Network Inference

Single Cell Network Inference

Development of multicellular organisms from a single cell is arguably one of the most fascinating phenomena in biology. Mechanistic understanding of such a complex process is an important scientific challenge. Our single cell work aligns with the development of a systems perspective framework to comprehend how individual  cellular states  emerge and collectively result in a homeostatic multicellular organism.

Team

Publications

Reiss, David J., Nitin S. Baliga, and Richard Bonneau. “Integrated Biclustering of Heterogeneous Genome-Wide Datasets for the Inference of Global Regulatory Networks.” BMC Bioinformatics 7 (2006): 280. https://doi.org/10.1186/1471-2105-7-280. Cite
Bonneau, Richard, Marc T. Facciotti, David J. Reiss, Amy K. Schmid, Min Pan, Amardeep Kaur, Vesteinn Thorsson, et al. “A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell.” Cell 131, no. 7 (December 28, 2007): 1354–65. https://doi.org/10.1016/j.cell.2007.10.053. Cite
Brooks, Aaron N., David J. Reiss, Antoine Allard, Wei-Ju Wu, Diego M. Salvanha, Christopher L. Plaisier, Sriram Chandrasekaran, Min Pan, Amardeep Kaur, and Nitin S. Baliga. “A System-Level Model for the Microbial Regulatory Genome.” Molecular Systems Biology 10 (2014): 740. Cite
Reiss, David J., Christopher L. Plaisier, Wei-Ju Wu, and Nitin S. Baliga. “CMonkey2: Automated, Systematic, Integrated Detection of Co-Regulated Gene Modules for Any Organism.” Nucleic Acids Research 43, no. 13 (July 27, 2015): e87. https://doi.org/10.1093/nar/gkv300. Cite

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