about

I am a postdoctoral fellow at the Lewis-Sigler Institute for Integrative Genomics. I recently received my PhD from the Department of Computer Science, advised by Olga Troyanskaya at Princeton University.

My research focus is in computational biology, where I develop machine learning and statistical methods to improve our understanding of the biological circuitry that underlies living organisms and how its dysregulation may lead to disease. More specifically, I have worked on modeling tissue and cell type specificity as well as disease progression, both by developing general methods (such as semi-supervised network integration) and in applying them to decipher the molecular underpinnings of diseases such as Alzheimer’s, Parkinson’s, and rheumatoid arthritis.

An important facet of my research is building intuitive, interactive systems as interfaces to the models and predictions that I develop, and I have built such systems whenever appropriate. For example, check out my cell-type-specific functional networks for human neurons relevant to Alzheimer’s, tissue-gene expression pattern predictions in the worm, or crowdsourcing game to annotate biological pathways.

I especially enjoy collaboration, working closely with experimental biologists and clinicians in many of my projects, including:

publications

  1. An integrative tissue-network approach to identify and test human disease genes

    Yao V*, Kaletsky R*, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG.
    Nature Biotechnology. Oct 2018.
  2. Enabling Precision Medicine through Integrative Network Models

    Yao V*, Wong AK*, Troyanskaya OG.
    Journal of Molecular Biology. Sep 2018.
  3. Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression

    Kaletsky R*, Yao V*, Williams A, Runnels AM, Tadych A, Zhou S, Troyanskaya OG, Murphy CT.
    PLoS Genetics. Aug 2018.
  4. A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data

    Rangan AV, McGrouther CC, Kelsoe J, Schork N, Stahl E, Zhu Q, Krishnan A, Yao V, Troyanskaya O, Bilaloglu S, Raghavan P, Bergen S, Jureus A, Landen M, Bipolar Disorders Working Group of the Psychiatric Genomics Consortium .
    PLoS Computational Biology. May 2018.
  5. Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder

    Krishnan A*, Zhang R*, Yao V, Theesfeld CL, Wong AK, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya OG.
    Nature Neuroscience. Nov 2016.
  6. Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans

    Watson E, Olin-Sandoval V, Hoy MJ, Li CH, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M, Walhout AJ.
    eLife. Jul 2016.
  7. FNTM: a server for predicting functional networks of tissues in mouse

    Goya J*, Wong AK*, Yao V*, Krishnan A, Homilius M, Troyanskaya OG.
    Nucleic Acids Research. Jul 2015.
  8. IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

    Wong AK, Krishnan A, Yao V, Tadych A, Troyanskaya OG.
    Nucleic Acids Research. Jul 2015.
  9. A community computational challenge to predict the activity of pairs of compounds

    Bansal Mukesh, .... , NCI-DREAM Community.
    Nature Biotechnology. Dec 2014.
  10. Nucleosome-coupled expression differences in closely-related species

    Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG.
    BMC Genomics. Sep 2011.

teaching

I have been the mentor and direct supervisor for several high school, undergraduate, and junior graduate students from diverse backgrounds, ranging from computer science majors to students with no programming experience at all. More specifically, my responsibilities have included initial project design based on the students’ backgrounds and interests, close working relationship throughout the project, as well as final presentation and paper writing guidance. Furthermore, several of these students have won awards for the work they completed with me.

I was a TA for COS 323: Computing for the Physical and Social Sciences both Fall of 2012 and 2013. This data science course had over 100 students and was focused on introducing principles of scientific computation (e.g., simulations, optimization algorithms) through real-world applications.

I also enjoy volunteering for outreach events. For example, I was one of the coaches for a Django Girls workshop at Princeton. This was a free programming workshop geared towards women with little or no technical background, introducing them to HTML, CSS, Python, and, of course, Django.

other

One of the side projects that I worked on as part of HackPrinceton was “What Would I Say?”—a fun Facebook app that takes a user’s statuses and generates new ones that sound roughly like them. It has had millions of users and been covered by several news outlets (including The New Yorker, PC Magazine, and ABC News).

I am a food aficionado and have probably eaten at ~83% of the restaurants in the Princeton area (working towards completion). Some of my favorite food items are the croissants at The Little Chef and ice cream at the bent spoon. Be sure to check them out if you’re ever in town!