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Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath 2020 Children's Mercy Kansas City

Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath

Research Days

No abstract provided.


The Evolving Management Of Aortic Valve Disease: Trends In The Utilization And Cost Of Savr, Tavr, And Medical Therapy, Andrew Goldsweig 2020 University of Nebraska Medical Center

The Evolving Management Of Aortic Valve Disease: Trends In The Utilization And Cost Of Savr, Tavr, And Medical Therapy, Andrew Goldsweig

Theses & Dissertations

Aortic stenosis (AS) and regurgitation (AR) may be treated with surgical aortic valve replacement (SAVR), transcatheter AVR (TAVR), or medical therapy (MT). Data are lacking regarding usage and cost of SAVR, TAVR, and MT for patients hospitalized with aortic valve disease. From the Nationwide Readmissions Database, we determined utilization and cost trends for SAVR, TAVR, and MT in patients with aortic valve disease admitted 2012-2016 for valve replacement, heart failure, unstable angina, non-ST-elevation myocardial infarction, or syncope. From 2012 through 2016, there was a 48.1% increase in the number of patients hospitalized for aortic valve disease annually. Overall, 19 ...


Molecular Characterization Of A Gene Encoding Insulin-Like Peptide 5 (Ilp5) In Drosophila Virilis, Nikolas R. Likourentzos, Jae H. Park 2020 University of Tennessee, Knoxville

Molecular Characterization Of A Gene Encoding Insulin-Like Peptide 5 (Ilp5) In Drosophila Virilis, Nikolas R. Likourentzos, Jae H. Park

Pursuit - The Journal of Undergraduate Research at the University of Tennessee

The study of the insulin-like peptides of Drosophila can provide insight of their similarities to mammalian insulin and their potential usage in treating human insulin-related diseases. In this study, we isolated and characterized cDNA encoding insulin-like peptide (ILP) 5 in D. virilis by using RNA purification, reverse transcription, and RACE protocols. Subsequently, various bioinformatic softwares were employed to predict peptide structure. The ILP5 gene (587 base pairs) codes for 121 amino acids that make up prepro-ILP5. After maturation, functional ILP5 is a peptide of two 25 amino acid chains, A- and B-chain, connected by two disulfide bonds. Sequencing genomic DNA ...


Using Bioinformatics Tools To Evaluate Potential Risks Of Food Allergy And To Predict Microbiome Functionality, Mohamed Abdelmoteleb 2020 University of Nebraska - Lincoln

Using Bioinformatics Tools To Evaluate Potential Risks Of Food Allergy And To Predict Microbiome Functionality, Mohamed Abdelmoteleb

Dissertations, Theses, & Student Research in Food Science and Technology

Novel foods and Genetically Engineered (GE) organisms are being developed for nutritional, industrial, and environmental applications. Dietary interventions have been used recently to mitigate methane emissions in ruminants. In this project, bioinformatics tools have been used to answer two main questions. The first question is the potential allergy risks for consumption of novel foods and GE organisms. The second question is the effects of dietary interventions on microbiome functionality related to methane production in ruminants.

To answer the first question, regulatory authorities in the United States and Europe now expect an evaluation of new proteins in novel foods or genetically ...


Comparative Analysis Of Metabolic Pathways Of Bacteria Used In Fermented Food, Keanu Hoang, Kiran Bastola 2020 University of Nebraska at Omaha

Comparative Analysis Of Metabolic Pathways Of Bacteria Used In Fermented Food, Keanu Hoang, Kiran Bastola

Theses/Capstones/Creative Projects

This study presents a novel methodology for analyzing metabolic pathways. Utilizing KEGG REST API through a Biopython package and file parser, data about whether or not a bacteria has an enzyme or not was extracted. The results found that differences in metabolic pathway enrichment values follow along the lines of genera and pathway type. In particular, bacteria found in food spoilage and commercial nitrogen fixing products had high values of enrichment.


A Study Of Matr3 And Its Effects On The Neural Progenitor Cells Of Xenopus Laevis Tadpoles, Kendall Branham 2020 William & Mary

A Study Of Matr3 And Its Effects On The Neural Progenitor Cells Of Xenopus Laevis Tadpoles, Kendall Branham

Undergraduate Honors Theses

Understanding the genes and mechanisms that regulate the highly important process of neurogenesis in the developing nervous system is crucial to uncovering why disease arises when this system is disrupted. Neural progenitor cells and their multipotent nature allow for the growth of a large pool of stem cells in the early stages of development, but the signal that leads these cells to the irreversible fate of becoming a neuron is unclear. The gene matr3 has been implicated in having a role in the maintenance of undifferentiated neural stem cells but its role needs further investigation to fully reveal how its ...


Transcriptomic Analysis Of Cytokine-Treated Tissue-Engineered Cartilage As An In Vitro Model Of Osteoarthritis, Jiehan Li 2020 Washington University in St. Louis

Transcriptomic Analysis Of Cytokine-Treated Tissue-Engineered Cartilage As An In Vitro Model Of Osteoarthritis, Jiehan Li

Engineering and Applied Science Theses & Dissertations

Osteoarthritis (OA), as the most common form of arthritis and a leading cause of disability worldwide, currently has no disease-modifying drugs. Inflammation plays an important role in cartilage degeneration in OA, and pro-inflammatory cytokines, IL-1β and TNF-α, have been shown to induce degradative changes along with aberrant gene expression in chondrocytes, the only resident cells in cartilage. The goal of this study was to further understand the transcriptomic regulation of tissue-engineered cartilage in response to inflammatory cytokines using an in vitro miPSC model system. We performed RNA sequencing for the IL-1β or TNF-α treated tissue-engineered cartilage derived from murine iPSCs ...


Sars-Cov-2 Receptor Ace2 Is An Interferon-Stimulated Gene In Human Airway Epithelial Cells And Is Detected In Specific Cell Subsets Across Tissues, Carly G. K. Ziegler, Yuming Cao, Zhiru Guo, Jennifer P. Wang, Robert W. Finberg, Manuel Garber, Alex K. Shalek, Jose Ordovas-Montanes, HCA Lung Biological Network 2020 Harvard Medical School

Sars-Cov-2 Receptor Ace2 Is An Interferon-Stimulated Gene In Human Airway Epithelial Cells And Is Detected In Specific Cell Subsets Across Tissues, Carly G. K. Ziegler, Yuming Cao, Zhiru Guo, Jennifer P. Wang, Robert W. Finberg, Manuel Garber, Alex K. Shalek, Jose Ordovas-Montanes, Hca Lung Biological Network

Coronavirus COVID-19 Publications by UMMS Authors

There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2), which causes the disease COVID-19. SARS-CoV-2 spike (S) protein binds angiotensin-converting enzyme 2 (ACE2), and in concert with host proteases, principally transmembrane serine protease 2 (TMPRSS2), promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues and the factors that regulate ACE2 expression remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 among tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung ...


Transcriptomic Profiling Reveals Extraordinary Diversity Of Venom Peptides In Unexplored Predatory Gastropods Of The Genus Clavus, Aiping Lu, Maren Watkins, Qing Li, Samuel D. Robinson, Gisela P. Concepcion, Mark Yandell, Zhiping Weng, Baldomero M. Olivera, Helena Safavi-Hemami, Alexander E. Fedosov 2020 Tongji University

Transcriptomic Profiling Reveals Extraordinary Diversity Of Venom Peptides In Unexplored Predatory Gastropods Of The Genus Clavus, Aiping Lu, Maren Watkins, Qing Li, Samuel D. Robinson, Gisela P. Concepcion, Mark Yandell, Zhiping Weng, Baldomero M. Olivera, Helena Safavi-Hemami, Alexander E. Fedosov

Open Access Articles

Predatory gastropods of the superfamily Conoidea number over 12,000 living species. The evolutionary success of this lineage can be explained by the ability of conoideans to produce complex venoms for hunting, defense and competitive interactions. Whereas venoms of cone snails (family Conidae) have become increasingly well studied, the venoms of most other conoidean lineages remain largely uncharacterized. In the present study we present the venom gland transcriptomes of two species of the genus Clavus that belong to the family Drilliidae. Venom gland transcriptomes of two specimens of Clavus canalicularis, and two specimens of Cv. davidgilmouri were analyzed, leading to ...


Chemical Modifications Of Adenine Base Editor Mrna And Guide Rna Expand Its Application Scope, Tingting Jiang, Xiao-Ou Zhang, Yueying Cao, Zhiping Weng, Wen Xue 2020 University of Massachusetts Medical School

Chemical Modifications Of Adenine Base Editor Mrna And Guide Rna Expand Its Application Scope, Tingting Jiang, Xiao-Ou Zhang, Yueying Cao, Zhiping Weng, Wen Xue

Open Access Articles

CRISPR-Cas9-associated base editing is a promising tool to correct pathogenic single nucleotide mutations in research or therapeutic settings. Efficient base editing requires cellular exposure to levels of base editors that can be difficult to attain in hard-to-transfect cells or in vivo. Here we engineer a chemically modified mRNA-encoded adenine base editor that mediates robust editing at various cellular genomic sites together with moderately modified guide RNA, and show its therapeutic potential in correcting pathogenic single nucleotide mutations in cell and animal models of diseases. The optimized chemical modifications of adenine base editor mRNA and guide RNA expand the applicability of ...


469— Life Or Death: Decision Making In Sexual Disease Treatment Matters, Jason Ipolito 2020 SUNY Geneseo

469— Life Or Death: Decision Making In Sexual Disease Treatment Matters, Jason Ipolito

GREAT Day

Syphilis is an STI that has recently made a resurgence in homosexual populations. When infected, a patient has two options: seek treatment immediately or do not seek treatment. I used a system of differential equations that includes susceptible, exposed, treatment receptive, treatment non-receptive, cured, and dead state variables in order to determine the relationships among transmission rate, treatment options, and death rate. My model suggests that an individual’s treatment option has a larger effect on death rate than the transmission rate inherent to the disease. The model also contains two sets of equilibria: an unstable trivial disease free condition ...


Mhcherrypan, A Novel Model To Predict The Binding Affinity Of Pan-Specific Class I Hla-Peptide, Xuezhi Xie 2020 The University of Western Ontario

Mhcherrypan, A Novel Model To Predict The Binding Affinity Of Pan-Specific Class I Hla-Peptide, Xuezhi Xie

Electronic Thesis and Dissertation Repository

The human leukocyte antigen (HLA) system or complex plays an essential role in regulating the immune system in humans. Accurate prediction of peptide binding with HLA can efficiently help to identify those neoantigens, which potentially make a big difference in immune drug development. HLA is one of the most polymorphic genetic systems in humans, and thousands of HLA allelic versions exist. Due to the high polymorphism of HLA complex, it is still pretty difficult to accurately predict the binding affinity. In this thesis, we presented a new algorithm to combine convolutional neural network and long short-term memory to solve this ...


Progress Presentation On The Proposed Function Of Protein 4diu Through Bioinformatics Analyses, Melissa Hoff 2020 Ursinus College

Progress Presentation On The Proposed Function Of Protein 4diu Through Bioinformatics Analyses, Melissa Hoff

Biochemistry and Molecular Biology Presentations

The BASIL project is a scientific inquiry project that aims to determine the function of a protein from its structure. Biochemistry students completed wet lab work, while structural biology students worked in silico. The purpose of this study was to determine the function of the protein with PDB ID: 4DIU. Bioinformatics analyses were completed using several databases: BLAST, Dali, Pfam, and Moltimate, and imaging of the protein was completed using PyMOL software. The BLAST database aligned the primary sequence with known protein sequences. The Dali database compared protein structure with known structures through global alignment. The Pfam database matched our ...


Dolphinnext: A Distributed Data Processing Platform For High Throughput Genomics, Onur Yukselen, Osman Turkyilmaz, Ahmet R. Ozturk, Manuel Garber, Alper Kucukural 2020 University of Massachusetts Medical School

Dolphinnext: A Distributed Data Processing Platform For High Throughput Genomics, Onur Yukselen, Osman Turkyilmaz, Ahmet R. Ozturk, Manuel Garber, Alper Kucukural

Open Access Articles

BACKGROUND: The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and databases make analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for highly parallel, flexible, portable, and reproducible data processing frameworks. Several platforms currently ...


Single-Cell Analysis Of Upper Airway Cells Reveals Host-Viral Dynamics In Influenza Infected Adults, Yuming Cao, Zhiru Guo, Pranitha Vangala, Elisa Donnard, Ping Liu, Patrick McDonel, Jose Ordovas Montanes, Alex K. Shalek, Robert W. Finberg, Jennifer P. Wang, Manuel Garber 2020 University of Massachusetts Medical School

Single-Cell Analysis Of Upper Airway Cells Reveals Host-Viral Dynamics In Influenza Infected Adults, Yuming Cao, Zhiru Guo, Pranitha Vangala, Elisa Donnard, Ping Liu, Patrick Mcdonel, Jose Ordovas Montanes, Alex K. Shalek, Robert W. Finberg, Jennifer P. Wang, Manuel Garber

University of Massachusetts Medical School Faculty Publications

Influenza virus infections are major causes of morbidity and mortality. Research using cultured cells, bulk tissue, and animal models cannot fully capture human disease dynamics. Many aspects of virus-host interactions in a natural setting remain unclear, including the specific cell types that are infected and how they and neighboring bystander cells contribute to the overall antiviral response. To address these questions, we performed single-cell RNA sequencing (scRNA-Seq) on cells from freshly collected nasal washes from healthy human donors and donors diagnosed with acute influenza during the 2017-18 season. We describe a previously uncharacterized goblet cell population, specific to infected individuals ...


Environmental Dna Metabarcoding Detects Mammal Use Of Stock Tanks And Natural Springs On The Prescott National Forest, K. A. Smith, Berenice Carreras Mendiolea, C. E. Benson, F. B. Anaya 2020 Montana State University - Billings

Environmental Dna Metabarcoding Detects Mammal Use Of Stock Tanks And Natural Springs On The Prescott National Forest, K. A. Smith, Berenice Carreras Mendiolea, C. E. Benson, F. B. Anaya

Discovery Day - Prescott

Recent research has shown the viability of environmental DNA (eDNA) analysis as a tool for identifying species presence in aquatic ecosystems. However, there is limited research indicating the feasibility of eDNA as a survey tool in water sources such as springs and stock tanks. Because of the scarcity of water in the high desert landscape of Arizona, natural springs and stock tanks are an important water resource. In this study, we examined whether 16S rRNA metabarcoding could detect mammal eDNA in springs and stock tanks in the Prescott National Forest. During summer 2019, we collected and analyzed water samples at ...


Cylindrical Similarity Measurement For Helices In Medium-Resolution Cryo-Electron Microscopy Density Maps, Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He 2020 Old Dominion University

Cylindrical Similarity Measurement For Helices In Medium-Resolution Cryo-Electron Microscopy Density Maps, Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He

College of Sciences Posters

Cryo-electron microscopy (cryo-EM) density maps at medium resolution (5-10 Å) reveal secondary structural features such as α-helices and β-sheets, but they lack the side chains details that would enable a direct structure determination. Among the more than 800 entries in the Electron Microscopy Data Bank (EMDB) of medium-resolution density maps that are associated with atomic models, a wide variety of similarities can be observed between maps and models. To validate such atomic models and to classify structural features, a local similarity criterion, the F1 score, is proposed and evaluated in this study. The F1 score is theoretically normalized to a ...


Multi-Label Model For Toxicity Prediction, Xiu Huan Yap, Michael L. Raymer 2020 Wright State University - Main Campus

Multi-Label Model For Toxicity Prediction, Xiu Huan Yap, Michael L. Raymer

Symposium of Student Research, Scholarship, and Creative Activities Materials

Most computational predictive models are specifically trained for a single toxicity endpoint. Since more than 1300 toxicity assays have been reported in the TOXCAST dashboard, achieving high coverage over this growing number of toxicity endpoints remains challenging. Furthermore, single-endpoint models lack the ability to learn dependencies between endpoints, such as those targeting similar biological pathways, which may be used to boost model performance. In this study, we characterize the performance of 3 multi-label classification (MLC) models, namely Classifier Chains (CC), Label Powersets (LP) and Stacking (SBR), on Tox21 challenge data. These MLC models employ the Problem Transformation approach, which is ...


Assembly And Identification Of Novel Viruses In The Aquatic Invertebrate Daphnia Magna, Freddy L. Gonzalez, Reilly O. Cooper, Clayton E. Cressler 2020 University of Nebraska - Lincoln

Assembly And Identification Of Novel Viruses In The Aquatic Invertebrate Daphnia Magna, Freddy L. Gonzalez, Reilly O. Cooper, Clayton E. Cressler

UCARE Research Products

Microbiome studies have been critical to understanding host health and life history. Many studies primarily focus on understanding the impacts of bacteria on the host, while fewer examine the impacts of viruses on host fitness or the interaction between viruses and bacteria within a host. Here, we utilized shotgun sequencing to identify whether viruses were present in the model organism Daphnia magna. VIBRANT, a bioinformatic tool that utilizes hybrid machine learning and protein similarity to identify lytic genomes and other novel viruses, was used on sequencing data from four samples of adult and juvenile Daphnia. We found a complete, novel ...


Gene-Based Clustering Algorithms: Comparison Between Denclue, Fuzzy-C, And Birch, Martin C. Nwadiugwu 2020 University of Nebraska at Omaha

Gene-Based Clustering Algorithms: Comparison Between Denclue, Fuzzy-C, And Birch, Martin C. Nwadiugwu

Interdisciplinary Informatics Faculty Publications

The current study seeks to compare 3 clustering algorithms that can be used in gene-based bioinformatics research to understand disease networks, protein-protein interaction networks, and gene expression data. Denclue, Fuzzy-C, and Balanced Iterative and Clustering using Hierarchies (BIRCH) were the 3 gene-based clustering algorithms selected. These algorithms were explored in relation to the subfield of bioinformatics that analyzes omics data, which include but are not limited to genomics, proteomics, metagenomics, transcriptomics, and metabolomics data. The objective was to compare the efficacy of the 3 algorithms and determine their strength and drawbacks. Result of the review showed that unlike Denclue and ...


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