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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Research Project #444388
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 Reprint Icon will take you to the publication reprint.)

Why do some predicted protein structures fold poorly? Benchmarking AlphaFold, ESMFold, and Boltz in maize Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.

Tools and resources at the maize genetics and genomics database (MaizeGDB) Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.