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Neuroscience Graduate Program at UCSF

Faculty - Michael Oldham, Ph.D.

The molecular basis of cellular identity in the human brain


Research Description

The overarching goal of my lab’s research is to understand the molecular basis of cellular identity in the human brain in health and disease.  Our work is motivated by a simple but powerful idea: by analyzing gene coexpression relationships in heterogeneous tissue samples, it is possible to isolate robust transcriptional signatures of distinct cell types and cellular processes in silico.  The engine of my lab is a computational pipeline for analyzing and characterizing gene coexpression relationships in large transcriptomic datasets.  We are using this pipeline to study the organization of the non-pathological, adult human brain transcriptome and to develop genome-wide, quantitative models of gene expression that will allow us to predict gene expression levels and identify transcriptional aberrations in any neurological condition, but with a particular emphasis on glioma.  We are also performing comparisons between humans and other species to identify cell type-specific transcriptional differences during brain development.  In the long run, we aspire to predict the cellular composition of any human brain specimen purely on the basis of gene expression.

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Current Projects

Participation in these projects generally ensures that lab members are fluent (or develop fluency) in computational and experimental research strategies:

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Lab Members

Kevin Kelley, Graduate Student

Sam Shelton, Postdoctoral Fellow

Raju Chandrasekhar, Postdoctoral Fellow

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Selected Publications

Liu JH, Nowakowski TJ, Pollen AA, Javaherian A, Kriegstein AR, Oldham MC. Radial glia require PDGFD-PDGFRß signalling in human but not mouse neocortex. Nature 515(7526): 264-268 (2014).

Oldham MC, Langfelder P, Horvath S. Network methods for describing sample relationships in genomic datasets: application to Huntington's disease. BMC Sys Biol 6(1): 63 (2012).

Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S, Geschwind DH. Functional organization of the transcriptome in human brain. Nat Neurosci 11(11): 1271-1282 (2008).

Oldham MC, Horvath S, Geschwind DH. Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci USA 103(47): 17973-17978 (2006).

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Michael Oldham, Ph.D.



Email

michael.oldham@ucsf.edu

Phone 415-502-5498

Fax 415-514-9792

Office Address

1450 3rd Street
Box 0520, room 487B
San Francisco, CA 94143

Other Websites

Broad Center

BMS

Google Scholar