Michael Oldham, PhD
Associate Professor
Neurological Surgery
School of Medicine

To this end, the Oldham lab generates and analyzes vast quantities of gene expression data from human brain samples and uses custom computational pipelines to identify and compare patterns of gene activity across many independent datasets. Lab members are particularly interested in understanding how patterns of gene activity in normal human brain samples are perturbed by disease, with an emphasis on adult malignant gliomas. Dr. Oldham is a faculty member in UCSF PhD programs for Neuroscience, Biomedical Sciences, Developmental and Stem Cell Biology, and Biomedical Informatics. The Oldham lab is located on the fourth floor of the Helen Diller Family Cancer Research Building at Mission Bay.

• Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective.
  Cell 2024 Mathur R, Wang Q, Schupp PG, Nikolic A, Hilz S, Hong C, Grishanina NR, Kwok D, Stevers NO, Jin Q, Youngblood MW, Stasiak LA, Hou Y, Wang J, Yamaguchi TN, Lafontaine M, Shai A, Smirnov IV, Solomon DA, …
• EPCO-39. CLARIFYING THE MOLECULAR CONSEQUENCES OF ONCOGENIC MUTATIONS THROUGH MULTISCALE AND MULTIOMIC ANALYSIS OF INDIVIDUAL TUMORS.
  Neuro-Oncology 2023 Patrick Schupp, Samuel Shelton, Daniel Brody, Rebecca Eliscu, Brett Johnson, Tali Mazor, Kevin Kelley, Matthew Potts, Michael McDermott, Eric Huang, Daniel Lim, Russell Pieper, Mitchel Berger, Joseph …
• Bulk and mosaic deletions of Egfr reveal regionally defined gliogenesis in the developing mouse forebrain.
  iScience 2023 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
• Generation of functional human oligodendrocytes from dermal fibroblasts by direct lineage conversion.
  Development (Cambridge, England) 2022 Tanabe K, Nobuta H, Yang N, Ang CE, Huie P, Jordan S, Oldham MC, Rowitch DH, Wernig M
• Abstract 3621: 3D spatial sampling and integrated omics reveal sources and patterning of intratumoral heterogeneity in glioblastoma.
  Cancer Research 2022 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 …
• Nests of dividing neuroblasts sustain interneuron production for the developing human brain.
  Science (New York, N.Y.) 2022 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 …
• ECOA-5. Integrative 3D spatial characterization of genomic and epigenomic intratumoral heterogeneity in glioblastoma.
  Neuro-Oncology Advances 2021 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 …
• ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects.
  The Journal of clinical investigation 2021 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
• Positive Controls in Adults and Children Support That Very Few, If Any, New Neurons Are Born in the Adult Human Hippocampus.
  The Journal of neuroscience : the official journal of the Society for Neuroscience 2021 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
• Diagnostic blood RNA profiles for human acute spinal cord injury.
  The Journal of experimental medicine 2021 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…
• Machine intelligence identifies soluble TNFa as a therapeutic target for spinal cord injury.
  Scientific reports 2021 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
• Profiling the mouse brain endothelial transcriptome in health and disease models reveals a core blood-brain barrier dysfunction module.
  Nature neuroscience 2019 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
• MicroRNA Ratios Distinguish Melanomas from Nevi.
  The Journal of investigative dermatology 2019 Torres R, Lang UE, Hejna M, Shelton SJ, Joseph NM, Shain AH, Yeh I, Wei ML, Oldham MC, Bastian BC, Judson-Torres RL
• Immunopeptidomics and Peptide Expression Profiles to Develop T-Cell Receptors Against Glioma-Associated Antigens.
  Neurosurgery 2019 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 …
• 786 A machine-learning classifier trained with microRNA ratios to distinguish melanomas from nevi.
  Journal of Investigative Dermatology 2019 R. Torres, U. Lang, N.M. Joseph, A.H. Shain, I. Yeh, M.L. Wei, M.C. Oldham, B. Bastian, R.L. Judson-Torres
• Does Adult Neurogenesis Persist in the Human Hippocampus?
  Cell stem cell 2018 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-…
• 1220 MicroRNA signature distinguishing nevi from primary melanoma.
  Journal of Investigative Dermatology 2018 R. Torres, U. Lang, S. Shelton, Y. Yeniay, N. Joseph, A. Shain, I. Yeh, M. Oldham, M.L. Wei, B. Bastian, R. Judson
• A Glial Signature and Wnt7 Signaling Regulate Glioma-Vascular Interactions and Tumor Microenvironment.
  Cancer cell 2018 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-…
• Human hippocampal neurogenesis drops sharply in children to undetectable levels in adults.
  Nature 2018 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,…
• GENE-33. THE 3D EVOLUTION AND IN VIVO GROWTH PATTERNS OF GLIOMA CELL POPULATIONS.
  Neuro-Oncology 2017 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, …
• IMMU-52. SELECTION OF GLIOMA T-CELL THERAPY TARGETS BASED ON THE ANALYSIS OF TUMOR IMMUNOPEPTIDOME AND EXPRESSION PROFILES.
  Neuro-Oncology 2017 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, …
• Genetic Characterization of Stromal Cells in High Grade Gliomas.
  International Journal of Radiation Oncology • Biology • Physics 2017 S. Choi, J. Hayes, S. Shelton, L. Jones, T. Mazor, S. Fouse, M. Oldham, J. Costello
• Correction: Pleiotropic Mechanisms Indicated for Sex Differences in Autism.
  PLoS genetics 2017 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
• Resolving stem and progenitor cells in the adult mouse incisor through gene co-expression analysis.
  eLife 2017 Seidel K, Marangoni P, Tang C, Houshmand B, Du W, Maas RL, Murray S, Oldham MC, Klein OD
• An FAK-YAP-mTOR Signaling Axis Regulates Stem Cell-Based Tissue Renewal in Mice.
  Cell stem cell 2017 Hu JK, Du W, Shelton SJ, Oldham MC, DiPersio CM, Klein OD
• Pleiotropic Mechanisms Indicated for Sex Differences in Autism.
  PLoS genetics 2016 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
• GENT-15. INTEGRATED MOLECULAR PROFILING OF HUMAN BRAIN TUMORS THROUGH MULTIOMIC ANALYSIS OF SERIAL SECTIONS (MASS).
  Neuro-Oncology 2016 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.…
• ANGI-04Olig2 REGULATES Wnt7b EXPRESSION AND VASCULATURE CHARACTERISTICS IN GLIOMA.
  Neuro-Oncology 2015 Amelie Griveau, Samuel Shelton, An-Chi Tien, Giorgio Seano, Tracy Yuen, Jennifer Sabo, Jasmine Lau, Arman Jahangiri, Emmanuelle Huillard, Joanna Phillips, Anders Persson, Michael Oldham, William Weiss…
• MPTH-29CONNECTING MUTANT GENOTYPES TO ABERRANT TRANSCRIPTIONAL SIGNATURES ACROSS SERIAL SECTIONS OF A HUMAN TUMOR.
  Neuro-Oncology 2015 Samuel Shelton, Brett Johnson, Tali Mazor, Matthew Potts, Michael McDermott, Eric Huang, Daniel Lim, Russell Pieper, Mitchel Berger, Joanna Phillips, Joseph Costello, Michael Oldham
• Radial glia require PDGFD-PDGFRβ signalling in human but not mouse neocortex.
  Nature 2014 Lui JH, Nowakowski TJ, Pollen AA, Javaherian A, Kriegstein AR, Oldham MC
• DISTINCT AND SEPARABLE ROLES FOR HISTONE METHYLTRANSFERASE EZH2 IN NEUROGENIC ASTROCYTES.
  Neuro-Oncology 2014 D. A. Lim, W. W. Hwang, R. D. Salinas, J. J. Siu, K. W. Kelley, R. N. Delgado, M. F. Paredes, A. Alvarez-Buylla, M. C. Oldham, D. A. Lim
• Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo.
  Cell stem cell 2013 Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA
• Human-specific regulation of MeCP2 levels in fetal brains by microRNA miR-483-5p.
  Genes & development 2013 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 transcriptional networks in the brain.
  Neuron 2012 Konopka G, Friedrich T, Davis-Turak J, Winden K, Oldham MC, Gao F, Chen L, Wang GZ, Luo R, Preuss TM, Geschwind DH
• Functional genomic analyses identify pathways dysregulated by progranulin deficiency, implicating Wnt signaling.
  Neuron 2011 Rosen EY, Wexler EM, Versano R, Coppola G, Gao F, Winden KD, Oldham MC, Martens LH, Zhou P, Farese RV, Geschwind DH
• Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons.
  Genome research 2011 Iwamoto K, Bundo M, Ueda J, Oldham MC, Ukai W, Hashimoto E, Saito T, Geschwind DH, Kato T
• Is my network module preserved and reproducible?
  PLoS computational biology 2011 Langfelder P, Luo R, Oldham MC, Horvath S
• Is human blood a good surrogate for brain tissue in transcriptional studies?
  BMC genomics 2010 Cai C, Langfelder P, Fuller TF, Oldham MC, Luo R, van den Berg LH, Ophoff RA, Horvath S
• Detecting network modules in fMRI time series: a weighted network analysis approach.
  NeuroImage 2010 Mumford JA, Horvath S, Oldham MC, Langfelder P, Geschwind DH, Poldrack RA
• The organization of the transcriptional network in specific neuronal classes.
  Molecular systems biology 2009 Winden KD, Oldham MC, Mirnics K, Ebert PJ, Swan CH, Levitt P, Rubenstein JL, Horvath S, Geschwind DH
• Functional Connectivity Using Weighted Voxel Coexpression Network Analysis.
  NeuroImage 2009 JA Mumford, RA Poldrack, MC Oldham, DH Geshwind, P Langfelder, S Horvath
• Gene Expression in the Evolution of the Human Brain.
  Encyclopedia of Neuroscience 2009 M.C. Oldham, D.H. Geschwind
• A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging.
  The Journal of neuroscience : the official journal of the Society for Neuroscience 2008 Miller JA, Oldham MC, Geschwind DH
• Genome-wide analyses of human perisylvian cerebral cortical patterning.
  Proceedings of the National Academy of Sciences of the United States of America 2007 Abrahams BS, Tentler D, Perederiy JV, Oldham MC, Coppola G, Geschwind DH
• Identification of the transcriptional targets of FOXP2, a gene linked to speech and language, in developing human brain.
  American journal of human genetics 2007 Spiteri E, Konopka G, Coppola G, Bomar J, Oldham M, Ou J, Vernes SC, Fisher SE, Ren B, Geschwind DH
• Human brain evolution: insights from microarrays.
  Nature reviews. Genetics 2004 Preuss TM, Cáceres M, Oldham MC, Geschwind DH