Projects

THE MAIZE GENETICS AND GENOMICS DATABASE Appropriated (D)   Accession Number: 413161

Publications (Clicking on the reprint icon will take you to the publication reprint.)

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.

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.

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.

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) - (11-Oct-10)

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.