Research Summary

I am a neuroscientist and Principal Investigator in the Department of Neurological Surgery and Brain Tumor Center at UCSF. The overarching goal of my research is to understand the molecular basis of cellular identity in the human brain in health and disease. We are particularly focused on glioma but are interested in other types of brain cancer as well. In pursuit of this goal, my lab develops and applies standardized approaches for deconstructing complex biological systems using novel computational and experimental strategies. My 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.

Research Funding

  • December 1, 2019 - November 30, 2024 - Decoding the molecular basis of cellular identity in adult malignant gliomas, Principal Investigator. Sponsor: NIH/NCI, Sponsor Award ID: R01CA244621
  • May 1, 2020 - March 31, 2024 - Multiscale transcriptional architecture of the human brain, Principal Investigator. Sponsor: NIH/NIMH, Sponsor Award ID: R01MH123156
  • December 5, 2017 - November 30, 2022 - Decoding the molecular basis of cellular identity in the human brain, Principal Investigator. Sponsor: NIH/NIMH, Sponsor Award ID: R01MH113896
  • August 15, 2018 - July 31, 2020 - Peripheral blood RNA biomarkers of recovery after spinal cord injury, Co-Investigator. Sponsor: NIH/NINDS, Sponsor Award ID: R21NS106981

Education

Duke University B.S., 1996, Psychology
University of California, Los Angeles (UCLA), Ph.D., 2009, Neuroscience
University of California, Los Angeles (UCLA), Postdoctoral, 2010, Human Genetics

Honors & Awards

  • 2002-2003
    Pre-doctoral Fellowship, Neuroscience Ph.D. Program, UCLA, Los Angeles, CA
  • 2008
    Eva Kavan Prize for Excellence in Research on the Brain, Brain Research Institute, UCLA, LosAngeles, CA
  • 2009
    UCSF Sandler Fellow, UCSF, San Francisco, CA
  • 2010
    Travel Fellow, Winter Conference on Brain Research, Breckenridge, CO
  • 2012
    Young Investigator, Sage Commons Congress, San Francisco, CA
  • 2016-2017
    Weill Institute for Neurosciences Scholar Award, UCSF
  • 2015-2016
    Program for Breakthrough Biomedical Research New Frontiers Research Award, UCSF

Selected Publications

  1. Munji RN, Soung AL, Weiner GA, Sohet F, Semple BD, Trivedi A, Gimlin K, Kotoda M, Korai M, Aydin S, Batugal A, Cabangcala AC, Schupp PG, Oldham MC, Hashimoto T, Noble-Haeusslein LJ, Daneman R Profiling the mouse brain endothelial transcriptome in health and disease models reveals a core blood-brain barrier dysfunction module.  View on PubMed
  2. Torres R, Lang UE, Hejna M, Shelton SJ, Joseph NM, Shain AH, Yeh I, Wei ML, Oldham MC, Bastian BC, Judson-Torres RL MicroRNA Ratios Distinguish Melanomas from Nevi.  View on PubMed
  3. Diego A Carrera, Josie Hayes, Sören Müller, Payal Watchmaker, Samuel Shelton, Nolbert Hilf, Toni Weinschenk, Oliver Schoor, Gary Kohanbash, Michael Oldham, Joseph Costello, Harpreet Singh, Hideho Okada Immunopeptidomics and Peptide Expression Profiles to Develop T-Cell Receptors Against Glioma-Associated Antigens.  View on PubMed
  4. R. Torres, U. Lang, N.M. Joseph, A.H. Shain, I. Yeh, M.L. Wei, M.C. Oldham, B. Bastian, R.L. Judson-Torres 786 A machine-learning classifier trained with microRNA ratios to distinguish melanomas from nevi.  View on PubMed
  5. 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 Does Adult Neurogenesis Persist in the Human Hippocampus?  View on PubMed
  6. Kelley KW, Nakao-Inoue H, Molofsky AV, Oldham MC Variation among intact tissue samples reveals the core transcriptional features of human CNS cell classes.  View on PubMed
  7. Oldham MC, Kreitzer AC Sequencing Diversity One Cell at a Time.  View on PubMed
  8. Raju CS, Spatazza J, Stanco A, Larimer P, Sorrells SF, Kelley KW, Nicholas CR, Paredes MF, Lui JH, Hasenstaub AR, Kriegstein AR, Alvarez-Buylla A, Rubenstein JL, Oldham MC Secretagogin is Expressed by Developing Neocortical GABAergic Neurons in Humans but not Mice and Increases Neurite Arbor Size and Complexity.  View on PubMed
  9. R. Torres, U. Lang, S. Shelton, Y. Yeniay, N. Joseph, A. Shain, I. Yeh, M. Oldham, M.L. Wei, B. Bastian, R. Judson 1220 MicroRNA signature distinguishing nevi from primary melanoma.  View on PubMed
  10. Griveau A, Seano G, Shelton SJ, Kupp R, Jahangiri A, Obernier K, Krishnan S, Lindberg OR, Yuen TJ, Tien AC, Sabo JK, Wang N, Chen I, Kloepper J, Larrouquere L, Ghosh M, Tirosh I, Huillard E, Alvarez-Buylla A, Oldham MC, Persson AI, Weiss WA, Batchelor TT, Stemmer-Rachamimov A, Suvà ML, Phillips JJ, Aghi MK, Mehta S, Jain RK, Rowitch DH A Glial Signature and Wnt7 Signaling Regulate Glioma-Vascular Interactions and Tumor Microenvironment.  View on PubMed
  11. Sorrells SF, Paredes MF, Cebrian-Silla A, Sandoval K, Qi D, Kelley KW, James D, Mayer S, Chang J, Auguste KI, Chang EF, Gutierrez AJ, Kriegstein AR, Mathern GW, Oldham MC, Huang EJ, Garcia-Verdugo JM, Yang Z, Alvarez-Buylla A Human hippocampal neurogenesis drops sharply in children to undetectable levels in adults.  View on PubMed
  12. Stephanie Hilz, Samuel J Shelton, Llewellyn Jalbert, Hang K Wong, Tali Mazor, Chibo Hong, Josie Hayes, Tracy Luks, Henrik Bengtsson, Annette Molinaro, Michael McDermott, Mitchel S Berger, Daniel Lim, Aaron Diaz, Joanna J Phillips, Susan Chang, Sarah Nelson, Michael C Oldham, Joseph Costello GENE-33. THE 3D EVOLUTION AND IN VIVO GROWTH PATTERNS OF GLIOMA CELL POPULATIONS.  View on PubMed
  13. Diego Carrera, Josie Hayes, Soeren Mueller, Samuel J Shelton, Toni Weinschenk, Colette Song, Jens Fritsche, Oliver Schoor, Sabrina Kuttruff-Coqui, Norbert Hilf, Gary Kohanbash, Payal Watchmaker, Michael C Oldham, Joseph Costello, Harpreet Singh, Hideho Okada IMMU-52. SELECTION OF GLIOMA T-CELL THERAPY TARGETS BASED ON THE ANALYSIS OF TUMOR IMMUNOPEPTIDOME AND EXPRESSION PROFILES.  View on PubMed
  14. S. Choi, J. Hayes, S. Shelton, L. Jones, T. Mazor, S. Fouse, M. Oldham, J. Costello Genetic Characterization of Stromal Cells in High Grade Gliomas.  View on PubMed
  15. Mitra I, Tsang K, Ladd-Acosta C, Croen LA, Aldinger KA, Hendren RL, Traglia M, Lavillaureix A, Zaitlen N, Oldham MC, Levitt P, Nelson S, Amaral DG, Hertz-Picciotto I, Fallin MD, Weiss LA Correction: Pleiotropic Mechanisms Indicated for Sex Differences in Autism.  View on PubMed
  16. Seidel K, Marangoni P, Tang C, Houshmand B, Du W, Maas RL, Murray S, Oldham MC, Klein OD Resolving stem and progenitor cells in the adult mouse incisor through gene co-expression analysis.  View on PubMed
  17. Hu JK, Du W, Shelton SJ, Oldham MC, DiPersio CM, Klein OD An FAK-YAP-mTOR Signaling Axis Regulates Stem Cell-Based Tissue Renewal in Mice.  View on PubMed
  18. Mitra I, Tsang K, Ladd-Acosta C, Croen LA, Aldinger KA, Hendren RL, Traglia M, Lavillaureix A, Zaitlen N, Oldham MC, Levitt P, Nelson S, Amaral DG, Hertz-Picciotto I, Fallin MD, Weiss LA Pleiotropic Mechanisms Indicated for Sex Differences in Autism.  View on PubMed
  19. Samuel J. Shelton, Brett E. Johnson, Tali Mazor, Matthew B. Potts, Michael F. McDermott, Eric J. Huang, Dan Lim, Russel O. Pieper, Mitchel S. Berger, Joanna J. Phillips, Joseph F. Costello, Michael C. Oldham GENT-15. INTEGRATED MOLECULAR PROFILING OF HUMAN BRAIN TUMORS THROUGH MULTIOMIC ANALYSIS OF SERIAL SECTIONS (MASS).  View on PubMed
  20. Lui H, Zhang J, Makinson SR, Cahill MK, Kelley KW, Huang HY, Shang Y, Oldham MC, Martens LH, Gao F, Coppola G, Sloan SA, Hsieh CL, Kim CC, Bigio EH, Weintraub S, Mesulam MM, Rademakers R, Mackenzie IR, Seeley WW, Karydas A, Miller BL, Borroni B, Ghidoni R, Farese RV, Paz JT, Barres BA, Huang EJ Progranulin Deficiency Promotes Circuit-Specific Synaptic Pruning by Microglia via Complement Activation.  View on PubMed

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