Browsing by Department "Computational Biology and Bioinformatics"
Now showing items 1-20 of 86
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A Bayesian Hierarchical Model with SNP-level Functional Priors Applied to a Pathway-wide Association Study.
(2010)Tremendous effort has been put into study of the etiology of complexdiseases including the breast cancer, type 2 diabetes,cardiovascular diseases, and prostate cancers. Despite large numbers of reported disease-associated ... -
A Cloud-Based Infrastructure for Cancer Genomics
(2020)The advent of new genomic approaches, particularly next generation sequencing (NGS) has resulted in explosive growth of biological data. As the size of biological data keeps growing at exponential rates, new methods for ... -
A Computational Synthesis of Genes, Behavior, and Evolution Provides Insights into the Molecular Basis of Vocal Learning
(2012)Vocal learning is the ability modify vocal output based on auditory input and is the basis of human speech acquisition. It is shared by few distantly related bird and mammal orders, and is thus very likely to be an example ... -
Analysis and Error Correction in Structures of Macromolecular Interiors and Interfaces
(2009)As of late 2009, the Protein Data Bank (PDB) has grown to contain over 70,000 models. This recent increase in the amount of structural data allows for more extensive explication of the governing principles of macromolecular ... -
Automated Microscopy and High Throughput Image Analysis in Arabidopsis and Drosophila
(2009)Development of a single cell into an adult organism is accomplished through an elaborate and complex cascade of spatiotemporal gene expression. While methods exist for capturing spatiotemporal expression patterns---in situ ... -
Bayesian meta-analysis models for heterogeneous genomics data
(2013)The accumulation of high-throughput data from vast sources has drawn a lot attentions to develop methods for extracting meaningful information out of the massive data. More interesting questions arise from how to combine ... -
Bayesian modeling of microbial physiology
(2017)Microbial population growth measurements are widespread in the study of microorganisms, providing insight into areas including genetics, physiology, and engineering. The most common models of microbial population growth ... -
Bayesian Multivariate Count Models for the Analysis of Microbiome Studies
(2019)Advances in high-throughput DNA sequencing allow for rapid and affordable surveys of thousands of bacterial taxa across thousands of samples. The exploding availability of sequencing data has poised microbiota research to ... -
Characterization of Gene Interaction and Assessment of Ld Matrix Measures for the Analysis of Biological Pathway Association
(2009)Leukotrienes are arachidonic acid derivatives long known for their inflammatory properties and their involvement with a number of human diseases, most notably asthma. Recently, leukotriene-based inflammation has also been ... -
Characterization of Gene-by-Age Interaction and Gene-by-Gene Interaction In Coronary Artery Disease
(2012)The success of genome-wide association studies (GWAS) has been limited by missing heritability and lack of biological relevance of identified variants. We sought to address these issues by characterizing interaction among ... -
Chromatin Determinants of the Eukaryotic DNA Replication Program
(2011)The accurate and timely replication of eukaryotic DNA during S-phase is of critical importance for the cell and for the inheritance of genetic information. Missteps in the replication program can activate cell cycle checkpoints ... -
Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data
(2015)Transcriptional regulation has been studied intensively in recent decades. One important aspect of this regulation is the interaction between regulatory proteins, such as transcription factors (TF) and nucleosomes, ... -
Computational Methods for Comparative Analysis of Rare Cell Subsets in Flow Cytometry
(2013)Automated analysis techniques for flow cytometry data can address many of the limitations of manual analysis by providing an objective approach for the identification of cellular subsets. While automated analysis has the ... -
Computational Methods For Functional Motif Identification and Approximate Dimension Reduction in Genomic Data
(2011)Uncovering the DNA regulatory logic in complex organisms has been one of the important goals of modern biology in the post-genomic era. The sequencing of multiple genomes in combination with the advent of DNA microarrays ... -
Computational Methods for Investigating Dendritic Cell Biology
(2011)The immune system is constantly faced with the daunting task of protecting the host from a large number of ever-evolving pathogens. In vertebrates, the immune response results from the interplay of two cellular systems: ... -
Computational Methods to Study Diversification in Pathogens, and Invertebrate and Vertebrate Immune Systems
(2010)Pathogens and host immune systems use strikingly similar methods of diversification. Mechanisms such as point mutations and recombination help pathogens escape the host immune system and similar mechanisms help the host ... -
Computational Processing of Omics Data: Implications for Analysis
(2013)In this work, I present four studies across the range of 'omics data types - a Genome- Wide Association Study for gene-by-sex interaction of obesity traits, computational models for transcription start site classification, ... -
Computational Protein Design with Non-proteinogenic Amino Acids and Small Molecule Ligands, with Applications to Protein-protein Interaction Inhibitors, Anti-microbial Enzyme Inhibitors, and Antibody Design
(2021)Computational protein design is a leading-edge technology to design novel protein with novel functions, as well as study the structure and function of known protein. Conventionally, most of the existing computational protein ... -
Computational Systems Biology of Saccharomyces cerevisiae Cell Growth and Division
(2014)Cell division and growth are complex processes fundamental to all living organisms. In the budding yeast, <italic>Saccharomyces cerevisiae</italic>, these two processes are known to be coordinated with one another as a cell's ... -
Constructing Mathematical Models of Gene Regulatory Networks for the Yeast Cell Cycle and Other Periodic Processes
(2014)We work on constructing mathematical models of gene regulatory networks for periodic processes, such as the cell cycle in budding yeast, using biological data sets and applying or developing analysis methods in the areas ...
