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 Corn Insects and Crop Genetics Research: Ames, IA
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ARS Home Midwest Area Ames, Iowa Corn Insects and Crop Genetics Research People & Locations







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.)
                            ProjectsMaizeGDB - Database and Computational Resources for Maize Genetics, Genomics, and Breeding Research
                                                    In-House Appropriated
                                                                    (D)Accession Number: 444388Sequencing, 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.)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.H. 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.Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications
                                                        

- (Peer Reviewed Journal)Sen, S., Woodhouse, M.R., 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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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.


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