Model Systems: Halobacterium
The Baliga group seeks to understand the physiological implications of these regulatory influences at the systems level.
Computational biology
cMonkey
has been adapted and improved for use with higher eukaryotic species such as Arabidopsis thaliana and Homo sapiens. This required the development of a gene expression microarray preprocessing pipeline for normalization and quality control, and the development of a framework for extracting the cis-regulatory regions that cMonkey utilizes for de novo motif detection. These improvements to cMonkey allowed identification of a set of co-regulated genes in a glioblastoma multiforme cancer dataset.
The Inferelator algorithm now has constraints on the inferred regulatory network models that enable Inferelator to use insights derived from high-resolution transcriptome and transcription factor binding data. A framework has been developed for systematic construction of ensemble network models that will enable direct correlations of transcription factors to the cis-regulatory regions to which they bind.
Microfluidics technology development
The Microfluidics and Imaging Core has proved to be a vital resource for device fabrication, and the expertise of Core personnel has led to improvements in the microfluidic platform for H. salinarum NRC-1. On-chip growth and gene expression profiles of durations over 2 weeks can now be reliably collected.
Software development
The Gaggle software is a component of the annual courses, Introduction to Systems Biology, and Proteomics Informatics.
The Gaggle Tool Creator (GTC) was developed, a web application that couples Gaggle functionality with data from 500 species through publicly available data sets. Using GTC, researchers can access and retrieve annotation, interaction, genomic, orthology and other available data, and integrate these data with the researcher's own data. Because GTC is fully Gaggle-compatible, data generated in analyses may be shared between all Gaggle-enabled desktop applications and web sites.
The genome browser has been applied to visualize high-density measurements of transcription and protein-DNA binding events in the context of the genome. It can now be applied to any sequenced organism through an automated import of genomic data from the UCSC genome browser and NCBI, as well as standard file formats. With this tool a transcriptome structure of Bacillus anthracis, as measured by RNA-seq, has been visualized. The browser has demonstrated interoperability using BioTapestry and the sea urchin genome. In addition, visualizations for protein-DNA binding interactions in human and yeast were assembled in collaboration with the Ranish group.
Firegoose has been integrated with an ISB proteomics tool (PIPE), and the Prion Disease Database (with Nils Gehlenborg at the European Bioinformatics Institute).
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