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MaizeGDB update: new tools, data and interface for the maize model organism database.

Andorf CM, Cannon EK, Portwood JL 2nd, Gardiner JM, Harper LC, Schaeffer ML, Braun BL, Campbell DA, Vinnakota AG, Sribalusu VV, Huerta M, Cho KT, Wimalanathan K, Richter JD, Mauch ED, Rao BS, Birkett SM, Sen TZ, Lawrence-Dill CJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1195-201. doi: 10.1093/nar/gkv1007. Epub 2015 Oct 1.


A computational platform to maintain and migrate manual functional annotations for BioCyc databases.

Walsh JR, Sen TZ, Dickerson JA.

BMC Syst Biol. 2014 Oct 12;8:115. doi: 10.1186/s12918-014-0115-1.


Sampling errors: Aristotle's suspect statistical skills.

Sen TZ.

Nature. 2014 Sep 18;513(7518):315. doi: 10.1038/513315f. No abstract available.


An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures.

Ilgu M, Fulton DB, Yennamalli RM, Lamm MH, Sen TZ, Nilsen-Hamilton M.

RNA. 2014 Jun;20(6):815-24. doi: 10.1261/rna.041145.113. Epub 2014 Apr 22.


Endoglucanases: insights into thermostability for biofuel applications.

Yennamalli RM, Rader AJ, Kenny AJ, Wolt JD, Sen TZ.

Biotechnol Biofuels. 2013 Sep 27;6(1):136. doi: 10.1186/1754-6834-6-136.


Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks.

Andorf CM, Honavar V, Sen TZ.

PLoS One. 2013;8(2):e56833. doi: 10.1371/journal.pone.0056833. Epub 2013 Feb 19.


Molecular simulation of fibronectin adsorption onto polyurethane surfaces.

Panos M, Sen TZ, Ahunbay MG.

Langmuir. 2012 Aug 28;28(34):12619-28. doi: 10.1021/la301546v. Epub 2012 Aug 16.


A rigid network of long-range contacts increases thermostability in a mutant endoglucanase.

Rader AJ, Yennamalli RM, Harter AK, Sen TZ.

J Biomol Struct Dyn. 2012;30(6):628-37. Epub 2012 Jun 26.


POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data.

Cannon EK, Birkett SM, Braun BL, Kodavali S, Jennewein DM, Yilmaz A, Antonescu V, Antonescu C, Harper LC, Gardiner JM, Schaeffer ML, Campbell DA, Andorf CM, Andorf D, Lisch D, Koch KE, McCarty DR, Quackenbush J, Grotewold E, Lushbough CM, Sen TZ, Lawrence CJ.

Int J Plant Genomics. 2011;2011:923035. doi: 10.1155/2011/923035. Epub 2011 Dec 27.


Dynamics of endoglucanase catalytic domains: implications towards thermostability.

Yennamalli RM, Wolt JD, Sen TZ.

J Biomol Struct Dyn. 2011 Dec;29(3):509-26.


MaizeGDB: curation and outreach go hand-in-hand.

Schaeffer ML, Harper LC, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Sen TZ, Lawrence CJ.

Database (Oxford). 2011 May 29;2011:bar022. doi: 10.1093/database/bar022. Print 2011.


The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.

Harper LC, Schaeffer ML, Thistle J, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Braun BL, Birkett SM, Lawrence CJ, Sen TZ.

Database (Oxford). 2011 May 9;2011:bar016. doi: 10.1093/database/bar016. Print 2011.


Thermostability in endoglucanases is fold-specific.

Yennamalli RM, Rader AJ, Wolt JD, Sen TZ.

BMC Struct Biol. 2011 Feb 3;11:10. doi: 10.1186/1472-6807-11-10.


Choosing a genome browser for a Model Organism Database: surveying the maize community.

Sen TZ, Harper LC, Schaeffer ML, Andorf CM, Seigfried TE, Campbell DA, Lawrence CJ.

Database (Oxford). 2010 Jul 6;2010:baq007. doi: 10.1093/database/baq007.


The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps.

Andorf CM, Lawrence CJ, Harper LC, Schaeffer ML, Campbell DA, Sen TZ.

Bioinformatics. 2010 Feb 1;26(3):434-6. doi: 10.1093/bioinformatics/btp556.


MaizeGDB becomes 'sequence-centric'.

Sen TZ, Andorf CM, Schaeffer ML, Harper LC, Sparks ME, Duvick J, Brendel VP, Cannon E, Campbell DA, Lawrence CJ.

Database (Oxford). 2009;2009:bap020. doi: 10.1093/database/bap020. Epub 2009 Dec 7.


The ribosome structure controls and directs mRNA entry, translocation and exit dynamics.

Kurkcuoglu O, Doruker P, Sen TZ, Kloczkowski A, Jernigan RL.

Phys Biol. 2008 Nov 24;5(4):046005. doi: 10.1088/1478-3975/5/4/046005.


MaizeGDB: The maize model organism database for basic, translational, and applied research.

Lawrence CJ, Harper LC, Schaeffer ML, Sen TZ, Seigfried TE, Campbell DA.

Int J Plant Genomics. 2008;2008:496957. doi: 10.1155/2008/496957.


Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.

Sen TZ, Kloster M, Jernigan RL, Kolinski A, Bujnicki JM, Kloczkowski A.

Biophys J. 2008 Apr 1;94(7):2482-91. doi: 10.1529/biophysj.107.116046. Epub 2008 Jan 4.


Predicting the order in which contacts are broken during single molecule protein stretching experiments.

SuĊ‚kowska JI, Kloczkowski A, Sen TZ, Cieplak M, Jernigan RL.

Proteins. 2008 Apr;71(1):45-60.

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