Michael Oldham, PhD

Associate Professor
M_NeuSrg-General
415-502-5498

The molecular basis of cellular identity in the human brain

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.

Current Projects

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

  1. Identifying the direct transcriptional consequences of specific driver mutations in glioma
  2. Developing standardized sampling and analytical strategies for maximizing the amount of molecular information that can be obtained from a single tissue specimen
  3.     
  4. Determining the functional consequences of cell type-specific transcriptional differences between humans and other species during brain development
  5. Modeling gene expression in the human brain

Lab Members

Sam Shelton, PhD
Postdoctoral Fellow
[email protected]

Chandra Sekhar Saki Raju, PhD
Postdoctoral Fellow
[email protected]

Kevin Kelley
Neuroscience Graduate Student
[email protected]

Lab Website

Publications

Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective.

M_Anatomy-General

Mathur R, Wang Q, Schupp PG, Nikolic A, Hilz S, Hong C, Grishanina NR, Kwok D, Stevers NO, Jin Q, Youngblood MW, Stasiak LA, Hou Y, Wang J, Yamaguchi TN, Lafontaine M, Shai A, Smirnov IV, Solomon DA, Chang SM, Hervey-Jumper SL, Berger MS, Lupo JM, Okada H, Phillips JJ, Boutros PC, Gallo M, Oldham MC, Yue F, Costello JF

Diagnostic blood RNA profiles for human acute spinal cord injury.

Kyritsis N, Torres-Espín A, Schupp PG, Huie JR, Chou A, Duong-Fernandez X, Thomas LH, Tsolinas RE, Hemmerle DD, Pascual LU, Singh V, Pan JZ, Talbott JF, Whetstone WD, Burke JF, DiGiorgio AM, Weinstein PR, Manley GT, Dhall SS, Ferguson AR, Oldham MC, Bresnahan JC, Beattie MS

Does Adult Neurogenesis Persist in the Human Hippocampus?

Paredes MF, Sorrells SF, Cebrian-Silla A, Sandoval K, Qi D, Kelley KW, James D, Mayer S, Chang J, Auguste KI, Chang EF, Gutierrez Martin AJ, Kriegstein AR, Mathern GW, Oldham MC, Huang EJ, Garcia-Verdugo JM, Yang Z, Alvarez-Buylla A