Program Faculty

Behnam Abasht
Email | (302) 831-8876

Genetics, Genomics, Bioinformatics

Computer Networks, Data Compression
http://www.cis.udel.edu/~amer/

Maciek Antoniewicz
Email | (302) 831-8960

Metabolic Engineering, Systems Biology
http://www.che.udel.edu/mranton

The Antoniewicz lab is developing next generation tools and techniques for analyzing, engineering and manipulating microbial and mammalian systems, applied to specific problems in biotechnology (e.g. biofuels) and medicine (e.g. obesity, diabetes). In our research we make use of modern techniques in metabolic engineering, metabolic flux analysis, stable-isotope labeling, tandem mass spectrometry, molecular biology, bioinformatics and computational biology.

Ryan Arsenault
Email | 302-831-7579

Kinomics, Microbiome, Peptide Array Design, Data Tools/Mining.
http://canr.udel.edu/faculty/arsenault-ryan-j/

The Arsenault lab studies cellular signal transduction through the use of high-throughput peptide array technology. We study animal health and infectious diseases, gut health and immunometabolism. Bioinformatics plays a role at all levels including peptide array design, data integration, data mining and data visualization. Applying peptide array technology to new species and new post-translational modifications and the development of new data tools are an important part of our ongoing research.

Brian Bahnson
Email | (302) 831-0786

Structural Biology, Molecular Modeling
http://www.udel.edu/chem/bahnson/

The Bahnson lab is exploring the fascinating catalytic power of enzymes with a focus on two related areas of interest: (i) x-ray crystallography is used to solve structures of substrate complexes and intermediates of enzyme catalyzed reactions and (ii) understanding the role of evolved ordered enzyme motions in catalysis.

Jennifer F Biddle
Email | (302) 645-4267

Microbial Populations and Processes in Subseafloor Marine Environments
http://www.ceoe.udel.edu/our-people/profiles/jfbiddle

Fidelma Boyd
Email | (302) 831-1088

Richard Braun
Email | (302) 831-1869

Mathematical models for tear film, ocular surface and blink dynamics; mathematical biology and medicine
http://www.math.udel.edu/~braun/

Richard Braun is an applied mathematician whose recent research focuses on dynamics of the tear film, ocular surface and blinking. He uses mathematical modeling, perturbation methods and computation methods to get results of interest to the ocular surface community.

Ben Carterette
Email | (302) 831-3185

Artificial Intelligence
http://ir.cis.udel.edu/~carteret/

Sunita Chandrasekaran
Email | 302-831-2714

Dr. Chandrasekaran's research interests include exploring high-level directive-based parallel programming models for heterogeneous HPC and embedded systems, exploring strategies to migrate scientific applications to current and future platforms, creating benchmark suites representing real-world applications to measure performance of computing systems, building validation and verification suites for validating parallel programming models and its conformance to the standard.

Sheng-Chih Chen
Email |

Sheng-Chih Chen leads the technology company Intelligent Computing Systems to develop software tools and provide data services. He is Adjunct Assistant Professor at the University of Delaware and Georgetown University Medical Center.

Our interests are broadly centered around neurological disease research, with specific interests 1) in the application of systems biology to understand the network of dysfunction underlying Huntington's disease and 2) in the development of novel tools for proteomics.

Prasad Dhurjati
Email | (302) 831-2879

Systems Biology and Systems Engineering, Biochemical Engineering, Knowledge-based Diagnostics, Applied Mathematics
http://www.che.udel.edu/dhurjati

Our current research combines three decades of expertise in biotechnology and artificial intelligence. Common to both these application areas are the use of dynamic models, qualitative domain knowledge and artificial intelligence approaches for data interpretation and knowledge integration. The research has resulted in a hundred publications, training of forty graduate students and postdoctoral researchers, and over fifty undergraduate research theses. We are currently combining our past expertise in biotechnology and knowledge-based systems to develop system level tools and models for analysis and integration of data and domain knowledge.

Shanshan Ding
Email | 302-831-1884

Dimension reduction, high dimensional data, machine learning, multivariate analysis, survival analysis, statistical applications to neuroimaging and genomic data
http://canr.udel.edu/faculty/ding-shanshan/

Vu Dinh
Email | (765) 237-8876

Mathematical and computational biology; Machine learning
http://vucdinh.github.io/

My research focuses on phylogenetics and applied probability/statistics, with an emphasis on the development of next-generation Markov chain Monte Carlo (MCMC) methods for phylogenetic inference. I am also interested in computational methods for experimental design and control of biological systems, as well as machine learning algorithms and their applications in applied sciences.

Melinda Duncan
Email | (302) 831-0533

Next generation RNA sequencing to gain biological insights into developmental biology and wound healing, image analysis, data mining of health records data
https://www.bio.udel.edu/users/mduncan

The Duncan lab uses anatomical, genetic, molecular and cell biology methods to investigate the molecular basis of blinding eye conditions, most notably cataracts. Diverse bioinformatic methods are used in this research as well. A current focus of the lab and possible topic for a research MS thesis in Bioinformatics and Computational Biology is the bioinformatic analysis of RNA-seq data generated from tissues with highly non-normal distributions of gene expression.

Hui Fang
Email | (302) 831-7238

Information Retrieval, Data Mining
http://www.ece.udel.edu/~hfang/

Pak-Wing Fok
Email | (302) 831-0637

Tissue Modeling, Stochastic Processes
http://udel.edu/~pakwing/

Pak-Wing Fok is an Applied Mathematician whose research centers on atherogenesis and plaque development. He is interested in the physical and biological processes that drive plaques to grow and later rupture, using a combination of mathematical modeling and computation to understand these complex phenomena.

Guang Gao
Email | (302) 831-8218

High Performance Computing, Data Mining
http://www.capsl.udel.edu/~ggao/

Pamela Green
Email |

The Green Lab studies RNA biology with emphasis on post-transcriptional control of gene expression at the genomic, epigenomic, molecular genetic, and biochemical levels. Our projects include genome-wide analyses of the human RNA degradome, the Arabidopsis RNA degradome in ribonuclease mutants, and noncoding RNAs, namely miRNAs and siRNAs associated with environmental and oxidative stress, aging, and tissue type. The work is carried out in model plants, food and bioenergy crop plants, marine invertebrates, and human cells.

Thomas Hanson
Email | (302) 831-3404

Microbial Genomics
http://www.ceoe.udel.edu/people/profile.aspx?tehanson

Keith Hopper
Email | (302) 731-7330

Genetics and evolution of insect host specificity
https://www.researchgate.net/profile/Keith_Hopper

The Hopper lab studies the genetics of host shifts in herbivores (genus Heliothis) and aphid parasitoids (genus Aphelinus) using laboratory experiments on host use behavior and quantitative genetics analyses of inter and intraspecific crosses to map QTL and determine genetic architecture. We also use modern methods of molecular phylogenetics to develop a robust phylogeny for species (~100) in the genus Aphelinus. To develop and genotype SNPs for QTL mapping and molecular phylogenetics, reduced-representation genomic libraries are generated. With these libraries, we are using next-generation sequencing to discover and genotype large numbers of SNP markers distributed across the genome

John Jungck
Email | (302) 831-2281

Dr. Jungck is primarily interested in four different areas of bioinformatics that are reflected in recent publications: 1)"Genetic Codes as Codes: Towards a Theoretical Basis for Bioinformatics;" 2)"Ka-me: A Voronoi Image Analyzer" that allows users to analyze biological images of polygonal tessellations such as dividing epithelia with computational geometry, graph theory, and spatial statistics; 3)"Evolutionary Bioinformatics: Making Meaning of Molecular Messages" with a focus on molecular phylogenetics; and "Bioinformatics education dissemination with an evolutionary problem solving perspective." Please visit http://bioquest.org/bedrock/ for bioinformatics education modules.

Chandra Kambhamettu
Email | (302) 831-8235

Biomedical Image analysis, Computer Vision/Graphics
http://www.cis.udel.edu/~chandra/

Calvin Keeler
Email | (302) 831-6473

Pathogenomics, Innate Immunity, Molecular Virology
http://ag.udel.edu/anfs/faculty/Keeler.html

Megan Killian
Email | (302) 257-1913

Mammalian genomics, genetics, mechanobiology, orthopedics, developmental biology
http://www.killianlab.com

The Killian lab in the Department of Biomedical Engineering at the University of Delaware is focused on research in Musculoskeletal Development and Rehabilitation. Our primary aim is to understand how dissimilar tissues form a structural and functional interface that allows our musculoskeletal system to function, grow, and adapt during development and following injury. We use in vivo experimental approaches that incorporate techniques from molecular biology, genetics, biomechanical engineering, and imaging to address how mechanical forces influence growth, development, and repair of musculoskeletal soft tissues.

David Kirchman
Email | (302) 654-4375

The Kirchman lab examines the role of heterotrophic and photoheterotrophic bacteria in elemental cycles of the oceans. Most of our work is focused on the carbon cycle and the processing of natural dissolved organic material in estuarine and coastal waters. Because the vast majority of these microbes cannot be cultivated, we use cultivation-independent approaches to identify bacteria and to explore the role of various types of bacteria in elemental cycles. We are also interested in what controls the growth, abundance, and biomass levels of bacteria over time and space. Current projects include work in the Delaware estuary, the Arctic Ocean, and in Antarctic Seas.

April Kloxin
Email | 302-831-3009

The April Kloxin Group seeks to understand important biological signals in tissue regeneration and disease using both a materials- and engineering-based approach. They design materials to mimic soft tissues, such as brain, muscle, and connective tissue, and whose properties can be modified at any location and time. These novel biomaterials are used as a flexible platform for cell culture to ask fundamental questions about how the environment surrounding a cell influences cell function and fate for tissue regeneration or disease progression. These findings are utilized to develop better strategies for tissue repair or disease treatment towards improving human health.

My research interests are nanomedicine, nanotoxicity, tissue engineering, drug discover, protein drug interaction and biomedical devices. Nanomedicine will have extraordinary and far-reaching implications for the medical profession, for the definition of disease, for the diagnosis and treatment of medical conditions including aging, and ultimately for the improvement and extension of natural human biological structure and function. Further, I am expanding nanomedicine approach to treat and diagnose diseases at early stage such as Alzheimer's, Parkinson's, brain trauma, cardiomyopathies, cancer, gene therapy and chronic lung disease.

Salil Lachke
Email | (302) 831-3040

Identify and functionally characterize regulatory pathways associated with mammalian eye development and disease.
http://www.bio.udel.edu/users/slachke

The Lachke lab uses systems-based approaches in combination with mouse and human genetics to identify genes critical to ocular development and function. We have developed a bioinformatics-based approach, iSyTE (integrated Systems Tool for Eye gene discovery) that has identified several novel candidate genes involved in lens development and disease. Opportunities are available for students with interest in developing tools for analyzing RNA-seq data generated from RNA-IP (Immuno Precipitation) experiments in the lens and lens-derived cells.

Kelvin Lee
Email | (302) 831-0344

Systems Biology, Proteomics, Genomics
http://www.leelab.org/

Kelvin Lee's research team works on problems relevant to the biopharmaceutical manufacturing community and to the Alzheimer's disease community. The group uses -omics tools and approaches to support ways to improve manufacturing of therapeutic proteins and antibodies and also uses stem cell based models of the blood-brain barrier to improve understanding and delivery of such molecules to address neurodegenerative diseases.

Jung-Youn Lee
Email | (302) 831-3230

Lee laboratory research is focused on understanding the role of cell-to-cell communication through plasmodesmata in plants by taking a multidisciplinary approach employing cell and molecular biology, biochemistry, genetics, and bioinformatics. Plasmodesmata are intercellular communication channels unique to plant systems that are considered one of the fundamental changes that occurred during the evolution of land plants. Yet, our understanding of this fundamental structure is quite limited. The Lee lab is tackling this problem by working towards unmystifying their molecular composition and architecture, control mechanisms, and roles in physiological and developmental processes.

Xiaoming Li
Email | (302) 831-0334

High Performance Computing and Applications
http://www.ece.udel.edu/~xli

Li's research is focused on the high-performance computing and its applications. Specifically, we develop code optimization techniques that accelerate programs on various computer platforms including multi-core processors and Graphic Processing Units (GPU's). Furthermore, we deliver near-peak performance for many widely used numerical routines such as FFT and BLAS. Our research propels the efficiency of computation, which ultimately caps the size and complexity of problems that can be solved by the computational approach in bioinformatics and related areas.

Li Liao
Email | (302) 831-3500

Identification/Prediction of Sequence and Structural Signatures of Protein, DNA and RNA; Systems Biology, with a focus on Protein-Protein Interaction Prediction and Regulatory Networks Inference; Comparative Genomics; Sequence Assembly
http://www.cis.udel.edu/~lliao

X. Lucas Lu
Email | 302-831-2401

Our research focuses on the mechanobiology in musculoskeletal system, in particular how cartilage and bone cells sense the mechanical forces generated from our physical activities and transfer the signals into orchestrated cellular activities. Using advanced mechanical methods, microscopy techniques, nanotechnology, proteomics and computational modeling, the mechano-chemical conversation between cartilage and bone at both molecular and cellular levels are investigated to understand the etiology of osteoarthritis and osteoporosis, and to find new therapeutic interventions aimed at the mitigation or treatment of these diseases.

Edward Lyman
Email | (302) 831-3519

Julia Maresca
Email | (302) 831-4391

Adam Marsh
Email | (302) 645-4367

Environmental Bioinformatics
http://www.ceoe.udel.edu/our-people/profiles/amarsh

Plant Genomics, Bioinformatics
https://www.danforthcenter.org/scientists-research/principal-investigators/blake-meyers

The primary emphasis of the Meyers lab is the analysis of small RNAs in plants. With our many collaborators, we have pioneered genomic analysis of small RNAs and their targets, working with "next-gen" sequencing technologies nearly since their invention. The Meyers lab continues to develop and apply novel informatics approaches for the analysis of RNA function in plants.

Anja Nohe
Email | (302) 831-2959

Systems Biology, Pathway Modeling, pbpk Modeling
http://www.bio.udel.edu/users/anohe

Terry Papoutsakis
Email | (302) 831-8376

Systems Biology, Metabolic Engineering
http://www.papoutsakis.org

Vijay Parashar
Email | (973) 715-4411

Structural Biology, Bacterial Signal transduction, discovery of novel anti-infectives
http://xtalsmgddp.wixsite.com/parasharlaboratory/people

Using a combination of structural (X-ray crystallography) and functional analyses, our laboratory determines the mechanistic basis of critical communication events during bacterial pathogenesis. This facilitates development of a novel class of anti-infectives that do not kill bacteria but target these communication events to curb bacterial behaviors leading to disease.

Mark Parcells
Email | (302) 831-0114

Molecular Virology, Tumor immunology, Vaccine Development and Testing
http://canr.udel.edu/faculty/parcells-mark

Sandeep Patel
Email | (302) 831-6024

Computational Chemistry; Machine Learning; Stochastic Processes
http://patelgroup.chem.udel.edu/joomla/

Dr. Patel uses a variety of computing paradigms (HPC, GPU, supercomputer, etc) for modeling at the quantum and classical levels, materials of relevance to biochemical processes. He is also interested in application of machine learning and artificial intelligence methods for developing computaitonal models, as well as analyzing large data sets wherever they may originate. Finally, he is interested in coupling machine learning / AI methods with current understanding of stochastic processes involved in biology, biochemistry, and mathematics.

P. Michael Peterson
Email | (302) 831-3672

Dr. Peterson has extensive experience in behavioral assessment and change. He is also an expert in health and media, social marketing and has developed and implemented numerous research studies related to behavior change via social marketing interventions. He has consulted with a wide variety of private, non-profit, and government agencies in the area of behavioral change and assessment. He also has been primary investigator on many grant projects that promote health in communities throughout the Mid-Atlantic region, and has created highly acclaimed cutting-edge tools for assessing health-related behavioral, psychosocial, and ecological measures.

Shawn Polson
Email | (302)831-3235

My research interests lie at the intersection of genomics and microbial ecology, examining the ways in which microorganisms and viruses affect and are affected by their environments. The lab is also involved in designing and implementing bioinformatics solutions for utilizing systems biology data (e.g. genomics, metagenomics, transcriptomics) to answer microbial and viral ecology questions. We apply these approaches in numerous environments including marine, freshwater, and soil ecosystems and various organism-associated microbiomes including oyster, coral, cattle, and soybean.

Jing Qiu
Email | 302-831-4550

Analysis of high dimensional data, statistical modeling of genomics data, gene expression data analysis, DNA methylation analysis, high dimensional equivalence test, confidence intervals for selected means, multiple testing, Bayesian modeling.
http://canr.udel.edu/faculty/jing-qiu

Biostatistics
http://ag.udel.edu/frec/faculty/rejto.html

Tania Roth
Email | (302) 831-2787

Behavioral epigenetics, early life stress
http://rothlab.psych.udel.edu/

We are interested in understanding how environmental factors, such as parenting behavior and social stress, can influence the development of behavior and psychiatric disorders. Our primary interests are centered on identifying epigenetic changes (i.e. DNA methylation) associated with early-life caregiving experiences, particularly maltreatment, and understanding their causal role in behavioral outcome

Gilberto Schleiniger
Email | (302) 831-1872

Mathematical Biology, Mathematical Modeling and Scientific Computation, Applications of Mathematics in Medicine
https://www.mathsci.udel.edu/people/faculty/schleini

Carl Schmidt
Email | (302) 831-1334

Avian Genomics
http://ag.udel.edu/anfs/faculty/Schmidt.html

Erica Selva
Email | (302) 831-6096

Signal Transduction
http://www.bio.udel.edu/people/erica-selva.php

Vijay Shanker
Email | (302) 831-1952

Natural Language Processing, Text Mining of Biomedical Literature, Machine Learning
http://www.cis.udel.edu/~vijay

Hagit Shatkay
Email | (302) 831-8622

Computational Biology, Medical Informatics, Bioinformatics, Machine Learning, Data and Text Mining, and their combination.
http://www.eecis.udel.edu/~shatkay/

Abhyudai Singh
Email | (302) 831-8677

Research in our lab is focused on developing mathematical and computational tools for studying the stochastic dynamics of gene-protein networks at a single cell resolution. By combining these computational techniques with high-throughput experimental data we map novel regulatory mechanisms within gene-protein networks. Of particular interests are sub-cellular biochemical networks underlying various disease systems. Current research uses coupled experimental-computational approaches to characterize gene regulatory networks encoded by pathogenic viruses such as Human Immunodeficiency Virus and Herpes viruses, and design strategies to manipulate these networks for therapeutic benefit.

Jia Song
Email | 302-831-2794

The Song lab uses computational, molecular biological, systems biology approaches such as next generation sequencing and proteomic approaches to understand the regulatory roles of microRNAs in early development.

Erin Sparks
Email | (302) 831-3428

Plant Development, Plant Molecular Biology, Plant Biomechanics
http://sites.udel.edu/canr-sparkslab/

The yield potential of agricultural crops is limited by the ability of plants to support their own weight and withstand external forces. The failure of plants to stay upright, termed lodging, can have a dramatic impact on crop yields. Lodging can occur when the stem breaks (stalk lodging) or when the root system loses contact with the soil and is up-rooted (root lodging). Although stalk lodging has been the focus of much research attention, it is suggested that root lodging is more prevalent. In some crops (e.g. corn and sorghum) specialized aerial roots, called brace roots, are thought to play an important role in stability to prevent root lodging. Yet, the benefit of brace roots to the plant and what makes a good brace root is unknown. Our lab focuses on understanding the development and function of brace roots in crops. We leverage techniques from engineering, computational biology, genetics, genomics, and molecular biology to address these research questions.

Michela Taufer
Email | (302) 831-0071

Grid Computing, Cloud Computing, Parallel Algorithms on Hybrid Computing Platforms (multi-cores, GPUs)
http://gcl.cis.udel.edu/personal/taufer/index.php

Kenneth VanGolen
Email | (302) 831-2669

Breast, Prostate and Pancreatic Cancer
http://www.bio.udel.edu/people/kenneth-van-golen.php

Shuo Wei
Email | (302) 831-1146

Regulation of cell signaling and proteolysis in development and disease
https://www.bio.udel.edu/users/swei

Research description: The Wei lab is interested in the regulation of cell signaling, in particular Wnt and PI3K/Akt signaling, by cell-surface metalloproteinases. Perturbations of these cellular processes can lead to severe birth defects as well as other diseases, such as tumors, arthritis and neurodegenerative diseases.

Randall Wisser
Email | (302) 831-1356

Plant and Fungal Genetics
http://ag.udel.edu/plsc/faculty/wisser.html

The Wisser plant breeding and genetics lab studies complex or quantitative trait variation as it applies to crop improvement. Investigations are centered on the genetics and biology of response to selection, environmental adaptation and disease resistance. Our laboratory provides a setting for students and professionals to explore biological questions relevant to plant improvement while developing fundamental skills in the fields of genetics, breeding, statistics, bioinformatics and molecular biology through a combination of field, laboratory and computational experimentation.

Eric Wommack
Email | (302) 831-4362

Microbial Ecology, viral ecology, metagenomics, genomics, molecular biology, bioinformatics
http://www.virusecology.org/MOVE/Home.html

Cathy Wu
Email | (302) 831-8869

Computational Systems Biology, Protein Structure and Function, Biological Text Mining and Ontology, Bioinformatics Cyberinfrastructure
http://bioinformatics.udel.edu/People/Cathy_Wu

Jingyi Yu
Email | (302) 831-0345

Computer Graphics, Computer Vision, Image and Video Processing, Novel Camera Designs
http://www.cis.udel.edu/~yu/

Xiaoke Zhang
Email |

Functional data analysis, longitudinal data analysis, smoothing, dimension reduction, statistical learning, and neuroimaging (EEG, fMRI).
https://sites.google.com/a/udel.edu/xkzhang/home

Ryan Zurakowski
Email | (302) 831-0331

Biomedical Engineering, Mathematical Biology, Evolutionary Modeling
http://sites.udel.edu/ryanz/