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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » People & Locations » Taner Sen
Taner Z Sen (PhD)
Crop Improvement and Genetics Research
Research Biologist

Phone: (510) 559-5982
Fax: (510) 559-5818

(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)

Projects
GrainGenes- A Global Data Repository for Small Grains
In-House Appropriated (D)
  Accession Number: 444625
Oat Pangenome Project Data Sharing Agreement
Non-Funded Cooperative Agreement (N)
  Accession Number: 440183
Curation of Nutrient-Associated Enzymes and Machine Learning Analysis of Mutational Effects in Enzymatic Activity in Wheat and Barley Pangenomes
Non-Assistance Cooperative Agreement (S)
  Accession Number: 446734

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.
Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii Reprint Icon - (Peer Reviewed Journal)
Grewal, S., Yang, C., Scholefield, D., Ashling, S., Ghosh, S., Swarbreck, D., Collins, J., Yao, E., Sen, T.Z., Wilson, M., Yant, L., King, I., King, J. 2024. Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii. Scientific Data. 11. Article 420. https://doi.org/10.1038/s41597-024-03260-w.
Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits Reprint Icon - (Peer Reviewed Journal)
Poretsky, E., Cagirici, H.B., 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. 14(5). Article jkae059. https://doi.org/10.1093/g3journal/jkae059.
A uniform gene and chromosome nomenclature system for oat (Avena spp.) Reprint Icon - (Peer Reviewed Journal)
Jellen, E.N., Wight, C.P., Spannagl, M., Blake, V.C., Chong, J., Herrmann, M., Howarth, C.N., Huang, Y., Juqing, J., Katsiotis, A., Langdon, T., Li, C., Park, R., Tinker, N.A., Sen, T.Z. 2024. A uniform gene and chromosome nomenclature system for oat (Avena spp.). Crop and Pasture Science. 75(1). Article CP23247. https://doi.org/10.1071/CP23247.
One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa) Reprint Icon - (Peer Reviewed Journal)
Wight, C.P., Blake, V.C., Jellen, E.N., Yao, E., Sen, T.Z., Tinker, N.A. 2024. One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa). Crop and Pasture Science. 75(2). Article CP23246. https://doi.org/10.1071/CP23246.
PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models Reprint Icon - (Peer Reviewed Journal)
Poretsky, E., Andorf, C.M., Sen, T.Z. 2024. PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models. Plant Direct. 7(12). Article e554. https://doi.org/10.1002/pld3.554.
Wheat data integration and FAIRification: IWGSC, GrainGenes, Ensembl and other data repositories Reprint Icon - (Book / Chapter)
Alaux, M., Dyer, S., Sen, T.Z. 2023. Wheat data integration and FAIRification: IWGSC, GrainGenes, Ensembl and other data repositories. In: Appels, R., Eversole, K., Feuillet, C., Gallagher, D., editors. The Wheat Genome. Cham, CH: Springer. p. 13-25. https://doi.org/10.1007/978-3-031-38294-9_2.
Data Sharing and Ontology use among Agricultural Genetics, Genomics and Breeding Databases and Resources of the AgBioData Consortium Reprint Icon - (Pre-print Publication)
Clarke, J., Cooper, L., Poelchau, M.F., Berardini, T., Elser, J., Farmer, A., Ficklin, S., Kumari, S., Laporte, M., Nelson, R., Sadohara, R., Selby, P., Thessen, A.E., Whitehead, B., Sen, T.Z. 2023. Data Sharing and Ontology use among Agricultural Genetics, Genomics and Breeding Databases and Resources of the AgBioData Consortium. ArXiv. arXiv:2307.08958. https://doi.org/10.48550/arXiv.2307.08958.
Co-expression pan-network reveals genes involved in complex traits within maize pan-genome Reprint Icon - (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 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.
Updated guidelines for gene nomenclature in wheat Reprint Icon - (Peer Reviewed Journal)
Boden, S.A., McIntosh, R.A., Uauy, C., Krattinger, S., Dubcovsky, J., Rogers, W., Xia, X., Badaeva, E.D., Bentley, A.R., Brown Guedira, G.L., Caccamo, M., Cattivelli, L., Chhuneja, P., Cockram, J., Contreras-Moreira, B., Dreisigacker, S., Edwards, D., Gonzalez, F., Guzman, C., Ikeda, T., Karsai, E.I., Nasuda, S., Pozniak, C., Prins, R., Sen, T.Z., Silva, P., Simkova, H., Zhang, Y. 2023. Updated guidelines for gene nomenclature in wheat. Theoretical and Applied Genetics. 136. Article 72. https://doi.org/10.1007/s00122-023-04253-w.
G4Boost: A machine learning-based tool for quadruplex identification and stability prediction Reprint Icon - (Peer Reviewed Journal)
Cagirici, H.B., Budak, H., Sen, T.Z. 2022. G4Boost: A machine learning-based tool for quadruplex identification and stability prediction. BMC Bioinformatics. 23. Article 240. https://doi.org/10.1186/s12859-022-04782-z.
Experimental and computational studies of cellulases as bioethanol enzymes Reprint Icon - (Peer Reviewed Journal)
Ranganathan, S., Mahesh, S., Suresh, S., Nagarajan, A., Sen, T.Z., Yennamalli, R.M. 2022. Experimental and computational studies of cellulases as bioethanol enzymes. Bioengineered. 13(5):14028-14046. https://doi.org/10.1080/21655979.2022.2085541.
Capturing wheat phenotypes at the genome level Reprint Icon - (Peer Reviewed Journal)
Hussain, B., Akpinar, B.A., Alaux, M., Algharib, A.M., Sehgal, D., Ali, Z., Aradottir, G.I., Batley, J., Bellec, A., Bentley, A.R., Cagirici, H.B., Cattivelli, L., Choulet, F., Cockram, J., Desiderio, F., Devaux, P., Dogramaci, M., Dorado, G., Dreisigacker, S., Edwards, D., El-Hassouni, K., Eversole, K., Fahima, T., Figueroa, M., Galvez, S., Gill, K.S., Govta, L., Gul, A., Hensel, G., Hernandez, P., Herrera, L.C., Ibrahim, A., Kilian, B., Korzun, V., Krugman, T., Li, Y., Liu, S., Mahmoud, A.F., Morgounov, A., Muslu, T., Naseer, F., Ordon, F., Paux, E., Perovic, D., Reddy, G.V., Reif, J.C., Reynolds, M., Roychowdhury, R., Rudd, J., Sen, T.Z., Sukumaran, S., Ozdemir, B.S., Tiwari, V., Ullah, N., Unver, T., Yazar, S., Appels, R., Budak, H. 2022. Capturing wheat phenotypes at the genome level. Frontiers in Plant Science. 13. Article 851079. https://doi.org/10.3389/fpls.2022.851079.
Predicting tissue-specific mRNA and protein abundance in maize: A machine learning approach Reprint Icon - (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.
GrainGenes: A data-rich repository for small grains genetics and genomics Reprint Icon - (Peer Reviewed Journal)
Yao, E., Blake, V.C., Cooper, L., Wight, C.P., Michel, S., Cagirici, H.B., Lazo, G.R., Birkett, C., Waring, D.J., Jannink, J., Holmes, I., Waters, A.J., Eickholt, D.P., Sen, T.Z. 2022. GrainGenes: A data-rich repository for small grains genetics and genomics. Database: The Journal of Biological Databases and Curation. 2022. Article baac034. https://doi.org/10.1093/database/baac034.
GrainGenes: Tools and content to assist breeders improving oat quality Reprint Icon - (Peer Reviewed Journal)
Blake, V.C., Wight, C.P., Yao, E., Sen, T.Z. 2022. GrainGenes: Tools and content to assist breeders improving oat quality. Foods. 11(7). Article 914. https://doi.org/10.3390/foods11070914.
Multiple variant calling pipelines in wheat whole exome sequencing Reprint Icon - (Peer Reviewed Journal)
Cagirici, B.H., Akpinar, B., Sen, T.Z., Budak, H. 2021. Multiple variant calling pipelines in wheat whole exome sequencing. International Journal of Molecular Sciences. 22(19). Article 10400. https://doi.org/10.3390/ijms221910400.
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.
mirMachine: a one-stop shop for plant miRNA annotation Reprint Icon - (Peer Reviewed Journal)
Cagirici, B.H., Sen, T.Z., Budak, H. 2021. mirMachine: a one-stop shop for plant miRNA annotation. The Journal of Visualized Experiments (JoVE). (171). Article e62430. https://www.doi.org/10.3791/62430.
Genome-wide discovery of G-quadruplexes in barley Reprint Icon - (Peer Reviewed Journal)
Cagirici, B.H., Budak, H., Sen, T.Z. 2021. Genome-wide discovery of G-quadruplexes in barley. Scientific Reports. 11. Article 7876. https://doi.org/10.1038/s41598-021-86838-3.
Building a successful international research community through data sharing: the case of wheat information system (WheatIS) Reprint Icon - (Peer Reviewed Journal)
Sen, T.Z., Caccamo, M., Edwards, D., Quesneville, H. 2020. Building a successful international research community through data sharing: the case of wheat information system (WheatIS). F1000Research. 9. Article 536. https://doi.org/10.12688/f1000research.23525.1.
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.
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.
LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants Reprint Icon - (Peer Reviewed Journal)
Cagirici, B.H., Galvez, S., Sen, T.Z., Budak, H. 2021. LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants. Functional and Integrative Genomics. 21(1): 195-204. https://doi.org/10.1007/s10142-021-00769-w.
LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants Reprint Icon - (Peer Reviewed Journal)
Cagirici, B.H., Galvez, S., Sen, T.Z., Budak, H. 2021. LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants. Functional and Integrative Genomics. 21:195-204. https://doi.org/10.1007/s10142-021-00769-w.
JBrowse Connect: a server API to connect JBrowse instances and users Reprint Icon - (Peer Reviewed Journal)
Yao, E., Buels, R., Stein, L., Sen, T.Z., Holmes, I. 2020. JBrowse Connect: a server API to connect JBrowse instances and users. PLoS Computational Biology. 16(8). https://doi.org/10.1371/journal.pcbi.1007261.
Genome-wide discovery of G-quadruplexes in wheat: distribution and putative functional roles Reprint Icon - (Peer Reviewed Journal)
Cagirici, H., Sen, T.Z. 2020. Genome-wide discovery of G-quadruplexes in wheat: distribution and putative functional roles. G3, Genes/Genomes/Genetics. 10(6). https://doi.org/10.1534/g3.120.401288.
Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize Reprint Icon - (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.
GrainGenes: centralized small grain resources and digital platform for geneticists and breeders - (Peer Reviewed Journal)
Blake, V.C., Woodhouse, M.R., Lazo, G.R., Odell, S.G., Wight, C.W., Tinker, N.A., Wang, Y., Gu, Y.Q., Birkett, C.L., Jannink, J., Matthews, D.E., Hane, D.L., Michel, S.L., Yao, E., Sen, T.Z. 2019. GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. Database: The Journal of Biological Databases and Curation. 2019.
PedigreeNet: A web-based pedigree viewer for biological databases Reprint Icon - (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.
Visualization, tools, and resources for wheat at GrainGenes - (Abstract Only)
Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region Reprint Icon - (Peer Reviewed Journal)
Arora, R., Bharyal, P., Sarswati, S., Sen, T.Z., Yennamalli, R.M. 2018. Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region. Journal of Molecular Graphics and Modeling. 88:1-10. https://doi.org/10.1016/j.jmgm.2018.12.012.
MaizeGDB 2018: The maize multi-genome genetics and genomics database Reprint Icon - (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.
Application of molecular simulations toward understanding cellulase mechanisms Reprint Icon - (Peer Reviewed Journal)
Arora, M., Yennamalli, R.M., Sen, T.Z. 2018. Application of molecular simulations toward understanding cellulase mechanisms. BioEnergy Research. 11:850-867. https://doi.org/10.1007/s12155-018-9944-x.
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture Reprint Icon - (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.
SNPversity: A web-based tool for visualizing diversity Reprint Icon - (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.
The art of curation at a biological database: principles and application Reprint Icon - (Peer Reviewed Journal)
Odell, S.G., Lazo, G.R., Woodhouse, M.R., Hane, D.L., Sen, T.Z. 2017. The art of curation at a biological database: principles and application. Current Plant Biology. 11-12:2-11. https://doi.org/10.1016/j.cpb.2017.11.001.
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.
The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize Reprint Icon - (Peer Reviewed Journal)
Walsh, J.R., Schaeffer, M.L., Zhang, P., Rhee, S.Y., Dickerson, J.A., Sen, T.Z. 2016. The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. BMC Systems Biology. 10:129. doi: 10.1186/s12918-016-0369-x.
The quality of metabolic pathway resources depends on initial enzymatic function assignments and level of manual curation: A case for maize - (Peer Reviewed Journal)
Walsh, J., Schaeffer, M.L., Zhang, P., Rhee, S., Dickerson, J., Sen, T.Z. 2016. The quality of metabolic pathway resources depends on initial enzymatic function assignments and level of manual curation: A case for maize. BMC Systems Biology. 10:129.
A clade-specific Arabidopsis gene connects primary metabolism and senescence - (Peer Reviewed Journal)
Jones, D.C., Zheng, W., Huang, S., Du, C., Zhao, X., Yennamalli, R., Sen, T.Z., Nettleton, D., Wurtele, E.S., Li, L. 2016. A clade-specific Arabidopsis gene connects primary metabolism and senescence. Frontiers in Plant Science. 7:983. doi: 10.3389/fpls.2016.00983.
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.
A computational platform to maintain and migrate manual functional annotations for BioCyc databases - (Peer Reviewed Journal)
Walsh, J.R., Sen, T.Z., Dickerson, J.A. 2014. A computational platform to maintain and migrate manual functional annotations for BioCyc databases. BMC Systems Biology. 8:115. DOI: 10.1186/s12918-014-0115-1.
Maize databases - (Book / Chapter)
Schaeffer, M.L., Sen, T.Z., Lawrence, C.J. 2014. Maize databases. In: Wusirika, R., Bohn, M., Lai, J., Kole, C., editors. Genetics, Genomics and Breeding of Maize. Boca Raton, FL: CRC Press. p. 215-235.
MaizeGDB: everything old is new again! [abstract] Reprint Icon - (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.
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.
Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks - (Peer Reviewed Journal)
Andorf, C.M., Honavar, V., Sen, T.Z. 2013. Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PLoS One. 8(2):e56833.
Maize metabolic network construction and transcriptome analysis - (Peer Reviewed Journal)
Monaco, M.K., Sen, T.Z., Dharmawardhana, P., Ren, L., Schaeffer, M.L., Amarasinghe, V., Thomason, J., Harper, E.C., Gardiner, J.M., Lawrence, C.J., Ware, D., Jaiswal, P., Naithani, S., Cannon, E. 2013. Maize metabolic network construction and transcriptome analysis. The Plant Genome. 6(1):DOI:10.3835/plantgenome2012.09.0025.
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.
Molecular simulation of fibronectin adsorption onto polyurethane surfaces - (Peer Reviewed Journal)
Panos, M., Sen, T.Z., Ahunbay, G.M. 2012. Molecular simulation of fibronectin adsorption onto polyurethane surfaces. Langmuir. 28(34):12619-12628.
A rigid network of long-range contacts increases thermostability in a mutant endoglucanase - (Peer Reviewed Journal)
Rader, A.J., Yennamalli, R.M., Harter, A.K., Sen, T.Z. 2012. A rigid network of long-range contacts increases thermostability in a mutant endoglucanase. Journal of Biomolecular Structure and Dynamics. DOI:10.1080/07391102.2012.689696.
A systematic approach to evolve aptamers with new specificities - (Abstract Only)
Ilgu, M., Yennamalli, R.M., Kleckler, M.M., Sen, T.Z., Lamm, M.H., Nilsen-Hamilton, M. 2012. A systematic approach to evolve aptamers with new specificities. Journal of Physical Chemistry. Paper No. 23.
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.
MaizeCyc: Metabolic networks in maize - (Abstract Only)
Monaco, M., Sen, T.Z., Ren, L., Dharmawardhana, P., Schaeffer, M.L., Amarasinghe, V., Thomason, J., Harper, E.C., Naithani, S., Gardiner, J.M., Lawrence, C.J., Ware, D., Pankaj, J. 2012. MaizeCyc: Metabolic networks in maize. Plant and Animal Genome Conference. 4:100-110.
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.
Metabolic and regulatory networks in gramene - (Abstract Only)
Dharmawardhana, P., Monaco, M., Amarasinghe, V., Preece, J., Wu, G., D'Eustachio, P., Thomason, J., Sen, T.Z., Gardiner, J.M., Harper, E.C., Schaeffer, M.L., Lawrence, C.J., Ware, D., Jaiswal, P. 2011. Metabolic and regulatory networks in gramene. Meeting Abstract. Paper No. 2.
MaizeCyc: Metabolic networks in maize - (Abstract Only)
Monaco, M., Sen, T.Z., Ren, L., Dharmawardhana, P., Schaeffer, M.L., Amarasinghe, V., Thomason, J., Harper, E.C., Naithani, S., Gardiner, J.M., Lawrence, C.J., Ware, D., Jaiswal, P. 2011. MaizeCyc: Metabolic networks in maize [abstract]. In: Conference on Genome Informatics, November 2-5, 2011, Cold Spring Harbor, New York. p. 1.
Dynamics of endoglucanase catalytic domains: implications towards thermostability - (Peer Reviewed Journal)
Yennamalli, R.M., Wolt, J.D., Sen, T.Z. 2011. Dynamics of endoglucanase catalytic domains: implications towards thermostability. Journal of Biomolecular Structure and Dynamics. 29(3):424-596.
Metabolic and regulatory networks for cereals - (Abstract Only)
Dharmawardhana, P., Monaco, M., Amarasinghe, V., Preece, J., D'Eustachio, P., Ren, L., Thomason, J., Sen, T.Z., Gardiner, J.M., Harper, E.C., Schaeffer, M.L., Lawrence, C.J., Ware, D., Jaiswal, P. 2011. Metabolic and regulatory networks for cereals. American Society of Plant Biologists Annual Meeting, August 6-10, 2011, Minneapolis, MN. Available: http://abstracts.aspb.org/pb2011/public/P21/P21021.html.
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.
Thermostability in endoglucanases is fold-specific - (Peer Reviewed Journal)
Yennamalli, R.M., Rader, A.J., Wolt, J.D., Sen, T.Z. 2011. Thermostability in endoglucanases is fold-specific. BMC Structural Biology. 11(10):1-15.
POPcorn: A PrOject Portal for corn - (Abstract Only)
Cannon, E., Birkett, S.M., Braun, B.L., Gardiner, J.M., Sen, T.Z., Lawrence, C.J. 2011. POPcorn: A PrOject Portal for corn. Plant and Animal Genome Conference. 2011(1):267.
Sequence, structure and dynamics analysis of thermostability in endoglucanases - (Abstract Only)
Yennamalli, R.M., Rader, A.J., Wolt, J.D., Sen, T.Z. 2011. Sequence, structure and dynamics analysis of thermostability in endoglucanases. Annual Biophysical Meeting. 2011(1):134.
MAIZEGDB.ORG, the Maize Genetics Cooperation and the 2500 MB B73 Genome-Generated Tsunami - (Abstract Only)
An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community - (Peer Reviewed Journal)
Bastow, R., Beynon, J., Estelle, M., Friesner, J., Grotewold, E., Lavagi, I., Lindsey, K., Meyers, B., Provart, N., Benfey, P., Birney, E., Braun, P., Brendel, V., Buell, R., Caccamo, M., Carrington, J., Cherry, M., Ecker, J., Eppig, J., Forster, M., Gutierrez, R., Hilson, P., Huala, E., Katari, M., Kersey, P., Kudla, J., Ma, H., Matsui, M., Matthews, K., May, S., Mayer, K., Millar, A., Millar, H., Mjolsness, E., Mockler, T., Nikolau, B., Nordborg, M., Rawlings, C., Schofield, P., Schoof, H., Schroeder, J., Sen, T.Z., Stanzione, D., Town, C., Toyoda, T., Vision, T., Walsh, S., Wang, X., Ware, D., Weckwerth, W., Yang, W. 2010. An international bioinformatics infrastructure to underpin the Arabidopsis community. The Plant Cell. 22(8):2530-2536.
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 Ribosome Shape Directs mRNA Translocation through Entrance and Exit Dynamics - (Peer Reviewed Journal)
Kurkcuoglu, O., Doruker, P., Sen, T.Z., Kloczkowski, A., Jernigan, R.L. 2008. The Ribosome Shape Directs mRNA Translocation through Entrance and Exit Dynamics. Physical Biology. 5(4):40005.
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.
Genome Browser Survey Results and Browser Selection for MaizeGDB - (Proceedings)
Sen, T.Z., Campbell, D.A., Schaeffer, M.L., Harper, E.C., Lawrence, C.J. 2008. Genome Browser Survey Results and Browser Selection for MaizeGDB. In: Genome Informatics Proceedings. Cold Spring Harbor Meeting Proceedings, Sept. 10-14, 2008, Hinxton, U.K. p. 1.
MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research - (Peer Reviewed Journal)
Lawrence, C.J., Harper, E.C., Schaeffer, M.L., Sen, T.Z., Seigfried, T.E., Campbell, D.A. 2008. MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research. International Journal of Plant Genomics. 2008:496957.
MaizeGDB as Chromosome Walking Companion - (Abstract Only)
Schaeffer, M.L., Campbell, D.A., Harper, E.C., Seigfried, T.E., Sen, T.Z., Lawrence, C.J. 2008. MaizeGDB as Chromosome Walking Companion. American Society of Plant Biologists Annual Meeting. p.106.
MaizeGDB's New Genome Browser Project - (Abstract Only)
Sen, T.Z., Seigfried, T.E., Campbell, D.A., Schaeffer, M.L., Harper, E.C., Lawrence, C.J. 2008. MaizeGDB's New Genome Browser Project. In: 50th Maize Genetics Conference Proceedings, February 27-March 2, 2008, Washington, D.C. p. 61.
Maize Genetics and Genomics Database - (Research Notes)
Schaeffer, M.L., Campbell, D.A., Seigfried, T.E., Harper, E.C., Sen, T.Z., Lawrence, C.J. 2008. Maize Genetics and Genomics Database. Maize Genetics Cooperation Newsletter. 82:82-83.
Plant cytogenetics in genome databases - (Book / Chapter)
Harper, E.C., Sen, T.Z., Lawrence, C.J. 2012. Plant cytogenetics in genome databases. In: Bass, H.W., Birchler, J.A., editors. Plant Cytogenetics. New York, NY: Springer. p. 311-322.
MaizeGDB Community Curation Tools - (Abstract Only)
Sen, T.Z., Campbell, D.A., Harper, E.C., Lawrence, C.J., Schaeffer, M.L., Seigfried, T.E. 2008. MaizeGDB Community Curation Tools. In: Annual International Plant & Animal Genome XVI Conference Proceedings, January 12-16, 2008, San Diego, CA. p. 940.
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