Our Assets: Technical Expertise

Children’s Mercy Hospitals

Shui Qing Ye, MD, PhD

Dr. Ye is a Professor in the Department of Pediatrics at Children’s Mercy Hospitals and Clinics and Department of Biomedical and Health Informatics, University of Missouri School of Medicine at Kansas City (UMKC) and the William R. Brown/Missouri Endowed Chair in Medical Genetics and Molecular Medicine at CMH and UMKC. Dr. Ye had served as the Director, Gene Expression Profiling Core in Center of Translational Respiratory Medicine in Johns Hopkins University School of Medicine from 2001 to 2005 and the Director, Molecular Resource Core in a NIH funded Program Project Grant on Lung Endothelial Pathobiology in University of Chicago Pritzker School of Medicine from 2005 to 2007. Dr. Ye edited a book entitled “Bioinformatics-A Practical Approach”, which was published  in 2008 by CRC Press (www.crepress.com). This book enjoys a rave review by covering most translational bioinformatics topics with 25 expert contributing authors from nine different world-class institutions of six different countries. He is planning to work on the second edition of this book at the invitation of the publisher, Dr. Sunil Nair. Dr. Ye now serves as the Director in the Core of Genetic Research at CMH, which provides next generation sequencing and data analysis services for medical researchers at CMH. Last year, his lab published a demonstrative RNA-seq technology video article (Cheranova et al., 2013) in J Vis Exp, The First Scientific Video Journal, at the editor’s invitation.

Kansas State University

Eduard Akhunov, PhD

Dr. Akhunov compares the genetic code of ancient wheat varieties to that of modern varieties with a goal of improving wheat for different growing conditions throughout the world.  He compares variation in the DNA sequence between ancient and modern wheat varieties to detect the variants of genes that were selected by breeders to make wheat cultivars that can be grown from Argentina to Norway and Russia.

Susan Brown, PhD

Dr. Brown is the Director of the Bioinformatics Center at Kansas State University.  Her research interests include evolution of gene regulatory networks, using segmentation in the red flour beetle, Tribolium castaneum as a model system. Genomics and Bioinformatics, focusing on genome sequence analysis Tribolium.  Dr. Brown has developed a variety of genetic and genomic tools that have established Tribolium as a genetic model organism. These include molecular recombination maps, DNA libraries and other molecular resources, RNAi, and the use of transposons in genome-wide insertional mutagenesis.

Doina Caragea, PhD

Dr. Caragea is the Associate Director of the Bioinformatics Center at Kansas State University.  Her research interests include artificial intelligence, machine learning, data mining and knowledge discovery, visual data mining, link analysis, ontologies and information integration, semantic web, bioinformatics.

John Fellers, PhD

Mapping and cloning genes in wheat for resistance to Karnal bunt, leaf rust, stem rust, scab, septoria, Hessian fly and viruses. Genomics approaches to identify new markers and expressed sequence tags for plant disease and insect resistance genes.

Karen Garrett, PhD

Dr. Garrett studies the ecology and ecological genomics of plant disease and other plant stressors. In agricultural systems, she works to improve plant disease management in US and tropical farming through resistance gene deployment and sustainable cultural practices. In natural systems, she studies plant-pathogen-environment interactions in tallgrass prairie and tropical forests. Some of her projects emphasize statistical and/or bioinformatic approaches and ecological modeling.

Jesse Poland, PhD

Dr. Poland serves as Associate Director of the Wheat Genetics Resource Center and Director of the Feed the Future Innovation Lab for Applied Wheat Genomics.  His research is focused on wheat genetics and germplasm improvement.  His laboratory is currently developing new marker technologies for use in breeding and association genetics. He is also focused on developing new breeding lines with resistance to important diseases of wheat; stem rust, stripe rust and leaf rust and abiotic stress tolerance to heat and drought.  In collaboration with public breeding programs, his laboratory is exploring the use of genomic selection methods in wheat breeding.  Dr. Poland is developing field-based high throughput phenotyping platforms to accelerate basic and applied genomics and breeding research.

Chris Toomajian, PhD

Areas of research include population and evolutionary genetics and genomics of plants and plant pathogens. Dr. Toomajian analyzes genome-scale DNA polymorphism datasets in order to infer the relative importance of processes such as mutation, recombination, genetic drift, migration, and natural selection in creating observed patterns of polymorphisms. He develops methods to infer recent instances of natural selection at the DNA level in order to identify adaptive genetic variation. He is interested in methods and datasets that allow for the statistical mapping of quantitative trait loci (complex traits) back to the genome in samples of unrelated individuals.

Frank White, PhD

Dr. White utilizes molecular genetic and genomic techniques for functional analyses of plant disease and mechanisms of resistance. Complete genome sequencing of plant pathogenic bacteria is used for gene discovery. Targeted mutagenesis techniques are  subsequently used for functional analysis. Transcriptional profiling is for gene discovery in rice, sorghum and wheat. RNA-meditated gene silencing and insertional mutanagenesis techniques are employed in the analysis of host/pathogen interactions. His principle organisms are rice and sorghum with related work in other species including wheat.

Saint Luke’s Health System

Suzanne Arnold, MD, MHA

Dr. Arnold is a Board Certified cardiologist devoting 30% of her time to clinical cardiology practice and 70% to outcomes research at MAHI.  She received her MD and MHA degrees from The Ohio State University and completed her internal medicine residency and clinical cardiology fellowship at Washington University in St. Louis.  She spent 3 years during her cardiology training doing outcomes research at MAHI through the AHA-PRT Award. She is a Clinical Associate at the UMKC School of Medicine. Dr. Arnold has produced numerous scientific contributions in the field of patients’ health status recovery after acute myocardial infarction and Trans-Aortic Valve Replacement (TAVR) and is a leader developing risk models for patients’ health status outcomes. She recently received a fundable score for creating shared decision-making tools to assist patients and providers considering TAVR interventions, based upon patients’ predicted survival and quality of life after treatment.

Paul Chan, MD, MSc

Dr. Chan is a Board Certified cardiologist devoting 25% of his time to clinical cardiology practice and 75% to outcomes research at MAHI through an NIH training grant.  He received his MD degree from the Johns Hopkins School of Medicine, his internal medicine and pediatrics residencies at the Brigham and Women’s and the Boston Children’s Hospitals, and his cardiology fellowship and masters in biostatistics & clinical research design at the University of Michigan Schools of Medicine and Public Health.  He is an Associate Professor of medicine at the UMKC School of Medicine.

Dr, Chan is an international authority on the management and outcomes of in-hospital cardiac arrest. He is widely published in the field, including landmark papers in the New England Journal of Medicine, JAMA, Lancet and Circulation. In 2013, he received the AHA’s Resuscitation Council’s highest recognition award for the field, the Dickinson W. Richards Memorial Lectureship. Currently, Dr. Chan is a member of the AHA’s Scientific Writing Group on Out-of-Hospital Cardiac Arrests and BLS Guidelines and the American College of Cardiology (ACC) Writing Group on Performance Measurement. He is also co-director of the Adult Task Force for the AHA’s National Registry for Cardiopulmonary Resuscitation.  In 2013, he received the AHA’s Resuscitation Council’s highest recognition award for the field, the Dickinson W. Richards Memorial Lectureship. His research interests include the appropriate use of technology in a manner that is cost-efficient and which optimizes patient outcomes, improves quality, and reduces disparities. He has numerous peer-reviewed publications.

Adnan Chhatriwalla, MD

Dr. Chhatriwalla is an interventional cardiologist with a focus on structural heart disease, patient outcomes and shared medical decision-making. He devotes 20% of his time to research and is the Co-PI of a grant from the Patient Centered Outcomes Research Institute (PCORI) to develop a shared decision-making tool for bare metal vs. drug eluting stents in patients undergoing percutaneous coronary intervention (PCI). He led the implementation efforts, from a physician’s perspective, of the ePRISM tool to deliver personalized medicine in the cath lab to improve the safety and outcomes of PCI.

Kensey Gosch, MS

Kensey Gosch serves as a biostatistician for the CV Outcomes Research. She supports numerous investigators analyzing data housed at MAHI and has published over 30 papers on cardiovascular outcomes. Her expertise includes hierarchical modeling, multiple imputation and propensity score methods. She continuously seeks to apply the most appropriate techniques, and has researched and introduced several contemporary methodologies to the Biostatistics group, including alternative regression models for estimating relative risk and shared frailty models for clustered time-to-event data.  She is also highly skilled in data management and has developed several Access databases for local researchers.  She has substantial experience using both SAS and R for data analyses.

Phil Jones, MS

Mr. Jones is the Senior Biostatistician for the Outcomes Group and manages the statistics and programming group for CV Outcomes Research at MAHI. In addition, he serves as the primary statistical liaison for Saint Luke’s Health System and for the Cardiovascular Outcomes Research Consortium, an international network of cardiovascular outcomes researchers. Mr. Jones has co-authored over 60 published clinical articles and has served as lead statistician on numerous grants and industry-funded studies. Mr. Jones has as Master’s degree from Iowa State University and over 12 years of experience in biostatistics and project leadership. His major statistical interests are in risk-adjustment, hierarchical data analysis, latent variable models and selection bias. He also has substantial experience with provider profiling methods, having developed internal models for physician performance reports and working closely with Saint Luke’s Health System leadership to improve hospital performance metrics using Bayesian methods.

In addition, Mr. Jones has extensive data management experience, including over 10 years experience with SAS and SQL, creation of several complex Access database applications, co-development of a conceptual model for a hierarchical patient-centric data warehouse, creation and direction of the Research Center’s analytic data repository, and authorship of internal standards for data organization and representation.  He is conversant with several other software packages and languages, including R, WinBugs and Visual Basic.  He is a highly skilled programmer, and has developed and maintains a large repository of macros for facilitating complex statistical analyses and for providing rapid, accurate and concise deliverables for customers.

Kevin Kennedy, MS

Mr. Kennedy is a masters-level statistician from Kansas State University who was been an instrumental part of the MAHI research department since 2008. He is the lead analysis for several of the ACC NCDR datasets, including the Cath/PCI, ACTION, ICD and CARE registries. He is an expert in the creation of risk-prediction models for quality assessment purposes. He supports numerous investigators throughout the country and has published over 50 peer-reviewed manuscripts. Mr. Kennedy also has extensive expertise linking clinical registry data, such as the NCDR, with large administrative claims data, such as the CMS data files.

Dmitry Grigoryev, MD, PhD

Dr. Grigoryev is an Assistant Professor in the Department of Pediatrics at Children’s Mercy Hospitals and Clinics and Department of Biomedical and Health Informatics, University of Missouri School of Medicine at Kansas City. Dr. Grigoryev received 2.5 years postdoctoral training in Bioinformatics at NCI/NIH, where he learned and mastered Python language. He then served as Head, Data Analysis Unit in the Gene Expression Profiling Core in Center of Translational Respiratory Medicine in Johns Hopkins University School of Medicine for 7 years. Now he serves the same capacity in our Core of Genetic Research at CMH. He has been a microarray data analysis guru. Now, he has developed the pipelines for RNA-seq and exome-seq data analysis in our core to support the next generation sequence application of our group as well as other investigators at CMH. 

Yan Li, PhD

Dr. Li is a PhD-level statistician who joined the MAHI research group in 2009. She obtained her PhD from the University of Florida in Gainesville and has been employed at MAHI ever since. She is an expert at working with large datasets, including the Cerner Healthfacts and AHA Get with the Guidelines Resuscitation database. She is an expert in the creation of risk-adjustment modeling and in handling clustered data. Her skills in handling missing data and the analysis of observational data for comparative effectiveness research are superb.

Mikhail Kosiborod, MD

Dr. Kosiborod is a Board Certified cardiologist devoting 50% of his time to clinical cardiology practice and 50% to outcomes research at MAHI.  He received his MD degree from Mount Sinai School of Medicine, his internal medicine residency and cardiology fellowship at Yale-New Haven Hospital.  He was a Robert Wood Johnson recipient having spent his research experience with Yale School of Medicine and the School of Public Health. He currently is an Associoate Professor of medicine at the UMKC School of Medicine.

Dr. Kosiborod is and internationally recognized authority on the intersection of diabetes and cardiovascular disease, having produced several of the landmark studies in the field. He is a member of the AHA’s Scientific Writing Group on Hyperglycemia in Acute Coronary Syndromes.  He also has served on the abstract grading committees for AHA’s Annual Scientific Forum on Quality of Care and Outcomes Research and the American College of Cardiology Scientific Sessions.  His research interests include clinically analyzing large datasets for glycemic control in ACS patients and anemia prevalence in heart failure.  He has numerous peer-reviewed publications.

John Spertus, MD, MPH

Dr. Spertus is a the Missouri/Lauer Endowed Chair and Tenured Professor at the UMKC-School of Medicine. He is an Adjunct Professor at Washington University in Saint Louis and the University of Kansas. He is a nationally recognized researcher and expert in the field of cardiovascular outcomes research, patient-centered health status measurement, quality of care and performance measure development. Recently, he has pioneered the implementation of personalized medicine, based upon the execution of risk prediction models in routine clinical care, to improve the safety and outcomes of cardiovascular care. He received his MD from University of San Francisco as well as his internal medicine residency.  His cardiology fellowship and MPH training were at the University of Washington.

Dr. Spertus has successfully led the Cardiovascular Outcomes Research section at the Mid America Heart Institute (MAHI) since 1996 where he serves as the Medical Director of Cardiovascular Outcomes Research. Dr Spertus has created the international standards for quantifying patient-centered outcomes, including the Seattle Angina Questionnaire, the Kansas City Cardiomyopathy Questionnaire and the Peripheral Artery Questionnaire. His grant portfolio includes a range of NIH, AHRQ, Foundation and industry projects amounting to over $35 million in the past 10 years.  He has over 500 peer-reviewed publications.

Dr. Spertus is the founder and President of the Cardiovascular Outcomes, Inc., a 501(c)3 organization which coordinates the Cardiovascular Outcomes Research Consortium (CORC). CORC is a dynamic collection of the country’s leading cardiovascular outcomes researchers and has conducted several ground-breaking studies of the health status outcomes of HF and ACS patients.  These registries have recently been leveraged for their detailed phenotypic description of patients’ outcomes to define the incremental prognostic importance of genetic polymorphisms and biomarkers.  He co-founded and currently chairs the AHA’s Annual Scientific Forum on Quality of Care and Outcomes Research and has served on numerous committees for the ACC, AHA, VA, IOM, AMA and United Healthcare. He holds 9 patents and in 2009, he launched a new company, Health Outcomes Sciences, to support and disseminate his work throughout the country.

Fengming Tang, MS

Ms. Tang is a programmer/statistician who has been with the MAHI Outcomes Research Group since 2007.  She is highly proficient in SAS and has had responsibility for the data management and creation of analytic datasets for the TRIUMPH study, a 26-center, post-MI registry that includes over 1600 data elements, including baseline and follow-up clinical data, as well as biomarker and genetic data; all emanating from diverse sources. She also oversees the data management and analysis of several American College of Cardiology National Cardiovascular Data Registries. She has been the lead analyst for the ACC’s PINNACLE database, which currently houses of 5 million outpatient records. These efforts have included numerous publications, quality assessment reports and CMS reporting for PQRS.

University of Kansas

Brian D. Ackley, PhD

Cell adhesion molecules drive neuronal development.  The brain is an amazing network of cells connected by axons and dendrites that form the conduits for our thoughts and actions. One of the fundamental questions of neuroscience is to understand how these connections form. As such these cells and their processes must differentiate appropriate partners from inappropriate targets. Neuroscientists have found that molecules outside the cells instruct all the stages of neural development. For example growth factors secreted from other cells instruct nerve cells to adopt the correct fate, diffusible cues inform neurons where potential synaptic partners might be located and cell surface cues can tell them when they have reached their targets. Work in the Ackley Lab seeks to understand the contribution of cell adhesion molecules to the process of neural development, and we use genetics, cell biology and biochemistry to approach to this problem. Using a bioinformatic approach, Ackley has created a list of all of the genes in the C. elegans genome predicted to be secreted into the extracellular space. This list (The Secretome) includes ~10,000 members. To facilitate understanding how each of these may contribute to development he is creating a library of RNAi clones directed against each member of the list. Ultimately this will provide a valuable rescoure to investigators wanting to probe the contribution of secreted molecules to pathways of interest.

Eric Deeds, PhD

A wide variety of processes in the cell depend on the function of large complexes. Dr. Deed’s research focuses on using computational modeling to understand how macromolecular structures assemble from their component parts. His work is aimed at providing fundamental insights into assembly mechanisms with the ultimate goal of developing strategies that could disrupt or enhance the assembly of medically relevant complexes. The results of his work also provide general rules that can be applied in the design and construction of synthetic complexes that will self-assembly efficiently.

In one set of projects, the Deeds group is considering the assembly dynamics of macromolecular structures that contain rings. Many important complexes, such as the proteasome, the chaperone GroEL, and the apoptosome involved in programmed cell death, consist either of single rings or of multiple rings stacked on top of one another. They have characterized some of the challenges that face simple ring-like structures as they assemble, and have discovered mechanisms that complexes could employ to assemble with optimal efficiency. The team is currently extending this work to the study of stacked rings, with a particular focus on complexes for which there is experimental evidence of self-assembly. The predictions of such models are tested through detailed analysis of the solved structures of complexes containing rings or stacked rings.

In a second set of projects, the Deed’s lab is taking a more systems-wide view and are characterizing assembly challenges that arise in the context of large Protein-Protein Interaction (PPI) networks. Assembly processes occur in the context of a large network in which each of the components of a complex may interact with many potential binding partners. By applying rule- and agent-based modeling techniques, the group has recently conducted the first dynamical simulations of complex formation in the context of a large PPI network. Such large complexes do not reliably assemble in these simulations, indicating that specific mechanisms have evolved to deal with assembly challenges that arise in large PPI networks. The team is currently extending this work to understand how cells have evolved to overcome these problems.

Wonpil Im, PhD

The research programs in the Im group focus on the applications of theoretical/computational methods to chemical and physical problems in biology and material science. Specific research interests and projects include 1) development of efficient and reliable tools for membrane protein modeling and studies of insertion, folding, and assembly of membrane proteins/peptides; 2) NMR & X-ray structure refinement of proteins and protein-DNA complexes using implicit solvent models; 3) ion channel activities such as ion permeation, selectivity, and gating at molecular level; 4) membrane fusion with simplified lipid molecules; and 5) theoretical/methodological developments with particular emphasis on implicit solvent models. In addition, the group is involved in developing the biomolecular simulation program CHARMM.

John Karanicolas, PhD

Dr. Karanicolas’ primary goal is to develop structure-based approaches for modulating protein function using small-molecules. He is exploring two parallel paths towards this overarching goal: the first is re-engineering proteins so that a small-molecule can be used to “turn on” function, and the second is identifying small-molecules that naturally complement and occlude a protein surface such that they can be used to “turn off” function.

In select cases, the ability to activate protein function with a pharmacological agent has already helped elucidate details of protein function in living cells. These cases, however, have been limited either by the fact that the strategy must be catered to a particular protein system or by relatively slow kinetics of activation. Karanicolas seeks to develop a very general approach for engineering small-molecule dependent function into proteins in a way that circumvents these problems. The novel strategy for activating protein function is predicated on adapting a well-known technique – chemical rescue – in an entirely new structure-based context.

Meanwhile, the ability to identify a small-molecule to inhibit a particular protein-protein interaction has long represented a promising avenue for therapeutic intervention in a variety of settings. The relative lack of success in this pursuit has led to a collective view that protein interactions represent a challenging therapeutic target. Karanicolas seeks to understand the root cause of these difficulties unlocking the vast potential associated with pharmacological inhibitors of protein interactions, and translate this understanding into new methods for identifying inhibitors with therapeutic potential. He developed a computational structure-based approach for distinguishing between sites that are suitable for small-molecule binding and those that are not.

Christian Ray, PhD

Physiological responses in growing organisms display tradeoffs between cost and benefit. In microbial metabolism, organismal fitness (often characterized by population growth rate) depends on networks of well-balanced metabolic fluxes. In gene regulation and signaling networks, physical limits on information flow play a decisive role in evolution. In either type of network, small-scale molecular mechanisms can have a powerful effect on larger-scale emergent physiology, creating critical transitions that determine cellular phenotypes and thus fitness.

Dr. Ray uses complementary theoretical and experimental methods to understand the relationship between the properties of critical transitions in single cells and evolutionary fitness. He uses mathematical and computational methods to predict cellular dynamics and guide the design of experiments with bacteria. Specifically, he directly measure the relationship between network dynamics and fitness, using either natural networks (such as the well-studied lac operon in E. coli) or synthetic constructs designed to test specific predictions.

Joanna Slusky, PhD

The Slusky lab is cross-disciplinary, bringing together computational biology, protein design, and molecular biology approaches.  The team assess the structural bioinformatics of OMPs and apply the results to de novo OMP protein design and to native OMP manipulation.  OMPs are a ripe target for cancer therapeutics. Mitochondria have recently become a focus of cancer therapies due to the fact that mitochondrial outer membrane permeabilization leads to apoptosis or necrosis. Dr. Slusky explores mitochondrial membrane permeabilization through manipulation of the OMP pores that already exist in the mitochondrial outer membrane. This may have pharmaceutical consequences because tumorigenic mitochondrial membranes can be selectively targeted in themselves as they have been shown to accumulate lipophilic cations.

Beyond this mechanistic understanding, knowledge of the relationship between OMP chemistry and structure will allow new OMPs to be designed for use in vaccines and will facilitate manipulation of native bacterial OMPs for custom tailored drug delivery systems that could shorten bacterial infections.  Outer membrane proteins have been used for the development of vaccines in three distinct ways: as antigens, as adjuvants and as fasteners to conjugate soluble antigens to outer membrane vesicles. Finally, because OMPs are the bacterial import machinery, drugs could be designed in such a way to manipulate OMPs such that those drugs can facilitate their own import into bacteria.

Ilya Vakser, PhD

Dr. Vakser’s research focuses on molecular modeling in the context of structural genomics and bioinformatics. The major goals are to develop approaches to the modeling of protein interactions and to design procedures for reconstruction of the network of connections between proteins in a genome. The number of protein-protein interactions in a genome is significantly larger than the number of individual proteins. Moreover, most protein structures will be models of limited accuracy. Thus the structure-based methods for building this network have to be (a) fast, and (b) insensitive to significant inaccuracies of modeled structures. The precision of these methods may be correlated with the precision of the protein structures – lower for less accurate models and higher for more exact models.

Vakser’s long-term goals are to understand the fundamental principles of protein interaction and to create a structure-based description of genomes. The primary current objectives are: development of methodology for an accurate prediction of the structure of protein complexes, docking in genome-wide databases of modeled protein structures, and development of the integrated environment for docking studies.

University of Kansas Medical Center

Brooke L. Fridley, PhD

Dr. Fridley’s research is focused primarily on development methods for data integration, including Bayesian methods, molecular clustering and gene set analysis approaches. Recently, she also started investigating and developing analysis methods for next-generation sequence data that will aid researchers in the interpretation of this high-dimensional data, including rare variants. In addition to her statistical research, she is actively involved in numerous genomic projects, primary in the area of cancer and cancer pharmacogenomics. Many of these studies deal with both candidate genes and genome-wide approaches, along with multiple types of genomic data, such as genotypic, methylation and mRNA expression.  Dr. Fridley is the Site Director for the K-INBRE Bioinformatics Core.

Devin Koestler, PhD

Dr. Koestler’s research involves the development and application of bioinformatics/statistical methodologies for analyzing high-throughput ‘omic’ data. He also has interests in epigenetics and molecular epidemiology, specifically DNA methylation and its implications for human health and disease.  In addition to his methodological interests, which include, multivariate statistics, mixture models, and mixed-effects models, he is also collaborating in the areas of environmental health, the human microbiome, and a wide variety of different epigenetics studies.  The shared theme across his collaborative research projects is the use of high-dimensional genomic data to gain further insight into some biological process.

Peter Smith, PhD

Dr. Smith’s research examines this interplay between nerve and target and the factors that govern neuronal growth and degeneration. He is especially interested in how this relationship is affected by gonadal steroid hormones such as estrogen. Ongoing projects examine mechanisms and consequences of neuroplasticity in peripheral tissues including: reorganization of cardiac innervation following myocardial infarction, which may contribute to sudden cardiac death; estrogen-induced remodeling of innervation of the reproductive tract; mechanisms by which nerve projections are pruned under normal and pathophysiological conditions; and the role of estrogen in the etiology of female pain syndromes.  Dr. Smith is the Director of KUMC’s Bioinformatics core.

University of Missouri

Jianlin Cheng, PhD

Dr. Cheng is an associate professor in the Computer Science Department at the University of Missouri. He is affiliated with the University of Missouri Informatics Institute, the National Center for Soybean Biotechnology, the Interdisciplinary Plant Group and the Bond Life Science Center. His research is focused on developing computational methods and tools for big biomedical data analysis. His research group has developed a number of software tools for analyzing protein structure and function, biological sequences and networks and 3-D genome structure, which are used by scientists around the world. His research has been supported by the National Institutes of Health, the National Science Foundation, the U.S. Department of Energy, the U.S. Department of Education and the University of Missouri. Cheng is a recipient of the NSF CAREER award and the MU College of Engineering’s junior faculty research award.

Ye Duan, PhD

Dr. Duan is an associate professor in the Computer Science Department at the University of Missouri. He has received research funding from the Department of Defense, the Army Research Lab, the Leonard Wood Institute, the Brain & Behavior Research Foundation, the National Geospatial-Intelligence Agency, the Thompson Center for Autism and the National Science Foundation. His area of research interests include computer graphics and visualization, computer vision and biomedical imaging, and geometric and physics-based modeling.

Trupti Joshi, PhD

Dr. Joshi is an assistant research professor in the Computer Science Department at the University of Missouri. Her interests are in the areas of bioinformatics and its application to biology and medical fields. Her research includes development of comprehensive web-based resources for multi-omics data integration, high-throughput biological data analyses and computational tools development for genomics and systems biology research.

Toni Kazik, PhD

Dr. Kazic is an associate professor in the Computer Science Department at the University of Missouri. She is currently working on methods to infer the structure of complex networks using the disease lesion mimic mutants of maize as a model system. Her work has included the development of an architecture for community query, deposit, review and curation of information on biochemical reactions, and the analysis of extant reaction networks. Kazic is a fellow of the American College of Medical Informatics and was an Invited Researcher to the Institute for New Generation Computer Technology. She served as a program director for the National Science Foundation in computational biology, and now consults for the National Institutes of Health and the National Science Foundation and is a member of several national and international scientific advisory bodies.

Dmitry Korkin, PhD

Dr. Korkin is an assistant professor in the Computer Science Department at the University of Missouri. His interests in bioinformatics are toward characterizing structure, function and evolution of protein assemblies and predicting host-pathogen interactions. A recipient of the National Science Foundation’s CAREER award, his research in machine learning involves developing a symbolic approach for inductive learning and classification and its applications. Before coming to MU, Korkin was a postdoctoral researcher at the University of California, San Francisco and Rockefeller University. His research is supported by the University of Missouri.

Yi Shang, PhD

Dr. Shang is a professor and director of graduate studies in the Computer Science Department. He has published more than 150 refereed papers in international journals and conferences, and has six U.S. patents. Shang has worked as a researcher for the University of Illinois and the Xerox Palo Alto Research Center. He has received research funding from the National Science Foundation, National Institutes of Health, the U.S. Army, DARPA, Microsoft and Raytheon.  His research interest include AI, combinatorial and nonlinear optimization, NN, GA, SAT, Web search, WSN, adaptive robotic control, traffic monitoring and control, mobile computing, location aware services, recommendation systems, and protein folding.

Chi-ren Shyu, PhD

Chi-Ren Shyu is professor and chairman of the Electrical and Computer Engineering Department and director of the University of Missouri Informatics Institute, a campuswide doctoral program in bioinformatics and health informatics.  His research interests include biomedical informatics, mHealth and eHealth, information retrieval, visual knowledge reasoning and data mining. Current project sponsors, in addition to the NSF, include the National Institutes of Health, the U.S. Department of Education and other for-profit and nonprofit organizations.

Gordon Springer, PhD

Dr. Springer is an associate professor in the Computer Science Department scientific director of the UM Bioinformatics Consortium. He also serves as MU’s director of Research Support Computing for the Division of Information Technology, MU’s campus computing organization. A former director of graduate studies for MU’s Computer Science Department, Springer has worked since the late 1980s with the MU Molecular Biology Program and in the Life Science Center to develop and support computer systems and software required to carry out various research projects that need computer analysis of biological data.

Dong Xu, PhD

Dr. Xu is professor and chair of the Computer Science Department, with appointments in the Christopher S. Bond Life Sciences Center and the MU Informatics Institute at the University of Missouri. His research includes protein structure prediction, high-throughput biological data analyses and in silico studies of plants, microbes and cancers. He has published more than 240 papers and is a recipient of the 2001 R&D 100 Award, 2003 Federal Laboratory Consortium’s Award of Excellence in Technology Transfer and 2010 Outstanding Achievement Award from International Society of Intelligent Biological Medicine. Xu is an editor in chief of International Journal of Functional Informatics and Personalized Medicine and associate editor in chief of IEEE/ACM Transactions on Computational Biology and Bioinformatics. He is an editorial board member of Current Protein and Peptide Science, Applied and Environmental Microbiology and International Journal of Data Mining and Bioinformatics.

University of Missouri–Kansas City

Jenifer Allsworth, PhD

Dr. Jenifer Allsworth joined the Department of Biomedical and Health Informatics at the School of Medicine at the University of Missouri-Kansas City as Research Associate Professor in 2013.  Prior to joining UMKC, she was Assistant Professor in the Department of Obstetrics and Gynecology at Washington University in St. Louis School of Medicine. With over 10 years of experience studying the health of women, Dr. Allsworth has been an investigator on multiple longitudinal large-scale population based epidemiologic studies in women’s health. Most recently, she has been an investigator on the Contraceptive CHOICE Project – an innovative study examining the impact of counseling and cost support on women’s selection and continuation of contraception.  She has also contributed to Project PROTECT, an intervention study to improve dual method contraceptive use, and the Study of Women’s Health across the Nation (SWAN), a multi-ethnic, longitudinal study of women’s health during the menopausal transition. Dr. Allsworth was a KL2 Clinical Research Scholar at Washington University in St. Louis and studied genetic epidemiology.

Her current research interests include: the impact of social factors, including race, violence, and poverty on obstetric and gynecologic outcomes; the use of social media for delivery of weight gain interventions among disadvantaged reproductive-aged women at risk for obesity; and the impact of alterations of the vaginal microbiome on health outcomes. Dr. Allsworth has 80 peer reviewed manuscripts published and 19 invited chapters and papers and in 2011 was honored as one of the top reviewers of the American Journal of Obstetrics & Gynecology.

Julie Banderas, PharmD, FCCP, BCPS

Dr. Banderas is a Professor in the Department of Medicine at the University of Missouri-Kansas City (UMKC) School of Medicine. She is also a tenured professor in the Department of Biomedical and Health Informatics. She was appointed as the first Assistant Dean for Graduate Studies for the School of Medicine in 2009 and also became Assistant Dean for Allied Health in 2012. She has been a Board Certified Pharmacotherapy Specialist since 1995. Dr. Banderas devotes a substantial amount of time to teaching clinical pharmacology and therapeutics at UMKC and is the course director for the course, Responsible Conduct of Research which is a required course for many graduate programs. She was a member of the UMKC Adult Health Sciences IRB for over 12 years and chaired the committee for 4 years.  Dr. Banderas’ research has primarily focused on HIV/AIDS.  She has served as a primary and co-investigator for NLM, CDC, and NIMH funded projects, including electronic access to consumer health information for persons affected by HIV, HIV transmission prevention and interventions to enhance adherence to antiretroviral therapies.

Peter Almenoff, MD, FCCP

Dr. Almenoff is the Vijay Babu Rayudu Endowed Chair of Patient Safety at UMKC and is a clinical professor of Biomedical and Health Informatics and Internal Medicine.  Dr. Almenoff serves as the Special Advisor in the Office of the Secretary (Healthcare Value), and Senior Fellow in the VA Center for Innovation. Dr. Almenoff was also appointed Director, Operational Analytics and Reporting in 2012. He oversees the Office of Operational Analytics and Reporting (OAR), including the Office of Productivity, Efficiency, and Staffing (OPES); Business Reporting; Operations and Management Support; and Field Analytics. He served as Assistant Deputy Undersecretary for Health for Quality and Safety for the Department of Veterans Affairs from 2008-2012 and provided leadership nationally in the area of outcomes research with specific attention to risk adjustment models.  He also served as the National Program Director for Pulmonary and Critical Care. In his role at the School of Medicine, Dr. Almenoff will advise the School in developing medical education programs and research programs that incorporate patient safety. Dr. Almenoff will also serve an advisory role to Saint Luke’s Hospital on the development of a clinical outcomes analytic program.

Donna M. Buchanan, PhD

Dr. Buchanan is a psychologist who works as a researcher and manager with the Cardiovascular and Outcomes Research Group at Saint Luke’s Mid America Heart Institute and is a Teaching Assistant Professor at the University of Missouri-Kansas City School of Medicine. She coordinates the research and publication activities of the national network of cardiovascular researchers comprising the Cardiovascular Outcomes Research Consortium and provides management oversight of the services provided by Saint Luke’s Mid America Heart Institute as an analytic center for the American College of Cardiology’s National Cardiovascular Data Registries. Prior to joining Saint Luke’s Mid America Heart Institute in 2005, she had 10 years of hospital-level administrative experience working for Missouri Department of Mental Health, including progressive executive positions of Director of Quality Management, Assistant Superintendent of Treatment, and Chief Operating Officer. She has extensive knowledge of healthcare regulatory standards, performance measures, and guidelines, and has provided consultation and project coordination for the development of national performance measurement reporting systems in both areas of behavioral health and cardiology.  Dr. Buchanan leads and has published research involving the association of depression and other psychosocial and behavioral characteristics with heart disease and outcomes.  Her research also involves using advanced statistical methods to determine the most appropriate ways to measure socioeconomic status to improve the rigor of future research aimed at better understanding and reducing socioeconomic-based disparities in healthcare and outcomes.

Jie Chen, PhD

Dr. Chen is currently a professor of statistics, chair of the Department of Mathematics and Statistics, and an adjunct Professor of the Department of Biomedical and Health Informatics at the University of Missouri-Kansas City.  Her research interests are in the areas of change point analysis, model selection criteria, applied statistics, statistics in bioinformatics, and genomics data modeling.  She has published over 40 articles in statistical research since 1995 and is the leading author of the book “Parametric Statistical Change Point Analysis” (Birkhaüser, 2000 and 2012) while the 2012 edition of the book includes applications in medicine, genetics, and finance.

Deendayal Dinakarpandian, PhD

Dr. Dinakarpandian is an Associate Professor in the Department of Computer Science and Electrical Engineering. He has an interdisciplinary background in the biological, medical and computational sciences. His research interests lie in data mining, machine learning and knowledge representation, with particular emphasis on methods with biological and medical applications. His work has been funded by the National Science Foundation and National Institutes of Health. He serves as the coordinator of the computational track for the School of Medicine graduate program in Bioinformatics, and the coordinator of the undergraduate Computer Science program. He has taught courses on databases, probability, data structures, bioinformatic algorithms and machine learning.

Mary M. Gerkovich, PhD

Dr. Gerkovich is an Associate Professor in the Department of Biomedical and Health Informatics. Her research area focuses on issues of management of chronic medical conditions and adherence to complicated medication regimens, and the occurrence of chronic medical conditions and utilization of services in a safety-net patient population. Her research goal is to identify patient-level and system-level changes and opportunities for reducing disparities in patients who are faced with challenges as the result of lack of personal resources and social support. This work includes the extraction of information from electronic health records and information collection directly from patients and providers. Dr. Gerkovich’s most recent research has the object of identifying factors that explain differences in engagement in medical care for treatment of chronic conditions, with an emphasis on factors that explain patients’ transitions between engagement and non-engagement in care. Dr. Gerkovich’s research program involves the collection of new data and the use of secondary data sources, such as national representative data samples, to address research questions. Her research methodology and statistical analysis expertise support this collaborative research and mentoring of students. In addition, she is trained in research methodology, statistical analysis, computer programming, and informatics, and is an author on over 50 peer-reviewed publications and many professional presentations. Dr. Gerkovich is a member of the American Medical Informatics Association (AMIA).

Earl Glynn, MS

Mr. Glynn is Principle Programmer/Analyst of the Center for Health Insights at the University of Missouri – Kansas City (UMKC). He received a BS in nuclear engineering and an MS in computer science from Kansas State University. Earl has applied a background in scientific computing and analytic methodology to solving a variety of R&D problems. Before joining UMKC, he was a scientific programmer at Stowers Institute. In addition to a number of large-scale analytics projects involving scientific, medical, engineering and open government data, Earl developed the imaging software in the Cerveillance Scope, which won a 1998 Silicon Prairie “Technology of the Year” award.

Timothy P. Hickman, MD, MEd, MPH

Dr. Hickman is an Associate Teaching Professor in the Department of Biomedical Health and Informatics, UMKC School of Medicine and in the Health Professions Education Program, Division of Counseling and Educational Psychology, UMKC School of Education.   His primary focus is on Culturally Appropriate Care, Social Determinants of Health and Health Disparities. He utilizes a transdisciplinary approach including curriculum development and instructional design for graduate students, medical students and continuing education; assessment of skills, knowledge and attitudes using a multi-modal approach; and exploring clinical decision support tools including evidence based guidelines, shared decision making and health literacy. Dr. Hickman holds a Graduate Certificate in biomedical informatics from the Department of Medical Informatics & Clinical Epidemiologyat the Oregon Health & Science University.

Mark Hoffman, PhD

Dr. Hoffman is Director of the Center for Health Insights at the University of Missouri – Kansas City (UMKC), where he also serves as an Associate Professor in the Department of Biomedical and Health Informatics and the Department of Pediatrics. He received his Ph.D. from the University of Wisconsin – Madison and performed post-doctoral research at the National Animal Disease Center in Ames Iowa. Before joining UMKC, he spent 16 years leading genomics, public health and research initiatives at Cerner Corporation, where he was a Vice President. He also was an adjunct professor in the UMKC School of Computing and Engineering for 9 years prior to joining the DBHI faculty.  In addition to his peer-reviewed publications, Mark is an inventor on 16 issued patents.

William E. Lafferty, MD

Dr. Lafferty is the Hicklin Endowed Chair, Office for Health Services and Public Health Outcomes Research at the School of Medicine at the University of Missouri-Kansas City. He works on projects that seek to balance cost, access, and quality of health care in new areas of public interest such as complementary and alternative medicine. Dr. Lafferty is a physician who studies, teaches, and performs health services research. Prior to joining UMKC, he was a Professor in the University of Washington’s School of Public Health in the Department of Health Services. His research interests include health policy decision making and cost, access, and quality issues having to do with health care. He is keenly interested in social justice issues and believes that ending poverty, racism, and other forms of discrimination is an important health intervention. He also did an infectious disease subspecialty fellowship at the University of Washington and continues work in the area of sexually transmitted infections. He has expertise in epidemiology, disease surveillance, analysis of secondary data sets, complementary medicine, and heath care outcomes research.

Praveen Rao, PhD

Dr. Praveen Rao is an Associate Professor in the Department of Computer Science Electrical Engineering at University of Missouri-Kansas City. He is also a collaborating faculty of the Center for Health Insights at UMKC. His research interests are in the areas of data management, big data and analytics, and health informatics. More specifically, his research work aims to solve fundamental data management problems that arise in data-intensive software applications by designing new algorithms, data structures, and software techniques. His research and outreach activities have been sponsored by the National Science Foundation, University of Missouri Research Board, Headquarters Counseling Center (KS), Kansas City Power and Light, Intel, and Amazon Web Services. In 2010, he received the IBM Smarter Planet Faculty Innovation Award. In 2013, he was one of the 14 professors world-wide to receive the IBM Big Data and Analytics Award. During 2001-2002, he worked as a software engineer at Amazon in Seattle.

Steve Simon, PhD

Dr. Simon is an Adjunct Research Professor in Biomedical and Health Informatics at the University of Missouri – Kansas City, and also serves as an independent statistical consultant. He received his Ph.D. from the University of Iowa. In addition to his research publications, Dr. Simon is author of a book. Statistical Evidence in Medical Trial, and the website P.Mean (at: http://www.pmean.com/). His research interests include accrual problems in clinical trials, information theory, monitoring adverse events in clinical trials, research ethics and risk adjustment models. Previously, Dr. Simon has worked in the College of Business at Bowling Green State University, at the National Institute for Occupational Safety and Health, and at Children’s Mercy Hospital.

Kim Smolderen, PhD

Dr. Smolderen is an Assistant Professor at the Biomedical & Health Informatics Department at the School of Medicine at UMKC and is affiliated as an Outcomes Research Scientist at the Saint Luke’s Mid America Heart Institute. She has led a 2-center observational registry that evaluated the prevalence of mood disorders in peripheral arterial disease (PAD) patients and its association with generic health status and clinical outcomes. Her doctoral work addressed the psychological burden in patients with PAD, focusing, for example, upon the prevalence of depression and how this disproportionately affects younger women. These results were based on an ongoing prospective PAD registry that she initiated in the Southern part of the Netherlands. Currently, she is the PI of two projects supported by the Patient Centered Outcomes Research Institute that are directed towards developing a multicenter US observational PAD registry with a focus on quantifying patient- centered outcomes as a function of their patient characteristics and administered treatments.

Lakshmi Venkitachalam, PhD

Dr. Venkitachalam is Assistant Professor in Epidemiology and Outcomes Research at the University of Missouri – Kansas City. As tenure-track faculty, Dr.Venkitachalam is developing an independent research agenda that supports and builds capacity to systematically address the implementation and evaluation of evidence-based clinical and public health initiatives to prevent and manage chronic conditions in underserved, low-resource settings. Her research and training experience thus far has allowed for multi-dimensional focus on clinical and patient-centered outcomes with emphasis on novel research methodology that includes comparison of standard and novel analytical methods in cardiovascular research. She has extensive experience in the use of large, secondary databases (derived from electronic medical records, multicenter registries), and has co-authored over 15 peer-reviewed publications, >40 abstracts at national conferences and 4 book chapters in premier textbooks in the field of cardiovascular epidemiology and outcomes research. Dr.Venkitachalam is the primary instructor for the graduate course on principles and application of epidemiology and mentors graduate and medical students in areas of health services and outcomes research.  She also serves as the director of the internship program at DBHI and in this capacity, builds collaborations with community organizations to identify training opportunities for students in the MS Bioinformatics program. Full bio is available at:  http://www.med.umkc.edu/dbhi/Faculty/venkitachalam.shtml

Karen B. Williams, PhD

Dr. Williams is Professor and Chair of Biomedical and Health Informatics at the University of Missouri-Kansas City School of Medicine.  She is a research methodologist with an emphasis in biostatistics and health outcomes research.  Dr. Williams’ previous service on the UMKC Adult Health Sciences Institutional Research Board, the Rinehart Foundation Research Support Committee and Director of the Clinical Research Center at the UMKC School of Dentistry makes her a valuable resource for pre-clinical and clinical researchers navigating through regulatory, research development and statistical analyses processes. Her research interests include clinical reasoning, health outcomes, oral health and health behavior.  Dr. Williams has assisted numerous research teams in developing and validating novel measurement instruments for use in research.  Additionally, she has served as a principal investigator, co-investigator and/or methodologist/biostatistician for numerous corporate and federally-funded (NCI, NCCAM and NIMH) grants aimed at evaluating behavioral strategies for reducing tobacco use, and improving adherence to medications in an HIV population; testing the effectiveness of Sutherlandia, a South African indigenous phytotherapy treatment for HIV+ patients; and Phase I, II and III clinical trials.

Gerald Wyckoff, PhD

Dr. Wyckoff is an Associate Professor in the School of Biological Sciences, Division of Molecular Biology and Biochemistry and holds a joint appointment in the School of Medicine, Department of Biomedical and Health Informatics.   A major effort of Dr. Wyckoff’s research has been to create a relational database of genomic sequences and associated information. This includes expression information, divergence information, protein function information, and positional information. This has bearing on several types of research dealing directly with the techniques and programs built to handle and query the data, but more importantly, observations made using this tool will lead to hypothesis testing experiments performed at the bench. His work is aimed at developing the informatics structure necessary to allow for the incorporation of many other types of research data, including protein structure, pathway information, and disease linkage information.

A bioinformatics approach allows for the analysis of large-scale genomic differences between species and comparison to polymorphism data within species. Dr. Wyckoff is utilizing these analyses to understand the processes affecting genes and genomes during evolution, including analyses of physico-chemical properties of individual amino acid changes in sets of genes. While constraint and random genetic drift are the primary forces acting on the evolution of gene sequences, positive selection does happen at the molecular level and can play a significant role in the development of specific gene sequences. Large-scale approaches help us to quantify the nature of positive and negative selection both within and between species.

Currently, Dr. Wyckoff is working on categorizing and annotating genes from a major macaque brain cDNA sequencing effort involving research groups from both Japan and the United States. This work is in parallel with ongoing database design work and my interest in rapidly evolving genes in primates.