Faculty Research
Computer Science
Biological Sciences
Chemistry
Mathematical Sciences
Philosophy
Computer Science Department
Dr. Karen Daniels' research interests are applied computational geometry, combinatorial optimization, geometric modeling, and packing/layout/covering problems. Her research support has come from NSF, and Harvard University, and has resulted in numerous publications. Her previous applied algorithms research has been in VLSI design (custom layout algorithms for a silicon compiler), geometric modeling (partitioning cubic B-spline curves), manufacturing (inventory level optimization for factory production and layout algorithms for apparel manufacturing), and telecommunications (channel assignment algorithms for wireless networking). Some of her work has been licensed to Gerber Technologies and is part of a commercial product. She is interested in the application of her expertise to molecular modeling, clustering and geometric covering. Her research group has begun work on computational geometry techniques for clustering algorithms. One of her current research interests is hemoglobin assembly simulation that would model molecular environments and facilitate a number of molecular dynamic simulations, each involving a different hypothesized hemoglobin formation process.
Dr. Georges Grinstein's research areas are broad, focusing on computer graphics, visualization, virtual environments, user interfaces and data mining of large and complex data sets, especially those from the medical sciences (e.g. gene and protein databases, clinical trials, patient files). His emphasis is on the modeling, analysis and visualization of complex information systems, currently with the focus on bioinformatics and cheminformatics. Dr. Grinstein holds several patents and his software research tools in use worldwide. He has published well over 100 papers, chaired a number of conferences and founded five companies. He has organized and taught numerous 1-5 day courses and workshops in the areas of visualization, data mining, the integration of databases and visualization, integration of data mining and visualization, for applications to bioinformatics, cheminformatics and medical informatics. An advisor to several pharmaceutical companies, he now co-directs the Institute for Visualization and Perception Research (IVPR) and the Center for Biomolecular and Medical Informatics.
Dr. Haim Levkowitz's research interests are in visualization, perception, color, sonification, graphics, Internet/Web, medical and bioinformatics applications. In 2004-2005, he was a Fulbright Scholar and Fellow in Brazil, State of Sao Paulo; and a Visiting Professor of Computer Science, University of Sao Paulo. He has authored Color Theory & Modeling for Computer Graphics, Visualization and Multimedia Applications, as well as more than 50 papers and book chapters. He is co-director of the Institute for Visualization and Perception Research.
Dr. Gary Livingston has five years of experience applying data mining tools to biomedical data. His research interests are primarily machine learning algorithms such as classification rule induction and Bayesian network learning and their (mostly biological) applications. Some of Dr. Livingston's current areas of application are gene expression analysis, pathway inference and analysis, and the use of machine learning to improve gene prediction.
Dr. Jie Wang's expertise is in network security, computational complexity, and applied algorithms and combinatorial optimizations. He studied a number of optimization problems arising in virtual colon endoscopy and radiosurgical treatment planning and devised an efficient algorithm to calculate the central path of 3D colon models. He also devised cryptographic protocols for secure network communications, anti-hacking tools and implementations of virtual private networks. These methods can be used to devise and implement a secure system for transmitting large, highly sensitive bioinformatics data sets. His interests are thus in the application of computational optimization problems arising in protein structure modeling and analysis, and in gene expression arrays; and in the development of security measures for transmission of large, highly sensitive bioinformatics data sets over the Internet, including queries and their answers. Dr. Wang has over 70 refereed publications, including 3 books. His research has been funded by NSF and Intel Corporation, with the total amount of $625,829 in the past two years.
Dr. Cindy Chen's research interests are Database Systems, XML Information Systems and Data Mining. She received her PhD. from UCLA and subsequently joined IBM T.J. Watson Researh Center and AT&T Labs as a postdoctoral fellow and visiting scientist, respectively. She is currently an assistant professor in the computer science department at UMass Lowell.
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Biological Sciences Department
Dr. Susan Braunhut has twenty years of research experience in tumor angiogenesis, radiotherapy and novel chemotherapeutics, retinoids and more recently in collaboration with Dr. Kenneth Marx, an interest in biosensors. She has supported her research laboratory as PI since 1986 and has received NIH, DOD, NSF and private funding. Her laboratory is exploring ways to improve the detection and treatment of human breast cancer. New chemotherapeutics under investigation include taxanes and retro-retinoids, and new adjunct therapies being studied utilize novel sensitizing agents with ionizing and non-ionizing radiation sources. Her laboratory studies the response of several human breast cancer cell lines and normal capillary endothelial cells to these novel treatments. The effectiveness of new therapeutic strategies is evaluated with regard to their direct effects on cancer cells and also their effects on the tumor vasculature. In collaboration with Dr. Marx, her laboratory is studying the use of cell based biosensors in drug discovery and pathogen detection.
Dr. Mark Hines is a microbial biogeochemist who studies elemental cycling in a variety of marine, fresh-water and terrestrial environments. His work focuses on trace gas production and anaerobic processes in wetlands and sediments, microbial transformations of mercury and other pollutants and bacterial diversity changes in response to environmental perturbations.
Dr. Michael Graves’ research interests in the genetic, molecular and cellular biology, and physiology of virus-host interactions have resulted in thirteen publications. Specifically, he studies the chlorella viruses, members of the family Phycodnaviridae, an extensive group that consists of large dsDNA (180 to 500 kbp) viruses that infect freshwater and marine algae. Genetically, these viruses are very complex; the genome of the type isolate, PBCV-1 contains ~375 protein-encoding genes as well as 11 tRNA genes. Most recently he is the PI on an NSF funded project entitled "Algal Virus Genomics" (EF0333197) the goal of which is to determine the sequences of additional chlorella virus genomes. Details about the project, including the sequences of finished virus genomes, can be found on Graves' lab webserver.
Dr. Brian Bettencourt's interests include molecular and phenotypic evolution, bioinformatics and ecological genetics. His research concerns ecological and evolutionary functional genomics, with dual foci on computational and genetic/biochemical approaches. He uses the multiple available Drosophila spp. genomes to identify genes under positive Darwinian selection, then conducts field and laboratory analyses of phenotypes to test hypotheses concerning the nature of selection. A current major thrust is studying the population genomics of polyglutamine repeat expansion, a model for neurodegenerative disease in humans, and the role of natural thermal stress and molecular chaperone expression in selection on repeat length.
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Department of Chemistry
Dr. Kenneth Marx’s research is broadly based. He is the Director of the Center for Intelligent Biomaterials and Co-Director of the Center for Biomolecular and Medical Informatics at UMass Lowell. His lab has produced over 160 refereed publications based upon multiple grant fundings from NIH, DARPA and the U.S. Army Research Office as well as projects funded by pharmaceutical and biotechnology companies. These are in the areas of physical biochemistry, biosensors, biomaterials, computational biochemistry and bio/cheminformatics. Dr. Marx was also a Co-Founder of AnVil, Inc. and has been a consultant to other biotechnology companies. Dr. Marx’s computational bio/cheminformatic approaches center around a number of areas that include the following topics. 1) Investigation of homopolymer tract frequency of occurrence, their significant enrichment, non-random genome location and function in a range of organisms across the phylogenetic spectrum. 2) Utilizing MELTSIM, (a statistical thermodynamic algorithm for simulating the melting properties of long DNA sequences) as a bioinformatics tool and to identify structural/energetic features in DNA sequences. 3) Utilization of new core algorithms for gene finding programs that employ physical property descriptors and informational theory metrics to discriminate exons from introns and to characterize quantitative aspects of specific DNA-protein interactions. 4) Data mining techniques have been utilized to discover novel gene and chemical compound relationships in NCI cancer compound public dataset and gene expression microarray datasets. This analysis has identified two novel subtypes of quinone compounds specifically effective against melanoma and leukemia cancer cell lines.
Dr. Melisenda McDonald's major fields of endeavor are protein, biophysical and analytical chemistry and her major research interests lie in macromolecular structure, function and assembly; multi-domain protein folding; static and rapid kinetic spectroscopic techniques to monitor in vitro physiochemical events. She has worked for over three decades on the biochemistry of human hemoglobin, a multisubunit allosteric prototype protein responsible for oxygen transport in the blood. Recent studies have focused on the incorporation of heme into the four globin subunits of tetrameric hemoglobin. Multidisciplinary approaches have included: recombinant site-directed mutagenesis & Soret spectral studies; data mining and integration (with Dr. Claypool); and molecular modeling and dynamics (with Dr. Daniels). Dr. McDonald has 62 peer reviewed publications, and her work has been funded by the National Heart, Lung and Blood Institute of the NIH.
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Mathematical Sciences
Professor Ann Marie Hurley is an active member of the Bioinformatics Program Committee. Her interests include biostatistics and experimental design. She represents the Biostatistics resource for the program.
Dr. Lee Jones’ research interests are statistical learning theory, neural networks, pattern recognition, probability and mathematical statistics, computational statistics, queue inferencing and transactional data analysis. Most recently his work has been in the area of estimation algorithms with high accuracy and exact inference methods and their applications to biomedical data. His research is supported by ONR, German Research Foundation, FHWA (Federal Highway Administration) and NSF. He has published in Annals of Statistics, Operations Research, and IEEE Transactions on Information Theory.
Dr. Konstantin Rybnikov has been working in statistical physics, graph rigidity theory, discrete and computational geometry. While his previous work in statistical physics was mostly related to glasses and elastic materials, he is now working on mathematical and computational approaches to shape and function of biomolecules. One of the directions of his work is the determination of rigid and flexible parts in a graph, realized in 3D space; he is especially interested in development of algorithms identifying rigid parts in a graph and how they are attached to each other, and in approaches to rigidity that incorporate the probabilistic point of view. His expertise is in rigidity theory and other areas of discrete and computational geometry pertaining to protein analysis.
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Philosophy
Dr. Eugene Mellican's work is in applied ethics. His research areas during the past 20 years ranged from engineering ethics to research ethics and numerous topics in biomedical ethics. With a special interest in scientific literacy, he has written about the way scientific issues are presented to the public. His publications include essays on scientific misconduct, teaching research ethics, the right to die, culturally constructed "diseases", breast implants and the challenge of an informed public. For eight summers he taught research ethics as part of a NSF Research Experiences for Undergraduates Program and presently as an online course for the Biomedical Engineering and Biotechnology graduate program. His present and future research interests focus on the ethical, legal, and social issues arising from the transforming power of genomics and the paradigm shift it is creating in the life sciences. He is particularly interested in such issues as intellectual property rights, conflicts of interest, the sharing of data, and the patenting of DNA sequences.
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