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 / 3D Structural Characterization of Genomes

Grace Aldrovandi

  • Microbiome

Hooman Allayee

  • GWAS for Complex Diseases

Eric Allen

  • How Do Firms Adjust to Energy Shocks? Evidence from Power Outages

Todd Alonzo

  • Statistical Methods for Medical Tests and Biomarkers

Oscar Aparicio

  • Analysis of DNA Replication Using High-Throughput Sequencing

Andrea Armani

  • Modeling of Optical Devices

Thalida Arpawong

  • Etiology of Emotional Resilience in Older Adults: Stress, Genes, and Behaviors

Shahab Asgharzadeh

  • Next Generation Sequencing Analyses of Childhood Neural Tumors

Pushpinder Bains

  • Characterization of Circulating Tumor Cells in Breast Cancer

George Ban-Weiss

  • Can Cool Pavements Counteract Climate Change in California?
  • Can Increased Use of Urban Vegetation Counter the Effects of Future Climate Change While Simultaneously Improving Air Quality?

Kayleigh Barnes

  • Medicare Bundled Payments

Burcin Becerik

  • Calibration of Building Energy Modeling

Thorsten Becker

  • Global Mantle Convection and Crustal Dynamics

Yehuda Ben-Zion

  • Earthquake Source Tensors in 3D

Ivan Bermejo-Moreno

  • High-Fidelity Simulations of Turbulent Flows

Carrie Breton

  • Prenatal Tobacco Smoke Exposure and TAM DNA Methylation

Roberta Brinton

  • P3 RNA-Seq Analyses

Todd Brun

  • Quantum Error Correction for Orbital Angular Momentum in Photons

Gully Burns

  • SciKnowMine
  • TechKnAcq

Peter Calabrese

  • Genetic Analysis Using Sperm Typing

Daniel Campo

  • UPC Genome Core

Preet Chaudhary

  • Clonal Events Influencing Treatment Response in Cancers of the Blood

Yibu Chen

  • Implementing Bioinformatics Software on Custom Computer Cluster

Liang Chen

  • Develop 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 Re-sequencing

Jongmoo Choi

  • Social Facial Expression Recognition

Brian Cohn

  • Hit-and-Run Biomechanics Study

David Conti

  • Statistical Methods in Genetic Epidemiology
  • Colon Cancer Family Registry
  • Childrens Health Study

Eileen Crimmins

  • Health and Retirement Study GWAS

Gage Crump

  • Genomic Analysis of Craniofacial Development

Pedro Diniz

  • Evaluation of Adaptive Multi-Threading for Resilient HPC Applications

Julian Domaradzki

  • Numerical Simulations of Turbulent Flows

Tomas Duffy

  • Circadian Gene Networks in Brachypodium

Christopher Edlund

  • NCCC Bioinformatics Core

Fokion Egolfopoulos

  • Aerodynamic and Kinetics Processes in Homogeneous and Heterogeneous Reacting Flows

Ian Ehrenreich

  • Genetic Variation in Microbes

Moh El-Naggar

  • Synchronous Parallel Kinetic Monte Carlo Simulations of Electron Transfer in the Cytochrome Networks of Bacterial Nanowires

Veronica Eliasson

  • Numerical Simulations on Shock Wave Focusing and Shock Dynamics

Julien Emile-Geay

  • C2D2 Modeling the Tropical Climate of the Past Millennium
  • P2C2: Regional Climate Reconstructions

Oleg Evgrafov

  • Transcriptome Sequencing of Neuronal Cell Lines from Patients with Schizophrenia

Robert Farley

  • ATPase MD Simulations
  • Selective Ion Permeation in Biology

Peggy Farnham

  • ChIP-seq Analysis Pipeline

Adam Fincham

  • Energy Transfer and Dynamics of Breaking Surface Gravity Waves

Steven Finkel

  • Whole-Genome Sequencing of E. Coli Populations throughout Multiple Phases of Growth

Meredith Franklin

  • Spatio-Temporal Statisitcal Analysis of Remote Sensing Data

Samuel Friedman

  • Agent-Based Cell Model

Cary Frydman

  • Neural Mechanisms of Stock Trading Biases

William Gauderman

  • Genome-Wide Association Analysis for Childhood Respiratory Outcomes

Sanford George

  • Archaeology Research in 3D Structure from Motion

Panayiotis Georgiou

  • Speech to Speech Translation
  • Behavioral Signal Processing for Motivational Interviewing

Roger Ghanem

  • Algorithms and Applications for Uncertainty Quantification

Stephan Haas

  • Magnetic Fields and Disorder in Quantum Spin Systems

Justin Haldar

  • Constrained Magnetic Resonance Image Reconstruction

Christoph Haselwandter

  • Linking Membrane Mechanics to Membrane Protein Structure

Dennis Hedgecock

  • Bioinformatic Support for Oyster Genomic Studies

John Heidemann

  • Los Angeles Network Data Exchange and Repository (LANDER) Project

Itay Hen

  • Simulating Quantum Annealers

Phillip Hendrickson

  • Large-Scale Hippocampal Model

Jerry Hobbs

  • Machine Reading

Thieo Hogen-Esch

  • Mechanisms of Anionic Isotactic Styrene Polymerizations
  • Evaluation of Aromatic Stacking of Cyclic Triazoles
  • Ring Opening Polymerizations of Cyclic Esters and N-Carboxyanhydrides

Behnam Jafarpour

  • Subsurface Flow and Transport Modeling, Simulation, and Optimization

Nir Jaimovich

  • Labor Flows and Immigration

Kristian Jessen

  • LBM Simulation of Flow and Transport

Erik Johnson

  • Computationally Efficient Design of Semiactive Control Strategies for Natural Hazard Mitigation

Christopher Jones

  • Disappearing Anomalies

Anand Joshi

  • Brain Shape Analysis using Spectral Geometry

Gideon Juve

  • Pegasus

Rehan Kapadia

  • Scaled Electron Devices

Vsevolod Katritch

  • Structure and Dynamics of Kappa Opioid Receptor

Sarah Kenny

  • Sigma

Kevin Knight

  • Statistical-Based Natural Language Processing

James Knowles

  • Analysis of DNA Sequences Generated with Next-Gen Technology

Chung-Chieh Kuo

  • Multimedia Technologies
  • TREC Video Understanding Experiments

Ite Laird

  • Epigenetic Profiling of Human Alveolar Epithelial Cells in Health and Disease

Darius Lakdawalla

  • Insurance Benefit Design

Julie Lang

  • Molecular Profiling of Circulating Tumor Cells

Fides Lay

  • Genome-Wide Nucleosome Occupancy and Methylome Sequencing

Natasha Lepore

  • Morphometry in Brain MR Images of Babies and Fetuses

Kristina Lerman

  • SciSIP

Naomi Levine

  • Impact of Submesoscale Processes on Marine Carbon Cycling
  • Microbial Diversity and Bio-Physical Interactions
  • Ecosystem Dynamics at SPOT

Lin Li

  • Investigating Mechanism of Hormonal Therapy Resistance Caused by ESR1 Mutation

Gangning Liang

  • Analyzing Cancer Epigenomes – Updated

Daniel Lidar

  • Simulations of the D-Wave Quantum Annealing Computer

Michael Lieber

  • DNA Sequence Alignment with Mouse Genome
  • Accumulation of Human DNA Mutations with Age

Eric Lin

  • On the Topographic Resonance Induced by a Tropical Storm – Continue

Patrick Lynett

  • Large-Scale Modeling of Wave-Driven Coastal Processes

Philip Maechling

  • SCEC/CME: Cyberinfrastructure for Earthquake System Science

Paul Marjoram

  • Marjoram Lab – Animal Behavior

Mara Mather

  • fMRI Analyses of Emotion and Cognition Studies

Andrew McMahon

  • Regulatory Programs of Neural Specification

Huaiyu Mi

  • Panther Pathway

Joshua Millstein

  • Identifying Prognostic Markers and Therapeutic Targets for Serious Ovarian Cancer

Hyungsik Moon

  • Heterogeneous Income Profiles Model

Gourab Mukherjee

  • Scalable, Consistent Clustering Methods with Applications in Single-Cell Expression Analysis

Frank Nagle

  • Bitcoin Transaction Network Analysis

Aiichiro Nakano

  • Ultrascale Atomistic Simulation of Chemical Reactions

Shrikanth Narayanan

  • Tracking Dynamics of Vocal Tract Shaping

Premkumar Natarajan

  • Graphics-Based Learning Approach Integrated with Vision Elements (GLAIVE)
  • Multilingual Automatic Document Classification and Translation (MADCAT)

Krishna Nayak

  • Magnetic Resonance Engineering Laboratory

Michael Neely

  • Optimization of High-Dimensional Nonparametric Maximum Likelihood Pharmacokinetic Population Distributions

Ramakant Nevatia

  • Video Content Analysis

Paul Newton

  • Cancer Metastasis Models Based on Evolutionary Game Theory

Toan Nguyen

  • Online Archive Video Converter

Feng Ni

  • Design of GPCP Ligands

Serguei Noujdine

  • Making the Complex Comprehensible: Approximate Bayesian Computation and Behavioral Dynamics

Elvia Nunez

  • Identification of Circulating Tumor Cells

Maria Ogneva

  • Predicting Revisions in Macroeconomic Indicators using Accounting Information

Antonio Ortega

  • Machine Learning using Graph Signal Processing for Big Data Applications

Kelly Peters

  • Structural Equation Modeling Tree to Extract Longitudinal Patterns of Changes from Big Data

Elena Pierpaoli

  • The Matter Power Spectrum at Small Scale
  • Reconstruct Dark Matter Mass Profile from Radio Emission in Galaxy Clusters

Fabien Pinaud

  • Multiparametric Single Molecule Tracking and Superresolution Imaging

Michelle Povinelli

  • Large-Scale Simulations of Microphotonic Devices

Michael Press

  • Discovery and Characterization of Molecular Alterations in Ovarian Cancers with Potential as Novel Therapeutic Targets

Oleg Prezhdo

  • Time-Domain Ab Initio Studies of Nanoscale Materials for Energy Applications

Emily Putnam-Hornstein

  • Children’s Data Network

David Pynadath

  • OpenMind

Peter Qin

  • Molecular Dynamics Analyses of Nitroxides Attached to Nucleic Acids

Cauligi Raghavendra

  • Brain MRI Data Analysis using Machine Learning Algorithms

Peter Ralph

  • Visualization and Statistics for Spatial Population Genomic Analysis

Golam Rasul

  • Ab Initio/GIAO-CCSD(T) 13C NMR Study of the Rearrangement Pathways and Dynamic Aspects of the Rapidly Equilibrating Carbocations

Edward Rhodes

  • Helioseismic Studies of Solar Internal Structure and Dynamics

Remo Rohs

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

Paul Ronney

  • Turbulent Combustion Simulations

Muhammad Sahimi

  • Towards a Molecular Model of SiC Nanoporous Membranes
  • Landfill Modeling and Estimation

Neil Segil

  • Epigenetic Analysis of Sensory Development and Regeneration of the Inner Ear

Fei Sha

  • Statistical Machine Learning

Robin Shakeshaft

  • Greens Function for Continuum Processes

Maryam Shanechi

  • Brain-Machine Interface for Neuropsychiatric Disorders

Ansgar Siemer

  • Exploration of Orb2 Fibril Core

Andrew Smith

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

Yann Staelens

  • USC Formula SAE team

Lowell Stott

  • Collaborative Research: Investigating Decadal Climate Predictability and Climate Impacts (IDCPI) on the Western United States

Daniel Stram

  • Analysis of Genome-Wide Genetics Data

Fengzhu Sun

  • Development of Computational Methods for Metagenomics Data Analysis

Pedro Szekely

  • DIG: Domain-Specific Insight Graphs

Alireza Tabatabaeenejad

  • AirMOSS

Milind Tambe

  • Finding Stackelberg Equilibria

Simon Tavare

  • Center of Excellence in Genomic Science: Genomic Analysis of the Genotype-to-Phenotype Map

Paul Thomas

  • Reconstructing the Evolution of All Known Genes

Matthew Thornton

  • Stem Cell Microenvironment in The Maintenance of Pluripotency and Reprogramming
  • Molecular Mechanisms in Myelomeningocoele

Xin Tong

  • Information Exchange in Social Networks: a Finite Population and Communication Perspective

Bryan Tysinger

  • Future Elderly Model – Future America Model

Anton Valouev

  • Cancer Genomics

David Van Den Berg

  • NGS Data and Infrastructure Analysis

Priya Vashishta

  • Billion Atom Molecular Dynamics Simulations of Energetic Materials

P. Thomas Vernier

  • Molecular Dynamics Simulations of Biomolecular Structures in Nanosecond, Megavolt-Per-Meter Pulsed Electric Fields

Greg Ver Steeg

  • Clustering with Prior Information
  • Discovering Structure in High-Dimensional Data through Correlation Explanation

Kai Wang

  • Next Generation Sequencing Data Analysis

Arieh Warshel

  • Computational Biophysics and Biochemistry

Richard Watanabe

  • The BetaGene Study
  • The GUARDIAN Study

Michael Waterman

  • Center of Excellence in Genomic Science: Genomic Analysis of the Genotype-to-Phenotype Map

Eric Watson

  • Origin and Accumulation of Hybrid Incompatibilities in Tigriopus Californicus

Randall Widelitz

  • Evolution and Development of Skin Appendages

John Wood

  • Simulation of MRI signal in Iron Laden Hepatic Tissue
  • Oxygen Contrast in Sickle Cell Disease

Jian Xu

  • New Regulators Of Cardiac Cell Plasticity

Ke-Thia Yao

  • CiSoft SEA

Zhong Zheng

  • KOR-Virtual Screen

Xianghong Zhou

  • Develop a Knowledge Base on Interconnections Among Diseases and a Bioinformatics Infrastructure for the MAPGen Consortium