formosa, R.7
Happe, S.8
-
121
-
-
84881486404
-
Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries
-
Laurie, M.T., Bertout, J.A., Taylor, S.D., Burton, J.N., Shendure, J.A. and Bielas, J.H. (2013) Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries. Biotechniques, 55, 61-67.
-
(2013)
Biotechniques
, vol.55
, pp. 61-67
-
-
Laurie, M.T.1
Bertout, J.A.2
Taylor, S.D.3
Burton, J.N.4
Shendure, J.A.5
Bielas, J.H.6
-
122
-
-
84962862007
-
Comparison of DNA quantification methods for next generation sequencing
-
Robin, J.D., Ludlow, A.T., LaRanger, R., Wright, W.E. and Shay, J.W. (2016) Comparison of DNA quantification methods for next generation sequencing. Sci. Rep., 6, doi:10.1038/srep24067.
-
(2016)
Sci. Rep.
, vol.6
-
-
Robin, J.D.1
Ludlow, A.T.2
LaRanger, R.3
Wright, W.E.4
Shay, J.W.5
-
123
-
-
64849115804
-
Digital PCR provides sensitive and absolute calibration for high throughput sequencing
-
White, R.A. 3rd, Blainey, P.C., Fan, H.C. and Quake, S.R. (2009) Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics, 10, doi:10.1186/1471-2164-10-116.
-
(2009)
BMC Genomics
, vol.10
-
-
White, R.A.1
Blainey, P.C.2
Fan, H.C.3
Quake, S.R.4
-
124
-
-
65349094759
-
Computational and analytical framework for small RNA profiling by high-throughput sequencing
-
Fahlgren, N., Sullivan, C.M., Kasschau, K.D., Chapman, E.J., Cumbie, J.S., Montgomery, T.A., Gilbert, S.D., Dasenko, M., Backman, T.W., Givan, S.A. et al. (2009) Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA, 15, 992-1002.
-
(2009)
RNA
, vol.15
, pp. 992-1002
-
-
Fahlgren, N.1
Sullivan, C.M.2
Kasschau, K.D.3
Chapman, E.J.4
Cumbie, J.S.5
Montgomery, T.A.6
Gilbert, S.D.7
Dasenko, M.8
Backman, T.W.9
Givan, S.A.10
-
125
-
-
80052521697
-
Synthetic spike-in standards for RNA-seq experiments
-
Jiang, L., Schlesinger, F., Davis, C.A., Zhang, Y., Li, R., Salit, M., Gingeras, T.R. and Oliver, B. (2011) Synthetic spike-in standards for RNA-seq experiments. Genome Res., 21, 1543-1551.
-
(2011)
Genome Res.
, vol.21
, pp. 1543-1551
-
-
Jiang, L.1
Schlesinger, F.2
Davis, C.A.3
Zhang, Y.4
Li, R.5
Salit, M.6
Gingeras, T.R.7
Oliver, B.8
-
126
-
-
84890565382
-
The role of replicates for error mitigation in next-generation sequencing
-
Robasky, K., Lewis, N.E. and Church, G.M. (2014) The role of replicates for error mitigation in next-generation sequencing. Nat. Rev. Genet., 15, 56-62.
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 56-62
-
-
Robasky, K.1
Lewis, N.E.2
Church, G.M.3
-
128
-
-
77956873627
-
Tackling the widespread and critical impact of batch effects in high-throughput data
-
Leek, J.T., Scharpf, R.B., Bravo, H.C., Simcha, D., Langmead, B., Johnson, W.E., Geman, D., Baggerly, K. and Irizarry, R.A. (2010) Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet., 11, 733-739.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 733-739
-
-
Leek, J.T.1
Scharpf, R.B.2
Bravo, H.C.3
Simcha, D.4
Langmead, B.5
Johnson, W.E.6
Geman, D.7
Baggerly, K.8
Irizarry, R.A.9
-
129
-
-
84887433583
-
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
-
t'Hoen, P.A., Friedlander, M.R., Almlof, J., Sammeth, M., Pulyakhina, I., Anvar, S.Y., Laros, J.F., Buermans, H.P., Karlberg, O., Brannvall, M. et al. (2013) Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat. Biotechnol., 31, 1015-1022.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 1015-1022
-
-
T'Hoen, P.A.1
Friedlander, M.R.2
Almlof, J.3
Sammeth, M.4
Pulyakhina, I.5
Anvar, S.Y.6
Laros, J.F.7
Buermans, H.P.8
Karlberg, O.9
Brannvall, M.10
-
130
-
-
84878234942
-
Characterizing and measuring bias in sequence data
-
Ross, M.G., Russ, C., Costello, M., Hollinger, A., Lennon, N.J., Hegarty, R., Nusbaum, C. and Jaffe, D.B. (2013) Characterizing and measuring bias in sequence data. Genome Biol., 14, doi:10.1186/gb-2013-14-5-r51.
-
(2013)
Genome Biol.
, vol.14
-
-
Ross, M.G.1
Russ, C.2
Costello, M.3
Hollinger, A.4
Lennon, N.J.5
Hegarty, R.6
Nusbaum, C.7
Jaffe, D.B.8
-
131
-
-
77955504378
-
Statistical design and analysis of RNA sequencing data
-
Auer, P.L. and Doerge, R.W. (2010) Statistical design and analysis of RNA sequencing data. Genetics, 185, 405-416.
-
(2010)
Genetics
, vol.185
, pp. 405-416
-
-
Auer, P.L.1
Doerge, R.W.2
-
132
-
-
79957882567
-
RNA-seq: Technical variability and sampling
-
McIntyre, L.M., Lopiano, K.K., Morse, A.M., Amin, V., Oberg, A.L., Young, L.J. and Nuzhdin, S.V. (2011) RNA-seq: technical variability and sampling. BMC Genomics, 12, doi:10.1186/1471-2164-12-293.
-
(2011)
BMC Genomics
, vol.12
-
-
McIntyre, L.M.1
Lopiano, K.K.2
Morse, A.M.3
Amin, V.4
Oberg, A.L.5
Young, L.J.6
Nuzhdin, S.V.7
-
133
-
-
84876097604
-
Comparison of analysis tools for miRNA high throughput sequencing using nerve crush as a model
-
Metpally, R.P., Nasser, S., Malenica, I., Courtright, A., Carlson, E., Ghaffari, L., Villa, S., Tembe, W. and Van Keuren-Jensen, K. (2013) Comparison of analysis tools for miRNA high throughput sequencing using nerve crush as a model. Front. Genet., 4, doi:10.3389/fgene.2013.00020.
-
(2013)
Front. Genet.
, vol.4
-
-
Metpally, R.P.1
Nasser, S.2
Malenica, I.3
Courtright, A.4
Carlson, E.5
Ghaffari, L.6
Villa, S.7
Tembe, W.8
Van Keuren-Jensen, K.9
-
134
-
-
84907500627
-
RNA-Seq gene profiling - A systematic empirical comparison
-
Fonseca, N.A., Marioni, J. and Brazma, A. (2014) RNA-Seq gene profiling-a systematic empirical comparison. PLoS One, 9, e107026.
-
(2014)
PLoS One
, vol.9
-
-
Fonseca, N.A.1
Marioni, J.2
Brazma, A.3
-
135
-
-
84855295457
-
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
-
Kircher, M., Sawyer, S. and Meyer, M. (2012) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res., 40, e3.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e3
-
-
Kircher, M.1
Sawyer, S.2
Meyer, M.3
-
136
-
-
80053194792
-
Base-calling for next-generation sequencing platforms
-
Ledergerber, C. and Dessimoz, C. (2011) Base-calling for next-generation sequencing platforms. Brief. Bioinform., 12, 489-497.
-
(2011)
Brief. Bioinform.
, vol.12
, pp. 489-497
-
-
Ledergerber, C.1
Dessimoz, C.2
-
137
-
-
48449094744
-
Alta-Cyclic: A self-optimizing base caller for next-generation sequencing
-
Erlich, Y., Mitra, P.P., delaBastide, M., McCombie, W.R. and Hannon, G.J. (2008) Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat. Methods, 5, 679-682.
-
(2008)
Nat. Methods
, vol.5
, pp. 679-682
-
-
Erlich, Y.1
Mitra, P.P.2
DelaBastide, M.3
McCombie, W.R.4
Hannon, G.J.5
-
138
-
-
55049090961
-
Probabilistic base calling of Solexa sequencing data
-
Rougemont, J., Amzallag, A., Iseli, C., Farinelli, L., Xenarios, I. and Naef, F. (2008) Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics, 9, doi:10.1186/1471-2105-9-431.
-
(2008)
BMC Bioinformatics
, vol.9
-
-
Rougemont, J.1
Amzallag, A.2
Iseli, C.3
Farinelli, L.4
Xenarios, I.5
Naef, F.6
-
139
-
-
70449371390
-
The challenges of sequencing by synthesis
-
Fuller, C.W., Middendorf, L.R., Benner, S.A., Church, G.M., Harris, T., Huang, X., Jovanovich, S.B., Nelson, J.R., Schloss, J.A., Schwartz, D.C. et al. (2009) The challenges of sequencing by synthesis. Nat. Biotechnol., 27, 1013-1023.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 1013-1023
-
-
Fuller, C.W.1
Middendorf, L.R.2
Benner, S.A.3
Church, G.M.4
Harris, T.5
Huang, X.6
Jovanovich, S.B.7
Nelson, J.R.8
Schloss, J.A.9
Schwartz, D.C.10
-
140
-
-
0031978181
-
Base-calling of automated sequencer traces using phred. II. Error probabilities
-
Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 186-194.
-
(1998)
Genome Res.
, vol.8
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
141
-
-
52649157765
-
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
-
Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from high-throughput 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
-
142
-
-
80052226692
-
Sequence-specific error profile of Illumina sequencers
-
Nakamura, K., Oshima, T., Morimoto, T., Ikeda, S., Yoshikawa, H., Shiwa, Y., Ishikawa, S., Linak, M.C., Hirai, A., Takahashi, H. et al. (2011) Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res., 39, e90.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. e90
-
-
Nakamura, K.1
Oshima, T.2
Morimoto, T.3
Ikeda, S.4
Yoshikawa, H.5
Shiwa, Y.6
Ishikawa, S.7
Linak, M.C.8
Hirai, A.9
Takahashi, H.10
-
143
-
-
77950361329
-
Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences?
-
Stein, A., Takasuka, T.E. and Collings, C.K. (2010) Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences? Nucleic Acids Res., 38, 709-719.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 709-719
-
-
Stein, A.1
Takasuka, T.E.2
Collings, C.K.3
-
144
-
-
65449144325
-
Evaluation of next generation sequencing platforms for population targeted sequencing studies
-
Harismendy, O., Ng, P.C., Strausberg, R.L., Wang, X., Stockwell, T.B., Beeson, K.Y., Schork, N.J., Murray, S.S., Topol, E.J., Levy, S. et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol., 10, doi:10.1186/gb-2009-10-3-r32.
-
(2009)
Genome Biol.
, vol.10
-
-
Harismendy, O.1
Ng, P.C.2
Strausberg, R.L.3
Wang, X.4
Stockwell, T.B.5
Beeson, K.Y.6
Schork, N.J.7
Murray, S.S.8
Topol, E.J.9
Levy, S.10
-
145
-
-
84865992574
-
A survey of error-correction methods for next-generation sequencing
-
Yang, X., Chockalingam, S.P. and Aluru, S. (2013) A survey of error-correction methods for next-generation sequencing. Brief. Bioinform., 14, 56-66.
-
(2013)
Brief. Bioinform.
, vol.14
, pp. 56-66
-
-
Yang, X.1
Chockalingam, S.P.2
Aluru, S.3
-
146
-
-
84860756398
-
Performance comparison of benchtop high-throughput sequencing platforms
-
Loman, N.J., Misra, R.V., Dallman, T.J., Constantinidou, C., Gharbia, S.E., Wain, J. and Pallen, M.J. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol., 30, 434-439.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 434-439
-
-
Loman, N.J.1
Misra, R.V.2
Dallman, T.J.3
Constantinidou, C.4
Gharbia, S.E.5
Wain, J.6
Pallen, M.J.7
-
147
-
-
84960345468
-
Illumina error profiles: Resolving fine-scale variation in metagenomic sequencing data
-
Schirmer, M., D'Amore, R., Ijaz, U.Z., Hall, N. and Quince, C. (2016) Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics, 17, doi:10.1186/s12859-016-0976-y.
-
(2016)
BMC Bioinformatics
, vol.17
-
-
Schirmer, M.1
D'Amore, R.2
Ijaz, U.Z.3
Hall, N.4
Quince, C.5
-
148
-
-
84962019811
-
Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells
-
Beltman, J.B., Urbanus, J., Velds, A., van Rooij, N., Rohr, J.C., Naik, S.H. and Schumacher, T.N. (2016) Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells. BMC Bioinformatics, 17, doi:10.1186/s12859-016-0999-4.
-
(2016)
BMC Bioinformatics
, vol.17
-
-
Beltman, J.B.1
Urbanus, J.2
Velds, A.3
Van Rooij, N.4
Rohr, J.C.5
Naik, S.H.6
Schumacher, T.N.7
-
149
-
-
34948842866
-
Accuracy and quality of massively parallel DNA pyrosequencing
-
Huse, S.M., Huber, J.A., Morrison, H.G., Sogin, M.L. and Welch, D.M. (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol., 8, doi:10.1186/gb-2007-8-7-r143.
-
(2007)
Genome Biol.
, vol.8
-
-
Huse, S.M.1
Huber, J.A.2
Morrison, H.G.3
Sogin, M.L.4
Welch, D.M.5
-
150
-
-
84856770811
-
Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample
-
Luo, C., Tsementzi, D., Kyrpides, N., Read, T. and Konstantinidis, K.T. (2012) Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One, 7, e30087.
-
(2012)
PLoS One
, vol.7
-
-
Luo, C.1
Tsementzi, D.2
Kyrpides, N.3
Read, T.4
Konstantinidis, K.T.5
-
152
-
-
75949108066
-
Galaxy: A web-based genome analysis tool for experimentalists
-
Blankenberg, D., Kuster, G.V., 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., doi:10.1002/0471142727.mb1910s89.
-
(2010)
Curr. Protoc. Mol. Biol.
-
-
Blankenberg, D.1
Kuster, G.V.2
Coraor, N.3
Ananda, G.4
Lazarus, R.5
Mangan, M.6
Nekrutenko, A.7
Taylor, J.8
-
153
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
-
(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
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
-
154
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks, J., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, doi:10.1101/gr.4086505.
-
(2010)
Genome Biol.
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
155
-
-
84897493652
-
ERNA: A graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing
-
Yuan, T., Huang, X., Dittmar, R.L., Du, M., Kohli, M., Boardman, L., Thibodeau, S.N. and Wang, L. (2014) eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. BMC Genomics, 15, doi:10.1186/1471-2164-15-176.
-
(2014)
BMC Genomics
, vol.15
-
-
Yuan, T.1
Huang, X.2
Dittmar, R.L.3
Du, M.4
Kohli, M.5
Boardman, L.6
Thibodeau, S.N.7
Wang, L.8
-
156
-
-
58849112575
-
Biogenesis of small RNAs in animals
-
Kim, V.N., Han, J. and Siomi, M.C. (2009) Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol., 10, 126-139.
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 126-139
-
-
Kim, V.N.1
Han, J.2
Siomi, M.C.3
-
157
-
-
84955353582
-
SAMSVM: A tool for misalignment filtration of SAM-format sequences with support vector machine
-
Yang, J., Ding, X., Sun, X., Tsang, S.-Y. and Xue, H. (2015) SAMSVM: A tool for misalignment filtration of SAM-format sequences with support vector machine. J. Bioinform. Comput. Biol., 13, doi:10.1142/s0219720015500250.
-
(2015)
J. Bioinform. Comput. Biol.
, vol.13
-
-
Yang, J.1
Ding, X.2
Sun, X.3
Tsang, S.-Y.4
Xue, H.5
-
158
-
-
84878629521
-
Benchmarking short sequence mapping tools
-
Hatem, A., Bozdaǧ, D., Toland, A.E. and Çatalyürek, Ü.V. (2013) Benchmarking short sequence mapping tools. BMC Bioinformatics, 14, doi:10.1186/1471-2105-14-184.
-
(2013)
BMC Bioinformatics
, vol.14
-
-
Hatem, A.1
Bozdaǧ, D.2
Toland, A.E.3
Çatalyürek, U.V.4
-
159
-
-
79960698975
-
Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
-
Kong, Y. (2011) Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics, 98, 152-153.
-
(2011)
Genomics
, vol.98
, pp. 152-153
-
-
Kong, Y.1
-
160
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17, 10-12.
-
(2011)
EMBnet.journal
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
161
-
-
84923867589
-
Rapid evaluation and quality control of next generation sequencing data with FaQCs
-
Lo, C.-C. and Chain, P.S.G. (2014) Rapid evaluation and quality control of next generation sequencing data with FaQCs. BMC Bioinformatics, 15, doi:10.1186/s12859-014-0366-2.
-
(2014)
BMC Bioinformatics
, vol.15
-
-
Lo, C.-C.1
Chain, P.S.G.2
-
162
-
-
78649358717
-
Quake: Quality-aware detection and correction of sequencing errors
-
Kelley, D.R., Schatz, M.C. and Salzberg, S.L. (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biol., 11, doi:10.1186/gb-2010-11-11-r116.
-
(2010)
Genome Biol.
, vol.11
-
-
Kelley, D.R.1
Schatz, M.C.2
Salzberg, S.L.3
-
163
-
-
79952178131
-
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
-
Gnerre, S., Maccallum, I., Przybylski, D., Ribeiro, F.J., Burton, J.N., Walker, B.J., Sharpe, T., Hall, G., Shea, T.P., Sykes, S. et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl. Acad. Sci. U.S.A., 108, 1513-1518.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 1513-1518
-
-
Gnerre, S.1
Maccallum, I.2
Przybylski, D.3
Ribeiro, F.J.4
Burton, J.N.5
Walker, B.J.6
Sharpe, T.7
Hall, G.8
Shea, T.P.9
Sykes, S.10
-
164
-
-
78049346632
-
De novo assembly and analysis of RNA-seq data
-
Robertson, G., Schein, J., Chiu, R., Corbett, R., Field, M., Jackman, S.D., Mungall, K., Lee, S., Okada, H.M., Qian, J.Q. et al. (2010) De novo assembly and analysis of RNA-seq data. Nat. Methods, 7, 909-912.
-
(2010)
Nat. Methods
, vol.7
, pp. 909-912
-
-
Robertson, G.1
Schein, J.2
Chiu, R.3
Corbett, R.4
Field, M.5
Jackman, S.D.6
Mungall, K.7
Lee, S.8
Okada, H.M.9
Qian, J.Q.10
-
165
-
-
84893443187
-
An extensive evaluation of read trimming effects on Illumina NGS data analysis
-
Del Fabbro, C., Scalabrin, S., Morgante, M. and Giorgi, F.M. (2013) An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One, 8, e85024.
-
(2013)
PLoS One
, vol.8
-
-
Del Fabbro, C.1
Scalabrin, S.2
Morgante, M.3
Giorgi, F.M.4
-
166
-
-
77957151956
-
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
-
Cox, M.P., Peterson, D.A. and Biggs, P.J. (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics, 11, doi:10.1186/1471-2105-11-485.
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Cox, M.P.1
Peterson, D.A.2
Biggs, P.J.3
-
167
-
-
84899995586
-
Software for pre-processing Illumina next-generation sequencing short read sequences
-
Chen, C., Khaleel, S.S., Huang, H. and Wu, C.H. (2014) Software for pre-processing Illumina next-generation sequencing short read sequences. Source Code Biol. Med., 9, doi:10.1186/1751-0473-9-8.
-
(2014)
Source Code Biol. Med.
, vol.9
-
-
Chen, C.1
Khaleel, S.S.2
Huang, H.3
Wu, C.H.4
-
168
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
170
-
-
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, doi:10.1186/gb-2009-10-3-r25.
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
171
-
-
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
-
172
-
-
67650711615
-
SOAP2: An improved ultrafast tool for short read alignment
-
Li, R., Yu, C., Li, Y., Lam, T.-W., Yiu, S.-M., Kristiansen, K. and Wang, J. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
-
(2009)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
Yu, C.2
Li, Y.3
Lam, T.-W.4
Yiu, S.-M.5
Kristiansen, K.6
Wang, J.7
-
173
-
-
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
-
174
-
-
79959640102
-
Evaluation of next-generation sequencing software in mapping and assembly
-
Bao, S., Jiang, R., Kwan, W., Wang, B., Ma, X. and Song, Y.-Q. (2011) Evaluation of next-generation sequencing software in mapping and assembly. J. Hum. Genet., 56, 406-414.
-
(2011)
J. Hum. Genet.
, vol.56
, pp. 406-414
-
-
Bao, S.1
Jiang, R.2
Kwan, W.3
Wang, B.4
Ma, X.5
Song, Y.-Q.6
-
175
-
-
84855722896
-
BarraCUDA - A fast short read sequence aligner using graphics processing units
-
Klus, P., Lam, S., Lyberg, D., Cheung, M., Pullan, G., McFarlane, I., Yeo, G.S.H. and Lam, B.Y.H. (2012) BarraCUDA-a fast short read sequence aligner using graphics processing units. BMC Res. Notes, 5, doi:10.1186/1756-0500-5-27.
-
(2012)
BMC Res. Notes
, vol.5
-
-
Klus, P.1
Lam, S.2
Lyberg, D.3
Cheung, M.4
Pullan, G.5
McFarlane, I.6
Yeo, G.S.H.7
Lam, B.Y.H.8
-
176
-
-
84878532952
-
SOAP3-dp: Fast, accurate and sensitive GPU-based short read aligner
-
Luo, R., Wong, T., Zhu, J., Liu, C.-M., Zhu, X., Wu, E., Lee, L.-K., Lin, H., Zhu, W., Cheung, D.W. et al. (2013) SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner. PLoS One, 8, e65632.
-
(2013)
PLoS One
, vol.8
-
-
Luo, R.1
Wong, T.2
Zhu, J.3
Liu, C.-M.4
Zhu, X.5
Wu, E.6
Lee, L.-K.7
Lin, H.8
Zhu, W.9
Cheung, D.W.10
-
177
-
-
84977534075
-
MICA: A fast short-read aligner that takes full advantage of many integrated core architecture (MIC)
-
Luo, R., Cheung, J., Wu, E., Wang, H., Chan, S.-H., Law, W.-C., He, G., Yu, C., Liu, C.-M., Zhou, D. et al. (2015) MICA: a fast short-read aligner that takes full advantage of many integrated core architecture (MIC). BMC Bioinformatics, 16, doi:10.1186/1471-2105-16-s7-s10.
-
(2015)
BMC Bioinformatics
, vol.16
-
-
Luo, R.1
Cheung, J.2
Wu, E.3
Wang, H.4
Chan, S.-H.5
Law, W.-C.6
He, G.7
Yu, C.8
Liu, C.-M.9
Zhou, D.10
-
179
-
-
84891818318
-
MiRBase: Annotating high confidence microRNAs using deep sequencing data
-
Kozomara, A. and Griffiths-Jones, S. (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res., 42, D68-D73.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D68-D73
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
180
-
-
84946094179
-
Rfam 12.0: Updates to the RNA families database
-
Nawrocki, E.P., Burge, S.W., Bateman, A., Daub, J., Eberhardt, R.Y., Eddy, S.R., Floden, E.W., Gardner, P.P., Jones, T.A., Tate, J. et al. (2015) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res., 43, D130-D137.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D130-D137
-
-
Nawrocki, E.P.1
Burge, S.W.2
Bateman, A.3
Daub, J.4
Eberhardt, R.Y.5
Eddy, S.R.6
Floden, E.W.7
Gardner, P.P.8
Jones, T.A.9
Tate, J.10
-
181
-
-
78650563218
-
Methods for allocating ambiguous short-reads
-
Lipson, D., Speed, T.P. and Taub, M. (2010) Methods for allocating ambiguous short-reads. Commun. Inform. Syst., 10, 69-82.
-
(2010)
Commun. Inform. Syst.
, vol.10
, pp. 69-82
-
-
Lipson, D.1
Speed, T.P.2
Taub, M.3
-
182
-
-
77949507153
-
RNA-Seq gene expression estimation with read mapping uncertainty
-
Li, B., Ruotti, V., Stewart, R.M., Thomson, J.A. and Dewey, C.N. (2010) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics, 26, 493-500.
-
(2010)
Bioinformatics
, vol.26
, pp. 493-500
-
-
Li, B.1
Ruotti, V.2
Stewart, R.M.3
Thomson, J.A.4
Dewey, C.N.5
-
183
-
-
83655163970
-
BM-map: Bayesian mapping of multireads for next-generation sequencing data
-
Ji, Y., Xu, Y., Zhang, Q., Tsui, K.-W., Yuan, Y., Norris, C., Liang, S. and Liang, H. (2011) BM-map: Bayesian mapping of multireads for next-generation sequencing data. Biometrics, 67, 1215-1224.
-
(2011)
Biometrics
, vol.67
, pp. 1215-1224
-
-
Ji, Y.1
Xu, Y.2
Zhang, Q.3
Tsui, K.-W.4
Yuan, Y.5
Norris, C.6
Liang, S.7
Liang, H.8
-
184
-
-
79952097693
-
Next generation sequencing of miRNAs - Strategies, resources and methods
-
Motameny, S., Wolters, S., Nürnberg, P. and Schumacher, B. (2010) Next generation sequencing of miRNAs-strategies, resources and methods. Genes, 1, 70-84.
-
(2010)
Genes
, vol.1
, pp. 70-84
-
-
Motameny, S.1
Wolters, S.2
Nürnberg, P.3
Schumacher, B.4
-
185
-
-
84899895387
-
A challenge for miRNA: Multiple isomiRs in miRNAomics
-
Guo, L. and Chen, F. (2014) A challenge for miRNA: multiple isomiRs in miRNAomics. Gene, 544, 1-7.
-
(2014)
Gene
, vol.544
, pp. 1-7
-
-
Guo, L.1
Chen, F.2
-
186
-
-
84855168259
-
MicroRNAs and their isomiRs function cooperatively to target common biological pathways
-
Cloonan, N., Wani, S., Xu, Q., Gu, J., Lea, K., Heater, S., Barbacioru, C., Steptoe, A.L., Martin, H.C., Nourbakhsh, E. et al. (2011) MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol., 12, doi:10.1186/gb-2011-12-12-r126.
-
(2011)
Genome Biol.
, vol.12
-
-
Cloonan, N.1
Wani, S.2
Xu, Q.3
Gu, J.4
Lea, K.5
Heater, S.6
Barbacioru, C.7
Steptoe, A.L.8
Martin, H.C.9
Nourbakhsh, E.10
-
187
-
-
84867736206
-
IsomiRs - The overlooked repertoire in the dynamic microRNAome
-
Neilsen, C.T., Goodall, G.J. and Bracken, C.P. (2012) IsomiRs-the overlooked repertoire in the dynamic microRNAome. Trends Genet., 28, 544-549.
-
(2012)
Trends Genet.
, vol.28
, pp. 544-549
-
-
Neilsen, C.T.1
Goodall, G.J.2
Bracken, C.P.3
-
188
-
-
38549141630
-
PiRNABank: A web resource on classified and clustered Piwi-interacting RNAs
-
Sai Lakshmi, S. and Agrawal, S. (2008) piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Nucleic Acids Res., 36, D173-D177.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D173-D177
-
-
Sai Lakshmi, S.1
Agrawal, S.2
-
189
-
-
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
-
190
-
-
84883368195
-
Software for computing and annotating genomic ranges
-
Lawrence, M., Huber, W., Pagès, H., Aboyoun, P., Carlson, M., Gentleman, R., Morgan, M.T. and Carey, V.J. (2013) Software for computing and annotating genomic ranges. PLoS Comput. Biol., 9, e1003118.
-
(2013)
PLoS Comput. Biol.
, vol.9
-
-
Lawrence, M.1
Huber, W.2
Pagès, H.3
Aboyoun, P.4
Carlson, M.5
Gentleman, R.6
Morgan, M.T.7
Carey, V.J.8
-
191
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
-
(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
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
192
-
-
84898618335
-
Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells
-
Zhao, S., Fung-Leung, W.-P., Bittner, A., Ngo, K. and Liu, X. (2014) Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One, 9, e78644.
-
(2014)
PLoS One
, vol.9
-
-
Zhao, S.1
Fung-Leung, W.-P.2
Bittner, A.3
Ngo, K.4
Liu, X.5
-
193
-
-
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
-
194
-
-
83455238345
-
GC-content normalization for RNA-Seq data
-
Risso, D., Schwartz, K., Sherlock, G. and Dudoit, S. (2011) GC-content normalization for RNA-Seq data. BMC Bioinformatics, 12, doi:10.1186/1471-2105-12-480.
-
(2011)
BMC Bioinformatics
, vol.12
-
-
Risso, D.1
Schwartz, K.2
Sherlock, G.3
Dudoit, S.4
-
195
-
-
65649126066
-
Transcript length bias in RNA-seq data confounds systems biology
-
Oshlack, A. and Wakefield, M.J. (2009) Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct, 4, doi:10.1186/1745-6150-4-14.
-
(2009)
Biol. Direct
, vol.4
-
-
Oshlack, A.1
Wakefield, M.J.2
-
196
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
-
Bullard, J.H., Purdom, E., Hansen, K.D. and Dudoit, S. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics, 11, doi:10.1186/1471-2105-11-94.
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Bullard, J.H.1
Purdom, E.2
Hansen, K.D.3
Dudoit, S.4
-
197
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
198
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
Robinson, M.D. and Oshlack, A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol., 11, doi:10.1186/gb-2010-11-3-r25.
-
(2010)
Genome Biol.
, vol.11
-
-
Robinson, M.D.1
Oshlack, A.2
-
199
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, doi:10.1186/gb-2010-11-10-r106.
-
(2010)
Genome Biol.
, vol.11
-
-
Anders, S.1
Huber, W.2
-
200
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M.I., Huber, W. and Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, doi:10.1186/s13059-014-0550-8.
-
(2014)
Genome Biol.
, vol.15
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
201
-
-
84925226706
-
Svaseq: Removing batch effects and other unwanted noise from sequencing data
-
Leek, J.T. (2014) svaseq: removing batch effects and other unwanted noise from sequencing data. Nucleic Acids Res., 42, e161.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. e161
-
-
Leek, J.T.1
-
202
-
-
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. Brief. Bioinform., 14, 671-683.
-
(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
Keime, C.7
Marot, G.8
Castel, D.9
Estelle, J.10
-
203
-
-
84934326250
-
The impact of normalization methods on RNA-Seq data analysis
-
Zyprych-Walczak, J., Szabelska, A., Handschuh, L., Górczak, K., Klamecka, K., Figlerowicz, M. and Siatkowski, I. (2015) The impact of normalization methods on RNA-Seq data analysis. Biomed Res. Int., 2015, doi:10.1155/2015/621690.
-
(2015)
Biomed Res. Int.
, vol.2015
-
-
Zyprych-Walczak, J.1
Szabelska, A.2
Handschuh, L.3
Górczak, K.4
Klamecka, K.5
Figlerowicz, M.6
Siatkowski, I.7
-
204
-
-
84863453861
-
Technical and biological variance structure in mRNA-Seq data: Life in the real world
-
Oberg, A.L., Bot, B.M., Grill, D.E., Poland, G.A. and Therneau, T.M. (2012) Technical and biological variance structure in mRNA-Seq data: life in the real world. BMC Genomics, 13, doi:10.1186/1471-2164-13-304.
-
(2012)
BMC Genomics
, vol.13
-
-
Oberg, A.L.1
Bot, B.M.2
Grill, D.E.3
Poland, G.A.4
Therneau, T.M.5
-
205
-
-
79958115654
-
A two-stage poisson model for testing RNA-Seq data
-
Auer, P.L. and Doerge, R.W. (2011) A two-stage poisson model for testing RNA-Seq data. Stat. Appl. Genet. Mol. Biol., 10, doi:10.2202/1544-6115.1627.
-
(2011)
Stat. Appl. Genet. Mol. Biol.
, vol.10
-
-
Auer, P.L.1
Doerge, R.W.2
-
206
-
-
79958117254
-
The NBP negative binomial model for assessing differential gene expression from RNA-Seq
-
Di, Y., Schafer, D.W., Cumbie, J.S. and Chang, J.H. (2011) The NBP negative binomial model for assessing differential gene expression from RNA-Seq. Stat. Appl. Genet. Mol. Biol., 10, doi:10.2202/1544-6115.1637.
-
(2011)
Stat. Appl. Genet. Mol. Biol.
, vol.10
-
-
Di, Y.1
Schafer, D.W.2
Cumbie, J.S.3
Chang, J.H.4
-
207
-
-
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
-
208
-
-
84876263777
-
EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments
-
Leng, N., Dawson, J.A., Thomson, J.A., Ruotti, V., Rissman, A.I., Smits, B.M.G., Haag, J.D., Gould, M.N., Stewart, R.M. and Kendziorski, C. (2013) EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics, 29, 1035-1043.
-
(2013)
Bioinformatics
, vol.29
, pp. 1035-1043
-
-
Leng, N.1
Dawson, J.A.2
Thomson, J.A.3
Ruotti, V.4
Rissman, A.I.5
Smits, B.M.G.6
Haag, J.D.7
Gould, M.N.8
Stewart, R.M.9
Kendziorski, C.10
-
209
-
-
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, doi:10.1186/1471-2105-11-422.
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Hardcastle, T.J.1
Kelly, K.A.2
-
210
-
-
84886557480
-
Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data
-
Li, J. and Tibshirani, R. (2013) Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat. Methods Med. Res., 22, 519-536.
-
(2013)
Stat. Methods Med. Res.
, vol.22
, pp. 519-536
-
-
Li, J.1
Tibshirani, R.2
-
211
-
-
84983732319
-
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package
-
Tarazona, S., Furi ó-Tarí, P., Turrà, D., Di Pietro, A., Nueda, M.J., Ferrer, A. and Conesa, A. (2015) Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package. Nucleic Acids Res., 43, e140.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. e140
-
-
Tarazona, S.1
Furió-Tarí, P.2
Turrà, D.3
Di Pietro, A.4
Nueda, M.J.5
Ferrer, A.6
Conesa, A.7
-
212
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth, G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, doi:10.2202/1544-6115.1027.
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
-
-
Smyth, G.K.1
-
213
-
-
84926507971
-
Limma powers differential expression analyses for RNA-sequencing and microarray studies
-
Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W. and Smyth, G.K. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, e47.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. e47
-
-
Ritchie, M.E.1
Phipson, B.2
Wu, D.3
Hu, Y.4
Law, C.W.5
Shi, W.6
Smyth, G.K.7
-
214
-
-
84896735766
-
Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
-
Law, C.W., Chen, Y., Shi, W. and Smyth, G.K. (2014) voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol., 15, doi:10.1186/gb-2014-15-2-r29.
-
(2014)
Genome Biol.
, vol.15
-
-
Law, C.W.1
Chen, Y.2
Shi, W.3
Smyth, G.K.4
-
215
-
-
84982781651
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B, 57, 289-300.
-
(1995)
J. R. Stat. Soc. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
216
-
-
84874677498
-
A comparison of methods for differential expression analysis of RNA-seq data
-
Soneson, C. and Delorenzi, M. (2013) A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics, 14, doi:10.1186/1471-2105-14-91.
-
(2013)
BMC Bioinformatics
, vol.14
-
-
Soneson, C.1
Delorenzi, M.2
-
217
-
-
84883644707
-
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
-
Rapaport, F., Khanin, R., Liang, Y., Pirun, M., Krek, A., Zumbo, P., Mason, C.E., Socci, N.D. and Betel, D. (2013) Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol., 14, doi:10.1186/gb-2013-14-9-r95.
-
(2013)
Genome Biol.
, vol.14
-
-
Rapaport, F.1
Khanin, R.2
Liang, Y.3
Pirun, M.4
Krek, A.5
Zumbo, P.6
Mason, C.E.7
Socci, N.D.8
Betel, D.9
-
218
-
-
84928199480
-
Comparison of software packages for detecting differential expression in RNA-seq studies
-
Seyednasrollah, F., Laiho, A. and Elo, L.L. (2015) Comparison of software packages for detecting differential expression in RNA-seq studies. Brief. Bioinformatics, 16, 59-70.
-
(2015)
Brief. Bioinformatics
, vol.16
, pp. 59-70
-
-
Seyednasrollah, F.1
Laiho, A.2
Elo, L.L.3
-
219
-
-
84945184668
-
Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns
-
Moulos, P. and Hatzis, P. (2015) Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns. Nucleic Acids Res., 43, e25.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. e25
-
-
Moulos, P.1
Hatzis, P.2
-
220
-
-
85017389483
-
Biomarkers discovery through multivariate statistical methods: A review of recently developed methods and applications in proteomics
-
Marcello Manfredi, E.R. (2013) Biomarkers discovery through multivariate statistical methods: a review of recently developed methods and applications in proteomics. J. Proteomics Bioinform., s3, doi:10.4172/jpb.S3-003.
-
(2013)
J. Proteomics Bioinform., S
, vol.3
-
-
Marcello Manfredi, E.R.1
-
221
-
-
9944247186
-
Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm)
-
Eriksson, L., Antti, H., Gottfries, J., Holmes, E., Johansson, E., Lindgren, F., Long, I., Lundstedt, T., Trygg, J. and Wold, S. (2004) Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm). Anal. Bioanal. Chem., 380, 419-429.
-
(2004)
Anal. Bioanal. Chem.
, vol.380
, pp. 419-429
-
-
Eriksson, L.1
Antti, H.2
Gottfries, J.3
Holmes, E.4
Johansson, E.5
Lindgren, F.6
Long, I.7
Lundstedt, T.8
Trygg, J.9
Wold, S.10
-
222
-
-
0035108235
-
A hierarchical unsupervised growing neural network for clustering gene expression patterns
-
Herrero, J., Valencia, A. and Dopazo, J. (2001) A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics, 17, 126-136.
-
(2001)
Bioinformatics
, vol.17
, pp. 126-136
-
-
Herrero, J.1
Valencia, A.2
Dopazo, J.3
-
223
-
-
0011646341
-
Estimating transformations for regression via additivity and variance stabilization
-
Tibshirani, R. (1988) Estimating transformations for regression via additivity and variance stabilization. J. Am. Stat. Assoc., 83, 394-405.
-
(1988)
J. Am. Stat. Assoc.
, vol.83
, pp. 394-405
-
-
Tibshirani, R.1
-
224
-
-
34249847958
-
PcaMethods - A bioconductor package providing PCA methods for incomplete data
-
Stacklies, W., Redestig, H., Scholz, M., Walther, D. and Selbig, J. (2007) pcaMethods-a bioconductor package providing PCA methods for incomplete data. Bioinformatics, 23, 1164-1167.
-
(2007)
Bioinformatics
, vol.23
, pp. 1164-1167
-
-
Stacklies, W.1
Redestig, H.2
Scholz, M.3
Walther, D.4
Selbig, J.5
-
225
-
-
70350694448
-
IntegrOmics: An R package to unravel relationships between two omics datasets
-
Le Cao, K.A., Gonzalez, I. and Dejean, S. (2009) integrOmics: an R package to unravel relationships between two omics datasets. Bioinformatics, 25, 2855-2856.
-
(2009)
Bioinformatics
, vol.25
, pp. 2855-2856
-
-
Le Cao, K.A.1
Gonzalez, I.2
Dejean, S.3
-
226
-
-
0036798238
-
Judging the quality of gene expression-based clustering methods using gene annotation
-
Gibbons, F.D. and Roth, F.P. (2002) Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res., 12, 1574-1581.
-
(2002)
Genome Res.
, vol.12
, pp. 1574-1581
-
-
Gibbons, F.D.1
Roth, F.P.2
-
227
-
-
77949269457
-
Gene expression profiling-clusters of possibilities
-
Bergkvist, A., Rusnakova, V., Sindelka, R., Garda, J.M., Sjogreen, B., Lindh, D., Forootan, A. and Kubista, M. (2010) Gene expression profiling-clusters of possibilities. Methods, 50, 323-335.
-
(2010)
Methods
, vol.50
, pp. 323-335
-
-
Bergkvist, A.1
Rusnakova, V.2
Sindelka, R.3
Garda, J.M.4
Sjogreen, B.5
Lindh, D.6
Forootan, A.7
Kubista, M.8
-
228
-
-
38049025722
-
Multivariate analysis of complex gene expression and clinical phenotypes with genetic marker data
-
Beyene, J., Tritchler, D., Bull, S.B., Cartier, K.C., Jonasdottir, G., Kraja, A.T., Li, N., Nock, N.L., Parkhomenko, E., Rao, J.S. et al. (2007) Multivariate analysis of complex gene expression and clinical phenotypes with genetic marker data. Genet. Epidemiol., 31(Suppl. 1), S103-S109.
-
(2007)
Genet. Epidemiol.
, vol.31
, pp. S103-S109
-
-
Beyene, J.1
Tritchler, D.2
Bull, S.B.3
Cartier, K.C.4
Jonasdottir, G.5
Kraja, A.T.6
Li, N.7
Nock, N.L.8
Parkhomenko, E.9
Rao, J.S.10
-
229
-
-
11344295027
-
Comparative analysis of clustering methods for gene expression time course data
-
Costa, I.G., Carvalho, F.d.A.T.d. and Souto, M.C.P.d. (2004) Comparative analysis of clustering methods for gene expression time course data. Genet. Mol. Biol., 27, 623-631.
-
(2004)
Genet. Mol. Biol.
, vol.27
, pp. 623-631
-
-
Costa, I.G.1
Carvalho, F.D.A.T.D.2
Souto, M.C.P.D.3
-
230
-
-
33644914709
-
The real-time polymerase chain reaction
-
Kubista, M., Andrade, J.M., Bengtsson, M., Forootan, A., Jonak, J., Lind, K., Sindelka, R., Sjoback, R., Sjogreen, B., Strombom, L. et al. (2006) The real-time polymerase chain reaction. Mol. Aspects Med., 27, 95-125.
-
(2006)
Mol. Aspects Med.
, vol.27
, pp. 95-125
-
-
Kubista, M.1
Andrade, J.M.2
Bengtsson, M.3
Forootan, A.4
Jonak, J.5
Lind, K.6
Sindelka, R.7
Sjoback, R.8
Sjogreen, B.9
Strombom, L.10
-
231
-
-
49249124314
-
Investigating the efficacy of nonlinear dimensionality reduction schemes in classifying gene and protein expression studies
-
Lee, G., Rodriguez, C. and Madabhushi, A. (2008) Investigating the efficacy of nonlinear dimensionality reduction schemes in classifying gene and protein expression studies. IEEE/ACM Trans. Comput. Biol. Bioinform., 5, 368-384.
-
(2008)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.5
, pp. 368-384
-
-
Lee, G.1
Rodriguez, C.2
Madabhushi, A.3
-
232
-
-
12244254135
-
Multi-and megavariate data analysis. Principles and applications
-
I. Eriksson, E. Johansson, N. Kettaneh-Wold and S. Wold, Umetrics Academy, Umeå 533
-
Shaffer, R.E. (2002) Multi-and megavariate data analysis. Principles and applications, I. Eriksson, E. Johansson, N. Kettaneh-Wold and S. Wold, Umetrics Academy, Umeå, 2001, ISBN 91-973730-1-X, 533pp. J. Chemom., 16, 261-262.
-
(2001)
J. Chemom.
, vol.16
, pp. 261-262
-
-
Shaffer, R.E.1
-
233
-
-
0037350844
-
Partial least squares for discrimination
-
Barker, M. and Rayens, W. (2003) Partial least squares for discrimination. J. Chemom., 17, 166-173.
-
(2003)
J. Chemom.
, vol.17
, pp. 166-173
-
-
Barker, M.1
Rayens, W.2
-
234
-
-
79959258968
-
Sparse PLS discriminant analysis: Biologically relevant feature selection and graphical displays for multiclass problems
-
Le Cao, K.A., Boitard, S. and Besse, P. (2011) Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems. BMC Bioinformatics, 12, doi:10.1186/1471-2105-12-253.
-
(2011)
BMC Bioinformatics
, vol.12
-
-
Le Cao, K.A.1
Boitard, S.2
Besse, P.3
-
235
-
-
0036083139
-
Orthogonal projections to latent structures (O-PLS)
-
Trygg, J. and Wold, S. (2002) Orthogonal projections to latent structures (O-PLS). J. Chemom., 16, 119-128.
-
(2002)
J. Chemom.
, vol.16
, pp. 119-128
-
-
Trygg, J.1
Wold, S.2
-
236
-
-
34347262093
-
PLS and dimension reduction for classification
-
Liu, Y. and Rayens, W. (2007) PLS and dimension reduction for classification. Comput. Stat., 22, 189-208.
-
(2007)
Comput. Stat.
, vol.22
, pp. 189-208
-
-
Liu, Y.1
Rayens, W.2
-
237
-
-
64849110688
-
Discriminating variable test and selectivity ratio plot: Quantitative tools for interpretation and variable (biomarker) selection in complex spectral or chromatographic profiles
-
Rajalahti, T., Arneberg, R., Kroksveen, A.C., Berle, M., Myhr, K.-M. and Kvalheim, O.M. (2009) Discriminating variable test and selectivity ratio plot: quantitative tools for interpretation and variable (biomarker) selection in complex spectral or chromatographic profiles. Anal. Chem., 81, 2581-2590.
-
(2009)
Anal. Chem.
, vol.81
, pp. 2581-2590
-
-
Rajalahti, T.1
Arneberg, R.2
Kroksveen, A.C.3
Berle, M.4
Myhr, K.-M.5
Kvalheim, O.M.6
-
238
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
Lewis, B.P., Burge, C.B. and Bartel, D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
239
-
-
60149095444
-
Most mammalian mRNAs are conserved targets of microRNAs
-
Friedman, R.C., Farh, K.K., Burge, C.B. and Bartel, D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
-
(2009)
Genome Res.
, vol.19
, pp. 92-105
-
-
Friedman, R.C.1
Farh, K.K.2
Burge, C.B.3
Bartel, D.P.4
-
240
-
-
38549124383
-
The microRNA.org resource: Targets and expression
-
Betel, D., Wilson, M., Gabow, A., Marks, D.S. and Sander, C. (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res., 36, D149-D153.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D149-D153
-
-
Betel, D.1
Wilson, M.2
Gabow, A.3
Marks, D.S.4
Sander, C.5
-
241
-
-
0842321501
-
MicroRNA targets in Drosophila
-
Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C. and Marks, D.S. (2003) MicroRNA targets in Drosophila. Genome Biol., 5, doi:10.1186/gb-2003-5-1-r1.
-
(2003)
Genome Biol.
, vol.5
-
-
Enright, A.J.1
John, B.2
Gaul, U.3
Tuschl, T.4
Sander, C.5
Marks, D.S.6
-
242
-
-
80051931399
-
A Lasso regression model for the construction of microRNA-target regulatory networks
-
Lu, Y., Zhou, Y., Qu, W., Deng, M. and Zhang, C. (2011) A Lasso regression model for the construction of microRNA-target regulatory networks. Bioinformatics, 27, 2406-2413.
-
(2011)
Bioinformatics
, vol.27
, pp. 2406-2413
-
-
Lu, Y.1
Zhou, Y.2
Qu, W.3
Deng, M.4
Zhang, C.5
-
243
-
-
84921424760
-
Posttranscriptional regulatory networks: From expression profiling to integrative analysis of mRNA and microRNA data
-
Meyer, S.U., Stoecker, K., Sass, S., Theis, F.J. and Pfaffl, M.W. (2014) Posttranscriptional regulatory networks: from expression profiling to integrative analysis of mRNA and microRNA data. Methods Mol. Biol., 1160, 165-188.
-
(2014)
Methods Mol. Biol.
, vol.1160
, pp. 165-188
-
-
Meyer, S.U.1
Stoecker, K.2
Sass, S.3
Theis, F.J.4
Pfaffl, M.W.5
-
244
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
245
-
-
84943193527
-
Integrative analysis of microRNA and mRNA data reveals an orchestrated function of microRNAs in skeletal myocyte differentiation in response to TNF-alpha or IGF1
-
Meyer, S.U., Sass, S., Mueller, N.S., Krebs, S., Bauersachs, S., Kaiser, S., Blum, H., Thirion, C., Krause, S., Theis, F.J. et al. (2015) Integrative analysis of microRNA and mRNA data reveals an orchestrated function of microRNAs in skeletal myocyte differentiation in response to TNF-alpha or IGF1. PLoS One, 10, e0135284.
-
(2015)
PLoS One
, vol.10
-
-
Meyer, S.U.1
Sass, S.2
Mueller, N.S.3
Krebs, S.4
Bauersachs, S.5
Kaiser, S.6
Blum, H.7
Thirion, C.8
Krause, S.9
Theis, F.J.10
-
246
-
-
79957578583
-
Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments
-
McCormick, K.P., Willmann, M.R. and Meyers, B.C. (2011) Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence, 2, doi:10.1186/1758-907X-2-2.
-
(2011)
Silence
, vol.2
-
-
McCormick, K.P.1
Willmann, M.R.2
Meyers, B.C.3
-
247
-
-
58749109023
-
Genevestigator v3: A reference expression database for the meta-analysis of transcriptomes
-
Hruz, T., Laule, O., Szabo, G., Wessendorp, F., Bleuler, S., Oertle, L., Widmayer, P., Gruissem, W. and Zimmermann, P. (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv. Bioinformatics, 2008, doi:10.1155/2008/420747.
-
(2008)
Adv. Bioinformatics
, vol.2008
-
-
Hruz, T.1
Laule, O.2
Szabo, G.3
Wessendorp, F.4
Bleuler, S.5
Oertle, L.6
Widmayer, P.7
Gruissem, W.8
Zimmermann, P.9
-
248
-
-
64749094910
-
Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases
-
Zimmermann, P., Laule, O., Schmitz, J., Hruz, T., Bleuler, S. and Gruissem, W. (2008) Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases. Mol. Plant, 1, 851-857.
-
(2008)
Mol. Plant
, vol.1
, pp. 851-857
-
-
Zimmermann, P.1
Laule, O.2
Schmitz, J.3
Hruz, T.4
Bleuler, S.5
Gruissem, W.6
|