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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







Carson  Andorf
                        Corn Insects and Crop Genetics Research

                        




                        
                        Computational Biologist
                        Phone: (515) 294-2019
                        
                        
                        Fax: (515) 294-2265(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: 444388Tools and Resources to Explore Maize Multi-omics Data
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 437908Development of a Pan Genome MaizeMine, a Flexible Data Warehouse and Analysis System for Exploring the Maize Pan Genome
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 440229Sequencing, 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.)Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits
                                                        

- (Peer Reviewed Journal)Poretsky, E., Cagirici, B.H., Andorf, C.M., Sen, T.Z. 2024. Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits. Genetics. https://doi.org/10.1093/g3journal/jkae059.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.PhosBoost: improved phosphorylation prediction using gradient boosting and protein language models
                                                        

- (Peer Reviewed Journal)Poretsky, E., Andorf, C.M., Sen, T.Z. 2023. PhosBoost: improved phosphorylation prediction using gradient boosting and protein language models. Journal of Plant Physiology. https://doi.org/10.1002/pld3.554.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.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.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.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
                                                        

- (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.Co-expression pan-network reveals genes involved in complex traits within maize pan-genome
                                                        

- (Peer Reviewed Journal)Cagirici, B.H., Andorf, C.M., Sen, T.Z. 2022. Co-expression pan-network reveals genes involved in complex traits within maize pan-genome. BMC Plant Biology. 22. Article 595. https://doi.org/10.1186/s12870-022-03985-z.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.Predicting tissue-specific mRNA and protein abundance in maize: A machine learning approach
                                                        

- (Peer Reviewed Journal)Cho, K., Sen, T.Z., Andorf, C.M. 2022. Predicting tissue-specific mRNA and protein abundance in maize: A machine learning approach. Frontiers in Artificial Intelligence. 5. Article 830170. https://doi.org/10.3389/frai.2022.830170.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.ABRIDGE: An ultra-compression software for SAM alignment files
                                                        

- (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
                                                        

- (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.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.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.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.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.PAST: the Pathway Association Study Tool for interpreting GWAS data in light of metabolic pathway data

- (Abstract Only)Warburton, M.L., Thrash, A., Andorf, C.M. 2020. PAST: the Pathway Association Study Tool for interpreting GWAS data in light of metabolic pathway data. 62nd Maize Genetics Conference Abstracts. P222.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.Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize
                                                        

- (Peer Reviewed Journal)Walsh, J.R., Woodhouse, M.R., Andorf, C.M., Sen, T.Z. 2020. Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize. Biomed Central (BMC) Plant Biology. 20. https://doi.org/10.1186/s12870-019-2218-8.Haplotype structure in commercial maize breeding programs in relation to key founder lines
                                                        

- (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
                                                        

- (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.Technological advances in maize breeding: Past, present and future
                                                        

- (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
                                                        

- (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.AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
                                                        

- (Peer Reviewed Journal)Harper, E.C., Campbell, J., Cannon, E.K., Jung, S., Main, D., Poelchau, M.F., Walls, R.L., Andorf, C.M., Arnaud, E., Berardini, T.Z., Birkett, C.L., Cannon, S.B., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C., Farmer, A., Ficklin, S., Grant, D.M., Grau, E., Hendon, N., Hu, Z., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M., Larmande, P., Lazo, G.R., McCarthy, F., Menda, N., Mungall, C., Munoz-Torres, M., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L., Sen, T.Z., Staton, M., Subramaniam, S., Karey, T., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M. 2018. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database: The Journal of Biological Databases and Curation. 2018(1):1-32. https://doi.org/10.1093/database/bay088.Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning
                                                        

- (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.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.Maize GO annotation—methods, evaluation, and review (maize-GAMER)
                                                        

- (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.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.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.Investigating diversity and possible functions of G-quadruplexes in regulatory regions of maize genes

- (Abstract Only)He, M., Andorf, C.M., Walley, J., Walia, H., Koch, K., Liu, P., Bass, H., Lawrence-Dill, C. 2016. Investigating diversity and possible functions of G-quadruplexes in regulatory regions of maize genes. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 85.Sequencing, assembly, and annotation of Maize B104 : A maize transformation resource

- (Abstract Only)Manchanda, N., Andorf, C.M., Ye, L., Wimalanathan, K., Rounsley, S., Wang, K., Lawrence-Dill, C. 2016. Sequencing, assembly, and annotation of Maize B104 : A maize transformation resource. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 92.Maize - GO annotation methods, evaluation, and review (Maize-GAMER)

- (Abstract Only)Wimalanathan, K., Friedberg, I., Andorf, C.M., Lawrence-Dill, C. 2016. Maize - GO annotation methods, evaluation, and review (Maize-GAMER). In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 87.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.Stewardship of the Maize B73 feference genome assembly

- (Abstract Only)Cannon, E., Rezaie, T., Dunfee, B., Jiao, Y., Schneider, V., Ware, D., Andorf, C.M. 2016. Stewardship of the Maize B73 feference genome assembly. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 64.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.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.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.MaizeGDB:  The Maize Genetics and Genomics Database.

- (Book / Chapter)Harper, E.C., Gardiner, J., Andorf, C.M., Lawrence, C.J. 2016. MaizeGDB:  The Maize Genetics and Genomics Database. In: Edwards, D. Plant Bioinformatics, Methods and Protocols. 2nd Edition. New York, NY: Humana Press. p.187-202.G-quadruplex (G4) motifs in the maize (Zea mays L.) genome are enriched at specific locations in thousands of genes coupled to energy status, hypoxia, low sugar, and nutrient deprivation

- (Peer Reviewed Journal)Andorf, C.M., Kopylov, M., Dobbs, D., Koch, K., Stroupe, M., Lawrence, C.J., Bass, H. 2014. G-quadruplex (G4) motifs in the maize (Zea mays L.) genome are enriched at specific locations in thousands of genes coupled to energy status, hypoxia, low sugar, and nutrient deprivation. Journal of Genetics and Genomics. 41(12):627-647. DOI: 10.1016/j.jgg.2014.10.004.MaizeGDB: everything old is new again! [abstract]
                                                        

- (Abstract Only)Andorf, C.M., Cannon, E., Portwood, J., Braun, B.L., Harper, E.C., Campbell, D.A., Schaeffer, M.L., Richter, J., Sen, T.Z., Lawrence, C.J. 2013. MaizeGDB: everything old is new again! [abstract]. In: Maize Genetics Conference, St. Charles, IL.  Mar. 14-17, 2013. p. 55.Compare Identity By Sequence Relationships of the Ames Diversity Panel using TYPSimSelector [abstract]
                                                        

- (Abstract Only)Mauch, E., Andorf, C.M., Millard, M.J., Romay, C., Buckler Iv, E.S., Gardner, C.A., Lawrence, C.J. 2013. Compare Identity By Sequence Relationships of the Ames Diversity Panel using TYPSimSelector [abstract]. In: Maize Genetics Conference, St. Charles, IL.  Mar. 14-17, 2013. p. 55.Metabolic pathway resources at MaizeGDB

- (Abstract Only)Sen, T.Z., Monaco, M., Chae, L., Dharmawardhana, P., Schaeffer, M.L., Dreher, K., Zhang, P., Naithani, S., Thomason, J., Harper, E.C., Gardiner, J., Cannon, E., Andorf, C.M., Campbell, D.A., Rhee, S.Y., Ware, D., Jaiswal, P., Lawrence, C.J. 2013. Metabolic pathway resources at MaizeGDB [abstract].  In: Proceedings of Maize Genetics Conference, March 14-17, St. Charles, Illinois. p. 3.MaizeGDB: enabling access to basic, translational, and applied research information

- (Proceedings)Lawrence, C.J., Andorf, C.M., Birkett, S., Braun, B.L., Campbell, D.A., Cannon, E., Gardiner, J., Harper, E.C., Portwood, J., Richter, J., Schaeffer, M.L., Sen, T.Z., Wimalanathan, K. 2012. MaizeGDB: enabling access to basic, translational, and applied research information. Meeting Proceedings. P. 233.POPcorn: An online resource providing access to distributed and diverse maize project data

- (Peer Reviewed Journal)Cannon, E.K., Birkett, S.M., Braun, B.L., Kodavali, S., Jennewein, D.M., Yilmaz, A., Antonescu, V., Antonescu, C., Harper, E.C., Gardiner, J.M., Schaeffer, M.L., Campbell, D.A., Andorf, C.M., Andorf, D., Lisch, D., Koch, K.K., McCarty, D.R., Quackenbush, J., Grotewold, E., Lushbough, C.M., Sen, T.Z., Lawrence, C.J. 2011. POPcorn: An online resource providing access to distributed and diverse maize project data. International Journal of Plant Genomics. 2011:Article 923035. Available http://www.hindawi.com/journals/ijpg/2011/923035.MaizeGDB, the maize model organism database

- (Abstract Only)Lawrence, C.J., Andorf, D., Andorf, C.M., Birkett, S.M., Braun, B.L., Cannon, E., Campbell, D.A., Gardiner, J.M., Harper, E.C., Rao, B., Schaeffer, M.L., Sen, T.Z. 2011. MaizeGDB, the maize model organism database. Meeting Abstract. P. 1.MaizeGDB: Curation and outreach go hand-in-hand

- (Peer Reviewed Journal)Schaeffer, M.L., Harper, E.C., Gardiner, J.M., Andorf, C.M., Campbell, D.A., Cannon, E.K., Sen, T.Z., Lawrence, C.J. 2011. MaizeGDB: Curation and outreach go hand-in-hand. Database: The Journal of Biological Databases and Curation. 2011:Article bar022. Available: http://database.oxfordjournals.org/content/2011/bar022.long.The MaizeGDB Genome Browser Tutorial: One example of database outreach to biologists via video

- (Peer Reviewed Journal)Harper, E.C., Schaeffer, M.L., Thistle, J., Gardiner, J., Andorf, C.M., Campbell, D.A., Cannon, E.K., Braun, B.L., Birkett, S., Lawrence, C.J., Sen, T.Z. 2011. The MaizeGDB Genome Browser Tutorial: One example of database outreach to biologists via video. Database: The Journal of Biological Databases and Curation. DOI: 10.1093/database/bar016:1.Reinventing MaizeGDB

- (Abstract Only)Andorf, C.M., Cannon, E.K., Braun, B.L., Birkett, S., Harper, E.C., Schaeffer, M.L., Gardiner, J., Jayasingam, D., Campbell, D.A., Sen, T.Z., Lawrence, C.J. 2011. Reinventing MaizeGDB. 53rd Annual Maize Genetics Conference Program and Abstracts. 1(1):33.MAIZEGDB.ORG, the Maize Genetics Cooperation and the 2500 MB B73 Genome-Generated Tsunami

- (Abstract Only)Choosing a Genome Browser for a Model Organism Database (MOD): Surveying the Maize Community

- (Peer Reviewed Journal)Sen, T.Z., Harper, E.C., Schaeffer, M.L., Andorf, C.M., Seigfried, T.E., Campbell, D.A., Lawrence, C.J. 2010. Choosing a Genome Browser for a Model Organism Database (MOD): Surveying the Maize Community. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/baq007. p. 1.Sequence Resources at MaizeGDB with Emphasis on POPcorn: A Project Portal for Corn

- (Proceedings)Lawrence, C.J., Cannon, E.K., Andorf, C.M., Campbell, D.A., Harper, E.C., Schaeffer, M.L., Sen, T.Z. 2010. Sequence Resources at MaizeGDB with Emphasis on POPcorn: A Project Portal for Corn [abstract]. 52nd Maize Genetics Conference Proceedings. p. 32.The Locus Lookup Tool at MaizeGDB: Identification of Genomic Regions in Maize by Integrating Sequence Information with Physical and Genetic Maps

- (Peer Reviewed Journal)Andorf, C.M., Lawrence, C.J., Harper, E.C., Schaeffer, M.L., Campbell, D.A., Sen, T.Z. 2010. The Locus Lookup Tool at MaizeGDB: Identification of Genomic Regions in Maize by Integrating Sequence Information with Physical and Genetic Maps. Bioinformatics. 26(3):434-436.MaizeGDB Becomes Sequence-centric

- (Peer Reviewed Journal)Sen, T.Z., Andorf, C.M., Schaeffer, M.L., Harper, E.C., Sparks, M., Duvick, J., Brendel, V., Cannon, E., Campbell, D.A., Lawrence, C.J. 2009. MaizeGDB Becomes Sequence-centric. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/bap020. p. 1.The MaizeGDB Genome Browser

- (Abstract Only)Sen, T.Z., Andorf, C.M., Campbell, D.A., Schaeffer, M.L., Harper, E.C., Lawrence, C.J. 2009. The MaizeGDB Genome Browser [abstract]. Maize Genetics Conference Abstracts. p. 28.The MaizeGDB Genome Browser

- (Abstract Only)Sen, T.Z., Andorf, C.M., Campbell, D.A., Schaeffer, M.L., Harper, E.C., Lawrence, C.J. 2009. The MaizeGDB Genome Browser [abstract]. Plant and Animal Genome Conference Proceedings. p. 1.


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