Bioinformatics Computing Laboratory (BCL)


Visit Dr. Aley...Stephen B. Aley, Ph.D., Professor, Department of Biological Sciences, and Associate Vice President for Research. He has worked and taught microbiology, parasitology, and bioinformatics since 1995, and is the PI and Program Director for the Howard Hughes Medical Institute Curriculum Grant at UTEP. He has extensive research experience in molecular biology and sequence analysis of human parasites (Giardia, Plasmodium), including five years involvement with genome project for Giardia lamblia. Current research interests include biochemistry and cell biology of Giardia lamblia, including host/parasite interactions and evolution of eurkaryotic organelles and biochemical pathways using bioinformatics computing tools. Dr. Aley is a member of the Executive Committee and Admission Committee in the Bioinformatics Program. Dr. Aley is the PI in the NIH-funded “Enhancement of Quantitative Science in Biology Curricula” and co-PI in the subcontract with Pittsburgh Supercomputing Center in NIH-funded projects for bioinformatics education and research. His expertise includes genome and sequence assembly techniques and the use of general bioinformatics computing tools.

 

Visit Dr. Almeida...Igor Almeida, Ph.D., Professor, Department of Biological Sciences. His research studies focus on structure and immunological roles of GPI-anchored glycoconjugates and lipids of Trypanosoma cruzi, trying to understand how the parasite modulates and evades the host immune response. His ultimate goal is the development of new therapeutic approaches for Chagas’ disease. His current five-year NIH-funded research project is a study on the molecular composition and function of T. cruzi shed vesicles. Also, he was involved in several collaborative studies with research groups from the US and abroad, aiming at the structural and functional characterization of glycoconjugates and lipids from various pathogens and disease vectors. Dr. Almeida is a member of the Research Committee in the Bioinformatics Program and has recently developed a web-based bioinformatics tool for glycosylation site prediction, OGPET, at ISOGlyP.utep.edu. As a resource faculty for BCL, he will provide bioinformatics support services in the areas of proteomics, mass spectrometry, and glycosylation site prediction.

 

 

Visit Dr. Bernal...Ricardo Bernal, Ph.D., Associate Professor, Department of Chemistry. The research interests of Dr. Bernal are primarily focused on the mechanisms that lead to the efficient and precise assembly of large macromolecular complexes from heterogeneous subunits. One project includes the three dimensional structure determination of bacteriophages that infect Pseudomonas aeruginosa, a human pathogen. These bacteriophages have been isolated from natural environments such as lakes and rivers. One of these viruses, bacteriophage EL, is an unusually large phage with a genome that is 211,215bp in length and has 201 predicted open reading frames. One of these open reading frames encodes a chaperonin that is similar to the E. coli GroEL chaperonin. His lab is currently working on the structure of this first and only known virus encoded chaperonin. Another focus of his lab is on the structure determination of V-type ATPases from various organisms. V-ATPases are enzymes that utilize the energy derived from ATP hydrolysis to pump protons against concentration gradients. These ATPases acidify organelles such as the yeast vacuole or can be utilized by cells such as osteoclasts to degrade bone. He will provide bioinformatics tools for cryo-EM data analysis, macromolecular assembly and X-ray crystallography analysis.

 

Visit Dr. Fuentes...

Olac Fuentes, Ph.D., Professor, Department of Computer Science. His major research area is machine learning and its applications to scientific data analysis, computer vision, robotics, and natural language processing. He is a member of the Colloquium Committee and Research Committee in the Bioinformatics Program. With his extensive research experience in machine learning, Dr. Fuentes is a supervising faculty in the project “RNAVLab: Virtual Laboratory for RNA Structure Predictions” funded by Texas ARP. His expertise includes the integration of machine learning techniques in developing bioinformatics computing tools, especially in areas related to RNA structure prediction methods.

 

 

 

 

Visit Dr. Kreinovich...

Vladik Kreinovich, Ph.D., Professor, Department of Computer Science. His research interests include interval computations and intelligent control. He is a member of the Executive Committee and Admission Committee in the Bioinformatics Program as a representative from the Department of Computer Science. He is a member of the editorial boards of many prestigious journals in his research areas, such as the International Journal of Reliable Computing, Journal of Applied Statistics and Intelligent Technology, and International Journal of Interval Computations. As a co-PI in the NSF-funded "CREST Cyber-ShARE Center of Excellence: A Center for Sharing Cyberresources to Advance Science and Education" and co-I in the NIH-funded “Enhancement of Quantitative Science in Biology Curricula,” Dr. Kreinovich has expertise using intelligent computing systems in data processing under uncertainty and intelligent data processing techniques for bioinformatics computing problems.

 

 

Visit Dr. Leung...

Ming-Ying Leung, Ph.D., Professor, Department of Mathematical Sciences, and Director, Bioinformatics and Computational Science Programs. Research interests include probabilistic modeling and statistical bioinformatics, focusing on applications of Markov models, Poisson approximations, and the scan statistics to DNA sequence analysis. Her current research theme is to develop a fast, efficient way to predict the 2-dimensional structures of ribonucleic acids (RNA) used by some viruses as their genomes (e.g., West Nile virus). As the PI for five research projects since 2003, Dr. Leung received grants from NIH, NSF, and Texas NHARP. In addition, she has also been co-PI or co-investigator for other NSF or NIH grants. She serves as a referee for many journals, reviewer for NIH and NSF grants, and members of various editorial boards and external advisory boards. Dr. Leung provides bioinformatics support services mainly in molecular sequence analysis, microarray analysis, RNA structure prediction, and DNA replication origin prediction.

 

 

Visit Dr. Narayan...

Mahesh Narayan, Ph.D., Professor, Department of Chemistry. His research interests include the investigation of mechanism of chaperone catalyzed protein folding reactions in order to develop small molecule mimics that can serve as chemotherapeutics. Folding studies on biomedically relevant proteins to unravel key intramolecular interactions that stabilize the native state. He also develops nanobiotechnological vehicles for drug delivery. Awards and Activities: European Union Travel Award; American Chemical Society Honorarium. Dr. Narayan is a member of the Research Committee and Chair of the Colloquium Committee in the Bioinformatics Program. His expertise includes proteomics, X-ray crystallography, and protein folding dynamics.

 

 

 

 

 

 

Visit Dr.Qian...

Wei Qian, Ph.D., Professor, Department of Electrical and Computer Engineering, and Director, Medical Imaging Informatics. Research interests include computer-aided cancer detection, diagnostic digital mammography, X-ray lung chest images, and lung CT images, with the use of neural networks, fuzzy logic, genetic algorithms and evolution algorithms in simulation, modeling, and design of high-performance and robust systems. Dr. Qian was awarded five US patents in the area of medical imaging; three of the patents were licensed and commercialized by the Kodak Company. For over 10 years, he has been involved in clinical trial studies and leading many research projects funded by state and federal agencies, private foundations, and industries, e.g., NSF, NIH, DOD, NASA, Susan G. Koman Breast Cancer Foundation, and GTE. As a BCL resource faculty, Dr. Qian’s expertise is mainly biomedical and molecular imaging with computational techniques using bioinformatics computing tools for cancer imaging and biomarker analysis.

 

 

Visit Dr. Sha...

Naijun Sha, Ph.D., Associate Professor, Department of Mathematical Sciences. Research interests include classification and clustering, variable selection technique with Bayesian approach applications to molecular biology, and wavelet method in statistics. He is the professional member of the American Statistical Association (ASA), Institute of Mathematical Statistics (IMS), and Mathematical Association of America (MAA) as well as reviewer for journals, such as Bioinformatics, Chemometrics and Intelligent Laboratory Systems, Theoretical Biology and Medical Modeling, and Biometrics. Dr. Sha is a member of the Admission Committee and Research Committee of the Bioinformatics Program with expertise in microarray analysis, statistical genetics, and computational techniques.

 

 

 

Visit Dr. Walsh...

Elizabeth Walsh, Ph.D., Professor, Department of Biological Sciences. NSF-funded research in molecular systematics and genotyping. Research interests include molecular systematics and evolutionary genetics. One of the NSF-funded ongoing projects is “Community Composition and Phylogeny of Basal Consumers in Chihuahuan Desert Waters” and she is serving as the Director for BBRC Toxicology Unit. Dr. Walsh is co-I in the NIH-funded “Enhancement of Quantitative Science in Biology Curricula” and a member of the Executive Committee and Research Committee in the Bioinformatics Program. She is actively involved in teaching bioinformatics core courses and supervising research projects for bioinformatics students, especially in their training of using bioinformatics computing tools. Her expertise as a BCL resource faculty includes general bioinformatics computational software, evolution and phylogenetic analysis, and toxicogenomics.

 

 

 

Chuan "River" Xiao, Ph.D.,  Associate Professor, Department of Chemistry. Research interests are mainly on viruses, which are small nano-machines that are assembled accurately from proteins and nucleic acids within the host cell. Understanding the assembly process can lead to not only the prevention of the harmfulness of viruses but also their utilization for biomedical purposes. His research focuses on the studies of viral assembly by combination of the structural determination techniques of cryo-EM and X-ray crystallography. Dr. Xiao is currently Chair of the Colloquium Committee in the Bioinformatics Program.

 

 

 

 

 

 

Visit Dr. Zhang...Jianying Zhang, M.D., Ph.D., Professor, Department of Biological Sciences. Research interests include cancer autoimmunity and cancer epidemiology. One of his several funded projects focuses on the use of autoantibodies as serological markers for detection and diagnosis of liver cancer in Hispanic population. Dr. Zhang has been an instructor for the bioinformatics core courses “Introduction to Bioinformatics II” (BINF 5352) and “Post-Genomic Analysis” (BINF 5354), and has expertise in bioinformatics tools for cancer research in areas such as proteomics, cancer informatics, and epidemiology.