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deep-learning

Mentors and Regional Facilitators
Name Region Skills Interests
Aniruddha Maiti ACCESS CSSN, Campus Champions
Alana Romanella Campus Champions
Michael Blackmon Campus Champions, ACCESS CSSN
Kevin Brandt Campus Champions, Great Plains, CCMNet
Bala Desinghu ACCESS CSSN, Campus Champions, CAREERS, Northeast
Daniel Morales Campus Champions
Deborah Penchoff Campus Champions
Daniel Howard ACCESS CSSN, Campus Champions, CCMNet, RMACC
David Liu CCMNet
David Ryglicki
Daniel Sierra-Sosa Campus Champions
Fan Chen ACCESS CSSN
Fernando Garzon ACCESS CSSN
Ibrahim Sheikh CAREERS
Jeffrey Weekley Campus Champions
Od Odbadrakh ACCESS CSSN
Lonnie Crosby Campus Champions, ACCESS CSSN
shuai liu ACCESS CSSN
Mohsen Ahmadkhani CCMNet, ACCESS CSSN
Michael Puerrer Campus Champions, Northeast
Maryam Taeb
Dr. Nabeel Alzahrani Campus Champions, CCMNet
Nect Admin Great Plains, Northeast, RMACC
Jeffrey J. Nuc… CAREERS, CCMNet
Renos Zabounidis Campus Champions
SAI MUKKAVILLI ACCESS CSSN, CCMNet, Campus Champions
Grant Scott Great Plains
Xiaoqin Huang ACCESS CSSN
Shaohao Chen Northeast
Simon Delattre
Mohammad Al-Tahat CAREERS, Campus Champions, CCMNet
William Lai ACCESS CSSN
Yongwook Song Kentucky

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Engagements

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MGHPCC

Yersinia pestis, the bacterium that causes the bubonic plague, uses a type III secretion system (T3SS) to inject toxins into host cells. The structure of the Y. pestis T3SS needle has not been modeled using AI or cryo-EM. T3SS in homologous bacteria have been solved using cryo-EM. Previously, we created possible hexamers of the Y. pestis T3SS needle protein, YscF, using CollabFold and AlphaFold2 Colab on Google Colab in an effort to understand more about the needle structure and calcium regulation of secretion. Hexamers and mutated hexamers were designed using data from a wet lab experiment by Torruellas et. al (2005). T3SS structures in homologous organisms show a 22 or 23mer structure where the rings of hexamers interlocked in layers. When folding was attempted with more than six monomers, we observed larger single rings of monomers. This revealed the inaccuracies of these online systems. To create a more accurate complete needle structure, a different computer software capable of creating a helical polymerized needle is required. The number of atoms in the predicted final needle is very high and more than our computational infrastructure can handle. For that reason, we need the computational resources of a supercomputer. We have hypothesized two ways to direct the folding that have the potential to result in a more accurate needle structure. The first option involves fusing the current hexamer structure into one protein chain, so that the software recognizes the hexamer as one protein. This will make it easier to connect multiple hexamers together. Alternatively, or additionally the cryo-EM structures of the T3SS of Shigella flexneri and Salmonella enterica Typhimurium can be used as models to guide the construction of the Y. pestis T3SS needle. The full AlphaFold library or a program like RoseTTAFold could help us predict protein-protein interactions more accurately for large structures. Based on our needs we have identified the TAMU ACES, Rockfish and Stampede-2 as promising resources for this project. The generated model of the Y. pestis T3SS YscF needle will provide insight into a possible structure of the needle. 

Status: Recruiting
AI for Business
San Diego State University

The research focus is to apply the pre-training techniques of Large Language Models to the encoding process of the Code Search Project, to improve the existing model and develop a new code searching model. The assistant shall explore a transformer or equivalent model (such as GPT-3.5) with fine-tuning, which can help achieve state-of-the-art performance for NLP tasks. The research also aims to test and evaluate various state-of-the-art models to find the most promising ones.

Status: Complete

People with Expertise

Yuan Qu

Rutgers University

Programs

CAREERS

Roles

student-facilitator

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Expertise

Alana Romanella

Virginia Polytechnic Institute and State University

Programs

Campus Champions

Roles

mentor, researcher/educator, research computing facilitator, Affinity Group Leader, Match SC

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Expertise

Amira Kefi

University of Illinois at Chicago

Programs

CCMNet

Roles

CCMNet

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Expertise

People with Interest

Elizabeth Leake

Programs

CCMNet

Roles

CCMNet

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Interests

Girish Ganesan

Rutgers University

Programs

CAREERS

Roles

student-facilitator

Interests

Iman Rahbari

University of Southern California

Programs

Campus Champions, ACCESS CSSN, CCMNet

Roles

mentor, researcher/educator, research computing facilitator, research software engineer, cssn, CCMNet

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Interests

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