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Clustering of genes into regulons using integrated modeling-COGRIM
Guang Chen, Shane T Jensen, Christian J Stoeckert, Jr
Genome Biol. 2007; 8(1): R4. Published online 2007 January 4. doi: 10.1186/gb-2007-8-1-r4
PMCID:
PMC1839128
Abstract Full Text PDF–680K Supplementary Material
 Is Cited by the Following 18 Articles in this Archive:
Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis
Logan J. Everett, Shane T. Jensen, Sridhar Hannenhalli
Nucleic Acids Res. 2011 July; 39(12): e78. Published online 2011 April 5. doi: 10.1093/nar/gkr172
PMCID:
PMC3130287
Abstract Full Text PDF–2.4M Supplementary Material
Motif-guided sparse decomposition of gene expression data for regulatory module identification
Ting Gong, Jianhua Xuan, Li Chen, Rebecca B Riggins, Huai Li, Eric P Hoffman, Robert Clarke, Yue Wang
BMC Bioinformatics. 2011; 12: 82. Published online 2011 March 22. doi: 10.1186/1471-2105-12-82
PMCID:
PMC3072956
Abstract Full Text PDF–1.1M Supplementary Material
LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data
Geert Geeven, Harold D. MacGillavry, Ruben Eggers, Marion M. Sassen, Joost Verhaagen, August B. Smit, Mathisca C. M. de Gunst, Ronald E. van Kesteren
Nucleic Acids Res. 2011 July; 39(13): 5313–5327. Published online 2011 March 21. doi: 10.1093/nar/gkr139
PMCID:
PMC3141251
Abstract Full Text PDF–5.4M Supplementary Material
TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information
Qi Liu, Yejun Tan, Tao Huang, Guohui Ding, Zhidong Tu, Lei Liu, Yixue Li, Hongyue Dai, Lu Xie
BMC Bioinformatics. 2010; 11(Suppl 11): S5. Published online 2010 December 14. doi: 10.1186/1471-2105-11-S11-S5
PMCID:
PMC3024863
Abstract Full Text PDF–710K Supplementary Material
Learning transcriptional networks from the integration of ChIP–chip and expression data in a non-parametric model
Ahrim Youn, David J. Reiss, Werner Stuetzle
Bioinformatics. 2010 August 1; 26(15): 1879–1886. Published online 2010 June 4. doi: 10.1093/bioinformatics/btq289
PMCID:
PMC2913654
Abstract Full Text PDF–424K Supplementary Material
Multilevel support vector regression analysis to identify condition-specific regulatory networks
Li Chen, Jianhua Xuan, Rebecca B. Riggins, Yue Wang, Eric P. Hoffman, Robert Clarke
Bioinformatics. 2010 June 1; 26(11): 1416–1422. Published online 2010 April 7. doi: 10.1093/bioinformatics/btq144
PMCID:
PMC2872001
Abstract Full Text PDF–342K Supplementary Material
Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
Matthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli
Algorithms Mol Biol. 2010; 5: 4. Published online 2010 January 4. doi: 10.1186/1748-7188-5-4
PMCID:
PMC2826332
Abstract Full Text PDF–711K
Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families
Larry N. Singh, Sridhar Hannenhalli
Nucleic Acids Res. 2010 January; 38(3): 738–749. Published online 2010 January. doi: 10.1093/nar/gkp989
PMCID:
PMC2817486
Abstract Full Text PDF–1.2M Supplementary Material
Uncovering transcriptional interactions via an adaptive fuzzy logic approach
Cheng-Long Chuang, Kenneth Hung, Chung-Ming Chen, Grace S Shieh
BMC Bioinformatics. 2009; 10: 400. Published online 2009 December 6. doi: 10.1186/1471-2105-10-400
PMCID:
PMC2797023
Abstract Full Text PDF–905K Supplementary Material
Transcriptional programs: Modelling higher order structure in transcriptional control
John E Reid, Sascha Ott, Lorenz Wernisch
BMC Bioinformatics. 2009; 10: 218. Published online 2009 July 16. doi: 10.1186/1471-2105-10-218
PMCID:
PMC2725141
Abstract Full Text PDF–504K Supplementary Material
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen Marchal
BMC Syst Biol. 2009; 3: 49. Published online 2009 May 7. doi: 10.1186/1752-0509-3-49
PMCID:
PMC2684101
Abstract Full Text PDF–426K Supplementary Material
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
Karen Lemmens, Tijl De Bie, Thomas Dhollander, Sigrid C De Keersmaecker, Inge M Thijs, Geert Schoofs, Ami De Weerdt, Bart De Moor, Jos Vanderleyden, Julio Collado-Vides, Kristof Engelen, Kathleen Marchal
Genome Biol. 2009; 10(3): R27. Published online 2009 March 6. doi: 10.1186/gb-2009-10-3-r27
PMCID:
PMC2690998
Abstract Full Text PDF–639K Supplementary Material
Variable Selection in Nonparametric Varying-Coefficient Models for Analysis of Repeated Measurements
Lifeng Wang, Hongzhe Li, Jianhua Z. Huang
J Am Stat Assoc. Author manuscript; available in PMC 2010 January 5.
Published in final edited form as: J Am Stat Assoc. 2008 December 1; 103(484): 1556–1569. doi: 10.1198/016214508000000788
PMCID:
PMC2801925
Abstract Full Text PDF–1.8M
Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
Huai Li, Ming Zhan
Bioinformatics. 2008 September 1; 24(17): 1874–1880. Published online 2008 June 27. doi: 10.1093/bioinformatics/btn332
PMCID:
PMC2519161
Abstract Full Text PDF–545K Supplementary Material
Systems biology-defined NF-κB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 status
Bin Yan, Guang Chen, Kunal Saigal, Xinping Yang, Shane T Jensen, Carter Van Waes, Christian J Stoeckert, Zhong Chen
Genome Biol. 2008; 9(3): R53. Published online 2008 March 11. doi: 10.1186/gb-2008-9-3-r53
PMCID:
PMC2397505
Abstract Full Text PDF–981K Supplementary Material
High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae
Hun-Goo Lee, Hyo-Soo Lee, Sang-Hoon Jeon, Tae-Hoon Chung, Young-Sung Lim, Won-Ki Huh
Genome Biol. 2008; 9(1): R2. Published online 2008 January 3. doi: 10.1186/gb-2008-9-1-r2
PMCID:
PMC2395236
Abstract Full Text PDF–1.4M Supplementary Material
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
Tineke Casneuf, Yves Van de Peer, Wolfgang Huber
BMC Bioinformatics. 2007; 8: 461. Published online 2007 November 26. doi: 10.1186/1471-2105-8-461
PMCID:
PMC2213692
Abstract Full Text PDF–497K Supplementary Material
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
Xiangdong Liu, Walter J Jessen, Siva Sivaganesan, Bruce J Aronow, Mario Medvedovic
BMC Bioinformatics. 2007; 8: 283. Published online 2007 August 3. doi: 10.1186/1471-2105-8-283
PMCID:
PMC1994961
Abstract Full Text PDF–1.4M Supplementary Material
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