Decoding the auxin code: uncovering new players in the auxin pathway through WGCNA analysis
Auxins are a class of phytohormones in plants which have an active role in growth and development. The Auxin hormone control pathway in maize meristem is not well studied and has significant scope for in-depth exploration. Previous studies have not shown much novel information about how Auxin is regulated. Weighted Gene co-expression analysis takes results from differentially expressed genes and organizes them into clusters and modules showing possible interactions and co-regulation. These clusters usually highlight unique interactions which cannot be seen by most other methods. We present our ongoing work in building gene co-regulatory networks using certain gene knockouts in…
RDF-Based Method to Uncover Implicit Health Communication Episodes from Unstructured Health Data
Health communication is the process that coordinates health services such as specimen transaction, oral interactions, medical records, and more. Healthcare workflows are based on communication established historically through the practice of healthcare or by the leadership in health institutions. However, during healthcare practices communication doesn’t flow according to plan; interpersonal miscommunication, technical glitches, information overload, etc. risk inefficient healthcare services. We hypothesize that health records contain information related to communication and we can retrieve it in order to address issues of communication. We present an informatics pipeline to retrieve health communication episodes from unstructured health data. The method uses Resource…
Comparison of histone patterns in orthologus regions between mouse and human tissues
With the advent of next-generation sequencing technologies, a considerable effort has been put into sequencing the epigenome of different species. The efforts such as “Encode” and “Roadmap” epigenomics projects provide an opportunity to compare epigenomes across species (especially between human and mouse). This study is an effort to understand how different histone modifications vary/co-appear between orthologus regions of the two species. In this work, we have also used various measures of orthologus similarity between each pair of orthologus genes and explore how histone modifications are conserved with respect to changes in these similarity measures. These measures of similarity include “gene…
Building an online quality improvement information exchange for home visiting programs in Missouri
Early childhood home visiting programs date back to the 1880s and deliver a vital public service of providing and connecting families with health, educational, and economic resources to support optimal development. Continuous quality improvement (CQI) consists of systematic and continuous actions that lead to measurable improvement in services for targeted groups. CQI initiatives (CQII) in home visiting programs have traditionally occurred within a local implementing agency (LIA), parent organization, or funding provision. LIA CQII are often lost to the benefit of external agencies facing similar challenges. We developed a web-based environment, the Gateway, to virtually connect and engage users within…
Genetic variation, population structure, and genome assembly of the threatened Neosho madtom catfish
The Neosho madtom (Noturus placidus) is a small catfish, generally less than 3 inches in length, unique to the Neosho-Spring River system within the Arkansas River Basin. It was federally listed as threatened in 1990, largely due to habitat loss. As part of conservation efforts, we generated whole genome Illumina paired-end sequence data from ten Neosho madtom (average 39X coverage) originating from three geographically separated subpopulations to evaluate genetic diversity and population structure. One slender madtom (Noturus exilis) was also sequenced as an outgroup. Although over 1 million variants were found between Neosho and slender madtom, only 86,155 SNPs were…
MUII Comprehensive Exam – Awatef Ben Ramadan
Steps in Transforming the Missouri Cancer Registry (MCR) from an Incidence Registry to a Survival Registry The Problem: Breast cancer is the most common invasive cancer among women of all races and ethnicities in the United States (US). About 12 percent of women will be diagnosed with breast cancer in one stage of their lives in the US. Significance: The Missouri Cancer Registry (MCR) needs to be transformed from an incidence registry to a survival registry to accurately measure the impact of Missouri public health programs. Using interactive mapping software reports of maps and statistics to improve data visualization and…
MUII Comprehensive Exam Announcement – Lynsey Whitacre
De novo assembly and comparison of whole genome consensus sequences for nine breeds of beef cattle With the recent rise in re-sequencing efforts fueled by next-generation short read sequencing technologies, we have lost sight of the overarching goal of trying to understand what functions a genetic variant has at the molecular level, which is one of the main reasons we started sequencing genomes to begin with. Instead, immense focus has been placed on identifying SNPs that are associated with important phenotypes. These association studies have undoubtedly allowed forward progression of the industry through genetics through providing variants that can be…
Quantification of selective constraint in the polyploid genomes of Arabidopsis thaliana and Brassica rapa
Polyploidy is an important mechanism in plant evolution. We are interested in studying how selective pressures change after a lineage experiences whole genome duplication (WGD) or triplication (WGT). Alpha duplication is the most recent WGD event in Arabidopsis. Then a WGT event occurred in genus Brassica when they diverged from Arabidopsis thaliana. We examined selection at both the population and the species level, by calculating the ratio of non-synonymous to synonymous polymorphisms (pN/pS) and computing Ka/Ks between species. In both lineages of Arabidopsis and Brassica, pN/pS values are larger than Ka/Ks, in accord with the expectation that most populations include…
Identifying Patients at Risk of High Healthcare Utilization
Objective: To develop a systematic and reproducible way to identify patients at increased risk for higher healthcare costs. Methods: Medical records were analyzed for 9,581 adults who were primary care patients in the University of Missouri Health System and who were enrolled in Medicare or Medicaid. Patients were categorized into one of four risk tiers as of October 1, 2013, and the four tiers were compared on demographic characteristics, number of healthcare episodes, and healthcare charges in the year before and the year after cohort formation. Results: The mean number of healthcare episodes and the sum of healthcare charges in…