Bioinformatics Commons^™

Classification Of Breast Cancer Patients Using Somatic Mutation Profiles And Machine Learning Approaches, Suleyman Vural

Theses & Dissertations

The high degree of heterogeneity observed in breast cancers makes it very difficult to classify cancer patients into distinct clinical subgroups and consequently limits the ability to devise effective therapeutic strategies. In this study, we explore the use of gene mutation profiles to classify, characterize and predict the subgroups of breast cancers. We analyzed the whole exome sequencing data from 358 ethnically similar breast cancer patients in The Cancer Genome Atlas (TCGA) project. Identified somatic and non-synonymous single nucleotide variants were assigned a quantitative score (C-score) that represents the extent of negative impact on the function of the gene. Using …

Finding Function In The Unknown, Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, Catherine Putonti

Bioinformatics Faculty Publications

Through high-throughput RNA sequencing (RNAseq), transcriptomes for a single cell, tissue, or organism(s) can be ascertained at a high resolution. While a number of bioinformatic tools have been developed for transcriptome analyses, significant challenges exist for studies of non-model organisms. Without a reference sequence available, raw reads must first be assembled de novo followed by the tedious task of BLAST searches and data mining for functional information. We have created a pipeline, PyRanger, to automate this process. The pipeline includes functionality to assess a single transcriptome and also facilitate comparative transcriptomic studies.

Identifying Gene-Gene Interactions That Are Highly Associated With Body Mass Index Using Quantitative Multifactor Dimensionality Reduction (Qmdr), Rishika De, Shefali S. Verma, Fotios Drenos, Emily R. Holzinger

Dartmouth Scholarship

Despite heritability estimates of 40–70% for obesity, less than 2% of its variation is explained by Body Mass Index (BMI) associated loci that have been identified so far. Epistasis, or gene-gene interactions are a plausible source to explain portions of the missing heritability of BMI. Using genotypic data from 18,686 individuals across five study cohorts – ARIC, CARDIA, FHS, CHS, MESA – we filtered SNPs (Single Nucleotide Polymorphisms) using two parallel approaches. SNPs were filtered either on the strength of their main effects of association with BMI, or on the number of knowledge sources supporting a specific SNP-SNP interaction in …

The Importance Of Physicochemical Characteristics And Nonlinear Classifiers In Determining Hiv-1 Protease Specificity, Timmy Manning, Paul Walsh

Department of Biological Sciences Publications

This paper reviews recent research relating to the application of bioinformatics approaches to determining HIV-1 protease specificity, outlines outstanding issues, and presents a new approach to addressing these issues. Leading machine learning theory for the problem currently suggests that the direct encoding of the physicochemical properties of the amino acid substrates is not required for optimal performance. A number of amino acid encoding approaches which incorporate potentially relevant physicochemical properties of the substrate are identified, and are evaluated using a nonlinear task decomposition based neuroevolution algorithm. The results are evaluated, and compared against a recent benchmark set on a nonlinear …

Expansion Of The Chlorovirus Genus By Studies On Virus Natural History And Chlorella Host Metabolism, Cristian F. Quispe

School of Biological Sciences: Dissertations, Theses, and Student Research

Inland waters cover about 2.5 percent of our planet and harbor huge numbers of known and unknown microorganisms including viruses. Viruses likely play dynamic, albeit largely undocumented roles in regulating microbial communities and in recycling nutrients in the ecosystem. Phycodnaviruses are a genetically diverse, yet morphologically similar, group of large dsDNA-containing viruses (160- to 560-kb) that inhabit aquatic environments. Members of the genus Chlorovirus are common in freshwater. They replicate in eukaryotic, single-celled, chlorella-like green algae that normally exist as endosymbionts of protists in nature. Very little is known about the natural history of the chloroviruses and how they achieve …

Application Of Hidden Markov Model Based Methods For Gaining Insights Into Protein Domain Evolution And Function, Amit Anil Upadhyay

Doctoral Dissertations

With the explosion in the amount of available sequence data, computational methods have become indispensable for studying proteins. Domains are the fundamental structural, functional and evolutionary units that make up proteins. Studying protein domains is an important part of understanding protein function and evolution. Hidden Markov Models (HMM) are one of the most successful methods that have been applied for protein sequence and structure analysis. In this study, HMM based methods were applied to study the evolution of sensory domains in microbial signal transduction systems as well as functional characterization and identification of cellulases in metagenomics datasets. Use of HMM …

Applications Of Evolutionary Bioinformatics In Basic And Biomedical Research, Ogun Adebali

Doctoral Dissertations

With the revolutionary progress in sequencing technologies, computational biology emerged as a game-changing field which is applied in understanding molecular events of life for not only complementary but also exploratory purposes. Bioinformatics resources and tools significantly help in data generation, organization and analysis. However, there is still a need for developing new approaches built based on a biologist’s point of view. In protein bioinformatics, there are several fundamental problems such as (i) determining protein function; (ii) identifying protein-protein interactions; (iii) predicting the effect of amino acid variants. Here, I present three chapters addressing these problems from an evolutionary perspective. Firstly, …

Glucose-Fructose Likely Improves Gastrointestinal Comfort And Endurance Running Performance Relative To Glucose-Only, P. B. Wilson, S. J, Ingraham

Athletic Performance Research

This study aimed to determine whether glucose-fructose (GF) ingestion, relative to glucose-only, would alter performance, metabolism, gastrointestinal (GI) symptoms, and psychological affect during prolonged running. On two occasions, 20 runners (14 men) completed a 120-min submaximal run followed by a 4-mile time trial (TT). Participants consumed glucose-only (G) or GF (1.2:1 ratio) beverages, which supplied ~1.3 g/min of carbohydrate. Substrate use, blood lactate, psychological affect [Feeling Scale (FS)], and GI distress were measured. Differences between conditions were assessed using magnitude-based inferential statistics. Participants completed the TT 1.9% (−1.9; −4.2, 0.4) faster with GF, representing a likely benefit. FS ratings were …

A New Method For Shear Wave Speed Estimation In Shear Wave Elastography, Aaron J. Engel, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Visualization of mechanical properties of tissue can aid in noninvasive pathology diagnosis. Shear wave elastography (SWE) measures the elastic properties of soft tissues by estimation of local shear wave propagation speed. In this paper, a new robust method for estimation of shear wave speed is introduced which has the potential for simplifying continuous filtering and real-time elasticity processing. Shear waves were generated by external mechanical excitation and imaged at a high frame rate. Three homogeneous phantoms of varying elastic moduli and one inclusion phantom were imaged. Waves propagating in separate directions were filtered and shear wave speed was estimated by …

Misrepresentation Of Carbohydrate For Exercise: ‘It Is Time To Bust The Myth Of Physical Inactivity And Obesity: You Cannot Outrun A Bad Diet’, Patrick B. Wilson

Athletic Performance Research

The contention from Malhotra et al1 regarding the unimportance of carbohydrate for exercise is misguided. First, the reference they provide is an editorial2 that should not be viewed as high-quality evidence. Several oft-cited exercise studies showing benefits with high-fat diets simultaneously utilized carbohydrate restoration strategies,3 which involves “carbohydrate loading” after a high-fat diet. Thus, the evidence provided does not contradict the established belief that carbohydrate is an important fuel for endurance exercise. Second, the authors’ use of the term “carbohydrate loading” is misleading in this context. No public health organizations advocate a diet containing carbohydrate in amounts used in “carbohydrate …

Intent Classification Of Short-Text On Social Media, Hemant Purohit, Guozhu Dong, Valerie L. Shalin, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

Social media platforms facilitate the emergence of citizen communities that discuss real-world events. Their content reflects a variety of intent ranging from social good (e.g., volunteering to help) to commercial interest (e.g., criticizing product features). Hence, mining intent from social data can aid in filtering social media to support organizations, such as an emergency management unit for resource planning. However, effective intent mining is inherently challenging due to ambiguity in interpretation, and sparsity of relevant behaviors in social data. In this paper, we address the problem of multiclass classification of intent with a use-case of social data generated during crisis …

Rare Occurrences Of Free-Living Bacteria Belonging To Sedimenticola From Subtidal Seagrass Beds Associated With The Lucinid Clam, Stewartia Floridana, Aaron M. Goemann

Masters Theses

Lucinid clams and their sulfur-oxidizing endosymbionts comprise two compartments of a three-stage, biogeochemical relationship among the clams, seagrasses, and microbial communities in marine sediments. A population of the lucinid clam, Stewartia floridana, was sampled from a subtidal seagrass bed at Bokeelia Island Seaport in Florida to test the hypotheses: (1) S. floridana, like other lucinids, are more abundant in seagrass beds than bare sediments; (2) S. floridana gill microbiomes are dominated by one bacterial operational taxonomic unit (OTU) at a sequence similarity threshold level of 97% (a common cutoff for species level taxonomy) from 16S rRNA genes; …

Apply Data Clustering To Gene Expression Data, Abdullah Jameel Abualhamayl Mr.

Electronic Theses, Projects, and Dissertations

Data clustering plays an important role in effective analysis of gene expression. Although DNA microarray technology facilitates expression monitoring, several challenges arise when dealing with gene expression datasets. Some of these challenges are the enormous number of genes, the dimensionality of the data, and the change of data over time. The genetic groups which are biologically interlinked can be identified through clustering. This project aims to clarify the steps to apply clustering analysis of genes involved in a published dataset. The methodology for this project includes the selection of the dataset representation, the selection of gene datasets, Similarity Matrix Selection, …

Biomechanical Performances Of Networked Polyethylene Glycol Diacrylate: Effect Of Photoinitiator Concentration, Temperature, And Incubation Time, Morshed Khandaker, Albert Orock, Stefano Tarantini, Jeremiah White, Ozlem Yasar

Publications and Research

Nutrient conduit networks can be introduced within the Polyethylene Glycol Diacrylate (PEGDA) tissue construct to enable cells to survive in the scaffold. Nutrient conduit networks can be created on PEGDA by macrochannel to nanochannel fabrication techniques. Such networks can influence the mechanical and cell activities of PEGDA scaffold. There is no study conducted to evaluate the effect of nutrient conduit networks on the maximum tensile stress and cell activities of the tissue scaffold.The study aimed to explore the influence of the network architecture on the maximum tensile stress of PEGDA scaffold and compared with the nonnetworked PEGDA scaffold. Our study …

A Survey Of The Common Loon (Gavia Immer) Genome Reveals Patterns Of Natural Selection, Zach G. Gayk

All NMU Master's Theses

With rapid advances in Next-Generation Sequencing technology, comparative genomics has become a viable method for studying the adaptation of species to their environment at the genome level. I investigated this in common loons (Gavia immer)—for which molecular adaptation has not been characterized—by finding signatures of positive selection as evidence for genomic adaptation.

I used Illumina short read sequencing data from a single female common loon to produce a fragmented assembly of the common loon (Gavia immer) genome. The resulting assembly had a contig N50 of 814 bp, a total length of 767,326,331 bp, and 45.7 % …

Early Seed Development Responses In Cereals Under Environmental Stresses, Kevin Begcy

Kevin Begcy

Plants are influenced by a large number of environmental factors. The search for higher yields at lower costs requires detailed knowledge of physiology, biochemistry, molecular and genetic level of plants, in order to optimize the relationship between different factors of production for maximum performance. Reproductive development has been demonstrated to be especially highly sensitive to environmental stresses. Within environmental stresses, drought and heat stress are the major restrictors of food production worldwide. With decreasing supplies of freshwater, increase in average temperature and predictions for the increased frequency of extreme precipitation events, there is a critical need for developing crops that …

Effectiveness Of Group Kickboxing As A Means To Improve Gait And Balance In Individuals With Ms, Kurt Jackson, Kimberly Edginton Bigelow, Christina Cooper, Harold L. Merriman

Harold L. Merriman

In recent years, there has been a particular emphasis on identifying and delivering appropriate therapeutic interventions that address the significant balance and gait impairments that affect individuals with multiple sclerosis (MS). Group interventions implemented in community settings have been especially of interest, including tai chi classes. Recently, the authors conducted a preliminary study to examine whether group kick-boxing, which requires more vigorous movements, might be a feasible intervention. Initial findings showed promise and led the authors to pursue a more rigorous follow-up study, with the objective of determining whether a 5-week group kickboxing class improved clinical measures of balance and …

The Evolution Of Thermotolerance A Characterization Of A Directionally Evolved Cyanobacterium, Nathen Emil Bopp

Masters Theses

Chaperone proteins are essential components in the maintenance and turnover of the proteome. Many chaperones play integral functions in the folding and unfolding of cellular substrates under many conditions, including heat stress. Most chaperones can be characterized into two categories; the typical ATP dependent chaperones and the ATP independent chaperones. One ATP independent chaperone class it the Small Heat Shock Proteins (sHSPs), which as molecular life vests and are thought to protect misfolding proteins from irreversible aggregation. One such organism, the cyanobacterium Synechocystis sp. PCC 6803, is an excellent model for the study and understanding of these proteins and their …

Complete Genome Sequence Of Spiroplasma Turonicum Strain Tab4ct, A Parasite Of A Horse Fly, Haematopota Sp. (Diptera: Tabanidae)., Robert E. Davis, Jonathan Shao, Yan Zhao, Gail E. Gasparich, Brady J. Gaynor, Nicole Donofrio

Gail Gasparich

Computational Methods For Biomarker Identification In Complex Disease, Amin Ahmadi Adl

USF Tampa Graduate Theses and Dissertations

In a modern systematic view of biology, cell functions arise from the interaction between molecular components. One of the challenging problems in systems biology with high-throughput measurements is discovering the important components involved in the development and progression of complex diseases, which may serve as biomarkers for accurate predictive modeling and as targets for therapeutic purposes. Due to the non-linearity and heterogeneity of these complex diseases, traditional biomarker identification approaches have had limited success at finding clinically useful biomarkers. In this dissertation we propose novel methods for biomarker identification that explicitly take into account the non-linearity and heterogeneity of complex …