Master’s Program in
Bioinformatics & Computational Biology

Program Faculty

  Behnam Abasht
Email | (302) 831-8876
Assistant Professor
Department of Animal and Food Sciences (ANFS)

http://sites.udel.edu/abashtlab/
Poultry Genetics and Genomics

  Paul Amer
Email | (302) 831-1944
Alumni Distinguished Professor
Department of Computer & Information Sciences (CIS)
Computer Networks, Data Compression
http://www.cis.udel.edu/~amer/

  Maciek Antoniewicz
Email | (302) 831-8960
DuPont Young Professor/Assistant Professor
Department of Chemical Engineering (ChE)
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.

  Brian Bahnson
Email | (302) 831-6335
Associate Professor
Department of Chemistry and Biochemistry
Structural Biology, Molecular Modeling
http://www.udel.edu/chem/bahnson/

  Jennifer F Biddle
Email | (302) 645-4267
Assistant Professor
Marine Biosciences
Microbial Populations and Processes in Subseafloor Marine Environments
http://www.ceoe.udel.edu/people/profile.aspx?jfbiddle

  Fidelma Boyd
Email | (302) 831-1088
Professor
Biological Sciences

http://www.bio.udel.edu/users/fboyd

  Richard Braun
Email | (302) 831-1869
Professor
Mathematical Sciences

http://www.math.udel.edu/~braun/
Richard Braun is an applied mathematician whose recent research focuses on dynamics of the tear film. 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
Assistant Professor
Department of Computer & Information Sciences (CIS)
Artificial Intelligence
http://ir.cis.udel.edu/~carteret/

  David Colby
Email | (302) 831-3649
Assistant Professor
Department of Chemical and Biomolecular Engineering

http://www.che.udel.edu/research_groups/colby/people/
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
Professor
Chemical Engineering and Mathematical Sciences
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.

  Melinda Duncan
Email | (302) 831-0533
Professor
Department of Biological Sciences
Structural Biology, Molecular Modeling
http://www.bio.udel.edu/people/melinda-duncan.php
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
Assistant Professor
Department of Electrical and Computer Engineering (ECE)
Information Retrieval, Data Mining
http://www.ece.udel.edu/~hfang/

  Pak-Wing Fok
Email | (302) 831-0637
Assistant Professor
Mathematical Sciences

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
Distinguished Professor
Department of Electrical and Computer Engineering (ECE)
High Performance Computing, Data Mining
http://www.capsl.udel.edu/~ggao/

  Pamela Green
Email |
Crawford H. Greenewalt Professor
Plant & Soil Sciences
Marine Biosciences

http://ag.udel.edu/plsc/faculty/pamgreen/index.html
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
Associate Professor
Marine Biosciences
Microbial Genomics
http://www.ceoe.udel.edu/people/profile.aspx?tehanson

  John Jungck
Email | (302) 831-2281
Director of Interdisciplinary Science Instruction
College of Arts & Sciences

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  
Associate Professor
Department of Computer & Information Sciences (CIS)
Biomedical Image analysis, Computer Vision/Graphics
http://www.cis.udel.edu/~chandra/

  Calvin Keeler
Email | (302) 831-6473
Professor
Department of Animal and Food Sciences (ANFS)
Pathogenomics, Innate Immunity, Molecular Virology
http://ag.udel.edu/anfs/faculty/Keeler.html

  David Kirchman
Email | (302) 654-4375
Maxwell P. and Mildred H. Professor
Marine Biosciences

http://www.ceoe.udel.edu/people/kirchman
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
Assistant Professor
Chemical Engineering & Materials Science and Engineering

http://www.AprilKloxinGroup.org
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.

  Arun Kumar
Email | (302) 831-4180
Assistant Professor
Medical Laboratory Sciences

http://www.udel.edu/chs/facultystaff/kumar.html
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
Assistant Professor
Biological Sciences

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) 831-1818
Gore Professor, Director of Delaware Biotechnology Institute
Department of Chemical Engineering
Systems Biology, Proteomics
http://www.leelab.org/

  Jung-Youn Lee
Email | (302) 831-3230
Associate Professor
Department of Plant & Soil Sciences (PLSC)

http://udel.edu/~jylee/plasmodesmata.html
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
Assistant Professor
Department of Electrical and Computer Engineering (ECE)
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
Associate Professor
Department of Computer & Information Sciences
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

  Lucas Lu
Email | 302-831-2401
Assistant Professor
Department of Mechanical Engineering

http://www.me.udel.edu/Faculty/l_lu.html
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
Assistant Professor
Physics & Astronomy

http://web.physics.udel.edu/about/directory/faculty/edward-r-lyman

  Julia Maresca
Email | (302) 831-4391
Assistant Professor
Civil and Environmental Engineering

http://www.ce.udel.edu/directories/profiles.html?jmaresca

  Adam Marsh
Email | (302) 645-4367
Associate Professor
Marine Biosciences
Environmental Bioinformatics
http://www.ceoe.udel.edu/people/profile.aspx?amarsh

  Blake Meyers
Email | (302) 831-3418
Edward F. and Elizabeth Goodman Rosenberg Professor
Plant & Soil Sciences
Plant Genomics, Bioinformatics
http://www.dbi.udel.edu/People/meyers.html
The Meyers lab uses bioinformatics and laboratory-based approaches to examine gene expression (mRNA), small RNA, and chromatin modifications in plants. We use short-read sequencing technologies for these studies and have developed a unique set of analytical tools and databases. These data are being used to determine patterns of gene expression under different developmental conditions or in different genetic backgrounds, to identify novel genes, and to understand the relationship between the genomic context of a gene and its activity. We work with members of the CBCB on genomic analysis and next-gen DNA sequencing data.

   Anja Nohe
Email | (302) 831-2959
Assistant Professor
Department of Biological Sciences (BIO)
Systems Biology, Pathway Modeling, pbpk Modeling
http://www.bio.udel.edu/people/anja-nohe.php

  Mia Papas
Email | 302-831-4990
Assistant Professor
Behavioral Health and Nutrition

http://www.udel.edu/chs/facultystaff/papas.html
Dr. Papas received her doctoral degree in epidemiology from Johns Hopkins University. Dr. Papas has authored over 30 peer reviewed articles investigating the built environment and adolescent overweight, growth rates among children with early growth deficiency, dietary habits of inner-city adolescent mothers, the influence of pain on adherence to mammography screening guidelines, and food insecurity in Hispanic families. Dr. Papas' expertise includes study designs, the assessment of screening tools, the analysis of longitudinal data, and the use of GIS in understanding the effect of place on health and health behaviors.

  Terry Papoutsakis
Email | (302) 831-8376
Eugene DuPont Professor
Department of Chemical Engineering (ChE)
Systems Biology, Metabolic Engineering
http://www.papoutsakis.org

  Sandeep Patel
Email | (302) 831-6024
Assistant Professor
Department of Chemistry and Biochemistry (CHEM)
Computational Chemistry
http://patelgroup.chem.udel.edu/joomla/

  P. Michael Peterson
Email | (302) 831-3672
Professor and Chair
Department of Behavorial Health and Nutrition

http://www.udel.edu/chs/facultystaff/peterson.html
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
Research Assistant Professor
Coordinator, Bioinformatics Core Facility
Department of Computer and Information Sciences (CIS)

http://bioinformatics.udel.edu/People/Polson
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.

  Lidia Rejto
Email | (302) 831-8034
Professor
Department of Food & Resource Economics (FREc)
Biostatistics
http://ag.udel.edu/frec/faculty/rejto.html

  Gilberto Schleiniger
Email | (302) 831-1872
Associate Professor
Department of Mathematical Sciences (MATH)
Mathematical Biology, Computational Biology, Mathematical Modeling and Scientific Computation
http://www.math.udel.edu/php/deptapps/profile.php?pid=schgilb

  Carl Schmidt
Email | (302) 831-1334
Associate Professor
Department of Animal and Food Sciences
Avian Genomics
http://ag.udel.edu/anfs/faculty/Schmidt.html

  Erica Selva
Email | (302) 831-6096
Associate Professor
Department of Biological Sciences
Signal Transduction
http://www.bio.udel.edu/people/erica-selva.php

  Vijay Shanker
Email | (302) 831-1952  
Professor
Department of Computer & Information Sciences (CIS)
Natural Language Processing, Text Mining of Biomedical Literature, Machine Learning
http://www.cis.udel.edu/~vijay

  Hagit Shatkay
Email | (302) 831-8622
Associate Professor
Computer and Information Sciences
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
Assistant Professor
Department of Electrical and Computer Engineering

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
Assistant Professor
Department of Biological Sciences

http://www.bio.udel.edu/people/jia-song.php
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.

  Michela Taufer
Email | (302) 831-0071
Associate Professor
Department of Computer & Information Sciences (CIS)
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
Assistant Professor
Department of Biological Sciences
Breast, Prostate and Pancreatic Cancer
http://www.bio.udel.edu/people/kenneth-van-golen.php

  Randall Wisser
Email | (302) 831-1356
Assistant Professor
Department of Plant & Soil Sciences (PLSC)
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
Professor
Department of Plant & Soil Sciences (PLSC)
Viral Genomics
http://www.virusecology.org/MOVE/Home.html

  Cathy Wu
Email | (302) 831-8869
Jefferson Professor
Computer & Information Sciences
Biological Sciences
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
Assistant Professor
Department of Computer & Information Sciences (CIS)
Computer Graphics, Computer Vision, Image and Video Processing, Novel Camera Designs
http://www.cis.udel.edu/~yu/

  Ryan Zurakowski
Email | (302) 831-0331
Assistant Professor
Department of Electrical and Computer Engineering (ECE)
Biomedical Engineering, Mathematical Biology, Evolutionary Modeling
http://www.ece.udel.edu/~ryanz/


 

Center for Bioinformatics & Computational Biology • 15 Innovation Way • Newark, DE 19711 • USA
Phone: 302-831-0161 • E-mail: bioinformatics@udel.edu

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