Omics

The BIO5 is the most influential cross collaborative initiative at the University of Arizona. Being a part of the BIO5 opens opportunities to collaborate within scientific fields outside of my specialty and promotes both academic and industrial partnerships. With my background in single-cell transcriptomics, hiPSC technology and heart disease, I hope to share my knowledge and learn from other BIO5 members. In becoming a member of BIO5, I aspire to enhance my research program an ultimately, make life changing discoveries.

We are a plant genomics lab who specialize in whole genome sequencing and assembly; with analyses of structural variation, gene modeling and transcriptomes. Our work on major projects of rice, corn, barley, etc, allows us to share our technical expertise with other researchers. Our research in plant and animal genomes, at the whole genome and transcriptome levels, will impact successful genetic selections toward the goal of feeding the 9 billion people toward the year 2050. Keywords: "Genome Sequencing", "PacBio", "Structural Genomics", "Plant Genetics", "DNA Extraction"

Dr. Zenhausern research interests encompass multiple scientific themes combining engineering and medicine to develop platform technologies with global impact for improving human life and the delivery systems of more comprehensive and personalized cares. In alignment with the fourth industrial revolution, Zenhausern and his team at the Center for Applied Nanobioscience and Medicine (ANBM) provides an interdisciplinary framework for advancing technological innovation from discoveries to medical products by partnering with governmental, clinical and industrial institutions across the globe, while training the next generation of students and professionals. Keywords: Technology Platforms Development; Integrated Biomedical Systems

Carol Soderlund, PhD, is an Associate Research Professor at the BIO5 Institute at the University of Arizona. While working on her PhD in Computer science in 1988, she collaborated with a biologist to develop one of the first gene prediction programs. She received a DOE Human Genome Distinguished Postdoctoral Fellowship hosted by Los Alamos National Laboratory, where she became involved with mapping the human genome. Her work continued at the Sanger Centre in the UK, which was on the forefront of sequencing the human genome. She developed the FPC software, which was used for mapping the human genome, and has since been the primary software package for mapping large genomes.Her primary research objective is to provide environments for biologists to run algorithms (both her own and existing software), with highly interactive graphics for query and display of the data and results. Towards this end, she has published seven software packages for various genomic problems, where the three most important are: (1) The FPC program mentioned above, which is still being used after its initial release 15 years ago and has been extended for next generation sequencing. (2) The SyMAP software for the computation, query and display for synteny for the comparison of plant genomes. (3) The Transcriptome Computational Workbench (TCW) for the analysis of the transcriptome across tissues or conditions, and across the species for finding shared and unique genes.Dr. Soderlund has published over 60 original research papers and 20 book chapters on a range of genomic problems. She has collaborated with a range of scientists on a variety of organisms and genomic problems, where the majority of the collaborations have been on mapping genomes and transcriptome analysis, but she has also been involved in metagenomics, sequencing, and host-pathogen interactions.

Dr. Schlenke's research program uses fruit flies in the genus Drosophila to understand the evolutionary genetics of host-parasite interactions. For example, his lab has developed several species of parasitic wasps, which are readily observed infecting Drosophila in nature and can be very specialized to particular host species, as model parasites. These wasps lay single eggs in Drosophila larvae and, once hatched, consume flies from the inside out. Flies mount cellular and behavioral defense responses against wasps, but wasps have adaptations for finding host fly larvae, suppressing host cellular immunity, and manipulating host behavior. The Schlenke lab uses a variety of "omics" tools to understand the molecular genetics of fly cellular immunity and wasp virulence, as well as patterns of host immunity and pathogen virulence coevolution across fly and wasp phylogenies. The Schlenke lab also studies the genetics and neurobiology of behaviors that flies use to avoid being infected by the wasps and to cure themselves once they are infected, including various self-medication behaviors.

Dr. Bonnie Hurwitz is an Assistant Professor of Biosystems Engineering at the University of Arizona and BIO5 Research Institute Fellow. She has worked as a computational biologist for nearly two decades on interdisciplinary projects in both industry and academia. Her research on the human/earth microbiome incorporates large-scale –omics datasets, high-throughput computing, and big data analytics towards research questions in “One Health”. In particular, Dr. Hurwitz is interested in the relationship between the environment, microbial communities, and their hosts. Dr. Hurwitz is well-cited for her work in computational biology in diverse areas from plant genomics to viral metagenomics with over 1200 citations

The Gutenkunst group studies the function and evolution of the complex molecular networks that comprise life. To do so, they integrate computational population genomics, bioinformatics, and molecular evolution. They focus on developing new computational methods to extract biological insight from genomic data and applying those methods to understand population history and natural selection.

Andrew Capaldi, PhD, researches the signaling pathways and transcription factors in a cell that are organized into circuits. They allow cells to process information and make decisions. For Dr. Capaldi, the work arises in understanding both how these circuits are built from their components, and how they function and malfunction. To address these questions, he is working to reverse engineer the circuitry that controls cell growth in budding yeast using a combination of genomic, proteomic and computational methods. http://capaldilab.mcb.arizona.edu