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Thyroid Cancer Informatics

Survival prediction is important both to clinicians and patients; ensuring the best course of treatment is selected to manage the thyroid cancer. In 2018, there was an estimated half a million new thyroid cancer diagnoses and 41,071 deaths. Unlike other tumors whose mortality has decreased over the last two decades, thyroid cancer mortality rates have increased. Existing risk

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A Case-Control based Genomic Analysis of Chronic Obstructive Pulmonary Disease

Chronic Obstructive Pulmonary Disease (COPD) is a respiratory illness that affects millions of people all over the world. It is a major cause of chronic morbidity and mortality and a serious global public health problem. COPD is the fourth leading cause of death worldwide. Although the environmental causes of COPD which predominantly include cigarette smoking

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Methods for Measuring Geodiversity in Large Overhead Imagery Datasets

This research introduces some of the first geo-computational methods to address a key gap in the artificial intelligence (AI) and big data literature as it relates to the geosciences and remote sensing: the lack of understanding of the global feature representativeness of labels in large remotely-sensed imagery (RSI) datasets. Issues of data fairness, heterogeneity and

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The Genescape Allele Catalog Development for Precise Identification of Causative SNPs

Next-generation sequencing (NGS) has become more popular in the modern-day. Large amounts of next-generation resequencing data have been generated and are available online for various organisms including soybeans. However, current genome-wide association study (GWAS) prediction tools simply identify the most significant SNP based on Manhattan plots and still have some limitations in pinpointing the exact

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Building a Population-based Childhood Cancer Data Ecosystem: Challenges and Opportunities for Informatics and Data Science

Childhood cancer is a relatively rare disease diagnosed in over 16,000 U.S. children and adolescents (ages 0 – 19) each year.  While 84% of children with cancer survive 5 years or more, cancer remains the second leading cause of death in children after accidents. Molecular variations make all childhood cancers extraordinarily rare and difficult to study.  The

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Evaluating the effectiveness of transfer-learning with DeepVariant

Genomic data has become ubiquitous for bioinformaticians; however, successfully inferring biological meaning depends upon the sensitive prediction of differences between genomes. The most popular method to infer short sequence variants is the Genome Analysis Toolkit (GATK). While GATK provides rigorous guidelines, the methods require knowledge-intensive refinement as software and sequencing technologies advance. A recent advancement

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Tool Development for Analyzing Arrhythmias in Fast Cardiac Magnetic Resonance Scans

Cardiac magnetic resonance (CMR) scanning provides a method to diagnose cardiac disease. For obtaining an effective image, the standard procedure of CMR requires patients to hold their breath during the scanning, but it is difficult for frail patients in clinic. Furthermore, standard CMR imaging depends upon averaging together regular cardiac cycles, which is disrupted by

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Using Big Data to Identify Possible External Risk Factors for Poorly Understood Cancers

Worldwide, cancer is the second leading cause of death (Cancer, 2012). There were 17 million new cases and 9.6 million cancer deaths worldwide in 2018, including approximately 1.7 million new U.S. cases and 600,000 U.S. cancer deaths (Cancer Facts & Figures 2018 | American Cancer Society, 2018; Worldwide Cancer Statistics, 2019). The worldwide incidence of cancer is expected to increase

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An Evaluation of Physician Burnout by EMR Use Characterization and Correlation

Burnout disproportionately affects healthcare workers and continues to rise.  This condition potentially contributes to cost, quality and patient safety risk in an already overburdened United States healthcare system.  While the causes of burnout are complex, evidence exists pointing to Electronic Medical Record use (EMR) as one major contributor due to the increased clerical burden that decreases patient

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Early Detection of Glaucoma Using Electronic Health Records

Glaucoma is the second leading cause of irreversible blindness worldwide. About 70 million people have glaucoma, and nearly 4.4 million people are blind from optic nerve damage due to undiagnosed glaucoma. Besides, the current glaucoma growth rate and its economic burdens are unsustainable. As a result, warrant a systematic evaluation for glaucoma risk assessment and

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