Margaret Woodhouse
Corn Insects and Crop Genetics Research
Computational Biologist
Phone: (515) 294-3122
Fax:
(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
Publications
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Fusarium Protein Toolkit: A web-based resource for structural and variant analysis of Fusarium species
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Kim, H., Haley, O., Portwood Ii, J.L., Harding, S.F., Proctor, R., Woodhouse, M.H., Sen, T.Z., Andorf, C.M. 2024. Fusarium Protein Toolkit: A web-based resource for structural and variant analysis of Fusarium species. BMC Microbiology. https://doi.org/10.1186/s12866-024-03480-5.
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Genomes, comparative genomics and pan-genomics tools and resources at the maize genetics and genomics database (MaizeGDB)
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Woodhouse, M.R., Portwood Ii, J.L., Sen, S., Hayford, R.K., Gardiner, J.M., Cannon, E.K., Haley, O., Andorf, C.M. 2024. Genomes, comparative genomics and pan-genomics tools and resources at the maize genetics and genomics database (MaizeGDB). Cold Spring Harbor Protocols. https://doi.org/10.1101/pdb.over108430.
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Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress
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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.
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A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize
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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.
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PanEffect: a pan-genome visualization tool for variant effects in maize
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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.
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Enhanced pan-genomic resources at the maize genetics and genomics database
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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.
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Maize feature store: a centralized resource to manage and analyze curated maize multi-omics features for machine learning applications
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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.
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PanEffect: A pan-genome visualization tool for variant effects in maize
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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.
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Stress response functional annotation using RNA expression in maize
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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.
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Maize Feature Store (MFS): A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications
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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.
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Pan-genome data at MaizeGDB
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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.
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MaizeGDB: Maize protein structure resources
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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.
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Maize protein structure resources at the maize genetics and genomics database
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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.
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FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology
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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.
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Association mapping across a multitude of traits collected in diverse environments in maize
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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.
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Association mapping across a multitude of traits collected in diverse environments identifies pleiotropic loci in maize
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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.
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qTeller: A tool for comparative multi-genomic gene expression analysis
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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.
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A pan-genomic approach to genome databases using maize as a model system
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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.
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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
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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.
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FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences
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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.
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The NAM genome assemblies and 2021 release of their official annotations at MaizeGDB
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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.
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Constructing Zea mays genes from RNA-Seq expression data using FINDER - a fully automated gene annotator
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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.
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History of the maize genome sequence assemblies
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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.
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Maize Genetics Committee on Outreach, Diversity, Inclusion, and Education (CODIE) 2020-2021 Update
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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.
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Sequence, assembly and annotation of maize inbred B104
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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.
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FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences
- (Pre-print Publication)
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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.
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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
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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.
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Gapless assembly of maize chromosomes using long-read technologies
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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.
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Effect of sequence depth and length in long-read assembly of the maize inbred NC358
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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.
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GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations
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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.
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