Research

Interests

High-performance computing: algorithms, parallel programming languages, compilers and architectures. Applications in Bioinformatics and Computational Biology.

Projects

• Transcriptome analysis from RNA-seq data (joint with Univ of Kentucky, supported by NIH and NSF).
  Project website and publications
• Runtime systems for task-parallel programming languages (joint with RENCI, supported by DoD and DOE).
  Maestro overview and publications
• Advanced Algorithms and Software for Problems in Computational Bio-Fluid Dynamics (Focused Research Group between UNC Applied Math and Computer Science, supported by NSF). Project website
• Previous projects: Carolina Center for Exploratory Genetic Analysis; Mining protein-family specific amino-acid packing patterns; Irregular Parallel Algorithms: algorithmic, language, compilation, and hardware techniques for high performance execution of unstructured problems;Time-adaptive techniques for accelerating n-body simulations; Software and development for the DeltaSphere 3D Scene Digitizer with Lars Nyland at 3rdTech, Inc.; Evaluation of Unified Paralllel C (UPC) parallel programming language and compilers; Problem-solving environment for multiphase subsurface flow and transport phenomena; Parallel Computing Resource for Structural Biology: parallel algorithms and implementations for Molecular Dynamics simulations; Proteus: a language for prototyping parallel algorithms; Architecture-independent design methodology for parallel algorithms; High performance implementation of parallel algorithms; Lattice gas methods for modeling fluid flow and contaminant transport in heterogeneous multiphase systems; CAETI: Software infrastructure for distributed educational applications

Research Collaborators

• Faculty: Jinze Liu (UKY Computer Science), Corbin Jones (Biology), Praveen Sethupathy (Genetics), Chuck Perou and Neil Hayes ( Cancer Genome Atlas Project at Lineberger Cancer Center), Bill Marzluff (Biochemistry & Biophysics), Perpetua Muganda (NCAT Biology), Casey Miller(Environmental Science and Engineering) and James McClure (VT Adv Res Comp), Lars Nyland (Nvidia)
• Students: Darshan Singh, Christian Orellana, David Marron, Joshua Welch, Previous students.

Publications

• A curated list of publications is maintained in Google Scholar
• • Publications in reverse chronological order
  • Publications by citation count (as computed by Google Scholar)
• Access to some recent publications organized by topic (not always up to date)

Conference and journal reviewing

• Program Committee, RECOMB/ISCB Conference on Regulatory and Systems Genomics
• Editorial Board, Journal of Scientific Programming.