-
1
-
-
33847032960
-
The mammalian epigenome
-
Bernstein, B.E., Meissner, A. and Lander, E.S. (2007) The mammalian epigenome. Cell, 128, 669-681.
-
(2007)
Cell
, vol.128
, pp. 669-681
-
-
Bernstein, B.E.1
Meissner, A.2
Lander, E.S.3
-
2
-
-
33846283385
-
The evolution of gene regulation by transcription factors and microRNAs
-
Chen, K. and Rajewsky, N. (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat. Rev. Genet., 8, 93-103.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 93-103
-
-
Chen, K.1
Rajewsky, N.2
-
3
-
-
33646738502
-
-
Pal, S. K. (ed.) Springer-Verlag Berlin Heidelberg
-
Zhang, M.Q. (2005) In: Pal, S. K. (ed.), PReMI. Springer-Verlag Berlin Heidelberg, Vol. 3776, pp. 31-38.
-
(2005)
PReMI
, vol.3776
, pp. 31-38
-
-
Zhang, M.Q.1
-
4
-
-
33646369393
-
Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band
-
Frigola, J., Song, J., Stirzaker, C., Hinshelwood, R.A., Peinado, M.A. and Clark, S.J. (2006) Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat. Genet., 38, 540-549.
-
(2006)
Nat. Genet.
, vol.38
, pp. 540-549
-
-
Frigola, J.1
Song, J.2
Stirzaker, C.3
Hinshelwood, R.A.4
Peinado, M.A.5
Clark, S.J.6
-
5
-
-
34249275353
-
Phenotypic plasticity and the epigenetics of human disease
-
Feinberg, A.P. (2007) Phenotypic plasticity and the epigenetics of human disease. Nature, 447, 433-440.
-
(2007)
Nature
, vol.447
, pp. 433-440
-
-
Feinberg, A.P.1
-
6
-
-
33751505540
-
DNA methylation profling of human chromosomes 6, 20 and 22
-
Eckhardt, F., Lewin, J., Cortese, R., Rakyan, V.K., Attwood, J., Burger, M., et al. (2006) DNA methylation profling of human chromosomes 6, 20 and 22. Nat. Genet., 38, 1378-1385.
-
(2006)
Nat. Genet.
, vol.38
, pp. 1378-1385
-
-
Eckhardt, F.1
Lewin, J.2
Cortese, R.3
Rakyan, V.K.4
Attwood, J.5
Burger, M.6
-
7
-
-
38849093314
-
The infuence of genetic variation on gene expression
-
Williams, R.B., Chan, E.K., Cowley, M.J. and Little, P.F. (2007) The infuence of genetic variation on gene expression. Genome Res., 17, 1707-1716.
-
(2007)
Genome Res.
, vol.17
, pp. 1707-1716
-
-
Williams, R.B.1
Chan, E.K.2
Cowley, M.J.3
Little, P.F.4
-
8
-
-
45549096818
-
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping
-
Bock, C., Walter, J., Paulsen, M. and Lengauer, T. (2008) Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res., 36, e55.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Bock, C.1
Walter, J.2
Paulsen, M.3
Lengauer, T.4
-
9
-
-
39449088572
-
Genome-wide approaches to studying chromatin modi-fcations
-
Schones, D.E. and Zhao, K. (2008) Genome-wide approaches to studying chromatin modi-fcations. Nat. Rev. Genet., 9, 179-191.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 179-191
-
-
Schones, D.E.1
Zhao, K.2
-
10
-
-
61649123317
-
EpiGRAPH: User-friendly software for statistical analysis and prediction of (epi-) genomic data
-
Bock, C., Halachev, K., Buch, J. and Lengauer, T. (2009) EpiGRAPH: User-friendly software for statistical analysis and prediction of (epi-) genomic data. Genome Biol., 10, R14.
-
(2009)
Genome Biol.
, vol.10
-
-
Bock, C.1
Halachev, K.2
Buch, J.3
Lengauer, T.4
-
11
-
-
33645777446
-
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure
-
Bock, C., Paulsen, M., Tierling, S., Mikeska, T., Lengauer, T. and Walter, J. (2006) CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet., 2, e26.
-
(2006)
PLoS Genet.
, vol.2
-
-
Bock, C.1
Paulsen, M.2
Tierling, S.3
Mikeska, T.4
Lengauer, T.5
Walter, J.6
-
12
-
-
34249723701
-
The human genomic melting map
-
Liu, F., Tostesen, E., Sundet, J.K., Jenssen, T.K., Bock, C., Jerstad, G.I., et al. (2007) The human genomic melting map. PLoS Comput. Biol., 3, e93.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Liu, F.1
Tostesen, E.2
Sundet, J.K.3
Jenssen, T.K.4
Bock, C.5
Jerstad, G.I.6
-
13
-
-
34347337742
-
CpG island mapping by epigenome prediction
-
Bock, C., Walter, J., Paulsen, M. and Lengauer, T. (2007) CpG island mapping by epigenome prediction. PLoS Comput. Biol., 3, e110.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Bock, C.1
Walter, J.2
Paulsen, M.3
Lengauer, T.4
-
14
-
-
57849159039
-
Functional analysis of a potassium-chloride co-transporter 3 (SLC12A6) promoter polymorphism leading to an additional DNA methylation site
-
Moser, D., Ekawardhani, S., Kumsta, R., Palmason, H., Bock, C., Athanassiadou, Z., et al. (2008) Functional analysis of a potassium-chloride co-transporter 3 (SLC12A6) promoter polymorphism leading to an additional DNA methylation site. Neuropsychopharmacology, 34, 458-467.
-
(2008)
Neuropsychopharmacology
, vol.34
, pp. 458-467
-
-
Moser, D.1
Ekawardhani, S.2
Kumsta, R.3
Palmason, H.4
Bock, C.5
Athanassiadou, Z.6
-
15
-
-
34250376884
-
A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
-
Blankenberg, D., Taylor, J., Schenck, I., He, J., Zhang, Y., Ghent, M., et al. (2007) A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res., 17, 960-964.
-
(2007)
Genome Res.
, vol.17
, pp. 960-964
-
-
Blankenberg, D.1
Taylor, J.2
Schenck, I.3
He, J.4
Zhang, Y.5
Ghent, M.6
-
16
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., 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
-
17
-
-
15844406550
-
HyPhy: Hypothesis testing using phylogenies
-
Pond, S.L., Frost, S.D. and Muse, S.V. (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics, 21, 676-679.
-
(2005)
Bioinformatics
, vol.21
, pp. 676-679
-
-
Pond, S.L.1
Frost, S.D.2
Muse, S.V.3
-
18
-
-
0034201441
-
EMBOSS: The European molecular biology open software suite
-
Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
19
-
-
20044384522
-
Mapping of genetic and epigenetic regulatory networks using microarrays
-
van Steensel, B. (2005) Mapping of genetic and epigenetic regulatory networks using microarrays. Nat. Genet., 37 Suppl, S18-24.
-
(2005)
Nat. Genet.
, vol.37
, Issue.SUPPL.
-
-
Van Steensel, B.1
-
20
-
-
37548999369
-
Computational epigenetics
-
Bock, C. and Lengauer, T. (2008) Computational epigenetics. Bioinformatics, 24, 1-10.
-
(2008)
Bioinformatics
, vol.24
, pp. 1-10
-
-
Bock, C.1
Lengauer, T.2
-
21
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinfor-matics
-
Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., et al. (2004) Bioconductor: open software development for computational biology and bioinfor-matics. Genome Biol., 5, R80.
-
(2004)
Genome Biol.
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
-
22
-
-
35748982895
-
Getting started in tiling microar-ray analysis
-
Liu, X.S. (2007) Getting started in tiling microar-ray analysis. PLoS Comput. Biol., 3, 1842-1844.
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 1842-1844
-
-
Liu, X.S.1
-
23
-
-
40449126726
-
Systematic evaluation of variability in ChIP-chip experiments using predefned DNA targets
-
Johnson, D.S., Li, W., Gordon, D.B., Bhattacharjee, A., Curry, B., Ghosh, J., et al. (2008) Systematic evaluation of variability in ChIP-chip experiments using predefned DNA targets. Genome Res., 18, 393-403.
-
(2008)
Genome Res.
, vol.18
, pp. 393-403
-
-
Johnson, D.S.1
Li, W.2
Gordon, D.B.3
Bhattacharjee, A.4
Curry, B.5
Ghosh, J.6
-
24
-
-
33747587864
-
Model-based analysis of tiling-arrays for ChIP-chip
-
Johnson, W.E., Li, W., Meyer, C.A., Gottardo, R., Carroll, J.S., Brown, M. and Liu, X.S. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. USA., 103, 12457-12462.
-
(2006)
Proc. Natl. Acad. Sci. USA.
, vol.103
, pp. 12457-12462
-
-
Johnson, W.E.1
Li, W.2
Meyer, C.A.3
Gottardo, R.4
Carroll, J.S.5
Brown, M.6
Liu, X.S.7
-
25
-
-
48449097251
-
QUMA: Quantifcation tool for methylation analysis
-
Kumaki, Y., M. Oda, and M. Okano. 2008. QUMA: quantifcation tool for methylation analysis. Nucleic Acids Res 36: W170-175.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Kumaki, Y.1
Oda, M.2
Okano, M.3
-
26
-
-
27744577751
-
BiQ Analyzer: Visualization and quality control for DNA methylation data from bisulfte sequencing
-
Bock, C., Reither, S., Mikeska, T., Paulsen, M., Walter, J. and Lengauer, T. (2005) BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfte sequencing. Bioinformatics, 21, 4067-4068.
-
(2005)
Bioinformatics
, vol.21
, pp. 4067-4068
-
-
Bock, C.1
Reither, S.2
Mikeska, T.3
Paulsen, M.4
Walter, J.5
Lengauer, T.6
-
27
-
-
38549131376
-
The UCSC Genome Browser Database: 2008 update
-
Karolchik, D., Kuhn, R.M., Baertsch, R., Barber, G.P., Clawson, H., Diekhans, M., et al. (2008) The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res., 36, D773-779.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Karolchik, D.1
Kuhn, R.M.2
Baertsch, R.3
Barber, G.P.4
Clawson, H.5
Diekhans, M.6
-
28
-
-
38549176691
-
Ensembl 2008
-
Flicek, P., Aken, B.L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., et al. (2008) Ensembl 2008. Nucleic Acids Res., 36, D707-714.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Flicek, P.1
Aken, B.L.2
Beal, K.3
Ballester, B.4
Caccamo, M.5
Chen, Y.6
-
29
-
-
33746051706
-
Computational prediction of methylation status in human genomic sequences
-
Das, R., Dimitrova, N., Xuan, Z., Rollins, R.A., Haghighi, F., Edwards, J.R., et al. (2006) Computational prediction of methylation status in human genomic sequences. Proc. Natl. Acad. Sci. U. S. A., 103, 10713-10716.
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, pp. 10713-10716
-
-
Das, R.1
Dimitrova, N.2
Xuan, Z.3
Rollins, R.A.4
Haghighi, F.5
Edwards, J.R.6
-
30
-
-
33748711235
-
Predicting methylation status of CpG islands in the human brain
-
Fang, F., Fan, S., Zhang, X. and Zhang, M.Q. (2006) Predicting methylation status of CpG islands in the human brain. Bioinformatics, 22, 2204-2209.
-
(2006)
Bioinformatics
, vol.22
, pp. 2204-2209
-
-
Fang, F.1
Fan, S.2
Zhang, X.3
Zhang, M.Q.4
-
31
-
-
1242296842
-
A comprehensive analysis of allelic methyla-tion status of CpG islands on human chromosome 21q
-
Yamada, Y., Watanabe, H., Miura, F., Soejima, H., Uchiyama, M., Iwasaka, T., et al. (2004) A comprehensive analysis of allelic methyla-tion status of CpG islands on human chromosome 21q. Genome Res., 14, 247-266.
-
(2004)
Genome Res.
, vol.14
, pp. 247-266
-
-
Yamada, Y.1
Watanabe, H.2
Miura, F.3
Soejima, H.4
Uchiyama, M.5
Iwasaka, T.6
-
32
-
-
33845703344
-
What is a support vector machine?
-
Noble, W.S. (2006) What is a support vector machine? Nat. Biotechnol., 24, 1565-1567.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1565-1567
-
-
Noble, W.S.1
-
33
-
-
63449103531
-
DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution
-
Zhang, Y., C. Rohde, S. Tierling, T.P. Jurkowski, C. Bock, D. Santacruz, S. Ragozin, R. Reinhardt, M. Groth, J. Walter, and A. Jeltsch. 2009. DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution. PLoS Genet 5: e1000438.
-
(2009)
PLoS Genet
, vol.5
-
-
Zhang, Y.1
Rohde, C.2
Tierling, S.3
Jurkowski, T.P.4
Bock, C.5
Santacruz, D.6
Ragozin, S.7
Reinhardt, R.8
Groth, M.9
Walter, J.10
Jeltsch, A.11
-
34
-
-
35348983887
-
A second generation human haplotype map of over 3.1 million SNPs
-
Frazer, K.A., Ballinger, D.G., Cox, D.R., Hinds, D.A., Stuve, L.L., Gibbs, R.A., et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-861.
-
(2007)
Nature
, vol.449
, pp. 851-861
-
-
Frazer, K.A.1
Ballinger, D.G.2
Cox, D.R.3
Hinds, D.A.4
Stuve, L.L.5
Gibbs, R.A.6
-
35
-
-
7444260846
-
The ENCODE (ENCyclopedia of DNA Elements) Project
-
ENCODE Project Consortium
-
ENCODE Project Consortium. (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306, 636-640.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
36
-
-
34547635063
-
HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifcations
-
Wang, G.P., Ciuff, A., Leipzig, J., Berry, C.C. and Bushman, F.D. (2007) HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifcations. Genome Res., 17, 1186-1194.
-
(2007)
Genome Res.
, vol.17
, pp. 1186-1194
-
-
Wang, G.P.1
Ciuff, A.2
Leipzig, J.3
Berry, C.C.4
Bushman, F.D.5
-
38
-
-
0003684449
-
-
Springer, New York
-
Hastie, T., Tibshirani, R. and Friedman, J.H. (2001) The elements of statistical learning: data mining, inference, and prediction. Springer, New York.
-
(2001)
The Elements of Statistical Learning: Data Mining, Inference, and Prediction
-
-
Hastie, T.1
Tibshirani, R.2
Friedman, J.H.3
-
39
-
-
84872256757
-
Machine learning and its applications to biology
-
Tarca, A.L., Carey, V.J., Chen, X.W., Romero, R. and Draghici, S. (2007) Machine learning and its applications to biology. PLoS Comput. Biol., 3, e116.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Tarca, A.L.1
Carey, V.J.2
Chen, X.W.3
Romero, R.4
Draghici, S.5
-
40
-
-
49649125042
-
Genome-scale DNA methylation maps of pluripotent and differentiated cells
-
Meissner, A., Mikkelsen, T.S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., 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.S.2
Gu, H.3
Wernig, M.4
Hanna, J.5
Sivachenko, A.6
|