Sofie Salama

  • Research Scientist in BIomolecular Engineering
  • HHMI Senior Scientist
  • Genomics Institute
  • Biomolecular Engineering
  • Center for Biomolecular Science & Engineering
  • 831-459-2814 (Office)
  • 831-459-1014 (lab)
  • Biomedical Sciences, Room 440
  • CBSE
  • I direct the Haussler Wet Lab, which is a portion of Professor David Haussler’s research group at UCSC and is primarily funded by the Howard Hughes Medical Institute. We work closely with the computational group, the Haussler Dry lab, to understand the evolution and function of non-protein coding regions of the human genome. A major focus is on identifying DNA elements and non-coding RNAs that play a role in specifying cortical neuron development. We use embryonic or induced pluripotent stem cell neural differentiation assays with human and primate stem cells followed by genomic characterization of this process using RNA-Seq, ChIP-Seq, etc. This approach allows us to identify both primate- and human-specific features of this important developmental pathway. In addition, we are examining the role of transposable elements in modifying our genome in both deleterious and beneficial ways. We study the cellular machinery that controls the proliferation of these elements and whether deregulation of these elements during reprogramming alters the genome of induced pluripotent stem cells. I also participate in the Haussler lab cancer genomics efforts, an ongoing collaboration with Professor Josh Stuart at UCSC. My work focuses on glioblastoma and lower grade gliomas primarily in the context of the Cancer Genome Atlas (TCGA), where I am a member of both disease analysis working groups. We focus on identifying mutations and genomic rearrangements present in individual tumors by analyzing DNA and RNA sequencing data. In addition we aim to characterize and categorize patient cohorts by integrating measurements of various gene features that affect its activity such as DNA copy number, DNA methylation, RNA expression and protein expression in a pathway context to infer the activity of proteins, complexes and processes. This type of analysis can reveal how disparate perturbations in individual tumors can lead to similar overall effects on critical cellular pathways underlying tumor development and disease progression. We bring this work back into the wet lab by making glioma driver mutations in pluripotent stem cells using CRISPR/Cas9 to assess their affects on growth, differentiation and drug sensitivity or these cells.
  • Molecular biology
  • Cell Biology
  • Stem Cells
  • Genomics
  • Neurobiology
  • Development
  • Cancer
  • Ph.D. in Molecular and Cell Biology, 1995, UC Berkeley
  • B.S. in Chemistry, 1989, University of Illinois

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