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Analysis Of Motif Distributions In Regions Of Endocytic Proteins, Chante Bethell, Zuzana Kadlecova, PhD, Stephanie J. Spielman, PhD 2019 Bioinformatics, Rowan University

Analysis Of Motif Distributions In Regions Of Endocytic Proteins, Chante Bethell, Zuzana Kadlecova, Phd, Stephanie J. Spielman, Phd

Student Research Symposium Posters

A short linear motif (SLiM) is a recurring pattern of approximately three to ten amino acids found in proteins. SLiMs are important for cellular signaling and the regulating of proteins, often times by acting as binding sites for protein-binding domains. While SLiMs exist both in ordered regions of proteins where there is a tertiary structure and in disordered regions where there is no structure, they are primarily functional in disordered regions. An important example of SLiM-mediated processes and the focus of this study is endocytosis. Endocytosis is the process by which cells engulf molecules from the extracellular environment. There are ...


Genome-Wide Association Studies In Maize And Sorghum, Preston Hurst 2019 University of Nebraska - Lincoln

Genome-Wide Association Studies In Maize And Sorghum, Preston Hurst

Theses, Dissertations, and Student Research in Agronomy and Horticulture

Genome-wide association studies are used to identify genetic variants associated with a particular phenotype. GWAS has been used in a variety of taxa, from humans, to fish to plants . The present analysis is focused on two species important to the human species: maize and sorghum. A GWAS in maize was carried out on the modification of the Ga1-s allele. The Ga1 locus has long been studied as being involved in a unilateral crossing barrier . However, it has long been suspected that the locus is modified by background genetic factors . GWAS was used to observe candidates for this modification. A series ...


The Full Genome Sequence Of An Antarctic Microbe Constructed Using A Rapid, Portable Sequencer And A Hybrid Assembly, Bruce Wyatt Boles 2019 University of Tennessee, Knoxville

The Full Genome Sequence Of An Antarctic Microbe Constructed Using A Rapid, Portable Sequencer And A Hybrid Assembly, Bruce Wyatt Boles

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Microbial genomes contain combinations of nucleotides that code for genes which subsequently determines the function of the cell. This information provides significant insight into the unique niche of microbes from extreme environments. Here we use two sequencing technologies, the Oxford Nanopore MinION with accompanying software and Illumina HiSeq, to generate a hybrid genome for a Shewanella strain isolated from an Antarctic glacier. Bioinformatic programs, Albacore and SPAdes, allowed us to decrease the time of genome assembly while also obtaining a large quantity of information related to the Shewanella sp. Our combined approach yielded a high quality genome assembly 5.3 ...


Crispr-Sonic: Targeted Somatic Oncogene Knock-In Enables Rapid In Vivo Cancer Modeling, Haiwei Mou, Deniz M. Ozata, Jordan L. Smith, Ankur Sheel, Suet-Yan Kwan, Soren Hough, Alper Kucukural, Zachary Kennedy, Yueying Cao, Wen Xue 2019 University of Massachusetts Medical School

Crispr-Sonic: Targeted Somatic Oncogene Knock-In Enables Rapid In Vivo Cancer Modeling, Haiwei Mou, Deniz M. Ozata, Jordan L. Smith, Ankur Sheel, Suet-Yan Kwan, Soren Hough, Alper Kucukural, Zachary Kennedy, Yueying Cao, Wen Xue

RNA Therapeutics Institute Publications

CRISPR/Cas9 has revolutionized cancer mouse models. Although loss-of-function genetics by CRISPR/Cas9 is well-established, generating gain-of-function alleles in somatic cancer models is still challenging because of the low efficiency of gene knock-in. Here we developed CRISPR-based Somatic Oncogene kNock-In for Cancer Modeling (CRISPR-SONIC), a method for rapid in vivo cancer modeling using homology-independent repair to integrate oncogenes at a targeted genomic locus. Using a dual guide RNA strategy, we integrated a plasmid donor in the 3'-UTR of mouse beta-actin, allowing co-expression of reporter genes or oncogenes from the beta-actin promoter. We showed that knock-in of oncogenic Ras and ...


Evolution Of Endurance Running Genes Across Primates, Natalia T. Grube 2019 CUNY Hunter College

Evolution Of Endurance Running Genes Across Primates, Natalia T. Grube

School of Arts & Sciences Theses

The endurance running hypothesis has emerged as a key idea to explain several unique anatomical, physiological, and genetic features of modern humans—among these features is the evolution of ACTN3 (Bramble & Lieberman 2004, Nature), a gene linked to human athletic performance. An additional gene linked to human endurance performance is ACE. Because endurance running is a uniquely human trait, I predicted that ACE and ACTN3 genes would be evolving adaptively in the human lineage when examined in a wider primatological framework. To test this I compiled ACE and ACTN3 genes from 14 primate species and phylogenetically tested if these genes ...


Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney 2019 University of Lynchburg

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point ...


Gogo: An Improved Algorithm To Measure The Semantic Similarity Between Gene Ontology Terms, Chenguang Zhao 2019 The University of Southern Mississippi

Gogo: An Improved Algorithm To Measure The Semantic Similarity Between Gene Ontology Terms, Chenguang Zhao

Master's Theses

Measuring the semantic similarity between Gene Ontology (GO) terms is an essential step in functional bioinformatics research. We implemented a software named GOGO for calculating the semantic similarity between GO terms. GOGO has the advantages of both information-content-based and hybrid methods, such as Resnik’s and Wang’s methods. Moreover, GOGO is relatively fast and does not need to calculate information content (IC) from a large gene annotation corpus but still has the advantage of using IC. This is achieved by considering the number of children nodes in the GO directed acyclic graphs when calculating the semantic contribution of an ...


Scl: A Lattice-Based Approach To Infer Three-Dimensional Chromosome Structures From Single-Cell Hi-C Data, Hao Zhu 2019 The University of Southern Mississippi

Scl: A Lattice-Based Approach To Infer Three-Dimensional Chromosome Structures From Single-Cell Hi-C Data, Hao Zhu

Master's Theses

In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.

We developed SCL (Single-Cell Lattice), a computational method to reconstruct three-dimensional (3D) structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3D cubic lattice. Metropolis-Hastings simulation and simulated annealing are used ...


Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig 2019 University of New Mexico

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in ...


Characterization Of The Φctx-Like Pseudomonas Aeruginosa Phage Dobby Isolated From The Kidney Stone Microbiota, Genevieve Johnson, Alan J. Wolfe, Catherine Putonti 2019 Loyola University Chicago

Characterization Of The Φctx-Like Pseudomonas Aeruginosa Phage Dobby Isolated From The Kidney Stone Microbiota, Genevieve Johnson, Alan J. Wolfe, Catherine Putonti

Biology: Faculty Publications and Other Works

Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37 152 bp genome that closely resembles the temperate P. aeruginosa ...


Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan 2019 Temple University

Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional ...


Similarities And Differences Between Variants Called With Human Reference Genome Hg19 Or Hg38, Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuantin Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong 2019 U.S. Food and Drug Administration

Similarities And Differences Between Variants Called With Human Reference Genome Hg19 Or Hg38, Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuantin Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong

Faculty Publications

Background

Reference genome selection is a prerequisite for successful analysis of next generation sequencing (NGS) data. Current practice employs one of the two most recent human reference genome versions: HG19 or HG38. To date, the impact of genome version on SNV identification has not been rigorously assessed.

Methods

We conducted analysis comparing the SNVs identified based on HG19 vs HG38, leveraging whole genome sequencing (WGS) data from the genome-in-a-bottle (GIAB) project. First, SNVs were called using 26 different bioinformatics pipelines with either HG19 or HG38. Next, two tools were used to convert the called SNVs between HG19 and HG38. Lastly ...


Predicting Protein Residue-Residue Contacts Using Random Forests And Deep Networks, Joseph Luttrell IV, Tong Liu, Chaoyang Zhang, Zheng Wang 2019 University of Southern Mississippi

Predicting Protein Residue-Residue Contacts Using Random Forests And Deep Networks, Joseph Luttrell Iv, Tong Liu, Chaoyang Zhang, Zheng Wang

Faculty Publications

No abstract provided.


A Note On Misspecification In General Linear Models With Correlated Errors For The Analysis Of Crossover Clinical Trials, Wei Wang, Ning Cong, Tian Chen, Hui Zhang, Bo Zhang 2019 University of Mississippi Medical Center

A Note On Misspecification In General Linear Models With Correlated Errors For The Analysis Of Crossover Clinical Trials, Wei Wang, Ning Cong, Tian Chen, Hui Zhang, Bo Zhang

Open Access Articles

Among various approaches to the repeated measures analysis in crossover clinical trials, the general linear models (GLMs) with correlated errors attract substantial attention due to their simplicity in model specification, implementation, and interpretation. The goal of this research note is to conduct simulation studies to numerically investigate the impact of model misspecification in the GLMs with correlated errors in the analysis of crossover trials. A series of synthetic two-treatment and three-treatment crossover trials were designed, and simulation studies were conducted to assess how treatment effect estimation, type I error rates, and power can be affected by misspecified period effects, carryover ...


Stress Response To Co2 Deprivation By Arabidopsis Thaliana In Plant Cultures, Souvik Banerjee, Oskar Siemianowski, Meiling Liu, Kara R. Lind, Xinchun Tian, Dan Nettleton, Ludovico Cademartiri 2019 Iowa State University

Stress Response To Co2 Deprivation By Arabidopsis Thaliana In Plant Cultures, Souvik Banerjee, Oskar Siemianowski, Meiling Liu, Kara R. Lind, Xinchun Tian, Dan Nettleton, Ludovico Cademartiri

Statistics Publications

After being the standard plant propagation protocol for decades, cultures of Arabidopsis thaliana sealed with Parafilm remain common today out of practicality, habit, or necessity (as in co-cultures with microorganisms). Regardless of concerns over the aeration of these cultures, no investigation has explored the CO2 transport inside these cultures and its effect on the plants. Thereby, it was impossible to assess whether Parafilm-seals used today or in thousands of older papers in the literature constitute a treatment, and whether this treatment could potentially affect the study of other treatments.For the first time we report the CO2concentrations in Parafilm-sealed cultures ...


Poster: Image Disguising For Privacy-Preserving Deep Learning, Sagar Sharma, Keke Chen 2019 Wright State University - Main Campus

Poster: Image Disguising For Privacy-Preserving Deep Learning, Sagar Sharma, Keke Chen

Keke Chen

No abstract provided.


Towards Practical Privacy-Preserving Analytics For Iot And Cloud Based Healthcare Systems, Sagar Sharma, Keke Chen, Amit P. Sheth 2019 Wright State University - Main Campus

Towards Practical Privacy-Preserving Analytics For Iot And Cloud Based Healthcare Systems, Sagar Sharma, Keke Chen, Amit P. Sheth

Keke Chen

Modern healthcare systems now rely on advanced computing methods and technologies, such as IoT devices and clouds, to collect and analyze personal health data at unprecedented scale and depth. Patients, doctors, healthcare providers, and researchers depend on analytical models derived from such data sources to remotely monitor patients, early-diagnose diseases, and find personalized treatments and medications. However, without appropriate privacy protection, conducting data analytics becomes a source of privacy nightmare. In this paper, we present the research challenges in developing practical privacy-preserving analytics in healthcare information systems. The study is based on kHealth - a personalized digital healthcare information system that ...


Poster: Privacy-Preserving Boosting With Random Linear Classifiers, Sagar Sharma, Keke Chen 2019 Wright State University - Main Campus

Poster: Privacy-Preserving Boosting With Random Linear Classifiers, Sagar Sharma, Keke Chen

Keke Chen

We propose SecureBoost, a privacy-preserving predictive modeling framework, that allows service providers (SPs) to build powerful boosting models over encrypted or randomly masked user submit- ted data. SecureBoost uses random linear classifiers (RLCs) as the base classifiers. A Cryptographic Service Provider (CSP) manages keys and assists the SP’s processing to reduce the complexity of the protocol constructions. The SP learns only the base models (i.e., RLCs) and the CSP learns only the weights of the base models and a limited leakage function. This separated parameter holding avoids any party from abusing the final model or conducting model-based attacks ...


Augmented Personalized Health: Using Semantically Integrated Multimodal Data For Patient Empowered Health Management Strategies, Amit P. Sheth, Hong Y. Yip, Utkarshani Jaimini, Dipesh Kadariya, Vaikunth Sridharan, R. Venkataramanan, Tanvi Banerjee, Krishnaprasad Thirunarayan, Maninder Kalra 2019 Wright State University - Main Campus

Augmented Personalized Health: Using Semantically Integrated Multimodal Data For Patient Empowered Health Management Strategies, Amit P. Sheth, Hong Y. Yip, Utkarshani Jaimini, Dipesh Kadariya, Vaikunth Sridharan, R. Venkataramanan, Tanvi Banerjee, Krishnaprasad Thirunarayan, Maninder Kalra

Krishnaprasad Thirunarayan

Healthcare as we know it is in the process of going through a massive change from:

1. Episodic to continuous

2. Disease-focused to wellness and quality of life focused

3. Clinic-centric to anywhere a patient is

4. Clinician controlled to patient empowered

5. Being driven by limited data to 360-degree, multimodal personal-public-population physical-cyber-social big data-driven URL: https://mhealth.md2k.org/2018-tech-showcase-home


Personalized Prediction Of Suicide Risk For Web-Based Intervention, Amanuel Alambo, Manas Gaur, Ugur Kursuncu, Krishnaprasad Thirunarayan, Jeremiah Schumm, Jyotishman Pathak, Amit P. Sheth 2019 Wright State University - Main Campus

Personalized Prediction Of Suicide Risk For Web-Based Intervention, Amanuel Alambo, Manas Gaur, Ugur Kursuncu, Krishnaprasad Thirunarayan, Jeremiah Schumm, Jyotishman Pathak, Amit P. Sheth

Krishnaprasad Thirunarayan

Across the United States, suicide is the second leading cause of death for people aged between 15 and 34, and younger people are more prone to mental health problems, suicidal thoughts, and behaviors. For instance, 80% of patients with Borderline Personality Disorder have suicide-related behaviors, and between 4-9% of them commit suicide. Moreover, the social stigma associated with mental health issues and suicide deter patients from sharing their experiences directly with others. In such a situation, social media that provides a free and open forum for voluntary expression can provide insights into suicide ideation and self-destructive behavior.

Reddit is a ...


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