My research focuses on developing probabilistic modeling and computational algorithms for bioinformatics analysis of biomolecular sequence data. In particular, I have developed Markov models, scan statistics, and computational algorithms to identify unusual palindromic patterns in the nucleotide sequences and have applied them to the analysis of genomic sequences of DNA and RNA viruses like the herpesviruses and SARS coronaviruses. I have also been developing efficient computational approaches for predicting secondary structures, including pseudoknots, of long RNA sequences. We have devised methods to circumvent the extremely high demands of memory and computing time in the structure prediction problem by using grid computing technologies available in the UTEP Border Biomedical Research Center Bioinformatics Computing Core Facility, where I serve as director. The research in these projects has resulted in several bioinformatics software packages publicly accessible online (bioinformatics.utep.edu/BCL). With broad research interests and experience in probabilistic modeling, algorithm design, and statistical bioinformatics, I have served as PI and co-PI in various projects for setting up and managing computational facilities for biomedical research and as director of the Bioinformatics and Computational Science Programs for administering graduate research training at UTEP. Over the past 20 years, my research has been funded by NIH, NSF, IBM, and the Texas NHARP in viral genome replication, sequence analysis, and RNA structural prediction with a long record of publication in these areas. In addition, I am involved in several collaborative research projects in identifying protein biomarkers for hepatocellular carcinoma, mammogram image analysis, HIV vaccine development, and pipeline implementation for bioinformatics analysis of exonic sequence variants in cancer-related genes.