Palo Alto, California, United States
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Publications

  • Parallel Bayesian global optimization of expensive functions

    Operations Research

    We consider parallel global optimization of derivative-free expensive-to-evaluate functions, and propose an efficient method based on stochastic approximation for implementing a conceptual Bayesian optimization algorithm proposed by Ginsbourger in 2008.

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  • Bayesian optimization for machine learning: A practical guidebook

    arXiv preprint arXiv:1612.04858

    We outline four example machine learning problems that can be solved using open source machine learning libraries, and highlight the benefits of using Bayesian optimization in the context of these common machine learning applications.

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  • ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.

    Bioinformatics

    Researchers need general purpose methods for objectively evaluating the accuracy of single and metagenome assemblies and for automatically detecting any errors they may contain. Current methods do not fully meet this need because they require a reference, only consider one of the many aspects of assembly quality or lack statistical justification, and none are designed to evaluate metagenome assemblies.
    In this article, we present an Assembly Likelihood Evaluation (ALE) framework that…

    Researchers need general purpose methods for objectively evaluating the accuracy of single and metagenome assemblies and for automatically detecting any errors they may contain. Current methods do not fully meet this need because they require a reference, only consider one of the many aspects of assembly quality or lack statistical justification, and none are designed to evaluate metagenome assemblies.
    In this article, we present an Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods.

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  • Solving Genomic Jigsaws

    DEIXIS Magazine

    A popular science style essay I wrote about my PhD research for a computational science magazine.

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  • Left handed beta helix models for mammalian prion fibrils.

    Prion

    We propose models for in vitro grown mammalian prion protein fibrils based upon left handed beta helices formed both from the N-terminal and C-terminal regions of the proteinase resistant infectious prion core. The C-terminal threading onto a beta-helical structure is almost uniquely determined by fixing the cysteine disulfide bond on a helix corner. In comparison to known left handed helical peptides, the resulting model structures have similar stability attributes including relatively low…

    We propose models for in vitro grown mammalian prion protein fibrils based upon left handed beta helices formed both from the N-terminal and C-terminal regions of the proteinase resistant infectious prion core. The C-terminal threading onto a beta-helical structure is almost uniquely determined by fixing the cysteine disulfide bond on a helix corner. In comparison to known left handed helical peptides, the resulting model structures have similar stability attributes including relatively low root mean square deviations in all atom molecular dynamics, substantial side-chain-to-side-chain hydrogen bonding, good volume packing fraction, and low hydrophilic/hydrophobic frustration. For the N-terminus, we propose a new threading of slightly more than two turns, which improves upon the above characteristics relative to existing three turn beta-helical models. The N-terminal and C-terminal beta helices can be assembled into eight candidate models for the fibril repeat units, held together by large hinge (order 30 residues) domain swapping, with three amenable to fibril promoting domain swapping via a small (five residue) hinge on the N-terminal side. Small concentrations of the metastable C-terminal beta helix in vivo might play a significant role in templating the infectious conformation and in enhancing conversion kinetics for inherited forms of the disease and explain resistance (for canines) involving hypothesized coupling to the methionine 129 sulfur known to play a role in human disease.

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Honors & Awards

  • 2016 Forbes 30 under 30

    Forbes

    http://www.forbes.com/30-under-30-2016/enterprise-tech/

  • Department of Energy Computational Science Graduate Fellowship

    -

    Four year full fellowship for PhD work. One of ~20 awarded each year nationally.

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