Program Faculty

Juw Won Park, PhD

Juw Won Park, Ph.D., Executive Committee Chair

Assistant Professor, Computer Engineering and Computer Science
University of Iowa

Email Juw Won Park
Phone: 502-852-1047

Publications on google scholarResearchgate publications

The research in the Dr. Perlin lab focuses on the evolution of interactions between pathogens and the hosts on which they cause disease. At present, this work has two main areas of emphasis: fungal/plant interactions and population dynamics of bacteria resistant to antibiotics.

Shizuka Uchida;

Shizuka Uchida, Ph.D., Executive Committee Vice Chair

Associate Professor, Medicine 
Japan Advanced Institute of Science and Technology

Email Shizuka Uchida
Phone: 502-854-0570

Researchgate publicationsPublications on LinkedIn

Dr. Uchida's research focuses on elucidating the functions of long non-coding RNAs (lncRNAs) using dry (bioinformatics) and wet (biology) lab techniques. He hopes to apply basic biology to rejuvenate ailing hearts by directing the differentiation of resident adult cardiac stem cells into functional cardiomyocytes using lncRNAs.

Eric Rouchka, D.Sc., Director

Eric Rouchka, Director of Graduate Studies

Professor, Computer Engineering and Computer Science
D.Sc., Washington University in St. Louis

Email Eric Rouchka
Phone: 502-852-3060

Publications on google scholarResearchgate publicationsPublications on ScopusPublications on LinkedInPublications on orcidPublications on ResearcherID

Dr. Rouchka's laboratory is primarily interested in algorithmic development and design for use with high throughput genomic and transcriptomic data. The laboratory has 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. Dr. Rouchka's team also uses publicly available next-generation sequence data for studying genomic variation.

Nigel Cooper

Nigel Cooper

Professor, Anatomical Sciences and Neurobiology
Ph.D., University of Tennessee Health Sciences Center

Email Nigel Cooper
Phone: 502-852-1474

Researchgate publicationsPublications on MendeleyPublications on ScopusPublications on LinkedIn

The research interests of Dr. Cooper's laboratory are related to signal transduction and gene networks in neurons. His group is currently funded to investigate cell death and cell survival pathways in animal models of retinal ischemia, and they 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.

The laboratory's 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.

Andrew P. DeFilippis

Andrew P. DeFilippis

Assistant Professor, Medicine
M.D., Georgetown University School of Medicine

Email Andrew DeFilippis
Phone: 502-852-7959

Researchgate publications

Some of Dr. DeFilippis's research interests include biomarker development for acute myocardial infarction (atherothrombotic and non-atherothrmbotic); cardiovascular risk prediction; plaque disruption and coronary thrombosis; and omics

Nigel Cooper

Ryan Gill

Associate Professor, Mathematics
Ph.D., The University of Texas at Dallas

Email Ryan Gill
Phone: 502-852-2729

Publications on Mendeley | Web of Science | MathScieNet

Some of Dr. Gill's research interests include Change-Point Problems, Generalized Linear Models

Theodore S. Kalbfleisch

Assistant Professor, Biochemistry and Molecular Biology
Ph.D., Boston University

Email Ted Kalbfleisch
Phone: 502-852-3060

Publications on ResearcherID

Dr. Kalbfleisch seeks to understand how our genetic makeup impacts whether or not we are healthy or sick. To that end, Ted works to build informatics infrastructure to make it possible for scientists and clinicians to develop and test hypotheses using the vast amount of genetic data that we are generating.

Ashok Kumar, PhD

Ashok Kumar

Professor, Anatomical Sciences and Neurobiology
Ph.D., University of Delhi

Email Ashok Kumar
Phone: 502-852-1133

 

Research in our laboratory is focused towards understanding the molecular and signaling mechanisms that regulate the acquisition and maintenance of skeletal muscle mass. For past five years, we have been investigating the proximal signaling mechanisms that regulate skeletal muscle atrophy, regeneration, and muscle hypertrophy. We are also investigating signaling mechanisms which regulate self-renewal and differentiation of satellite cells in myogenic lineage. Moreover, we are studying the pathophysiological mechanisms which mediate the disease progression in muscular dystrophy. Using animal models, we also study molecular mechanisms regulating skeletal muscle wasting during cancer cachexia. We use several cutting-edge biochemistry, molecular biology, and physiology techniques including tissue-specific transgenic and knockout mice, microarray, quantitative real-time PCR, RNA interference, viral vectors, primary mouse muscle cell cultures, flow cytometry, mass spectrometry, muscle contraction studies, and various immunohistochemical and morphometric methods in our ongoing research.

Jiaxu, PhD

 

Jiaxu Li

Assistant Professor, Mathematics
Ph.D., Arizona State University

Email Jiaxu Li
Phone: 502-852-6828

Publications on orcid

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.

Richard Kerber, PhD

 

Michael Merchant

Associate Professor, Division of Nephrology & Hypertension
Ph.D., University of Arkansas, Fayetteville (Geren)

Email Michael Merchant
Phone: 502-852-0245

Researchgate publicationsPublications on LinkedInPublications on orcid

Research Goal: To utilize high resolution mass spectrometry methods to gain insight on human disease

Research Interests

  • Translational research - the discovery and understanding of biomarkers of renal disease
  • Basic Research - Mechanisms of renal function decline and fibrosis
  • Basic Research - Mechanisms for the transition from acute to chronic disease

John Pani Ph.D.

John Pani Ph.D.

Professor, Psychological and Brain Sciences
University of Illinois

Email John Pani
Phone: (502) 852-3956

Publications on google scholar

Dr. Pani's research interests are in visualization and spatial understanding as they relate to learning and expert knowledge. With the special opportunities for visualization and learning provided by modern computation, his recent work has focused on developing ground breaking computer-based systems for learning. Current work is focused in two areas: 1) research and development of 3D computer-based learning of neuroanatomy; 2) in collaboration with the bioinformatics group here, Dr. Pani and his colleagues are evaluating methods for visualization of complex network data. Other recent projects have included experimental study of spatial reasoning (mostly concerning spatial transformations), and characterizing visual skill in the practice of microscopy in histology (the microanatomy of biological tissues).

Over recent years, the methods being used to explore cognition range from naturalistic studies of experienced practitioners (e.g., of microscopy) through tightly controlled experiments to the development of new computer graphical models and computer-based learning technologies.

Michael Perlin

Michael Perlin, Ph.D.

Professor, Biology
University of Chicago

Email Michael Perlin
Phone: 502-852-5944

Publications on google scholar

The research in the Dr. Perlin lab focuses on the evolution of interactions between pathogens and the hosts on which they cause disease. At present, this work has two main areas of emphasis: fungal/plant interactions and population dynamics of bacteria resistant to antibiotics.

Jeffrey C. Petruska, Ph.D.

Jeffrey C. Petruska, Ph.D.

Assistant Professor, Anatomical Sciences and Neurobiology
University of Florida

Email Jeffrey Petruska
Phone: 502-852-8057

Publications on google scholar

In terms of biological principles, Dr. Petruska investigates the cellular and molecular mechanisms regulating anatomical and electrophysiological plasticity of neurons, focusing on the peripheral nervous system and spinal cord. His group is particularly interested in the interaction between, and co-regulation of, the anatomical and electrophysiological properties of neurons. These principles are studied in the context of spinal cord injury and the spinal pain system (particularly in the context of damage to peripheral tissue which is a common and chronic issue for the SCI population and is an etiological factor in the development of chronic pain).

In terms of biomedical questions, hwe investigates:
1) the mechanisms controlling axonal collateral sprouting (growth of non-injured axons) in the adult nervous system, particularly considering how these mechanisms contrast with those of axonal regeneration (growth of injured axons);
2) the mechanisms and consequences of sensory neuron responses to damage of peripheral tissue (e.g., skin, muscle, viscera), particularly contrasting this with the response of sensory neurons to nerve injury;
3) the effects of spinal cord injury and post-SCI plasticity-inducing treatments on the function of motor and sensory neurons.
These hypothesis-driven projects are well-coordinated when viewed in the context of my long-term vision – understanding how sensory input to the spinal cord below an injury influences the function of the remaining circuitry. It is my proposition that the combined effects of spinal cord injury and inflammatory and/or tissue-damaging secondary conditions (e.g., systemic inflammation, pressure sores, bladder infection, bowel impaction) act in concert to induce “circuit dysfunction” in the spinal cord caudal to an injury due to an unchecked, overactive, and highly plastic spinal nociceptive system. Unfortunately, SCI-related secondary conditions are rarely considered in basic neuroscience research, in spite of their high degree of clinical relevance and importance to the SCI community. On the other hand, the status of spinal circuits below an injury is a topic of a great deal of basic science study, but principally in the context of acute lacerations intended to determine the role of specific tracts, and much less-so in the context of clinically-modelled SCI. The status of these circuits after SCI is increasingly more important with the accumulation of data demonstrating the efficacy of activity-dependent task-specific training (i.e., physical therapy), and the reliance of that therapy on both appropriate sensory input and “healthy” caudal spinal cord circuitry.

Liz O'Brien, Ph.D.

Anil Rai, Ph.D.

Head, Centre of Agricultural Bioinformatics at Indian Agricultural Statistics Research Institute (IASRI), New Delhi
Indian Agricultural Research Institute, New Delhi

  • Development of models/methodologies/procedures/tools for analysis of biological/omics data.
  • Design and development of biological/genomics data bases/data warehouse and web resources for omics data analysis.
  • Design and development of efficient computational and informatics solutions for management and analysis large biological/omics data sets.
  • Modeling and analysis of data from large scale phenomics in agriculture.
  • Applications of geo-informatics/ spatial models/ statistics in agricultural surveys.
  • Survey Sampling and policy research
  • Teaching and training in the field of bioinformatics, statistics and computer applications.
Shesh Rai, Ph.D.

Shesh Rai Ph.D.

Professor, Bioinformatics and Biostatistics
University of Waterloo

Email Shesh Rai
Phone: 502-852-4030

Researchgate publicationsPublications on ScopusPublications on LinkedInPublications on orcid

Dr. Rai is thoroughly experienced in designing (sample size) and analyzing retrospective/prospective studies in cancer and other clinical and basic science researches and behavioral interventions. He pursues 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 samplng weights in log-linear models, and characterization and estimation of population risk.

David Schultz, PhD

David Schultz Ph.D.

Associate Professor, Biology
Pennsylvania State University

Email David Schultz
Phone: 502-852-5938

Publications on Scopus

Dr. Schultz's lab’s research is focused on the biochemistry, biotechnology and bioactivity of plant chemicals. My laboratory uses a wide range of approaches from basic biochemistry and molecular biology/biotechnology through whole system physiology. His lab has expertise in natural product purification and identification, bioactivity assessment and bioengineering plant production of targeted products. The goal of his lab is to identify and test target plant chemicals for unique bioactive properties then to identify the genetic elements required for heterologous production and to use biotechnology approaches to produce these target molecules at higher levels for human use. His laboratory also works to understand the biosynthesis of unusual monoenoic fatty acids that could function as biofuels/petroleum replacement products with an ultimate goal of bioengineering unusual monoene production in oilseed crops. Their work is often highly interdisciplinary and thus we have long-term collaborative projects focused on the inhibitory role of anacardic acid on breast cancer (Dr. Carrie Klinge, UofL Department of Biochemistry and Molecular Biology), the role(s) of spices in the Apiaceae family and dark berries in preventing lung and/or breast cancer (Dr. Ramesh Gupta, UofL Department of Pharmacology and Toxicology) and plant/pathogen interactions (Dr. Mike Perlin, UofL Biology Department).

Deborah Yoder-Himes, PhD

Deborah Yoder-Himes Ph.D.

Assistant Professor, Biology
Michigan State University

Email Deborah Yoder-Himes
Phone: 502-852-0991

Publications on Pubmed

Our long term goal is to investigate the evolution of virulence properties, transmission from the environment to humans, and the ecology of opportunistic bacterial respiratory pathogens in humans and the environment. To achieve these goals, we have three projects currently in the lab.

  1. Comparative transcriptomics in polymicrobial cultures
  2. To define and pursue Burkholderia cepacia complex virulence factors and potential vaccine targets
  3. Testing environmental, particularly airborne, Burkholderia and Pseudomonas strains for biofilm properties and gene expression