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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » People & Locations » Margaret Woodhouse
Margaret Woodhouse
Corn Insects and Crop Genetics Research
Computational Biologist

Phone: (515) 294-3122
Fax:

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Projects
MaizeGDB - Database and Computational Resources for Maize Genetics, Genomics, and Breeding Research
In-House Appropriated (D)
  Accession Number: 444388
Sequencing, Mapping, and Analysis of Maize Genomes and Variant Data Important to Maize Breeding Programs
Non-Assistance Cooperative Agreement (S)
  Accession Number: 442724

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Application of RF diffusion to predict interspecies protein-protein interactions between fungal pathogens and cereal crops Reprint Icon - (Pre-print Publication)
Haley, O.C., Harding, S., Sen, T.Z., Woodhouse, M.R., Kim, H.-S., Andorf, C. 2024. Application of RFdiffusion to predict interspecies protein-protein interactions between fungal pathogens and cereal crops. bioRxiv. https://doi.org/10.1101/2024.09.17.613523.
Fusarium Protein Toolkit: A web-based resource for structural and variant analysis of Fusarium species Reprint Icon - (Peer Reviewed Journal)
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.
Genomes, comparative genomics and pan-genomics tools and resources at the maize genetics and genomics database (MaizeGDB) Reprint Icon - (Book / Chapter)
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.
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.
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.
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.
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 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.