Informatics

CCTS Informatics provides the infrastructure to collect structured clinical data at the point of care; export it to a data warehouse that also contains genomic and other biological information; and use the data for clinical, translational and outcomes research from bench to bedside and back. 

From genomics data mining to custom software development targeted at clinical, educational or research initiatives, we offer a broad spectrum of informatics solutions to investigators.



Services & Tools

Consultations

One-on-one informatics consultations

Data/Analysis

  • Next Generation Sequence Analysis
  • Microarray Analysis
  • Enterprise Data Warehousing Initiative
  • Aggregate Cohort Estimator
  • Data Storage/Safety

Tools

  • MOUSER — voluntary database of mouse strains used by labs on the UAB campus
  • AKI Assistant (Drug-Gene-Retriever) — PubMed search engine for detecting associations between publications, drugs, genes, and diseases
  • Custom program wrappers — developed to support integration of new analytic tools into the Next-Gen bioinformatics analysis platform, Galaxy
  • Kaizen — Facebook application supporting medical education
  • The Cancer Registry Informatics Initiative — registry and quality alert system to expedite reporting to national disease registries and to enhance local reporting through improved monitoring and collection of reliable data
  • Natural Language Processing — processing of unstructured, text-based medical records

Team


Elliot J. Lefkowitz, PhD
Director
205-934-1946
elliotl@uab.edu
Dr. Lefkowitz is a Professor in the Department of Microbiology. His research focuses on the genomics and evolution of microorganisms, especially viruses;  the development and use of bioinformatics tools and techniques to support genomics research; and the provision of informatics support across the full spectrum of biomedical research. In addition to serving as Director of Informatics for the CCTS, he is also Director of Bioinformatics for the UAB Center for AIDS Research, and Director of Bioinformatics for the UAB Microbiome Facility.
Jonas S. Almeida, PhD
Co-Director
205-975-3286
jalmeida@uab.edu
Dr. Almeida is Chair of the Data Working group of the Advisory Committee of the National Science Foundation Directorate for Biological Sciences. His computational research and tool development is focused on the integration of biomolecular and clinical data and the advancement of personalized medicine through the development of tools required to support the use of these data for patient care, including development of novel informatics algorithms and the corresponding software libraries to the development of novel integrative computational infrastructure, especially supporting the use of genomic data.
Eta S. Berner, EdD
Co-Director
205-975-8219
eberner@uab.edu
Dr. Berner is a former member of the Board of Directors of the American Medical Informatics Association, the External Scientific Panel for NHGRI’s Emerge Network and the Technical Expert Panel for the AHRQ Clinical Decision Support Initiative.  She is responsible for the development and oversight of CCTS Informatics educational activities and works with others at UAB to oversee and develop policies concerning consent and governance issues surrounding the use of clinical data for research.
Geoff Gordon, MSEE
Co-Director
205-297-9495
gdgordon@uab.edu
Mr. Gordon is an IT Director for the Health System Information Services division of UAB Health System, responsible for Web Development and the Enterprise Data Warehousing Iniative.  He has been working in clinical analytics for the past 3 years and has over 20 years of software development experience, 15 in healthcare.
James H. Willig, MD, MSPH
Co-Director
205-996-5753
jwillig@uab.edu
Dr. Willig is the Medical Informatics Director of the UAB 1917 AIDS Clinic, Co-Director of the UAB HIV-Research and Informatics Service Center, and Director of Clinical Informatics for the UAB Health System Information Services. He also serves as the physician lead for the Clinical Data Warehouse Research Working Group. His own research involves the development and use of informatics tools and methods to support patient care, especially for patients living with HIV.
Matthew Wyatt, MSHI
Assistant Director
205-934-0660
mwyatt@uabmc.edu
Mr. Wyatt provides operational management for all aspects of Informatics day-to-day activities. He is responsible for oversight of institutional collaborative projects including those related to clinical data warehousing, clinical data capture at the point of care, and clinical data extraction.
Keith Bobitt
Senior System Analyst
205-934-2508
kbobitt@uab.edu
Mr. Bobitt is a Senior System Analyst and Java developer. He is developing systems to extract data from i2b2 and VDW based Clinical Data Warehouses for cohort discovery and Java based software for direct database access of VDW systems and RESTful web interface access of i2b2 systems.
David K. Crossman, PhD
Instructor
205-996-4045
dkcrossm@uab.edu


Dr. Crossman is an Instructor in the Department of Genetics. He directs the Bioinformatics Facility at the Heflin Center for Human Genetics and is responsible for the initial processing and analysis of Next-Gen Sequencing data obtained for Genomics’ Illumina sequencers. He provides CCTS investigators with expertise in microarray analysis, Next-Gen Sequencing analysis, mass spectrometry proteomics analysis, and Systems Biology pathway analysis.
Don Dempsey, MS
Programmer
205-934-9522
ddempsey@uab.edu
Mr. Dempsey is a web and Java developer who is responsible for the development of many of our web-based applications and databases. This includes working with clinical and translational researchers to create data capture forms and clinical, outcomes, and bioinformatics databases; assisting researchers with analysis and extraction of data from the Clinical Data Warehouse; developing new clinical and bioinformatics tools; and specific programming needed to develop the tools and systems supporting the needs of individual investigators.
Curtis Hendrickson
Research Associate
205-975-5240
curtish@uab.edu
Mr. Hendrickson provides expertise in data collection, integration, and reporting. This includes scientific database design, implementation, and support, as well as in web site design, web application development, and project management. He also supports a variety of bioinformatics-related services including Next-Gen Sequencing analysis, detection of sequence variants, and detection of gene regulatory motifs.
Ranjit Kumar, PhD
Research Associate
205-934-2508
rkumar@uab.edu
Dr. Kumar’s research has focused on whole genome transcriptome analysis of bacterial pathogens, which led to identification of numerous novel non-coding RNAs and proteins. He has also worked on host-pathogen protein-protein interactions by developing a non-redundant web based relational database that has advanced capabilities for host-pathogen interaction storage, retrieval, and data mining. He provides bioinformatics support and application development to investigators, especially focusing on the analysis of Next-Gen Sequencing data including microbiome and metagenomic analysis. He is responsible for the installation, maintenance, and support of all associated tools and data sources supporting microbiome analysis, and he has developed and is currently supporting the analytical pipeline used by the CCTS to support the analysis of data derived from human microbiome studies.
John Osborne, MS
Research Associate
205-975-5240
ozborn@uab.edu
Mr. Osborne works with clinical and translational researchers to create data capture forms and clinical, outcomes, and bioinformatics databases; assists researchers with analysis and extraction of data from the data warehouses; and works extensively with UAB investigators on the analysis of Next-Gen Sequencing data derived from patients enrolled in clinical research studies. He also develops new approaches and applications to support the extraction of clinical information from free-text records in order to store that information in structured database fields.


Education

A number of UAB departments offer courses that provide extensive opportunities for informatics education. Course descriptions can be found in the UAB Graduate Catalog.

Department of Biostatistics

  • BST 675 Introduction to Statistical Genetics
  • BST 676 Statistical Bioinformatics

Department of Computer and Information Sciences

  • CS640 Bioinformatics I
  • CS641 Bioinformatics II

Department of Genetics

Department of Health Services Administration

  • M.S. Health Informatics (MSHI)
  • HI 600 Analysis and Design of Health Information Systems
  • HI 601 Databases and Data Modeling
  • HI 602 Clinical and Administrative Systems
  • HI 605 Communications and Networks
  • HI 612 Organizational Behavior and Leadership
  • HI 615 Decision Support Systems
  • HI 620 Security and Privacy in Health Care
  • HI 640 Introduction to Health Informatics and Health Care Delivery

School of Nursing

  • NUR 643 Introduction to Nursing Informatics
  • NUR 733 Informatics for Advanced Practice Nursing
  • NNI 621 Conceptual Basis for Informatics Practice
  • NNI 622 The Information System Life Cycle

Section on Statistical Genetics

  • NIGMS-Funded Short Courses
  • NHGRI Next Generation Sequencing Short Courses
  • Professional Development
  • Upcoming Seminars
  • Courses and Events Archive


Partners

In partnership with the other UAB entities, we have been the driving force behind many of the institutional informatics changes that have occurred over the past five years. CCTS Informatics personnel are providing leadership for endeavors such as: establishment of the UAB Informatics Working Group, use of Next-Generation Sequencing analytics, and the Enterprise Data Warehousing Initiative.

The CCTS serves as a link to informatics resources within our Partner Network. Our partners provide a wide range of services and have broad expertise in biomedical informatics and genomics. The available resources are always evolving and being expanded within this network, with each partner representing a potential collaborative site for investigators. Some of these partners are listed below:

  • Heflin Center for Genomic Science
  • Division of Informatics, Department of Pathology
  • Section on Statistical Genetics
  • Center for AIDS Research
  • The HudsonAlpha Institute for Biotechnology

Download a PDF of a current list of Informatics Experts and Expertise for the CCTS Partners.  On the list, highlighted in yellow, the primary contact(s) for these institutions (LSU, Tulane, UMMC, UAB).

Known contacts at other institutions are as follows:

Auburn 

Eric Peatman, PhD
Associate Professor
Auburn University School of Fisheries
Aquaculture and Aquatic Sciences

203 Swingle Hall
Auburn University, AL 36849
Lab (334) 844-4085
Office (334) 844-9319
peatmer@auburn.edu

HAIB

Devin Absher, PhD
Investigator
HudsonAlpha Institute for Biotechnology
601 Genome Way NW
Huntsville, AL 35806
(256) 327-0400

dabsher@hudsonalpha.com

LSU

Lucio Miele, MD, PhD
Professor of Medicine
Director for Inter-Institutional Programs
Stanley Scott Cancer Center, LSU Health Sciences Campus
New Orleans, LA  70112
Phone:  (504) 210-3433
New Orleans, LA 70112

Pennington Biomedical Research Center, LSU System
Ron Horswell, PhD
Director of Biomedical Informatics
6400 Perkins Road
Baton Rouge, LA 70808
Phone 225-763-2737
Fax (HCSD): (225) 922-1502
Email:   Ronald.Horswell@pbrc.edu  or rhorsw@lsuhsc.edu


Tulane
Michelle R. Lacey, PhD
6823 St. Charles Avenue
New Orleans, LA  70118
Phone:  (504) 862-3439
Email:  mlacy1@tulane.edu

UAB
Elliot J. Lefkowitz, PhD
Professor, Department of Microbiology
Director of Informatics, Center for Clinical and Translational Science
Director, Molecular and Genetic Bioinformatics Facility, Center for AIDS Research
Director, Bioinformatics Core, Microbiome Facility
BBRB 276 
Birmingham, AL  35294-2170

Phone:  (205) 934-1946
Email:  ElliotL@uab.edu

UMMC (University of Mississippi Medical Center)
Chindo Hicks, PhD
Associate Professor, Department of Medicine
Director, Cancer Bioinformatics Core
Member, Cancer Genetics Program

PhD, Statistical Genetics 1995, University of Copenhagen, Denmark
2500 N State St.
Cancer Institute, Room G659
Arthur Guyton Research Center
Jackson, MS 39216
Phone: (601) 815-6829
E-mail: 
chicks2@umc.edu


South
Alabama

Dan Roach, MD
Acting Director of the Center for Strategic Health Innovation
(251) 414-8170
Email:  droach@southalabama.edu




Archived Presentations


The Application and Analysis of Next Generation Sequencing Technologies (5/27/11)

Some presentations below are password protected:

  • Stephen Barnes: Can The 'Cloud' rescue computing?
  • Elliot Lefkowitz: Getting your NextGen data analyzed at UAB
  • Mark Prichard: Identifying molecular targets of antiviral drugs by deep sequencing
  • Eric E. Smith, Illumina, Inc.: CASAVA 1.8
  • Eric E. Smith, Illumina, Inc.: Illumina NextGen File Formats




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The UAB Center for Clinical and Translational Science (CCTS) is part of the Clinical and Translational Science Award program funded by the National Center for Advancing Translational Sciences at the National Institutes of Health (NIH) (grant number UL1 TR000165). The content of this website is solely the responsibility of UAB and does not necessarily represent the official views of the NIH.

NIH Funding Acknowledgment — All publications resulting from the use of CCTS resources are required to credit the CCTS grant by including the NIH funding acknowledgment and must comply with NIH Public Access Policy.