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Recent Articles in Bioinformatics
Comparative Analyses Of Microbial Genomes To Identify Molecular Markers For Different Groups Of Prokaryotes, Vaibhav Bhandari McMaster University
Comparative Analyses Of Microbial Genomes To Identify Molecular Markers For Different Groups Of Prokaryotes, Vaibhav Bhandari
Open Access Dissertations and Theses
Currently centered on molecular data, bacterial and archaeal relationships are often based on their relative branching in 16S rRNA based phylogenetic trees. The availability of numerous bacterial genome sequences over the past two decades has provided new information for insights previously inaccessible to the field of taxonomy. Through utilization of comparative genomics, numerous molecular markers in the form of insertions and deletions within conserved regions of proteins, also known as Conserved Signature Indels or CSIs, have been discovered for various prokaryotic taxa. Using these techniques, we have analyzed relationships among the bacterial phyla of Thermotogae and Synergistetes and the conglomeration ...
A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer Loyola University Chicago
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 ...
Pathway Distiller - Multisource Biological Pathway Consolidation, Mark S. Doderer, Zachry Anguiano, Uthra Suresh, Ravi Dashnamoorthy, Alexander J. R. Bishop, Yidong Chen University of Massachusetts Medical School
Pathway Distiller - Multisource Biological Pathway Consolidation, Mark S. Doderer, Zachry Anguiano, Uthra Suresh, Ravi Dashnamoorthy, Alexander J. R. Bishop, Yidong Chen
Open Access Articles
BACKGROUND: One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets.
METHODS: After gene set enrichment finds representative pathways for large ...
Interpretation, Stratification And Validation Of Sequence Variants Affecting Mrna Splicing In Complete Human Genome Sequences, Ben C. Shirley Western University
Interpretation, Stratification And Validation Of Sequence Variants Affecting Mrna Splicing In Complete Human Genome Sequences, Ben C. Shirley
University of Western Ontario - Electronic Thesis and Dissertation Repository
The Shannon Human Splicing Pipeline software has been developed to analyze variants on a genome-scale. Evidence is provided that this software predicts variants affecting mRNA splicing. Variants are examined through information-based analysis and the context of novel mutations as well as common and rare SNPs with splicing effects are displayed. Potential natural and cryptic mRNA splicing variants are identified, and inactivating mutations are distinguished from leaky mutations. Mutations and rare SNPs were predicted in genomes of three cancer cell lines (U2OS, U251 and A431), supported by expression analyses. After filtering, tractable numbers of potentially deleterious variants are predicted by the ...
An Investigation Of Gene Networks Influenced By Low Dose Ionizing Radiation Using Statistical And Graph Theoretical Algorithms, Sudhir Naswa University of Tennessee, Knoxville
An Investigation Of Gene Networks Influenced By Low Dose Ionizing Radiation Using Statistical And Graph Theoretical Algorithms, Sudhir Naswa
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 ...
Utilizing Nmr Spectroscopy And Molecular Docking As Tools For The Structural Determination And Functional Annotation Of Proteins, Jaime Stark University of Nebraska - Lincoln
Utilizing Nmr Spectroscopy And Molecular Docking As Tools For The Structural Determination And Functional Annotation Of Proteins, Jaime Stark
Student Research Projects, Dissertations, and Theses - Chemistry Department
With the completion of the Human Genome Project in 2001 and the subsequent explosion of organisms with sequenced genomes, we are now aware of nearly 28 million proteins. Determining the role of each of these proteins is essential to our understanding of biology and the development of medical advances. Unfortunately, the experimental approaches to determine protein function are too slow to investigate every protein. Bioinformatics approaches, such as sequence and structure homology, have helped to annotate the functions of many similar proteins. However, despite these computational approaches, approximately 40% of proteins still have no known function. Alleviating this deficit will ...
Radiomics Of Nsclc: Quantitative Ct Image Feature Characterization And Tumor Shrinkage Prediction, Luke Hunter Texas Medical Center Library
Radiomics Of Nsclc: Quantitative Ct Image Feature Characterization And Tumor Shrinkage Prediction, Luke Hunter
UT GSBS Dissertations and Theses (Open Access)
Radiomics is the high-throughput extraction and analysis of quantitative image features. For non-small cell lung cancer (NSCLC) patients, radiomics can be applied to standard of care computed tomography (CT) images to improve tumor diagnosis, staging, and response assessment.
The first objective of this work was to show that CT image features extracted from pre-treatment NSCLC tumors could be used to predict tumor shrinkage in response to therapy. This is important since tumor shrinkage is an important cancer treatment endpoint that is correlated with probability of disease progression and overall survival. Accurate prediction of tumor shrinkage could also lead to individually ...
The Effect Of The R1648h Sodium Channel Mutation On Neuronal Excitability: A Model Study, Christopher Locandro, Robert Clewley Georgia State University
The Effect Of The R1648h Sodium Channel Mutation On Neuronal Excitability: A Model Study, Christopher Locandro, Robert Clewley
Georgia State Undergraduate Research Conference
No abstract provided.
Health Care Informatics Support Of A Simulated Study, Zeinab Salari Far University of Wisconsin Milwaukee
Health Care Informatics Support Of A Simulated Study, Zeinab Salari Far
Theses and Dissertations
The objective of this project is to assess the value of REDCap (Harris, 2009) by conducting a simulated breast cancer clinical trial and demonstration. REDCap is a free, secure, web-based application designed to support data capture for research studies. To assess REDCap's value, we conducted a simulation of a clinical trial study designed to compare the use of two new technologies for breast cancer diagnosis and treatment with current best practice breast cancer diagnosis and treatment. We call the trial, "Real-Time Operating Room BC Diagnostic Treatment (RORBCDT)". The RORBCDT clinical trial is designed to assess the value of a ...
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 The University of Texas
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 ...
The Problem Of Too Many Statistical Tests: Subgroup Analyses In A Study Comparing The Effectiveness Of Online And Live Lectures, David M. Lane University of South Florida
The Problem Of Too Many Statistical Tests: Subgroup Analyses In A Study Comparing The Effectiveness Of Online And Live Lectures, David M. Lane
The more statistical analyses performed in the analysis of research data, the more likely it is that one or more of the conclusions will be in error. Multiple statistical analyses can occur when the sample contains several subgroups and the researchers perform separate analyses for each subgroup. For example, separate analyses may be done for different ethnic groups, different levels of education, and/or for both genders. Media reports of research frequently omit information on the number of subgroup analyses performed thus leaving the reader with insufficient information to assess the validity of the conclusions. This article discusses the problems ...
An Integrated Encyclopedia Of Dna Elements In The Human Genome, Ian Dunham, Ewan Birney, Bryan R. Lajoie, Amartya Sanyal, Xianjun Dong, Melissa Greven, Xinying Lin, Jie Wang, Troy W. Whitfield, Jiali Zhuang, Job Dekker, Zhiping Weng, Gaurav Jain, ENCODE Project Consortium University of Massachusetts Medical School
An Integrated Encyclopedia Of Dna Elements In The Human Genome, Ian Dunham, Ewan Birney, Bryan R. Lajoie, Amartya Sanyal, Xianjun Dong, Melissa Greven, Xinying Lin, Jie Wang, Troy W. Whitfield, Jiali Zhuang, Job Dekker, Zhiping Weng, Gaurav Jain, Encode Project Consortium
Program in Systems Biology Publications and Presentations
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence ...
Error Correction In Next Generation Dna Sequencing Data, Michael Z. Molnar Western University
Error Correction In Next Generation Dna Sequencing Data, Michael Z. Molnar
Electronic Thesis and Dissertation Repository
Motivation: High throughput Next Generation Sequencing (NGS) technologies can sequence the genome of a species quickly and cheaply. Errors that are introduced by NGS technologies limit the full potential of the applications that rely on their data. Current techniques used to correct these errors are not sufficient, and a more efficient and accurate program is needed to correct errors.
Results: We have designed and implemented RACER (Rapid Accurate Correction of Errors in Reads), an error correction program that targets the Illumina genome sequencer, which is currently the dominant NGS technology. RACER combines advanced data structures with an intricate analysis of ...
Transcriptional Analysis Of Cervical Epithelial Cell Responses To Hiv-1, Andrew A. Block University of Nebraska - Lincoln
Transcriptional Analysis Of Cervical Epithelial Cell Responses To Hiv-1, Andrew A. Block
Dissertations and Theses in Biological Sciences
Human Immunodeficiency Virus type 1 (HIV-1) infection causes a growing pandemic throughout the world, of which women comprise 51% of people who live with HIV-1, more than 60% in sub-Saharan Africa. HIV-1 infections of women are mainly acquired through female reproductive tract where cervical and vaginal epithelial cells are the first line of defense. Although HIV-1 does not directly infect epithelial cells, HIV-1 obligatorily interacts with and crosses over epithelial layer to infect susceptible target cells, mainly CD4+ T cells, in the lamina propria to initiate an infection. However, the mechanism and ramification of the interaction of HIV-1 and epithelial ...
Sulfate Reducing Communities In Aquifer Systems Can Be Reliably Stimulated By Addition Of Complex Nutrients, Matthew Bryan Scholz University of Tennessee, Knoxville
Sulfate Reducing Communities In Aquifer Systems Can Be Reliably Stimulated By Addition Of Complex Nutrients, Matthew Bryan Scholz
The disseration presented below is the summation of research into the potential roles of microbial communities associated with aquifers of Bangladesh contaminated with naturally occuring arsenic. These investigations also included experimental microcosm experiments to assess the role of nutrients supplementation of complex carbon sources (molasses), and inorganic sulfate (MgSO4), on both the solubility of arsenic to determine the feasibility of this method for the goal of performing in situ bioremediation. Community structure and functional gene profiling was performed on all samples, as well as detection of community shifts following amendments predicted to encourage the growth of sulfate reducting microorganisms (SRM ...
Effects Of Pristane On Growth Of Pink Salmon (Oncorhynchus Gorbuscha), Brielle D. Kemis, Bonita Nelson California Polytechnic State University
Effects Of Pristane On Growth Of Pink Salmon (Oncorhynchus Gorbuscha), Brielle D. Kemis, Bonita Nelson
STEM Teacher and Researcher (STAR) Program Posters
Pristane is a naturally occurring hydrocarbon that is generated by copepods in marine ecosystems. Organisms that eat copepods do not readily metabolize pristane, which causes it to accumulate throughout the marine food web. Understanding how pristane affects marine fish is essential because pristane is often used as a bioindicator in lab studies and may be influencing results in those studies. Also, this hydrocarbon may significantly reduce growth of marine fish in the wild. A previous study indicated that pristane is an appetite suppressant and growth retardant in fish. However, the study implemented a feeding regime with unnaturally high levels of ...
Isaac: An Improved Structural Annotation Of Attc And An Initial Application Thereof, Judith C. Szamosi McMaster University
Isaac: An Improved Structural Annotation Of Attc And An Initial Application Thereof, Judith C. Szamosi
Open Access Dissertations and Theses
We introduce new software (ISAAC: Improved Structural Annotation of attC) to annotate cassette arrays in bacterial integrons by ﬁnding attI and attC sites, and to provide detailed annotation of the attC sites for analysis. We demonstrate an initial application of ISAAC by annotating the cassette complements of all the integrons we identiﬁed in the RefSeq bacterial genome database, and providing an analysis of the patterns of nucleotide frequencies at the structurally important positions in the attCs we’ve found.
Rpos Regulon Modulation By Environmental Selection, Sarah M. Chiang McMaster University
Rpos Regulon Modulation By Environmental Selection, Sarah M. Chiang
Open Access Dissertations and Theses
Regulatory interactions evolve to incorporate new genomic material and contribute to bacterial diversity. These regulatory interactions are flexible and likely provide bacteria with a means of rapid environmental adaptation. In this thesis, the RpoS regulon is used as a model system to investigate the hypothesis that regulon composition and expression are modified according to environmental pressures. Several novel findings are presented, namely the distribution of RpoS homologs in bacteria, the flexibility of the RpoS regulon, and the effect of diverse environmental pressures on RpoS regulon expression. Based on phylogenetic and reciprocal best hits analyses, RpoS was determined to be conserved ...
Lateral Gene Transfer In Operons And Its Effects On Neighbouring Genes, Asher Pasha McMaster University
Lateral Gene Transfer In Operons And Its Effects On Neighbouring Genes, Asher Pasha
Open Access Dissertations and Theses
Prokaryotes evolve, in part, by lateral gene transfer (LGT). This transfer of genetic material is likely important in the evolution of operons, a group of genes that are transcribed as a single mRNA. Genes that are transferred may then be integrated into genomes by homologous recombination. In this thesis, it was proposed that homologous recombination is the mechanism of integration of laterally transferred genes into operons. To investigate this proposal, a phylogenetic tree of Bacillus was inferred using DNA sequence alignments. LGT was inferred using a parsimony algorithm, and operons were inferred using OperonDB. Homologous recombination breakpoints were identified by ...
Optimal Clustering Techniques For Metagenomic Sequencing Data, Erik T. Cameron Western University
Optimal Clustering Techniques For Metagenomic Sequencing Data, Erik T. Cameron
Electronic Thesis and Dissertation Repository
Metagenomic sequencing techniques have made it possible to determine the composition of bacterial microbiota of the human body. Clustering algorithms have been used to search for core microbiota types in the vagina, but results have been inconsistent, possibly due to methodological differences. We performed an extensive comparison of six commonly-used clustering algorithms and four distance metrics, using clinical data from 777 vaginal samples across 5 studies, and 36,000 synthetic datasets based on these clinical data. We found that centroid-based clustering algorithms (K-means and Partitioning around Medoids), with Euclidean or Manhattan distance metrics, performed well. They were best at correctly ...
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Risk Factors Of Follicular Lymphoma, Shuangge Ma
An Integrated Encyclopedia Of Dna Elements In The Human Genome, Zhiping Weng, Job Dekker, Bryan Lajoie, Troy Whitfield, Xianjun Dong, Amartya Sanyal, Gaurav Jain, Jie Wang, Melissa Greven, Xinying Lin, Jiali Zhuang
Statistical Analyses And Reproducible Research, Robert Gentleman, Duncan Temple Lang
Members’ Discoveries: Fatal Flaws In Cancer Research, Jeffrey Morris
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