Computational Biology Commons^™

The Host Gatekeeper: Using The Flagellar Pathway To Understand Symbiont Host Adaptation, Adam R. Pollio

Graduate Theses, Dissertations, and Problem Reports

The acquisition of microbial partners is a strategy used by a diverse group of arthropods to overcome ecological barriers that might normally make certain niches uninhabitable. The unique phylogenetic opportunities attainable from the natural experiment of the Sodalis-allied clade allow for better understanding of how molecular structures evolve through time. Here, we focus on the evolution of the flagellar synthesis pathway, due to its complexity and ability to diverge in response to ecological pressures. We used this molecular pathway and natural experiment to show that normal evolutionary outcomes associated with symbiosis (i.e., genome reduction) do not explain the predicted conservation …

Evaluation Of The Performance Of Probabilistic Genotyping Software On Complex Mixture Samples, Kristen Newland

Graduate Theses, Dissertations, and Problem Reports

Probabilistic genotyping systems use sophisticated algorithms to aid DNA analysts with complex mixture interpretation. These systems are used to generate a likelihood ration (LR) which is used to provide the analyst with the statistical weight of the match between an evidence profile and a known contributor. Complex mixtures occur from samples consisting of more than two contributors and samples that have experienced degradation or consist of low template quantity.

This study was performed to compare the performance of three mixture analysis software tools on the same set of samples to determine the capabilities of each software, false inclusions, and false …

Mathematical Models Of Cellular Signaling And Supramolecular Self-Assembly, Pratip Rana

Theses and Dissertations

Synthetic biologists endeavor to predict how the increasing complexity of multi-step signaling cascades impacts the fidelity of molecular signaling, whereby cellular state information is often transmitted with proteins diffusing by a pseudo-one-dimensional stochastic process. We address this problem by using a one-dimensional drift-diffusion model to derive an approximate lower bound on the degree of facilitation needed to achieve single-bit informational efficiency in signaling cascades as a function of their length. We find that a universal curve of the Shannon-Hartley form describes the information transmitted by a signaling chain of arbitrary length and depends upon only a small number of physically …

Machine Learning Prediction Of Glioblastoma Patient One-Year Survival, Andrew Du '20, Warren Mcgee, Jane Y. Wu

Student Publications & Research

Glioblastoma (GBM) is a grade IV astrocytoma formed primarily from cancerous astrocytes and sustained by intense angiogenesis. GBM often causes non-specific symptoms, creating difficulty for diagnosis. This study aimed to utilize machine learning techniques to provide an accurate one-year survival prognosis for GBM patients using clinical and genomic data from the Chinese Glioma Genome Atlas. Logistic regression (LR), support vector machines (SVM), random forest (RF), and ensemble models were used to identify and select predictors for GBM survival and to classify patients into those with an overall survival (OS) of less than one year and one year or greater. With …

A Transcriptomic Exploration Of Hawaiian Drosophilid Development And Evolution, Madeline M. Chenevert

University of New Orleans Theses and Dissertations

One in four known species of fruit flies inhabit the Hawaiian Islands. From a small number of colonizing flies, a wide range of species evolved, some of which managed to reverse-colonize other continental environments. In order to explore the developmental pathways, which separate the Hawaiian Drosophila proper and the Scaptomyza group that contains reverse-colonized species, the transcriptomes of two better-known species in each group, Scaptomyza anomala and Drosophila grimshawi, were analyzed to find changes in gene expression between the two groups. This study describes a novel transcriptome for S. anomala studies as well as unusual changes in gene expression …

Overlap Matrix Completion For Predicting Drug-Associated Indications, Menhyun Yang, Huimin Luo, Yaohang Li, Fang-Xiang Wu, Jianxin Wang

Computer Science Faculty Publications

Identification of potential drug-associated indications is critical for either approved or novel drugs in drug repositioning. Current computational methods based on drug similarity and disease similarity have been developed to predict drug-disease associations. When more reliable drug- or disease-related information becomes available and is integrated, the prediction precision can be continuously improved. However, it is a challenging problem to effectively incorporate multiple types of prior information, representing different characteristics of drugs and diseases, to identify promising drug-disease associations. In this study, we propose an overlap matrix completion (OMC) for bilayer networks (OMC2) and tri-layer networks (OMC3) to predict potential drug-associated …

Deepep: A Deep Learning Framework For Identifying Essential Proteins, Min Zeng, Min Li, Fang-Xiang Wu, Yaohang Li, Yi Pan

Computer Science Faculty Publications

Background: Essential proteins are crucial for cellular life and thus, identification of essential proteins is an important topic and a challenging problem for researchers. Recently lots of computational approaches have been proposed to handle this problem. However, traditional centrality methods cannot fully represent the topological features of biological networks. In addition, identifying essential proteins is an imbalanced learning problem; but few current shallow machine learning-based methods are designed to handle the imbalanced characteristics. Results: We develop DeepEP based on a deep learning framework that uses the node2vec technique, multi-scale convolutional neural networks and a sampling technique to identify essential proteins. …

Finding And Analyzing De Novo Mutations In The Exomes Of Parent-Offspring Trios Of Spontaneous Chiari Malformation Type 1 Patients, Brian Leon Ricardo

Arts & Sciences Electronic Theses and Dissertations

Chiari Malformation Type 1 (CM1) is a neurodevelopmental disorder that occurs when one of the cerebellar tonsils herniates past the foramen magnum causing headaches, motor or sensory deficits, sleep apnea, and difficulty swallowing. This disorder is estimated to affect 1% of the population but due to the need of neuroimaging for diagnosis and the presence of asymptomatic patients there is still uncertainty about the exact proportion of the population affected. CM1 often presents itself with other neurodevelopmental disorders such as syringomyelia, scoliosis, and known genetic syndromes such as Klippel-Feil and Marfan syndromes. Twin, family, and familial clustering studies have established …

Chasing The Genetics Of Ascites In Broilers Using Whole Genome Resequencing, Alia Parveen

Graduate Theses and Dissertations

We are using whole genome resequencing to identify chromosomal regions associated with resistance or susceptibility to ascites, a form of pulmonary hypertension syndrome, meat-type chickens. Previous Genome Wide Association Studies (GWAS) based on Single Nucleotide Polymorphisms (SNPs) have identified regions on chromosomes 2, 9 and Z. Despite several GWAS and further genotyping, there are no reliable or potential markers for ascites phenotype. We have completed screening of Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms in ascites resistant and susceptible birds from the relaxed, REL, line derived from a commercial elite broiler line. DNA samples from resistant and susceptible birds …

Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold

Doctoral Dissertations

Soils serve as massive carbon sinks, but their ability to continue this ecological service is contingent on how the resident soil microbial community will respond to the ongoing climate crisis. One key dimension of the microbial response to warming is its carbon use efficiency (CUE), or the fraction of carbon taken up by an organism which is allocated to growth rather than respiration. However, the scientific community is still in the early stages of understanding the drivers, consequences - and even accurate measurements of - CUE. In this dissertation, I first quantified the variability of CUE and its responsiveness to …

Tal Effector-Nucleotide Targeter (Tale-Nt) 2.0: Tools For Tal Effector Design And Target Prediction, Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. Vandyk, Adam J. Bogdanove

Nicholas J. Booher

Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the DNA target, with some degeneracy. A TAL effector-nucleotide binding code that links repeat type to specified nucleotide enables prediction of genomic binding sites for TAL effectors and customization of TAL effectors for use in DNA targeting, in particular as custom transcription factors for engineered gene regulation and as site-specific nucleases for genome editing. We have developed a suite of web-based tools called TAL Effector-Nucleotide Targeter 2.0 (TALE-NT 2.0;https://boglab.plp.iastate.edu/) that enables design …

Characterization And Amplification Of Retrotransposable Elements Platy-1 And Alu In The Cebidae Lineage Of Platyrrhine Primates, Jessica Storer

LSU Doctoral Dissertations

Alu mobile elements are much more than “junk DNA”. Inherent properties such as high copy number, small ~300 bp size, and their nearly homoplasy-free nature make these elements particularly useful in resolving primate phylogenies. In addition, shared sequence features and identity with the Alu element allow for discovery of new SINE retrotransposons, such as the Platyrrhine-limited Platy-1 element. Building on previous research of subfamily analysis, the Platy-1 and Alu elements can be used not only to explore the controversial New World monkey (NWM) phylogeny, but also the mode and tempo of their amplification in different primate genera and species.

Chapter …

Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Network Structure And Dynamics Of Biological Systems, Deena R. Schmidt

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Loop Homology Of Bi-Secondary Structures, Andrei Bura

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Identifying Potential Cancer Driver Genes By Genomic Data Integration., Yong Chen, Jingjing Hao, Wei Jiang, Tong He, Xuegong Zhang, Tao Jiang, Rui Jiang

Yong Chen

Cancer is a genomic disease associated with a plethora of gene mutations resulting in a loss of control over vital cellular functions. Among these mutated genes, driver genes are defined as being causally linked to oncogenesis, while passenger genes are thought to be irrelevant for cancer development. With increasing numbers of large-scale genomic datasets available, integrating these genomic data to identify driver genes from aberration regions of cancer genomes becomes an important goal of cancer genome analysis and investigations into mechanisms responsible for cancer development. A computational method, MAXDRIVER, is proposed here to identify potential driver genes on the basis …

Towards A Mathematical Model Of Motility Using Dictyostelium Discoideum: Proteins And Geometric Features That Regulate Bleb-Based Motility, Zully Santiago

Dissertations, Theses, and Capstone Projects

A variety of biological functions depend on actin organization. The organization of actin is tightly regulated by a plethora of extracellular and intracellular signaling, scaffolding, and actin-binding proteins. Dysfunctions in this regulation lead to immune diseases, increased susceptibility to pathogens, neurodegenerative diseases, developmental disorders, and cancer metastasis. A variety of actin-dependent processes, including cell motility, are regulated by several proteins of interest: Paxillin, a scaffolding protein; WASP, an actin nucleating protein; SCAR/WAVE, another WASP family actin nucleating protein; Talin, a cortex-to-membrane binding protein; Myosin II, an F-actin contracting motor protein; and Protein Kinase C, a protein kinase. D. discoideum cells …

Using Machine Learning For Antimicrobial Resistant Dna Identification, Jason I. Lingle, John Santerre

SMU Data Science Review

In this paper, we present a novel machine learning-based methodology for identifying bacteria DNA sub-sequences that are associated with antimicrobial resistance. The dramatic rise in cases of antibiotic resistant bacteria has been an increasing threat across the globe as the existing treatments are rendered ineffective in treating most of these cases due to mutations of their DNA. Among the most recent bacteria to display antimicrobial resistance (AMR) is Neisseria Gonorrhea with the first global treatment failure taking place in 2016. In 2018, new cases of resistance to multiple, high levels of antibiotics were reported in the United Kingdom and Australia. …

Phylogenetic Trees And Networks Can Serve As Powerful And Complementary Approaches For Analysis Of Genomic Data, Christopher Blair, Cécile Ané

Publications and Research

Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point-of-view we highlight some of the strengths and limitations …

Effective Statistical Energy Function Based Protein Un/Structure Prediction, Avdesh Mishra

University of New Orleans Theses and Dissertations

Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D structure, have dynamic characteristics and therefore, exist in multiple states. Based on …