Chi-Ren Shyu

Chi-Ren Shyu
University of Missouri | Mizzou · Institute for Data Science and Informatics

Doctor of Philosophy

About

234
Publications
32,682
Reads
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3,522
Citations
Introduction
CR Shyu is the founding director of the University of Missouri Institute for Data Science and Informatics and Paul K. and Dianne Shumaker Endowed Professor of Engineering. His research interests include explainable AI, biomedical informatics, geospatial analytics, visual analytics, digital clinical trials, and data mining. He is a fellow of American Medical Informatics Association.
Additional affiliations
June 2014 - October 2016
University of Missouri
Position
  • Chair
September 2000 - present
University of Missouri
Position
  • Paul K. and Dianne Shumaker Endowed Professor
August 1999 - July 2000
Purdue University
Position
  • PostDoc Position
Education
January 1995 - August 1999
Purdue University
Field of study
  • Electrical and Computer Engineering
August 1993 - December 1994
Purdue University
Field of study
  • Electrical Engineering

Publications

Publications (234)
Article
Full-text available
Background Circulating tumor cells (CTCs) are liquid biopsies that represent micrometastatic disease and may offer unique insights into future recurrences in non-small cell lung cancer (NSCLC). Due to CTC rarity and limited stability, no stable CTC-derived xenograft (CDX) models have ever been generated from non-metastatic NSCLC patients directly....
Article
Background: Patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may have an increased risk of acute cardiovascular events in the convalescent period. Aims: To determine whether patients with pneumonia associated with SARS-CoV-2 infection have an increased risk of cardiovascular events during the convalescent period....
Article
Full-text available
After the COVID-19 pandemic reached Missouri, the Show-Me ECHO (Extension for Community Healthcare Outcomes) project initiated COVID-19 ECHO virtual knowledge-sharing networking sessions. These live-interactive weekly sessions inform participants about up-to-date evidence-based recommendations and guidelines through expert didactic lectures followe...
Article
Background: A clinical trial management system (CTMS) is a suite of specialized productivity tools that manage clinical trial processes from study planning to closeout. Using CTMSs has shown remarkable benefits in delivering efficient, auditable, and visualizable clinical trials. However, the current CTMS market is fragmented, and most CTMSs fail...
Article
Background: Circulating tumor cells (CTCs) represent micrometastatic disease and may offer unique insights into future recurrences in lethal malignancies, including non-small cell lung cancer (NSCLC). Due to CTC rarity and limited stability, no CTC-derived xenograft (CDX) models have ever been generated from non-metastatic NSCLC patients directly....
Article
Recent studies report increased frequency of hyperglycemic and hyperketotic emergencies in youth with T1D and coronavirus disease 20 (COVID-19) . Morbidity and mortality risk may be increased in individuals who develop diabetic ketoacidosis (DKA) or hyperglycemic hyperosmolar syndrome (HHS) with concurrent COVID-infection. Using a Cerner RealWorld...
Article
Full-text available
Background Case series without control groups suggest that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may result in cognitive deficits and dementia in the post-infectious period. Methods Adult pneumonia patients with SARS-CoV-2 infection (index hospitalization) and age, gender, and race/ethnicity matched contemporary co...
Article
Objectives: Acute ischemic stroke patients with severe acute respiratory syndrome coronavirus maybe candidates for acute revascularization treatments (intravenous thrombolysis and/or mechanical thrombectomy). Materials and Methods: We analyzed the data from 62 healthcare facilities to determine the odds of receiving acute revascularization treatmen...
Preprint
BACKGROUND A clinical trial management system (CTMS) is a suite of specialized productivity tools that manage clinical trial processes from study planning to closeout. Using CTMS has shown remarkable benefits in delivering efficient, auditable, and visualizable clinical trials. However, the current CTMS market is fragmented and most CTMSs fail to m...
Article
Full-text available
Breast cancer (BC) is the leading cause of death among female patients with cancer. Patients with triple-negative breast cancer (TNBC) have the lowest survival rate. TNBC has substantial heterogeneity within the BC population. This study utilized our novel patient stratification and drug repositioning method to find subgroups of BC patients that sh...
Article
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Recent advances in deep learning have shown many successful stories in smart healthcare applications with data-driven insight into improving clinical institutions’ quality of care. Excellent deep learning models are heavily data-driven. The more data trained, the more robust and more generalizable the performance of the deep learning model. However...
Preprint
BACKGROUND Enabling the use of spatial context is vital to understanding today’s digital health problems. Any given location is associated with many different contexts. The strategic transformation of population health, epidemiology, and eHealth studies require vast amounts of integrated digital data. Needed is a novel analytical framework designed...
Article
Background: Enabling the use of spatial context is vital to understanding today's digital health problems. Any given location is associated with many different contexts. The strategic transformation of population health, epidemiology, and eHealth studies require vast amounts of integrated digital data. Needed is a novel analytical framework design...
Article
Objectives Acute ischemic stroke patients with severe acute respiratory syndrome coronavirus maybe candidates for acute revascularization treatments (intravenous thrombolysis and/or mechanical thrombectomy). Materials and Methods We analyzed the data from 62 healthcare facilities to determine the odds of receiving acute revascularization treatment...
Article
Full-text available
Monocarboxylate transporter 2 (MCT2) is a major high-affinity pyruvate transporter encoded by the SLC16A7 gene, and is associated with glucose metabolism and cancer. Changes in the gut microbiota and host immune system are associated with many diseases, including cancer. Using conditionally expressed MCT2 in mice and the TC1 lung carcinoma model, w...
Article
Full-text available
Objective: To identify differences in short-term outcomes of patients with coronavirus disease 2019 (COVID-19) according to various racial/ethnic groups. Design: Analysis of Cerner de-identified COVID-19 dataset. Setting: A total of 62 health care facilities. Participants: The cohort included 49,277 adult COVID-19 patients who were hospitali...
Article
Background To identify whether the risk of intracerebral hemorrhage is higher in patients with coronavirus disease 2019 (COVID-19), we compared the risk factors, comorbidities, and outcomes in patients intracerebral hemorrhage and COVID-19 and those without COVID-19.Methods We analyzed the data from the Cerner deidentified COVID-19 data set derived...
Article
Background: Intracranial hemorrhage (including subarachnoid hemorrhage) has been reported in 0.3 to 1.2% of patients with coronavirus disease 2019 (COVID-19). However, no study has evaluated the risk of subarachnoid hemorrhage in COVID-19 patients. Methods: We analyzed the data from 62 healthcare facilities using the Cerner de-identified COVID-1...
Article
Full-text available
Colorectal cancer (CRC) remains one of the deadliest malignancies worldwide despite recent progress in treatment strategies. Though immune checkpoint inhibition has proven effective for a number of other tumors, it offers benefits in only a small group of CRC patients with high microsatellite instability. In general, heterogenous cell groups in the...
Article
Full-text available
Enabling precision medicine requires developing robust patient stratification methods and developing drugs tailored to homogeneous subgroups of patients from a heterogeneous population. Developing de novo drugs is expensive and time consuming with an ultimately low FDA approval rate. These limitations make developing new drugs for a small portion o...
Article
Background: A better understanding of re-infection after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has become one of the healthcare priorities in the current pandemic. We determined the rate of re-infection, associated factors and mortality during follow up in a cohort of patients with SARS-CoV-2 infection. Methods:...
Article
Background and Purpose: Acute ischemic stroke may occur in patients with Coronavirus disease 2019 but risk factors, in hospital events, and outcomes are not well studied in large cohorts. We identified risk factors, co-morbidities, and outcomes in patients with Coronavirus disease 2019 with or without acute ischemic stroke and compared with patient...
Article
Background and Purpose Acute ischemic stroke may occur in patients with coronavirus disease 2019 (COVID-19), but risk factors, in-hospital events, and outcomes are not well studied in large cohorts. We identified risk factors, comorbidities, and outcomes in patients with COVID-19 with or without acute ischemic stroke and compared with patients with...
Article
Clinical trials are essential for discovering new treatments, but there are multiple challenges to patient recruitment, patient engagement, and cost containment. Virtual clinical trials (VCT) are an innovative approach that provides potential solutions by conducting home-based, rather than site-based, clinical trials. Virtual clinical trials are st...
Article
Full-text available
Background: Identifying patient-specific flow of signal transduction perturbed by multiple single-nucleotide alterations is critical for improving patient outcomes in cancer cases. However, accurate estimation of mutational effects at the pathway level for such patients remains an open problem. While probabilistic pathway topology methods are gaini...
Article
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Visual reasoning is critical in many complex visual tasks in medicine such as radiology or pathology. It is challenging to explicitly explain reasoning processes due to the dynamic nature of real-time human cognition. A deeper understanding of such reasoning processes is necessary for improving diagnostic accuracy and computational tools. Most comp...
Article
CAPRI challenges offer a variety of blind tests for protein‐protein interaction prediction. In CAPRI Rounds 38‐45, we generated a set of putative binding modes for each target with an FFT‐based docking algorithm, and then scored and ranked these binding modes with a proprietary scoring function, ITScorePP. We have also developed a novel web server,...
Article
Full-text available
Health Information Exchange (HIE) exhibits remarkable benefits for patient care such as improving healthcare quality and expediting coordinated care. The Office of the National Coordinator (ONC) for Health Information Technology is seeking patient-centric HIE designs that shift data ownership from providers to patients. There are multiple barriers...
Preprint
BACKGROUND Data coordination across multiple healthcare facilities has become increasingly important for many emerging healthcare applications. Distrust has been recognized as a key barrier to the success of such applications. Leveraging blockchain technology could provide potential solutions that bring trust between data providers and receivers by...
Article
Full-text available
Background Data coordination across multiple health care facilities has become increasingly important for many emerging health care applications. Distrust has been recognized as a key barrier to the success of such applications. Leveraging blockchain technology could provide potential solutions tobuild trust between data providers and receivers by...
Article
Full-text available
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 con...
Article
The output of the majority of NLP based informatics pipelines for structurization of free-text lack an ability to recover and convey implicit information , found in diagnostic reports. Such information is readily perceived and taken into account by a human reader as a contextual component. Here, we have developed a method to model contextual inform...
Conference Paper
Introduction: Low cytotoxic T lymphocyte (CTLs) infiltration and poor immunogenicity in the breast cancer (BC) microenvironment is a challenge to treatment with immune checkpoint (ICK) inhibitors. However, ICK inhibitors were recently approved by the FDA in triple-negative breast cancer (TNBC), which are characterized by high levels of tumor infilt...
Article
Full-text available
Background: Colorectal cancer (CRC) is the second leading cancer killer in the US today and patients with metastatic disease have only a 14% 5-year survival. One of the most impactful recent advances in cancer therapy, immune checkpoint inhibition, has not been shown to be effective for the majority of these patients. In this study, we use The Can...
Article
Full-text available
Background: Free-text sections of pathology reports contain the most important information from a diagnostic standpoint. However, this information is largely underutilized for computer-based analytics. The vast majority of NLP-based methods lack a capacity to accurately extract complex diagnostic entities and relationships among them as well as to...
Article
30 Background: Colorectal cancer (CRC) is the second-leading cause of cancer mortality in the US today. Recent advances in immunotherapy have only been shown to benefit a limited subgroup of patients with CRC. In other malignancies, activation of Toll-like receptors (TLRs) has been shown to overcome resistance to immunotherapy, such as immune check...
Article
25 Background: Low cytotoxic T lymphocyte (CTLs) infiltration in colorectal cancer (CRC) tumors is a challenge to treatment with immune checkpoint inhibitors. Consensus molecular subtypes (CMS) classify patients based on tumor attributes, and CMS1 patients include the majority of patients with high CTL infiltration and “inflamed” tumors. Epigenetic...
Conference Paper
Full-text available
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 con...
Article
T cell lymphoblastic leukemia (T-ALL) is an aggressive cancer arising from transformed thymocytes. Most human T-ALL involves hyperactive NOTCH signaling that is often caused by activating NOTCH mutations. However, the identification of specific molecular signals that might induce or select for mutation and transformation are incompletely understood...
Patent
Full-text available
Method, system and media for authenticating a subject as a user. Embodiments generate visual stories specific to the user and for which the subject must select the corresponding images from among a plurality of decoy images. Gaze tracking can be used to determine which images the user has selected without allowing an observer to learn which images...
Article
Full-text available
Finding small homogeneous subgroup cohorts in large heterogeneous populations is a critical process for hypothesis development in biomedical research. Concurrent computational approaches are still lacking in robust answers to the question “what hypotheses are likely to be novel and to produce clinically relevant results with well thought-out study...
Article
Merging geospatial analytics with big data approaches provides a mechanism for leveraging and maximizing uses of traditional survey data to further extant work in meaningful ways. This study examines the income inequality hypothesis, which proposes that ecological (summary-level) income inequality is harmful for population health. However, findings...
Article
Full-text available
Medical calculators play an important role as a component of specific clinical decision support systems that synthesize measurable evidence and can introduce new medical guidelines and standards. Understanding the features of calculators is important for calculator adoption and clinical acceptance. This paper presents a novel classification system...
Article
Introduction: Health disparity affects both urban and rural residents, with evidence showing that rural residents have significantly lower health status than urban residents. Health equity is the commitment to reducing disparities in health and in its determinants, including social determinants. Objective: This article evaluates the reach and co...
Article
Background and objectives: Medical calculators synthesize measurable evidence and help introduce new medical guidelines and standards. Some medical calculators can fulfill the role of CDS for Meaningful Use purposes. However, there are barriers for clinicians to use medical calculators in practice. Objectives of this study were to determine whethe...
Conference Paper
Full-text available
Understanding differences and similarities between scanpaths has been one of the primary goals for eye tracking research. Sequences of areas of interest mapped from fixations are a major focus for many analytic techniques since these sequences directly relate to the semantic meaning of the visual input. Many studies analyze complete sequences while...
Article
Background: Constant interruptions and continual data flow result in information overload for clinicians and become barriers to identification and extraction of relevant patient data and its correct interpretation. The aim of the study was to describe the types, frequencies, and impact of intensive care unit (ICU) interruptions on patient safety e...
Article
Introduction: Most breast tumors respond poorly to immunotherapy. Triple-negative breast cancer (TNBC) breast tumors are thought to be more immunogenic than other breast cancer subtypes (luminal A/B or HER2+). Increased immune response in TNBC are characterized by high levels of tumor infiltrating T lymphocyte (TIL) composition that would predict e...
Article
Full-text available
"Blockchain" is a distributed ledger technology originally applied in the financial sector. This technology ensures the integrity of transactions without third-party validation. Its functions of decentralized transaction validation, data provenance, data sharing, and data integration are a good fit for the needs of health information exchange and c...
Conference Paper
Full-text available
Blockchain" is a distributed ledger technology originally applied in the financial sector. This technology ensures the integrity of transactions without third-party validation. Its functions of decentralized transaction validation, data provenance, data sharing, and data integration are a good fit for the needs of health information exchange and cl...
Article
Full-text available
Though the genetic etiology of autism is complex, our understanding can be improved by identifying genes and gene-gene interactions that contribute to the development of specific autism subtypes. Identifying such gene groupings will allow individuals to be diagnosed and treated according to their precise characteristics. To this end, we developed a...
Article
Full-text available
Background Visual heuristics of pathology diagnosis is a largely unexplored area where reported studies only provided a qualitative insight into the subject. Uncovering and quantifying pathology visual and nonvisual diagnostic patterns have great potential to improve clinical outcomes and avoid diagnostic pitfalls. Methods Here, we present PathEdE...
Article
Full-text available
Eye Gaze Pattern Analysis of Whole Slide Image Viewing Behavior in PathEdEx Platform - Volume 23 Issue S1 - Ilker Ersoy, Misha Kovalenko, Chi-Ren Shyu, Richard Hammer, Dmitriy Shin