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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.orgShow Less
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Courses
- ACCApplied Cyberinfrastructure Concepts
- IBIIntroductory Biology I
Grants
- HIGH INTENSITY PHENOTYPING SITES: A Multi-Scale, Multi-Modal Sensing and Sense-Making Cyber-Ecosystem for Genomes to Fields
Principal Investigator (PI)
2020
$497.5K
Active - TRTech-PGR: Identification and Characterization of Stress-Responsive and Evolutionary Conserved Epitranscriptome Modification Sites in Plant Transcriptomes
Principal Investigator (PI)
2020
$430.6K
Active - NIFA AG2PI Collaborative: Creating a Shared Vision across Crop and Livestock Communities
Principal Investigator (PI)
2020
$20.1K
Active - Augmented Reality GUI for Bioenergy Crop Phenotyping and Precision Agriculture
Co-Investigator (COI)
2019
$2.1M
Active - RESEARCH-PGR: Elucidating the Role of the Epitranscriptome on Adaptation to Abiotic Stresses in Cereals
Principal Investigator (PI)
2019
$358.1K
Active - IPA (Intergovernmental Personnel Act Assignment) for Eric Lyons
Principal Investigator (PI)
2018
$250.5K
- Multifactorial Methods and Bioinformatics Tools Of Big Data Analysis For Genomic Discovery And Application in Livestock Species
Principal Investigator (PI)
2018
$16.2K
- Structural, Functional, and Evolutionary Analysis of Long Non-coding RNAs in Control of Stress Response and the Epigenome in Diverse Plant Species (REU)
Co-Investigator (COI)
2016
$18.0K
- Polyploidy and plasticity in the crop Brassicas
Principal Investigator (PI)
2014
$812.5K
- iAnimal: cyberinfrastructure enabling animal breeding genetics and genomics
Principal Investigator (PI)
2013
$499.2K
Technologies / Patents
News
- Despite COVID, UArizona Reports Strong Year for Innovation and Commercialization
2021
- 'Howl-itosis' a Problem? UArizona Inventor Creates Bacteria Strain to Quell Bad Dog Breath
2021
- I-Squared Awards Honor Researchers and Technology Champions
2019
- Citizen Science Program Has a Research Payoff
2018
- CyVerse Receives Third NSF Award for Enabling Data Science
2018
- Students Use CyVerse to Help Predict Mosquito-Borne Diseases
2017
- NSF's iPlant Collaborative Rebrands to CyVerse
2016
- Looking for the Missing Link in RNA Molecules
2015
- iPlant Taming the 'Big Data Beast'
2015
- Parker Antin: Leading Life Science Initiatives
2015
- How Happiness Came Into Beings
2015
- New Genome Research Illuminates Bird, Crocodile Evolution
2014
- UA Science Could Make Canola Oil More Nutritious, and Broccoli More Tasty
2014
- Carnivorous Plant Throws Out ‘Junk’ DNA
2013
- UA Scientists Help Decipher Origin of Flowers
2013
- UA-Led Research Collaborative Awarded $50M to Advance Cyberinfrastructure for the Life Sciences
2013
- Mystery Peeled Off Banana Genome
2012
- Super Computing Meets the World of Biology
2012
Publications (141)
Recent
- NowCasting-Nets: Representation Learning to Mitigate Latency Gap of Satellite Precipitation Products Using Convolutional and Recurrent Neural Networks
2022
- Darwinian genomics and diversity in the tree of life
2022
- A chickpea genetic variation map based on the sequencing of 3,366 genomes (vol 599, pg 622, 2021)
2022
- Community Perspectives: Genome to Phenome in Agricultural Sciences
2022
- A comparative genomics examination of desiccation tolerance and sensitivity in two sister grass species
2022
- Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae
2022
- MegaStitch: Robust Large Scale Image Stitching
2022
- Ten simple rules to ruin a collaborative environment
2022
- Improvements on Multiway ICP Registration for Reconstructing Individual Plants from 3D Field Scans
2021
- Messenger RNA 5′ NAD+ capping is a dynamic regulatory epitranscriptome mark that is required for proper response to abscisic acid in Arabidopsis
2021
- A chickpea genetic variation map based on the sequencing of 3,366 genomes
2021
- Identification and Functional Annotation of Long Intergenic Non-coding RNAs in the Brassicaceae
2021
- Ten simple rules to cultivate transdisciplinary collaboration in data science
2021
- StarBLAST: a scalable BLAST+ solution for the classroom
2021
- Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis
2021
- A conserved long intergenic non-coding RNA containing snoRNA sequences, lncCOBRA1, affects Arabidopsis germination and development
2021
- Convergent evolution of polyploid genomes from across the eukaryotic tree of life
2021
- The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
2021
- Ten simple rules for organizing a data science workshop
2020
- CyVerse 2020
2020
- Plant science decadal vision 2020--2030: Reimagining the potential of plants for a healthy and sustainable future
2020
- Elucidating the Function of a Novel Long Non-Coding RNA during Arabidopsis development
2020
- Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data
2020
- Origin and evolution of the octoploid strawberry genome
2019
- Comparative Genomic and Transcriptomic Analyses of Functionally Characterized Arabidopsis lncRNAs Reveals Conservation in Unexpected Places
2019
- Tail wags the dog? Functional gene classes driving genome-wide GC content in Plasmodium spp.
2019
- Hybrid Conflict, Biased Gene Losses and Developmental Innovation: The Continuing Impact of Ancient Polyploidies on Genome Structure and Function
2019
- Author Correction: Origin and evolution of the octoploid strawberry genome (Nature Genetics,(2019), 51, 3,(541-547), 10.1038/s41588-019-0356-4)
2019
- Data from: Origin and evolution of the octoploid strawberry genome
2019
- Chickspress: a resource for chicken gene expression
2019
- From Alpha-Duplication to Triplication and Sextuplication
2018
- Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization
2018
- N6-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis
2018
- A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B)
2018
- EPIC-CoGe: managing and analyzing genomic data
2018
- Patterns of population variation in two paleopolyploid eudicot lineages suggest that dosage-based selection on homeologs is long-lived
2018
- A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model
2018
- Models for similarity distributions of syntenic homologs and applications to phylogenomics
2018
- CoGe: Scaling to 33,000 genomes (and beyond)
2018
- Erratum: Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
2018
- Science Citation Knowledge Extractor
2018
- CoGe LoadExp+: A web-based suite that integrates next-gen sequencing data analysis workflows and visualization
2017
- An ALMA and MagAO study of the substellar companion GQ Lup B
2017
- Leveraging CyVerse resources for de novo comparative transcriptomics of underserved (non-model) organisms
2017
- Comparative Genomics Using CoGe, Hook, Line, and Sinker
2017
- iAnimal: Cyberinfrastructure to Support Data-driven Science
2017
- Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments
2017
- Wild tobacco genomes reveal the evolution of nicotine biosynthesis
2017
- Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
2017
- Evolinc: A tool for the identification and evolutionary comparison of long intergenic non-coding RNAs
2017
- FractBias: a graphical tool for assessing fractionation bias following polyploidy
2017
- A global view of RNA-protein interactions identifies post-transcriptional regulators of root hair cell fate
2017
- SynMap2 and SynMap3D: web-based whole-genome synteny browsers
2017
- Bringing your tools to CyVerse Discovery Environment using Docker [version 3; referees: 3 approved]
2016
- Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida
2016
- Bringing your tools to CyVerse discovery environment using Docker
2016
- Comparative genomics of gene families in relation with metabolic pathway for gene candidates highlighting
2016
- A New Approach to Space Domain Awareness at the University of Arizona
2016
- Scaling GIS analysis tasks from the desktop to the cloud utilizing contemporary distributed computing and data management approaches: A case study of project-based learning and cyberinfrastructure concepts
2016
- A genomic analysis of factors driving lincRNA diversification: lessons from plants
2016
- The genome of black raspberry (Rubus occidentalis)
2016
- The Trees in the Peaks
2016
- fRNAkenseq: a Powered-by-iPlant RNA Sequencing Analysis Platform
2016
- High-contrast imaging in the cloud with klipReduce and Findr
2016
- P1039 Bioinformatics resources for animal genomics using CyVerse cyberinfrastructure
2016
- The iPlant collaborative: cyberinfrastructure for enabling data to discovery for the life sciences
2016
- Bringing your tools to CyVerse Discovery Environment using Docker [version 1; referees: awaiting peer review]
2016
- The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences.
2016
- Introduction to CoGe
2016
- ALLMAPS: robust scaffold ordering based on multiple maps
2015
- Designing and Evaluating Scientific Workflows for Big Data Interactions
2015
- Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates
2015
- Plant paleopolyploidy
2015
- Genome Biology and Evolution Advance Access published November 11, 2015 doi: 10.1093/gbe/evv219
2015
- A Genomic and Transcriptomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants
2015
- SynFind: compiling syntenic regions across any set of genomes on demand
2015
- Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum
2015
- The pineapple genome and the evolution of CAM photosynthesis
2015
- Scaling Critical Zone analysis tasks from desktop to the cloud utilizing contemporary distributed computing and data management approaches: A case study for project based learning of Cyberinfrastructure concepts
2015
- Optical mapping in plant comparative genomics
2015
- Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)
2014
- Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
2014
- Syntenic Sequence Conservation Between and Within Papaya Genes
2014
- Comparative Genomics of Grass Genomes using CoGe
2014
- Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC
2014
- Comparative genomics reveals insights into avian genome evolution and adaptation
2014
- Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
2014
- EPIC-CoGe: Functional and diversity comparative genomics
2014
- EPIC CoGe: demonstration
2014
- Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
2014
- Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants
2014
- DNA methylation profiles at the human Th2 locus in BAC transgenic mice point to novel putative regulatory elements (IRM6P. 720)
2014
- Syntenic Analysis of Banana's Paleopolyploidy Events
2014
- Architecture and evolution of a minute plant genome
2013
- The Amborella genome and the evolution of flowering plants
2013
- Early History of the Angiosperms
2013
- Matthew Vaughn
2013
- Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
2013
- Ancient eudicot hexaploidy meets ancestral eurosid gene order
2013
- Nelumbo nucifera [data set]
2013
- The dynamics of functional classes of plant genes in rediploidized ancient polyploids
2013
- From data to function: Functional modeling of poultry genomics data
2013
- Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family
2013
- Ancient angiosperm hexaploidy meets ancestral eudicot gene order
2012
- The banana (Musa acuminata) genome and the evolution of monocotyledonous plants
2012
- Maintaining Turfgrass Coverage Under High Traffic Conditions
2012
- The evolution of genome structure
2012
- Loss of syd-1 from R7 neurons disrupts two distinct phases of presynaptic development
2012
- Taking the next step: building an Arabidopsis information portal
2012
- Genome-wide analysis of syntenic gene deletion in the grasses
2012
- Long identical multispecies elements in plant and animal genomes
2012
- Unleashing the genome of Brassica rapa
2012
- Ancient angiosperm hexaploidy meets gene order reconstruction of the eudicot ancestor
2012
- Using genomic sequencing for classical genetics in E. coli K12
2011
- Screening synteny blocks in pairwise genome comparisons through integer programming
2011
- Is Overseeding With Supina Bluegrass a Viable Option?
2011
- The iPlant collaborative
2011
- The iPlant Collaborative: Cyberinfrastructure for Plant Biology
2011
- The compact Salaginella genome identifies changes in gene content associated with the evolution of vascular plants
2011
- OMG! Orthologs in multiple genomes--competing graph-theoretical formulations
2011
- Comparative genomics with maize and other grasses: from genes to genomes!
2011
- MaizeGDB—Past, Present, and Future.
2011
- The Selaginella genome identifies genetic changes associated with the evolution of vascular plants
2011
- The evolution of a high copy gene array in Arabidopsis
2010
- Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs
2010
- Maize GEvo: A Comparative DNA Sequence Alignment Visualization and Research Tool
2009
- The Sorghum bicolor genome and the diversification of grasses.
2009
- Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
2008
- CoGe, a new kind of comparative genomics platform: Insights into the evolution of plant genomes
2008
- The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
2008
- Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids
2008
- The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids
2008
- How to usefully compare homologous plant genes and chromosomes as DNA sequences
2008
- Many or most genes in
2008
- G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis
2007
- Arabidopsis intragenomic conserved noncoding sequence
2007
- Differential inhibition of inducible T cell cytokine secretion by potent iron chelators
2005
- Culture-independent molecular analysis of microbial constituents of the healthy human outer ear
2003
- PATHOGENESIS AND IMMUNITY-Multiple Nucleocapsid Packaging of Autographa californica Nucleopolyhedrovirus Accelerates the Onset of Systemic Infection in Trichoplusia ni
1999
- Multiple nucleocapsid packaging of Autographa californica nucleopolyhedrovirus accelerates the onset of systemic infection in Trichoplusia ni
1999