-
1
-
-
57049122389
-
A large genome center's improvements to the Illumina sequencing system
-
Quail, M.A., I. Kozarewa, F. Smith, A. Scally, P. J. Stephens, R. Durbin, H. Swerdlow, and D.J. Turner. 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
-
2
-
-
63949083912
-
Amplif-cation-free Illumi na sequencing-l ibrary preparation facilitates improved mapping and assembly of (G+C)-biased genomes
-
Kozarewa, I., Z. Ning, M.A. Quail, M.J. Sanders, M. Berriman, and D.J. Turner. 2009. Amplif-cation-free Illumi na sequencing-l ibrary preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods 6:291-295.
-
(2009)
Nat. Methods
, vol.6
, pp. 291-295
-
-
Kozarewa, I.1
Ning, Z.2
Quail, M.A.3
Sanders, M.J.4
Berriman, M.5
Turner, D.J.6
-
3
-
-
84866953427
-
CEL-Seq: Single-cel l R NA-Seq by multiplexed linear amplifcation
-
Hashimshony, T., F. Wagner, N. Sher, and I. Yanai. 2012. CEL-Seq: single-cel l R NA-Seq by multiplexed linear amplifcation. Cel l Rep 2:666-673.
-
(2012)
Cel L Rep
, vol.2
, pp. 666-673
-
-
Hashimshony, T.1
Wagner, F.2
Sher, N.3
Yanai, I.4
-
4
-
-
84864880991
-
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
-
Ramsköld, D., S. Luo, Y. C. Wa n g, R. Li, Q. Deng, O.R. Faridani, G.A. Daniels, I. Khrebtukova, et al. 2012. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechnol. 30:777-782.
-
(2012)
Nat. Biotechnol
, vol.30
, pp. 777-782
-
-
Ramsköld, D.1
Luo, S.2
Wang, Y.C.3
Li, R.4
Deng, Q.5
Faridani, O.R.6
Daniels, G.A.7
Khrebtukova, I.8
-
5
-
-
84876085773
-
Quartz-Seq: A highly reproducible and sensitive single-cel l R NA sequencing method, revea ls non-genetic gene-expression heterogeneity
-
Sasagawa, Y., I. Nikaido, T. Hayashi, H. Danno, K. D. Uno, T. Imai, and H.R. Ueda. 2013. Quartz-Seq: a highly reproducible and sensitive single-cel l R NA sequencing method, revea ls non-genetic gene-expression heterogeneity. Genome Biol. 14:R31.
-
(2013)
Genome Biol
, vol.14
-
-
Sasagawa, Y.1
Nikaido, I.2
Hayashi, T.3
Danno, H.4
Uno, K.D.5
Imai, T.6
Ueda, H.R.7
-
6
-
-
84872194966
-
Two methods for full-length RNA sequencing for low quantities of cells and single cells
-
Pan, X., R.E. Durrett, H. Zhu, Y. Tanaka, Y. Li, X. Zi, S.L. Marjani, G. Euskirchen, et al. 2013. Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc. Natl. Acad. Sci. USA 110:594-599.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 594-599
-
-
Pan, X.1
Durrett, R.E.2
Zhu, H.3
Tanaka, Y.4
Li, Y.5
Zi, X.6
Marjani, S.L.7
Euskirchen, G.8
-
7
-
-
84877751402
-
Quantitative transcriptomics using designed primer-based amplification
-
Bhargava, V., P. Ko, E. Willems, M. Mercola, and S. Subramaniam. 2013. Quantitative transcriptomics using designed primer-based amplification. Scientific reports 3:1740.
-
(2013)
Scientific Reports
, vol.3
, pp. 1740
-
-
Bhargava, V.1
Ko, P.2
Willems, E.3
Mercola, M.4
Subramaniam, S.5
-
8
-
-
67349146589
-
mRNA-Seq whole-transcriptome analysis of a single cell
-
Tang, F., C. Barbacioru, Y. Wang, E. Nordman, C. Lee, N. Xu, X. Wang, J. Bodeau, et al. 2009. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Met hods 6:377-382.
-
(2009)
Nat. Met Hods
, vol.6
, pp. 377-382
-
-
Tang, F.1
Barbacioru, C.2
Wang, Y.3
Nordman, E.4
Lee, C.5
Xu, N.6
Wang, X.7
Bodeau, J.8
-
9
-
-
79959403670
-
Characterization of the single-cell transcriptional landscape by highly multiplex R NA-seq
-
Islam, S., U. Kjallquist, A. Moliner, P. Zajac, J.B. Fan, P. Lonnerberg, and S. Linnarsson. 2011. Characterization of the single-cell transcriptional landscape by highly multiplex R NA-seq. Genome Res. 21: 1160-1167.
-
(2011)
Genome Res
, vol.21
, pp. 1160-1167
-
-
Islam, S.1
Kjallquist, U.2
Moliner, A.3
Zajac, P.4
Fan, J.B.5
Lonnerberg, P.6
Linnarsson, S.7
-
10
-
-
84871461434
-
Genome-wide detection of single-nucleotide and copy-number variations of a single human cell
-
Zong, C., S. Lu, A.R. Chapman, and X.S. Xie. 2012. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338:1622-1626.
-
(2012)
Science
, vol.338
, pp. 1622-1626
-
-
Zong, C.1
Lu, S.2
Chapman, A.R.3
Xie, X.S.4
-
11
-
-
84864258558
-
Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm
-
Wang, J., H.C. Fan, B. Behr, and S.R. Quake. 2012. Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150:402-412.
-
(2012)
Cell
, vol.150
, pp. 402-412
-
-
Wang, J.1
Fan, H.C.2
Behr, B.3
Quake, S.R.4
-
12
-
-
83055180102
-
Evaluation of a transposase protocol for rapid generation of shotgun high- throughput sequencing libraries from nanogram quantities of DNA
-
Marine, R., S.W. Polson, J. Ravel, G. Hatfull, D. Russell, M. Sullivan, F. Syed, M. Dumas, and K.E. Wommack. 2011. Evaluation of a transposase protocol for rapid generation of shotgun high- throughput sequencing libraries from nanogram quantities of DNA. Appl. Environ. Microbiol. 77:8071-8079.
-
(2011)
Appl. Environ. Microbiol
, vol.77
, pp. 8071-8079
-
-
Marine, R.1
Polson, S.W.2
Ravel, J.3
Hatfull, G.4
Russell, D.5
Sullivan, M.6
Syed, F.7
Dumas, M.8
Wommack, K.E.9
-
13
-
-
82355193803
-
Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing
-
Knierim, E., B. Lucke, J.M. Schwarz, M. Schuelke, and D. Seelow. 2011. Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing. PLoS ONE 6:e28240.
-
(2011)
PLoS ONE
, vol.6
-
-
Knierim, E.1
Lucke, B.2
Schwarz, J.M.3
Schuelke, M.4
Seelow, D.5
-
14
-
-
14944374438
-
Distributions of exons and introns in the human genome
-
Sakharkar, M.K., V.T. Chow, and P. Kangueane. 2004. Distributions of exons and introns in the human genome. In Silico Biol. 4:387-393.
-
(2004)
In Silico Biol
, vol.4
, pp. 387-393
-
-
Sakharkar, M.K.1
Chow, V.T.2
Kangueane, P.3
-
15
-
-
77956340995
-
Comprehensive comparative a na lysis of strand-specifc RNA sequencing methods
-
Levin, J.Z., M. Yassour, X. Adiconis, C. Nusbaum, D. A. Tompson, N. Friedman, A. Gnirke, and A. Regev. 2010. Comprehensive comparative a na lysis of strand-specifc RNA sequencing methods. Nat. Methods 7:709-715.
-
(2010)
Nat. Methods
, vol.7
, pp. 709-715
-
-
Levin, J.Z.1
Yassour, M.2
Adiconis, X.3
Nusbaum, C.4
Tompson, D.A.5
Friedman, N.6
Gnirke, A.7
Regev, A.8
-
16
-
-
69549112743
-
Digital transcriptome profling using selective hexamer priming for cDNA synthesis
-
Armour, C.D., J.C. Castle, R. Chen, T. Babak, P. Loerch, S. Jackson, J.K. Shah, J. Dey, et al. 2009. Digital transcriptome profling using selective hexamer priming for cDNA synthesis. Nat. Methods 6:647-649.
-
(2009)
Nat. Methods
, vol.6
, pp. 647-649
-
-
Armour, C.D.1
Castle, J.C.2
Chen, R.3
Babak, T.4
Loerch, P.5
Jackson, S.6
Shah, J.K.7
Dey, J.8
-
17
-
-
0035046755
-
Reverse transcriptase template switching: A SMART approach for full-length cDNA library construction
-
Zhu, Y.Y., E.M. Machleder, A. Chenchik, R. Li, and P. D. Siebert. 2001. Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques 30:892-897.
-
(2001)
Biotechniques
, vol.30
, pp. 892-897
-
-
Zhu, Y.Y.1
Machleder, E.M.2
Chenchik, A.3
Li, R.4
Siebert, P.D.5
-
18
-
-
79951694175
-
A nalyzing and minimizing PCR amplifcation bias in Illumina sequencing l ibraries
-
Aird, D., M.G. Ross, W. S. Chen, M. Danielsson, T. Fennell, C. Russ, D. B. Jafe, C. Nusbaum, and A. Gnirke. 2011. A nalyzing and minimizing PCR amplifcation bias in Illumina sequencing l ibraries. Genome Biol. 12: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
Jafe, D.B.7
Nusbaum, C.8
Gnirke, A.9
-
19
-
-
84893629592
-
Ligation biasinillumina next-generation DNA libraries: Implications for sequencing ancient genomes
-
Seguin-Orlando, A., M. Schubert, J. Clary, J. Stagegaard, M.T. Alberdi, J.L. Prado, A. Prieto, E. Willerslev, and L. Orlando. 2013. Ligation biasinillumina next-generation DNA libraries: implications for sequencing ancient genomes. PLoS ONE 8:e78575.
-
(2013)
PLoS ONE
, vol.8
-
-
Seguin-Orlando, A.1
Schubert, M.2
Clary, J.3
Stagegaard, J.4
Alberdi, M.T.5
Prado, J.L.6
Prieto, A.7
Willerslev, E.8
Orlando, L.9
-
20
-
-
84857271408
-
Length and GC-biases during sequencing library amplification: A comparison of various polymerase-bufer systems with ancient and modern DNA sequencing libraries
-
Dabney, J. and M. Meyer. 2012. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-bufer 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
-
21
-
-
84855219212
-
Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes
-
Oyola, S.O., T. D. Otto, Y. Gu, G. Maslen, M. Manske, S. Campino, D.J. Turner, B. Macinnis, et al. 2012. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 13:1.
-
(2012)
BMC Genomics
, vol.13
, pp. 1
-
-
Oyola, S.O.1
Otto, T.D.2
Gu, Y.3
Maslen, G.4
Manske, M.5
Campino, S.6
Turner, D.J.7
Macinnis, B.8
-
22
-
-
78649773164
-
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
-
Adey, A., H.G. Morrison, Asan, X. Xun, J.O. Kitzman, E.H. Turner, B. Stackhouse, A.P. MacKenzie, et al. 2010. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol. 11: R119.
-
(2010)
Genome Biol
, vol.11
-
-
Adey, A.1
Morrison, H.G.2
Asan3
Xun, X.4
Kitzman, J.O.5
Turner, E.H.6
Stackhouse, B.7
Mackenzie, A.P.8
-
23
-
-
78651304279
-
Whole-genome molecular haplotyping of single cells
-
Fan, H.C., J. Wang, A. Potanina, and S.R. Quake. 2011. Whole-genome molecular haplotyping of single cells. Nat. Biotechnol. 29: 51-57.
-
(2011)
Nat. Biotechnol
, vol.29
, pp. 51-57
-
-
Fan, H.C.1
Wang, J.2
Potanina, A.3
Quake, S.R.4
-
24
-
-
79953766940
-
Tumour evolution inferred by single-cell sequencing
-
Navin, N., J. Kendall, J. Troge, P. Andrews, L. Rodgers, J. McIndoo, K. Cook, A. Stepansky, et al. 2011. Tumour evolution inferred by single-cell sequencing. Nature 472:90-94.
-
(2011)
Nature
, vol.472
, pp. 90-94
-
-
Navin, N.1
Kendall, J.2
Troge, J.3
Andrews, P.4
Rodgers, L.5
McIndoo, J.6
Cook, K.7
Stepansky, A.8
-
25
-
-
84863338168
-
Direct, genome-wide assessment of DNA mutations in single cells
-
Gundry, M., W. Li, S.B. Maqbool, and J. Vijg. 2012. Direct, genome-wide assessment of DNA mutations in single cells. Nucleic Acids Res. 40:2032-2040.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 2032-2040
-
-
Gundry, M.1
Li, W.2
Maqbool, S.B.3
Vijg, J.4
-
26
-
-
84893594630
-
Genome analyses of single human oocytes
-
Hou, Y., W. Fan, L. Yan, R. Li, Y. Lian, J. Huang, J. Li, L. Xu, et al. 2013. Genome analyses of single human oocytes. Cell 155:1492-1506.
-
(2013)
Cell
, vol.155
, pp. 1492-1506
-
-
Hou, Y.1
Fan, W.2
Yan, L.3
Li, R.4
Lian, Y.5
Huang, J.6
Li, J.7
Xu, L.8
-
27
-
-
0034830935
-
Rapid amplifcation of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplifcation
-
Dean, F. B., J.R. Nelson, T. L. Giesler, and R.S. Lasken. 2001. Rapid amplifcation of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplifcation. Genome Res. 11:1095-1099.
-
(2001)
Genome Res
, vol.11
, pp. 1095-1099
-
-
Dean, F.B.1
Nelson, J.R.2
Giesler, T.L.3
Lasken, R.S.4
-
28
-
-
50849100742
-
Efcient microR NA capture and bar-cod ing via enzymatic oligonucleotide adenylation
-
Vigneault, F., A.M. Sismour, and G.M. Church. 2008. Efcient microR NA capture and bar-cod ing via enzymatic oligonucleotide adenylation. Nat. Methods 5:777-779.
-
(2008)
Nat. Methods
, vol.5
, pp. 777-779
-
-
Vigneault, F.1
Sismour, A.M.2
Church, G.M.3
-
29
-
-
78650281342
-
New methods for next generation sequencing based microRNA expression profling
-
Buermans, H.P., Y. Ariyurek, G. van Ommen, J.T. den Dunnen, and P.A. t'Hoen. 2010. New methods for next generation sequencing based microRNA expression profling. BMC Genomics 11:716.
-
(2010)
BMC Genomics
, vol.11
, pp. 716
-
-
Buermans, H.P.1
Ariyurek, Y.2
van Ommen, G.3
den Dunnen, J.T.4
T'Hoen, P.A.5
-
30
-
-
77955452809
-
Long antisense non-coding RNAs and their role in transcription and oncogenesis
-
Morris, K. V. and P. K. Vogt. 2010. Long antisense non-coding RNAs and their role in transcription and oncogenesis. Cell Cycle 9:2544-2547.
-
(2010)
Cell Cycle
, vol.9
, pp. 2544-2547
-
-
Morris, K.V.1
Vogt, P.K.2
-
31
-
-
84879671055
-
Pervasive transcription of the human genome produces thousands of previously unidentifed long intergenic noncoding R NAs
-
Ha ngauer, M.J., I. W. Vaughn, and M. T. McManus. 2013. Pervasive transcription of the human genome produces thousands of previously unidentifed long intergenic noncoding R NAs. PLoS Genet. 9:e1003569.
-
(2013)
PLoS Genet
, vol.9
-
-
Hangauer, M.J.1
Vaughn, I.W.2
McManus, M.T.3
-
32
-
-
70350653808
-
Transcriptome ana lysis by strand-specific sequencing of complementary DNA
-
Parkhomchuk, D., T. Borodina, V. Amstislavskiy, M. Banaru, L. Hallen, S. K robitsch, H. Lehrach, A. Soldatov. 2009. Transcriptome ana lysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 37: e123.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Parkhomchuk, D.1
Borodina, T.2
Amstislavskiy, V.3
Banaru, M.4
Hallen, L.5
Robitsch, S.K.6
Lehrach, H.7
Soldatov, A.8
-
33
-
-
36148972085
-
Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
-
Perocchi, F., Z. Xu, S. Clauder-Munster, and L.M. Steinmetz. 2007. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res. 35:e128.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Perocchi, F.1
Xu, Z.2
Clauder-Munster, S.3
Steinmetz, L.M.4
-
34
-
-
25444523728
-
Novel isothermal, l inear nucleic acid amplifcation systems for highly multiplexed applications
-
Kurn, N., P. Chen, J.D. Heath, A. Kopf-Sill, K.M. Stephens, and S. Wang. 2005. Novel isothermal, l inear nucleic acid amplifcation systems for highly multiplexed applications. Clin. Chem. 51:1973-1981.
-
(2005)
Clin. Chem
, vol.51
, pp. 1973-1981
-
-
Kurn, N.1
Chen, P.2
Heath, J.D.3
Kopf-Sill, A.4
Stephens, K.M.5
Wang, S.6
-
35
-
-
84902840108
-
Technical variations in low-input RNA-seq methodologies
-
Bhargava, V. H., Ordoukhanian, P; Mercola, M; Subramaniam, S. 2014. Technical variations in low-input RNA-seq methodologies. Sci Rep. 4: 3678.
-
(2014)
Sci Rep
, vol.4
, pp. 3678
-
-
Bhargava, V.H.1
Ordoukhanian, P.2
Mercola, M.3
Subramaniam, S.4
-
36
-
-
84864453787
-
The ribosome profling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
-
Ingolia, N.T., G.A. Brar, S. Rouskin, A.M. McGeachy, and J.S. Weissman. 2012. The ribosome profling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7:1534-1550.
-
(2012)
Nat. Protoc
, vol.7
, pp. 1534-1550
-
-
Ingolia, N.T.1
Brar, G.A.2
Rouskin, S.3
McGeachy, A.M.4
Weissman, J.S.5
-
37
-
-
84880820841
-
Genome-wide annotation and quantitation of translation by ribosome profling
-
Chapter 4:Unit 418
-
Ingolia, N.T., G.A. Brar, S. Rouskin, A.M. McGeachy, and J.S. Weissman. 2013. Genome-wide annotation and quantitation of translation by ribosome profling. Curr Protoc Mol Biol Chapter 4:Unit 418.
-
(2013)
Curr Protoc Mol Biol
-
-
Ingolia, N.T.1
Brar, G.A.2
Rouskin, S.3
McGeachy, A.M.4
Weissman, J.S.5
-
38
-
-
84889681532
-
SHAPE-Seq: High-Troughput RNA Structure Analysis
-
Mortimer, S.A., C. Trapnell, S. Aviran, L. Pachter, and J.B. Lucks. 2012. SHAPE-Seq: High-Troughput RNA Structure Analysis. Curr Protoc Chem Biol. 4:275-297.
-
(2012)
Curr Protoc Chem Biol
, vol.4
, pp. 275-297
-
-
Mortimer, S.A.1
Trapnell, C.2
Aviran, S.3
Pachter, L.4
Lucks, J.B.5
-
39
-
-
84855306099
-
Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA
-
Parkinson, N.J., S. Maslau, B. Ferneyhough, G. Zhang, L. Gregory, D. Buck, J. Ragoussis, C.P. Ponting, and M.D. Fischer. 2012. Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Res. 22:125-133.
-
(2012)
Genome Res
, vol.22
, pp. 125-133
-
-
Parkinson, N.J.1
Maslau, S.2
Ferneyhough, B.3
Zhang, G.4
Gregory, L.5
Buck, D.6
Ragoussis, J.7
Ponting, C.P.8
Fischer, M.D.9
-
40
-
-
84869234288
-
Limitations and possibilities of low cell number ChIP-seq
-
Gilfillan, G.D., T. Hughes, Y. Sheng, H.S. Hjorthaug, T. Straub, K. Gervin, J.R. Harris, D.E. Undlien, and R. Lyle. 2012. Limitations and possibilities of low cell number ChIP-seq. BMC Genomics 13:645.
-
(2012)
BMC Genomics
, vol.13
, pp. 645
-
-
Gilfillan, G.D.1
Hughes, T.2
Sheng, Y.3
Hjorthaug, H.S.4
Straub, T.5
Gervin, K.6
Harris, J.R.7
Undlien, D.E.8
Lyle, R.9
-
41
-
-
79959327151
-
Counting individual DNA molecules by the stochastic attachment of diverse labels
-
Fu, G.K., J. Hu, P.H. Wang, and S.P. Fodor. 2011. Counting individual DNA molecules by the stochastic attachment of diverse labels. Proc. Natl. Acad. Sci. USA 108:9026-9031.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 9026-9031
-
-
Fu, G.K.1
Hu, J.2
Wang, P.H.3
Fodor, S.P.4
-
42
-
-
84856398949
-
Digital RNA sequencing minimizes sequence-dependent bias and amplifcation noise with optimized single-molecule barcodes
-
Shiroguchi, K., T.Z. Jia, P.A. Sims, and X.S. Xie. 2012. Digital RNA sequencing minimizes sequence-dependent bias and amplifcation noise with optimized single-molecule barcodes. Proc. Natl. Acad. Sci. USA 109:1347-1352.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 1347-1352
-
-
Shiroguchi, K.1
Jia, T.Z.2
Sims, P.A.3
Xie, X.S.4
-
43
-
-
78751682536
-
Overcoming bias and systematic errors in next generation sequencing data
-
Taub, M.A., H. Corrada Bravo, and R.A. Irizarry. 2010. Overcoming bias and systematic errors in next generation sequencing data. Genome Med. 2: 87.
-
(2010)
Genome Med
, vol.2
, pp. 87
-
-
Taub, M.A.1
Corrada Bravo, H.2
Irizarry, R.A.3
-
44
-
-
77956873627
-
Tackling the widespread and critical impact of batch efects in high-throughput data
-
Leek, J.T., R.B. Scharpf, H.C. Bravo, D. Simcha, B. Langmead, W. E. Johnson, D. Geman, K. Baggerly, and R.A. Irizarry. 2010. Tackling the widespread and critical impact of batch efects 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
-
45
-
-
84884558982
-
Monitoring of technical variation in quantitative high-throughput datasets
-
Lauss, M., I. Visne, A. Kriegner, M. Ringner, G. Jonsson, and M. Hoglund. 2013. Monitoring of technical variation in quantitative high-throughput datasets. Cancer Inform. 12:193-201.
-
(2013)
Cancer Inform
, vol.12
, pp. 193-201
-
-
Lauss, M.1
Visne, I.2
Kriegner, A.3
Ringner, M.4
Jonsson, G.5
Hoglund, M.6
-
46
-
-
84860198538
-
Structural biasin T4 R NA ligase-mediated 3′-adapter ligation
-
Zhuang, F., R.T. Fuchs, Z. Sun, Y. Zheng, and G.B. Robb. 2012. Structural biasin T4 R NA ligase-mediated 3′-adapter ligation. Nucleic Acids Res. 40:e54.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Zhuang, F.1
Fuchs, R.T.2
Sun, Z.3
Zheng, Y.4
Robb, G.B.5
-
47
-
-
84860389888
-
RNA-ligase-dependent biases in miR NA representation in deep-sequenced small RNA cDNA libraries
-
Ha f ner, M., N. Renwick, M. Brown, A. Mihailovic, D. Holoch, C. Lin, J.T. Pena, J.D. Nusbaum, et al. 2011. RNA-ligase-dependent biases in miR NA representation in deep-sequenced small RNA cDNA libraries. R NA 17:1697-1712.
-
(2011)
R NA
, 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
-
48
-
-
84866979410
-
Reducing ligation bias of smal l R NAs in libraries for next generation sequencing
-
Sorefan, K., H. Pais, A.E. Hall, A. Kozomara, S. Grifths-Jones, V. Moulton, and T. Dalmay. 2012. Reducing ligation bias of smal l R NAs in libraries for next generation sequencing. Si lence. 3:4.
-
(2012)
Si Lence
, vol.3
, pp. 4
-
-
Sorefan, K.1
Pais, H.2
Hall, A.E.3
Kozomara, A.4
Grifths-Jones, S.5
Moulton, V.6
Dalmay, T.7
-
49
-
-
77449121614
-
Ta r g e t-enrichment strategies for next-generation sequencing
-
Mamanova, L., A.J. Coffey, C.E. Scott, I. Kozarewa, E.H. Turner, A. Kumar, E. Howard, J. Shendure, and D.J. Turner. 2010. Ta r g e t-enrichment strategies for next-generation sequencing. Nat. Methods 7:111-118.
-
(2010)
Nat. Methods
, vol.7
, pp. 111-118
-
-
Mamanova, L.1
Coffey, A.J.2
Scott, C.E.3
Kozarewa, I.4
Turner, E.H.5
Kumar, A.6
Howard, E.7
Shendure, J.8
Turner, D.J.9
-
50
-
-
78651390679
-
Sequencing antibody repertoires: The next generation
-
Fischer, N. 2011. Sequencing antibody repertoires: the next generation. MAbs 3:17-20.
-
(2011)
MAbs
, vol.3
, pp. 17-20
-
-
Fischer, N.1
-
51
-
-
59849113821
-
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
-
Gnirke, A., A. Melnikov, J. Maguire, P. Rogov, E.M. LeProust, W. Brockman, T. Fennell, G. Giannoukos, et al. 2009. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27:182-189.
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 182-189
-
-
Gnirke, A.1
Melnikov, A.2
Maguire, J.3
Rogov, P.4
Leproust, E.M.5
Brockman, W.6
Fennell, T.7
Giannoukos, G.8
-
52
-
-
36549021060
-
Genome-wide in situ exon capture for selective resequencing
-
Hodges, E., Z. Xuan, V. Balija, M. Kramer, M.N. Molla, S.W. Smith, C.M. Middle, M.J. Rodesch, et al. 2007. Genome-wide in situ exon capture for selective resequencing. Nat. Genet. 39:1522-1527.
-
(2007)
Nat. Genet
, vol.39
, pp. 1522-1527
-
-
Hodges, E.1
Xuan, Z.2
Balija, V.3
Kramer, M.4
Molla, M.N.5
Smith, S.W.6
Middle, C.M.7
Rodesch, M.J.8
-
53
-
-
84884826911
-
Te next-generation sequencing revolution and its impact on genomics
-
Koboldt, D. C., K.M. Steinberg, D. E. Larson, R.K. Wilson, and E.R. Mardis. 2013. Te next-generation sequencing revolution and its impact on genomics. Cell 155: 27-38.
-
(2013)
Cell
, vol.155
, pp. 27-38
-
-
Koboldt, D.C.1
Steinberg, K.M.2
Larson, D.E.3
Wilson, R.K.4
Mardis, E.R.5
-
54
-
-
70449339945
-
Microdroplet-based PCR enrichment for large-scale targeted sequencing
-
Tewhey, R., J.B. Warner, M. Nakano, B. Libby, M. Medkova, P. H. David, S.K. Kotsopoulos, M.L. Samuels, et al. 2009. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat. Biotechnol. 27:1025-1031.
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 1025-1031
-
-
Tewhey, R.1
Warner, J.B.2
Nakano, M.3
Libby, B.4
Medkova, M.5
David, P.H.6
Kotsopoulos, S.K.7
Samuels, M.L.8
-
55
-
-
80053520872
-
Application of microdroplet PCR for large-scale targeted bisulfte sequencing
-
Komori, H.K., S.A. La Mere, A. Torkamani, G.T. Hart, S. Kotsopoulos, J. Warner, M.L. Samuels, J. Olson, et al. 2011. Application of microdroplet PCR for large-scale targeted bisulfte sequencing. Genome Res. 21:1738-1745.
-
(2011)
Genome Res
, vol.21
, pp. 1738-1745
-
-
Komori, H.K.1
la Mere, S.A.2
Torkamani, A.3
Hart, G.T.4
Kotsopoulos, S.5
Warner, J.6
Samuels, M.L.7
Olson, J.8
-
56
-
-
33751524657
-
Uniform amplifcation of multiple DNAs by emu lsion PCR
-
Hori, M., H. Fukano, and Y. Suzuki. 2007. Uniform amplifcation of multiple DNAs by emu lsion PCR. Biochem. Biophys. Res. Commun. 352:323-328.
-
(2007)
Biochem. Biophys. Res. Commun
, vol.352
, pp. 323-328
-
-
Hori, M.1
Fukano, H.2
Suzuki, Y.3
-
57
-
-
84865339168
-
I nte grat ed nex t-g enerat io n seque nci ng of 16S rDNA and metaproteomics diferentiate the healthy urine microbiome from asymptomatic bacteriu ria in neuropathic bladder associated with spinal cord injur y
-
Fouts, D.E., R. Pieper, S. Szpakowski, H. Pohl, S. Knoblach, M.J. Suh, S.T. Huang, I. Ljungberg, et al. 2012. I nte grat ed nex t-g enerat io n seque nci ng of 16S rDNA and metaproteomics diferentiate the healthy urine microbiome from asymptomatic bacteriu ria in neuropathic bladder associated with spinal cord injur y. J. Transl. Med. 10:174.
-
(2012)
J. Transl. Med
, vol.10
, pp. 174
-
-
Fouts, D.E.1
Pieper, R.2
Szpakowski, S.3
Pohl, H.4
Knoblach, S.5
Suh, M.J.6
Huang, S.T.7
Ljungberg, I.8
-
58
-
-
79955033419
-
Ectopic B - cell clusters that infltratetrans -planted human kidneys are clonal
-
Cheng, J., A. Torkamani, R.K. G rover, T. M. Jones, D.I. Ruiz, N.J. Schork, M.M. Quigley, F.W. Hall, et al. 2011. Ectopic B - cell clusters that infltratetrans -planted human kidneys are clonal. Proc. Natl. Acad. Sci. USA 108:5560-5565.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 5560-5565
-
-
Cheng, J.1
Torkamani, A.2
Rover, R.K.G.3
Jones, T.M.4
Ruiz, D.I.5
Schork, N.J.6
Quigley, M.M.7
Hall, F.W.8
-
59
-
-
83255193503
-
Aptamer selection by high-throughput sequencing and informatic analysis
-
Hoon, S., B. Zhou, K. D. Janda, S. Brenner, and J. Scolnick. 2011. Aptamer selection by high-throughput sequencing and informatic analysis. Biotechniques 51:413-416.
-
(2011)
Biotechniques
, vol.51
, pp. 413-416
-
-
Hoon, S.1
Zhou, B.2
Janda, K.D.3
Brenner, S.4
Scolnick, J.5
-
60
-
-
84864353628
-
Efcient and sequence-independent replication of DNA containing a third base pair establishes a functiona l six-letter genetic alphabet
-
Malyshev, D.A., K. Dhami, H.T. Quach, T. Lavergne, P. Ordoukhanian, A. Torkamani, and F. E. Romesberg. 2012. Efcient and sequence-independent replication of DNA containing a third base pair establishes a functiona l six-letter genetic alphabet. Proc. Natl. Acad. Sci. USA 109:12005-12010.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 12005-12010
-
-
Malyshev, D.A.1
Dhami, K.2
Quach, H.T.3
Lavergne, T.4
Ordoukhanian, P.5
Torkamani, A.6
Romesberg, F.E.7
-
61
-
-
75549083380
-
Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase
-
Lahr, D.J. and L.A. Katz. 2009. Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase. Biotechniques 47: 857-866.
-
(2009)
Biotechniques
, vol.47
, pp. 857-866
-
-
Lahr, D.J.1
Katz, L.A.2
-
62
-
-
83355173006
-
Reducing the efects of PCR amplifcation and sequencing artifacts on 16S rRNA-based studies
-
Schloss, P. D., D. Gevers, and S.L. Westcott. 2011. Reducing the efects of PCR amplifcation and sequencing artifacts on 16S rRNA-based studies. PLoS ON E 6:e27310.
-
(2011)
PLoS ON E
, vol.6
-
-
Schloss, P.D.1
Gevers, D.2
Westcott, S.L.3
-
63
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar, R.C., B.J. Haas, J.C. Clemente, C. Quince, and R. Knight. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinfor-matics 27:2194-2200.
-
(2011)
Bioinfor-matics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
64
-
-
84863392983
-
Illumina mate-paired DNA sequencing-librar y preparation using Cre-Lox recombination
-
Van Nieuwerburgh, F., R.C. Thompson, J. Ledesma, D. Deforce, T. Gaasterland, P. Ordoukhanian, and S.R. Head. 2012. Illumina mate-paired DNA sequencing-librar y preparation using Cre-Lox recombination. Nucleic Acids Res. 40:e24.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
van Nieuwerburgh, F.1
Thompson, R.C.2
Ledesma, J.3
Deforce, D.4
Gaasterland, T.5
Ordoukhanian, P.6
Head, S.R.7
-
65
-
-
84855481366
-
Generation of long insert pairs using a Cre-LoxP Inverse PCR approach
-
Peng, Z., Z. Zhao, N. Nath, J. L. Froula, A. Clum, T. Zhang, J. F. Cheng, A.C. Copeland, et al. 2012. Generation of long insert pairs using a Cre-LoxP Inverse PCR approach. PLoS ONE 7: e29437.
-
(2012)
PLoS ONE
, vol.7
-
-
Peng, Z.1
Zhao, Z.2
Nath, N.3
Froula, J.L.4
Clum, A.5
Zhang, T.6
Cheng, J.F.7
Copeland, A.C.8
-
66
-
-
84869502241
-
ChIP-seq and beyond: New and improved methodologies to detect and characterize protein-DNA interactions
-
Furey, T. S. 2012. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat. Rev. Genet. 13:840-852.
-
(2012)
Nat. Rev. Genet
, vol.13
, pp. 840-852
-
-
Furey, T.S.1
-
67
-
-
84884829249
-
Mapping human epigenomes
-
Rivera, C.M. and B. Ren. 2013. Mapping human epigenomes. Cell 155:39-55.
-
(2013)
Cell
, vol.155
, pp. 39-55
-
-
Rivera, C.M.1
Ren, B.2
-
68
-
-
79959360046
-
Application of ChIP-Seq a nd related techniques to the study of immune function
-
Northrup, D.L. and K. Zhao. 2011. Application of ChIP-Seq a nd related techniques to the study of immune function. Immunity 34:830-842.
-
(2011)
Immunity
, vol.34
, pp. 830-842
-
-
Northrup, D.L.1
Zhao, K.2
-
69
-
-
78751605211
-
Chromatin condensation via the condensin II complex is required for peripheral T-cell quiescence
-
Rawlings, J.S., M. Gatzka, P. G. Tomas, and J.N. Ihle. 2011. Chromatin condensation via the condensin II complex is required for peripheral T-cell quiescence. EMBO J. 30:263-276.
-
(2011)
EMBO J
, vol.30
, pp. 263-276
-
-
Rawlings, J.S.1
Gatzka, M.2
Tomas, P.G.3
Ihle, J.N.4
-
70
-
-
80053388216
-
W hole- genome chromatin profling from lim ited numbers of cel ls using nano-ChIP-seq
-
Adli, M. and B.E. Bernstein. 2011. W hole- genome chromatin profling from lim ited numbers of cel ls using nano-ChIP-seq. Nat. Protoc. 6:1656-1668.
-
(2011)
Nat. Protoc
, vol.6
, pp. 1656-1668
-
-
Adli, M.1
Bernstein, B.E.2
-
71
-
-
84899487669
-
Profling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq
-
Jayaseelan, S., F. Doyle, and S.A. Tenenbaum. 2013. Profling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq. Methods.
-
(2013)
Methods
-
-
Jayaseelan, S.1
Doyle, F.2
Tenenbaum, S.A.3
-
72
-
-
18444383371
-
Protein families and R NA recognition
-
Chen, Y. and G. Varani. 2005. Protein families and R NA recognition. FEBS J. 272:2088-2097.
-
(2005)
FEBS J
, vol.272
, pp. 2088-2097
-
-
Chen, Y.1
Varani, G.2
-
73
-
-
0029071516
-
Protein-RNA recognition
-
Draper, D.E. 1995. Protein-RNA recognition. Annu. Rev. Biochem. 64:593-620.
-
(1995)
Annu. Rev. Biochem
, vol.64
, pp. 593-620
-
-
Draper, D.E.1
-
74
-
-
44449166478
-
RNA-binding proteins and post-transcriptional gene regulation
-
Glisovic, T., J.L. Bachorik, J. Yong, and G. Dreyfuss. 2008. RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett. 582:1977-1986.
-
(2008)
FEBS Lett
, vol.582
, pp. 1977-1986
-
-
Glisovic, T.1
Bachorik, J.L.2
Yong, J.3
Dreyfuss, G.4
-
75
-
-
84875229872
-
How cel ls get the message: Dynamic assembly and function of mRNA-protein complexes
-
Müller-McNicoll, M. and K.M. Neugebauer. 2013. How cel ls get the message: dynamic assembly and function of mRNA-protein complexes. Nat. Rev. Genet. 14: 275-287.
-
(2013)
Nat. Rev. Genet
, vol.14
, pp. 275-287
-
-
Müller-McNicoll, M.1
Neugebauer, K.M.2
-
76
-
-
80051726311
-
Matrin 3 binds and stabilizes mR NA
-
Salton, M., R. Elkon, T. Borodina, A. Davydov, M.L. Yaspo, E. Halperin, and Y. Shiloh. 2011. Matrin 3 binds and stabilizes mR NA. PLoS ONE 6:e23882.
-
(2011)
PLoS ONE
, vol.6
-
-
Salton, M.1
Elkon, R.2
Borodina, T.3
Davydov, A.4
Yaspo, M.L.5
Halperin, E.6
Shiloh, Y.7
-
77
-
-
78651408754
-
Identification of neuronal R N A targets of TDP-43-containing ribonucleoprotein complexes
-
Sephton, C.F., C. Cenik, A. Kucukural, E.B. Dammer, B. Cenik, Y. Han, C.M. Dewey, F. P. Roth, et al. 2011. Identification of neuronal R N A targets of TDP-43-containing ribonucleoprotein complexes. J. Biol. Chem. 286:1204-1215.
-
(2011)
J. Biol. Chem
, vol.286
, pp. 1204-1215
-
-
Sephton, C.F.1
Cenik, C.2
Kucukural, A.3
Dammer, E.B.4
Cenik, B.5
Han, Y.6
Dewey, C.M.7
Roth, F.P.8
-
78
-
-
78650253763
-
Genome-wide identifcation of polycomb-associated RNAs by RIP-seq
-
Zhao, J., T. K. Ohsumi, J.T. Kung, Y. Ogawa, D.J. Grau, K. Sarma, J.J. Song, R.E. Kingston, et al. 2010. Genome-wide identifcation of polycomb-associated RNAs by RIP-seq. Mol. Cell 40:939-953.
-
(2010)
Mol. Cell
, vol.40
, pp. 939-953
-
-
Zhao, J.1
Ohsumi, T.K.2
Kung, J.T.3
Ogawa, Y.4
Grau, D.J.5
Sarma, K.6
Song, J.J.7
Kingston, R.E.8
-
79
-
-
84887331330
-
Finding the active genes in deep R NA-seq gene expression studies
-
Hart, T., H.K. Komori, S. Lamere, K. Podshivalova, and D.R. Salomon. 2013. Finding the active genes in deep R NA-seq gene expression studies. BMC Genomics 14:778.
-
(2013)
BMC Genomics
, vol.14
, pp. 778
-
-
Hart, T.1
Komori, H.K.2
Lamere, S.3
Podshivalova, K.4
Salomon, D.R.5
-
80
-
-
0242497663
-
CLIP identifes Nova-regulated RNA networks in the brain
-
Ule, J., K.B. Jensen, M. Ruggiu, A. Mele, A. Ule, and R.B. Darnell. 2003. CLIP identifes Nova-regulated RNA networks in the brain. Science 302:1212-1215.
-
(2003)
Science
, vol.302
, pp. 1212-1215
-
-
Ule, J.1
Jensen, K.B.2
Ruggiu, M.3
Mele, A.4
Ule, A.5
Darnell, R.B.6
-
81
-
-
27944508215
-
CLIP: A method for identifying protein-RNA interaction sites in living cells
-
Ule, J., K. Jensen, A. Mele, and R.B. Darnell. 2005. CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 37:376-386.
-
(2005)
Methods
, vol.37
, pp. 376-386
-
-
Ule, J.1
Jensen, K.2
Mele, A.3
Darnell, R.B.4
-
82
-
-
84934437354
-
CL I P: Cros s -linking a nd immunoprecipitation of in vivo R NA targets of R NA-binding proteins
-
Jensen, K.B. and R.B. Darnell. 2008. CL I P: cros s -linking a nd immunoprecipitation of in vivo R NA targets of R NA-binding proteins. Methods Mol. Biol. 488:85-98.
-
(2008)
Methods Mol. Biol
, vol.488
, pp. 85-98
-
-
Jensen, K.B.1
Darnell, R.B.2
-
83
-
-
56549105330
-
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
-
Licatalosi, D.D., A. Mele, J.J. Fak, J. Ule, M. Kayikci, S.W. Chi, T. A. Clark, A.C. Schweitzer, et al. 2008. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456:464-469.
-
(2008)
Nature
, vol.456
, pp. 464-469
-
-
Licatalosi, D.D.1
Mele, A.2
Fak, J.J.3
Ule, J.4
Kayikci, M.5
Chi, S.W.6
Clark, T.A.7
Schweitzer, A.C.8
-
84
-
-
77954387023
-
ICLIP reveals the function of hnRNP particles in splicing at individual nucleot ide resolution
-
König, J., K. Zarnack, G. Rot, T. Curk, M. K ayikci, B. Zupan, D.J. Turner, N.M. Luscombe, and J. Ule. 2010. iCLIP reveals the function of hnRNP particles in splicing at individual nucleot ide resolution. Nat. S t r uct. Mol. Biol. 17:909-915.
-
(2010)
Nat. S T R Uct. Mol. Biol
, vol.17
, pp. 909-915
-
-
König, J.1
Zarnack, K.2
Rot, G.3
Curk, T.4
Ayikci, M.K.5
Zupan, B.6
Turner, D.J.7
Luscombe, N.M.8
Ule, J.9
-
85
-
-
37349130959
-
Identifcation of microRNAs and other small regulatory RNAs using cDNA library sequencing
-
Hafner, M., P. Landgraf, J. Ludwig, A. Rice, T. Ojo, C. Lin, D. Holoch, C. Lim, and T. Tuschl. 2008. Identifcation of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 44: 3-12.
-
(2008)
Methods
, vol.44
, pp. 3-12
-
-
Hafner, M.1
Landgraf, P.2
Ludwig, J.3
Rice, A.4
Ojo, T.5
Lin, C.6
Holoch, D.7
Lim, C.8
Tuschl, T.9
-
86
-
-
77950920903
-
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
-
Hafner, M., M. Landthaler, L. Burger, M. Khorshid, J. Hausser, P. Berninger, A. Rothballer, M. Ascano, Jr., et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141:129-141
-
(2010)
Cell
, vol.141
, pp. 129-141
-
-
Hafner, M.1
Landthaler, M.2
Burger, L.3
Khorshid, M.4
Hausser, J.5
Berninger, P.6
Rothballer, A.7
Ascano, M.8
-
87
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic diferences
-
Lister, R., M. Pelizzola, R.H. Dowen, R.D. Hawkins, G. Hon, J. Tonti-Filippini, J.R. Nery, L. Lee, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic diferences. Nature 462:315-322.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.5
Tonti-Filippini, J.6
Nery, J.R.7
Lee, L.8
-
88
-
-
84878292277
-
Transcriptiona l and epigenetic dynamics during specification of human embr yonic stem cells
-
Giford, C.A., M.J. Ziller, H. Gu, C. Trapnell, J. Donaghey, A. Tsankov, A.K. Shalek, D.R. Kelley, et al. 2013. Transcriptiona l and epigenetic dynamics during specification of human embr yonic stem cells. Cell 153: 1149-1163.
-
(2013)
Cell
, vol.153
, pp. 1149-1163
-
-
Giford, C.A.1
Ziller, M.J.2
Gu, H.3
Trapnell, C.4
Donaghey, J.5
Tsankov, A.6
Shalek, A.K.7
Kelley, D.R.8
-
89
-
-
84875457313
-
Conventional and nanotech-niques for DNA methylation profling
-
Shanmuganathan, R., N.B. Basheer, L. Amirthalingam, H. Muthukumar, R. Kaliaperumal, and K. Shanmugam. 2013. Conventional and nanotech-niques for DNA methylation profling. J. Mol. Diagn. 15:17-26.
-
(2013)
J. Mol. Diagn
, vol.15
, pp. 17-26
-
-
Shanmuganathan, R.1
Basheer, N.B.2
Amirthalingam, L.3
Muthukumar, H.4
Kaliaperumal, R.5
Shanmugam, K.6
-
90
-
-
0037372003
-
Epigenetic regulation of gene expression: How the genome integrates intrinsic a nd environmental signa ls
-
Jaenisch, R. and A. Bird. 2003. Epigenetic regulation of gene expression: how the genome integrates intrinsic a nd environmental signa ls. Nat. Genet. 33(Suppl):245-254.
-
(2003)
Nat. Genet
, vol.33
, Issue.SUPPL.
, pp. 245-254
-
-
Jaenisch, R.1
Bird, A.2
-
91
-
-
73249137306
-
DNA methylation of cancer genome
-
Cheung, H.H., T. L. Lee, O. M. Rennert, and W. Y. Chan. 2009. DNA methylation of cancer genome. Birth Defects Res. C Embryo Today 87:335-350.
-
(2009)
Birth Defects Res. C Embryo Today
, vol.87
, pp. 335-350
-
-
Cheung, H.H.1
Lee, T.L.2
Rennert, O.M.3
Chan, W.Y.4
-
92
-
-
77954661906
-
DNA hy p omet hy l ation in ca ncer cells
-
Ehrlich, M. 2009. DNA hy p omet hy l ation in ca ncer cells. Epigenomics. 1:239-259.
-
(2009)
Epigenomics
, vol.1
, pp. 239-259
-
-
Ehrlich, M.1
-
94
-
-
77953860649
-
The role of epigenetics in the pathology of diabetic complications
-
Villeneuve, L.M. and R. Natarajan. 2010. The role of epigenetics in the pathology of diabetic complications. A m. J. Physiol. Rena l Physiol. 299: F14-F25.
-
(2010)
A M. J. Physiol. Rena L Physiol
, vol.299
-
-
Villeneuve, L.M.1
Natarajan, R.2
-
96
-
-
77953248367
-
Discovering disease-specific biomarker genes for cancer diagnosis and progno si s
-
Huang, H.C., S. Zheng, V. VanBuren, and Z. Zhao. 2010. Discovering disease-specific biomarker genes for cancer diagnosis and progno si s. Technol. Cancer Res. Treat. 9:219-230.
-
(2010)
Technol. Cancer Res. Treat
, vol.9
, pp. 219-230
-
-
Huang, H.C.1
Zheng, S.2
Vanburen, V.3
Zhao, Z.4
-
97
-
-
84875290402
-
Genome-wide DNA methylation analysis using massively paral lel sequencing technologies
-
Suzuki, M. and J.M. Greally. 2013. Genome-wide DNA methylation analysis using massively paral lel sequencing technologies. Semin. Hematol. 50: 70-77.
-
(2013)
Semin. Hematol
, vol.50
, pp. 70-77
-
-
Suzuki, M.1
Greally, J.M.2
-
98
-
-
84876120904
-
Deciphering the epigenetic code: An overview of DNA methyl-ation analysis methods
-
Umer, M. and Z. Herceg. 2013. Deciphering the epigenetic code: an overview of DNA methyl-ation analysis methods. Antioxid. Redox Signal. 18:1972-1986.
-
(2013)
Antioxid. Redox Signal
, vol.18
, pp. 1972-1986
-
-
Umer, M.1
Herceg, Z.2
-
99
-
-
0014933620
-
Specifc deamination of RNA by sodium bisulphite
-
Shapiro, R., B.I. Cohen, and R.E. Servis. 1970. Specifc deamination of RNA by sodium bisulphite. Nature 227:1047-1048.
-
(1970)
Nature
, vol.227
, pp. 1047-1048
-
-
Shapiro, R.1
Cohen, B.I.2
Servis, R.E.3
-
100
-
-
40749109894
-
Shotgu n bisu lphite sequencing of the Arabidopsis genome reveals DNA methyl-ation patterning
-
Cokus, S.J., S. Feng, X. Zhang, Z. Chen, B. Merriman, C.D. Haudenschild, S. Pradhan, S.F. Nelson, et al. 2008. Shotgu n bisu lphite sequencing of the Arabidopsis genome reveals DNA methyl-ation patterning. Nature 452:215-219.
-
(2008)
Nature
, vol.452
, pp. 215-219
-
-
Cokus, S.J.1
Feng, S.2
Zhang, X.3
Chen, Z.4
Merriman, B.5
Haudenschild, C.D.6
Pradhan, S.7
Nelson, S.F.8
-
101
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister, R., R.C. O'Malley, J. Tonti-Filippini, B.D. Gregory, C.C. Berry, A.H. Millar, and J.R. Ecker. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-536.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
Gregory, B.D.4
Berry, C.C.5
Millar, A.H.6
Ecker, J.R.7
-
102
-
-
84857784165
-
Libra ry-free methylation sequenci ng with bisulfte padlock probes
-
Diep, D., N. Plongthongkum, A. Gore, H.L. Fung, R. Shoemaker, and K. Zhang. 2012. Libra ry-free methylation sequenci ng with bisulfte padlock probes. Nat. Methods 9:270-272.
-
(2012)
Nat. Methods
, vol.9
, pp. 270-272
-
-
Diep, D.1
Plongthongkum, N.2
Gore, A.3
Fung, H.L.4
Shoemaker, R.5
Zhang, K.6
-
103
-
-
84886860116
-
TET enzymes, TDG and the dynamics of DNA demethylation
-
Kohli, R.M. and Y. Zhang. 2013. TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502:472-479.
-
(2013)
Nature
, vol.502
, pp. 472-479
-
-
Kohli, R.M.1
Zhang, Y.2
-
104
-
-
84861221693
-
Quantitative sequencing of 5-methylcy tosine and 5-hydrox ymethylcytosine at single-base resolution
-
Booth, M.J., M.R. Branco, G. Fic z, D. Oxley, F. Krueger, W. Reik, and S. Balasubramanian. 2012. Quantitative sequencing of 5-methylcy tosine and 5-hydrox ymethylcytosine at single-base resolution. Science 336:934-937.
-
(2012)
Science
, vol.336
, pp. 934-937
-
-
Booth, M.J.1
Branco, M.R.2
Ficz, G.3
Oxley, D.4
Krueger, F.5
Reik, W.6
Balasubramanian, S.7
-
105
-
-
84861990517
-
Base-resolution analysis of 5 -hydroxymethylcy tosine in the Mamm
-
Yu, M., G.C. Hon, K.E. Szulwach, C.X. Song, L. Zhang, A. Kim, X. Li, Q. Dai, et al. 2012. Base-resolution analysis of 5 -hydroxymethylcy tosine in the Mamm. Genome. Cell 14 9:1368-1380.
-
(2012)
Genome. Cell
, vol.14
, Issue.9
, pp. 1368-1380
-
-
Yu, M.1
Hon, G.C.2
Szulwach, K.E.3
Song, C.X.4
Zhang, L.5
Kim, A.6
Li, X.7
Dai, Q.8
-
106
-
-
84856453032
-
Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine
-
Song, C.X., T. A. Clark, X.Y. Lu, A. Kislyuk, Q. Dai, S. W. Turner, C. He, and J. Korlach. 2012. Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat. Methods 9:75-77.
-
(2012)
Nat. Methods
, vol.9
, pp. 75-77
-
-
Song, C.X.1
Clark, T.A.2
Lu, X.Y.3
Kislyuk, A.4
Dai, Q.5
Turner, S.W.6
He, C.7
Korlach, J.8
-
107
-
-
84865061978
-
Genome-wide distribution of 5-formyl-cytosine i n embr yonic stem cel ls is associated with transcription and depends on thymine DNA glyco-sylase
-
Raiber, E.A., D. Beraldi, G. Ficz, H.E. Burgess, M.R. Branco, P. Murat, D. Oxley, M.J. Booth, et al. 2012. Genome-wide distribution of 5-formyl-cytosine i n embr yonic stem cel ls is associated with transcription and depends on thymine DNA glyco-sylase. Genome Biol. 13:R69.
-
(2012)
Genome Biol
, vol.13
-
-
Raiber, E.A.1
Beraldi, D.2
Ficz, G.3
Burgess, H.E.4
Branco, M.R.5
Murat, P.6
Oxley, D.7
Booth, M.J.8
-
108
-
-
84876946045
-
Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics
-
Shen, L., H. Wu, D. Diep, S. Yamaguchi, A.C. D'Alessio, H.L. Fung, K. Zhang, and Y. Zhang. 2013. Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell 153:692-706.
-
(2013)
Cell
, vol.153
, pp. 692-706
-
-
Shen, L.1
Wu, H.2
Diep, D.3
Yamaguchi, S.4
D'Alessio, A.C.5
Fung, H.L.6
Zhang, K.7
Zhang, Y.8
-
109
-
-
84876907152
-
Genome-wide profl ing of 5-formylcy tosine reveals its roles in epigenetic priming
-
Song, C.X., K.E. Szulwach, Q. Dai, Y. Fu, S.Q. Mao, L. Lin, C. Street, Y. Li, et al. 2013. Genome-wide profl ing of 5-formylcy tosine reveals its roles in epigenetic priming. Cell 153:678-691.
-
(2013)
Cell
, vol.153
, pp. 678-691
-
-
Song, C.X.1
Szulwach, K.E.2
Dai, Q.3
Fu, Y.4
Mao, S.Q.5
Lin, L.6
Street, C.7
Li, Y.8
-
110
-
-
27844529344
-
Proposed methods for testing and selecting the ERCC external RNA controls
-
External RN Controls Consortium
-
External RN Controls Consortium. 2005. Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 6:150.
-
(2005)
BMC Genomics
, vol.6
, pp. 150
-
-
-
111
-
-
79551524281
-
Comprehensive identif-cation and quantifcation of microbial transcrip-tomes by genome-wide unbiased methods
-
Mäder, U., P. Nicolas, H. Richard, P. Bessieres, and S. Aymerich. 2011. Comprehensive identif-cation and quantifcation of microbial transcrip-tomes by genome-wide unbiased methods. Curr. Opin. Biotechnol. 22:32-41.
-
(2011)
Curr. Opin. Biotechnol
, vol.22
, pp. 32-41
-
-
Mäder, U.1
Nicolas, P.2
Richard, H.3
Bessieres, P.4
Aymerich, S.5
-
112
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Wang, Z., M. Gerstein, and M. Snyder. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10: 57-63.
-
(2009)
Nat. Rev. Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
113
-
-
84877768911
-
RNA sequencing of cancer reveals novel spl icing a lterations
-
Eswaran, J., A. Horvath, S. Godbole, S. D. Reddy, P. Mudvari, K. Ohshiro, D. Cyanam, S. Nair, et al. 2013. RNA sequencing of cancer reveals novel spl icing a lterations. Scientifc reports 3:1689.
-
(2013)
Scientifc Reports
, vol.3
, pp. 1689
-
-
Eswaran, J.1
Horvath, A.2
Godbole, S.3
Reddy, S.D.4
Mudvari, P.5
Ohshiro, K.6
Cyanam, D.7
Nair, S.8
-
114
-
-
84872180043
-
RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum
-
Zhao, C., C. Waalwijk, P. J. de Wit, D. Tang, and T. van der Lee. 2013. RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum. BMC Genomics 14:21.
-
(2013)
BMC Genomics
, vol.14
, pp. 21
-
-
Zhao, C.1
Waalwijk, C.2
de Wit, P.J.3
Tang, D.4
van der Lee, T.5
-
115
-
-
80053566222
-
Small RNAs derived from longer non-coding R NAs
-
Röther, S. and G. Meister. 2011. Small RNAs derived from longer non-coding R NAs. Biochimie 93:1905-1915.
-
(2011)
Biochimie
, vol.93
, pp. 1905-1915
-
-
Röther, S.1
Meister, G.2
-
117
-
-
79959317018
-
Whole transcriptome analysis: What are we still missing? Wiley interdisciplinary reviews
-
Saxena, A. and P. Carninci. 2011. Whole transcriptome analysis: what are we still missing? Wiley interdisciplinary reviews. Systems biology and medicine 3: 527-543.
-
(2011)
Systems Biology and Medicine
, vol.3
, pp. 527-543
-
-
Saxena, A.1
Carninci, P.2
-
118
-
-
84893620730
-
Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabi-dopsis
-
In press
-
Wang, H., P. J. Chung, J. Liu, I.C. Jang, M. Kean, J. Xu, and N.H. Chua. 2014. Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabi-dopsis. Genome Res. (In press.)
-
(2014)
Genome Res
-
-
Wang, H.1
Chung, P.J.2
Liu, J.3
Jang, I.C.4
Kean, M.5
Xu, J.6
Chua, N.H.7
|