-
1
-
-
34249026300
-
High-Resolution Profiling of Histone Methylations in the Human Genome
-
[87]
-
Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., Zhao, K., et al. (2007), "High-Resolution Profiling of Histone Methylations in the Human Genome, " Cell, 129, 823-837. [87]
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
2
-
-
84865790047
-
An Integrated Encyclopedia of DNA Elements in the Human Genome
-
[87]
-
Bernstein, B. E., Birney, E., Dunham, I., Green, E. D., Gunter, C., Snyder, M., et al. (2012), "An Integrated Encyclopedia of DNA Elements in the Human Genome, " Nature, 489, 57. [87]
-
(2012)
Nature
, vol.489
, pp. 57
-
-
Bernstein, B.E.1
Birney, E.2
Dunham, I.3
Green, E.D.4
Gunter, C.5
Snyder, M.6
-
3
-
-
0032329029
-
Asymptotic Normality of the Maximum-Likelihood Estimator for General Hidden Markov Models
-
[81,93]
-
Bickel, P. J., Ritov, Y., and Ryden, T. (1998), "Asymptotic Normality of the Maximum-Likelihood Estimator for General Hidden Markov Models, " The Annals of Statistics, 26, 1614-1635. [81,93]
-
(1998)
The Annals of Statistics
, vol.26
, pp. 1614-1635
-
-
Bickel, P.J.1
Ritov, Y.2
Ryden, T.3
-
4
-
-
54949147307
-
F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags
-
[88]
-
Boyle, A. P., Guinney, J., Crawford, G. E., and Furey, T. S. (2008), "F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags, " Bioinformatics, 24, 2537-2538. [88]
-
(2008)
Bioinformatics
, vol.24
, pp. 2537-2538
-
-
Boyle, A.P.1
Guinney, J.2
Crawford, G.E.3
Furey, T.S.4
-
5
-
-
0002837834
-
Statistical Analysis of Time Series: Some Recent Developments
-
(with discussion), [80]
-
Cox, D. R., Gudmundsson, G., Lindgren, G., Bondesson, L., Harsaae, E., Laake, P., Juselius, K., and Lauritzen, S. L. (1981), "Statistical Analysis of Time Series: Some Recent Developments" (with discussion), Scandinavian Journal of Statistics, 8, 93-115. [80]
-
(1981)
Scandinavian Journal of Statistics
, vol.8
, pp. 93-115
-
-
Cox, D.R.1
Gudmundsson, G.2
Lindgren, G.3
Bondesson, L.4
Harsaae, E.5
Laake, P.6
Juselius, K.7
Lauritzen, S.L.8
-
6
-
-
3843066519
-
Observation-Driven Models for Poisson Counts
-
[80]
-
Davis, R. A., Dunsmuir, W. T.M., and Streett, S. B. (2003), "Observation-Driven Models for Poisson Counts, " Biometrika, 90, 777-790. [80]
-
(2003)
Biometrika
, vol.90
, pp. 777-790
-
-
Davis, R.A.1
Dunsmuir, W.T.M.2
Streett, S.B.3
-
7
-
-
1542784653
-
Empirical Bayes Analysis of a Microarray Experiment
-
[87]
-
Efron, B., Tibshirani, R., Storey, J. D., and Tusher, V. (2001), "Empirical Bayes Analysis of a Microarray Experiment, " Journal of the American Statistical Association, 96, 1151-1160. [87]
-
(2001)
Journal of the American Statistical Association
, vol.96
, pp. 1151-1160
-
-
Efron, B.1
Tibshirani, R.2
Storey, J.D.3
Tusher, V.4
-
8
-
-
1542784498
-
Variable Selection via Nonconcave Penalized Likelihood and Its Oracle Properties
-
[80,81,84]
-
Fan, J., and Li, R. (2001), "Variable Selection via Nonconcave Penalized Likelihood and Its Oracle Properties, " Journal of the American Statistical Association, 96, 1348-1360. [80,81,84]
-
(2001)
Journal of the American Statistical Association
, vol.96
, pp. 1348-1360
-
-
Fan, J.1
Li, R.2
-
9
-
-
77949352853
-
A Selective Overview of Variable Selection in High Dimensional Feature Space
-
[81]
-
Fan, J., and Lv, J. (2010), "A Selective Overview of Variable Selection in High Dimensional Feature Space, " Statistica Sinica, 20, 101. [81]
-
(2010)
Statistica Sinica
, vol.20
, pp. 101
-
-
Fan, J.1
Lv, J.2
-
10
-
-
0034641720
-
Overexpression of MYC Causes p53-Dependent g2 Arrest of Normal Fibroblasts
-
[93]
-
Felsher, D.W., Zetterberg, A., Zhu, J., Tlsty, T., and Bishop, J. M. (2000), "Overexpression of MYC Causes p53-Dependent g2 Arrest of Normal Fibroblasts, " Proceedings of the National Academy of Sciences, 97, 10544-10548. [93]
-
(2000)
Proceedings of the National Academy of Sciences
, vol.97
, pp. 10544-10548
-
-
Felsher, D.W.1
Zetterberg, A.2
Zhu, J.3
Tlsty, T.4
Bishop, J.M.5
-
11
-
-
84862556734
-
Fast Sparse Regression and Classification
-
[80]
-
Friedman, J. H. (2008), "Fast Sparse Regression and Classification, " International Journal of Forecasting, 28, 722-738. [80]
-
(2008)
International Journal of Forecasting
, vol.28
, pp. 722-738
-
-
Friedman, J.H.1
-
12
-
-
77949374262
-
Variable Selection for Regression Models With Missing Data
-
[83]
-
Garcia, R. I., Ibrahim, J. G., and Zhu, H. (2010), "Variable Selection for Regression Models With Missing Data, " Statistica Sinica, 20, 149. [83]
-
(2010)
Statistica Sinica
, vol.20
, pp. 149
-
-
Garcia, R.I.1
Ibrahim, J.G.2
Zhu, H.3
-
15
-
-
55749094855
-
An Integrated Software System for Analyzing Chip-Chip and Chip-Seq Data
-
[78,91]
-
Ji, H., Jiang, H., Ma, W., Johnson, D. S., Myers, R. M., andWong, W. H. (2008), "An Integrated Software System for Analyzing Chip-Chip and Chip-Seq Data, " Nature Biotechnology, 26, 1293-1300. [78,91]
-
(2008)
Nature Biotechnology
, vol.26
, pp. 1293-1300
-
-
Ji, H.1
Jiang, H.2
Ma, W.3
Johnson, D.S.4
Myers, R.M.5
Wong, W.H.6
-
16
-
-
35348854001
-
Variable Selection in Finite Mixture of Regression Models
-
[80,81,82,84,93]
-
Khalili, A., and Chen, J. (2007), "Variable Selection in Finite Mixture of Regression Models, " Journal of the American Statistical Association, 102, 1025-1038. [80,81,82,84,93]
-
(2007)
Journal of the American Statistical Association
, vol.102
, pp. 1025-1038
-
-
Khalili, A.1
Chen, J.2
-
17
-
-
33947201809
-
Analysis of the Vertebrate Insulator Protein ctcf Binding Sites in the Human Genome
-
[87]
-
Kim, T. H., Abdullaev, Z. K., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., and Ren, B. (2007), "Analysis of the Vertebrate Insulator Protein ctcf Binding Sites in the Human Genome, " Cell, 128, 1231. [87]
-
(2007)
Cell
, vol.128
, pp. 1231
-
-
Kim, T.H.1
Abdullaev, Z.K.2
Smith, A.D.3
Ching, K.A.4
Loukinov, D.I.5
Green, R.D.6
Zhang, M.Q.7
Lobanenkov, V.V.8
Ren, B.9
-
18
-
-
61349098460
-
Differential Chromatin Marking of Introns and Expressed Exons by h3k36me3
-
[91]
-
Kolasinska-Zwierz, P., Down, T., Latorre, I., Liu, Liu, X. S., and Ahringer, J. (2009), "Differential Chromatin Marking of Introns and Expressed Exons by h3k36me3, " Nature Genetics, 41, 376-381. [91]
-
(2009)
Nature Genetics
, vol.41
, pp. 376-381
-
-
Kolasinska-Zwierz, P.1
Down, T.2
Latorre, I.3
Liu, L.X.S.4
Ahringer, J.5
-
19
-
-
80054712249
-
A Statistical Framework for the Analysis of Chip-Seq Data
-
[78,79,80]
-
Kuan, P. F., Chung, D., Pan, G., Thomson, J. A., Stewart, R., andKeles, S. (2011), "A Statistical Framework for the Analysis of Chip-Seq Data, " Journal of the American Statistical Association, 106, 891-903. [78,79,80]
-
(2011)
Journal of the American Statistical Association
, vol.106
, pp. 891-903
-
-
Kuan, P.F.1
Chung, D.2
Pan, G.3
Thomson, J.A.4
Stewart, R.5
Keles, S.6
-
20
-
-
34249099730
-
Combined Action of phd and Chromo Domains Directs the rpd3s hdac to Transcribed Chromatin
-
[91]
-
Li, B., Gogol, M., Carey, M., Lee, D., Seidel, C., and Workman, J. L. (2007), "Combined Action of phd and Chromo Domains Directs the rpd3s hdac to Transcribed Chromatin, " Science, 316, 1050-1054. [91]
-
(2007)
Science
, vol.316
, pp. 1050-1054
-
-
Li, B.1
Gogol, M.2
Carey, M.3
Lee, D.4
Seidel, C.5
Workman, J.L.6
-
21
-
-
84876943255
-
The Histone Mark h3k36me3 Regulates Human DNA Mismatch Repair Through Its Interaction With mutsα
-
[91]
-
Li, F., Mao, G., Tong, D., Huang, J., Gu, L., Yang, W., and Li, G.-M. (2013), "The Histone Mark h3k36me3 Regulates Human DNA Mismatch Repair Through Its Interaction With mutsα, " Cell, 153, 590-600. [91]
-
(2013)
Cell
, vol.153
, pp. 590-600
-
-
Li, F.1
Mao, G.2
Tong, D.3
Huang, J.4
Gu, L.5
Yang, W.6
Li, G.-M.7
-
22
-
-
8744241621
-
Leukemia/Lymphoma-Related Factor, a POZ Domain-Containing Transcriptional Repressor, Interacts With Histone Deacetylase-1 and Inhibits Cartilage Oligomeric Matrix Protein Gene Expression and Chondrogenesis
-
[92]
-
Liu, C.-J., Prazak, L., Fajardo, M., Yu, S., Tyagi, N., and Di Cesare, P. E. (2004), "Leukemia/Lymphoma-Related Factor, a POZ Domain-Containing Transcriptional Repressor, Interacts With Histone Deacetylase-1 and Inhibits Cartilage Oligomeric Matrix Protein Gene Expression and Chondrogenesis, " Journal of Biological Chemistry, 279, 47081-47091. [92]
-
(2004)
Journal of Biological Chemistry
, vol.279
, pp. 47081-47091
-
-
Liu, C.-J.1
Prazak, L.2
Fajardo, M.3
Yu, S.4
Tyagi, N.5
Di Cesare, P.E.6
-
23
-
-
0016640079
-
Human Chronic Myelogenous Leukemia Cell-Line With Positive Philadelphia Chromosome
-
[91]
-
Lozzio, C. B., and Lozzio, B. B. (1975), "Human Chronic Myelogenous Leukemia Cell-Line With Positive Philadelphia Chromosome, " Blood, 45, 321-334. [91]
-
(1975)
Blood
, vol.45
, pp. 321-334
-
-
Lozzio, C.B.1
Lozzio, B.B.2
-
24
-
-
0036750717
-
Exact Computation of the Observed InformationMatrix for HiddenMarkovModels
-
[83]
-
Lystig, T. C., and Hughes, J. P. (2002), "Exact Computation of the Observed InformationMatrix for HiddenMarkovModels, " Journal of Computational and Graphical Statistics, 11, 678-689. [83]
-
(2002)
Journal of Computational and Graphical Statistics
, vol.11
, pp. 678-689
-
-
Lystig, T.C.1
Hughes, J.P.2
-
25
-
-
0031090158
-
On the EM Algorithm for Overdispersed Count Data
-
[80]
-
McLachlan, G. J. (1997), "On the EM Algorithm for Overdispersed Count Data, " Statistical Methods in Medical Research, 6, 76-98. [80]
-
(1997)
Statistical Methods in Medical Research
, vol.6
, pp. 76-98
-
-
McLachlan, G.J.1
-
26
-
-
0000251971
-
Maximum Likelihood Estimation via the ECM Algorithm: A General Framework
-
[82]
-
Meng, X.-L., and Rubin, D. B. (1993), "Maximum Likelihood Estimation via the ECM Algorithm: A General Framework, " Biometrika, 80, 267-278. [82]
-
(1993)
Biometrika
, vol.80
, pp. 267-278
-
-
Meng, X.-L.1
Rubin, D.B.2
-
27
-
-
77954041808
-
Hpeak: An HMM-Based Algorithm for Defining Read-Enriched Regions in ChIP-Seq Data
-
[78,79]
-
Qin, Z. S., Yu, J., Shen, J., Maher, C. A., Hu, M., Kalyana-Sundaram, S., Yu, J., and Chinnaiyan, A. M. (2010), "Hpeak: An HMM-Based Algorithm for Defining Read-Enriched Regions in ChIP-Seq Data, " BMC Bioinformatics, 11, 369. [78,79]
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 369
-
-
Qin, Z.S.1
Yu, J.2
Shen, J.3
Maher, C.A.4
Hu, M.5
Kalyana-Sundaram, S.6
Yu, J.7
Chinnaiyan, A.M.8
-
28
-
-
79960614727
-
ZINBA Integrates Local CovariatesWith DNA-Seq Data to Identify Broad and Narrow Regions of Enrichment, Even Within Amplified Genomic Regions
-
[78,79,80,84,87,88,91]
-
Rashid, N. U., Giresi, P. G., Ibrahim, J. G., Sun, W., and Lieb, J. D. (2011), "ZINBA Integrates Local CovariatesWith DNA-Seq Data to Identify Broad and Narrow Regions of Enrichment, Even Within Amplified Genomic Regions, " Genome Biology, 12, R67. [78,79,80,84,87,88,91]
-
(2011)
Genome Biology
, vol.12
-
-
Rashid, N.U.1
Giresi, P.G.2
Ibrahim, J.G.3
Sun, W.4
Lieb, J.D.5
-
29
-
-
1042290351
-
The swi/snf Complex chromatin and Cancer
-
[92]
-
Roberts, C. W. M., and Orkin, S. H. (2004), "The swi/snf Complex chromatin and Cancer, " Nature Reviews Cancer, 4, 133-142. [92]
-
(2004)
Nature Reviews Cancer
, vol.4
, pp. 133-142
-
-
Roberts, C.W.M.1
Orkin, S.H.2
-
30
-
-
60149112271
-
Peakseq Enables Systematic Scoring of ChIP-Seq Experiments Relative to Controls
-
[78]
-
Rozowsky, J., Euskirchen, G., Auerbach, R. K., Zhang, Z. D., Gibson, T., Bjornson, R., Carriero, N., Snyder, M., and Gerstein, M. B. (2009), "Peakseq Enables Systematic Scoring of ChIP-Seq Experiments Relative to Controls, " Nature Biotechnology, 27, 66-75. [78]
-
(2009)
Nature Biotechnology
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
Zhang, Z.D.4
Gibson, T.5
Bjornson, R.6
Carriero, N.7
Snyder, M.8
Gerstein, M.B.9
-
31
-
-
0000120766
-
Estimating the Dimension of a Model
-
[80]
-
Schwarz, G. (1978), "Estimating the Dimension of a Model, " The Annals of Statistics, 6, 461-464. [80]
-
(1978)
The Annals of Statistics
, vol.6
, pp. 461-464
-
-
Schwarz, G.1
-
32
-
-
70449434105
-
Bayespeak:Bayesian Analysis of ChIP-Seq Data
-
[78,79]
-
Spyrou, C., Stark, R., Lynch, A. G., and Tavaré, S. (2009), "Bayespeak:Bayesian Analysis of ChIP-Seq Data, " BMC Bioinformatics, 10, 299. [78,79]
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 299
-
-
Spyrou, C.1
Stark, R.2
Lynch, A.G.3
Tavaré, S.4
-
33
-
-
77956644615
-
Genomewide Multiple-Loci Mapping in Experimental Crosses by Iterative Adaptive Penalized Regression
-
[81]
-
Sun, W., Ibrahim, J. G., and Zou, F. (2010), "Genomewide Multiple-Loci Mapping in Experimental Crosses by Iterative Adaptive Penalized Regression, " Genetics, 185, 349. [81]
-
(2010)
Genetics
, vol.185
, pp. 349
-
-
Sun, W.1
Ibrahim, J.G.2
Zou, F.3
-
34
-
-
84875537133
-
Epigenetic Reprogramming in Cancer
-
[93]
-
Suvà, M. L., Riggi, N., andBernstein, B. E. (2013), "Epigenetic Reprogramming in Cancer, " Science, 339, 1567-1570. [93]
-
(2013)
Science
, vol.339
, pp. 1567-1570
-
-
Suvà, M.L.1
Riggi, N.2
Bernstein, B.E.3
-
35
-
-
84865755978
-
The Accessible Chromatin Landscape of the Human Genome
-
[91,93]
-
Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012), "The Accessible Chromatin Landscape of the Human Genome, " Nature, 489, 75-82. [91,93]
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
Rynes, E.2
Humbert, R.3
Vierstra, J.4
Maurano, M.T.5
Haugen, E.6
Sheffield, N.C.7
Stergachis, A.B.8
Wang, H.9
Vernot, B.10
-
36
-
-
85194972808
-
Regression Shrinkage and Selection via the Lasso
-
[80]
-
Tibshirani, R. (1996), "Regression Shrinkage and Selection via the Lasso, " Journal of the Royal Statistical Society, Series B, 58, 267-288. [80]
-
(1996)
Journal of the Royal Statistical Society, Series B
, vol.58
, pp. 267-288
-
-
Tibshirani, R.1
-
37
-
-
34347392874
-
Nup98-nsd1 Links h3k36 Methylation to hox-a Gene Activation and Leukaemogenesis
-
[91]
-
Wang, G. G., Cai, L., Pasillas, M. P., and Kamps, M. P. (2007), "Nup98-nsd1 Links h3k36 Methylation to hox-a Gene Activation and Leukaemogenesis, " Nature Cell Biology, 9, 804-812. [91]
-
(2007)
Nature Cell Biology
, vol.9
, pp. 804-812
-
-
Wang, G.G.1
Cai, L.2
Pasillas, M.P.3
Kamps, M.P.4
-
38
-
-
53749092745
-
An HMM Approach to Genome-Wide Identification of Differential Histone Modification Sites From ChIP-Seq Data
-
[79]
-
Xu, H., Wei, C. L., Lin, F., and Sung, W. K. (2008), "An HMM Approach to Genome-Wide Identification of Differential Histone Modification Sites From ChIP-Seq Data, " Bioinformatics, 24, 2344-2349. [79]
-
(2008)
Bioinformatics
, vol.24
, pp. 2344-2349
-
-
Xu, H.1
Wei, C.L.2
Lin, F.3
Sung, W.K.4
-
39
-
-
0013136164
-
A Regression Model for Time Series of Counts
-
[80]
-
Zeger, S. L. (1988), "A Regression Model for Time Series of Counts, " Biometrika, 75, 621. [80]
-
(1988)
Biometrika
, vol.75
, pp. 621
-
-
Zeger, S.L.1
-
40
-
-
0024204207
-
Markov Regression Models for Time Series: A Quasi-Likelihood Approach
-
[80]
-
Zeger, S. L., and Qaqish, B. (1988), "Markov Regression Models for Time Series: A Quasi-Likelihood Approach, " Biometrics, 44, 1019-1031. [80]
-
(1988)
Biometrics
, vol.44
, pp. 1019-1031
-
-
Zeger, S.L.1
Qaqish, B.2
-
41
-
-
77649284492
-
Nearly Unbiased Variable Selection Under Minimax Concave Penalty
-
[80]
-
Zhang, C. H. (2010), "Nearly Unbiased Variable Selection Under Minimax Concave Penalty, " The Annals of Statistics, 38, 894-942. [80]
-
(2010)
The Annals of Statistics
, vol.38
, pp. 894-942
-
-
Zhang, C.H.1
-
42
-
-
53849146020
-
Model-Based Analysis of ChIP-Seq (MACS)
-
[88]
-
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., et al. (2008a), "Model-Based Analysis of ChIP-Seq (MACS), " Genome Biology, 9, R137. [88]
-
(2008)
Genome Biology
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
-
43
-
-
50949097455
-
Modeling ChIP Sequencing in Silico With Applications
-
[91]
-
Zhang, Z. D., Rozowsky, J., Snyder, M., Chang, J., and Gerstein, M. (2008b), "Modeling ChIP Sequencing in Silico With Applications, " PLoS Comput Biol, 4, e1000158. [91]
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Zhang, Z.D.1
Rozowsky, J.2
Snyder, M.3
Chang, J.4
Gerstein, M.5
-
44
-
-
33846114377
-
The Adaptive Lasso and Its Oracle Properties
-
[80]
-
Zou, H. (2006), "The Adaptive Lasso and Its Oracle Properties, " Journal of the American Statistical Association, 101, 1418-1429. [80]
-
(2006)
Journal of the American Statistical Association
, vol.101
, pp. 1418-1429
-
-
Zou, H.1
|