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Ranked prediction of p53 targets using hidden variable dynamic modeling
Martino Barenco, Daniela Tomescu, Daniel Brewer, Robin Callard, Jaroslav Stark, Michael Hubank
Genome Biol. 2006; 7(3): R25. Published online 2006 March 31. doi: 10.1186/gb-2006-7-3-r25
PMCID:
PMC1557743
Abstract Full Text PDF–1.5M Supplementary Material
 Is Cited by the Following 16 Articles in this Archive:
Identification of novel targets for breast cancer by exploring gene switches on a genome scale
Ming Wu, Li Liu, Christina Chan
BMC Genomics. 2011; 12: 547. Published online 2011 November 3. doi: 10.1186/1471-2164-12-547
PMCID:
PMC3269833
Abstract Full Text PDF–1.9M Supplementary Material
Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern
Binhua Tang, Xuechen Wu, Ge Tan, Su-Shing Chen, Qing Jing, Bairong Shen
BMC Syst Biol. 2010; 4(Suppl 2): S3. Published online 2010 September 13. doi: 10.1186/1752-0509-4-S2-S3
PMCID:
PMC2982690
Abstract Full Text PDF–1.2M Supplementary Material
Targetfinder.org: a resource for systematic discovery of transcription factor target genes
Szymon M. Kiełbasa, Nils Blüthgen, Michael Fähling, Ralf Mrowka
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W233–W238. Published online 2010 May 11. doi: 10.1093/nar/gkq374
PMCID:
PMC2896086
Abstract Full Text PDF–247K
Major role for mRNA stability in shaping the kinetics of gene induction
Ran Elkon, Eitan Zlotorynski, Karen I Zeller, Reuven Agami
BMC Genomics. 2010; 11: 259. Published online 2010 April 21. doi: 10.1186/1471-2164-11-259
PMCID:
PMC2864252
Abstract Full Text PDF–610K Supplementary Material
Model-based method for transcription factor target identification with limited data
Antti Honkela, Charles Girardot, E. Hilary Gustafson, Ya-Hsin Liu, Eileen E. M. Furlong, Neil D. Lawrence, Magnus Rattray
Proc Natl Acad Sci U S A. 2010 April 27; 107(17): 7793–7798. Published online 2010 April 12. doi: 10.1073/pnas.0914285107
PMCID:
PMC2867914
Abstract Full Text PDF–347K Supplementary Material
An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis
Yi Zhang, Kim A Hatch, Joanna Bacon, Lorenz Wernisch
BMC Syst Biol. 2010; 4: 37. Published online 2010 March 31. doi: 10.1186/1752-0509-4-37
PMCID:
PMC2867773
Abstract Full Text PDF–772K
Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53
Junbai Wang, Tianhai Tian
BMC Bioinformatics. 2010; 11: 36. Published online 2010 January 19. doi: 10.1186/1471-2105-11-36
PMCID:
PMC2832896
Abstract Full Text PDF–405K Supplementary Material
Dissection of a complex transcriptional response using genome-wide transcriptional modelling
Martino Barenco, Daniel Brewer, Efterpi Papouli, Daniela Tomescu, Robin Callard, Jaroslav Stark, Michael Hubank
Mol Syst Biol. 2009; 5: 327. Published online 2009 November 17. doi: 10.1038/msb.2009.84
PMCID:
PMC2795478
Abstract Full Text PDF–2.5M Supplementary Material
Response of heterogeneous ribonuclear proteins (hnRNP) to ionizing radiation and their involvement in DNA damage repair
Benjamin Haley, Tatjana Paunesku, Miroslava Protić, Gayle E Woloschak
Int J Radiat Biol. Author manuscript; available in PMC 2009 November 30.
Published in final edited form as: Int J Radiat Biol. 2009 August; 85(8): 643–655. doi: 10.1080/09553000903009548
PMCID:
PMC2785495
Abstract Full Text PDF–1.2M
A dynamic network of transcription in LPS-treated human subjects
Junhee Seok, Wenzhong Xiao, Lyle L Moldawer, Ronald W Davis, Markus W Covert
BMC Syst Biol. 2009; 3: 78. Published online 2009 July 28. doi: 10.1186/1752-0509-3-78
PMCID:
PMC2729748
Abstract Full Text PDF–5.7M
Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data
Paul D. W. Kirk, Michael P. H. Stumpf
Bioinformatics. 2009 May 15; 25(10): 1300–1306. Published online 2009 March 17. doi: 10.1093/bioinformatics/btp139
PMCID:
PMC2677737
Abstract Full Text PDF–575K Supplementary Material
Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering
Giusy Della Gatta, Mukesh Bansal, Alberto Ambesi-Impiombato, Dario Antonini, Caterina Missero, Diego di Bernardo
Genome Res. 2008 June; 18(6): 939–948. doi: 10.1101/gr.073601.107
PMCID:
PMC2413161
Abstract Full Text PDF–787K
Molecular portrait of cisplatin induced response in human testis cancer cell lines based on gene expression profiles
Nur Duale, Birgitte Lindeman, Mitsuko Komada, Ann-Karin Olsen, Ashild Andreassen, Erik J Soderlund, Gunnar Brunborg
Mol Cancer. 2007; 6: 53. Published online 2007 August 21. doi: 10.1186/1476-4598-6-53
PMCID:
PMC1988831
Abstract Full Text PDF–528K Supplementary Material
Bayesian model-based inference of transcription factor activity
Simon Rogers, Raya Khanin, Mark Girolami
BMC Bioinformatics. 2007; 8(Suppl 2): S2. Published online 2007 May 3. doi: 10.1186/1471-2105-8-S2-S2
PMCID:
PMC1892071
Abstract Full Text PDF–697K
Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets
Buyong Ma, Yongping Pan, Jie Zheng, Arnold J. Levine, Ruth Nussinov
Nucleic Acids Res. 2007 May; 35(9): 2986–3001. Published online 2007 April 16. doi: 10.1093/nar/gkm192
PMCID:
PMC1888811
Abstract Full Text PDF–1.0M Supplementary Material
Correction of scaling mismatches in oligonucleotide microarray data
Martino Barenco, Jaroslav Stark, Daniel Brewer, Daniela Tomescu, Robin Callard, Michael Hubank
BMC Bioinformatics. 2006; 7: 251. Published online 2006 May 9. doi: 10.1186/1471-2105-7-251
PMCID:
PMC1508160
Abstract Full Text PDF–1.5M Supplementary Material
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