Comparative genomics

N2N developed a parallel, distributed-memory framework for comparative motif discovery

The increasing number of sequenced organisms has opened new possibilities for the computational discovery of cis-regulatory elements ('motifs') based on phylogenetic footprinting. Word-based, exhaustive approaches are among the best performing algorithms, however, they pose significant computational challenges as the number of candidate motifs to evaluate is very high. In this contribution, we describe a parallel, distributed-memory framework for de novo comparative motif discovery.

POSTDOCTORAL RESEARCH ASSOCIATE IN COMPARATIVE GENOMICS AT THE CHICAGO BOTANIC GARDEN

We are hiring a postdoctoral research associate for 2.5 years to lead the genome sequencing efforts of an NSF-funded, Phylogenetic Systematics grant titled “Evaluating the contributions of horizontally transferred bacterial genes and endogenous duplication events to the diversification of diatoms”. This project integrates transcriptomics, phylogenomics, and genome sequencing to understand the role of horizontal gene transfer and whole genome duplication in the diversification of diatoms.

Accepted paper: PLAZA 3.0: an access point for plant comparative genomics

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees, and detailed information about genome organization can easily be queried and visualized.

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