-
1
-
-
84863986133
-
Functions of dna methylation: Islands, start sites, gene bodies and beyond
-
Jones, P. A. (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet., 13, 484-492.
-
(2012)
Nat. Rev. Genet
, Issue.13
, pp. 484-492
-
-
Jones, P.A.1
-
2
-
-
0028096611
-
High sensitivity mapping of methylated cytosines
-
Clark, S. J., Harrison, J., Paul, C. L. and Frommer, M. (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res., 22, 2990-2997.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 2990-2997
-
-
Clark, S.1
Harrison, J.2
Paul, C.L.3
Frommer, M.4
-
3
-
-
70450217879
-
Human dna methylomes at base resolution show widespread epigenomic differences
-
Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q. M. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 315-322.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.3
Hawkins, R.4
Hon, G.5
Tonti-Filippini, J.6
Nery, J.7
Lee, L.8
Ye, Z.9
Ngo, Q.M.10
-
4
-
-
49649125042
-
Genome-scale dna methylation maps of pluripotent and differentiated cells
-
Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B. et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature, 454, 766-770.
-
(2008)
Nature
, vol.454
, pp. 766-770
-
-
Meissner, A.1
Mikkelsen, T.2
Gu, H.3
Wernig, M.4
Hanna, J.5
Sivachenko, A.6
Zhang, X.7
Bernstein, B.8
Nusbaum, C.9
Jaffe, D.B.10
-
5
-
-
84871702441
-
The dynamics of genome-wide dna methylation reprogramming in mouse primordial germ cells. Mol
-
Seisenberger, S., Andrews, S., Krueger, F., Arand, J., Walter, J., Santos, F., Popp, C., Thienpont, B., Dean, W. and Reik, W. (2012) The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol. Cell, 48, 849-862.
-
(2012)
Cell
, Issue.48
, pp. 849-862
-
-
Seisenberger, S.1
Andrews, S.2
Krueger, F.3
Arand, J.4
Walter, J.5
Santos, F.6
Popp, C.7
Thienpont, B.8
Dean, W.9
Reik, W.10
-
6
-
-
84871688621
-
Analysing and interpreting dna methylation data
-
Bock, C. (2012) Analysing and interpreting DNA methylation data. Nat. Rev. Genet., 13, 705-719.
-
(2012)
Nat. Rev. Genet
, Issue.13
, pp. 705-719
-
-
Bock, C.1
-
7
-
-
70350697851
-
Updates to the rmap short-read mapping software
-
Smith, A. D., Chung, W. Y., Hodges, E., Kendall, J., Hannon, G., Hicks, J., Xuan, Z. and Zhang, M. Q. (2009) Updates to the RMAP short-read mapping software. Bioinformatics, 25, 2841-2842.
-
(2009)
Bioinformatics
, vol.25
, pp. 2841-2842
-
-
Smith, A.1
Chung, W.2
Hodges, E.3
Kendall, J.4
Hannon, G.5
Hicks, J.6
Xuan, Z.7
Zhang, M.Q.8
-
8
-
-
78549291439
-
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel dna sequencing
-
Coarfa, C., Yu, F., Miller, C. A., Chen, Z., Harris, R. A. and Milosavljevic, A. (2010) Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. BMC Bioinformatics, 11, 572.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 572
-
-
Coarfa, C.1
Yu, F.2
Miller, C.A.3
Chen, Z.4
Harris, R.A.5
Milosavljevic, A.6
-
9
-
-
68949141599
-
Bsmap: Whole genome bisulfite sequence mapping program
-
Xi, Y. and Li, W. (2009) BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics, 10, 232.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 232
-
-
Xi, Y.1
Li, W.2
-
10
-
-
77951125407
-
Bs seeker: Precise mapping for bisulfite sequencing
-
Chen, P. Y., Cokus, S. J. and Pellegrini, M. (2010) BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics, 11, 203.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 203
-
-
Chen, P.Y.1
Cokus, S.J.2
Pellegrini, M.3
-
11
-
-
79957868920
-
Bismark: A flexible aligner and methylation caller for bisulfite-seq applications
-
Krueger, F. and Andrews, S. R. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-1572.
-
(2011)
Bioinformatics
, Issue.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
12
-
-
80051921569
-
Methylcoder: Software pipeline for bisulfite-treated sequences
-
Pedersen, B., Hsieh, T. F., Ibarra, C. and Fischer, R. L. (2011) MethylCoder: software pipeline for bisulfite-treated sequences. Bioinformatics, 27, 2435-2436.
-
(2011)
Bioinformatics
, Issue.27
, pp. 2435-2436
-
-
Pedersen, B.1
Hsieh, T.2
Ibarra, C.3
Fischer, R.4
-
13
-
-
40549107988
-
Pash 2.0: Scaleable sequence anchoring for next-generation sequencing technologies
-
Coarfa, C. and Milosavljevic, A. (2008) Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. Pacific Symposium on Biocomputing, 13, 102-113.
-
(2008)
Pacific Symposium on Biocomputing
, vol.13
, pp. 102-113
-
-
Coarfa, C.1
Milosavljevic, A.2
-
14
-
-
79551621409
-
Readdepth: A parallel r package for detecting copy number alterations from short sequencing reads
-
Miller, C. A., Hampton, O., Coarfa, C. and Milosavljevic, A. (2011) ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One, 6, e16327.
-
(2011)
PLoS One
, vol.6
-
-
Miller, C.A.1
Hampton, O.2
Coarfa, C.3
Milosavljevic, A.4
-
15
-
-
40749109894
-
Shotgun bisulphite sequencing of the arabidopsis genome reveals dna methylation patterning
-
Cokus, S. J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C. D., Pradhan, S., Nelson, S. F., Pellegrini, M. and Jacobsen, S. E. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 452, 215-219.
-
(2008)
Nature
, vol.452
, pp. 215-219
-
-
Cokus, S.1
Feng, S.2
Zhang, X.3
Chen, Z.4
Merriman, B.5
Haudenschild, C.6
Pradhan, S.7
Nelson, S.8
Pellegrini, M.9
Jacobsen, S.E.10
-
16
-
-
84872573541
-
Pass-bis: A bisulfite aligner suitable for whole methylome analysis of illumina and solid reads
-
Campagna, D., Telatin, A., Forcato, C., Vitulo, N. and Valle, G. (2013) PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. Bioinformatics, 29, 268-270.
-
(2013)
Bioinformatics
, Issue.29
, pp. 268-270
-
-
Campagna, D.1
Telatin, A.2
Forcato, C.3
Vitulo, N.4
Valle, G.5
-
17
-
-
84866860274
-
Batmeth: Improved mapper for bisulfite sequencing reads on dna methylation
-
Lim, J. Q., Tennakoon, C., Li, G., Wong, E., Ruan, Y., Wei, C. L. and Sung, W. K. (2012) BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biol., 13, R82.
-
(2012)
Genome Biol
, vol.13
-
-
Lim, J.Q.1
Tennakoon, C.2
Li, G.3
Wong, E.4
Ruan, Y.5
Wei, C.L.6
Sung, W.K.7
-
18
-
-
84864035039
-
Fast and sensitive mapping of bisulfite-treated sequencing data
-
Otto, C., Stadler, P. F. and Hoffmann, S. (2012) Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics, 28, 1698-1704.
-
(2012)
Bioinformatics
, Issue.28
, pp. 1698-1704
-
-
Otto, C.1
Stadler, P.F.2
Hoffmann, S.3
-
19
-
-
84861563688
-
Comparison of alignment software for genome-wide bisulphite sequence data
-
Chatterjee, A., Stockwell, P. A., Rodger, E. J. and Morison, I. M. (2012) Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Res., 40, e79.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Chatterjee, A.1
Stockwell, P.A.2
Rodger, E.J.3
Morison, I.M.4
-
20
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short dna sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. and Salzberg, S. L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
21
-
-
40049104732
-
Soap: Short oligonucleotide alignment program
-
Li, R., Li, Y., Kristiansen, K. and Wang, J. (2008) SOAP: short oligonucleotide alignment program. Bioinformatics, 24, 713-714.
-
(2008)
Bioinformatics
, vol.24
, pp. 713-714
-
-
Li, R.1
Li, Y.2
Kristiansen, K.3
Wang, J.4
-
22
-
-
78650688321
-
Season of conception in rural gambia affects dna methylation at putative human metastable epialleles
-
Waterland, R. A., Kellermayer, R., Laritsky, E., Rayco-Solon, P., Harris, R. A., Travisano, M., Zhang, W., Torskaya, M. S., Zhang, J., Shen, L. et al. (2010) Season of conception in rural gambia affects DNA methylation at putative human metastable epialleles. PLoS Genet., 6, e1001252.
-
(2010)
PLoS Genet
, vol.6
-
-
Waterland, R.A.1
Kellermayer, R.2
Laritsky, E.3
Rayco-Solon, P.4
Harris, R.A.5
Travisano, M.6
Zhang, W.7
Torskaya, M.S.8
Zhang, J.9
Shen, L.10
-
23
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J., 17, 10-12.
-
(2011)
EMBnet J
, Issue.17
, pp. 10-12
-
-
Martin, M.1
-
24
-
-
79251555660
-
Venndiagram: A package for the generation of highly-customizable venn and euler diagrams in r
-
Chen, H. and Boutros, P. C. (2011) VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics, 12, 35.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 35
-
-
Chen, H.1
Boutros, P.C.2
-
25
-
-
77951770756
-
Bedtools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A. R. and Hall, I. M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
-
(2010)
Bioinformatics
, Issue.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
26
-
-
33847736948
-
Optimizing annealing temperature overcomes bias in bisulfite pcr methylation analysis
-
Shen, L., Guo, Y., Chen, X., Ahmed, S. and Issa, J. P. (2007) Optimizing annealing temperature overcomes bias in bisulfite PCR methylation analysis. Biotechniques, 42, 48-58.
-
(2007)
Biotechniques
, vol.42
, pp. 48-58
-
-
Shen, L.1
Guo, Y.2
Chen, X.3
Ahmed, S.4
Issa, J.P.5
-
27
-
-
84856498057
-
Dna methylome analysis using short bisulfite sequencing data
-
Krueger, F., Kreck, B., Franke, A. and Andrews, S. R. (2012) DNA methylome analysis using short bisulfite sequencing data. Nat. Methods, 9, 145-151.
-
(2012)
Nat. Methods
, Issue.9
, pp. 145-151
-
-
Krueger, F.1
Kreck, B.2
Franke, A.3
Andrews, S.R.4
-
28
-
-
77957932941
-
Comparison of sequencing-based methods to profile dna methylation and identification of monoallelic epigenetic modifications
-
Harris, R. A., Wang, T., Coarfa, C., Nagarajan, R. P., Hong, C., Downey, S. L., Johnson, B. E., Fouse, S. D., Delaney, A., Zhao, Y. et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnol., 28, 1097-1105.
-
(2010)
Nat. Biotechnol
, Issue.28
, pp. 1097-1105
-
-
Harris, R.1
Wang, T.2
Coarfa, C.3
Nagarajan, R.4
Hong, C.5
Downey, S.6
Johnson, B.7
Fouse, S.8
Delaney, A.9
Zhao, Y.10
-
29
-
-
84866853818
-
Bsmooth: From whole genome bisulfite sequencing reads to differentially methylated regions
-
Hansen, K. D., Langmead, B. and Irizarry, R. A. (2012) BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol., 13, R83.
-
(2012)
Genome Biol
, vol.13
-
-
Hansen, K.D.1
Langmead, B.2
Irizarry, R.A.3
-
30
-
-
84876042374
-
In-solution hybrid capture of bisulfite-converted dna for targeted bisulfite sequencing of 174 adme genes
-
Ivanov, M., Kals, M., Kacevska, M., Metspalu, A., Ingelman-Sundberg, M. and Milani, L. (2013) In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes. Nucleic Acids Res., 41, e72.
-
(2013)
Nucleic Acids Res
, Issue.41
-
-
Ivanov, M.1
Kals, M.2
Kacevska, M.3
Metspalu, A.4
Ingelman-Sundberg, M.5
Milani, L.6
|