Researchers and Projects

Here are some of the researchers collaborating with Pitt CRC on large scale projects. Along with names of PIs and projects are allocations of computing time by Service Units (SU). Projects such as these requiring more than 10,000 SUs submit allocation proposals. Projects using 10,000 or fewer SUs do not require proposals.allocations. Allocations shown here also specify the resource by type of compute node (except in a few cases).

  • SMP: Shared Memory Framework
  • HTC: High Throughput Computing
  • MPI: Message Passing Interface
  • GPU: Graphics Processing Units

Find detailed descriptions of compute node types at https://crc.pitt.edu/Resource-Description-Proposal-Language.

 

Steven Abramowitch, associate professor, Department of Bioengineering
"Maternal Geometric and Material Property Predictors of Vaginal Birth-Related Injuries"
Allocation: 1,100,000 on SMP, 75,000 on GPI, until 01/20/21

 

Stefania Albanesi, professor, Department of Economics
Project 1: Lessons of the 2007-2009 Financial Crisis: The Role of Real Estate Investors and Long Term Consequences for the Young
Project 2: Labor Supply and Labor Demand Trends and Changing Business Cycles
Project 3: Heterogeneity and Macroeconomics: Various Topics Relating to Consumer Credit Markets
Allocation: 300,000 on SMP, 30,000 on MPI, 50,000 on GPU, until 08/07/20 
Read about Professor Albanesi’s Pitt CRC collaborations:

 “Pitt economics professor revisits the 2007-2009 financial crisis”
"Stefania Albanesi returns to CRC to create a new model credit score"

 

Matthew Barry, assistant professor, Department of Mechanical Engineering and Materials Science
Project 1: "Thermal-Fluid-Electric Coupled Modeling of Integrated Thermoelectric Devices”
Project 2: "Applied Computational Fluid Dynamics Laboratory Allocation Request - Multi-physics Systems Modeling and Integration of High-performance Computing into Classrooms"
Allocation: 1,300,000 on SMP, 1,500,000 on MPI, 250,000 on GPU, until 02/04/21

Read about Professor Barry’s Pitt CRC collaboration: “Power from the exhaust pipe”

 

Anna Balazs, distinguished professor, Department of Chemical & Petroleum Engineering
Project 1: "Designing Chemically Responsive Elastic Sheets"
Project 2: “Towards Creating Tunable Hierarchically Structured STEM Gels”
Project 3: “Biomimicry Among Chemically Active Synthetic Objects”
Project 4: “Chemical and hydrodynamic instabilities produced by enzymatic surface reactions”
Project 5: “Liquid Crystalline Elastomer Simulations”
Allocation: 1,300,000 on SMP, 100,000 on MPI, 50,000 on GPU, until 07/11/20

 

Ramon Bataller, professor, School of Medicine
"Use of Single Cell RNA-seq and Whole Exome sequencing to Investigate Molecular Mechanisms of Severe Alcoholic Hepatitis"
Allocation: 65,000 on HTC, until 02/23/21

 

Riyue Bao, Co-Director of Bioinformatics at UPMC Hillman Cancer Center & Research
associate professor, Department of Medicine
"Translational Bioinformatics to Drive Therapeutic and Treatment Advances in Cancer"
Allocation: 500,000 on HTC, until 12/18/20

 

Panagiotis (Takis) Benos, professor, Department of Computational and Systems Biology
“Probabilistic graphical models for modeling transcriptomic differences of response to a prophylactic cancer vaccine
Allocation: 30,000 on HTC until 02/25/20

 

Jon Boyle, associate professor, Department of Biological Sciences
"de novo genome assembly of Toxoplasma gondii and its relative using Nanopore MinION sequencing"
Allocation: 280,000 on HTC, until 10/16/20

 

Tullia Bruno, assistant professor, Department of Immunology
"Single-cell RNAseq Analysis of Peripheral Blood and Tumor Infiltrating Immune Cells from Patients with Solid Tumors"
Allocation: 25,000 on HTC, until 3/27/21

 

Peter Brusilovsky, professor, School of Computing and Information
"Open Corpus Personalized Learning"
Allocation: 100,000 on GPU, until 05/15/20

Andrew Bunger, associate professor, Department of Chemical & Petroleum Engineering
"Numerical Simulation of Sleeve Fracturing for Measurement of In Situ Stresses"
Allocation: 40,000 on SMP, until 04/03/20

 

Uma Chandran, associate professor, Department of Biomedical Informatics
Co-Director, Cancer Boinformatics Services, UPMC Hillman Cancer Center
"Genomics Analysis by the University of Pittsburgh shared resources –the Cancer Bioinformatics Services and the Genomics Analysis Core"
Allocation: 200,000 on HTC, until 12/10/20

 

Chung-Chou Chang, professor, Department of Medicine
"Chang Biostatistics Research Group"
Allocation: 500,000 on HTC, until 02/27/20

 

Yu Cheng, associate professor, Department of Statistics
"Dynamic Multivariate Normative Comparison and Risk Screening for Alzheimer's Disease Progression"
Allocation: 1,000,000 on MPI, until 11/24/20

 

Maria, Chikina, assisstant professor, Computational & Systems Biology
"Statistically Rigorous Computational Methods to Link Genotypes to Phenotypes"
Allocation: 500,000 on HTC, until 04/16/21

Lillian Chong, associate professor, Department of Chemistry
“Simulations of diffusion-controlled chemical reactions in explicit solvent”
Allocation: 3,200,000 on MPI until 04/25/20

Read about Professor Chong’s Pitt CRC collaboration: “Lillian Chong focuses on under explored regions”

 

Nathan Clark, associate professor, Department of Computational and Systems Biology
“Using Comparative Genomics to Provide Functional Annotation of Genomes”
Allocation: 380,000 on HTC until 01/28/20

 

Michael Colaresi, William S. Dietrich II Chair, Department of Political Science
Project 1. Organize, parse and analyze millions of documents from human rights reports.
Project 2. Analyze documents and press releases from more than 100 Human Rights NGOs to assess the comparative effectiveness of approaches to governments in addressing human rights issues – cooperatively engaging versus “naming and shaming.”
Project 3: Create a Bayesian generative model of Wikipedia editing to identify conflict of interest editing.
Project 4: Track political violence at a high spatial and temporal resolution for the continent of Africa and make predictions for approximately 1.25 million grid-cells on the continent, three months in advance, on a rolling basis.
Allocation: 289,000 on SMP, 10,000 on MPI until 02/21/20

Read about Professor Colaresi’s Pitt CRC collaboration: “Parsing human rights via machine learning”

 

Corey Clifford, postdoc, and Goetz Veser, professor, Department of Chemical and Petroleum Engineering
"Process Intensification in the Specialty Chemicals Industry: Understanding the Interplay Between Reaction, Heat-, and Mass-Transfer"
500,000 on MPI until 05/28/20

                                                        

Meihong Deng, research assistant professor, Department of Surgery
“Single-cell RNA Sequencing Reveals A New Monocyte Trajectory in Mouse Polytrauma Model”
Allocation: 156,120 on HTC until 04/07/20

Samuel Dickerson, assisstant professor, Electrical and Computer Engineering
"Vitual Reality Hands-Off Render Program"
Allocation: 24,000 on GPU until 04/17/21

 

Robert Ferris, Director, UPMC Hillman Cancer Center
"Next-Generation Sequencing Analysis of Squamous Cell Carcinomas (SCCs)"
Allocation: 121,000 on HTC, until 12/18/20

 

Peyman Givi, distinguished professor, Mechanical Engineering & Materials Science
James T. MacLeod professor, Mechanical Engineering and Petroleum Engineering
"Large Eddy Simulation of Supersonic Turbulent Combustion"
Allocation: 600,000 on SMP, 2,000,000 on MPI, 1,000 on GPU, until 06/19/20

 

Sarah Hainer, assistant professor, Department of Biological Sciences
"Chromatin-Mediated Mechanisms of Transcription Regulation in ES cells"
Allocation: 75,000 on HTC until 06/22/2021

 

Jamie Hanson, assistant professor, Psychology
"Investigating the reliability of brain segmentation algorithms: Focusing on Hippocampal and Amygdala Subdivisions"
Allocation: 16,783 on HTC, until 08/08/20

 

Daqing He, professor, School of Computing and Information
"Sentence Simplification through Deep Learning Model"
Allocation: 570,000 on SMP, 100,000 on GPU, until 05/08/20

 

Raúl Hernández Sánchez, assistant professor, Department of Chemistry
"Tubularenes: redefining carbon-based nanotubes"
Allocation: 650,000 on SMP, until 09/29/20

 

Jingtong Hu, assistant professor, Department of Electrical and Computer Engineering
"Efficient Data Transmission Between Transiently Powered Sensors "
Allocation: 1,000 on SMP, 80,000 on GPU, until 03/27/21

 

Geoffrey Hutchison, associate professor, Department of Chemistry
“Data-Driven Quantum Chemical Calculations for Molecular Materials Design”
Allocation: 800,000 on SMP, 10,000 on GPU until 04/16/21

 

Theodore Huppert, associate professor, Department of Electrical and Computer Engineering
"Advanced Statistical Models for Functional Near-infrared Spectroscopy Imaging Analysis"
Allocation: 728,000 on SMP, until 10/16/20

Tamer Ibrahim, professor, Bioengineering Department
"7 Tesla Bioengineering Research Program (7TBRP) and Radiofrequency (RF) Research Facility Imaging Research"
Allocation: 1,300,000 on SMP, 1,200,000 on MPI, until 03/27/21

 

Jong H. Jeong, professor, Biostatistics, School of Public Health
“Inference on Win Ratio for Clustered Semi-Competing Risk Data”
Allocation: 500,000 on HTC until 02/21/2020

 

J. Karl Johnson, W.K. Whiteford Professor, Department of Chemical and Petroleum Engineer
“Computational Design of New Materials for Energy and Environmental Applications”
Allocation: 1,700,000 on SMP, 2,700,000 on  MPI until 04/16/21

Read about Professor Johnson's CRC collaboration: "CRC associate director in Catalysis Science $ Technology"

 

Ken Jordan, Richard King Mellon Professor and Distinguished Professor of Computational Chemistry
Co-Director, Center for Simulation and Modeling
"Computational Resources to Support Projects in Electronic Structure Theory"
Allocation: 200,000 on SMP, 1,940,000 on MPI, 8,000 on GPU, until 06/19/20

 

Chae Ryon Kang, assistant professor, Biostatistics in Pitt School of Public Health
“Individualized treatment recommendation to optimize multiple rare event binary outcomes with application to mother-infant pairs from high-risk pregnancy studies”
Allocation: 500,000 on HTC until 01/30/2021

 

John Keith, associate professor, Department of Chemical & Petroleum Engineering
"Modeling local solvation effects in renewable energy catalysis and sustainability"
Allocation: 1,900,000 on SMP, 1,800,000 on MPI, until 04/08/20

 

Kang Kim, associate professor, Department of Medicine
"Ultrasound super-resolution imaging of vasa vasorum in atherosclerotic plaques"
Allocation: 153,600 on SMP until 05/27/20

 

David Koes, assistant professor, Department of Computational & Systems Biology
“Deep Generative Models for Drug Discovery”
Allocation: 100,000 on GPU until 02/28/20

 

Daniel Lambrecht, Department of Chemistry
"Exploring silyl ketenes for next-generation rigid rod polymers"
Allocation: 503,000 on SMP, until 04/16/21

 

Adrian Lee, professor, Department of Pharmacology and Chemical Biology
“Interrogating Genetic Drivers of Metastatic and Recurrent Breast and Ovarian Cancer”
Allocation: 500,000 on HTC until 01/24/20

 

Sangyeop Lee, assisstant professor, Department of Mechanical Engineering & Materials Science
"Machine Learning Enabled Study of Phonon Transport across Grain Boundaries from First Principles"
Allocation: 1,000,000 on MPI, until 06/28/20

 

Peng Liu, assistant professor, Department of Chemistry
“Computational Studies of Transition-Metal-Catalyzed Organic Reactions”
Allocation: 1,300,000 on SMP, 3,200,000 on MPI,  100,000 on GPU until 3/30/21

Read about Professor Liu’s Pitt CRC collaboration: “Pitt CRC computation guides catalyst design”

 

 

Shuchang Liu, assisstant professor, Department of Pathology
"Comprehensive statistical mining of genomic data of hepatocellular carcinoma"
Allocation: 50,000 on HTC, until 06/19/20

 

W. Vincent Liu, professor, department of Physics & Astronomy
"Computational exploration for quantum information scrambling of spin chains beyond standard short-range interaction"
Allocation: 1,240,000 on SMP, until 04/02/20

 

Cecilia Lo, Distinguished Professor, Department of Developmental Biology
"The Complex Genetic Etiology of Congenital Heart Disease"
Allocation: 200,000 on HTC, until 1/16/21

 

Anna Manelis, assistant professor, Department of Psychiatry
“Aberrant brain functioning during working memory tasks in mood disorders across diagnoses and age groups: Secondary data analysis”
Allocation: 75,000 on SMP until 02/29/2020

 

James McKone, assistant professor, Department of Chemical and Petroleum Engineering
"Design of Reducible Metal Oxide Hydrogenation Catalysts"
Allocation: 659,000 on MPI until 04/02/21

 

Rami Melhem, professor, School  of Computing and Information
“Shadow Computing and Sparse Big Data Analytics on HPC systems”
200,000 on MPI until 01/30/21

 

Prahlad G. Menon, assistant professor, Department of Bioengineering
“Hemodynamics Indices and Shape-Based Models of Left Atrial Appendage to Enhance Stroke Prediction in Atrial Fibrillation”
Allocation: 1,200,000 on SMP until 07/02/21

 

Lucas Mentch, assisstant professor, Department of Statistics
"Variable Selection and Hypothesis Testing for Supervised Learning"
Allocation: 1,500,000 on MPI, 36,000 on GPU, until 12/18/20

 

Yannis Mpourmpakis, assistant professor, Department of Chemical and Petroleum Engineering
Project 1. “Oxygen Reduction Reaction (ORR) over Ligand-Protected MNCs”
Project 2. “Ligand Removal Kinetics in MNC Catalysis”
Project 3. “Identifying Generalized Structure-Activity Relationships for the Dehydrogenation (DH) of Alkanes on Oxides”
Project 4. "Computational Investigation of Catalytic, Optical, and Structural Properties of Nanomaterials"
Allocation: 3,200,000 million on MPI, 1,300,000 on SMP until Jan. 16, 2021

 

Matthew Nicotra, assisstant professor, Department of Surgery
"Genomics and Proteomics of Hydractinia allorecognition"
Allocation: 241,920 on HTC, until 07/11/20

 

Steffi Oesterreich, professor, Department of Pharmacology and Chemical Biology
“Interrogating Genetic Drivers of Endocrine Therapy Resistance in Breast Cancer and the Tumor Microenvironment”
Allocation: 500,000 on HTC until 04/23/20

 

Ashok Panigrahy, professor, School of Medicine
"Identifying Population Subgroups in Neurological rs-fMRI Using Unsupervised Machine Learning"
Allocation: 580,000 on SMP, until 11/06/20

 

Hyun Jung Park, assisstant professor, Department of Human Genetics
"Identifying therapeutic microRNAs in immunotherapy clinical trial data"
Allocation: 200,000 on HTC, until 05/08/20

610,000

James M. Pipas, professor, Department of Biological Sciences
“Exploring the viral universe and its effects on cellular pathways”
Allocation: 100,000 on HTC until 04/23/20

Read about Professor Pipas’ Pitt CRC collaboration at: “Pitt researchers hunt viruses in Project Premonition”

 

Amanda Poholek, director, HSSC@CHP NextGen Sequencing Core Facility, School of Medicine, Department of Pediatrics
“Epigenetic and Transcription Factor Control of Immune Cell Differentiation”
Allocation: 40,000 on HTC until 01/16/21

 

Jiantao Pu, associate professor, Department of Radiology
"Improving Diagnosis of Small Airways Disease (SAD) Using Deep Learning Technology"
Allocation: 50,000 on GPU, until 08/08/20

 

Dhivyaa Rajasundaram, research assisstant professor, Department of Pediatrics
"Bioinformatics Core Facility at Children’s Hospital of Pittsburgh"
Allocation: 150,000 on HTC, 50,000 on MPI, until 07/17/20

 

Caroline Runyan, assisstant professor, Department of Neuroscience
"Diverse activity dynamics of inhibitory subtypes across mouse neocortex"
Allocation: 928,000 on SMP, until 04/16/20

 

Daniel Sadowsky, assisstant professor, Department of Chemistry
"Mechanistic Modeling of the Degradation of Hydro(chloro)fluoroether Anesthetics with Ab Initio Electronic Structure Calculations"
Allocation: 25,000 on SMP, until 10/16/20

 

Wissam Saidi, associate professor, Department of Mechanical Engineering & Materials Science
"Multiscale Investigations of Functional Materials"
Allocation: 1,200,000 on SMP, 200,000 on HTC, 3,100,000 on MPI, 60,000 on GPU, until 11/06/20

 

Sunil Saxena, professor and Department Chair, Department of Chemistry
"Accurately measuring DNA by copper based pulsed electron spin resonance"
Allocation: 50,000 on SMP, until 07/11/20

 

Harinder Singh, professor, Department of Immunology
"Regulatory DNA sequences controlling gene expression in immune cells"
Allocation: 20,000 on SMP, 100,000 on HTC, 20,000 on MPI, until 10/03/20

 

William Stauffer, assisstant professor, Department of Neurobiology
"Single cell profiling of macaque brain and screening of monkey-specific promotors"
Allocation: 500,000 on HTC, until 10/16/20

 

David Swigon, associate professor, Department of Mathematics
"Dynamics if Knotted DNA in Ionized Fluid"
Allocation: 858,000 on SMP, until 10/16/20

 

Kathryn Torok, associate professor, Department of Pediatrics
"Defining the skin transcriptional profile of pediatric localized scleroderma"
Allocation: 40,000 on HTC, until 07/11/20

 

Jonathan Vande Geest, professor, Departments of Bioengineering, Ophthalmology, Mechanical Engineering and Materials Science.
“Studying the Racioethnic disparity in Primary Open Angle Glaucoma: A proposal for computational resources”
Allocation: 125,000 on MPI, 350,000 on SMP until April 16, 2020

 

Sachin Velankar, associate professor, Department of Chemical & Petroleum Engineering
"Wrinkle and fold instability in biological and polymeric layered systems"
Allocation: 75,000 on SMP, until 08/07/20

 

Shyam Visweswaran, associate professor, Department of Biomedical Informatics
"Predictive modeling in the development of a Learning Electronic Medical Record System"
Allocation: 152,000 on MPI, 50,000 on GPU, until 10/16/20

 

Guofeng Wang, associate professor, Department of Mechanical Engineering and Materials Science
"Computational Study of PGM-Free Eelctrocatalysts"
Total allocation: 4,500,000 until 03/12/21

 

Junmei Wang, associate professor, Department of Pharmaceutical Sciences
Project 1. Developing the 2nd Generation of the General AMBER Force field.
Project 2. Developing New Algorithm for Alchemical Free Energy Calculations.
Project 3. Developing a New End-Point Free Energy Calculation Method - Extended Linear Interaction Energy
Allocation: 875,000 on SMP, 100,000 on GPU until 12/29/20

 

Xiaosong Wang, associate professor, Department of Pathology
"Genome-wide quantification of new biological and pathological functions of genes and pathways"
Allocation: 488,000 on HTC, until 02/05/21

 

Christopher Wilmer, professor, Department of Petroleum and Chemical Engineering
Project 1. Structure Property Relationships of Porous Crystals
Project 2. Predicting MOF Conductivity
Project 3. PUFF (Pitt Universal Force-Field) development
Project 4. MOF Sensor Arrays
Project 5. Nanoscale Diffusion of Molecular Machines
Allocation: 100,000 on MPI, 700,000 on SMP until 01/16/20

 

Xiang-Qun Xie, professor, School of Pharmacy, Computational Chemical Genomics Screening (CCGS) Center
NIH NIDA National Center of Excellence for Computational Drug Abuse Research (CDAR)
Allocation: 875,000 on SMP, 100,000 on GPU

 

Hassane Zarour, professor, Department of Immunology
"Evaluating Melanoma-induced Immunosuppression"
Allocation: 50,000 on HTC, until 11/12/20