Oct. 2, 2019
LARGE-SCALE SOYBEAN GENOME-WIDE VARIATION WORKFLOW AND ASSOCIATION ANALYSIS USING DEEP LEARNING
With the advances in next-generation sequencing technology and significant reduction in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations, and apply the knowledge towards improvements in traits. To facilitate large-scale NGS resequencing data analysis of genomic variations efficiently, we developed a systematic solution using high-performance computing environment, cloud data storage resources and graphics processing unit computing with cutting-edge deep learning approach. The solution contains an integrated and optimized variant calling workflow called ‘PGen’, a quantitative phenotype prediction model using convolutional neural network and an algorithm to study genome-wide association…
Oct. 1, 2019
Extension of the informatics framework for the structurization of free text diagnostic reports
In this seminar presentation, we will briefly discuss our recent project to extend our informatics pipeline for the structurization of free-text diagnostic reports with an information theory-based approach. We will focus on the steps of this approach that are for quantifying and measuring information in free text diagnostic reports. This is a work in progress.
Sep. 24, 2019
Analysis of Curated Toll-Like-Receptor Co-expression Network Reveals associations among RNAseq Expression and Immune system modulation in patients with Colorectal Cancer
This project is concerned with improving immune system capabilities in the context of immunotherapy for colorectal cancer treatments. Immunotherapies called checkpoint inhibitors are monoclonal antibody treatments that have been proven to be effective in small percentages of sample populations, especially upon a combination of treatments (e.g. PD-1 with CTLA-4). However, the effectiveness of the treatment response often accompanied by contraindications of autoimmunity. Allocation of our efforts towards computational modeling of communication networks specific to TLR signaling affords a more intimate study of innate immunity, and the corresponding responses generated, as they pertain to the Tumor Microenvironment. Targeting the mechanisms…
Sep. 24, 2019
Addressing Challenges of Deep Learning for Post-Disaster Damage Classification
The effectiveness of natural disaster response functions has increasingly relied on information extracted from remotely-sensed imagery – particularly for the time-critical and often large-scale task of assessing post-disaster damage to the built environment. Despite a recent push to operationalize deep learning (DL) technologies to assist this task, several overlooked and unaddressed challenges limit DL’s applicability. First, very little DL research in the remote sensing domain utilizes the geographic variation in objects of interest or ancillary spatial data layers as features which could help the algorithms learn. Second, there is a scarcity of labelled training data depicting the effects of common…
Sep. 11, 2019
The Role of Informatics in the Implementation of Population Precision Health
Abstract: Precision health is an emerging concept in healthcare. Coupled with the movement towards Learning Healthcare Systems, there is an opportunity to transform how care and prevention are imagined. To realize this vision requires collection and analysis of large amounts of disparate data, development of knowledge from the data, and seamless ways to deliver the knowledge back to clinicians and, increasingly, patients. Informatics is expected to play a key role in precision health. In this presentation, Dr. Williams will provide some background and philosophy on different terms in current use, will introduce Geisinger’s MyCode Community Health Initiative—the largest implemented population…
Aug. 28, 2019
Using Geospatial Context: Facilitating Geospatial Analysis in Research
This presentation will briefly review the Geospatial Context Big Table status and its current evolution. Then the presentation turns to two projects that have used or are using geospatial context in the analysis and visualization of their results. The first project is a zoonotic disease study originally undertaken as a class project and lab rotation. The second is a study of Thyroid Cancer and possible exposome radiation influences and population stability metrics. In each case focus will be on developing focus and assembling data and possible surrogates, compiling into units of analysis, and the modeling of those relationships.
Aug. 19, 2019
Applying Blockchain Technology to Enhance Clinical Trial Recruitment
Patient recruitment for clinical trials is known to be a challenging aspect of clinical research. There are multiple competing concerns from the sponsor, patient and principal investigator’s perspectives resulting in most clinical trials not meeting recruitment requirements on time. Conducting under-enrolled clinical trials affects the power of conclusive results or causes premature trial termination. Blockchain is a distributed ledger technology originally applied in the financial sector. Its features as a peer-to-peer system with publicly audited transactions, data security, and patient privacy are a good fit for the needs of clinical trials recruitment. The “Smart Contract” is a programmable self-executing protocol…
July 25, 2019
Graduate Research Assistantship in Biomedical Imaging Informatics (available Aug. 2019):
Many heart patients have not benefitted from MR scans due to technical limitations. A Ph.D. student is sought to further develop the new TRENDimaging software package to analyze complex and irregular heart motions. This will support wider application of ultrafast cardiac MR scans. The position is supported by a new grant from the American Heart Association. More information about the research group is available at: https://cafnrfaculty.missouri.edu/vandoren/ Those with background or interests in scientific computing, biomedical imaging, software engineering, and / or statistical approaches of data science are invited to submit a resume with contact information for two to three…
July 10, 2019