Feb. 8, 2018
MU-LOC: A Deep Neural Network Method for Predicting Mitochondrially 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 complex targeting sequences containing either an N-terminal pre-sequence or a multitude of internal signals. Compared with experimental approaches, computational predictions provide an efficient way to infer subcellular localization of a protein. However, it is still challenging to predict plant mitochondrially localized proteins accurately due to various limitations. Consequently, the performance of current tools can be improved with new data and new machine-learning methods. We present MU-LOC, a novel computational approach for large-scale…
Jan. 31, 2018
An Analysis of Diabetes Mobile Applications Features Compared to AADE7TM: Addressing Self-Management Behaviors in People with Diabetes
Diabetes Self-management (DSM) applications (apps) have been designed to improve knowledge of diabetes and self-management behaviors. However, few studies have systematically examined if diabetes apps followed the American Association of Diabetes Educators (AADE) Self-Care BehaviorsTM guidelines. The purpose of this study was to compare the features of current DSM apps to the AADE7TM guidelines. In two major app stores, we used three search terms to capture a wide range of diabetes apps. Apps were excluded based on five exclusion criteria. A multidisciplinary team analyzed and classified the features of each app based on the AADE7TM. We conducted interviews with six…
Jan. 28, 2018
Collaborations across disciplines: MU Thyroid Nodule Electronic Database (MU-TNED), a multidisciplinary informatics approach
Thyroid nodules are common findings and thyroid cancer is projected to be one of the leading causes of cancer in women. The EHR includes the necessary data needed to connect clinical research with patient outcomes. The objective for this project was to develop and validate a usable informatics tool for clinicians and researchers to record, analyze, and be able to manipulate the clinical and research data to benefit all collaborators. The tool was specifically designed to enable follow-up in a longitudinal manner to support multiple aspects of research. The informatics tool MU-TNED was designed with a multidisciplinary team including the…
Dec. 1, 2017
Use of the N-ary Relational Schema to Atomize Compound Relational Triples
Electronic medical records document health information in structured format and in unstructured free text format. Health information in structured format contains laboratory results, vital signs, patient demographics etc. The unstructured free text is the prime source of healthcare information documenting providers’ interpretations of health conditions, diagnoses, medical interventions, impressions, etc. In order to uncover unknown information and search for patterns in health data with computational methods, we need to structure the unstructured free text data. For that, we use information extraction, a computational technique for analyzing free text and deriving structured information. Extracted information from free text can be represented…
Nov. 26, 2017
Effects of evolutionary pressure on histone modifications
With the advent of next-generation sequencing technologies, a considerable effort has been put into sequencing the epigenomes 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 orthologous regions of the two species. In this work, we have used various measures of orthologous similarity between each pair of orthologous genes and explore how histone modifications are conserved with respect to changes in these similarity measures. These measures of similarity include “codon usage…
Nov. 3, 2017
Investigating genome composition in multiple bee species
The honey bee Apis mellifera was the first eusocial animal to have its genome assembled. Analysis of the complete draft sequence of the honey bee genome revealed several interesting features compared with the other metazoan genomes: a low but heterogeneous GC content, an overabundance of CpG dinucleotides and a lack of repetitive elements. The average GC content of the honey bee genome is only 33%, but GC content is highly heterogeneous, ranging from 11% to 67%, with a bimodal distribution. Furthermore, unlike genes in most other metazoans, honey bee genes are overly abundant in regions of low GC content (<30%).
Oct. 23, 2017
A Geospatial Health Context Table for Supporting Public Health Research
This project develops a Big Data table that allows researchers to query across and among multiple data sources integrated by location. The big table created in this way uses location as the fundamental linkage between data sets. This is the power of geospatial analysis and forms the foundation for the development and interaction with the Health Context Table. The approach utilizes a dense point file populated with attribution derived or obtained directly from public data sources and associated geospatial analysis. The database created extends across the entire continental United States comprising over 300 million points. The data table has at…
Sep. 26, 2017
Blockchain Technologies for Healthcare – Technical Challenges and Potential Applications
Blockchain is a technology of distributed ledger originally applied in the financial world. Bitcoin is one of the most adoptable cryptocurrencies based on Blockchain technique. The success of Bitcoin in technology means Blockchain has the potential for decentralized transaction validation, data provenance, data sharing, and data integration in different fields. Ethereum is a Blockchain-based platform with smart contract functionality inside. Smart contract is similar to coded protocol which enforce the workflow of data sharing. To date, most of academic papers for Blockchain in non-financial domains are still very conceptual and creating skepticism about the applicability of the technology and what it can achieve. At MU, we are experiencing the Ethereum platform to develop informatics tools for…
Sep. 12, 2017
Data Mining for Genetic Combinations Relevant to Autism Subtypes
Autism is characterized by a complex set of behavioral, social, and cognitive deficits. Extensive variation of these phenotypes suggests the existence of autism subtypes that likely have distinct genetic etiologies. The lack of unifying genotypes common to autism patients supports this subtype structure, and suggests that the onset of autism is due to combinations of genetic factors. The ability to precisely diagnose autism subtypes using genetic markers would lead to earlier and more specific treatments and improve outcomes, stressing the need for research which increases our understanding of the genetic etiologies of autism subtypes. In this research, we identify combinations…