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Identification Of Circrna Biomarkers In Osteosarcoma: An Updated Systematic Review And Meta-Analysis, Chunbin Zhou, Lois Balmer, Manshu Song, Gehendra Mahara, Kezhou Wu, Wei Wang, Hu Wang

Research outputs 2022 to 2026

Circular RNAs (circRNAs) play a crucial role in cancer development and progression. This study aimed to identify potential circRNA biomarkers for osteosarcoma. Articles published from January 2010 to September 2023 were searched across eight databases to compare circRNA expression profiles in osteosarcoma and control samples (human, animal and cell lines). Meta-analysis was conducted under a random effects model. Subgroup analysis of circRNAs in different samples and tissues was performed. Diagnostic value was evaluated using receiver operator characteristic curves. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis explored functions of circRNA host genes. A circRNA-miRNA-mRNA axis …

Systematic Comparison Of Propensity Score Matching And Structural Causal Modeling For Clinical Applications, With A Case Study Of Albumin Treatment For Acute Kidney Injury (Aki) Patients: Propensity Score Matching Vs. Structural Causal Models, Layaal Khellah

Student Research Symposium

Introduction:

Propensity Score Matching (PSM) and Structural Causal Models (SCMs) are key approaches in causal inference for treatment evaluation and clinical decisions, both rooted in the potential outcome framework but differing in their foundations—PSM follows Rubin's Causal Model, while SCMs adhere to the Structural Theory of Causation.

Methods:

Our study compares PSM and SCMs in clinical contexts, focusing on albumin as an AKI treatment. We examine each method's steps, highlighting differences. Using data from AKI patients with cirrhosis, we assess albumin’s treatment efficacy with both PSM and SCMs, offering insights into their performance in estimating causal effects..

Results:

PSM and …

An Investigation Of Information Structures In Dna, Joel Mohrmann

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

The information-containing nature of the DNA molecule has been long known and observed. One technique for quantifying the relationships existing within the information contained in DNA sequences is an entity from information theory known as the average mutual information (AMI) profile. This investigation sought to use principally the AMI profile along with a few other metrics to explore the structure of the information contained in DNA sequences.

Treating DNA sequences as an information source, several computational methods were employed to model their information structure. Maximum likelihood and maximum a posteriori estimators were used to predict missing bases in DNA sequences. …

Creating Interpretable Deep Learning Models To Identify Species Using Environmental Dna Sequences, Samuel Waggoner

Honors College

This research aims to develop an interpretable and fast machine learning (ML) model for identifying species using environmental DNA (eDNA). eDNA is a technique used to detect the presence or absence of species in an ecosystem by analyzing the DNA that animals naturally leave behind in water or soil. However, there can be millions of sequences to classify and the reference databases are sizeable, so traditional methods such as BLAST are slow. Convolutional neural networks (CNNs) have been shown to be 150 times faster at classifying sequences. In this work, we create a CNN that achieves 92.5% accuracy, surpassing the …

The Genomics Of Champ1: Insights Into Their Cell-Type Specificity And Developmental Trajectories, Zoe Marie Van Caugherty

MUSC Theses and Dissertations

Chromosome alignment maintaining phosphoprotein 1(CHAMP1) is a gene that encodes a zinc finger protein that is involved in in the maintenance of kinetochore-microtubule attachment and regulating chromosome segregation in mitosis. (Itoh et al., 2011) CHAMP1 mutations have been shown to be major risk factors for neurodevelopmental disorders (NDDs) and autism spectrum disorder (ASD).(Asakura et al., 2021; Isidor et al., 2016; Levy et al., 2022) Although there is information on the link between CHAMP1 mutations and NDD, the role of CHAMP1 in regulating processes of human cortical development, namely, neurogenesis, proliferation, and electrophysiological properties of newly born neurons, is unknown. This …

Bioinformatics To Guide Musculoskeletal Modeling: A Retrospective Study From Olympic Water Polo Athletes, Dhruv Seshadri, Tony Del Vecchio, Hayley Whitney, Tim Gabbett

International Journal of Exercise Science: Conference Proceedings

GNYACSM Original Research Abstract

Bioinformatics to Guide Musculoskeletal Modeling: A Retrospective Study from Olympic Water Polo Athletes

DEL VECCHIO TONY, WHITNEY HAYLEY, GABBETT TIM

Seshadri Lab; Bioengineering; Lehigh University; Bethlehem, PA

Category: Masters

Advisor / Mentor: Seshadri, Dhruv dhs223@lehigh.edu

ABSTRACT

There is a pressing need for effective injury prevention methods to mitigate time-loss injuries. This study aims to develop a robust injury risk assessment model for water polo athletes by assessing the interplay between load-response metrics, and leveraging artificial intelligence to forecast wellness based on prior assessments.

PURPOSE

Water polo athletes present with upper extremity injuries in the hip, knee, …

In-Silico Analysis For Structural And Functional Characterization Of Phosphorus-Starvation Tolerance 1 (Pstol1) Gene, Quratulain Mehdi Khan, Muhammad Aqeel, Maryam Murtaza, Wajya Ajmal, Muhammad Uzair, Sajid Fiaz, Kotb A. Attia, Asmaa M. Abushady, Itoh Kimiko, Muhammad Ramzan Khan, Ghulam Muhammad Ali

Turkish Journal of Agriculture and Forestry

As an important macro element for all living cells, phosphorus is essential in agricultural production systems as well and is required in large quantities by elite varieties of crops to maintain yields. Approximately 70% of worldwide cultivated land suffers from phosphorous deficiency, and it has recently been estimated that worldwide phosphorous resources will be shattered by the end of this century thus increasing the demand for crops to be more efficient in their P usage. A greater understanding of how plants can maintain yield with lower phosphorous availability is highly desirable to both breeders and farmers, therefore, significant to develop …

Mmappr2: An Improved Bioinformatics Approach To Find Novel Genes, Aiden Cardall, Jonathon T. Hill, Kyle Johnsen, Connor Ward, Maliha Tasnim, Jared Taylor

Library/Life Sciences Undergraduate Poster Competition 2024

Introduction

• New genes are commonly found by randomly inducing mutations in model organisms.

• Mapping the mutations to the genome to find novel genes is difficult, time-consuming, and expensive.

• We created a bioinformatics program, MMAPPR, to automate this process.

• Here, we introduce a new algorithm, MMAPPR2, which requires little to no bioinformatics knowledge to use.

• MMAPPR2 makes several improvements that allow it to identify genes more rapidly and precisely.

• MMAPPR2 will aid the rapid identification of genes in a wide range of species and developmental systems.

Determining The Role Of Noncoding Insertion And Deletion Mutations In Lung Cancer, Zachary Everton, Matthew H. Bailey

Library/Life Sciences Undergraduate Poster Competition 2024

Background

● Cancer is a disease in which cells grow and divide at an uncontrolled rate and cause damage to surrounding tissue and is caused by mutations in the cells’ DNA.

● Though some cancer-causing mutations are inherited from parents, most cancer-causing mutations emerge over the course of a person’s life and are localized to the tumor. These localized mutations are also known as somatic mutations.

● The human genome is over 6.27 billion base pairs long and cannot be read from end to end; instead it is read in small pieces that are aligned to best-matching sequences in the …

Advances In Methods For Trna Sequencing And Quantification, Nigam H. Padhiar, Upendra Katneni, Anton A. Komar, Yuri Motorin, Chava Kimchi-Sarfaty

Biological, Geological, and Environmental Faculty Publications

In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification …

Protein-Protein Interactions In Cell Cycle Proteins: An In Silico Investigation Of Two Important Players, Andriele Eichner

Dissertations, Theses, and Capstone Projects

The examination of the cell cycle carries significant implications for the biology, health, and overall existence of all living things. These implications span from the development and growth of these organisms to the aging process and cancer, as well as the potential of stem cell therapies to repair diseases and injuries. Numerous proteins of the cell cycle are essential for cellular division and proliferation and are widely conserved over the course of evolution. In this work, we aimed to investigate the molecular processes of protein-protein interactions in cell cycle proteins, centering on two key players: Cdc6 in budding yeast and …

Bnfo 135-002: Programming For Bioinformatics​​, Jun Wu

Computer Science Syllabi

No abstract provided.

Developing Partnerships For Academic Data Science Consulting And Collaboration Units, Marianne Huebner, Laura Bond, Felesia Stukes, Joel Herndon, David J. Edwards, Gina-Maria Pomann

Biomolecular Research Center Publications and Presentations

Data science consulting and collaboration units (DSUs) are core infrastructure for research at universities. Activities span data management, study design, data analysis, data visualization, predictive modelling, preparing reports, manuscript writing and advising on statistical methods and may include an experiential or teaching component. Partnerships are needed for a thriving DSU as an active part of the larger university network. Guidance for identifying, developing and managing successful partnerships for DSUs can be summarized in six rules: (1) align with institutional strategic plans, (2) cultivate partnerships that fit your mission, (3) ensure sustainability and prepare for growth, (4) define clear expectations in …

Using Single Cell Genomics To Explore The Impact Of Marine Viruses On Microbial Respiration., Paxton Tomko

MCB Articles

Viral metabolic reprograming of marine prokaryotes, through the use of virally encoded auxiliary metabolic genes (AMGs), plays a critical role in marine ecosystem function by influencing biochemical cycles and genetic diversity in these environments. Despite the fundamental role viruses play in global environmental ecosystems, they remain an understudied aspect of microbial ecology and evolution, in part due to the methods available for studying virus host interactions in natural systems. Thus far, metagenomic analyses have been used to study the interactions of virus host pairs, but these types of analyses have their limitations in accurately linking viruses to hosts, or culture-based …

Genome-Based Pathogenicity Potential Of Salmonella Isolated From Diverse Sources, Jared Mr Crocco

Theses and Dissertations (Comprehensive)

Bacterial human pathogens are among the leading causes of death around the world, especially in low income and developing countries. One important element in a bacterium’s ability to cause disease are genes that directly contribute to pathogenicity called virulence factors. A second significant aspect are antimicrobial resistance genes which allow microorganisms to persist in the presence of antimicrobial agents. In this project I aimed to determine if Salmonella isolated from different sources differed in pathogenicity profiles based on the complement of genes identified through genomic analysis. Accordingly, Salmonella genomes were organized into 8 groups: animal, clinical, human, environmental, food, water …

Functionality Of The Type Vi Secretion System (T6ss) In Providencia Alcalifaciens., Katherine Hood

UVM Patrick Leahy Honors College Senior Theses

The Providencia genus is a member of the Enterobacteriaceae family of bacteria and is a set of emerging, opportunistic pathogens that are known to cause urinary tract infections and gastroenteritis (Shah et al., 2019). Specifically, Providencia alcalifaciens has been linked to several diarrheal outbreaks worldwide, raising public safety concerns (Shah et al., 2019; Shah et al., 2015; Hinenoya et al., 2009; Yoh et al., 2005). The genome of P. alcalifaciens 205/92, a clinical isolate, has been sequenced and was found to contain numerous genes with homology to many virulence factors in pathogenic Gram-negative bacteria including a type VI secretion system …

Deep Learning In Bioinformatics, Malik Yousef, Jens Allmer

Turkish Journal of Biology

Deep learning is a powerful machine learning technique that can learn from large amounts of data using multiple layers of artificial neural networks. This paper reviews some applications of deep learning in bioinformatics, a field that deals with analyzing and interpreting biological data. We first introduce the basic concepts of deep learning and then survey the recent advances and challenges of applying deep learning to various bioinformatics problems, such as genome sequencing, gene expression analysis, protein structure prediction, drug discovery, and disease diagnosis. We also discuss future directions and opportunities for deep learning in bioinformatics. We aim to provide an …

Unsupervised Multi-Resolution Analysis Of Protein-Protein Abundance Patterns In Infectious Exacerbation Of Copd, Eric Everingham

Theses

Despite consistently appearing as a top 5 cause of death domestically and internationally, understandings of the underlying biological interactions of COPD remain insufficient. Particularly, early identification of highly vulnerable patients that may experience more severe infectious exacerbation is a challenge during diagnostics. This project leverages unsupervised clustering and multi-resolution decomposition of proteomic abundance profiles in a small cohort of COPD subjects to identify candidate biomarkers of heightened exacerbation risk. As part of an ongoing study, serum and sputum samples were collected during well visits (stable illness) from n=67 subjects, and analyzed using quantitative proteomics. A scores principal component analysis was …

Csrp1 Expression Is Associated With A Mesenchymal, Stroma-Rich Tumor Profile And Poor Prognosis In Colon Cancer, Seçi̇l Demi̇rkol Canli

Turkish Journal of Medical Sciences

Background/aim: Cysteine and glycine-rich protein 1 (CSRP1) is involved in the cysteine-rich protein family and is a marker of smooth muscle lineages. In colon cancer, the expression of this gene is associated with poor prognosis. In this study, the aim was to reevaluate its prognostic relationship in independent cohorts and explore potential underlying biological processes that are linked to aggressive behavior in tumors with high CSRP1 expression, such as epithelial-to-mesenchymal transition (EMT), stromal fractions in the tumor microenvironment, and consensus molecular subtypes (CMSs). Materials and methods: RNA sequencing (RNAseq)-, microarray-, and single-cell RNAseq (scRNAseq)-based transcriptomic data were obtained from public …

Towards Improved Genomic Surveillance Of Organisms, Joseph L. Sevigny

Doctoral Dissertations

DNA and RNA sequencing is an indispensable tool for the surveillance and monitoring of organisms. Technological advances and research opportunities over the past several years have transformed and driven my research questions; from understanding the impacts of environmental perturbations on complex benthic communities, to tracking and understanding emerging pathogens like SARS-CoV-2. All of them revolve around the use of DNA sequencing to ask fundamental questions about our understanding genomes and their relationship to phenotype and the environment. The advent of sequencing-based characterization has revolutionized our approach to studying organismal communities on a large scale, offering the ability to analyze vast …

Genomic Characterization Of Adolescent And Young Adult Cancers: Investigation Of Ewing Sarcoma Susceptibility And Chornobyl Thyroid Tumors, Olivia Lee

Dissertations & Theses (Open Access)

Adolescent and young adult (AYA) cancers, diagnosed between the ages of 15 and 39, can exhibit distinctive genetic and molecular characteristics. Reported epidemiologic findings and treatment outcomes based on pediatric and adult cancer studies are often not suitable for application to the AYA population, underscoring the need for more thorough genomic research. Advances in sequencing technologies have enabled comprehensive analyses of complex genomic characteristics of AYA cancers, crucial for understanding the underlying biology of these malignancies. Here, I have utilized advanced sequencing techniques and integrated analytic approaches to describe important genomic features in two different AYA cancer types: Ewing Sarcoma …

Algorithmic And Computational Approaches For Improving The Efficiency Of Mobile Genomic Element Discovery, A Bioinformatics Framework, Fatema Shormin

All Theses

Through this research, we are showcasing the application of computational approaches to the discoveries in the life sciences spectrum. Our current research not only focused on mobile genetic elements but also developed the computational methods that enabled these findings. We combined the biology sciences and computer science in our research, which is essentially multidisciplinary. To that end, this research intricately probed the role and implications of mobile genetic elements, emphasizing transposable elements. These dynamic components wielded substantial influence over genomic architecture's structure, function, and evolutionary adaptations. An integral component of our study is the innovative computational tool, Target/IGE Retriever (TIGER), …

Engaging Students In A Genetics Course-Based Undergraduate Research Experience Utilizing Caenorhabditis Elegans In Hybrid Learning To Explore Human Disease Gene Variants, Natalie Forte, Virginia Veasey, Bethany Christie, Amira Carter, Marli Hanks, Alan Holderfield, Taylor Houston, Anil Challa, Ashley Turner

Research, Publications & Creative Work

Genetic analysis in model systems using bioinformatic approaches provides a rich context for a concrete and conceptual understanding of gene structure and function. With the intent to engage students in research and explore disease biology utilizing the nematode Caenorhabditis elegans model, we developed a semester-long course-based undergraduate research experience (CURE) in a hybrid (online/in-person) learning environment—the gene-editing and evolutionary nematode exploration CURE (GENE-CURE). Using a combination of bioinformatic and molecular genetic tools, students performed structure-function analysis of disease-associated variants of uncertain significance (VUS) in human orthologs. With the aid of a series of workshop-style research sessions, students worked in teams …

Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone

Complex Biosystems PhD Program: Dissertations

The task of gene prediction has been largely stagnant in algorithmic improvements compared to when algorithms were first developed for predicting genes thirty years ago. Rather than iteratively improving the underlying algorithms in gene prediction tools by utilizing better performing models, most current approaches update existing tools through incorporating increasing amounts of extrinsic data to improve gene prediction performance. The traditional method of predicting genes is done using Hidden Markov Models (HMMs). These HMMs are constrained by having strict assumptions made about the independence of genes that do not always hold true. To address this, a Convolutional Neural Network (CNN) …

Structure V-1: A Mississippian Mica Workshop In Kershaw County, South Carolina, John Mclellan Dodge

Theses and Dissertations

This thesis reanalyzes the pottery assemblage of Structure V-1 at the Mulberry site (38KE12). Because Structure V-1 was originally hypothesized to be evidence of a late seventeenth century occupation at the Mulberry site, the framework I use for this research focuses on identifying evidence of community coalescence after Mulberry’s initial occupation ended. However, new evidence from both the pottery and radiocarbon analysis conclusively dates the structure to around the sixteenth century Mulberry I phase. With that new date in mind, I explore the role mica craft production within Structure V-1 might have had in linking the community at Mulberry to …

Performing A High-Throughput Virtual Screening (Hvts) To Identify Potential Therapeutic Targets Of Yb-1 Protein, Omar Karkoutly, Anupam Dhasmana, Kristopher Ezell, Kyle Doxtater, Vijian Dhevan, Subhash C. Chauhan, Manish Tripathi

Research Symposium

Background: Hepatocellular carcinomas (HCCs) is a primary malignancy of the liver. Hispanic-Texans have several risk factors and disparities that compound the risk of HCC diagnosis and treatment. The most used chemotherapeutic drug against HCC is sorafenib, but many liver cancers have developed a resistance to this drug. The knockdown of Y-box binding protein-1 (YB-1) has been shown to greatly increase sensitivity to sorafenib. In this study, we will discuss identification of potential YB-1 inhibitors, which can lead to re-sensitization of liver cancer cells to sorafenib.

Methodology: The RCSB protein data bank (pdb) was used to retrieve the crystal structure of …

A Prospective Randomized Clinical Trial To Assess Antibiotic Pocket Irrigation On Tissue Expander Breast Reconstruction, Jennifer N Walker, Blake M Hanson, Tayler Hunter, Shelby R Simar, Jesus M Duran Ramirez, Chloe L P Obernuefemann, Rajiv P Parikh, Marissa M Tenenbaum, Julie A Margenthaler, Scott J Hultgren, Terence M Myckatyn

Journal Articles

Bacterial infection is the most common complication following staged post-mastectomy breast reconstruction initiated with a tissue expander (TE). to limit bacterial infection, antibiotic irrigation of the surgical site is commonly performed despite little high-quality data to support this practice. We performed a prospective randomized control trial to compare the impact of saline irrigation alone to a triple antibiotic irrigation regimen (1 g cefazolin, 80 mg gentamicin, and 50,000 units of bacitracin in 500 mL of saline) for breast implant surgery. The microbiome in breasts with cancer (

Repurposing Normal Chromosomal Microarray Data To Harbor Genetic Insights Into Congenital Heart Disease, Nephi Walton, Hoang Nguyen, Sara Procknow, Darren Johnson, Alexander Anzelmi, Patrick Jay

Department of Medicine Faculty Papers

About 15% of congenital heart disease (CHD) patients have a known pathogenic copy number variant. The majority of their chromosomal microarray (CMA) tests are deemed normal. Diagnostic interpretation typically ignores microdeletions smaller than 100 kb. We hypothesized that unreported microdeletions are enriched for CHD genes. We analyzed "normal" CMAs of 1762 patients who were evaluated at a pediatric referral center, of which 319 (18%) had CHD. Using CMAs from monozygotic twins or replicates from the same individual, we established a size threshold based on probe count for the reproducible detection of small microdeletions. Genes in the microdeletions were sequentially filtered …

Bnfo 135: Programming For Bioinformatics​​, Jun Wu

Computer Science Syllabi

No abstract provided.

Generative Ai-Assisted Pathway Analysis And Interpretation Of Rna-Seq Experiment Data, Junguk Hur

AI Assignment Library

No abstract provided.