Eric Lyons, Ph.DEric Lyons, PhD, is an Assistant Professor at the University of Arizona’s School of Plant Sciences. He is an expert in plant comparative genomics and life-science cyberinfrastructure. He has published over 30 peer-reviewed research articles, four book chapters, and maintains the widely used comparative genomics platforms CoGe and EPIC-CoGe. He is a Co-PI on the NSF funded iPlant Collaborative and is dedicated to democratizing access to cyberinfrastructure for all life science research. His research group has been supported by the Gordon and Betty Moore Foundation, the US National Science Foundation, and the US Department of Agriculture. He is a triple graduate (BA, MS, PhD) from the University of California, Berkeley, and spent several years working in pharmaceutical, biotechnology, bioinformatic companies. He teaches a project-based learning course called Applied Concepts in Cyberinfrastructure.
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Matt BomhoffMatt Bomhoff graduated from Arizona State University with a degree in Computer Systems Engineering. For the last nine years he has worked as a Bioinformatics Software Engineer at the University of Arizona. He enjoys all aspects of scientific software development, from building analytical pipelines to user interfaces. He finds CoGe a particularly exciting project to work on because of its wide use and innovative tools..
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Asher Baltzell
Asher Baltzell is a Ph.D student at the University of Arizona in the Genetics GIDP. He works with Dr. Lyons lab investigating vertebrate genome structure/evolution, lincRNA functional identification and evolution, and working towards developing revolutionary ways of visualizing modern genomic data sets. His current projects include, but are not limited to, (1) working with dopamine receptors in 50 newly-sequenced Avian species as a model for understanding gene identification and evolution in new genomes, (2) integrating functionality for visualizing and analyzing personal genetic data in the comparative genomics platform CoGe, and (3) working at developing a 3D technologies for visualizing and understanding genomic data.
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Sean Davey
Sean Davey earned his Masters in Computer Science from the University of Arizona. He has done software development in proteomics and genomics at the University of Arizona for Daniel Liebler, Serrine Lau, Parker Antin and Eric Lyons. He developed and continues to work on GEISHA (Gallus Expression in Situ Hybridization Analysis) (http://geisha.arizona.edu/geisha/), Bird Base (http://birdbase.arizona.edu), and the Chicken Gene Nomenclature Consortium (http://birdgenenames.org). Recently he’s joined the CoGe team and works to improve backend technologies.
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Heather Lent
Heather Lent earned a double B.A. in linguistics and Russian language from the University of Arizona. She is now a second year graduate student studying Human Language Technology in the Department of Linguistics at the University of Arizona. She specializes in natural language processing (NLP) and computational linguistics, specifically, in the application of NLP to bioinformatics (known as bioNLP) and machine learning, information retrieval, and language modeling with probabilistic context free grammars. She was first introduced to bioNLP at the Bioinformatics Lab in the School of Engineering at Ewha Womans University in Seoul, South Korea, where she utilizes NLP techniques (Hidden Markov Models, N-grams, etc) for more accurate human promoter element recognition and prediction, as well as data mining biomedical literature for text summarization purposes.
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Andy Sposato
Andy Sposato is an undergraduate student at the University of Arizona. She is pursuing a major in Molecular and Cellular Biology and a minor in Gender and Women's Studies while also working in Dr. Lyons' lab as an intern. She is researching gene families of the Brassicas with Dr. Blake Joyce and is approaching this project more from a biological side with the intent of picking up some useful skills from the computer science aspect. Andy also works with a professor of Conservation Biology, editing and contributing to papers from the graduate students in Dr. Laura Lopez-Hoffman's lab to gain valuable experience in scientific writing.
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Stephanie ZawadaStephanie Zawada is an Electrical & Computer Engineering M.S. student working on database development for the Legume Federation and CoGe website design. She is also a co-investigator in the lab of Marvin J. Slepian, M.D., examining the clinical integration of biomedical research data. A biochemistry major, she graduated from the University of Arizona as the 2015 Robie Gold Medal Senior and Brown Foundation Distinguished Scholar in Entrepreneurship for her undergraduate work at the intersection of patient engagement, IT, and life science policy.
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Andreina Siri, Ph.DAndreina Castillo Siri earned her Ph.D. on Evolutionary Biology at Arizona State University. She then became a Postdoc on Dr. Eric Lyons laboratory and a member of the CoGe development team. She specializes on the study of evolutionary patterns inside the genus Plasmodium, a parasitic group capable of infecting a wide variety of vertebrate hosts and the causal agent of malaria in humans. As part of her graduate research, she studied the effects of natural selection, recombination and gene gain/loss events in Plasmodium spp. Currently, she is evaluating the numerous unique features of Plasmodium genome evolution using the CoGe platform, working on documenting her analyses using CoGe as a guideline for future researchers, and developing new research ideas to be implemented to the CoGe platform.
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Grace LoganGrace is a senior at University High School who is conducting a research project with the help of Dr. Lyons’ lab. She previously completed a research project on genetically engineered Bt corn through the Bio 5 KEYS Internship Program. She plans to pursue a major in a biological science field in her post-secondary education career. Outside of school she works at a local winery where she explores how various fields of science combine in the art of wine making.
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Past Members
Blake Joyce, Ph.D
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Haibao Tang, Ph.D
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AJ Stangl
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Evan Briones
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Alex Frank
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