Research Labs

Ann L Fruhling, Ph.D.

Research in Health and Consumer Informatics
Dr. Fruhling, Professor, is the founding Director of the School of Interdisciplinary Informatics at UNO and a Charles W. and Margre H. Durham Distinguished Professor of College of Information Science and Technology. The School offers four degrees: Cybersecurity, Bioinformatics, Biomedical Informatics, and IT Innovation. Since 2004, Dr. Fruhling has served as Director of the Public Health Informatics Research Laboratory, employing several FTEs and supporting many GAships and over 70 undergraduate, graduate, and doctoral students. She has over 100 publications and has been a PI/Co-PI on research projects totaling over $8.53M.

Dr. Fruhling's research focuses on health informatics and evaluating and improving human-computer interaction efficiency and effectiveness in the healthcare and public health domains. Since 2002, she has been the PI of an emergency response system and bioterrorism surveillance system for public health laboratories called STATPack™, which has been deployed in over 65 health laboratories. Dr. Fruhling is a Co-PI on an NIH R01, ARHQ grant that focuses on optimizing the EHR for cardiac care and the PI for a UNO/UNMC collaborative grant sponsored by the Department of Transportation and awarded by UNL’s University Transportation Center that is conducting research and development to minimize the health impact to first responders in the case of a HAZMAT transportation incident using internet of things (IoT). In addition, Dr. Fruhling is a Co-PI for the Biomedical Informatics KCA that supports the UNMC NIH IDeA Center for Translational Research.

Publications [Google Scholar]

Dario Ghersi, M.D., Ph.D.

Dr. Ghersi received an M.D. from the University of Genoa with a thesis on computational immunology in 2004. From 2004 to 2005 he worked as a Research Associate in the Department of Rheumatology at the Hospital for Joint Diseases in New York City. In 2005 he enrolled in the Ph.D. program in Computational Biology at Mount Sinai School of Medicine working on the structural bioinformatics of protein binding, and he graduated in 2010. He was a Postdoctoral Fellow at Princeton University from 2010 to 2014, where he worked on large-scale genome sequencing data. In 2011 he was awarded a postdoctoral fellowship from the American-Italian Cancer Foundation. He joined the University of Nebraska at Omaha in 2014 as an Assistant Professor of Biomedical Informatics in the School of Interdisciplinary Informatics.

Publications [Google Scholar]

Jonathan Clayton, DVM, Ph.D.

The Clayton Lab is studying host-microbiome interactions in humans and nonhuman primates. We are using nonhuman primates as a model for studying the effects of variations in dietary fiber and other dietary compounds, as well as lifestyle factors associated with modernized society, on the microbiome and metabolic health.

Dr. Clayton received his Doctor of Veterinary Medicine (D.V.M.) and his Doctor of Philosophy (Ph.D.) in Comparative and Molecular Biosciences from the University of Minnesota. For his Ph.D. thesis research, he used nonhuman primates as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. During his Ph.D., Dr. Clayton founded the Primate Microbiome Project (PMP) with the intended purpose to develop a systematic map of variation in microbiome structure and function across all primates and to relate this to primate health, evolution, behavior, and conservation.

The Clayton Lab are currently extending our research to explore in detail causal mechanisms for microbiome-modulated metabolic diseases including diabetes and obesity, as well as neurological/behavioral diseases such as stress. We do this using both in vitro and in vivo experiments, including, but not limited to, next-generation sequencing, anaerobic and aerobic culture, germ-free mouse models, and marmoset models.

Publications [Google Scholar]

Kate Cooper, Ph.D.

Dr. Kathryn (Kate) M. Cooper joined the School of Interdisciplinary Informatics at UNO in 2015 and has been a member of the UNO Bioinformatics Research group since September 2005. Her research has focused on application of network science to biomedical data; including network modeling of gene expression data can be functionally interpreted to further understand cellular systems. She has also worked work on developing structural filters in high performance computing environments for analysis of large biological networks; this work explores the relationship between known graph theoretic properties and potential function in protein protein interaction networks as well as correlation networks. She has also collaborated on projects exploring how graphs can be effective tools for modeling systems in broader areas of biomedical and health informatics, such as the spread of infectious disease and the modeling co-occurrence of terms in food products labels. Her current research interests are exploring the impact of diet on the microbiome for prevention of disease using consumer health informatics.

Publications [Google Scholar]

Guoqing Lu, Ph.D.

Dr. Lu’s group is interested in a broad spectrum of bioinformatics problems, ranging from sequence analysis, genome comparisons, to system-level biological interactions. His research spans both theoretical and applied bioinformatics, with a focus on comparative genomics and evolutionary informatics. Dr. Lu’s lab has a number of ongoing research projects, which include the pathogen-host-drug interaction networks at the systems biology level and the invasive species-native community interactions and feedback at the ecosystem level. His lab developed and is currently maintaining several bioinformatics systems, including Phylomarker and FluGenome.

Publications [Google Scholar]

Hesham H. Ali, Ph.D.

Dr. Ali Research and Creative Interests
Bioinformatics
Wireless Networks
Graph Modeling
Design and Analysis of Algorithms
Mobile Computing
Scheduling

Kiran Bastola, Ph.D.

Dr. Bastola goal as a teacher is to enable students to discover new possibilities and develop skills that open new doors of opportunity. My research is highly interdisciplinary and lies at the intersection between computational and biological sciences with an emphasis on integrating and analyzing large biomedical data sets. I believe, while research provides an opportunity to change the world, teaching and mentoring provide opportunities to make lasting impacts on individuals. Research area of interest include Mitochondrial Biology, Public Health Genomics and Pharmacognosy.

Martina Clarke, Ph.D.

Dr. Clarke’s research areas include: user-centered design, usability evaluations of health information technology, needs assessment, and clinical workflow analysis. In other words, her research is focused on integrating information technology into healthcare in a way that does not negatively impact clinicians and patients.Her research focuses on reducing documentation burden among care providers, specifically, shared living providers and other direct support professionals.

Publications [Google Scholar]

Paul H. Davis, PhD

Dr. Davis interested in Toxoplasma gondii, which is a zoonotic human parasite with worldwide distribution. Approximately 30% of the U.S. population is chronically infected with T. gondii, frequently acquired from infected cats or ingesting undercooked meats.

In addition to its classical association with fetal malformation and abortion (a leading cause of congenital neuropathy, affecting >1/1000 live births in the US), toxo­plasmosis also afflicts the growing ranks of immunocompromised individuals (cancer and transplant patients, as well victims of HIV). Following infection,bradyzoite cysts invade and permanently reside within tissues, and are completely resistant to chemotherapy. 

Recently, studies suggest that chronic parasite infection affects human behavior; thus the need to more closely examine this parasite stage is increasing. Our research involves studying the formation of this intra-tissue bradyzoite cyst using genomic and genetic approaches, both in vitro and in vivo.   

Moreover, the causative agent of malaria, P. falciparum, shares a close genetic relationship to T. gondii, the latter of which is a frequently used model for malaria research. Due to the ease of growth and genetic manipulation, we utilize T. gondii to investigate several recently tested compounds showing anti-parasitic activity in vitro, in an attempt to develop novel anti-malarial treatments

Babu Guda, Ph.D.

Research in Computational Biology, Genomics, and Precision Medicine
Dr. Guda has interdisciplinary training background in molecular biology, computer science and computational biology, with over 25 years of experience in bioinformatics research that includes analysis of a variety of high throughput data from genomics-based experiments. He published over 135 peer-reviewed research articles, with about half of them resulting from his own research work, which cover a wide range of topics related to genomics, bioinformatics, systems biology, neuroscience, precision medicine, and machine learning. Dr. Guda is also the founding director of the Bioinformatics and Systems Biology (BSB) Core facility at the University of Nebraska Medical Center (UNMC) that currently supports over 250 independent investigators in the Midwest region. BSB core offers a broad range of bioinformatic services related to the analysis of next-generation sequencing (exome, RNAseq, ChIPseq, bisulfite methylation, microRNA and SNP arrays, and metagenomics data), proteomics and metabolomics data, protein sequence and structure analysis that include homology modeling, database searching, functional characterization of genes and gene products, and pathway and network analysis. Dr. Guda developed and taught several graduate courses in Bioinformatics and mentored over 60 undergraduate and graduate students, postdocs and junior faculty, combined, in the bioinformatics field. He served on numerous study sections and review panels of NSF, NIH, and DoD, served on the external advisory boards of program projects and on the editorial boards of peer-reviewed journals. Dr. Guda is also serving as an active administrator at UNMC through his roles as the Chief Bioinformatics and Research Computing Officer reporting to the Vice Chancellor for Research and as Assistant Dean for Research Development reporting to the Dean, College of Medicine. He served on several high-level leadership search committees both at UNMC and the University of Nebraska.

Publications [PubMed][Google Scholar]

Jordan Rowley, Ph.D.

Principles of 3D Chromatin Organization
Chromatin is deliberately arranged in the 3D nucleus so that genomic loci can influence each other long-range. The organization of chromatin is altered during development, in response to hormonal signaling, and after heat shock, indicating that the nucleus is a dynamic environment. Abnormal 3D chromatin organization is implicated in diseases such as aberrant limb formation, cancer, and embryonic lethality. My overall goal is to discover mechanisms driving the establishment and dynamics of 3D chromatin organization. Specifically, Dr. Rowley aim to elucidate how looping, insulation, and transvection occur.

Publications [Google Scholar]

Walter (Scott) Campbell, Ph.D.

Dr. Campbell is an Associate Professor for the Pathology, Microbiology, and Immunology department, Sr. Director of Research Technoloiges - UNMC and Director of Pathology and Public Health Informatics.   Dr. Campbell completed his doctoral training at UNMC in health informatics in 2013.  Prior to his academic training, Dr. Campbell earned a Masters of Business Administration (University of Wisconsin – Madison, 1990).  He began his career in the food industry and later in the automotive industry serving in  a variety of capacities.  In 1998, he started his own company focused on medical office computer management systems including billing systems and electronic health records.  He has directly participated in the implementation of approximately 100 electronic health record software systems and practice management systems in the ambulatory care environment.

Shibiao Wan, Ph.D.

Research in Bioinformatics, Machine Learning and Computational Biology

Dr. Shibiao Wan is currently an Assistant Professor in the Department of Genetics, Cell Biology and Anatomy at University of Nebraska Medical Center (UNMC). He is also the Assistant Director for Bioinformatics and Systems Biology Core at UNMC. Before joining UNMC, Dr. Wan was a Bioinformatics Research Scientist at St. Jude Children's Research Hospital, one of the top pediatric cancer hospitals in US. Dr. Wan received his postdoctoral training in University of Pennsylvania (2017-19) and Princeton University (2016-17). Currently, Dr. Wan is particularly interested in single cell analysis, multi-omics analysis, spatial transcriptomics, and machine learning for processing large-scale biological data. With more than 12 years of experience in bioinformatics, machine learning, and computational biology, Dr. Wan has published >40 articles in prestigious journals like Genome Research, Nature Communications, Science Advances, Circulation Research, Nature Aging, Briefings in Bioinformatics, and Bioinformatics.  Dr. Wan is an academic editor for BioMed Research International and a guest associate editor for a series of high-impact journals including Frontiers in Cell and Developmental Biology, Frontiers in Pharmacology, Biology, Frontiers in Genetics, and Genes. He is a TPC member for >20 machine learning related international conferences including IEEE ICTAI and IEEE IAICT. Dr. Wan is also a reviewer for >50 prestigious journals including Nucleic Acids Research, Genomic Medicine, Briefings in Bioinformatics, British Journal of Cancer, and IEEE TNNLS. He is a recipient of the global peer review awards (top 1%) in “Cross-Field” and “Biology and Biochemistry” in 2019 awarded by Clarivate. Dr. Wan is also an Outstanding Young Alumni Awardee in 2022.

Publication [Google Scholar]