"Comparative inference and analysis of regulatory networks: from yeast to fly"
Event details
| Date | 10.03.2011 |
| Hour | 16:15 |
| Speaker | Dr. Sushmita Roy, Broad Institute - IC Faculty candidate |
| Location |
INM10
|
| Category | Conferences - Seminars |
Abstract : Transcriptional networks specify the set of connections between transcription factors and target genes, and drive cellular decisions under different spatial and temporal contexts. I will present computational methods for understanding regulatory networks spanning two very different temporal contexts, a developmental context, and an evolutionary context. I will first present an integrative approach to infer the regulatory network for the fly, Drosophila melanogaster. We used to network structure to predict expression and process annotation of target genes, demonstrating the functional value of the connections of the network. In the second part of my talk, I will present a novel multi-species clustering algorithm, Arboretum that can be used to infer expression clusters and their evolutionary histories of multiple organisms. We applied Arboretum to glucose starvation expression data of 15 ascomycete yeast species and identified five expression patterns that are all conserved across the 15 species. Analysis of cluster assignments of extant and ancestral species identified several gene sets with conserved phylogenetic patterns characteristic of life-style specific adaptations. Finally, we studied gene duplications using Arboretum and found that although duplicates do not change the overall expression patterns, they enable more divergence in clusters across species. Our results are consistent with known transcriptional responses under carbon limitation and provide new insights into the evolutionary patterns of other novel groups of genes. Arboretum is a general algorithm that is applicable to any hierarchically related dataset.
Bio : Sushmita Roy is a Computing Innovation post-doctoral fellow at the Broad Institute of Harvard and MIT.
Sushmita got her Bachelor in Computer Engineering from the Univ. of Pune (pronounced as poonay), India, and her PhD from the Univ of New Mexico. Sushmita's research focuses on developing machine learning algorithms for the inference and analysis of biological networks.
Links
Practical information
- General public
- Free
Contact
- Christine Moscioni