 |
|
|
Stuart KimAcademic Appointments
Appointment
Organization
Professor
Professor (By courtesy)
Professor
|
Postdoctoral Advisees
Yelena Budovskaya,
Sarah Kummerfeld,
Xiao Liu,
Dror Sagi,
Adolfo Sanchez-Blanco
Web Site Links
Research/Lab website:
Stuart Kim Lab
Research Interests
Global analysis of conserved genetic modules
DNA microarrays provide us with a first step towards uncovering gene function on a global scale. Functionally-related genes often exhibit expression patterns that are correlated under a large number of diverse conditions in DNA microarray experiments. Furthermore, gene interactions that are physiologically significant should be conserved through evolution, so that orthologous pairs of genes should show similar expression correlations in DNA microarray data from diverse organisms.
We are assembling all available DNA microarray data from several key organisms (human, mouse, fly, worm and yeast), and finding sets of orthologs that are co-expressed in multiple organisms. This conservation implies that these genes are functionally related. Furthermore, in addition to learning about the function of individual genes, we can use the network to analyze entire sets of genes in order to understand the system as a whole.
Molecular analysis of human aging.
We propose to elucidate mechanisms of human aging at the molecular level. A powerful approach to understand molecular changes associated with age is to use DNA chips to profile gene expression changes during human lifetime across the entire genome. We are using the kidney to study human aging because this organ shows a strong decline in function with age.
Our first goal is to generate a molecular profile showing how nearly every gene is expressed in the kidney with respect to age. We have already collected 74 kidneys from patients ranging in age from 27 to 92 years. We will use Affymetrix DNA chips to profile expression levels from each of these kidneys, thereby forming a genome-wide time course for aging in the kidney. Our preliminary analysis of analysis of genes from only half of the genome shows 215 aging regulated genes. These are the first molecular markers for human aging in the kidney, and analysis of the rest of the genome will certainly elucidate more biomarkers for aging.
DNA microarrays provide us with a first step towards uncovering gene function on a global scale. Functionally-related genes often exhibit expression patterns that are correlated under a large number of diverse conditions in DNA microarray experiments. Furthermore, gene interactions that are physiologically significant should be conserved through evolution, so that orthologous pairs of genes should show similar expression correlations in DNA microarray data from diverse organisms.
We are assembling all available DNA microarray data from several key organisms (human, mouse, fly, worm and yeast), and finding sets of orthologs that are co-expressed in multiple organisms. This conservation implies that these genes are functionally related. Furthermore, in addition to learning about the function of individual genes, we can use the network to analyze entire sets of genes in order to understand the system as a whole.
Molecular analysis of human aging.
We propose to elucidate mechanisms of human aging at the molecular level. A powerful approach to understand molecular changes associated with age is to use DNA chips to profile gene expression changes during human lifetime across the entire genome. We are using the kidney to study human aging because this organ shows a strong decline in function with age.
Our first goal is to generate a molecular profile showing how nearly every gene is expressed in the kidney with respect to age. We have already collected 74 kidneys from patients ranging in age from 27 to 92 years. We will use Affymetrix DNA chips to profile expression levels from each of these kidneys, thereby forming a genome-wide time course for aging in the kidney. Our preliminary analysis of analysis of genes from only half of the genome shows 215 aging regulated genes. These are the first molecular markers for human aging in the kidney, and analysis of the rest of the genome will certainly elucidate more biomarkers for aging.
Publications
- Kim SK, "Common aging pathways in worms, flies, mice and humans." The Journal of Experimental Biology 2007; 210: 1607-1612 More »
- Kim SK, Rulifson EJ "Conserved mechanisms of glucose sensing and regulation by Drosophila corpora cardiaca cells." Nature 2004; 431: 7006: 316-20 More »
- Stuart JM, Segal E, Koller D, Kim SK "A gene-coexpression network for global discovery of conserved genetic modules." Science 2003; 302: 5643: 249-55 More »
- Roy PJ, Stuart JM, Lund J, Kim SK "Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans." Nature 2002; 418: 6901: 975-9 More »
- Rulifson EJ, Kim SK, Nusse R "Ablation of insulin-producing neurons in flies: growth and diabetic phenotypes." Science 2002; 296: 5570: 1118-20 More »
10 publications: view full list
