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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Research Project #434521
Research Project: MaizeGDB: Enabling Access to Basic, Translational, and Applied Research Information

Location: Corn Insects and Crop Genetics Research

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

Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications Reprint Icon - (Peer Reviewed Journal)
Sen, S., Woodhouse, M.H., Portwood II, J.L., Andorf, C.M. 2023. Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications. Database: The Journal of Biological Databases and Curation . 2023. Article baad078. https://doi.org/10.1093/database/baad078.

Pan-genome data at MaizeGDB - (Abstract Only)
Cannon, E.K., Portwood II, J.L., Hayford, R., Gardiner, J., Woodhouse, M.H., Andorf, C.M. 2023. Pan-genome data at MaizeGDB. Maize Annual Meetings. 66.

Maize Feature Store (MFS): A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications - (Abstract Only)
Sen, S., Woodhouse, M.H., Portwood II, J.L., Andorf, C.M. 2023. Maize Feature Store (MFS): A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications. Maize Annual Meetings. 69.

MaizeGDB: Maize protein structure resources - (Abstract Only)
Andorf, C.M., Portwood II, J.L., Sen, S., Hayford, R., Cannon, E.K., Gardiner, J., Woodhouse, M.H. 2023. MaizeGDB: Maize protein structure resources. Maize Annual Meetings. 65.

Stress response functional annotation using RNA expression in maize - (Abstract Only)
Hayford, R., Woodhouse, M.H., Portwood II, J.L., Sen, S., Gardiner, J., Cannon, E.K., Andorf, C.M. 2023. Stress response functional annotation using RNA expression in maize. Maize Annual Meetings. 68.

Maize protein structure resources at the maize genetics and genomics database Reprint Icon - (Peer Reviewed Journal)
Woodhouse, M.H., Portwood II, J.L., Sen, S., Hayford, R.K., Gardiner, J.M., Cannon, E.K., Harper, L.C., Andorf, C.M. 2023. Maize protein structure resources at the maize genetics and genomics database. Genetics. 224(1).Article iyad016. https://doi.org/10.1093/genetics/iyad016.

FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology Reprint Icon - (Peer Reviewed Journal)
Andorf, C.M., Sen, S., Hayford, R.K., Portwood II, J.L., Cannon, E.K., Harper, L.C., Gardiner, J.M., Sen, T.Z., Woodhouse, M.H. 2022. FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology. bioRxiv. https://doi.org/10.1101/2022.11.10.516002.

Association mapping across a multitude of traits collected in diverse environments in maize Reprint Icon - (Peer Reviewed Journal)
Mural, R.V., Sun, G., Grzybowski, M., Tross, M.C., Jin, H., Smith, C., Newton, L., Andorf, C.M., Woodhouse, M.H., Thompson, A.M., Sigmon, B., Schnable, J.C. 2022. Association mapping across a multitude of traits collected in diverse environments in maize. Gigascience. 11.Article giac080. https://doi.org/10.1093/gigascience/giac080.

Association mapping across a multitude of traits collected in diverse environments identifies pleiotropic loci in maize Reprint Icon - (Pre-print Publication)
Mural, R.V., Sun, G., Grzybowski, M., Tross, M.C., Jin, H., Smith, C., Newton, L., Andorf, C.M., Woodhouse, M.H., Thompson, A.M., Sigmon, B., Schnable, J.C. 2022. Association mapping across a multitude of traits collected in diverse environments identifies pleiotropic loci in maize. bioRxiv. https://doi.org/10.1101/2022.02.25.480753.

ABRIDGE: An ultra-compression software for SAM alignment files Reprint Icon - (Pre-print Publication)
Banerjee, S., Andorf, C.M. 2022. ABRIDGE: An ultra-compression software for SAM alignment files. bioRxiv. https://doi.org/10.1101/2022.01.04.474935.

qTeller: A tool for comparative multi-genomic gene expression analysis Reprint Icon - (Peer Reviewed Journal)
Woodhouse, M.H., Sen, S., Schott, D., Portwood II, J.L., Freeling, M., Walley, J.W., Andorf, C.M., Schnable, J.C. 2021. qTeller: A tool for comparative multi-genomic gene expression analysis. Bioinformatics. 38(1): 236-242. https://doi.org/10.1093/bioinformatics/btab604.

A pan-genomic approach to genome databases using maize as a model system Reprint Icon - (Peer Reviewed Journal)
Woodhouse, M.H., Cannon, E.K., Portwood II, J.L., Harper, E.C., Gardiner, J.M., Schaeffer, M.L., Andorf, C.M. 2021. A pan-genomic approach to genome databases using maize as a model system. Biomed Central (BMC) Plant Biology. 21. Article 385. https://doi.org/10.1186/s12870-021-03173-5.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes Reprint Icon - (Peer Reviewed Journal)
Hufford, M.B., Seetharam, A.S., Woodhouse, M.H., Chougle, K.M., Ou, S., Liu, J., Ricci, W.A., Guo, T., Olson, A., Qiu, Y., Portwood II, J.L., Cannon, E.K., Andorf, C.M., Ware, D., Dawe, K.R. et al. 2021. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science. 373(6555):655-662. https://doi.org/10.1126/science.abg5289.

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences Reprint Icon - (Peer Reviewed Journal)
Banerjee, S., Bhandary, P., Woodhouse, M.H., Sen, T.Z., Wise, R.P., Andorf, C.M. 2021. FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. BMC Bioinformatics. 22. Article 205. https://doi.org/10.1186/s12859-021-04120-9.

Maize Genetics Committee on Outreach, Diversity, Inclusion, and Education (CODIE) 2020-2021 Update - (Abstract Only)
Andorf, C.M., Bartlett, M., Bass, H., De Leon, N., Doyle, E., Durham Brooks, T., Fowler, J., Jackson, D., Lubkowitz, M., Makarevitch, I., Morais De Sousa, S., Portwood Ii, J.L., Praud, S., Woodhouse, M.H., Yandeau-Nelson, M., Warburton, M.L. 2021. Maize Genetics Committee on Outreach, Diversity, Inclusion, and Education (CODIE) 2020-2021 Update. Maize Annual Meetings. 83.

The NAM genome assemblies and 2021 release of their official annotations at MaizeGDB - (Abstract Only)
Cannon, E.K., Woodhouse, M.H., Andorf, C.M., Gardiner, J., Harper, E.C., Portwood Ii, J.L., Schaeffer, M.L. 2021. The NAM genome assemblies and 2021 release of their official annotations at MaizeGDB. Maize Annual Meetings. 76.

MaizeMine facilitates meta-analysis of diverse data sets through genomic data integration - (Abstract Only)
Gardiner, J.M., Triant, D.A., Walsh, A., Andorf, C.M., Elsik, C.G. 2021. MaizeMine facilitates meta-analysis of diverse data sets through genomic data integration. In: Maize Annual Meeting, March 8-12, 2021, Virtual Meeting. p.69.

History of the maize genome sequence assemblies - (Abstract Only)
Harper, E.C., Gardiner, J.M., Schaeffer, M.L., Cannon, E.K., Portwood Ii, J.L., Woodhouse, M.H., Andorf, C.M. 2021. History of the maize genome sequence assemblies. Maize Annual Meetings. 59.

Sequence, assembly and annotation of maize inbred B104 - (Abstract Only)
Manchanda, N., Chougule, K., Olson, A., Fengler, K., Seetharam, A., Liaca, V., Zastrow-Hayes, G., Wei, S., Braun, I., Lopez, M.D., Ployaram, W., Zarecor, S., Lu, Z., Walley, J., Yandeau-Nelson, M., Wang, K., Adams, D., Ware, D., Schmitz, B., Woodhouse, M.H., Lauter, N.C., Andorf, C.M., Lawrence-Dill, C., Hufford, M. 2021. Sequence, assembly and annotation of maize inbred B104. Maize Annual Meetings. 76.

Constructing Zea mays genes from RNA-Seq expression data using FINDER - a fully automated gene annotator - (Abstract Only)
Banerjee, S., Bhandary, P., Woodhouse, M.H., Sen, T.Z., Wise, R.P., Andorf, C.M. 2021. Constructing Zea mays genes from RNA-Seq expression data using FINDER - a fully automated gene annotator. Maize Annual Meetings. 41.

FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences Reprint Icon - (Pre-print Publication)
Banerjee, S., Bhandary, P., Woodhouse, M.H., Sen, T.Z., Wise, R.P., Andorf, C.M. 2021. FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. bioRxiv. https://doi.org/10.1101/2021.02.04.429837.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes Reprint Icon - (Pre-print Publication)
Hufford, M.B., Seetharam, A.S., Woodhouse, M.H., Chougie, K.M., Ou, S., Liu, J., Ricci, W.A., Guo, T., Olson, A., Qiu, Y., Portwood Ii, J.L., Cannon, E.K., Andorf, C.M., Ware, D., Dawe, K.R., et all. 2021. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. bioRxiv. https://doi.org/10.1101/2021.01.14.426684.

MaizeMine: A data mining warehouse for the maize genetics and genomics database (MaizeGDB) Reprint Icon - (Peer Reviewed Journal)
Shamimuzzaman, M., Gardiner, J.M., Walsh, A.T., Triant, D.A., Le Tourneau, J.J., Tayal, A., Unni, D.R., Nguyen, H.H., Portwood Ii, J.L., Cannon, E.K., Andorf, C.M., Elsik, C.G. 2020. MaizeMine: A data mining warehouse for the maize genetics and genomics database (MaizeGDB). Frontiers in Plant Science. 11. Article 592730. https://doi.org/10.3389/fpls.2020.592730.

Gapless assembly of maize chromosomes using long-read technologies Reprint Icon - (Peer Reviewed Journal)
Liu, J., Seetharam, A.S., Chougule, K.M., Ou, S., Swentowsky, K.W., Gent, J.I., Llaca, V., Woodhouse, M.H., Manchanda, N., Presting, G.G., Kurdna, D.A., Alabady, M., Hirsch, C.N., Fengler, K.A., Ware, D., Michael, T.P., Hufford, M.B., Dawe, R.K. 2020. Gapless assembly of maize chromosomes using long-read technologies. Genome Biology. 21. https://doi.org/10.1186/s13059-020-02029-9.

Effect of sequence depth and length in long-read assembly of the maize inbred NC358 Reprint Icon - (Peer Reviewed Journal)
Ou, S., Liu, J., Chougule, K., Fungtammasan, A., Seetharam, A., Stein, J., Llaca, V., Manchanda, N., Gilbert, A., Wei, S., Ware, D., Woodhouse, M.H., et all. 2020. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications. 11. https://doi.org/10.1038/s41467-020-16037-7.

GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations Reprint Icon - (Peer Reviewed Journal)
Manchanda, N., Portwood II, J.L., Woodhouse, M.H., Seetharam, A., Lawrence-Dill, C.J., Andorf, C.M., Hufford, M. 2020. GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations. BMC Genomics. 21. https://doi.org/10.1186/s12864-020-6568-2.

Haplotype structure in commercial maize breeding programs in relation to key founder lines Reprint Icon - (Peer Reviewed Journal)
Coffman, S.M., Hufford, M.B., Andorf, C.M., Lubberstedt, T. 2019. Haplotype structure in commercial maize breeding programs in relation to key founder lines. Theoretical and Applied Genetics. 133:547-561. https://doi.org/10.1007/s00122-019-03486-y.

MaizeDIG: Maize Database of Images and Genomes Reprint Icon - (Peer Reviewed Journal)
Cho, K., Portwood II, J.L., Gardiner, J., Harper, E.C., Lawrence-Dill, C., Friedberg, I., Andorf, C.M. 2019. MaizeDIG: Maize Database of Images and Genomes. Frontiers in Plant Science. 10:1050. https://doi.org/10.3389/fpls.2019.01050.

Technological advances in maize breeding: Past, present and future Reprint Icon - (Peer Reviewed Journal)
Andorf, C.M., Beavis, W.D., Hufford, M., Lubberstedt, T., Smith, S., Suza, W., Wang, K., Woodhouse, M., Yu, J. 2019. Technological advances in maize breeding: Past, present and future. Journal of Theoretical and Applied Genetics. 132(32):817-849. https://doi.org/10.1007/s00122-019-03306-3.

MaizeGDB 2018: The maize multi-genome genetics and genomics database Reprint Icon - (Peer Reviewed Journal)
Portwood II, J.L., Woodhouse, M.R., Cannon, E.K., Gardiner, J., Harper, E.C., Schaeffer, M.L., Walsh, J., Sen, T.Z., Cho, K., Braun, B.L., Dietze, M., Dunfee, B., Elsik, C.G., Manchanda, N., Coe, E., Sachs, M.M., Stinard, P.S., Tolbert, J.P., Zimmerman, S.A., Andorf, C.M. 2018. MaizeGDB 2018: The maize multi-genome genetics and genomics database. Nucleic Acids Research. 47(D1):D1146-D1154. https://doi.org/10.1093/nar/gky1046.

MaizeGDB: How phenotype curation has co-evolved with genomic representations - (Abstract Only)
Harper, E.C., Gardiner, J., Portwood Ii, J.L., Cho, K., Woodhouse, M.R., Cannon, E.K., Lawrence-Dill, C., Freidberg, I., Andorf, C.M. 2018. MaizeGDB: How phenotype curation has co-evolved with genomic representations. Meeting Abstract. https://www.ars.usda.gov/research/publications/publication/?seqNo115=355949.

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning Reprint Icon - (Peer Reviewed Journal)
Zhou, N., Siegel, Z.D., Zarecor, S., Lee, N., Campbell, D.A., Andorf, C.M., Nettleton, D., Lawrence-Dill, C.J., Ganapathysubramanian, B., Kelly, J.W., Friedberg, I. 2018. Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning. PLoS Computational Biology. 14(7):e1006337. https://doi.org/10.1371/journal.pcbi.1006337.

Maize GO annotation—methods, evaluation, and review (maize-GAMER) Reprint Icon - (Peer Reviewed Journal)
Wimalanathan, K., Friedberg, I., Andorf, C.M., Lawrence-Dill, C. 2018. Maize GO annotation—methods, evaluation, and review (maize-GAMER). Plant Direct. 2(4):e00052. https://doi.org/10.1002/pld3.52.