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, Sponsor Award ID: R01CA244621
  • May 1, 2020 - March 31, 2024 - Multiscale transcriptional architecture of the human brain , Principal Investigator . Sponsor: NIH, 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, Sponsor Award ID: R01MH113896
  • August 15, 2018 - July 31, 2021 - Peripheral blood RNA biomarkers of recovery after spinal cord injury , Co-Investigator . Sponsor: NIH, Sponsor Award ID: R21NS106981


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. Zhang X, Xiao G, Johnson C, Cai Y, Horowitz ZK, Mennicke C, Coffey R, Haider M, Threadgill D, Eliscu R, Oldham MC, Greenbaum A, Ghashghaei HT. Bulk and mosaic deletions of Egfr reveal regionally defined gliogenesis in the developing mouse forebrain. iScience. 2023 Mar 17; 26(3):106242.  View on PubMed
  2. Tanabe K, Nobuta H, Yang N, Ang CE, Huie P, Jordan S, Oldham MC, Rowitch DH, Wernig M. Generation of functional human oligodendrocytes from dermal fibroblasts by direct lineage conversion. Development. 2022 10 15; 149(20).  View on PubMed
  3. Radhika Mathur, Qixuan Wang, Patrick Schupp, Ana Nikolic, Takafumi Yamaguchi, Stephanie Hilz, Chibo Hong, Ivan Smirnov, Marisa LaFontaine, Joanna Phillips, Susan Chang, Yan Li, Janine Lupo, Paul Boutros, Marco Gallo, Michael Oldham, Feng Yue, Joseph Costello. Abstract 3621: 3D spatial sampling and integrated omics reveal sources and patterning of intratumoral heterogeneity in glioblastoma. Cancer Research. 2022 Jun 15; 82(12_Supplement):3621-3621.  View on PubMed
  4. Paredes MF, Mora C, Flores-Ramirez Q, Cebrian-Silla A, Del Dosso A, Larimer P, Chen J, Kang G, Gonzalez Granero S, Garcia E, Chu J, Delgado R, Cotter JA, Tang V, Spatazza J, Obernier K, Ferrer Lozano J, Vento M, Scott J, Studholme C, Nowakowski TJ, Kriegstein AR, Oldham MC, Hasenstaub A, Garcia-Verdugo JM, Alvarez-Buylla A, Huang EJ. Nests of dividing neuroblasts sustain interneuron production for the developing human brain. Science. 2022 01 28; 375(6579):eabk2346.  View on PubMed
  5. Radhika Mathur, Qixuan Wang, Patrick Schupp, Stephanie Hilz, Chibo Hong, Ivan Smirnov, Marisa Lafontaine, Devika Nair, Sriranga Iyyanaki, Joanna Phillips, Susan Chang, Yan Li, Janine Lupo, Michael Oldham, Feng Yue, Joseph Costello. ECOA-5. Integrative 3D spatial characterization of genomic and epigenomic intratumoral heterogeneity in glioblastoma. Neuro-Oncology Advances. 2021 Jul 5; 3(Supplement_2):ii2-ii2.  View on PubMed
  6. Qiu H, Lee S, Shang Y, Wang WY, Au KF, Kamiya S, Barmada SJ, Finkbeiner S, Lui H, Carlton CE, Tang AA, Oldham MC, Wang H, Shorter J, Filiano AJ, Roberson ED, Tourtellotte WG, Chen B, Tsai LH, Huang EJ. ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects. J Clin Invest. 2021 04 01; 131(7).  View on PubMed
  7. Sorrells SF, Paredes MF, Zhang Z, Kang G, Pastor-Alonso O, Biagiotti S, Page CE, Sandoval K, Knox A, Connolly A, Huang EJ, Garcia-Verdugo JM, Oldham MC, Yang Z, Alvarez-Buylla A. Positive Controls in Adults and Children Support That Very Few, If Any, New Neurons Are Born in the Adult Human Hippocampus. J Neurosci. 2021 03 24; 41(12):2554-2565.  View on PubMed
  8. 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. Diagnostic blood RNA profiles for human acute spinal cord injury. J Exp Med. 2021 03 01; 218(3).  View on PubMed
  9. Huie JR, Ferguson AR, Kyritsis N, Pan JZ, Irvine KA, Nielson JL, Schupp PG, Oldham MC, Gensel JC, Lin A, Segal MR, Ratan RR, Bresnahan JC, Beattie MS. Machine intelligence identifies soluble TNFa as a therapeutic target for spinal cord injury. Sci Rep. 2021 02 09; 11(1):3442.  View on PubMed
  10. 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. Nat Neurosci. 2019 11; 22(11):1892-1902.  View on PubMed
  11. 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. J Invest Dermatol. 2020 01; 140(1):164-173.e7.  View on PubMed
  12. 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. Neurosurgery. 2019 Sep 1; 66(Supplement_1).  View on PubMed
  13. 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. Journal of Investigative Dermatology. 2019 May 1; 139(5):s136.  View on PubMed
  14. 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? Cell Stem Cell. 2018 12 06; 23(6):780-781.  View on PubMed
  15. Kelley KW, Nakao-Inoue H, Molofsky AV, Oldham MC. Variation among intact tissue samples reveals the core transcriptional features of human CNS cell classes. Nat Neurosci. 2018 09; 21(9):1171-1184.  View on PubMed
  16. Oldham MC, Kreitzer AC. Sequencing Diversity One Cell at a Time. Cell. 2018 08 09; 174(4):777-779.  View on PubMed
  17. 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. Cereb Cortex. 2018 06 01; 28(6):1946-1958.  View on PubMed
  18. 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. Journal of Investigative Dermatology. 2018 May 1; 138(5):s207.  View on PubMed
  19. 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. Cancer Cell. 2018 05 14; 33(5):874-889.e7.  View on PubMed
  20. 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. Nature. 2018 03 15; 555(7696):377-381.  View on PubMed

Go to UCSF Profiles, powered by CTSI