Southern All of Us Network

Principal Investigator (PI): Bruce Korf

Informatics Lead: James Cimino

In collaboration with the HudsonAlpha Institute for Biotechnology in Huntsville, this program is aimed at preventing and treating disease, including certain types of cancer, heart problems, and genetic disorders. The AGHI also includes a major focus on research, through which data from test results will be used to advance scientific understanding of the role that genes play in health and disease.

Press Release Link: https://www.joinallofus.org/southern

Duration of Grant: 7/1/2018 – 6/30/2023

Center for Clinical and Translational Science

PI: Robert P. Kimberly

Informatics Director: James Cimino

Co-Investigators: Jake ChenAmy Wang

The vision of the Center for Clinical and Translational Science (CCTS) is to reduce health disparities in diseases disproportionately represented within the Deep South as we accelerate discovery to improve human health. To accomplish this, the CCTS will 1) develop a vibrant, diverse clinical and translational research workforce, 2) catalyze a collaborative, integrated data analytics and informatics ecosystem, 3) work closely with local constituencies to address health issues of particular significance to our region and will share best practices in pursuit of community engaged studies to enhance culturally sensitive participation, safety, confidentiality and effectiveness, 4) support the ethical conduct of scientifically rigorous pilot and clinical research, and 5) use quantitative and qualitative assessment and feedback to assure that training and research programs meet the needs of its scientific constituencies and the goals of the CCTS.

Press Release Link: https://www.uab.edu/ccts/

Duration of Grant: 5/6/2019 – 4/30/2024

Integrating Genomic Risk Assessment for Chronic Disease Management in a Diverse Population – the eMERGE Consortium

PI’s: Nita Limdi, James Cimino

The project aims to develop race-specific genomic risk assessments, establish methods to implement these assessments and management in clinical care is the vital first step to leverage the power of genomics to prevent disease. In the United States, 60% of adults have at least one chronic disease and 40% have two or more.  Although research has identified genomic signatures of common diseases, genomic risk assessments are not used in clinical care to identify, and if appropriate, pre-treat patients at high risk for developing disease. 

Press Release Link: https://grantome.com/grant/NIH/U01-HG011167-01

Duration of Grant: 7/1/2020 – 4/30/2025

CRITICAL: Collaborative Resource for Intensive care Translational science, Informatics, Comprehensive Analytics, and Learning

PI: Jim Cimino

Working with Northwestern University, we aim to establish a large cross-CTSA collaborative critical care data sharing by leveraging the existing CTSA collaborative networks. With the diversified racial, ethnic and geographic profiles from the above CTSAs, we will be able to support fair and generalizable algorithms for advanced patient monitoring and decision support. The proposed project will provide best practice guidance to and set up exemplary examples for nationwide CTSAs. It will also support the cultivation of next generation medical AI researchers.

Press Release Link: https://www.scholars.northwestern.edu/en/projects/critical-collaborative-resource-for-intensive-care-translational-

Duration of Grant: 8/15/2021 – 7/31/2025

Improving Electronic Health Record Usability and Usefulness with a Patient-Specific Clinical Knowledge Base

PI: Jim Cimino

Co-Investigators: Tiago ColicchioJohn Osborne

This project seeks to improve the usability and usefulness of a patient’s electronic health record by enhancing the record with knowledge that makes clinical context explicit through representation of relationships among the various concepts in the record. We will build on previous work that defines the concepts and ontology of such relationships (about causality, intention of tests and treatments, and assessment of effect of therapy) by adding them to the elements that are already in the record (such as problems, tests, medications and diagnoses).

Duration of Grant: September 2021 – July 2023

Heterogeneity in African Ancestry SLE: Implications for Targeted Therapy

PI’s: Alexander Rosenberg, Chris Scharer

Also known as “Bioinformatics, Data Management and Integration,” the project has the goal of developing an informatics environment (data warehouse, integrative and analytical tools) for many types of data that will be collected for this cohort (e.g. flow cytometry, RNAseq, ATACseq, DNA methylation, single cell RNAseq and repertoire sequencing). The team on this project will coordinate program-wide ‘omics data processing, data management and downstream analysis, while assisting in requirements assessment, data modeling, data storage strategies, implementation, and ETL process development.

Press Release Link: How to Better Treat Lupus in Black Patients

Duration of Grant: 9/1/2021 – 8/30/2024

Building and InnovatinG: Digital heAlth Technology and Analytics (BIGDATA)

PI: James Willig

Co-Investigator: Amy Wang

The goal of this research core is to harness mobile and digital health technologies, informatics, real-world data, and advanced analytics to support broad base of investigators both within and outside UAB. The main priority is to bring innovative informatics and translational tools and methods to the research community with a focus on promoting innovative and synergistic research in rheumatologic and musculoskeletal diseases.

Duration of Grant: 9/15/2020 – 7/31/2024

Cancer Deep Phenotyping from Electronic Medical Records

PI: Gergana Savova

Co-Investigator: John Osborne

This project intends to evaluate and extend “deep phenotyping” reportable cancer case detection based on DeepPhe, by expanding previous Natural Language Processing and machine learning work on reportable case detection to codify both reportable cancer and cancer recurrence vocabularies and incorporate them into the DeepPhe Ontology. A detection algorithm will be implemented for cancer recurrence mentions, episodes and patients in DeepPhe and with the purpose of evaluating its ability to detect recurrence in previously detected reportable cancer cases at UAB.

Duration of Grant: 09/01/2021 - 08/31/2023

Automating Delirium Identification and Risk Prediction in Electronic Health Records

PI: Richard E. Kennedy

Co-Investigator: John Osborne

Delirium, or acute confusional state, affects 30-40% of hospitalized older adults, with the added cost of care estimated to be up to $7 billion. Although originally conceptualized as a transient disorder, delirium is now recognized to have significant consequences, including increased risk of death, functional decline, and long-term cognitive impairment. In this proposal, we present a novel approach to the identification of delirium based on large-scale data mining (i.e. pattern recognition) algorithms using machine learning and natural language processing applied to electronic health record (EHR) data, which will automate chart-based determination of delirium status and risk prediction.

Duration of Project: 02/15/2019 - 12/31/2022

Building and InnovatinG: Digital heALTH Technology and Analytics (BIGDATA)

PI: Jeffrey R. Curtis

Co-Investigator: John Osborne

Through the encompassing of three distinct and synergistic cores (Data Capture and Integration [DCI] Resource Core, Methodologic, and Administrative), the BIGDATA CCCR will bring innovative HIT tools and methods to the research community to effectively advance the NIAMS mission. Methods of advancing the NIAMS mission will include the following: promotion of innovative and musculoskeletal disease-focused research while expediting clinical, translational and informatics-related projects; fostering the development, refinement, and application of existing and de novo digital technology data through our Data Capture and Integration Core, and promote the training of both junior and established clinical and translational investigators in the current methods of clinical informatics and digital health tools applicable to the NIAMS mission through diverse enrichment activities overseen by our Administrative Core.

Duration of Project: 09/15/2020 - 07/31/2024

Opioid Use Disorder Center of Excellence

PI: Sue Feldman

Co-Investigator: John Osborne

The goal of this project is to support the identification and treatment of opiate use disorder cases in Alabama.

Duration of Project: 10/01/2021 - 9/30/2026

Automating Delirium Identification and Risk Prediction in Electronic Health Records

PI’s: Richard Kennedy and John Osborne

The project goal is to process the de-identification of delirium patient data, including clinical distribution and distribution of the resource.

Duration of Project: 02/15/2019 - 12/31/2022

Structural Variation Analysis With and Without a Reference Genome

PI: Zechen Chong

This project aims to develop efficient algorithms to SV analysis for organisms both with and without a reference and to study the SV formation mechanisms based on global genomic architecture, while obtaining accurate SV characterization and understanding their formation mechanisms using new sequencing data.

Duration of Grant/Project: 7/1/2020 – 6/30/2025

Biological Comparisons Among Three Derivative Models of Glioma Patient Cancers Under Microenvironmental Stress

PI: Christopher Willey

The aim of this project is to build patient-derived xenograft models of glioblastoma patient tumors, both experimentally and computationally, to help understand mechanisms of tumor growth and radiation resistance.

Project/Proposal Start and End Date: 09/17/2018 – 08/31/2023

Glioblastoma Tumor Microenvironmental Influence on Acquired and Inherent Cancer Therapy Resistance

PI: Christopher Willey

The goal is to extend the U01 work with new in vitro and new in vivo aims using 3D bioprinting and microbiome manipulation of models of GBM.

Project/Proposal Start and End Date: 09/17/2020 – 06/30/2023

B Cell Intrinsic Interferon-B Regulates Autoreactive B Cell Development

PI: John D. Mountz

The goal of this project is to under B cell developmental trajectory using single-cell sequencing technologies.

Project/Proposal Start and End Date: 02/13/2018 – 01/31/2023

Characterization of the Lupus Nephritis microRNAome

PI: Elizabeth E. Brown

To use next-generation sequencing technologies to understand how microRNAs changes over diverse samples of the Lupus patients during various disease progression stages.

Project/Proposal Start and End Date: 09/07/2018 – 08/31/2023

Role of Bone Marrow Tregs in Maintaining Stromal Cell Function

PI: Robert Welner

An essential participant in immune regulation, regulatory T cells (Tregs) are now known for their non-canonical functions. Here, we describe a bone marrow Treg subpopulation that maintains stromal cells. Our goals are to further characterize marrow Tregs, and to specifically dissect the role of Treg secreted interleukin-10 (IL-10) signaling pathways in the maintenance of mesenchymal stromal cells. These results identify a unique Treg subset, and an innovative secreted factor that regulates stromal cell abundance, differentiation, and function.

Project/Proposal Start and End Date: 09/15/2020 - 05/31/2024

Credentialing Next Generation Human Giloma Models for Precision Therapeutics

PI: Ryan C. Miller

The aims of this multi-PI proposal are to develop and molecularly credential human iGBM models against patient-derived xenograft (PDX) models. iGBM harbor predefined combinations of glioma mutations engineered via CRISPR editing of human induced pluripotent stem cells (iPSC). Serial engraftment of neural progenitor cell (NPC) derivatives of edited iPSCs yields GBM (iGBM). These models will be molecularly credentialed via RNA-seq, ATAC-seq, whole exome seq, and a novel kinome proteomics technique – multiplex inhibitor beads-mass spectrometry (MIB-MS).

Project/Proposal Start and End Date: 01/12/2022 – 12/31/2026

Identifying Secreted Protein Networks Affecting Human Pancreatic Islet Function in Type 2 Diabetes Using Public Omic Databases

PI: Sushant Bhatnagar

The aim of this project is to characterize secreted proteins and their networks from public T2D bulk RNA-seq data.

Project/Proposal Start and End Date: 09/01/2021 – 08/30/2023