Collaborators
Andrew Severin
Andrew Severin is the manager of the Genome Informatics Facility. My group works at the interface between genetics and bioinformatics translating big data into informative data for interesting biological questions. I work with a wide variety of organisms from viruses, mycoplasmas and bacteria to soybean, maize, Arabidopsis, potato, nematode, pig, painted turtle, bees, wasps, zebrafish, abalone and yellowtailtuna. My broader research interests include understanding how a genome relates to a phenotype from a systems biology approach and comparative genomics. The first step in this process has been the main focus for the last few years, which is the ability to create genomic resources for comparison (assembly, annotation, visualization) of many related organisms
Sivanandan Chudalayandi
My expertise is in the field of molecular biology, genetics and computational biology, modern biological research routinely produce large scale data that aid in shedding light on a phenomena or point us in a newer research direction. As an Associate Scientist at the Genome Informatics Facility, I work as a bioinformatics liaison for the USDA community at large, I contribute to the community by way of tutorials, online discussions etc. I also collaborate with researchers in my capacity as computational biologist to perform data driven discovery.
Rick E. Masonbrink
I am fortunate to work as a research scientist in the Genome Informatics Facility at Iowa State University, where I am surrounded by highly skilled bioinformaticians and constantly exposed to new ideas and approaches. This dynamic environment fosters my passion for science and my curiosity to keep learning and growing. With the support of the USDA, I have had the opportunity to create workshops and tutorials, and I also assist our faculty and industry collaborators through fee-for-service work. Over the years, I’ve been involved in a wide range of projects, developing and applying bioinformatics pipelines tailored to specific needs. I have also gained considerable experience in Hi-C scaffolding and genome annotation. I view this continuous exchange of ideas as key to my growth as both a researcher and a contributing member of the broader scientific community.
Aleksandra Badaczewska
Alex is a Research Scientist IV at the Genome Informatics Facility at Iowa State University. Her academic background is in Chemistry and Biotechnology, with a Ph.D. in Computational Biology and broad experience in programming and designing web applications. She develops a comprehensive collection of highly customizable visualization solutions for Bioinformatics and supports software optimization for the USDA Geospatial analyses.
Sharu Paul
Sharu is a Visiting Scientist at the Genome Informatics Facility at Iowa State University. His background is in Biotechnology with a Ph.D. in Genetics and Genomics. He is using a diverse array of bioinformatic analyses to solve big data problems and contribute to developing workshops and tutorials for USDA scientists.
Maryam Sayadi
I have recently joined the Genome Informatics Facility at Iowa State University. I am mostly involved in generating and updating bioinformatics tutorials. My background is protein structure and function through molecular modeling simulations. My goal is a multidisciplinary approach involving protein interaction and structure and gene regulation.
Arun S. Seetharam
My main interests are in the fields of bioinformatics and evolutionary genomics. Currently, I am working on various projects involving next-generation sequencing including the first de novo assembly of a teosinte genome. I am also developing pipelines to streamline the assembly and annotation process for newly sequenced organisms. My long-term goal is to study the genome organization and evolution of grass species.
Jennifer Chang
I am an Iowa State University graduate, with a PhD in Bioinformatics and Computational Biology. I have been programming (in one language or another) since 2006 and have an interest in data visualization and software development. My research focus has been on analyzing and merging networks, monitoring the evolution of influenza A viruses in swine, and writing cross-platform pipelines. In 2020, I joined the Genomics Informatics Facility in the hopes of developing interdisciplinary pipelines and tutorials to meet the needs of the widespread research community.
Swapna Menon
Swapna is a bioinformatics freelancer based in India. Her formal qualifications include an M.S. in Molecular Sciences and an M. Phil. in Bioinformatics. She analyzes microarray and NGS data for research groups in academic institutions. She helps clients with experimental design and sequence data issues. Earlier, she taught bioinformatics in universities in Kochi. The sequencing technologies are advancing. Bioinformatics software and analyses methods are keeping pace. Practicing bioinformatics requires knowledge of statistics, information technology and NGS technologies and, biology. Open source software and educational resources are vital for all bioinformatics practitioners.
Margaret Woodhouse
I am computational biologist for the USDA maize database MaizeGDB. My research interests are in comparative and evolutionary genomics. I have helped to develop MaizeGDB into a multi-genome, pan-genome database. I also collaborate with various universities and agencies in the United States and around the world to sequence, assemble, analyze, and steward the genomes of maize. My long-term goal is to harness the power of deep learning and the enormous amount of plant genomic and functional data to predict the functions of loci in maize.