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University of Louisville Bioinformatics

Bioinformatics Faculty


Nigel Cooper
(ASNB)
Nigel Cooper, Ph.D.
Professor
Vice Chair for Research
Department of Anatomical Sciences and Neurobiology
email
web site

The research interests of my laboratory are related to signal transduction and gene networks in neurons. We are currently funded to investigate cell death and cell survival pathways in animal models of retinal ischemia, and we propose to establish signature events related to this blinding disorder. Discoveries in this field may lead to better therapeutic interventions. The relationship between the expressions of miRs and mRNAs is one area under investigation. Our interests in bioinformatics include the potential for biomarker discovery as well as for the development of tools, resources, and other infrastructures for life sciences research. The promise of bioinformatics is that it will allow an investigator to reach beyond his/her own computational capacity to access and integrate multiple and disparate sources of information and to manage the complexities of scale inherent in genomic, molecular, cellular, and organismal systems.

Collaborating investigators in my laboratory include:

  • Wei Fan, M.D., Ph.D. - Visiting Professor, Ophthalmologist
  • Mexia Zhang, M.D. - Visiting Professor, Ophthalmologist
  • Xiang-Ping Wang, Ph.D. - Postdoctoral Research Associate
  • Jovan D. Rebollado-Mendez, Ph.D. - Postdoctoral Research Associate
  • Na Zhou - graduate student on rotation, fall 2010.


Ted Kalbfleisch
(BMB)
Ted Kalbfleisch, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology
email
web site

The majority of my experience over the last 14 years has been in the development and implementation of data and process management systems for the management and analysis of high throughput datasets. The bulk of this experience has been in the areas of sequence and genotype data. I believe that the design an implementation of interoperable systems is essential to the advancement of science in this high throughput age. Although web browsers have been effective tools for disseminating information, web services that allow programmatic access to datasets empowers scientists to analyze data systematically, and in a high throughput fashion. A major focus of my work the last five years has been the development of a web services based data management system for single nucleotide polymorphisms, genotypes, and the raw data from which they were derived. This system is currently supporting research at the USDA, and within my lab.


Ashok Kumar
(ASNB)
Ashok Kumar, Ph.D.
Associate Professor
Department of Anatomical Sciences and Neurobiology
email
web site

My primary research interest is to understand the molecular and genetic mechanisms governing skeletal muscle development, plasticity, and pathology. We are using a number of bioinformatics tools, microarray, genetic mouse models, and biochemical techniques to investigate the role of various signaling pathways, micro RNAs, and gene networks in skeletal muscle metabolism at cellular, tissue, and system levels.


Jiaxu Li
(Math)
Jiaxu Li, Ph.D.
Assistant Professor
Department of Mathematics
email

Dr. Jiaxu Li's research interest include ordinary differential equations, delay differential equations, dynamical systems and mathematical biology and medicine. His primary goal is to investigate the dynamic behaviors in complex systems in life sciences. He expects that biological mechanisms and insights can be revealed by modeling the systems and analyzing such models.


Jeffrey Petruska
(ASNB)
Jeffrey Petruska, Ph.D.
Assistant Professor
Department of Anatomical Sciences and Neurobiology
Kentucky Spinal Cord Injury Research Center
Joint: Department of Neurological Surgery
email
website

The theme of the research in the Petruska lab is neural plasticity - changes in neural structure and synaptic communication. Their studies are generally in the context of spinal cord injury (SCI) and of pain, primarily using in vivo rodent models. Dr. Petruska has developed novel tools and model systems in order to examine plasticity at every level from molecules to behavior. In collaboration with the laboratory of Dr. Eric Rouchka, the Petruska lab is currently engaged in examining the mechanisms of an understudied process of axonal plasticity - collateral sprouting - where non-injured neurons generate new axon branches and make new connections.


Shesh Rai
(B&B)
Shesh N. Rai, Ph.D.
Director, Biostatistics Shared Facility
Professor and Wendell Cherry Chair in Clinical Trial Research
James Graham Brown Cancer Center
Department of Bioinformatics and Biostatistics
email

Thoroughly experienced in designing (SAMPLE SIZE) and analyzing retrospective/prospective studies in CANCER and other CLINICAL and BASIC SCIENCE researches and BEHAVIORAL INTERVENTIONS; pursue developing statistical methods with real applications in heterogeneity in CLINICAL STUDIES, threshold DOSE-RESPONSE models, SURVIVAL ANALYSIS with incomplete and correlated data, efficient estimation in MIXED effects (REPEATED measure) models, robust estimation in high-dimension data (BIOINFORMATICS), effects of SAMPLING weights in log-linear models, and characterization and estimation of POPULATION RISK.


Eric Rouchka
(CECS)
Eric Rouchka, D.Sc.
Associate Professor
Department of Computer Engineering and Computer Science
email
web site
pubmed,IEEE Xplore

The University of Louisville Bioinformatics Laboratory under the direction of Dr. Rouchka is primarily interested in algorithmic development and design for use with high throughput genomic and transcriptomic data. We have ongoing research in the areas of understanding gene regulation from both a transcriptional and translational point of view as well as in the area of systems biology for understanding cross-tissue signalling through an ongoing collaboration with the Petruska lab. We also use publicly available next-generation sequence data for studying genomic variation.


John Trent
(Medicine)
John O. Trent, Ph.D.
Associate Professor
Department of Medicine
Director, Molecular Modeling Core Facility
James Graham Brown Cancer Center
email
web site

My group uses numerous computational techniques to complement experimental approaches aimed at understanding macromolecular interactions. The methods include molecular dynamics, free energy perturbation calculations, and Monte-Carlo methods as applied to real world problems. The combination of modeling techniques with different experimental modalities such as NMR, X-ray diffraction and thermodynamic methods is synergistic, and is the key to understanding structure and function.


Xiang Zhang
(Chemistry)
Xiang Zhang, Ph.D.
Associate Professor
Department of Chemistry
email
web site

We are interested in biomolecular quantification and network analyses using a systems biology approach. Our goal is to decode the disease mechanisms using advanced bioinformatic methodologies and modern analytical techniques. The bioanalytical research in our group exploits practical and efficient high-throughput technologies for the analyses of complex mixtures derived from living systems. Our bioinformatics research develops informatic systems that enable mining of high throughput data for identification and quantification of molecular networks and 'systems level' knowledge assembly.


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