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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







John L Portwood
                        Corn Insects and Crop Genetics Research

                        




                        
                        IT Specialist
                        Phone: (515) 294-6794
                        
                        
                        Fax: (515) 294-8359(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            **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.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.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.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.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.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.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.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.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.MaizeMine: A data mining warehouse for the maize genetics and genomics database (MaizeGDB)
                                                        

- (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.BonnMu: a novel sequence-indexed resource of transposon induced maize mutations for functional genomics studies
                                                        

- (Peer Reviewed Journal)Marcon, C.; Altrogge, L.; Win Y.N.; Stöcker, T.; Gardiner, J.M.; Portwood, J.L. 2nd; Opitz, N.; Kortz, A.; Baldauf, J.A.; Hunter, C.T.; McCarty, D.R.; Koch, K.E.*; Schoof, H.; Hochholdinger, F. 2020 BonnMu: A sequence-indexed resource of transposon-Induced maize mutations for functional genomics studies. Plant Physiology 184(2):620-631. https://doi.org/10.1104/pp.20.00478GenomeQC: 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.MaizeDIG: Maize Database of Images and Genomes
                                                        

- (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.PedigreeNet: A web-based pedigree viewer for biological databases
                                                        

- (Peer Reviewed Journal)Braun, B.L., Schott, D.A., Portwood Ii, J.L., Andorf, C.M., Sen, T.Z. 2019. PedigreeNet: A web-based pedigree viewer for biological databases. Bioinformatics. 1-3. https://doi.org/10.1093/bioinformatics/btz208.MaizeGDB 2018: The maize multi-genome genetics and genomics database
                                                        

- (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.The maize W22 genome provides a foundation for functional genomics and transposon biology
                                                        

- (Peer Reviewed Journal)Springer, N., Anderson, S., Andorf, C.M., Ahern, K., Bai, F., Barad, O., Barbazuk, W., Bass, H.W., Baruch, K., Gen-Zvi, G., Buckler IV, E.S., Bukowski, R., Campbell, M.S., Cannon, E.K., Chomet, P., Dawe, R., Davenport, R., Dooner, H.K., He Du, L., Du, C., Easterling, K., Gault, C., Guan, J., Jander, G., Hunter III, C.T., Jiao, Y., Koch, K.E., Kol, G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D.R., Noshay, J., Portwood II, J.L., Ronen, G., Settles, M.A., Shem-Tov, D., Shi, J., Soifer, I., Stein, J.C., Suzuki, M., Vera, D.L., Vollbrecht, E., Vrebalov, J.T., Ware, D., Wei, X., Wimalanathan, K., Woodhouse, M.R., Xiong, W., Brutnell, T.P. 2018. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics. 50:1282-1288. https://doi.org/10.1038/s41588-018-0158-0.SNPversity: A web-based tool for visualizing diversity
                                                        

- (Peer Reviewed Journal)Schott, D.A., Vinnakota, A.G., Portwood II, J.L., Andorf, C.M., Sen, T.Z. 2018. SNPversity: A web-based tool for visualizing diversity. Database: The Journal of Biological Databases and Curation. https://doi.org/10.1093/database/bay037.Surveying the maize community for their diversity and pedigree visualization needs to prioritize tool development and curation

- (Peer Reviewed Journal)Sen, T.Z., Braun, B., Schott, D., Portwood II, J.L., Schaeffer, M.L., Harper, E.C., Cannon, E.K., Andorf, C.M. 2017. Surveying the maize community for their diversity and pedigree visualization needs to prioritize tool development and curation. Database: The Journal of Biological Databases and Curation.  doi: 10.1093/database/bax031.MaizeGDB: New tools and resource

- (Abstract Only)Portwood II, J.L., Cannon, E., Braun, B., Harper, E.C., Gardiner, J.M., Schaeffer, M.L., Brumfield, M., Cho, K., Dunfee, B., Schott, D., Sen, T.Z., Andorf, C.M. 2016. MaizeGDB: New tools and resource. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 62.New trait data at MaizeGDB

- (Abstract Only)Schaeffer, M.L., Portwood II, J.L., Gardiner, J.M., Andorf, C.M. 2016. New trait data at MaizeGDB. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 62.Breeder survey, tools, and resources to visualize diversity and pedigree relationships at MaizeGDB

- (Abstract Only)Sen, T.Z., Braun, B.L., Schott, D.A., Portwood II, J.L., Schaeffer, M.L., Harper, E.C., Gardiner, J.M., Cannon, E.K., Andorf, C.M. 2016. Breeder survey, tools, and resources to visualize diversity and pedigree relationships at MaizeGDB. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 63.MaizeGDB video tutorials, feedback booth and introducing the agBioData working group

- (Abstract Only)Harper, E.C., Enger, A., Schaeffer, M.L., Gardiner, J.M., Braun, B., Cannon, E., Portwood II, J.L., Sen, T.Z., Andorf, C.M. 2016. MaizeGDB video tutorials, feedback booth and introducing the agBioData working group. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 63.Sequence, assembly and annotation of the maize W22 genome

- (Abstract Only)Andorf, C.M., Ahem, K., Bai, F., Barad, O., Barbazuk, B.W., Bass, H.W., Baruch, K., Ben-Zvi, G., Buckler Iv, E.S., Bukowski, R., Davenport, R., Dooner, H.K., He Du, L., Du, C., Easterling, K.A., Gault, C.M., Guan, J., Jander, G., Jiao, Y., Koch, K., Kol, G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D., Portwood II, J.L., Ronen, G., Settles, M.A., Shem-Tov, D., Soifer, I., Springer, N.M., Suzuki, M., Vera, D., Vollbrecht, E., Vrebalov, J.T., Ware, D., Wimalanathan, K., Xiong, W., Brutnell, T. 2016. Sequence, assembly and annotation of the maize W22 genome. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 91.MaizeGDB update:  New tools, data, and interface for the maize model organism database

- (Peer Reviewed Journal)Andorf, C.M., Cannon, E., Portwood II, J.L., Gardiner, J.M., Harper, E.C., Schaeffer, M.L., Braun, B.L., Campbell, D.A., Vinnakota, A.G., Sribalusa, V.V., Huerta, M., Cho, K., Wimalanathan, K., Richter, J.D., Mauch, E.D., Rao, B.S., Birkett, S.M., Sen, T.Z., Lawrence, C.J. 2016. MaizeGDB update: New tools, data, and interface for the maize model organism database. Nucleic Acids Research. 44 (D1):D1195-201. doi:10.1093/nar/gkv1007.


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