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Informatics

James Cimino, MD, as the inaugural director of the UAB Informatics InstituteThe CCTS is proud to welcome James Cimino, MD, as the inaugural director of the UAB Informatics Institute, established in June 2014. Cimino, previously chief of the Laboratory for Informatics Development at the National Institutes of Health's Clinical Center and a senior scientist at the National Library of Medicine, is a national leader in biomedical informatics. Read the full story here.

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.

biomedical summer series2Summer 2015:  CCTS Biomedical Informatics Seminar Series
This series will consist of a series of seminars, presentations and online lectures covering key topics in biomedical and health informatics for clinical and translational science researchers and the resources related to these topics at UAB.  There will be reading materials accompanying the presentations.  There are a total of five live seminars and three online sessions.  Each live session will be approximately an hour. The first of the live presentations will be on Wednesday June 3, from 3-4 p.m, and the rest of will occur on Wednesdays at the same time (3-4 p.m.) as indicated on the schedule below.  Online presentations will be available on weeks when there are no live presentations.  The specific dates and topics are listed below.  The seminar will take place at the UAB Pittman Center for Advanced Medical Studies (PCAMS).  Here is a schedule of presentations and course description and course description and course description.  For more information, please email Eta S. Berner, EdD



Services & Tools


Study Enrollment Feasibility

Feasibility review is a process to make sure that a proposed study has a greater probability of being successfully completed.  The CCTS can help investigators generate an aggregate assessment of potentially eligible patients for any clinical study.  

You may submit an inquiry by choosing either of the links below, or contact us directly:

Aggregate Data Request for Enrollment Feasibility    Individual Data Request for Recruitment a/o Analysis
 

Consultations

One-on-one informatics consultations

Data/Analysis

  • Next Generation Sequence Analysis
  • Microarray Analysis
  • Enterprise Data Warehousing Initiative
  • 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


James J. Cimino, MD
Director
UAB Informatics Institute
205-996-1958
ciminoj@uab.edu
James J. Cimino, M.D., is the inaugural director of the Informatics Institute in the School of Medicine at the University of Alabama at Birmingham. The institute was established by the Board of Trustees of the University of Alabama System in June 2014.

Cimino, who previously was the chief of the Laboratory for Informatics Development at the National Institutes of Health's Clinical Center and a senior scientist at the National Library of Medicine, is a national leader in the burgeoning field of biomedical informatics. He is one of the few informaticians in the prestigious Institute of Medicine and co-editor of the most influential textbook on informatics, Biomedical Informatics: Computer Applications in Health Care and Biomedicine, Fourth Edition.
Elliot J. Lefkowitz, PhD
Director of CCTS Informatics
Professor of Microbiology
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.
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.
Travis Ptacek, PhD
Postdoctoral Fellow
205-934-3727
tptacek@uab.edu
Dr. Ptacek received his PhD in Genetics from UAB in 2013.  His past research involved studies of genetic variants, single nucleotide and structural, within large case-control disease cohorts in a mixed wet and dry lab setting. He role within CCTS Informatics is to provide expertise in next generation sequence analysis, and in the managing, assembly and curation of large genetic/patient/animal databases. He is also involved in projects that require genomic assembly, comparative genomics, genomic variant (SNP and structural) discovery, evaluation, and curation, RNAseq analysis including transcript discovery, ChIP seq analysis, and analysis of microbiome data.
Liam Van Der Pol, MS
Bioinformation II

205-934-2508
liamvdp@uab.edu
Mr. Van Der Pol received his Masters degree in Bioinformatics in 2013 from Indiana University, Bloomington, IN.  For his Master’s thesis he worked on a project building a transcriptome for Wolbachia. This project sought to examine the genes being expressed by the bacterial parasite Wolbachia post-infection in the model organism host D. melanogaster, by purifying prokaryotic RNA from host tissue and sequencing with Illumina RNA-seq then assembling transcripts with the Trinity assembler. Mr. Van Der Pol is responsible for providing bioinformatics support to CCTS investigators.  He supports other bioinformatics team members by providing consults to investigators and working with other CCTS informatics personnel to ensure that the needs of investigators are met. He also manages the UAB Galaxy installation and the use of high performance computing resources to support bioinformatics analysis.
Dale Johnson, MS
Senior System Analyst
205-996-5659
rdalej@uab.edu

Mr. Johnsons is a Data Warehouse Developer III responsible for the development of i2b2 as part of the Enterprise Data Warehouse infrastructure.  His is responsible for the development and maintenance of custom loading for UAB clinical data into i2b2 as well as preparing UAB’s i2b2 instance(s) for SHRINE and PCORnet participation.  Mr. Johnson has BS and MS degrees in computer science and has worked in IT as an instructor and software developer for 30 years.  His primary strengths are Oracle database programming and web development.  He has more than 16 years of experience with Oracle databases and Oracle PL/SQL programming and 9 years of experience with medical information systems.  He has been with UAB since 2006, working on the UAB Oracle administrative workflow team, and now CCTS.  


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, CCTS Informatics has 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.

CCTS Informatics also serves as a link to informatics personnel and 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. These Partners include:

    Auburn University
    The HudsonAlpha Institute for Biotechnology
    Louisiana State University Health Sciences Center New Orleans (LSU)
    Pennington Biomedical Research Center
    Tulane University Health Services Center
    University of Mississippi Medical Center (UMMC)
    University of South Alabama (USA)

Download a PDF of a current list of Informatics Experts and Expertise for CCTS Informatics at UAB and for CCTS Partners.

The primary informatics contacts for CCTS Partner 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:  mlacey1@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




 
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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.