Sep. 10, 2021

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 are well-documented, to this date the genetic underpinnings of COPD remain largely unknown. Furthermore, in the current landscape of a respiratory pandemic, COPD patients are at a much higher risk for developing other respiratory illnesses and co-morbidities. In this study we use genomic data from…

Sep. 7, 2021

Large Scale Study of the Long-Term Effects of COVID-19 Infection Using Aggregated EHR Data

COVID-19 is known to have complex multi-system effects but the lasting effects of infection remain poorly understood. With the number of confirmed infections globally surpassing 200 million it is more important than ever to understand the potential long-term implications of COVID-19 infection on patient health. We have created a pipeline to analyze data from over 1.4 billion medical encounters recorded in the Cerner Real World Data EHR database. We apply this pipeline to analyze the effect of COVID-19 infection on the rate of subsequent new dementia diagnoses 30+ days after the infection period in patients hospitalized with pneumonia with no…

Aug. 30, 2021

FASTAptameR 2.0: A Web Server for Combinatorial Selections Analysis

Combinatorial selection strategies are powerful tools that allow researchers to simulate selective pressures over time on randomized sequence libraries. This is important for lead discovery and optimization and for understanding selection dynamics. Given the evolutionary nature of these experiments, high-fitness sequences will enrich, whereas low-fitness sequences will deplete. These experiments can generate large magnitudes of data, thus driving a need for high-throughput sequence (HTS) analyses that can utilize sequence-specific evolutionary trajectories. Recently, the selections field has benefitted from several software for HTS analysis. However, these software have a high entrance barrier for many users because they are only accessible through…

May 17, 2021

MD – Informatics PhD student, Cynthia Tang, wins the American College of Physicians 2021 National Virtual e-Poster Competition

Cynthia Tang is a first-year MD- Informatics PhD program student in Dr. Henry Wan’s lab. In her poster presentation “Assessing the clinical, epidemiological, and molecular implications of SARS-CoV-2 in Missouri”, Cynthia presented her research findings on SARS-CoV-2 viruses. In the May 14, 2021 American College of Physicians (ACP) town hall meeting, the Award Committee announced this news and said that ~600 abstracts were submitted in the medical student division, and 200 were selected as finalists to compete in the ePoster competition. Cynthia was one of five national research winners. Congratulations to Cynthia and Henry!  https://www.acponline.org/membership/residents/competitions-awards/acp-national-abstract-competitions/…

April 29, 2021

Bioinformatics Research and Collaboration in the Era of Big Data and Precision Medicine

As we have entered the precision medicine and big data science era, there are many unmet challenges on identifying the disease related information from large, heterogeneous data, and translating the findings for clinical use. Among these challenges, one is how to effectively identify driver mutations and genes in cancer genomes, especially those with the potential for druggable targets for the development of molecularly targeted cancer therapies. In this talk, I will first review the computational methods and tools for detecting cancer driver genes and mutations from cancer big data. Then, I will present our informatics approaches for identifying cancer mutations…

April 29, 2021

Detection of changes in allelic frequencies due to selection on complex traits in the genomes of pigs from four genetic lines using generation proxy selection mapping

Most economically relevant traits in pig breeding programs are controlled by numerous causal variants spread across the genome and undergo selection pressure to improve the genetic merit of commercial pigs.  As a result, small changes in allele frequency over relatively short time scales are induced at these loci.  Identification of genomic loci that exhibit directional changes in allele frequency due to artificial selection identifies areas of the genome that can aid in genetic improvement of populations of pigs.  Thus, the objective of this research was to use Generation Proxy Selection Mapping (GPSM) of the dependent variable birth date to detect…

April 12, 2021

CANCER PRIORITY BY RACE

Cancer is one of the most common and deadly diseases and its incidence is increasing. There are over one hundred types of cancer and they have a varied impact on society and the individuals affected. Racial disparities play a role in the outcome of many diseases. How does race impact the types of cancer that should be prioritized? How does incidence rate, death rate, and stage at diagnosis vary by race/ethnicity? Could cancer rates be improved by considering race/ethnicity? Please contact Robert Sanders (sandersrl@missouri.edu) for Zoom information.

April 12, 2021

De-novo SuperTranscriptome assembly from the nodal root growth zone of maize inbred line FR697

Certain cultivars of maize show increased resistance to water deficit conditions by maintenance of root growth. To better understand the molecular mechanisms related to this adaption, nodal root growth zone samples were collected from the reference inbred line B73 and inbred line FR697, which exhibits a relatively greater ability to maintain root elongation under water deficits. Plants were grown under various water stress levels in both field and controlled environment settings. FR697-specific RNA-Seq datasets were generated and used for a de-novo transcriptome assembly to characterize any genotype-specific genetic features. The assembly was aided by an Iso-Seq library of transcripts generated…

March 23, 2021

Design and Evaluation of a Longitudinal Method to Measure Physician Burnout in the Clinical Workflow

Burnout, a condition characterized by emotional exhaustion, listlessness, and an inability to cope, is demonstrably more prevalent among healthcare providers than other occupations.  Burnout is fundamentally a longitudinal problem, but traditional instruments for measurement such as the Maslach Burnout Inventory (MBI) and the Professional Fulfillment Index (PFI) are time-consuming, expensive, and complex to administer, making it prohibitive to collect repeated measures to capture burnout feedback with weekly, monthly or even yearly frequency. A Single-Item Burnout Measure (SIBM) has been previously validated to highly correlate to the emotional exhaustion dimension of the MBI, and thus can serve as a proxy measure…