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…

A Metagenomic Analysis of the Effect of Residual Feed Intake on Rumen Metabolism

Ruminant animals have a symbiotic relationship with gastrointestinal microorganisms in the rumen where microbes degrade compounds that can be used in the host animal’s metabolism. Currently, changes in the diet or feed efficiency of the sheep results in differences to the rumen’s microbiota population. By using a metabolic approach, the effects of differing residual feed intake (RFI) on the rumen’s microbiome are analyzed to determine the network interface between the host’s metabolism and rumen microbiome. These findings demonstrate important network structure differences between low and high RFI animals providing a greater understanding of the complexities in the rumen ecosystem.

Big Data Colloquium Distinguished Speaker – Dr. Jianjiong Gao

Thanks to the advancements of technology such as next-generation sequencing, an overwhelming amount of cancer genomics data has been generated by large-scale cancer genomics projects such as The Cancer Genome Atlas (TCGA). This has imposed an increasing challenge in the translation of the wealth of the resulting “big data” into biological discoveries and clinical applications. In this talk, I will present two major platforms we developed at Memorial Sloan Kettering Cancer Center to address this challenge: cBioPortal and OncoKB. The cBioPortal for Cancer Genomics (http://cbioportal.org/) collects, integrates, and visualizes multi-dimensional, high-level cancer genomics and clinical data. It was specifically…

Diabetes Self-Management Applications: Focus Group Findings from Elderly Diabetic Patients

The number of mobile diabetes self-management (DSM) apps has risen. However, it is not certain whether these apps provide effective DSM for elderly diabetic patients. The purpose of this study was to identify barriers in functionality and usability related to needs of elderly diabetic patients for DSM apps. We conducted two focus groups with 10 older diabetic patients. Participants completed a set of DSM tasks using nine representative DSM apps on iPads. They answered a questionnaire which included basic information, System Usability Scale (SUS), app specific questions, and open-ended questions. We found DSM apps did not adhere to diabetes guidelines.

Big Data Colloquium Distinguished Speaker – Dr. Philip S. Yu

The problem of big data has become increasingly importance in recent years. On the one hand, big data is an asset that potentially can offer tremendous value or reward to the data owners. On the other hand, it poses tremendous challenges to distil the value out of the big data. The very nature of big data poses challenges not only due to its volume, and velocity of being generated, but also its variety, where variety means the data can be collected from various sources with different formats from structured data to text to network/graph data, etc. In this talk, we…

MUII’s Data Science and Analytics Master’s Program to Deliver Cutting-Edge Training to the NGA with $12 Million Federal Contract

The University of Missouri College of Engineering has just been awarded a five-year, $12 million contract to deliver a comprehensive data science education program that will provide cutting-edge analytical training for the NGA workforce and potentially other members of the U.S. Intelligence Community (IC). This new program will address key education and training needs identified by NGA. The program is a collaboration between the MU College of Engineering’s Center for Geospatial Intelligence (CGI) and the MU Informatics Institute’s Data Science and Analytics (DSA) master’s degree program. The newly established effort is part of the NGA College’s Learning Outreach program that partners with qualified…

Soybean science blooms with supercomputers

Soybean Knowledge Base (SoyKB) project finds and shares comprehensive genetic and genomic soybean data through support of NSF-sponsored XSEDE high performance computing. SoyKB helps scientists improve soybean traits. XSEDE Stampede supercomputer 370,000 core hour allocation used in resequencing of over 1,000 soybean germplasm lines. XSEDE ECSS established Pegasus workflow that optimized SoyKB for supercomputers. SoyKB migrated workflow to XSEDE Wrangler data intensive supercomputer. http://www.nsf.gov/news/news_summ.jsp?cntn_id=189594&WT.mc_id=USNSF_195&WT.mc_ev=click