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<!DOCTYPE html>
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    <title>Ray Berkeley</title>
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        <p>
          I'm a staff scientist in the <a href="https://herziklab.com">Herzik Lab</a> at <a href="https://chemistry.ucsd.edu">UC San Diego</a>,
          where I am developing machine learning methods for curating particle image stacks generated by single-particle
          cryogenic electron microscopy experiments.
        </p>

        <p>
          Before working in the Herzik Lab, I completed my Ph.D. in the <a href="http://debelouchinalab.ucsd.edu">Debelouchina
          Lab</a>, also at UCSD. My research focused on understanding
          structural aspects of biomolecular phase transitions and protein self-assembly. This work fostered my interests in
          structural biology of systems that are heterogeneous at micro- or mesoscales, and my excitement about methods
          capable of interrogating them–especially solid-state NMR, cryo-EM and cryo-ET, and molecular dynamics. During my time in Galia's lab
          I also enjoyed keeping up with developments in cheminformatics and structural bioinformatics.
        </p>

        <p>
          I spent most of the early parts of my PhD learning about how to work with the intrinsically disordered
          protein FUS LC, which is a model protein for biomolecular phase separation. FUS (and FUS LC) has been shown to
          form biomolecular condensates that age into rigid structures that are associated with ALS pathology. We used
          MAS NMR and coarse-grained molecular dynamics simulations <a
          href="https://www.sciencedirect.com/science/article/pii/S0006349521001430">to investigate</a> how the structure
          and dynamics of FUS LC and an ALS-associated FUS LC G156E mutant change during this maturation process. More
          recently, I've been using solid-state MAS NMR and cryoEM <a
          href="https://scholar.google.com/citations?view_op=view_citation&hl=en&user=wuk3_NgAAAAJ&citation_for_view=wuk3_NgAAAAJ:Tyk-4Ss8FVUC">to
          investigate</a> the behavior of HSPB1, a small heat shock protein, in the context of various aging-related
          intrinsically disordered proteins that form liquid-liquid droplets, aggregates, and ordered fibrils.
        </p>

        <p>
          I had the opportunity to do a number of side projects during grad school, with one of my favorites
          being an investigation of small molecules that are capable of modulating biomolecular condensates. This is a
          topic that I'm particularly excited about as it blends my interests in medicinal chemistry and cheminformatics
          with cool structural biology. We wrote <a href="https://pubs.rsc.org/en/content/articlehtml/2022/sc/d2sc04907d">a perspective</a>
          that discusses some molecules that exhibit this behavior.
        </p>

        <p>
          Before UCSD, I spent four years as an undergraduate researcher in the <a href="https://lokey.chemistry.ucsc.edu">Lokey Lab</a>
          at <a href="https://science.ucsc.edu/department/chemistry/">UC Santa Cruz</a>, where I became interested in
          non-Lipinskian molecules and protein-protein interactions and developed a love for cheminformatics and Python
          programming. I also spent a few months in the <a href="http://conway.chem.ox.ac.uk">Conway Lab</a> at the <a
          href="https://www.chem.ox.ac.uk">University of Oxford</a> where I had the opportunity to learn about chemical
          tools for studying BRD4, which sparked an interest in chromatin and chromatin remodeling. In between UCSC and
          UCSD, I spent a year and a half in <a
          href="https://www.linkedin.com/company/mendel-biological-solutions/about/">industry</a> where I worked at a
          natural products drug discovery company screening microbial extracts for natural products capable of enhancing
          crop performance.
        </p>

        <p>
          I live in San Diego and spend quite a bit of time in the SF Bay Area. I'm easiest to reach by email at
          rberkele[at]ucsd[dot]edu. You can also find me on <a href="https://twitter.com/ray_berkeley">Twitter</a>, <a
          href="https://www.linkedin.com/in/raymondberkeley/">LinkedIn</a> and <a
          href="https://github.com/ray-berkeley">GitHub</a>, although I'm not too active on those platforms.
        </p>

        <p>
          An up-to-date list of my publications is available on <a
          href="https://scholar.google.com/citations?hl=en&user=wuk3_NgAAAAJ&view_op=list_works&sortby=pubdate">Google
          Scholar</a>.
        </p>
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        <img src="./assets/images/BPS_2023.JPG" alt="This is what I look like">
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