Understanding disease through integrated molecular and clinical analyses
Abstract:Traditional biomedical experiments are designed to study a single cohort for a single disease using a single technology. By studying disease with such a narrow lens, researchers make discoveries that are not reproducible because they are not representative of the real heterogeneity of disease. By integrating data from over 40 studies and 7,000 patients, we establish a robust signature of disease which correlates with disease activity and persists across blood, tissue, and sorted cell populations. We compare relationships of 104 diseases based on molecular and clinical manifestations from 41,000 gene expression samples and 2 million patient records. Finally, we contextualize…
Epigenetic adaptation to environment in long lives trees
Oak represents a valuable natural resource across Northern Hemisphere ecosystems, attracting a large research community studying its genetics, ecology, conservation, and management. Here we introduce a draft genome assembly of valley oak (Quercus lobata) using Illumina, PacBio and Dovetail sequencing of adult leaf tissue of a tree found in an accessible, well-studied, natural southern California population. We next utilize this genome to carry out landscape epigenetics studies. DNA methylation in plants affects transposon silencing, transcriptional regulation and thus phenotypic variation. One unanswered question is whether DNA methylation could be involved in local adaptation of plant populations to their environments. If methylation…
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…
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…
Analysis of Influence of Additional Diagnostic Clues During Pathology Diagnosis
Traditional pathology diagnostic process routinely relies on disease-specific diagnostic clues. We propose an informatics pipeline to identify and quantify additional diagnostic clues that, in addition to traditional disease-specific clues, can improve diagnostic outcomes and decrease the chance of diagnostic pitfalls. We used our PathEdEx whole-slide imaging platform to record user activities related to diagnosing a cancerous tissue slide along with the biological features that were noted in the tissue by the examining pathologist as relevant to the diagnosis. To identify and quantify additional diagnostic clues that can improve diagnosis, we extended association rule mining techniques to measure information gain of the additional…
A Blockchain Platform for Healthcare
Although Blockchain is much more investigated within the financial sector, it is gradually edging into other industries such as healthcare. Blockchain provides a trust mechanism in a cyber-system. Various last mile issues left to be resolved for establishing an end to end trust cyber physical system. This talk will discuss various aspects of blockchain last mile issues applied in the medical area. Especially, for data integrity, trust and secure data sharing technology specially fit for precision medicine supporting patient centric healthcare model. This is an international collaboration project among Asia University, Taiwan, China Medical University Hospital, Taiwan, University of Missouri,…
MUII Dissertation Defense-Awatef Ben Ramadan
Steps in Transforming the Missouri Cancer Registry (MCR) from an Incidence Registry to a Survival Registry Female Breast cancer (FBC) is the most common invasive cancer among women of all races and ethnicities in the United States (US). We aimed to estimate FBC burden in Missouri in terms of FBC incidence, mortality and survival rates; to visualize these results; and to assess the usability of the Missouri Cancer Registry and Research Center’s (MCR-ARC)’s interactive maps. FBC survival data were calculated from 2004 to 2010 after matching MCR’s FBC cases with Missouri death records, Social Security Death Index (SSDI),…
MUII Dissertation Defense-Lynsey Whitacre
Alternative Applications of Whole Genome De Novo Assembly in Animal Genomics Improvements in whole genome sequencing technologies have allowed substantial increases in the amount of data that can be generated on a single individual. This has facilitated many de novo genome assembly projects in the animal sciences. The overarching goal of de novo assembly is to overlap sequencing reads to construct contiguous sequences, also known as contigs or scaffolds, representing the genome. Once a high quality de novo assembly is constructed, it is often used to determine variation in the genome or simply as a reference for future resequencing projects.
MUII Dissertation Defense- Rhonda Archie
Information Technology (IT) Interconnectivity in a Rural Health Setting: A Conceptual Model Current and past developments in Health (HIT) systems in rural settings have focused on the use of electronic health records by health professionals. These systems were conducted in standalone mode, or coupled with the integration of HIT systems of two or more other HIT systems. In addition, this lack of interconnectivity involved diminished coordination in information sharing among the systems (Bahensky 2008; McCullough 2009). Grossman (2006) and Kevin (2008) investigated the state of HIT systems’ interconnectivity using networks in a rural health setting to promote sharing and…