Genomics

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

Rod Wing, PhD, and his lab, The Arizona Genomics Institute, specialize in building what geneticists call a physical map of a genome- a crucial foundation of any genome sequencing effort. AGI has earned a reputation for providing extremely high-quality maps, as documented in previous sequencing efforts leading to the genome sequences of rice and corn. The genome sequence will allow scientists to locate and identify genes that can improve and strengthen crops and increase yield in order to help solve the Earth’s looming food crisis by creating new strains of the cereal crops that make up 60% of humankind’s diet. Keywords: Genome Biology, Genome Sequencing/Assembly/Annotation, Food Security, Rice

Microbe-host interactions Specifically microbial pathogenesis Concomitant immune response with respect to host age

Bruce Walsh is a Professor of Ecology and Evolutionary Biology at the University of Arizona and also a Professor in the College of Public Health. He is also an Adjunct Professor in the Departments of Animal Sciences, Plant Sciences, and Molecular and Cellular Biology, and the former Chair of two Graduate Interdisciplinary Programs: Genetics and Statistics. Dr. Walsh is internationally known for his work on the genetics of complex traits, and is coauthor of the leading graduate text on Quantitative Genetics. He is a frequently-invited speaker at national and international meetings, being a keynote speaker at the last Two World Congresses in Quantitative Genetics (China and Scotland) as well as at the most recent Gordon Conference in Quantitative Genetics. Dr. Walsh routinely teaches several international graduate/ post-graduate courses each year in areas ranging from animal and plant breeding, to evolutionary genetics, to human applications, and has taught in Australia, Belgium, China, Costa Rica, Denmark, Finland, Holland, Korea, New Zealand, Portugal, Scotland, and Sweden in additional to numerous domestic short courses. Most recently, in conjunction with BIO5, he has started the Tucson Winter Institute in Plant Breeding, whose propose is to train academic and industry plant breeders from around the world in the latest techniques in genomics, statistics, and bioinformatics as they relate to improving plant production. Keywords: "Statistical Genetics" "plant and animal breeding"

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.

Our laboratory is both experimental and computational. We use next-generation sequencing technologies to measure genome-wide molecular phenotypes. By leveraging the interconnected relationships between DNA sequence, transcription factor binding, chromatin modification, and gene expression, we study how cells achieve context-appropriate expression patterns and signal responsiveness. Lab Website: www.romanoskilab.com Keywords: Genetics, Genomics, Vascular Biology, Bioinformatics

Our lab investigates how the ecology of a species shapes patterns of variation at multiple levels (genes, pathways, transcriptomes, genomes, physiology, behavior and life history), how populations adapt to environmental shifts (natural or human created), how genetic architecture can dictate the evolutionary trajectory of populations, the implication of ecological adaptation in the process of speciation and the role of sexual selection and sexual conflict in the evolution of reproductive incompatibilities. Our research revolves around these fundamental aspects of evolutionary biology. We work on a group of cactophilic Drosophila that inhabit the deserts of North America. These Drosophila species are an excellent system to study given that their ecology is well understood and the fact that we can perform many genetic, genomic, manipulative and life history experiments. In addition to utilizing the cactophilic Drosophila system we have ongoing projects on the agrigenomics of the agricultural pests, Drosophila suzukii (spotted wing Drosophila) and Helicoverpa zea (corn earworm). Keywords: Evolutionary, ecological and agricultural genomics

Eric Lyons, PhD is an assistant professor at the University of Arizona School of Plant Sciences. Dr. Lyons is internationally known for his work in understanding the evolution, structure, and dynamics of genomes. Core to his research activities is the development of software systems for managing and analyzing genomic data and cyberinfrastructure for the life sciences.Dr. Lyons has published over 30 original research papers and 5 book chapters, many in collaboration with investigators from around the world. He is a frequent presenter at national and international meetings, and has been invited to teach workshops on the analysis of genomic data to plant, vertebrate, invertebrate, microbe, and health researchers.Prior to joining the faculty in the School of Plant Sciences, Dr. Lyons worked with the iPlant Collaborative developing cyberinfrastructure, and managing its scientific activities. In addition, he spent five years working in industry at biotech, pharmaceutical, and software companies. Dr. Lyons’ core software system for managing and analyzing genomic data is called CoGe, and is available for use at http://genomevolution.org