Faculty active in this area of research are listed below. For a brief description of their research interests, click on their name in the list. Clicking on the name at the beginning of the brief description links to their detailed personal website.

Jake Chen, PhD, Department of Genetics and Computer Science
Elliot Lefkowitz, PhD, Department of Microbiology
Alexander Rosenberg, PhD, Department of Microbiology
Hemant Tiwari, PhD, Department of Biostatistics

Jake Chen, PhD Dr. Chen conducts research in “translational bioinformatics”—the science of collecting, representing, storing, retrieving and processing data and knowledge for the improvement of human health. His research interest focus on systems biology, data mining, advanced visual analytics for therapeutic discovery and clinical decision-making applications. He has published more than 150 peer-reviewed scientific papers and edited two bioinformatics books, “Biological Database Modeling” and “Biological Data Mining”. He has organized many conferences, including BIOKDD—a workshop series at the Annual ACM Knowledge Discovery and Data Mining Conference annually for two decades. In his previous position as a faculty in Indiana University, he was named a finalist as “Indiana’s Technology Educator of the Year” for his contribution to informatics research, education, and entrepreneurship in the state of Indiana.

Elliot Lefkowitz, PhD Research interests are directed at contributing to the understanding of microbial genomics and evolution by developing and utilizing computational tools and bioinformatics techniques to mine sequence and other data for significant patterns characteristic of function and/or evolution. This includes research on the genomics and evolutionary history of many virus species, as well as the complete genomic sequencing and annotation of various bacterial species. I have been part of the teams that have sequenced the complete genomes of ectromelia virus, monkeypox virus, rabbitpox virus, Ureaplasma urealyticum, Streptococcus pneumoniae strain R6, and Mycoplasma hyopneumoniae. My work on basic bioinformatics tool development has included the development of new algorithms for the detection of viral regulatory motifs; tools for the identification of viral genes; the development and utilization of High Performance Computing tools for bioinformatics analysis; and the development and use of tools for analyzing patterns of viral evolution. I have also been Principal Investigator of the Viral Bioinformatics Resource Center, an NIH-sponsored effort to develop Bioinformatics Resource Centers (BRCs) for Biodefense and Emerging or Re-Emerging Infectious Diseases. I also serve as Data Secretary for the International Committee on Taxonomy of Viruses (ICTV). In this role, I provide support to the ICTV for handling of viral taxonomy proposals; communicate the results of ICTV deliberations to the scientific community; and interact with various international agencies such as the NIH National Center for Biotechnology Information to incorporate the official, ICTV virus taxonomy into their own taxonomic databases.

As Director of CCTS and CFAR Informatics, in addition to providing informatics research support and collaboration, Dr. Lefkowitz is also responsible for providing educational opportunities to campus investigators to enhance their knowledge, understanding, and application of informatics data and analytical tools in support of their own research interests.

Alexander Rosenberg, PhD Dr. Rosenberg’s group works on bioinformatics related to immunology. One major focus is the application of bioinformatics to develop analytical methods and tools for the study of adaptive immune receptor repertoires using next generation sequencing (AIRR-seq). They have been developing a pipeline and downstream analysis tool set focused on immunoglobulin heavy chain sequence data from B cell subsets through which users can interrogate many aspects of repertoires, including clonality, mutation properties and relatedness between cell subsets, tissues or across time. More recently they are extending analysis and visualization tools to work with single cell 10x VDJ (and transcriptomic) data. This work supports studies in vaccinology, autoimmunity, infectious disease and allergy, and is useful for answering basic questions about the development of immune system responses. The lab is also interested in novel approaches for visualization of complex biological data, including the integration of data from multiple high-throughput platforms.

Hemant Tiwari, PhD Dr. Tiwari's current research interests include Genetic Linkage Analysis, Disequilibrium Mapping, Genome-Wide Association Studies, Copy number variations (CNVs) Structural variations (SV), Epigenetics, Pharmacogenetics/ Pharmacogenomics, Gene expression, Exome sequencing, Pathway and network analysis, Bioinformatics, Metabolomics, and Population Genetics. He has extensive record of productive collaborations in searching for genes for obesity, diabetes, cardiovascular diseases, Rheumatoid Arthritis, SLE, Stroke, Cancer, and Multiple Sclerosis, to name few.