Computational Biology Commons^™

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Computer Science: Faculty Publications & Other Works

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we ...

Annotation Of Genes Responsible For Synthesis Of Uroporphyrinogen Iii From L-Glutamate, The First Half Of Of The Pathway Of Heme Biosynthetic Pathway, In Kytococcus Sedentarius., Vignesh M. Iyer

Master's Level Graduate Research Conference

Genome annotation is a set of algorithmic software tools that allows complete sequencing of an organism’s genome. Kytococcus sedentarius is a gram positive bacterium, with callus degrading activity, closely associated with pitted keratolysis. The objective of this study was to annotate the genes in Kytococcus sedentarius strain 541 (DSM 20547) responsible for heme biosynthesis, involving the formation of uroporphyrinogen III from L-Glutamate. Metabolic functions of individual genes were characterized using the Integrated Microbial Genome Annotation Collaboration Toolkit (IMG-ACT) developed by the Joint Genome Institute (University of California, CA). Sequence based similarity was identified using BLAST and T-COFFEE. Cellular localization ...

An Investigation Of Gene Networks Influenced By Low Dose Ionizing Radiation Using Statistical And Graph Theoretical Algorithms, Sudhir Naswa

Doctoral Dissertations

Increased application of radiation in health and security sectors has raised concerns about its deleterious effects. Ionizing radiation (IR) less than 10cGys is considered low dose ionizing radiation (LDIR) by the National Research Committee to assess health risks from exposure to low levels of IR.

It is hard to extract the effects of mild stimulus such as LDIR on gene expression profiles using simple differential expression. We hypothesized that differential correlation instead would capture the effects of LDIR on mutual relationships between genes. We tested this hypothesis on expression profiles from five inbred strains of mice treated with LDIR. Whereas ...

Global Quantitative Assessment Of The Colorectal Polyp Burden In, Patrick M. Lynch, Jeffrey S. Morris, William A. Ross, Miguel A. Rodriguez-Bigas, Juan Posadas, Rossa Khalaf, Diane M. Weber, Valerie O. Sepeda, Bernard Levin, Imad Shureiqi

Jeffrey S. Morris

Background: Accurate measures of the total polyp burden in familial adenomatous polyposis (FAP) are lacking. Current assessment tools include polyp quantitation in limited-field photographs and qualitative total colorectal polyp burden by video.

Objective: To develop global quantitative tools of the FAP colorectal adenoma burden.

Design: A single-arm, phase II trial.

Patients: Twenty-seven patients with FAP.

Intervention: Treatment with celecoxib for 6 months, with before-treatment and after-treatment videos posted to an intranet with an interactive site for scoring.

Main Outcome Measurements: Global adenoma counts and sizes (grouped into categories: less than 2 mm, 2-4 mm, and greater than 4 mm) were ...

Improving Specimen Identification: Informative Dna Using A Statistical Bayesian Method, Melanie Lou

Open Access Dissertations and Theses

This work investigates the assignment of unknown sequences to their species of origin. In particular, I examine four questions: Is existing (GenBank) data reliable for accurate species identification? Does a segregating sites algorithm make accurate species identifications and how does it compare to another Bayesian method? Does broad sampling of reference species improve the information content of reference data? And does an extended model (of the theory of segregating sites) describe the genetic variation in a set of sequences (of a species or population) better? Though we did not find unusually similar between-species sequences in GenBank, there was evidence of ...

Physiologically-Based Pharmacokinetic Modeling Of Acetaminophen Metabolism And Toxicity, David M. Ng, Ali Navid

STEM Teacher and Researcher (STAR) Program Posters

Acetaminophen is a common analgesic and antipyretic. Metabolism of acetaminophen and acetaminophen-induced liver necrosis are predicted using physiologically-based pharmacokinetic (PBPK) modeling. Pharmacokinetic means the model determines where the drug is distributed in the body over time. Physiologically-based means the anatomy and physiology of the human body is reflected in the structure and functioning of the model. Acetaminophen is usually safe and effective when taken as recommended, but consumption at higher levels may lead to liver damage. Additionally, other factors such as alcoholic liver disease, smoking, and malnutrition affect the maximum safe dose of acetaminophen.

Dramatic Shifts In Benthic Microbial Eukaryote Communities Following The Deepwater Horizon Oil Spill, Holly M. Bik, Kenneth M. Halanych, Jyotsna Sharma, W. Kelley Thomas

Hubbard Center for Genome Studies (HCGS)

Benthic habitats harbour a significant (yet unexplored) diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we present an intensive evaluation of microbial eukaryote communities prior to and following oiling around heavily impacted shorelines. Our results show significant changes in community structure ...

Recognition Models To Predict Dna-Binding Specificities Of Homeodomain Proteins, Ryan G. Christensen, Metewo Selase Enuameh, Marcus Blaine Noyes, Michael H. Brodsky, Scot A. Wolfe, Gary D. Stormo

Program in Gene Function and Expression Publications and Presentations

MOTIVATION: Recognition models for protein-DNA interactions, which allow the prediction of specificity for a DNA-binding domain based only on its sequence or the alteration of specificity through rational design, have long been a goal of computational biology. There has been some progress in constructing useful models, especially for C(2)H(2) zinc finger proteins, but it remains a challenging problem with ample room for improvement. For most families of transcription factors the best available methods utilize k-nearest neighbor (KNN) algorithms to make specificity predictions based on the average of the specificities of the k most similar proteins with defined ...

Classification Of Genomic Sequences By Latent Semantic Analysis, Samuel F. Way

Electrical Engineering Theses and Dissertations

Evolutionary distance measures provide a means of identifying and organizing related organisms by comparing their genomic sequences. As such, techniques that quantify the level of similarity between DNA sequences are essential in our efforts to decipher the genetic code in which they are written.

Traditional methods for estimating the evolutionary distance separating two genomic sequences often require that the sequences first be aligned before they are compared. Unfortunately, this preliminary step imposes great computational burden, making this class of techniques impractical for applications involving a large number of sequences. Instead, we desire new methods for differentiating genomic sequences that eliminate ...