March 14, 2016
Sequence mining of EMR log data to understand clinician workflow
Modeling clinical workflow is an important pre-cursor to understanding how clinicians interact with an EMR and its features. Common methods of assessing clinical workflow include video recording or direct observations, or through directed user experience testing in a controlled environment. Assessing clinical workflow within an EMR can also be accomplished by analyzing EMR log data, which can provide an unbiased view of EMR use. Using log data to build workflow patterns requires appropriate pre-processing of the log data, and the use of several types of data mining techniques: frequent pattern mining, sequence mining, and sub-graph mining. This talk will…
March 7, 2016
Transformation of the advance care planning process through the use of an online computer-assisted instruction program and electronic health record enhancements at the University of Missouri
The Institute of Medicine report (1997) defines a good death as “good care at the end of life…depend[ant] on strong interpersonal skills, clinical knowledge, and technical proficiency, and it is informed by scientific evidence, values, and personal and professional experience” [1]. With only one-third of Americans having an advance directive [2], the failure to identify, choose, and define personal health preferences in end-of-life care has largely prevented the United States healthcare system from providing “good deaths” to many. The central hypothesis of this study is that through the development and deployment of a novel and meaningful tool, users will…
Feb. 29, 2016
Visualization of Female Breast Cancer Burden in Missouri
Background: In 2011, the female breast cancer incidence rate was about 120 per 100,000 population and the mortality rate was 24 per 100,000 population in Missouri. There is a critical need to build fact sheets in the form of interactive and dynamic map reports of accurate breast cancer burden among Missouri resident women at the sub-state and state level. Cancer incidence and mortality rates were traditionally displayed in data tables. Data tables meet the needs of some users. Aim: Use data visualization software to produce easily understood interactive reports with maps that display breast cancer incidence, survival and mortality…
Feb. 22, 2016
Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation
It has long been a challenge to determine the genetic origin of new characters in the evolution. The molecular mechanisms behind many morphological innovations are still unknown, including such striking evolutionary transitions as the appearance of the placenta. Our approach is based on using orthology to link genotype to phenotype. Orthology describes a relation between homologous genes (or chromosomal segments) that last diverged by a speciation event. Orthologous genes are often used to study evolutionary history because they tend to be conservative in molecular and biological functions. Using our orthology assignment pipeline, we have inferred orthologs in 38, primarily mammalian,…
Feb. 8, 2016
A Computational Pipeline for Comparative Study of Guide RNAs for CRISPR-CAS Genome Editing Systems
CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR Associated Proteins ) systems were recently developed into genome editing tools. Given their strength in multiplex targeting and easy programmability, CRISPR-CAS systems are already widely applied in academia and industry. While existing detection approaches could capture CRISPR arrays based on prior knowledge of sequence features, such predicted CRISPR arrays may lack essential structural features to enable RNA-processing for further immunity mechanism. Moreover, for efficient design of single guided RNA, unmet needs may remain to comprehensively discover structural features of CAS-nuclease/guide RNA complexes Here, we discuss a two-step seed-and-extend approach using a distributed computing environment, to detect CRISPR…
Feb. 8, 2016
A Deep Neural Network Method for Predicting Mitochondria-Localized Proteins in Plants
Targeting and translocation of proteins to the appropriate subcellular compartments is crucial for cell organization and function. Newly synthesized proteins are transported to mitochondria with the assistance of targeting sequences, which are complex, containing either an N-terminal presequence or a multitude of internal signals to target this organelle. Compared with experimental approaches, computational predictions provide an efficient and cost-effective way to infer subcellular localization for any given protein. However, it is still challenging to predict plant mitochondrial localized proteins accurately due to various limitations, and the performance of current tools is unsatisfactory. We present a novel computational approach for large-scale…
Feb. 1, 2016
An embarrassingly parallel application: High accuracy mapping of copy number variable regions
Finding gene copy number variation in a species is the cornerstone of genomic research. Most CNV finding tools and methods rely on comparing samples to the reference genome and on detecting certain signatures in the alignment data. These methods are robust and are significantly accurate, however they are not perfect. Different tools have various levels of success. Early research had access to few genome samples and these disadvantages could be overcome by using multiple tools for each study. With the development of significantly fast and cheap sequencing machines, a large numbers of samples can be produced in a short amount of time.
Jan. 25, 2016
Measuring the Speed and Efficacy of Clinical Decision Making through Medication History Visualizations
The rapid advancements in our ability to store, extract, and analyze data in the 20th and 21st century is overwhelming care providers. Large, diverse, complex and/or longitudinal datasets are continuously generated from a variety of instruments, sensors and/or computer-based transactions. Considering increased use of electronic medical records (EMRs) as a result of the American Recovery and Reinvestment Act of 2009, combined with a high frequency of poly-pharmacy patients, the number of mismanaged patients and medication errors has increased. Our study, holding all other things constant, hypothesizes that modifying the visual representation of the medication history within an EMR will increase…
Nov. 2, 2015
Identification of the causal mutation for a congenital limb abnormality in Mediterranean river buffalo
Mediterranean river buffalo have recently undergone strong selection for increased quality and quantity of milk for mozzarella cheese production. Strong selection for traits such as milk production are often associated with increased inbreeding, leading to decreased genetic diversity and an increase in genetic disease prevalence. Transverse hemimelia (TH) is a congenital developmental abnormality characterized by the absence of a variable portion of the distal limbs. It occurs at the rate of approximately 2-5% in Mediterranean river buffalo populations and causes significant production loss in affected animals as well as in carriers of the disease, which are eliminated from the breeding…