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Michael Oldham, PhD

TitleAssistant Professor
SchoolUCSF School of Medicine
DepartmentNeurological Surgery
Address1450 3rd Street
San Francisco CA 94158
Phone415-502-5498
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    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.


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    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. Seidel K, Marangoni P, Tang C, Houshmand B, Du W, Maas RL, Murray S, Oldham M, Klein OD. Resolving stem and progenitor cells in the adult mouse incisor through gene co-expression analysis. Elife. 2017 May 05; 6. PMID: 28475038.
      View in: PubMed
    2. 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 M. Secretagogin is Expressed by Developing Neocortical GABAergic Neurons in Humans but not Mice and Increases Neurite Arbor Size and Complexity. Cereb Cortex. 2017 Apr 26; 1-13. PMID: 28449024.
      View in: PubMed
    3. Hu JK, Du W, Shelton SJ, Oldham M, DiPersio CM, Klein OD. An FAK-YAP-mTOR Signaling Axis Regulates Stem Cell-Based Tissue Renewal in Mice. Cell Stem Cell. 2017 Apr 18. PMID: 28457749.
      View in: PubMed
    4. Mitra I, Tsang K, Ladd-Acosta C, Croen LA, Aldinger KA, Hendren RL, Traglia M, Lavillaureix A, Zaitlen N, Oldham M, Levitt P, Nelson S, Amaral DG, Herz-Picciotto I, Fallin MD, Weiss LA. Pleiotropic Mechanisms Indicated for Sex Differences in Autism. PLoS Genet. 2016 Nov; 12(11):e1006425. PMID: 27846226.
      View in: PubMed
    5. Lui H, Zhang J, Makinson SR, Cahill MK, Kelley KW, Huang HY, Shang Y, Oldham M, 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 5; 165(4):921-35. PMID: 27114033.
      View in: PubMed
    6. Kelley KW, Oldham M. Transcriptional architecture of the human brain. Nat Neurosci. 2015 Nov 25; 18(12):1699-701. PMID: 26605877.
      View in: PubMed
    7. Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham M, 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; PMCID: PMC4583716 [Available on 09/24/16].
    8. Parchem RJ, Moore N, Fish JL, Parchem JG, Braga TT, Shenoy A, Oldham M, 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 4; 12(5):760-73. PMID: 26212322.
      View in: PubMed
    9. Lui JH, Nowakowski TJ, Pollen AA, Javaherian A, Kriegstein AR, Oldham M. Radial glia require PDGFD-PDGFRß signalling in human but not mouse neocortex. Nature. 2014 Nov 13; 515(7526):264-8. PMID: 25391964; PMCID: PMC4231536.
    10. Potts MB, Siu JJ, Price JD, Salinas RD, Cho MJ, Ramos AD, Hahn J, Margeta M, Oldham M, 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; PMCID: PMC4420187.
    11. Hwang WW, Salinas RD, Siu JJ, Kelley KW, Delgado RN, Paredes MF, Alvarez-Buylla A, Oldham M, Lim DA. Distinct and separable roles for EZH2 in neurogenic astroglia. Elife. 2014; 3:e02439. PMID: 24867641; PMCID: PMC4032491.
    12. Parchem RJ, Ye J, Judson RL, LaRussa MF, Krishnakumar R, Blelloch A, Oldham M, Blelloch R. Two miRNA clusters reveal alternative paths in late-stage reprogramming. Cell Stem Cell. 2014 May 1; 14(5):617-31. PMID: 24630794; PMCID: PMC4305531.
    13. Qiu H, Lee S, Shang Y, Wang WY, Au KF, Kamiya S, Barmada SJ, Finkbeiner S, Lui H, Carlton CE, Tang AA, Oldham M, 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; PMCID: PMC3938263.
    14. 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 M. 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; PMCID: PMC3909648.
    15. Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham M, 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 2; 12(5):616-28. PMID: 23583100; PMCID: PMC3662805.
    16. Han K, Gennarino VA, Lee Y, Pang K, Hashimoto-Torii K, Choufani S, Raju CS, Oldham M, 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 1; 27(5):485-90. PMID: 23431031; PMCID: PMC3605462.
    17. Konopka G, Friedrich T, Davis-Turak J, Winden K, Oldham M, 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; PMCID: PMC3645834.
    18. Oldham M, Langfelder P, Horvath S. Network methods for describing sample relationships in genomic datasets: application to Huntington's disease. BMC Syst Biol. 2012; 6:63. PMID: 22691535; PMCID: PMC3441531.
    19. Rosen EY, Wexler EM, Versano R, Coppola G, Gao F, Winden KD, Oldham M, 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; PMCID: PMC3633414.
    20. Iwamoto K, Bundo M, Ueda J, Oldham M, 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; PMCID: PMC3083085.
    21. Langfelder P, Luo R, Oldham M, Horvath S. Is my network module preserved and reproducible? PLoS Comput Biol. 2011; 7(1):e1001057. PMID: 21283776; PMCID: PMC3024255.
    22. Cai C, Langfelder P, Fuller TF, Oldham M, 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; 11:589. PMID: 20961428; PMCID: PMC3091510.
    23. Mumford JA, Horvath S, Oldham M, Langfelder P, Geschwind DH, Poldrack RA. Detecting network modules in fMRI time series: a weighted network analysis approach. Neuroimage. 2010 Oct 1; 52(4):1465-76. PMID: 20553896; PMCID: PMC3632300.
    24. Winden KD, Oldham M, 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; PMCID: PMC2724976.
    25. Oldham M, 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; PMCID: PMC2756411.
    26. Miller JA, Oldham M, Geschwind DH. A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci. 2008 Feb 6; 28(6):1410-20. PMID: 18256261; PMCID: PMC2902235.
    27. Abrahams BS, Tentler D, Perederiy JV, Oldham M, Coppola G, Geschwind DH. Genome-wide analyses of human perisylvian cerebral cortical patterning. Proc Natl Acad Sci U S A. 2007 Nov 6; 104(45):17849-54. PMID: 17978184; PMCID: PMC2077018.
    28. 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; PMCID: PMC2276350.
    29. Oldham M, 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; PMCID: PMC1693857.
    30. Oldham M, 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
    31. Oldham M, Geschwind DH. Deconstructing language by comparative gene expression: from neurobiology to microarray. Genes Brain Behav. 2006; 5 Suppl 1:54-63. PMID: 16417618.
      View in: PubMed
    32. Oldham M, Geschwind DH. Evolutionary genetics: the human brain -- adaptation at many levels. Eur J Hum Genet. 2005 May; 13(5):520-2. PMID: 15756295.
      View in: PubMed
    33. Preuss TM, Cáceres M, Oldham M, Geschwind DH. Human brain evolution: insights from microarrays. Nat Rev Genet. 2004 Nov; 5(11):850-60. PMID: 15520794.
      View in: PubMed
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