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. 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
  2. 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 Apr 01; 131(7).  View on PubMed
  3. 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
  4. 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
  5. 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 Feb 09; 11(1):3442.  View on PubMed
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. Oldham MC, Kreitzer AC. Sequencing Diversity One Cell at a Time. Cell. 2018 08 09; 174(4):777-779.  View on PubMed
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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. Neuro-Oncology. 2017 Nov 6; 19(suppl_6):vi99-vi99.  View on PubMed
  18. 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. Neuro-Oncology. 2017 Nov 6; 19(suppl_6):vi124-vi124.  View on PubMed
  19. 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. International Journal of Radiation Oncology • Biology • Physics. 2017 Oct 1; 99(2):e68.  View on PubMed
  20. 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. PLoS Genet. 2017 Jun; 13(6):e1006831.  View on PubMed

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