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Michael Oldham, PhD

Title(s)Assistant Professor, Neurological Surgery
SchoolSchool of Medicine
Phone415-502-5498
ORCID ORCID Icon0000-0001-7633-6932 Additional info
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    Collapse Biography 
    Collapse Education and Training
    UCLA, Los Angeles, CAPhD06/2009Neuroscience
    Duke University, Durham, NCBS05/1992Psychology (major), Chemistry (minor)
    Collapse Awards and Honors
    UCSF2016  - 2017Weill Institute for Neurosciences Scholar Award
    UCSF2015  - 2016Program for Breakthrough Biomedical Research New Frontiers Research Award
    UCLA2008  - 2008Eva Kavan Prize for Excellence in Research on the Brain

    Collapse Overview 
    Collapse Overview
    I am an Assistant Professor in the Department of Neurological Surgery and Brain Tumor Research Center at UCSF. My lab uses novel computational and experimental strategies to study the molecular basis of cellular identity in the human brain in health and disease. Much of 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. More generally, we have found that the covariance structure of omics data contains an enormous amount of untapped information about the molecular and cellular organization of biological systems. We have developed a computational pipeline to extract this information and are applying it to samples from normal human brain samples and brain tumors. These efforts will produce mathematical definitions of neurobiological cell types under a range of conditions and reveal the critical molecular features that promote and maintain cellular identity in the human brain in health and disease.

    Collapse Research 
    Collapse Research Activities and Funding
    Peripheral blood RNA biomarkers of recovery after spinal cord injury
    NIH/NINDS R21NS106981Aug 15, 2018 - Jul 31, 2020
    Role: Co-Investigator
    Decoding the molecular basis of cellular identity in the human brain
    NIH/NIMH R01MH113896Dec 5, 2017 - Nov 30, 2022
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
    Collapse Websites
    Collapse In The News
    Collapse Faculty Mentoring

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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. 2019 Aug 22. PMID: 31580842.
      View in: PubMed
    2. 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. PMID: 30526879.
      View in: PubMed
    3. 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. PMID: 30154505.
      View in: PubMed
    4. Oldham MC, Kreitzer AC. Sequencing Diversity One Cell at a Time. Cell. 2018 08 09; 174(4):777-779. PMID: 30096308.
      View in: PubMed
    5. 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. PMID: 28449024.
      View in: PubMed
    6. 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. PMID: 29681511.
      View in: PubMed
    7. 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. PMID: 29513649.
      View in: PubMed
    8. 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. PMID: 28591140.
      View in: PubMed
    9. 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. Elife. 2017 05 05; 6. PMID: 28475038.
      View in: PubMed
    10. 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. Cell Stem Cell. 2017 07 06; 21(1):91-106.e6. PMID: 28457749.
      View in: PubMed
    11. 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. PLoS Genet. 2016 11; 12(11):e1006425. PMID: 27846226.
      View in: PubMed
    12. 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. Cell. 2016 May 05; 165(4):921-35. PMID: 27114033.
      View in: PubMed
    13. Kelley KW, Oldham MC. Transcriptional architecture of the human brain. Nat Neurosci. 2015 Dec; 18(12):1699-701. PMID: 26605877.
      View in: PubMed
    14. Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham MC, Diaz A, Lim DA, Leyrat AA, West JA, Kriegstein AR. Molecular identity of human outer radial glia during cortical development. Cell. 2015 Sep 24; 163(1):55-67. PMID: 26406371.
      View in: PubMed
    15. Parchem RJ, Moore N, Fish JL, Parchem JG, Braga TT, Shenoy A, Oldham MC, Rubenstein JL, Schneider RA, Blelloch R. miR-302 Is Required for Timing of Neural Differentiation, Neural Tube Closure, and Embryonic Viability. Cell Rep. 2015 Aug 04; 12(5):760-73. PMID: 26212322.
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    16. Lui JH, Nowakowski TJ, Pollen AA, Javaherian A, Kriegstein AR, Oldham MC. Radial glia require PDGFD-PDGFRß signalling in human but not mouse neocortex. Nature. 2014 Nov 13; 515(7526):264-8. PMID: 25391964.
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    17. Potts MB, Siu JJ, Price JD, Salinas RD, Cho MJ, Ramos AD, Hahn J, Margeta M, Oldham MC, Lim DA. Analysis of Mll1 deficiency identifies neurogenic transcriptional modules and Brn4 as a factor for direct astrocyte-to-neuron reprogramming. Neurosurgery. 2014 Oct; 75(4):472-82; discussion 482. PMID: 24887289.
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    18. Hwang WW, Salinas RD, Siu JJ, Kelley KW, Delgado RN, Paredes MF, Alvarez-Buylla A, Oldham MC, Lim DA. Distinct and separable roles for EZH2 in neurogenic astroglia. Elife. 2014 May 27; 3:e02439. PMID: 24867641.
      View in: PubMed
    19. Parchem RJ, Ye J, Judson RL, LaRussa MF, Krishnakumar R, Blelloch A, Oldham MC, Blelloch R. Two miRNA clusters reveal alternative paths in late-stage reprogramming. Cell Stem Cell. 2014 May 01; 14(5):617-31. PMID: 24630794.
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    20. 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. 2014 Mar; 124(3):981-99. PMID: 24509083.
      View in: PubMed
    21. Molofsky AV, Glasgow SM, Chaboub LS, Tsai HH, Murnen AT, Kelley KW, Fancy SP, Yuen TJ, Madireddy L, Baranzini S, Deneen B, Rowitch DH, Oldham MC. Expression profiling of Aldh1l1-precursors in the developing spinal cord reveals glial lineage-specific genes and direct Sox9-Nfe2l1 interactions. Glia. 2013 Sep; 61(9):1518-32. PMID: 23840004.
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    22. Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell. 2013 May 02; 12(5):616-28. PMID: 23583100.
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    23. Han K, Gennarino VA, Lee Y, Pang K, Hashimoto-Torii K, Choufani S, Raju CS, Oldham MC, Weksberg R, Rakic P, Liu Z, Zoghbi HY. Human-specific regulation of MeCP2 levels in fetal brains by microRNA miR-483-5p. Genes Dev. 2013 Mar 01; 27(5):485-90. PMID: 23431031.
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    24. Konopka G, Friedrich T, Davis-Turak J, Winden K, Oldham MC, Gao F, Chen L, Wang GZ, Luo R, Preuss TM, Geschwind DH. Human-specific transcriptional networks in the brain. Neuron. 2012 Aug 23; 75(4):601-17. PMID: 22920253.
      View in: PubMed
    25. Oldham MC, Langfelder P, Horvath S. Network methods for describing sample relationships in genomic datasets: application to Huntington's disease. BMC Syst Biol. 2012 Jun 12; 6:63. PMID: 22691535.
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    26. Rosen EY, Wexler EM, Versano R, Coppola G, Gao F, Winden KD, Oldham MC, Martens LH, Zhou P, Farese RV, Geschwind DH. Functional genomic analyses identify pathways dysregulated by progranulin deficiency, implicating Wnt signaling. Neuron. 2011 Sep 22; 71(6):1030-42. PMID: 21943601.
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    27. Iwamoto K, Bundo M, Ueda J, Oldham MC, Ukai W, Hashimoto E, Saito T, Geschwind DH, Kato T. Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons. Genome Res. 2011 May; 21(5):688-96. PMID: 21467265.
      View in: PubMed
    28. Langfelder P, Luo R, Oldham MC, Horvath S. Is my network module preserved and reproducible? PLoS Comput Biol. 2011 Jan 20; 7(1):e1001057. PMID: 21283776.
      View in: PubMed
    29. Cai C, Langfelder P, Fuller TF, Oldham MC, Luo R, van den Berg LH, Ophoff RA, Horvath S. Is human blood a good surrogate for brain tissue in transcriptional studies? BMC Genomics. 2010 Oct 20; 11:589. PMID: 20961428.
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    30. Mumford JA, Horvath S, Oldham MC, Langfelder P, Geschwind DH, Poldrack RA. Detecting network modules in fMRI time series: a weighted network analysis approach. Neuroimage. 2010 Oct 01; 52(4):1465-76. PMID: 20553896.
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    31. Winden KD, Oldham MC, Mirnics K, Ebert PJ, Swan CH, Levitt P, Rubenstein JL, Horvath S, Geschwind DH. The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol. 2009; 5:291. PMID: 19638972.
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    32. Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S, Geschwind DH. Functional organization of the transcriptome in human brain. Nat Neurosci. 2008 Nov; 11(11):1271-82. PMID: 18849986.
      View in: PubMed
    33. Miller JA, Oldham MC, Geschwind DH. A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci. 2008 Feb 06; 28(6):1410-20. PMID: 18256261.
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    34. Spiteri E, Konopka G, Coppola G, Bomar J, Oldham M, Ou J, Vernes SC, Fisher SE, Ren B, Geschwind DH. Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain. Am J Hum Genet. 2007 Dec; 81(6):1144-57. PMID: 17999357.
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    35. Abrahams BS, Tentler D, Perederiy JV, Oldham MC, Coppola G, Geschwind DH. Genome-wide analyses of human perisylvian cerebral cortical patterning. Proc Natl Acad Sci U S A. 2007 Nov 06; 104(45):17849-54. PMID: 17978184.
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    36. Oldham MC, Horvath S, Geschwind DH. Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A. 2006 Nov 21; 103(47):17973-8. PMID: 17101986.
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    37. Oldham MC, Geschwind DH. Comparative genomics: grasping human transcriptome evolution: what does it all mean? Heredity (Edinb). 2006 May; 96(5):339-40. PMID: 16552432.
      View in: PubMed
    38. Oldham MC, Geschwind DH. Deconstructing language by comparative gene expression: from neurobiology to microarray. Genes Brain Behav. 2006; 5 Suppl 1:54-63. PMID: 16417618.
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    39. Oldham MC, Geschwind DH. Evolutionary genetics: the human brain -- adaptation at many levels. Eur J Hum Genet. 2005 May; 13(5):520-2. PMID: 15756295.
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    40. Preuss TM, Cáceres M, Oldham MC, Geschwind DH. Human brain evolution: insights from microarrays. Nat Rev Genet. 2004 Nov; 5(11):850-60. PMID: 15520794.
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