Interactive Dynamic Environments Using Image-Based Modeling and Rendering. - Timothy A. Davis 002; Stephen P. Ficklin (Eurographics (Short Presentations), 2003)

GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research. - Sook Jung; Christopher Jesudurai; Margaret Staton; Zhidian Du; Stephen P. Ficklin; Ilhyung Cho; Albert G. Abbott; Jeffrey Tomkins; Dorrie Main (BMC Bioinform., 2004)

Tripal: a construction toolkit for online genome databases. - Stephen P. Ficklin; Lacey-Anne Sanderson; Chun-Huai Cheng; Margaret Staton; Taein Lee; Ilhyung Cho; Sook Jung; Kirstin E. Bett; Doreen Main (Database J. Biol. Databases Curation, 2011)

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. - Lacey-Anne Sanderson; Stephen P. Ficklin; Chun-Huai Cheng; Sook Jung; F. Alex Feltus; Kirstin E. Bett; Dorrie Main (Database J. Biol. Databases Curation, 2013)

Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. - F. Alex Feltus; Stephen P. Ficklin; Scott M. Gibson; Melissa C. Smith (BMC Syst. Biol., 2013)

The Genome Database for Rosaceae (GDR): year 10 update. - Sook Jung; Stephen P. Ficklin; Taein Lee; Chun-Huai Cheng; Anna Blenda; Ping Zheng; Jing Yu 002; Aureliano Bombarely; Ilhyung Cho; Sushan Ru; Kate Evans; Cameron Peace; et al. (Nucleic Acids Res., 2014)

CottonGen: a genomics, genetics and breeding database for cotton research. - Jing Yu 002; Sook Jung; Chun-Huai Cheng; Stephen P. Ficklin; Taein Lee; Ping Zheng; Don Jones; Richard G. Percy; Dorrie Main (Nucleic Acids Res., 2014)

Understanding Software Platforms for In-Memory Scientific Data Analysis: A Case Study of the Spark System. - Xuechen Zhang 001; Ujjwal Khanal; Xinghui Zhao; Stephen P. Ficklin (ICPADS, 2016)

Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. - Sook Jung; Taein Lee; Stephen P. Ficklin; Jing Yu 002; Chun-Huai Cheng; Dorrie Main (Database J. Biol. Databases Curation, 2016)

New extension software modules to enhance searching and display of transcriptome data in Tripal databases. - Ming Chen; Nathan Henry; Abdullah Almsaeed; Xiao Zhou; Jill L. Wegrzyn; Stephen P. Ficklin; Margaret Staton (Database J. Biol. Databases Curation, 2017)

Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases. - Sook Jung; Taein Lee; Chun-Huai Cheng; Stephen P. Ficklin; Jing Yu 002; Jodi L. Humann; Dorrie Main (Database J. Biol. Databases Curation, 2017)

blend4php: a PHP API for galaxy. - Connor Wytko; Brian Soto; Stephen P. Ficklin (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)

Making sense of performance in in-memory computing frameworks for scientific data analysis: A case study of the spark system. - Xuechen Zhang 001; Ujjwal Khanal; Xinghui Zhao; Stephen P. Ficklin (J. Parallel Distributed Comput., 2018)

Association Mapping for Forest Trees with CartograTree. - Nic Herndon; Taylor Falk; Emily S. Grau; Sook Jung; Stephen P. Ficklin; Dorrie Main; Margaret E. Staton; Jill L. Wegrzyn (Application of Semantic Technology in Biodiversity Science, 2018)

GPU Implementation of Pairwise Gaussian Mixture Models for Multi-Modal Gene Co-Expression Networks. - Benjamin T. Shealy; Josh J. R. Burns; Melissa C. Smith; F. Alex Feltus; Stephen P. Ficklin (IEEE Access, 2019)

Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps. - Katheryn Buble; Sook Jung; Jodi L. Humann; Jing Yu 002; Chun-Huai Cheng; Taein Lee; Stephen P. Ficklin; Heidi Hough; Bradford Condon; Margaret E. Staton; Jill L. Wegrzyn; Dorrie Main (Database J. Biol. Databases Curation, 2019)

Growing and cultivating the forest genomics database, TreeGenes. - Taylor Falk; Nic Herndon; Emily S. Grau; Sean Buehler; Peter Richter 001; Sumaira Zaman; Eliza M. Baker; Risharde Ramnath; Stephen P. Ficklin; Margaret Staton; Frank Alex Feltus; Sook Jung; et al. (Database J. Biol. Databases Curation, 2019)

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. - Shawna Spoor; Chun-Huai Cheng; Lacey-Anne Sanderson; Bradford Condon; Abdullah Almsaeed; Ming Chen; Anthony Bretaudeau; Helena Rasche; Sook Jung; Dorrie Main; Kirstin E. Bett; Margaret Staton; et al. (Database J. Biol. Databases Curation, 2019)

15 years of GDR: New data and functionality in the Genome Database for Rosaceae. - Sook Jung; Taein Lee; Chun-Huai Cheng; Katheryn Buble; Ping Zheng; Jing Yu 002; Jodi L. Humann; Stephen P. Ficklin; Ksenija Gasic; Kristin Scott; Morgan Frank; Sushan Ru; et al. (Nucleic Acids Res., 2019)

Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata. - Bradford Condon; Abdullah Almsaeed; Sean Buehler; Christopher P. Childers; Stephen P. Ficklin; Margaret E. Staton; Monica Poelchau (Database J. Biol. Databases Curation, 2020)

Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases. - Shawna Spoor; Connor Wytko; Brian Soto; Ming Chen; Abdullah Almsaeed; Bradford Condon; Nic Herndon; Heidi Hough; Sook Jung; Meg Staton; Jill L. Wegrzyn; Dorrie Main; et al. (Database J. Biol. Databases Curation, 2020)

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. - Margaret Staton; Ethalinda Cannon; Lacey-Anne Sanderson; Jill L. Wegrzyn; Tavis K. Anderson; Sean Buehler; Irene Cobo-Simón; Kay Faaberg; Emily S. Grau; Valentin Guignon; Jessica Gunoskey; Blake Inderski; et al. (Briefings Bioinform., 2021)

Named Data Networking for Genomics Data Management and Integrated Workflows. - Cameron Ogle; David Reddick; Coleman McKnight; Tyler Biggs; Rini Pauly; Stephen P. Ficklin; F. Alex Feltus; Susmit Shannigrahi (Frontiers Big Data, 2021)

Addressing noise in co-expression network construction. - Josh J. R. Burns; Benjamin T. Shealy; Mitchell S. Greer; John A. Hadish; Matthew McGowan; Tyler Biggs; Melissa C. Smith; F. Alex Feltus; Stephen P. Ficklin (Briefings Bioinform., 2022)

GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure. - John A. Hadish; Tyler Biggs; Benjamin T. Shealy; M. Reed Bender; Coleman McKnight; Connor Wytko; Melissa C. Smith; F. Alex Feltus; Loren A. Honaas; Stephen P. Ficklin (BMC Bioinform., 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)