Papers Using DREM (original) (raw)

Below are examples of papers using the Dynamic Regulatory Events Miner (DREM) as part of the data analysis:

• Mendoza-Parra MA, Walia M, Sankar M, Gronemeyer H.Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics.Molecular Systems Biology 7:538, 2011.
• Dikicioglu D, Karabekmez E, Rash B, Pir P, Kirdar B, Oliver SG. How yeast re-programmes its transcriptional profile in response to different nutrient impulses. BMC Systems Biology 5:148, 2011.
• Zinman G, Brower-Sinning R, Emeche CH, Ernst J, Huang GT, Mahony S, Myers AJ, O'Dee DM, Flynn JL, Nau GJ, Ross TM, Salter RD, Benos PV, Bar-Joseph Z, Morel PA.Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque.PLoS One 6:e22401, 2011.
• The modENCODE Consortium et al.Identification of functional elements and regulatory circuits by_Drosophila_ modENCODE.Science. 330: 1787-1797, 2010.
• Gu F., Hsu H-K., Hsu P-Y, Wu J., Ma Y., Parvin J., Huang T.H-M. and Jin V.X. Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data. BMC Systems Biology 4: 170, 2010.
• Kaur A., Van P.T., Busch C.R., Robinson C.K., Pan M., Pang W.L., Reiss D.J., DiRuggiero J., and Baliga N.S. Coordination of frontline defense mechanisms under severe oxidative stress. Molecular Systems Biology 6:393, 2010.
• Bonander N., Ferndahl C., Mostad P., Wilks M.DB., Chang C., Showe L., Gustafsson L., Larsson C. and Bill R.M. Transcriptome analysis of a respiratory Saccharomyces cerevisiae strain suggests the expression of its phenotype is glucose insensitive and predominantly controlled by Hap4, Cat8 and Mig1.BMC Genomics. 9: 365, 2008.
• Ernst J., Beg Q.K., Kay K.A., Balazsi G., Oltvai Z.N., and Bar-Joseph Z. A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli. PLoS Computational Biology. 4: e1000044, 2008.