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Agricultural Research ServiceORCID 0000-0002-0678-8754Unclaimed ORCID profile · follow to get notified of new preprints
9 papers
Recent·Most cited
John L. Portwood, Ethalinda K. S. Cannon, Olivia C. Haley, Laura E. Tibbs‐Cortes, Carson M. Andorf, Margaret Roth Woodhouse
The paper introduces a new pangenome viewer for maize that integrates graph and linear genome visualization to enhance structural variation analysis and locus characterization.
bioRxiv · Sep 4, 2026 · PreprintGenomics
Laura E. Tibbs‐Cortes, Olivia C. Haley, John L. Portwood, Ethalinda K. S. Cannon, Margaret Roth Woodhouse, Carson M. Andorf
The paper introduces a web tool and R package for analyzing the evolutionary origins of maize proteins, providing interactive visualizations and gene data for 26 maize inbreds.
Bioinformatics Advances · Jan 1, 2026Peer-reviewedBioinformatics
Olivia C. Haley, Laura E. Tibbs‐Cortes, Rita K. Hayford, Stephen F. Harding, Margaret Roth Woodhouse, Ethalinda K. S. Cannon, Jack M. Gardiner, John L. Portwood, Taner Z. Sen, Hye-Seon Kim, Carson M. Andorf
The paper benchmarks AlphaFold, ESMFold, and Boltz in maize to assess their performance on plant proteins, finding lower confidence scores and geometry issues in less conserved proteins.
bioRxiv · Jul 5, 2025 · PreprintBioinformatics
Michelle C. Stitzer, Arun Somwarpet Seetharam, Armin Scheben, Sheng‐Kai Hsu, Aimee J Schulz, Taylor AuBuchon‐Elder, Mohamed El-Walid, Taylor H. Ferebee, Charles O. Hale, Thuy La, Zong-Yan Liu, Sarah J. McMorrow, Patrick J. Minx, Alyssa R. Phillips, Michael Syring, , Matthew B. Hufford
The paper examines genome evolution in maize and related grasses, revealing variable outcomes of polyploidy across species.
bioRxiv · Jan 22, 2025 · PreprintEvolutionary Biology
Carson M. Andorf, Olivia C. Haley, Rita K. Hayford, John L. Portwood, Stephen Harding, Shatabdi Sen, Ethalinda K. S. Cannon, Jack M. Gardiner, Hye-Seon Kim, Margaret Roth Woodhouse
PanEffect visualizes variant effects across 51 maize genomes using ESM scores, enabling exploration of 550 million amino acid substitutions and 2.3 million natural variations.
Bioinformatics · Feb 1, 2024Peer-reviewedBioinformatics
Carson M. Andorf, Shatabdi Sen, Rita K. Hayford, John L. Portwood, Ethalinda K. S. Cannon, Lisa C. Harper, Jack M. Gardiner, Taner Z. Sen, Margaret Roth Woodhouse
FASSO combines sequence and structure orthology to improve ortholog prediction across species, annotating over 270,000 functions in plant and outgroup proteomes.
bioRxiv · Nov 10, 2022 · PreprintBioinformatics
Paul Otyama, Kelly D. Chenault Chamberlin, Peggy Ozias‐Akins, Michelle A. Graham, Ethalinda K. S. Cannon, Steven B. Cannon, Gregory E. MacDonald, Noelle Lynette Anglin
This study identifies SNPs and their interactions associated with fatty acid composition in peanut, revealing pleiotropy and epistasis in genetic control.
G3 Genes Genomes Genetics · Nov 9, 2021Peer-reviewedGenomics
Matthew B. Hufford, Arun Somwarpet Seetharam, Margaret Roth Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew J. Olson, Yinjie Qiu, Rafael Della Coletta, Silas B. Tittes, Asher I. Hudson, Alexandre P. Marand, Sharon Wei, , R. Kelly Dawe
A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.
Science · Aug 5, 2021Peer-reviewedGenomics
Paul Otyama, Roshan Kulkarni, Kelly D. Chenault Chamberlin, Peggy Ozias‐Akins, Ye Chu, Lori M. Lincoln, Gregory E. MacDonald, Noelle Lynette Anglin, Sudhansu Dash, David J. Bertioli, David Fernández‐Baca, Michelle A. Graham, Steven B. Cannon, Ethalinda K. S. Cannon
The paper genotypes a peanut core collection, identifies genetic clusters, and links them to botanical varieties and biogeography.
G3 Genes Genomes Genetics · Sep 4, 2020Peer-reviewedGenomics