A5040135909- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Herpesvirus Infections and Treatments
- Machine Learning in Bioinformatics
- HIV Research and Treatment
- Bacteriophages and microbial interactions
- Glycosylation and Glycoproteins Research
- Plant Virus Research Studies
- Tryptophan and brain disorders
- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- Distributed and Parallel Computing Systems
- Optimization and Search Problems
- Genomics and Rare Diseases
- Cytomegalovirus and herpesvirus research
- Gene expression and cancer classification
- Trypanosoma species research and implications
- Computational Drug Discovery Methods
- Enzyme Catalysis and Immobilization
- Distributed systems and fault tolerance
- Advanced Data Storage Technologies
- Data Mining Algorithms and Applications
- Fractal and DNA sequence analysis
- Image and Signal Denoising Methods
The University of Texas at El Paso
2013-2025
University of Delaware
2008
Leiden University
2008
The University of Texas at Austin
2007
The University of Texas at San Antonio
1991-2005
National University of Singapore
2005
Stanford University
1988
University of Hong Kong
1984
In this paper we formulate the static load balancing problem in single class job distributed systems as a cooperative game among computers. It is shown that Nash Bargaining Solution (NBS) provides Pareto optimal allocation which also fair to all jobs. We propose and present structure of NBS For an algorithm for computing derived. show fairness index is, always 1 using means Finally, performance our scheme compared with other existing schemes.
Pseudoknots have been recognized to be an important type of RNA secondary structures responsible for many biological functions. PseudoBase, a widely used database pseudoknot developed at Leiden University, contains over 250 records pseudoknots obtained in the past 25 years through crystallography, NMR, mutational experiments and sequence comparisons. To promptly address growing analysis requests researchers on bring together information from multiple sources across Internet single platform,...
The relative abundance and rarity of DNA words have been recognized in previous biological studies to implications for the regulation, repair, evolutionary mechanisms a genome. In this paper, we review several different measures words, including z-scores, representation ratios, cross-ratios, that appeared recent literature, examine concordance among them using human cytomegalovirus genome sequence. We then rank all length k = 2,..., 5 seven herpesvirus genomes according their abundance, as...
Mucin-type O-glycosylation is one of the most common posttranslational modifications proteins. The abnormal expression various polypeptide GalNAc-transferases (GalNAc-Ts) which initiate and define sites are linked to many cancers other diseases. Current O-glycosyation prediction programs utilize O-glycoproteomics data obtained without regard transferase isoform (s) responsible for glycosylation. With 20 different GalNAc-Ts in humans, having an ability predict interpret terms specific...
Efficient (linear time) algorithms are described for identifying global molecular sequence features allowing errors including repeats, matches between sequences, dyad symmetry pairings, and other patterns. A multiple alignment algorithm is also described. Specific applications given to hepatitis B viruses the J5-C (J, joining; C, constant) region of immunoglobulin kappa gene.
While separated by large expanses of dry terrain unsuitable for aquatic biota, aridland waters possess high biodiversity. How micrometazoans disperse to, and colonize, these isolated ephemeral habitats are not well understood. We used a multi-faceted approach including wind tunnel rehydration experiments, next-generation sequencing to assess potential movement diapausing propagules invertebrates anemochory across regional scales (102-105 km). Wind experiments using playa sediments with added...
Hispanic adults have an increased incidence of type 2 diabetes (T2D) at a younger age and diagnosis certain cancers, including liver, stomach, colorectal, which may be attributed to metabolic health. Several key health indicators, such as hemoglobin A1c (HbA1c), body mass index (BMI), waist-to-hip ratio (WHR), been linked obesity. The purpose this pilot study was explore the complex relationships between socio-behavioral factors that lead syndrome (e.g., HbA1c) chronic inflammation...
Overactive Janus kinases (JAKs) are known to drive leukemia, making them well-suited targets for treatment. We sought identify new JAK-activating mutations and instead found a JAK1-inactivating pseudokinase mutation, V666G. In contrast other that canonically lead an active kinase, the JAK1 V666G mutation led under-activation seen by reduced phosphorylation. To understand functional role of in modifying kinase activity we investigated its influence on JAK within Interleukin-2 pathway. not...
We analyze certain self-organizing filing techniques when accesses are assumed to be dependent on each other. The stream of requests for accessing records in a file is modelled as Markov chain. A general framework introduced obtain the asymptotic search cost memory-free heuristic. move-to-front heuristic studied detail. formula cost, which generalizes that case independent accesses, obtained. Numerical examples performance transposition provided, and compared with
Abstract A serious difficulty in concurrent programming of a distributed system is how to deal with scheduling and load balancing such which may consist heterogeneous computers. In this paper, we formulate the static load‐balancing problem single class job systems as cooperative game among The computers comprising are modeled M/M/1 queueing systems. It shown that Nash bargaining solution (NBS) provides an optimal (operation point) for it also fair solution. We propose present structure NBS....
Ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Their secondary structures are crucial for the RNA functionality, prediction of is widely studied. Our previous research shows that cutting long sequences into shorter chunks, predicting chunks independently using thermodynamic methods, reconstructing entire structure from predicted chunk can yield better accuracy than sequence as a whole. The chunking, prediction,...
Many empirical studies show that there are unusual clusters of palindromes, closely spaced direct and inverted repeats around the replication origins herpesviruses. In this paper, we introduce two new scoring schemes to quantify spatial abundance palindromes in a genomic sequence. Based on these schemes, computational method predict locations is developed. When our predictions compared with 39 known or annotated 19 herpesviruses, close 80% located within 2% genome length. A list predicted...
HLA-A 0201-restricted virus-specific CD8(+) CTL do not appear to control HIV effectively in vivo. To enhance the immunogenicity of a highly conserved subdominant epitope, TV9 (TLNAWVKVV, p24 Gag(19-27)), mimotopes were designed by screening large combinatorial nonapeptide library with TV9-specific primed vitro from healthy donors. A mimic peptide low binding affinity 0201, TV9p6 (KINAWIKVV), was studied further. Parallel cultures vitro-primed showed that consistently activated cross-reactive...
The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. Haller's organ, located in the tick's forelegs, crucial host detection and mating. To facilitate development new technologies better control this agricultural pest, we aimed to sequence annotate transcriptome R. australis forelegs associated tissues, including organ. As G protein-coupled receptors (GPCRs) are an important family eukaryotic proteins studied as...
With the identification of a novel coronavirus associated with
Replication origins are considered important sites for understanding the molecular mechanisms involved in DNA replication. Many computational methods have been developed predicting their locations archaeal, bacterial and eukaryotic genomes. However, a prediction method designed particular kind of genomes might not work well another. In this paper, we propose AT excursion method, which is score-based approach, to quantify local abundance genomic sequences use identified high scoring segments...
Abstract The Illumina Infinium HumanMethylation27 (Illumina 27K) BeadChip assay is a relatively recent high-throughput technology that allows over 27,000 CpGs to be assayed. 27K methylation data less commonly used in comparison gene expression bioinformatics. It provides critical need find the optimal feature ranking (FR) method for handling high dimensional data. FR on classifier not well known, and choosing best performing becomes more challenging setting. Therefore, identifying...
Replication of their DNA genomes is a central step in the reproduction many viruses. Procedures to find replication origins, which are initiation sites process, therefore great importance for controlling growth and spread such Existing computational methods viral origin prediction have mostly been tested within family herpesviruses. This paper proposes new approach by least-squares support vector machines (LS-SVMs) tests its performance not only on herpes but also collection caudoviruses...
Despite the computing power of emerging technologies, predicting long RNA secondary structures with thermodynamics-based methods is still infeasible, especially if include complex motifs such as pseudoknots. This paper presents preliminary results on rebuilding by an extensive and systematic sampling nucleotide chunks. The approach merges significant found in single prediction chunks are supported grid technology part RNAVLab functionality. Significant identified chunk merged a structure...