Lab
Quackenbush Lab
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Statement of Research Interest
As the sequence of the human genome unfolds over the next three to five years, our challenge will be to annotate the emerging data by providing a functional analysis of its gene content. This will require that we find all the genes within that sequence, determine their functions, and come to understand the transcriptional networks that underlie cellular metabolism and provide the link between genotype and phenotype.
The Genome Project marks a fundamental transition in the way in which this is going to be done; it marks a shift from small scale, single gene approaches to a more economical and efficient whole-genome approach. Our goal is the elucidation of gene function on a genomic scale and an analysis of genes and their interactions using advanced techniques such as cDNA microarraying.
In order to provide that crucial understanding, we are applying cDNA microarray analysis to a variety of systems. With funding from the National Cancer Institute's Cancer Genome Anatomy Project, we have assembled a collection of 30,000 cDNA clones representing distinct human transcripts. In collaboration with Timothy Yeatman of the H. Lee Moffitt Cancer Center, these will be used to identify genes that are expressed in a tissue or tumor-stage specific fashion and so develop a "molecular fingerprint" that can be used to classify human cancers, and ultimately direct treatment of those tumors.
We are also engaged in expression analysis in a variety of model systems. In collaboration with Steven Ekker of the University of Minnesota Medical School, and Keith Cheng and Glenn Gerhard of the Penn State Hershey Medical Center, we have begun a pilot project to examine gene expression patterns in zebrafish. Our ultimate aim is to combine the unique genetic resources available in zebrafish to build a database linking genotype, expression, and phenotype.
In collaboration with Commander Dan Carucci of the Naval Medical Research Institute, we are examining gene expression in Plasmodium falciparum in order determine parasite stage-specific expression patterns with the goal of using that information to combat malarial infection.
We are also working closely with other groups doing expression studies at TIGR, including Norman Lee, who is studing gene expression in rat, and Steven Gill, Karen Ketchum, and Scott Peterson, who are examining expression in a variety of microbial systems.
Much of the intellectual development underlying our eukaryotic arraying work is based on our analysis of the existing, publicly available EST data. EST sequences are compared and clustered, then assembled to produce a representation of the transcribes sequences within the genome. The assembled Gene Indices, available to the research community, include assembled transcripts for human, mouse, rat, zebrafish, Arabidopsis, rice, and tomato.
The Genome Project marks a fundamental transition in the way in which this is going to be done; it marks a shift from small scale, single gene approaches to a more economical and efficient whole-genome approach. Our goal is the elucidation of gene function on a genomic scale and an analysis of genes and their interactions using advanced techniques such as cDNA microarraying.
In order to provide that crucial understanding, we are applying cDNA microarray analysis to a variety of systems. With funding from the National Cancer Institute's Cancer Genome Anatomy Project, we have assembled a collection of 30,000 cDNA clones representing distinct human transcripts. In collaboration with Timothy Yeatman of the H. Lee Moffitt Cancer Center, these will be used to identify genes that are expressed in a tissue or tumor-stage specific fashion and so develop a "molecular fingerprint" that can be used to classify human cancers, and ultimately direct treatment of those tumors.
We are also engaged in expression analysis in a variety of model systems. In collaboration with Steven Ekker of the University of Minnesota Medical School, and Keith Cheng and Glenn Gerhard of the Penn State Hershey Medical Center, we have begun a pilot project to examine gene expression patterns in zebrafish. Our ultimate aim is to combine the unique genetic resources available in zebrafish to build a database linking genotype, expression, and phenotype.
In collaboration with Commander Dan Carucci of the Naval Medical Research Institute, we are examining gene expression in Plasmodium falciparum in order determine parasite stage-specific expression patterns with the goal of using that information to combat malarial infection.
We are also working closely with other groups doing expression studies at TIGR, including Norman Lee, who is studing gene expression in rat, and Steven Gill, Karen Ketchum, and Scott Peterson, who are examining expression in a variety of microbial systems.
Much of the intellectual development underlying our eukaryotic arraying work is based on our analysis of the existing, publicly available EST data. EST sequences are compared and clustered, then assembled to produce a representation of the transcribes sequences within the genome. The assembled Gene Indices, available to the research community, include assembled transcripts for human, mouse, rat, zebrafish, Arabidopsis, rice, and tomato.
Lab Members
| Pertea, Geo Research Staff | Sultana, Razvan Research Staff |