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Selected Projects

R-package: Immune Cells Analysis Software Toolkit using Machine Learning and Deep Learning

iCAT [ https://github.com/BioHPC/iCAT (private yet) ]
Project: Machine learning based high-throughput immune cell receptor sequencing analysis to inform immunological response
Skills: R, R-shiny, Machine Learning, Deep Learning
Collaborator: Dr. Richard DiPaolo, Saint Louis Univ. School of Medicine
Papers: [20]

R-package: Gene Length Depenent Analysis for Neuronal Conversion

LONGO [ https://github.com/BioHPC/LONGO ]
Project: Gene Length-Dependent Expression Analysis Tool in Neuronal Cells
Skills: R, R-shiny, BioMart, GO analysis
Collaborator: Dr. Andrew Yoo, Washington Univ. School of Medicine
Papers: [19]

Scalable Genome Assembly Algorithms

SORA [ https://github.com/BioHPC/SORA ]
Project: Scalable Overlap-Graph Reduction Algorithms for Genome Assembly using Apache Spark on Cloud
Skills: Spark, GraphX, Amazon Cloud, Scala, Python, Shell
Papers: [21], [18]

Metagenomics Analysis

SIGMA(W) [ https://github.com/BioHPC/SigmaW, http://sigma.omicsbio.org/ ]
Project: Strain-level genome identification algorithm for biosurveillance using high-performance computing
Skills: C++, Python, MPI, OpenMP, Supercomputer
Papers: [15]
OMEGA [ http://omega.omicsbio.org/ ]
Project: An overlap-graph de novo metagenome assembler
Skills: C++, Python
Papers: [12]

Cell Cycle Modeling and Stochastic Simulation using HPC

ForStoch [ https://github.com/BioHPC/ForStoch, ]
Project: Parallel Dynamic Load Balancing for Ensembles of Stochastic Simulation
Project: Implicit Stochastic Simulation Algorithm for Chemical Kinetics
Skills: Fortran, Java, C++, MPI, OpenMP, Supercomputer
Papers: [16], [14], [8], [4]
JigCell [ http://jigcell.cs.vt.edu/ ]
Project: Developing algorithms to simulate cell cycle model with stochastic methods.
Skills: Fortran, Java, C++, MPI, OpenMP, Supercomputer
Papers: [7], [3], [2]

Internships during PhD program

Pfizer Inc
Project: MATLAB on the HPC Grid: Maximizing and Optimizing the Capability in Phameceutical Modeling and Simulation
Skills: MATLAB, MATLAB Parallel Computing Toolbox, Distributed Computing Server
Sandia National Lab
Project: Investigating massive parallel genomic search application, mpiBLAST, on a macroscale simulator (SST/Macro)
Skills: C++, Python, MPI, OpenMP, Supercomputer
Papers: [10], [6]