Research Project: MaizeGDB - Database and Computational Resources for Maize Genetics, Genomics, and Breeding Research

Location: Corn Insects and Crop Genetics Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

MaizeGDB phylostrata tool: exploring evolutionary origins of maize proteins - (Peer Reviewed Journal)

Using the MaizeGDB genome browser to evaluate gene model annotation quality and gain functional insights - (Abstract Only)
Portwood II, J.L., Tibbs-Cortes, L., Haley, O., Cannon, E.K., Gardiner, J., Woodhouse, M.H., Andorf, C.M. 2026. Using the MaizeGDB genome browser to evaluate gene model annotation quality and gain functional insights. Maize Genetics Conference Abstracts.

AI-ready genomics and multi-omic functional annotation at MaizeGDB - (Abstract Only)
Haley, O., Tibbs-Cortes, L., Harding, S., Cannon, E.K., Portwood II, J.L., Gardiner, J.M., Woodhouse, M.H., Andorf, C.M. 2026. AI-ready genomics and multi-omic functional annotation at MaizeGDB. Maize Genetics Conference Abstracts.

How large-scale genotyping benefits the maize community - (Abstract Only)
Grover, C., Hufford, M.B., Ross-Ibarra, J., Woodhouse, M.H., Andorf, C.M. 2026. How large-scale genotyping benefits the maize community. Maize Genetics Conference Abstracts.

MaizeGDB phylostrata tool: exploring evolutionary origins of maize proteins - (Pre-print Publication)
Tibbs-Cortes, L., Haley, O.C., Portwood III, J.L., Cannon, E.K., Woodhouse, M.H., Andorf, C.M. 2025. MaizeGDB phylostrata tool: exploring evolutionary origins of maize proteins. bioRxiv. https://doi.org/10.64898/2025.12.19.695500.

Fishing for a reelGene: evaluating gene models with evolution and machine learning - (Peer Reviewed Journal)
Schulz, A.J., Zhai, J., AuBuchon-Elder, T., Andorf, C.M., El-Walid, M.Z., Ferebee, T.H., Gilmore, E.H., Hufford, M.B., Johnson, L.C., Kellogg, E.A., La, T., Long, E., McMorrow, S.J., Miller, Z.R., Portwood II, J.L., Romay, M., Seetharam, A.S., Stitzer, M.C., Woodhouse, M.H., Wrightsman, T., Buckler IV, E.S., Monier, B., Hsu, S. 2025. Fishing for a reelGene: evaluating gene models with evolution and machine learning. The Plant Journal. https://doi.org/10.1111/tpj.70483.

Why do some predicted protein structures fold poorly? Benchmarking AlphaFold, ESMFold, and Boltz in maize - (Pre-print Publication)
Haley, O., Tibbs-Cortes, L., Hayford, R.K., Harding, S., Woodhouse, M.H., Cannon, E.K., Gardiner, J.M., Portwood II, J.L., Sen, T.Z., Kim, H., Andorf, C.M. 2025. Why do some predicted protein structures fold poorly? Benchmarking AlphaFold, ESMFold, and Boltz in maize. bioRxiv. Article 2025.07.05.663230. https://doi.org/10.1101/2025.07.05.663230.

Extensive genome evolution distinguishes maize within a stable tribe of grasses - (Pre-print Publication)
Stitzer, M., Seetharam, A., Scheben, A., Hsu, S., Schultz, A., Aubuchon-Elder, T., Hale, C., Syring, M., Minx, P., Pasquet, R., Mcallister, C., Malcomber, S., Traiperm, P., Layton, D., Zhong, J., Costich, D., Fengler, K., Harris, C., Irelan, Z., Llaca, V., Parakka, P., Zastrow-Hayes, G., Dawe, R., Woodhouse, M.H., Cannon, E.K., Portwood II, J.L., Andorf, C.M., El-Walid, M., Mcmorrow, S., Ferebee, T., Wrightsman, T., Liu, Z., Phillips, A., Zhai, J., Albert, P., Birchler, J., Siepel, A., Ross-Ibarra, J., Romay, M., Kellogg, E., Buckler IV, E.S., Hufford, M. 2025. Extensive genome evolution distinguishes maize within a stable tribe of grasses. bioRxiv. Article 2025.01.22.633974. https://doi.org/10.1101/2025.01.22.633974.

Maize and wild relatives show distinct patterns of genome downsizing following polyploidy - (Pre-print Publication)
Snodgrass, S.J., Woodhouse, M.R., Stitzer, M., Hufford, M.B. 2025. Maize and wild relatives show distinct patterns of genome downsizing following polyploidy. bioRxiv. https://doi.org/10.1101/2024.12.24.630189.

Guidelines for gene and genome assembly nomenclature - (Peer Reviewed Journal)
Cannon, E.K., Molik, D.C., Wright, A., Zhang, H., Honaas, L.A., Chougule, K., Dyer, S. 2025. Guidelines for gene and genome assembly nomenclature. Genetics. https://doi.org/10.1093/genetics/iyaf006.

A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize - (Peer Reviewed Journal)
Andorf, C.M., Ross-Ibarra, J., Seetharam, A., Hufford, M., Woodhouse, M.H. 2024. A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize. G3: Genes, Genomes, Genetics. https://doi.org/10.1093/g3journal/jkae281.

Tools and resources at the maize genetics and genomics database (MaizeGDB) - (Book / Chapter)
Woodhouse, M.H., Portwood II, J.L., Sen, S., Hayford, R.K., Gardiner, J.M., Cannon, E.K., Haley, O., Andorf, C.M. 2024. Tools and resources at the maize genetics and genomics database (MaizeGDB). Cold Spring Harbor Protocols. https://doi.org/10.1101/pdb.over108430.

Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress - (Peer Reviewed Journal)
Hayford, R.K., Haley, O., Cannon, E.K., Portwood II, J.L., Gardiner, J.M., Andorf, C.M., Woodhouse, M.H. 2024. Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress. BMC Genomics. https://doi.org/10.1186/s12864-024-10443-7.

A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize - (Pre-print Publication)
Andorf, C.M., Ross-Ibarra, J., Seetharam, A., Hufford, M., Woodhouse, M.H. 2024. A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize. bioRxiv. https://doi.org/10.1101/2024.04.30.591904.

PanEffect: a pan-genome visualization tool for variant effects in maize - (Peer Reviewed Journal)
Andorf, C.M., Haley, O., Hayford, R.K., Portwood II, J.L., Harding, S.F., Sen, S., Cannon, E.K., Gardiner, J.M., Kim, H., Woodhouse, M.R. 2024. PanEffect: a pan-genome visualization tool for variant effects in maize. Bioinformatics. 40(2). Article btae073. https://doi.org/10.1093/bioinformatics/btae073.

Enhanced pan-genomic resources at the maize genetics and genomics database - (Peer Reviewed Journal)
Cannon, E.K., Portwood II, J.L., Hayford, R.K., Hayley, O.C., Gardiner, J.M., Andorf, C.M., Woodhouse, M.R. 2024. Enhanced pan-genomic resources at the maize genetics and genomics database. Genetics. 227(1). https://doi.org/10.1093/genetics/iyae036.

PanEffect: A pan-genome visualization tool for variant effects in maize - (Pre-print Publication)
Andorf, C.M., Haley, O., Hayford, R., Portwood Ii, J.L., Sen, S., Cannon, E.K., Gardiner, J.M., Woodhouse, M.H. 2023. PanEffect: A pan-genome visualization tool for variant effects in maize. bioRxiv. Article 09.25.559155. https://doi.org/10.1101/2023.09.25.559155.