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UNO Bioinformatics

Bioinformatics Faculty Members

The faculty members listed below have been instrumental in implementing the Bioinformatics undergraduate degree program at UNO. They have initiated new Bioinformatics courses that were first offered during the 2005-2006 academic year and have begun to establish the foundations for the NE-INBRE (Idea Networks of Biomedical Research Excellence) Scholars Program within the UNO Bioinformatics program. Each of them serves as a NE-INBRE Associate, and they assist scholars with ongoing research projects.

They have recently been part of several research grants that have been awarded to UNO entitled "Construction of a Targeted Rhesus Macaque Microarray," "IDeA Networks for Biomedical Research Excellence," "Informatics Center for Life Sciences," and "Nebraska Training Network in Functional Genomics."

  • Hesham H. Ali, Ph.D
    PKI 172C

    Dean Ali is a professor of Computer Science and the Lee D. and Willa Seemann Distinguished Dean of the College of IS&T at UNO. He received his Ph.D. in Computer Science from the University of Nebraska-Lincoln. He is also the deputy director for computational sciences of the Nebraska Informatics Center for Life Center (NICLS), and a member of Nebraska Center for Biosecurity. He has published many articles and books in the areas of algorithmic graph theory, scheduling, parallel computing and fault-tolerant networks.

    He has been leading a Bioinformatics Research Group at UNO that focuses on developing computational approaches used to identify and classify biological organisms, with the goal of complementing the current experimental approaches in predicting a wide range of events that range from potential virus outbreaks to bio-terrorism. Two titles of his research projects that are currently taking place are “Regulatory Motif Detection in Bacteria” and “Epidemiological Study of Enterovirus – A Web Based Tracking System.”

    Other areas of his research include the development of graph analysis and generation tools and the application of graph theory in parallel computing and VLSI design.

  • Dhundy (Kiran) Bastola, Ph.D
    PKI 177D

    Dr. Bastola has recently joined the Bioinforamtics faculty in the College of IS&T.

    In recent years biological database searching has been solved predominately via local alignment heuristics, pattern matching, and comparison of short statistically significant patterns. While these approaches have unlocked many clues as to sequence relationships, they are limited in that they do not provide searching capabilities based on whole genome or multiple target sequences. The focus of Dr. Bastola's laboratory is in developing alternative approaches to the commonly used heuristic searching method that uses local or global alignment. Relative Complexity Measure (RCM), which calculates organism relatedness based on the overall complexity of the sequences is one such example of alternative approaches. His lab is currently pursuing to implement this approach in the “Advance Molecular Identification System” that has two major components (1) database management system and (2) novel searching algorithm that involves genomic, proteomic, transcriptomic and other high-throughput data.

  • Bruce Chase, Ph.D.
    Allwine 514B

    Dr. Chase is an associate professor in the Department of Biology at the College of Arts and Sciences. He received his Ph.D. in Biology from Yale University in New Haven, Connecticut.

    Dr. Chase is working toward a better understanding of Parkinson's disease: "With clinical collaborators at the University of Thessaly in Greece, I can use gene chip technology to assay the levels of the products of about 40,000 human genes in the blood of Parkinsonian patients. We then can use bioinformatics methods to identify the constellation of genes whose products together serve as a biomarker for Parkinson's disease."

  • Zhengxin Chen, Ph.D.
    PKI 281C

    Dr. Chen is a professor in the Department of Computer Science at the College of IS&T. He received his Ph.D. in Computer Science from Louisiana State University. During the fall of 2005, he is teaching CSCI 2980 (Topics: Visualization Bioinformatics), CSCI 8390 (Advanced Topics Database Management), CSCI 9350 (Mathematical and Logical Foundations of Data Mining), and CSCI 4850/8856 (Database Management Systems). He also taught an undergrad/graduate course entitled "Database search and Pattern discovery in Bioinformatics" in the spring of 2005.

    His research interests include artificial intelligence, database management systems, intelligent information retrieval, and database search and data mining in bioinformatics. One of his ongoing research topics includes an IST Data Mining project entitled “Text mining for Antimicrobial Peptides.” He is currently supervising a master's thesis for developing an XML Database for RNA data, a master's project for an Electronic Medical Records System with Integrated Clinical Decision Support, and a Ph.D. thesis on text mining. He has also co-chaired a Master’s project on HIV-1 Medicated Neuronal Damage and a thesis on cluster analysis on time series data involving microarrays.

  • Parvathi Chundi, Ph.D.
    PKI 281A

    Dr. Chundi is an assistant professor in the Department of Computer Science at the College of IS&T. She received her Ph.D in Computer Science from the University at Albany in Albany, NY.

    Her research interests include areas like moving object databases, data mining, bioinformatics, and replicated and distributed databases. Some of her current research titles include “Text mining of Medline data” and “A system of moving sensor” related to wireless technology. One current research topic involves using publicly available domain knowledge to enhance text mining techniques such as document clustering, text classification, and trend analysis that are used to extract previously unknown information from unstructured documents.

  • Guoqing Lu, Ph.D.
    Allwine Hall 214D

    Dr. Lu is an assistant professor in the Department of Biology at the College of Arts and Sciences. He received his Ph.D. in Biology from Laval University in 2000. Dr. Lu has two M.Sc. degrees respectively in Computer Science and Biology. He did his postdoctoral training in Bioinformatics in the Center for Bioinformatics at the University of McGill. Before joining UNO, Dr Lu was the director of the Bioinformatics Core Research Facility at the University of Nebraska-Lincoln.

    His research focuses on the development of bioinformatics algorithms and database systems in order to have a better understanding of how genes or non-coding regions give each organism its unique characteristics. Dr. Lu’s group is developing an in silico data mining tool to predict gene regions that are likely to reflect the true evolutionary history and thus can be used as genetic markers for constructing species phylogeny. In addition, Dr. Lu’s group is developing algorithms and software tools for genotyping influenza A virus based on the whole genome sequences. His group has a couple of other projects underway.

  • Mark A. Pauley, Ph.D.
    PKI 174H

    Dr. Pauley is a Senior Research Fellow and a professor in the Department of Computer Science in the College of IS&T. He received his Ph.D. in Physical Chemistry from the University of Nebraska-Lincoln. He also did post-baccalaureate studies in Computer Science at the University of North Carolina at Chapel Hill/North Carolina State University. During the fall of 2005, he is teaching CSCI 2980 (Topics: Intro to Web Development) and CSCI 2980 (Topics: Intro to Bioinformatics).

    His research interests include object-oriented programming and Bioinformatics. Particularly, the past couple of years, he has worked on making an Affymetrix GeneChip for the rhesus macaque monkey by developing the algorithms and procedures necessary to acquire sequence information from the 3' end of non-human primate orthologs of human genes. He developed software to align mRNA with genomic sequence in order to identify terminal exons of human genes.

  • William E Tapprich, Ph.D
    Allwine Hall 211D

    Dr. Tapprich is a professor in the UNO Department of Biology as well the chair of the department. He received his Ph.D. at the University of Montana in 1986.

    The overall goal of Dr. Tapprich’s research is to understand the structure and function of RNA molecules. Most of his work has focused on ribosomal RNA (rRNA), characterizing the role of the RNA in protein synthesis (Thompson et al 2001, Vila et al 1994). He has recently embarked on a new area of investigation studying the structure and function of viral RNA molecules.