-
1
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
-
(2010)
Genome Biol.
, vol.11
-
-
Anders, S.1
Huber, W.2
-
2
-
-
0034281086
-
Comparing the success of different prediction software in sequence analysis: A review
-
Bajić, V.B. (2000) Comparing the success of different prediction software in sequence analysis: a review. Brief. Bioinform., 1, 214-228.
-
(2000)
Brief. Bioinform.
, vol.1
, pp. 214-228
-
-
Bajić, V.B.1
-
3
-
-
34249026300
-
High-Resolution Profiling of histone methylations in the human genome
-
Barski, A. et al. (2007) High-Resolution Profiling of histone methylations in the human genome. Cell, 129, 823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
-
4
-
-
84861548193
-
Summarizing and correcting the GC content bias in high-throughput sequencing
-
Benjamini, Y. and Speed, T.P. (2012) Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res., 40, e72.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Benjamini, Y.1
Speed, T.P.2
-
5
-
-
77957333749
-
13 - Histone modification therapy of cancer
-
Zdenko, Herceg and Toshikazu, Ushijima (eds) Academic Press, United States
-
Biancotto, C. et al. (2010) 13 - histone modification therapy of cancer. In: Zdenko, Herceg and Toshikazu, Ushijima (eds) Advances in Genetics. Academic Press, United States, pp. 341-386.
-
(2010)
Advances in Genetics.
, pp. 341-386
-
-
Biancotto, C.1
-
6
-
-
78651430230
-
Control-free calling of copy number alterations in deepsequencing data using GC-content normalization
-
Boeva, V. et al. (2011) Control-free calling of copy number alterations in deepsequencing data using GC-content normalization. Bioinformatics, 27, 268-269.
-
(2011)
Bioinformatics
, vol.27
, pp. 268-269
-
-
Boeva, V.1
-
7
-
-
84856561659
-
Control-FREEC: A tool for assessing copy number and allelic content using next-generation sequencing data
-
Boeva, V. et al. (2012a) Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics, 28, 423-425.
-
(2012)
Bioinformatics
, vol.28
, pp. 423-425
-
-
Boeva, V.1
-
8
-
-
84867325570
-
Nebula - A web-server for advanced ChIP-seq data analysis
-
Boeva, V. et al. (2012b) Nebula - a web-server for advanced ChIP-seq data analysis. Bioinformatics, 28, 2517-2519.
-
(2012)
Bioinformatics
, vol.28
, pp. 2517-2519
-
-
Boeva, V.1
-
9
-
-
23844537411
-
Homeobox D10 induces phenotypic reversion of breast tumor cells in a three-dimensional culture model
-
Carrio, M. et al. (2005) Homeobox D10 induces phenotypic reversion of breast tumor cells in a three-dimensional culture model. Cancer Res., 65, 7177-7185.
-
(2005)
Cancer Res.
, vol.65
, pp. 7177-7185
-
-
Carrio, M.1
-
10
-
-
78650192632
-
Transcriptional repression of DLEC1 associates with the depth of tumor invasion in oral squamous cell carcinoma
-
Chan, W.H. et al. (2010) Transcriptional repression of DLEC1 associates with the depth of tumor invasion in oral squamous cell carcinoma. Oral Oncol., 46, 874-879.
-
(2010)
Oral Oncol.
, vol.46
, pp. 874-879
-
-
Chan, W.H.1
-
11
-
-
84861964081
-
Systematic evaluation of factors influencing ChIP-seq fidelity
-
Chen, Y. et al. (2012) Systematic evaluation of factors influencing ChIP-seq fidelity. Nat. Methods, 9, 609-614.
-
(2012)
Nat. Methods
, vol.9
, pp. 609-614
-
-
Chen, Y.1
-
12
-
-
77649271805
-
Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity
-
Coolen, M.W. et al. (2010) Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat. Cell Biol., 12, 235-246.
-
(2010)
Nat. Cell Biol.
, vol.12
, pp. 235-246
-
-
Coolen, M.W.1
-
13
-
-
84867233454
-
Long-range epigenetic silencing of chromosome 5q31 protocadherins is involved in early and late stages of colorectal tumorigenesis through modulation of oncogenic pathways
-
Dallosso, A.R. et al. (2012) Long-range epigenetic silencing of chromosome 5q31 protocadherins is involved in early and late stages of colorectal tumorigenesis through modulation of oncogenic pathways. Oncogene, 31, 4409-4419.
-
(2012)
Oncogene
, vol.31
, pp. 4409-4419
-
-
Dallosso, A.R.1
-
15
-
-
0030970688
-
Expression and functions of EGF, FGF and TGFbetagrowth- factor family members and their receptors in invasive human transitional- cell-carcinoma cells
-
De Boer, W.I. et al. (1997) Expression and functions of EGF, FGF and TGFbetagrowth- factor family members and their receptors in invasive human transitional- cell-carcinoma cells. Int. J. Cancer, 71, 284-291.
-
(1997)
Int. J. Cancer
, vol.71
, pp. 284-291
-
-
De Boer, W.I.1
-
16
-
-
52649157765
-
Substantial biases in ultra-short read data sets from highthroughput DNA sequencing
-
Dohm, J.C. et al. (2008) Substantial biases in ultra-short read data sets from highthroughput DNA sequencing. Nucleic Acids Res., 36, e105-e105.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Dohm, J.C.1
-
17
-
-
33947315736
-
Cancer epigenomics: DNA methylomes and histone-modification maps
-
Esteller, M. (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat. Rev. Genet., 8, 286-298.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 286-298
-
-
Esteller, M.1
-
18
-
-
48249140621
-
FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology
-
Fejes, A.P. et al. (2008) FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics, 24, 1729-1730.
-
(2008)
Bioinformatics
, vol.24
, pp. 1729-1730
-
-
Fejes, A.P.1
-
19
-
-
33646369393
-
Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band
-
Frigola, J. et al. (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
-
20
-
-
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
-
21
-
-
84862988654
-
Genome-wide bovine H3K27me3 modifications and the regulatory effects on genes expressions in peripheral blood lymphocytes
-
He, Y. et al. (2012) Genome-wide bovine H3K27me3 modifications and the regulatory effects on genes expressions in peripheral blood lymphocytes. PLoS One, 7, e39094.
-
(2012)
PLoS One
, vol.7
-
-
He, Y.1
-
22
-
-
79953152547
-
EpiChIP: Gene-by-gene quantification of epigenetic modification levels
-
Hebenstreit, D. et al. (2011) EpiChIP: gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Res., 39, e27.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Hebenstreit, D.1
-
23
-
-
22044455309
-
HOXB13 is downregulated in colorectal cancer to confer TCF4-mediated transactivation
-
Jung, C. et al. (2005) HOXB13 is downregulated in colorectal cancer to confer TCF4-mediated transactivation. Br. J. Cancer, 92, 2233-2239.
-
(2005)
Br. J. Cancer
, vol.92
, pp. 2233-2239
-
-
Jung, C.1
-
24
-
-
57449100870
-
Design and analysis of ChIP-seq experiments for DNA-binding proteins
-
Kharchenko, P.V. et al. (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol., 26, 1351-1359.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1351-1359
-
-
Kharchenko, P.V.1
-
25
-
-
79953060951
-
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
-
Kharchenko, P.V. et al. (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature, 471, 480-485.
-
(2011)
Nature
, vol.471
, pp. 480-485
-
-
Kharchenko, P.V.1
-
26
-
-
33847076849
-
Chromatin modifications and their function
-
Kouzarides, T. (2007) Chromatin modifications and their function. Cell, 128, 693-705.
-
(2007)
Cell
, vol.128
, pp. 693-705
-
-
Kouzarides, T.1
-
27
-
-
55449105221
-
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains
-
Ku, M. et al. (2008) Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet., 4, e1000242.
-
(2008)
PLoS Genet.
, vol.4
-
-
Ku, M.1
-
28
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B. et al. (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
-
29
-
-
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
-
30
-
-
0029656012
-
Up-regulation of HOXC6, HOXD1, and HOXD8 homeobox gene expression in human neuroblastoma cells following chemical induction of differentiation
-
Manohar, C.F. et al. (1996) Up-regulation of HOXC6, HOXD1, and HOXD8 homeobox gene expression in human neuroblastoma cells following chemical induction of differentiation. Tumour Biol., 17, 34-47.
-
(1996)
Tumour Biol.
, vol.17
, pp. 34-47
-
-
Manohar, C.F.1
-
31
-
-
54249097887
-
Agglomerative epigenetic aberrations are a common event in human breast cancer
-
Novak, P. et al. (2008) Agglomerative epigenetic aberrations are a common event in human breast cancer. Cancer Res., 68, 8616-8625.
-
(2008)
Cancer Res.
, vol.68
, pp. 8616-8625
-
-
Novak, P.1
-
32
-
-
76249097734
-
Genome Alteration Print (GAP): A tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
-
Popova, T. et al. (2009) Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol., 10, R128.
-
(2009)
Genome Biol.
, vol.10
-
-
Popova, T.1
-
33
-
-
77954041808
-
HPeak: An HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
-
Qin, Z.S. et al. (2010) HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics, 11, 369.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 369
-
-
Qin, Z.S.1
-
34
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson, G. et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods, 4, 651-657.
-
(2007)
Nat. Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.1
-
35
-
-
78651271733
-
Integrative genomics viewer
-
Robinson, J.T. et al. (2011) Integrative genomics viewer. Nat. Biotechnol., 29, 24-26.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
-
36
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
-
Rozowsky, J. et al. (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol., 27, 66-75.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
-
37
-
-
77951605788
-
The Hox genes and their roles in oncogenesis
-
Shah, N. and Sukumar, S. (2010) The Hox genes and their roles in oncogenesis. Nat. Rev. Cancer, 10, 361-371.
-
(2010)
Nat. Rev. Cancer
, vol.10
, pp. 361-371
-
-
Shah, N.1
Sukumar, S.2
-
38
-
-
33751530055
-
Regional copy number-independent deregulation of transcription in cancer
-
Stransky, N. et al. (2006) Regional copy number-independent deregulation of transcription in cancer. Nat. Genet., 38, 1386-1396.
-
(2006)
Nat. Genet.
, vol.38
, pp. 1386-1396
-
-
Stransky, N.1
-
39
-
-
84875634162
-
Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
-
Thorvaldsdóttir, H. et al. (2012) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform., 14, 178-192.
-
(2012)
Brief. Bioinform.
, vol.14
, pp. 178-192
-
-
Thorvaldsdóttir, H.1
-
40
-
-
78651277534
-
A novel epigenetic phenotype associated with the most aggressive pathway of bladder tumor progression
-
Vallot, C. et al. (2011) A novel epigenetic phenotype associated with the most aggressive pathway of bladder tumor progression. JNCI J. Natl Cancer Inst., 103, 47-60.
-
(2011)
JNCI J. Natl Cancer Inst.
, vol.103
, pp. 47-60
-
-
Vallot, C.1
-
41
-
-
84935113569
-
Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
-
Viterbi, A. (1967) Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Info. Theory, 13, 260-269.
-
(1967)
IEEE Trans. Info. Theory
, vol.13
, pp. 260-269
-
-
Viterbi, A.1
-
42
-
-
53749092745
-
An HMMapproach to genome-wide identification of differential histone modification sites from ChIP-Seq data
-
Xu, H. et al. (2008) An HMMapproach to genome-wide identification of differential histone modification sites from ChIP-Seq data. Bioinformatics, 24, 2344-2349.
-
(2008)
Bioinformatics
, vol.24
, pp. 2344-2349
-
-
Xu, H.1
-
43
-
-
77952857912
-
A signal-noise model for significance analysis of ChIP-seq with negative control
-
Xu, H. et al. (2010) A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics, 26, 1199-1204.
-
(2010)
Bioinformatics
, vol.26
, pp. 1199-1204
-
-
Xu, H.1
-
44
-
-
60349109571
-
DLEC1 is a functional 3p22.3 tumour suppressor silenced by promoter CpG methylation in colon and gastric cancers
-
Ying, J. et al. (2009) DLEC1 is a functional 3p22.3 tumour suppressor silenced by promoter CpG methylation in colon and gastric cancers. Br. J. Cancer, 100, 663-669.
-
(2009)
Br. J. Cancer
, vol.100
, pp. 663-669
-
-
Ying, J.1
-
45
-
-
80053217575
-
ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity
-
Young, M.D. et al. (2011) ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res., 39, 7415-7427.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 7415-7427
-
-
Young, M.D.1
-
46
-
-
67650711619
-
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
-
Zang, C. et al. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics, 25, 1952-1958.
-
(2009)
Bioinformatics
, vol.25
, pp. 1952-1958
-
-
Zang, C.1
-
47
-
-
84864714031
-
Functional dissection of hoxd cluster genes in regulation of neuroblastoma cell proliferation and differentiation
-
Zha, Y. et al. (2012) functional dissection of hoxd cluster genes in regulation of neuroblastoma cell proliferation and differentiation. PLoS One, 7, e40728.
-
(2012)
PLoS One
, vol.7
-
-
Zha, Y.1
-
48
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y. et al. (2008)Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
-
(2008)
Genome Biol.
, vol.9
-
-
Zhang, Y.1
|