Principal Investigators and Projects

Below is a list of the principal investigators and projects currently supported by the Center for High-Performance Computing.

Frank Alber
Image Analysis in Cryo-Electron Tomograms/3DStructural Characterization of Genomes

Hooman Allayee
GWAS for Complex Diseases

Andrea Armani
Modeling of Optical Devices

Prithviraj Banerjee
Human Motion Detection and Tracking for Video

James Baurley
Algorithm to Learn Pathway Structure

Thorsten Becker
Global Mantle Convection and Crustal Dynamics

Todd Brun
Quantum Error Correction for Orbital Angular Momentum in Photons

Nikolaus Buenning
Investigating the Current Drought affecting the Western U.S.

Peter Calabrese
Genetic Analysis Using Sperm Typing

Gary Chen
Simulation of Genetic Variation in Mixed Populations

Liang Chen 
Developing Statistical Methods for High-Throughput Sequencing Data Analysis and Gene Expression Regulation Analysis

Ting Chen
Computational Analysis of Metagenomic Sequencing Data/Robust and Portable Workflow-Based Tolls for mRNA and Genome Resequencing

Yibu Chen
Implementing Bioinformatics Software on a Custom Computer Cluster

Limei Cheng 
Pneuma Extension

Keith Chin 
Atomistic Simulation of Protein/Surface Interaction and Protein/Surfactant Interaction

David Conti
Statistical Methods in Genetic Epidemiology

Stephen Cronin
Plasmon Resonant Nanostructures

Enoch Dames
Combustion Chemistry

Julian Domaradzki
Numerical Simulations of Turbulent Flows

Fokion Egolfopoulos
Aerodynamic and Kinetics Processes in Homogeneous and Heterogeneous Reacting Flows

Ian Ehrenreich
Genetic Variation in Microbes

Julien Emile-Geay
Modeling the Tropical Climate of the Past Millennium

Robert Farley
ATPase Molecular Dynamics Simulations

Masabumi Furuhata
Market Mechanisms for Agent Coordination

William Gauderman
Genome-Wide Association Analysis for Childhood Respiratory Outcomes

Panayiotis Georgiou
Behavioral Signal Processing for Motivational Interviewing

Roger Ghanem
Algorithms and Applications for Uncertainty Quantification

Aman Goel
Semantic Annotation Using Conditional Random Fields

Sam Gustman
Conversion of the USC Shoah Foundation Institute Video Testimonies into Multiple Digital Formats

Stephan Haas
Magnetic Fields and Disorder in Quantum Spin Systems

John Heidemann
Los Angeles Network Data Exchange and Repository (LANDER) Project

Phillip Hendrickson
Large-Scale Hippocampal Model

Jerry Hobbs
Machine Reading

Mohamadreza Hosseini
Southern California Air Quality Study

Eduard Hovy
Semantics-Oriented Natural Language Processing Research

Kung-Chuan Hsu
Quantum Key Expansion

Manish Jain
Finding Stackelberg Equilibria

Sewoong Jung
Particle Tracking Using Lattice Boltzmann Method

Ardeshir Kianercy
Boltzmann Q-learning Network Formation

Samuel Kim
Topic Models

Kevin Knight
Statistical-Based Natural Language Processing

James Knowles
Analysis of DNA Sequences Generated with Next-Gen Technology

Amy Koid
Using Metagenomics to Interrogate the Functional and Genomic Diversity of Picoeukaryotes at the San Pedro Ocean Time Series

Georgios Konstantinidis
Query Reformulation for Health Data Integration

Anna Krylov
Theory and Practice of Electronic Structure Calculations

C.C. Jay Kuo 
TREC Video Understanding Experiments

Manish Kurse
Structure and Function of the Fingers’ Tendinous Apparatus

Jun-Young Kwak
Sustainable Energy Project

Jiin Lee 
Computational Fluid Dynamic Analysis of Bridges Exposed to Hurricane Waves

Mihye Lee
Burea van Dijk Data Work

Natasha Lepore 
Morphometry in Brain MRI Images of Babies and Fetuses

Kristina Lerman 
Social Media Dynamics

Yiyu Li
Molecular Modeling of Protein Structures

Michael Lieber
DNA Sequence Alignment with Mouse Genome

Patrick Lynett
Large-Scale Modeling of Wave-Driven Coastal Processes

Philip Maechling
Cyberinfrastructure for Earthquake System Science

Leandro Marcolino
The Multi-Agent Monte Carlo Go Algorithm

Paul Marjoram
CNV Calling and Evolutionary Modeling for Tumors

Mara Mather
fMRI Analyses of Emotion and Cognition Studies

Patric Muggli
Full-Scale Modeling of High-Energy Particle Accelerators

Aiichiro Nakano
Ultrascale Atomistic Simulation of Chemical Reactions

Shrikanth Narayanan
Tracking Dynamics of Vocal Tract Shaping

Nouri Neamati
Virtual Screening of Large Databases of Small-Molecule Drugs

Ramakant Nevatia
Video Content Analysis

Magnus Nordborg
Genotype-Phenotype Map

Elnaz Nouri
Inverse Reinforcement Learning

Sergey Nuzhdin
Approximate Bayesian Computation and Behavioral Dynamics

John O’Brien
Energy Frontiers Research Center

Michelle Povinelli
Large-Scale Simulations of Microphotonic Devices

Kristen Pudenz
Adiabatic Quantum Algorithms

Peter Qin
Molecular Dynamics Analyses of Nitroxides Attached to Nucleic Acids

Lars Rahm
High-Energy Density Materials

Edward Rhodes
Helioseismic Studies of Solar Internal Structure and Dynamics

Remo Rohs
High-Throughput Analysis of DNA Shape on a Genome-Wide Basis

Daniel Ruderman
Modeling Tumor/Host Interaction

Robert Sacker
Modeling the Formation of E. Coli Morphotypes

Muhammad Sahimi
Landfill Modeling and Estimation

Patrick Schopf
Computer Simulations of Chemical Reactions in Enzymes and Solution

Fei Sha
Analysis of Statistical Methods in Machine Learning

Abhishek Sharma
Job Scheduling for Data Centers

Manoj Singh
Computational Biochemistry

Andrew Smith
Analytic Tools to Examine High-Resolution and Genome-Scale DNA Methylation Data

Darko Stefanovski
Steered Molecular Dynamics of P-Type ATPases

Lowell Stott
Analyzing California Climate Change

Alexander Stram
Increasing Accessibility to 1000 Genomes Data

Daniel Stram
Genome-Wide Association Scans

Fengzhu Sun
Computational Methods for Metagenomic Data Analysis

Alireza Tabatabaeenejad
Airborne Microwave Observatory of Subcanopy and Subsurface (AirMOSS)

Yaqi Tao
Kondo Effect by Friedel Artificially Inserted Resonance (FAIR) Method

Alexander Tartakovsky
MURI Air Force Project

Simon Tavaré
Genomic Analysis of the Genotype-to-Phenotype Map

Paul Thomas
Reconstructing the Evolution of All Known Genes

Barry Thompson
Stereoregular Electroactive Polymers

Matthew Thornton
Stem Cell Microenvironment in the Maintenance of Pluripotency and Reprogramming

Cong Trinh
Symmetry Breaking of Zinc Dipyrrine Compounds

Sinchai Tsao
Large-Scale Volumetric Segmentation in Vascular Dementia, Mild Cognitive Impairment, and Alzheimer’s Disease

Anton Valouev
Cancer Genomics

Priya Vashishta
Billion Atom Molecular Dynamics Simulations of Energetic Materials

Tom Vernier
Molecular Dynamics Simulations of Biomolecular Structures in Nanosecond, Megavolt-per-Meter Pulsed Electric Fields

Greg Ver 
Steeg Clustering with Prior Information

Nathan Walworth
Cyanobacterial Transcriptomics

Chen Wang
Routing Courier Delivery Services with Urgent Demand

Fang Wang
Asymmetric Catalysis

Fangyue Wang
Anchor Text Aggregation Research

Joseph Wang
High-Performance Computer Particle Simulation

Kai Wang
Next Generation Sequencing Data Analysis

Pan Wang
Attrition and Skewness in Longitudinal Twin Studies: A Comparative Study of Structural Equation Modeling (SEM) Estimation Methods

Arieh Warshel
Computational Biophysics and Biochemistry

Richard Watanabe
The BetaGene Study

Michael Waterman
Genomic Analysis of the Genotype-to-Phenotype Map

John Wood
Cortical Mapping in Thalassemia Major

Daiying Wu
Analysis of ChIP-Seq Data

Shanshan Xu
Multivariate Regression

Maocai Yan
Molecular Modeling of APOBEC and Design of Anti-HIV Molecules

Size Zheng
Molecular Dynamics (MD) Simulation Using GROMACS Software

Xianghong Zhou
Development of a Knowledge Base for Interconnections among Diseases and a Bioinformatics Infrastructure for the MAPGen Consortium