All Publications


  • Exploratory Gene Ontology Analysis with Interactive Visualization. Scientific reports Zhu, J., Zhao, Q., Katsevich, E., Sabatti, C. 2019; 9 (1): 7793

    Abstract

    The Gene Ontology (GO) is a central resource for functional-genomics research. Scientists rely on the functional annotations in the GO for hypothesis generation and couple it with high-throughput biological data to enhance interpretation of results. At the same time, the sheer number of concepts (>30,000) and relationships (>70,000) presents a challenge: it can be difficult to draw a comprehensive picture of how certain concepts of interest might relate with the rest of the ontology structure. Here we present new visualization strategies to facilitate the exploration and use of the information in the GO. We rely on novel graphical display and software architecture that allow significant interaction. To illustrate the potential of our strategies, we provide examples from high-throughput genomic analyses, including chromatin immunoprecipitation experiments and genome-wide association studies. The scientist can also use our visualizations to identify gene sets that likely experience coordinated changes in their expression and use them to simulate biologically-grounded single cell RNA sequencing data, or conduct power studies for differential gene expression studies using our built-in pipeline. Our software and documentation are available at http://aegis.stanford.edu .

    View details for DOI 10.1038/s41598-019-42178-x

    View details for PubMedID 31127124

  • QFMatch: multidimensional flow and mass cytometry samples alignment SCIENTIFIC REPORTS Orlova, D. Y., Meehan, S., Parks, D., Moore, W. A., Meehan, C., Zhao, Q., Ghosn, E. B., Herzenberg, L. A., Walther, G. 2018; 8: 3291

    Abstract

    Part of the flow/mass cytometry data analysis process is aligning (matching) cell subsets between relevant samples. Current methods address this cluster-matching problem in ways that are either computationally expensive, affected by the curse of dimensionality, or fail when population patterns significantly vary between samples. Here, we introduce a quadratic form (QF)-based cluster matching algorithm (QFMatch) that is computationally efficient and accommodates cases where population locations differ significantly (or even disappear or appear) from sample to sample. We demonstrate the effectiveness of QFMatch by evaluating sample datasets from immunology studies. The algorithm is based on a novel multivariate extension of the quadratic form distance for the comparison of flow cytometry data sets. We show that this QF distance has attractive computational and statistical properties that make it well suited for analysis tasks that involve the comparison of flow/mass cytometry samples.

    View details for PubMedID 29459702