The COMBINE lab was created in the fall of 2014, when Rob Patro joined the Department of Computer Science at Stony Brook University. In 2019, the lab moved to the Department of Computer Science at the University of Maryland. Our research interests span many areas of computational / algorithmic genomics, but our core focus is on the development of algorithms, data structures, and statistical inference methods for analyzing high-throughput sequencing data.

Research Interests

The research interests of our lab broadly span many areas of computational biology and bioinformatics. Some of our main areas of interest include:

  • Algorithms for high-throughput transcriptomics (RNA-seq)
    • assembly, quantification, de novo analysis, differential expression
    • gene expression analysis of single-cell sequencing data (specifically, single-cell RNA-seq)
  • Data structures for indexing genomes and raw genomic data
    • data structures for building, indexing and querying one or more reference genomes
    • data structures for indexing collections of tens of thousands of raw sequencing experiments
  • Applications of approximate and data-driven representations and data structures in bioinformatics