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3,377 full-text articles. Page 6 of 129.

Transcription Factor Binding Site Clusters Identify Target Genes With Similar Tissue-Wide Expression And Buffer Against Mutations., Peter Rogan, Ruipeng Lu 2019 The University of Western Ontario

Transcription Factor Binding Site Clusters Identify Target Genes With Similar Tissue-Wide Expression And Buffer Against Mutations., Peter Rogan, Ruipeng Lu

Biochemistry Publications

Background: The distribution and composition of cis-regulatory modules composed of transcription factor (TF) binding site (TFBS) clusters in promoters substantially determine gene expression patterns and TF targets. TF knockdown experiments have revealed that TF binding profiles and gene expression levels are correlated. We use TFBS features within accessible promoter intervals to predict genes with similar tissue-wide expression patterns and TF targets using Machine Learning (ML). Methods: Bray-Curtis Similarity was used to identify genes with correlated expression patterns across 53 tissues. TF targets from knockdown experiments were also analyzed by this approach to set up the ML framework. TFBSs were ...


Evaluating Predixcan’S Ability To Predict Differential Expression Between Alcoholics And Non-Alcoholics, John E. Drake Jr 2019 Virginia Commonwealth University

Evaluating Predixcan’S Ability To Predict Differential Expression Between Alcoholics And Non-Alcoholics, John E. Drake Jr

Theses and Dissertations

PrediXcan is a recent software for the imputation of gene expression from genotype data alone. Using an overlapping set of transcriptome datasets from postmortem brain tissues of donors with alcohol use disorder and neurotypical controls, which were generated by two different platforms (e.g., Arraystar and Affymetrix), and an additional unrelated transcriptome dataset from lung tissue, we sought to evaluate PrediXcan’s ability to impute gene expression and identify differentially expressed genes. From the Arraystar platform, 1.3% of matched genes between the measured and imputed expression had a Pearson correlation ≥ 0.5. Our attempt to replicate this finding using ...


The Impact Of Household Biocides And Antibiotics On Aquatic Microbial Community Composition, Abdulaziz Saud M Alrashdi 2019 Michigan Technological University

The Impact Of Household Biocides And Antibiotics On Aquatic Microbial Community Composition, Abdulaziz Saud M Alrashdi

Dissertations, Master's Theses and Master's Reports

Triclosan (TCS) is antimicrobial agent that is used in a lot of consumer products, including toothpaste, liquid and bar soap, and cosmetics. TCS has been found in many lakes and rivers in the United States. However, The Food and Drug Administration (FDA) banned TCS recently and it will no longer be used in household products. Despite the recent ban, TCS is known to persist in the environment and may have long-term impacts. We conducted an experiment on using fresh water from three locations Houghton, Green Bay and the Huron Mountains. Our goals in the study is to assess the impact ...


Empathi: An Ontology For Emergency Managing And Planning About Hazard Crisis, Manas Gaur, Kaeedeh Shekarpour, Amelia Gyrard, Amit P. Sheth 2019 Wright State University - Main Campus

Empathi: An Ontology For Emergency Managing And Planning About Hazard Crisis, Manas Gaur, Kaeedeh Shekarpour, Amelia Gyrard, Amit P. Sheth

Kno.e.sis Publications

In the domain of emergency management during hazard crises, having sufficient situational awareness information is critical. It requires capturing and integrating information from sources such as satellite images, local sensors and social media content generated by local people.
A bold obstacle to capturing, representing and integrating such heterogeneous and diverse information is lack of a proper ontology which properly conceptualizes this domain, aggregates and unifies datasets. Thus, in this paper, we introduce empathi ontology which conceptualizes the core concepts describing the domain of emergency managing and planning of hazard crises.
Although empathi has a coarse-grained view, it considers the necessary ...


A Genome Wide Survey Of The Insertion Sequences In Halanaerobium Hydrogeniformans, A Haloalkaliphilic Anaerobic Bacterium, Kody Austin Bassett 2019 Missouri University of Science and Technology

A Genome Wide Survey Of The Insertion Sequences In Halanaerobium Hydrogeniformans, A Haloalkaliphilic Anaerobic Bacterium, Kody Austin Bassett

Masters Theses

"Insertion sequences (IS) are the smallest prokaryotic transposable elements. These mobile genes are highly diverse in size and structure, making them difficult to study. The transposition activity of insertion sequences has a significant role in evolution by enabling genomic plasticity via genome rearrangements. Insertion sequences are largely uncharacterized and thus methods to improve the ability to accurately identify, annotate, and infer genomic impact of insertion sequences is limited. A sequential set of methods using readily available genomic and bioinformatic tools was developed to accurately identify insertion sequences. This method was used to perform an entire genome survey of Halanaerobium hydrogeniformans ...


Methods For Joint Normalization And Comparison Of Hi-C Data, John C. Stansfield 2019 Virginia Commonwealth University

Methods For Joint Normalization And Comparison Of Hi-C Data, John C. Stansfield

Theses and Dissertations

The development of chromatin conformation capture technology has opened new avenues of study into the 3D structure and function of the genome. Chromatin structure is known to influence gene regulation, and differences in structure are now emerging as a mechanism of regulation between, e.g., cell differentiation and disease vs. normal states. Hi-C sequencing technology now provides a way to study the 3D interactions of the chromatin over the whole genome. However, like all sequencing technologies, Hi-C suffers from several forms of bias stemming from both the technology and the DNA sequence itself. Several normalization methods have been developed for ...


Predicting Evolution And Inferring Its Consequences, Silas Benjamin Tittes 2019 University of Colorado at Boulder

Predicting Evolution And Inferring Its Consequences, Silas Benjamin Tittes

Ecology & Evolutionary Biology Graduate Theses & Dissertations

This dissertation concerns the roles of genetic and environmental factors in producing trait variation in evolving populations, with an emphasis on the creation and use of statistical tools that facilitate predictions. The research concerns evolution across a variety of spatial and temporal scales and environmental conditions. In each study I employ statistical approaches to make predictions about how observed trait variation is derived from variation due to the environment, or genetics, or the interaction between the two. The first chapter investigates the evolution of species' performance curves through the construction of a Bayesian model that facilitates comparisons among groups. The ...


Gene Ontology-Guided Force-Directed Visualization Of Protein Interaction Networks, James Lowell King 2019 Nova Southeastern University

Gene Ontology-Guided Force-Directed Visualization Of Protein Interaction Networks, James Lowell King

CCE Theses and Dissertations

Protein interaction data is being generated at unprecedented rates thanks to advancements made in high throughput techniques such as mass spectrometry and DNA microarrays. Biomedical researchers, operating under budgetary constraints, have found it difficult to scale their efforts to keep up with the ever-increasing amount of available data. They often lack the resources and manpower required to analyze the data using existing methodologies. These research deficiencies impede our ability to understand diseases, delay the advancement of clinical therapeutics, and ultimately costs lives.

One of the most commonly used techniques to analyze protein interaction data is the construction and visualization of ...


Citationally Enhanced Semantic Literature Based Discovery, John David Fleig 2019 Nova Southeastern University

Citationally Enhanced Semantic Literature Based Discovery, John David Fleig

CCE Theses and Dissertations

We are living within the age of information. The ever increasing flow of data and publications poses a monumental bottleneck to scientific progress as despite the amazing abilities of the human mind, it is woefully inadequate in processing such a vast quantity of multidimensional information. The small bits of flotsam and jetsam that we leverage belies the amount of useful information beneath the surface. It is imperative that automated tools exist to better search, retrieve, and summarize this content. Combinations of document indexing and search engines can quickly find you a document whose content best matches your query - if the ...


Comparative Analysis Of Dna Isolation Methods For The Human Microbiome, Hannah Chatwin 2019 University of Colorado, Boulder

Comparative Analysis Of Dna Isolation Methods For The Human Microbiome, Hannah Chatwin

Undergraduate Honors Theses

The human microbiome is made up of millions of microbes coexisting in and on us with involvement in health and disease. The exact mechanisms by which this occurs have yet to be fully elucidated. Due to high variability in the composition of each person’s microbiome, it requires large numbers of people to begin to identify some of these processes. A major road block to generating large data sets for analysis is the high cost of DNA isolation from large collections of phenotypically well-characterized human subjects. This study explores the possible application of an inexpensive alternative DNA isolation method utilizing ...


Sequence Analysis Of The Ren1 Genomic Region From The Grapevine ‘Kishmish Vatkana’, Dani Joseph 2019 Missouri State University

Sequence Analysis Of The Ren1 Genomic Region From The Grapevine ‘Kishmish Vatkana’, Dani Joseph

MSU Graduate Theses

The REN1 region of the grapevine ‘Kishmish Vatkana’ was mapped as the locus that confers resistance to the economically important disease, grape powdery mildew. The purpose of this work was to extend the nucleotide sequence information of this region. By sequencing a heretofore unknown bacterial artificial chromosome clone, the sequence information of this region was extended by 46,890 nucleotides. Sequencing was performed using the third-generation sequencing method, named Oxford Nanopore Technology (ONT). In order to improve the accuracy of the sequence data, a modified ONT library preparation method was developed. ONT sequencing of a library prepared with the modified ...


Post-Transcriptional Regulation Of The Eulkaryotic Transcriptome By The Covalent Rna Modicication N6-Methyladenosine, Stephen J. Anderson 2019 University of Pennsylvania

Post-Transcriptional Regulation Of The Eulkaryotic Transcriptome By The Covalent Rna Modicication N6-Methyladenosine, Stephen J. Anderson

Publicly Accessible Penn Dissertations

Post-Transcriptional regulation of the eukaryotic transcriptome by the covalent RNA modification N6-methyladenosine

Stephen James Anderson

Brian Gregory

Once a messenger RNA molecule is transcribed, a myriad of RNA fate decisions must be made. How these fate decisions are made is often unclear, and elucidating factors determining these fate outcomes is an essential task in order to fully understand gene regulation. One poorly- understood but undoubtedly important factor in post-transcriptional gene regulation is the covalent modification of ribonucleotides. Much like DNA can have chemical groups added to a nucleotide within its primary sequence, RNA can be modified in a similar manner ...


Genetic Insights Into Latent Autoimmune Diabetes In Adults, Rajashree Mishra 2019 University of Pennsylvania

Genetic Insights Into Latent Autoimmune Diabetes In Adults, Rajashree Mishra

Publicly Accessible Penn Dissertations

‘Latent autoimmune diabetes in adults’ (LADA) is a controversial subtype of diabetes characterized by initial insulin independency and the presence of diabetes associated autoantibodies. As a result, LADA is often misclassified and can represent 5-10% of apparent type 2 diabetes (T2D) cases and is potentially more prevalent than childhood-onset type 1 diabetes (T1D). Despite LADA sharing features with the two better characterized classic diabetes subtypes, the genetic etiology of LADA remains largely unknown. Once there is a more accurate definition of LADA, there will be an improvement in diabetes classification and consequently better treatment and therapeutic interventions. The objective of ...


Detecting Ancient Balancing Selection: Methods And Application To Human, Katherine Siewert 2019 University of Pennsylvania

Detecting Ancient Balancing Selection: Methods And Application To Human, Katherine Siewert

Publicly Accessible Penn Dissertations

Balancing selection can maintain genetic variation in a population over long evolutionary time periods. Identifying genomic loci under this type of selection not only elucidates selective pressures and adaptations but can also help interpret common genetic variation contributing to disease. Summary statistics which capture signatures in the site frequency spectrum are frequently used to scan the genome to detect loci showing evidence of balancing selection. However, these approaches have limited power because they rely on imprecise signatures such as a general excess of heterozygosity or number of genetic variants. A second class of statistics, based on likelihoods, have higher power ...


Mendelian Randomization And Single Cell Deconvolution: Two Problems In Statistics Genetics, Xuran Wang 2019 University of Pennsylvania

Mendelian Randomization And Single Cell Deconvolution: Two Problems In Statistics Genetics, Xuran Wang

Publicly Accessible Penn Dissertations

Finding interpretable targets within the genome for diseases is a primary goal of biomedical research. This thesis focuses on developing statistical models and methods for analysis of high throughput genomic and transcriptomic sequencing data with the goal of finding actionable targets of two types, disease-associated genes and disease-implicated cell types.

Traditional genome wide association studies(GWAS) focus on finding the association between genetic variants and diseases. However, GWAS results are often difficult to interpret, and they do not directly lead to an understanding of the true biological mechanism of diseases. Following GWAS findings, we can study the causal effect by ...


The Human Lung Viral Microbiome In Health And Disease, Arwa Abbas 2019 University of Pennsylvania

The Human Lung Viral Microbiome In Health And Disease, Arwa Abbas

Publicly Accessible Penn Dissertations

Vast and diverse microbial communities (the microbiome) are distinct at different human body sites and strongly influence health and disease. Specifically, the respiratory tract microbiome is thought to influence outcomes after lung transplantation, the only therapeutic option for end-stage lung diseases. Studies dissecting the role of the microbiome on pulmonary health should also include the viral microbiome (virome), which is less-studied due to unique challenges in identifying these small, diverse, self-replicating genetic elements. Organ transplantation is accompanied by immunosuppression, which can result in reactivation of latent viruses, transfer of viruses from organ donor to recipient, and increased susceptibility to viral ...


Mass Spectrometry: An Ideal Method For Rna Modification Analysis, Samuel Peter Wein 2019 University of Pennsylvania

Mass Spectrometry: An Ideal Method For Rna Modification Analysis, Samuel Peter Wein

Publicly Accessible Penn Dissertations

Currently there is no good way to measure and find the exact location of multiple RNA modifications. Existing technology can effectively find single varieties of modifications, but cannot identify co-occurrence. As the field of proteomics has shown, mass spectrometry is a powerful and versatile technique assessing broad ranges of chemical modifications in the context of the cellular environment. In this project I used our expertise in proteomics to build a mass spectrometry based platform for identifying RNA modifications. I have since set up both software and analytical platforms querying RNA modifications, and used this platform to survey human tRNA samples ...


Algorithms For Synteny-Based Phylostratigraphy And Gene Origin Classification, Zebulun Arendsee 2019 Iowa State University

Algorithms For Synteny-Based Phylostratigraphy And Gene Origin Classification, Zebulun Arendsee

Graduate Theses and Dissertations

With every newly sequenced species we discover hundreds of novel protein coding genes. Many of these "orphan" genes have been experimentally proven to have dramatic functions in development, sexual dimorphism, pathogen resistance, and social traits like symbiosis. Whereas in the past, researchers viewed genes as the product of continuous variation acting on ancient material, we now know that novel genes may arise de novo from non-genic sequence. Thus evolutionary experimentation is not limited to tweaking existing genes or their regulatory patterns. Any orphan genes that arose in the distant past, should appear today as lineage-specific genes (or gene families). The ...


Data Collection Curated With An Application Ontology Describes The Methods And Results Upon Performing An Ex-Vivo Voltage-Clamp Assay On Outer Hair Cells Of The Mammalian Cochlea, Brenda Farrell, Jason Bengtson 2019 Kansas State University

Data Collection Curated With An Application Ontology Describes The Methods And Results Upon Performing An Ex-Vivo Voltage-Clamp Assay On Outer Hair Cells Of The Mammalian Cochlea, Brenda Farrell, Jason Bengtson

BCM Research Data

This data collection describes the electrical properties of outer hair cells isolated from the mammalian cochlea of the domestic guinea pig. This data was obtained by performing whole-cell patch clamp voltage clamp assay on cells and monitoring the electrical admittance during a DC voltage ramp. The membrane capacitance was then calculated at each membrane potential from this admittance, and the voltage-independent and voltage-dependent membrane capacitance was determined upon further analysis. In some case the DC conductance was also measured by interrogation of the cell with voltage-step function which was calculated from the change in the mean steady-state current with respect ...


A Computational Method For Predicting Functional Effects Of Cancer-Related Genetic Sequence Variants, Bofei None Wang 2019 University of Texas at El Paso

A Computational Method For Predicting Functional Effects Of Cancer-Related Genetic Sequence Variants, Bofei None Wang

Open Access Theses & Dissertations

Rapid advances in next generation sequencing (NGS) technologies provide many oppor- tunities to identify associations between genetic sequence variants (GSV) and diseases, which may lead to better clinical diagnosis and treatments. OncoMiner is a bioinformatics pipeline developed at UTEP (OncoMiner.utep.edu) for mining NGS data. It can identify exonic sequence variants, link them with associated literatures, visualize genomic locations and compare their occurrence frequencies among dierent groups. However, the current version of OncoMiner is limited to accepting only a specic input le format provided by the Otogenetics NGS Lab Services. The main objectives of my current work are (1 ...


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