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Fractal Analysis Of Dna Sequences, Christian G. Arias, Pedro Antonio Moreno Phd, Carlos Tellez 2016 Universidad del Valle - Colombia - Georgia Institute of Technology

Fractal Analysis Of Dna Sequences, Christian G. Arias, Pedro Antonio Moreno Phd, Carlos Tellez

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Strategies To Avoid Overfitting Of Mcmc Bayesian Learning In Some Biological Applications, Diego M. Garcia 2016 Universidad del Valle - Colombia

Strategies To Avoid Overfitting Of Mcmc Bayesian Learning In Some Biological Applications, Diego M. Garcia

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Using Citizen Science And Remote Sensing Data To Model Hummingbird Migration, Sarah R. Supp, Laura J. Graham, Frank A. La Sorte, Tina A. Cormier, Gil Bohrer, Donald Powers, Susan Wethington, Kevin Guay, Patrick Jantz, Scott Goetz, Catherine H. Graham 2016 University of Maine

Using Citizen Science And Remote Sensing Data To Model Hummingbird Migration, Sarah R. Supp, Laura J. Graham, Frank A. La Sorte, Tina A. Cormier, Gil Bohrer, Donald Powers, Susan Wethington, Kevin Guay, Patrick Jantz, Scott Goetz, Catherine H. Graham

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Modeling The Spread Of The Zika Virus At The 2016 Olympics, Triona S. Matheson, Brian Satterthwaite, Hannah L. Callender 2016 University of Portland

Modeling The Spread Of The Zika Virus At The 2016 Olympics, Triona S. Matheson, Brian Satterthwaite, Hannah L. Callender

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Analyzing The Γδ T Cell Receptor Sequences Of Patients With Celiac Disease, Alanna P. Gary 2016 University of Chicago

Analyzing The Γδ T Cell Receptor Sequences Of Patients With Celiac Disease, Alanna P. Gary

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Modeling Of Human Circadian Clock: Per3 Provides Molecular Support For Behavioral Observations, Ha T. Vu 2016 Colgate University

Modeling Of Human Circadian Clock: Per3 Provides Molecular Support For Behavioral Observations, Ha T. Vu

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


1. Types Of Alignment: Presentations & Demos Assignment, Sarah O'Leary-Driscoll 2016 Illinois Mathematics and Science Academy

1. Types Of Alignment: Presentations & Demos Assignment, Sarah O'Leary-Driscoll

Sequence Alignments

Pairwise Alignment: DNA

Pairwise Alignment: Protein

Multiple Sequence Alignment: DNA

Multiple Sequence Alignment: Protein


Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers 2016 The Graduate Center, City University of New York

Comparative Population Genomics And Speciation Of Snakes Across The North American Deserts, Edward A. Myers

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Understanding the process of speciation is of central interest to evolutionary biologists. Speciation can be studied using a phylogeographic approach, by identifying regions that promote lineage divergence, addressing whether speciation has occurred with gene flow, and when extended to multiple taxa, addressing if the same patterns of speciation are shared across codistributed groups with different ecologies. Here I examine the comparative phylogeographic histories and population genomics of thirteen snake taxa that are widely distributed and co-occur across the arid southwest of North America. I first quantify the degree to which these species groups have a shared history of population divergence ...


Optimizing Gdna Purification And Qpcr Techniques For Specific Detection And Enumeration Of Probiotic Bacteria, Katelynn C. Lee, Jennifer VanderKelen, Christopher Kitts 2016 California Polytechnic State University, San Luis Obispo

Optimizing Gdna Purification And Qpcr Techniques For Specific Detection And Enumeration Of Probiotic Bacteria, Katelynn C. Lee, Jennifer Vanderkelen, Christopher Kitts

STAR (STEM Teacher and Researcher) Program Posters

Probiotics are live microorganisms, like bacteria and yeast, which are thought to provide health benefits when ingested. Large manufacturers produce blends of probiotics for supplementing the diets of agriculturally important animals. Commercial probiotic products are labeled with the number of cells present at the time of manufacture. Our assignment was to develop an assay which can be used to quantify the number of specific lactic acid bacteria present in certain probiotic products, thus verifying the number reported on the product labels. This quantification process involves isolating genomic DNA (gDNA) from the given samples and then running the DNA through a ...


Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager 2016 University of Wisconsin-La Crosse

Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager

Spora: A Journal of Biomathematics

The development of an embryo from a fertilised egg to a multicellular organism proceeds through numerous steps, with the formation of the three germ layers (endoderm, mesoderm, ectoderm) being one of the first. In this paper we study the mesendoderm (the tissue that collectively gives rise to both mesoderm and endoderm) gene regulatory network for two species, \textit{Xenopus laevis} and the axolotl (\textit{Ambystoma mexicanum}) using Boolean networks. We find that previously-established bistability found in these networks can be reproduced using this Boolean framework, provided that some assumptions used in previously-published differential equations models are relaxed. We conclude by ...


Bayesian Networks To Assess The Newborn Stool Microbiome, William E. Bennett Jr. 2016 Washington University in St. Louis

Bayesian Networks To Assess The Newborn Stool Microbiome, William E. Bennett Jr.

Engineering and Applied Science Theses & Dissertations

In human stool, a large population of bacterial genes and transcripts from hundreds of genera coexist with host genes and transcripts. Assessments of the metagenome and transcriptome are particularly challenging, since there is a great deal of sequence overlap among related species and related genes. We sequenced the total RNA content from stool samples in a neonate using previously-described methods. We then performed stepwise alignment of different populations of RNA sequence reads to different indices, including ribosomal databases, the human genome, and all sequenced bacterial genomes. Each pool of RNA at each alignment step was subjected to compression to assess ...


Using Electronic Health Record Data To Identify Prostate Cancer Patients That May Qualify For Active Surveillance, Andrew J. Knighton, Tom Belnap, Kim Brunisholz, Kelly Huynh, Jay T. Bishoff 2016 Intermountain Healthcare

Using Electronic Health Record Data To Identify Prostate Cancer Patients That May Qualify For Active Surveillance, Andrew J. Knighton, Tom Belnap, Kim Brunisholz, Kelly Huynh, Jay T. Bishoff

eGEMs (Generating Evidence & Methods to improve patient outcomes)

Introduction: The introduction of the protein-specific antigen (PSA) test in care means that prostate cancer (PCa) is being detected earlier and more frequently. The result of increased screening using PSA, digital rectal examination and awareness of prostate was an increase in the number of men with low risk cancers. Active surveillance has become a viable alternative to immediate treatment with surgery, radiation and other forms of localized treatment. Evidence suggests that there is no significant difference in mortality rates between AS and surgery. In addition, patients may potentially delay other complications associated with surgery, radiation or deprivation therapy.

Methods: This ...


Structure-Function Analysis And Characterization Of Metalloproteins., Sen Yao 2016 University of Louisville

Structure-Function Analysis And Characterization Of Metalloproteins., Sen Yao

Electronic Theses and Dissertations

Metalloproteins are proteins that can bind at least one metal ion as a cofactor. They utilize metal ions for a variety of biological purposes, and are essential for all domains of life. Due to the ubiquity of metalloprotein’s involvement across these processes across all domains of life, how proteins coordinate metal ions for different biochemical functions is of great relevance to understanding the implementation of these biological processes. One of the most important aspects of metal binding is its coordination geometry (CG), which often implies functional activities. Most of the current studies are based on the assumption of previously ...


Computational Analyses Of Mrna Ribosome Loading In Arabidopsis Thaliana, Joseph Benjamin Ernest 2016 University of Tennessee, Knoxville

Computational Analyses Of Mrna Ribosome Loading In Arabidopsis Thaliana, Joseph Benjamin Ernest

Doctoral Dissertations

Translation of mRNA into protein is a critical step in gene expression, but the principles guiding its regulation at the genome level are not completely understood. Translation can be quantified at a genome scale by measuring the ribosome loading of mRNA—the extent to which mRNA is associated with ribosomes. In this dissertation, I present investigations into how genome-wide ribosome loading is controlled in Arabidopsis thaliana. In chapter 1, I give an overview of regulation of ribosome loading and translation. In chapter 2, I present research demonstrating for the first time that genome-wide ribosome loading in plants is partially controlled ...


Protein Residue-Residue Contact Prediction Using Stacked Denoising Autoencoders, Joseph Bailey Luttrell IV 2016 The University of Southern Mississippi

Protein Residue-Residue Contact Prediction Using Stacked Denoising Autoencoders, Joseph Bailey Luttrell Iv

Honors Theses

Protein residue-residue contact prediction is one of many areas of bioinformatics research that aims to assist researchers in the discovery of structural features of proteins. Predicting the existence of such structural features can provide a starting point for studying the tertiary structures of proteins. This has the potential to be useful in applications such as drug design where tertiary structure predictions may play an important role in approximating the interactions between drugs and their targets without expending the monetary resources necessary for preliminary experimentation. Here, four different methods involving deep learning, support vector machines (SVMs), and direct coupling analysis were ...


Metabolomics Approaches To Decipher The Antibacterial Mechanisms Of Yerba Mate (Ilex Paraguariensis) Against Staphylococcus Aureus And Salmonella Enterica Serovar Typhimurium, Caroline Sue Rempe 2016 University of Tennessee, Knoxville

Metabolomics Approaches To Decipher The Antibacterial Mechanisms Of Yerba Mate (Ilex Paraguariensis) Against Staphylococcus Aureus And Salmonella Enterica Serovar Typhimurium, Caroline Sue Rempe

Doctoral Dissertations

The increasing prevalence of drug-resistant pathogens is an urgent problem that requires novel methods of bacterial control. Plant extracts inhibit bacterial pathogens and could contain antibacterial compounds with novel mechanisms of action. Yerba mate, a common South American beverage made from Ilex paraguariensis, has antibiotic activity against a broad range of bacterial pathogens. In this work, an attempt was first made to characterize the antibacterial source of an aqueous yerba mate extract by generating a series of extract fractions, collecting GC-MS and antibacterial activity profiles, and then ranking the hundreds of compounds by their presence in fractions with high antibacterial ...


Data Development And Analysis Pathways For Marine Mammals And Turtles: Creating A User Interface, Sarina Fernandez, Warren Asfazadour, Eric Archer, Lisa Komoroske 2016 California Polytechnic State University, San Luis Obispo

Data Development And Analysis Pathways For Marine Mammals And Turtles: Creating A User Interface, Sarina Fernandez, Warren Asfazadour, Eric Archer, Lisa Komoroske

STAR (STEM Teacher and Researcher) Program Posters

A major obstacle in genetic research is developing streamlined methods for analyzing large amounts of data. The statistical computer programming language R provides users with the ability to develop packages containing specific functions in order to create more accessible data analysis pipelines. However, writing code in R can still be intimidating to those with little to no coding experience. Fortunately, the R package shiny provides a framework for developing web applications based on R functions. Using shiny, we developed a user-friendly web application containing functions of the R package strataG. The strataG package contains several functions for summarizing genetic data ...


Use Of Clustering Techniques For Protein Domain Analysis, Eric Rodene 2016 University of Nebraska - Lincoln

Use Of Clustering Techniques For Protein Domain Analysis, Eric Rodene

Computer Science and Engineering: Theses, Dissertations, and Student Research

Next-generation sequencing has allowed many new protein sequences to be identified. However, this expansion of sequence data limits the ability to determine the structure and function of most of these newly-identified proteins. Inferring the function and relationships between proteins is possible with traditional alignment-based phylogeny. However, this requires at least one shared subsequence. Without such a subsequence, no meaningful alignments between the protein sequences are possible. The entire protein set (or proteome) of an organism contains many unrelated proteins. At this level, the necessary similarity does not occur. Therefore, an alternative method of understanding relationships within diverse sets of proteins ...


The Histone H3k9 Demethylase Kdm3a Promotes Anoikis By Transcriptionally Activating Pro-Apoptotic Genes Bnip3 And Bnip3l, Victoria E. Pedanou, Stephane Gobeil, Sebastien Tabaries, Tessa M. Simone, Lihua Julie Zhu, Peter M. Siegel, Michael R. Green 2016 University of Massachusetts Medical School

The Histone H3k9 Demethylase Kdm3a Promotes Anoikis By Transcriptionally Activating Pro-Apoptotic Genes Bnip3 And Bnip3l, Victoria E. Pedanou, Stephane Gobeil, Sebastien Tabaries, Tessa M. Simone, Lihua Julie Zhu, Peter M. Siegel, Michael R. Green

Open Access Articles

Epithelial cells that lose attachment to the extracellular matrix undergo a specialized form of apoptosis called anoikis. Here, using large-scale RNA interference (RNAi) screening, we find that KDM3A, a histone H3 lysine 9 (H3K9) mono- and di-demethylase, plays a pivotal role in anoikis induction. In attached breast epithelial cells, KDM3A expression is maintained at low levels by integrin signaling. Following detachment, integrin signaling is decreased resulting in increased KDM3A expression. RNAi-mediated knockdown of KDM3A substantially reduces apoptosis following detachment and, conversely, ectopic expression of KDM3A induces cell death in attached cells. We find that KDM3A promotes anoikis through transcriptional activation ...


End Sequence Analysis Toolkit (Esat) Expands The Extractable From Single Cell Rna-Seq Experiments, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim Artyomov, Manuel Garber 2016 University of Massachusetts Medical School

End Sequence Analysis Toolkit (Esat) Expands The Extractable From Single Cell Rna-Seq Experiments, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim Artyomov, Manuel Garber

Open Access Articles

RNA-seq protocols that focus on transcript termini are well-suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). As predicted by the telescripting model for transcriptional bursts, ESAT detected an LPS-stimulated shift to shorter 3'-isoforms that was not evident by conventional computational methods. Then, droplet-based microfluidics was used to generate 1,000 ...


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