Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. - Taner Z. Sen; Andrzej Kloczkowski; Robert L. Jernigan; Changhui Yan; Vasant G. Honavar; Kai-Ming Ho; Cai-Zhuang Wang; Yungok Ihm; Haibo Cao; Xun Gu; Drena Dobbs (BMC Bioinform., 2004)

GOR V server for protein secondary structure prediction. - Taner Z. Sen; Robert L. Jernigan; Jean Garnier; Andrzej Kloczkowski (Bioinform., 2005)

Functional clustering of yeast proteins from the protein-protein interaction network. - Taner Z. Sen; Andrzej Kloczkowski; Robert L. Jernigan (BMC Bioinform., 2006)

Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM). - Haitao Cheng; Taner Z. Sen; Robert L. Jernigan; Andrzej Kloczkowski (Bioinform., 2007)

MaizeGDB becomes 'sequence-centric'. - Taner Z. Sen; Carson M. Andorf; Mary L. Schaeffer; Lisa C. Harper; Michael E. Sparks; Jon Duvick; Volker P. Brendel; Ethalinda K. S. Cannon; Darwin A. Campbell; Carolyn J. Lawrence (Database J. Biol. Databases Curation, 2009)

Choosing a genome browser for a Model Organism Database: surveying the Maize community. - Taner Z. Sen; Lisa C. Harper; Mary L. Schaeffer; Carson M. Andorf; Trent E. Seigfried; Darwin A. Campbell; Carolyn J. Lawrence (Database J. Biol. Databases Curation, 2010)

The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps. - Carson M. Andorf; Carolyn J. Lawrence; Lisa C. Harper; Mary L. Schaeffer; Darwin A. Campbell; Taner Z. Sen (Bioinform., 2010)

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video. - Lisa C. Harper; Mary L. Schaeffer; Jordan Thistle; Jack M. Gardiner; Carson M. Andorf; Darwin A. Campbell; Ethalinda K. S. Cannon; Bremen L. Braun; Scott M. Birkett; Carolyn J. Lawrence; Taner Z. Sen (Database J. Biol. Databases Curation, 2011)

MaizeGDB: curation and outreach go hand-in-hand. - Mary L. Schaeffer; Lisa C. Harper; Jack M. Gardiner; Carson M. Andorf; Darwin A. Campbell; Ethalinda K. S. Cannon; Taner Z. Sen; Carolyn J. Lawrence (Database J. Biol. Databases Curation, 2011)

A computational platform to maintain and migrate manual functional annotations for BioCyc databases. - Jesse R. Walsh; Taner Z. Sen; Julie A. Dickerson (BMC Syst. Biol., 2014)

The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. - Jesse R. Walsh; Mary L. Schaeffer; Peifen Zhang; Seung Yon Rhee; Julie A. Dickerson; Taner Z. Sen (BMC Syst. Biol., 2016)

MaizeGDB update: new tools, data and interface for the maize model organism database. - Carson M. Andorf; Ethalinda K. S. Cannon; John L. Portwood II; Jack M. Gardiner; Lisa C. Harper; Mary L. Schaeffer; Bremen L. Braun; Darwin A. Campbell; Abhinav G. Vinnakota; Venktanaga V. Sribalusu; Miranda Huerta; Kyoung Tak Cho; et al. (Nucleic Acids Res., 2016)

Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation. - Taner Z. Sen; Bremen L. Braun; David A. Schott; John L. Portwood II; Mary L. Schaeffer; Lisa C. Harper; Jack M. Gardiner; Ethalinda K. S. Cannon; Carson M. Andorf (Database J. Biol. Databases Curation, 2017)

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. - Lisa C. Harper; Jacqueline D. Campbell; Ethalinda K. S. Cannon; Sook Jung; Monica Poelchau; Ramona L. Walls; Carson M. Andorf; Elizabeth Arnaud; Tanya Z. Berardini; Clayton L. Birkett; Steven B. Cannon; James D. Carson; et al. (Database J. Biol. Databases Curation, 2018)

SNPversity: a web-based tool for visualizing diversity. - David A. Schott; Abhinav G. Vinnakota; John L. Portwood II; Carson M. Andorf; Taner Z. Sen (Database J. Biol. Databases Curation, 2018)

GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. - Victoria C. Blake; Margaret Woodhouse; Gerard R. Lazo; Sarah G. Odell; Charlene P. Wight; Nicholas A Tinker; Yi Wang 052; Yong Q. Gu; Clayton L. Birkett; Jean-Luc Jannink; Dave E. Matthews; David L. Hane; et al. (Database J. Biol. Databases Curation, 2019)

PedigreeNet: a web-based pedigree viewer for biological databases. - Bremen L. Braun; David A. Schott; John L. Portwood II; Carson M. Andorf; Taner Z. Sen (Bioinform., 2019)

MaizeGDB 2018: the maize multi-genome genetics and genomics database. - John L. Portwood II; Margaret Woodhouse; Ethalinda K. S. Cannon; Jack M. Gardiner; Lisa C. Harper; Mary L. Schaeffer; Jesse R. Walsh; Taner Z. Sen; Kyoung Tak Cho; David A. Schott; Bremen L. Braun; Miranda Dietze; et al. (Nucleic Acids Res., 2019)

FINDER: A fully automated pipeline to FIND accurate gene structures from proteins and RNA-Seq expression data. - Sagnik Banerjee; Margaret Woodhouse; Roger P. Wise; Priyanka Bhandary; Taner Z. Sen; Carson M. Andorf (BCB, 2020)

The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics (short paper). - Laurel Cooper; Marie-Angélique Laporte; Justin Elser; Victoria Carollo Blake; Taner Z. Sen; Chris Mungall; Elizabeth Arnaud; Pankaj Jaiswal (ICBO/ODLS, 2020)

JBrowse Connect: A server API to connect JBrowse instances and users. - Eric Yao; Robert M. Buels; Lincoln Stein; Taner Z. Sen; Ian H. Holmes (PLoS Comput. Biol., 2020)

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. - Sagnik Banerjee; Priyanka Bhandary; Margaret Woodhouse; Taner Z. Sen; Roger P. Wise; Carson M. Andorf (BMC Bioinform., 2021)

GrainGenes: a data-rich repository for small grains genetics and genomics. - Eric Yao; Victoria C. Blake; Laurel Cooper; Charlene P. Wight; Steve L. Michel; H. Busra Cagirici; Gerard R. Lazo; Clayton L. Birkett; David J. Waring; Jean-Luc Jannink; Ian H. Holmes; Amanda J. Waters; et al. (Database J. Biol. Databases Curation, 2022)

G4Boost: a machine learning-based tool for quadruplex identification and stability prediction. - H. Busra Cagirici; Hikmet Budak; Taner Z. Sen (BMC Bioinform., 2022)

Predicting Tissue-Specific mRNA and Protein Abundance in Maize: A Machine Learning Approach. - Kyoung Tak Cho; Taner Z. Sen; Carson M. Andorf (Frontiers Artif. Intell., 2022)

Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium. - Jennifer L. Clarke; Laurel D. Cooper; Monica F. Poelchau; Tanya Z. Berardini; Justin Elser; Andrew D. Farmer; Stephen P. Ficklin; Sunita Kumari; Marie-Angélique Laporte; Rex T. Nelson; Rie Sadohara; Peter Selby; et al. (Database J. Biol. Databases Curation, 2023)

Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data. - Elly Poretsky; Victoria C. Blake; Carson M. Andorf; Taner Z. Sen (Database J. Biol. Databases Curation, 2025)