Computer Science Research Works: Recent submissions

Now showing items 1-5 of 118

    • MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets 

      Liu, Bo; Pop, Mihai (Springer Nature, 2011-04-28)
      Enabled by rapid advances in sequencing technology, metagenomic studies aim to characterize entire communities of microbes bypassing the need for culturing individual bacterial members. One major goal of metagenomic studies ...
    • Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences 

      Liu, Bo; Gibbons, Theodore; Ghodsi, Mohammad; Treangen, Todd; Pop, Mihai (Springer Nature, 2011-07-27)
      A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences ...
    • CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing 

      Angiuoli, Samuel V; Matalka, Malcolm; Gussman, Aaron; Galens, Kevin; Vangala, Mahesh; Riley, David R; Arze, Cesar; White, James R; White, Owen; Fricke, W Florian (Springer Nature, 2011-08-30)
      Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput ...
    • Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis 

      Niranjan, Tejasvi S; Adamczyk, Abby; Bravo, Héctor Corrada; Taub, Margaret A; Wheelan, Sarah J; Irizarry, Rafael; Wang, Tao (Springer Nature, 2011-09-28)
      Sequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants. We report an effective Illumina sequencing strategy utilizing pooled samples with novel quality (Srfim) and ...
    • Exploiting sparseness in de novo genome assembly 

      Ye, Chengxi; Sam Ma, Zhanshan; Cannon, Charles H; Pop, Mihai; Yu, Douglas W (Springer Nature, 2012-04-19)
      The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. In this paper, we demonstrate that constructing a sparse ...