Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites. - Jill L. Wegrzyn; Thomas M. Drudge; Faramarz Valafar; Vivian Hook (BMC Bioinform., 2008)

PineSAP - sequence alignment and SNP identification pipeline. - Jill L. Wegrzyn; Jennifer M. Lee; John Liechty; David B. Neale (Bioinform., 2009)

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut. - Sandeep Chakraborty; Monica Britton; Jill L. Wegrzyn; Timothy Butterfield; Basuthkar J. Rao; Charles A. Leslie; Mallikarjuna Aradhaya; David B. Neale; Keith Woeste; Abhay Dandekar (F1000Research, 2015)

CartograTree: Enabling landscape genomics for forest trees. - Nic Herndon; Emily S. Grau; Iman Batra; Steven A. Demurjian; Hans A. Vasquez-Gross; Margaret E. Staton; Jill L. Wegrzyn (PeerJ Prepr., 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)

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)

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)

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)

gFACs: Gene Filtering, Analysis, and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks. - Madison Caballero; Jill L. Wegrzyn (Genom. Proteom. Bioinform., 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 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)