Gaasterland Lab
Research Projects
The MAGPIE (Multipurpose Automated Genome Project Investigation Environment) system for genome annotation anchors the Laboratory. At the most general level, MAGPIE accepts genomic sequence as input, identifies genomic features within regions of the input sequence, and constructs static logical models of molecular systems from the features encoded in the genome.
EGRET is the sister annotation system to Magpie used for eukaryotic genomes.
The TANGO (Transcriptome ANalysis of GenOmes) system for gene expression data analysis is a sister system to MAGPIE that associates dynamic gene expression data with static genome features. TANGO accepts as input gene expression images and gene intensity values tables from spotted microarray hybridizations and from Affymetrix GeneChip™ hybridizations. The system provides intelligent assistance to a biologist user to prepare each hybridization for further clustering and analysis.
As the number of genomes sequenced rises exponentially over the next few years, automated systems that can generate reliable and informative annotations will become indispensable. To address this issue, we have begun work on HERON (Human Emulated Reasoning for Objective Notations), currently a simple algorithm for identifying the 'best' description line from a series of homology-based sequence matches. At present, HERON performs well, but is limited in its analyses. We are working to expand HERON's capabilities and facilitate truly accurate, automated annotation of genomes.
HERON workflow
Sandpiper Sandpiper
Sandpiper (Structural Genomics Target Selection) is part of the Structural Genomics project conducted by the New York Structural Genomics Research Consortium (NYSGRC).
Gaasterland Bio/CV Current Research in the Lab Publications: Abstracts and Links Lab Members Computational Resources