Stephen P. Ficklin

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 22

Top Topics

Interactive Visual

Software Platform

Scientific Data Analysis

Top Venues

Database J. Biol. Databases Curation

Nucleic Acids Res.

Briefings Bioinform.

Publications

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, Anne E. Thessen, Brandon Whitehead, Taner Z. Sen
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium. Database J. Biol. Databases Curation 2023 (2023)
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, Anne E. Thessen, Brandon Whitehead, Taner Z. Sen
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the AgBioData Consortium. CoRR (2023)
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
GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure. BMC Bioinform. 23 (1) (2022)
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
Addressing noise in co-expression network construction. Briefings Bioinform. 23 (1) (2022)
Cameron Ogle, David Reddick, Coleman McKnight, Tyler Biggs, Rini Pauly, Stephen P. Ficklin, F. Alex Feltus, Susmit Shannigrahi
Named Data Networking for Genomics Data Management and Integrated Workflows. Frontiers Big Data 4 (2021)
Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill L. Wegrzyn, Tavis Anderson, Sean Buehler, Irene Cobo-Simón, Kay Faaberg, Emily S. Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski, Sook Jung, Kelly Lager, Dorrie Main, Monica Poelchau, Risharde Ramnath, Peter Richter, Joe West, Stephen P. Ficklin
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. Briefings Bioinform. 22 (6) (2021)
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, F. Alex Feltus, Stephen P. Ficklin
Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases. Database J. Biol. Databases Curation 2020 (2020)
Bradford Condon, Abdullah Almsaeed, Sean Buehler, Christopher P. Childers, Stephen P. Ficklin, Margaret E. Staton, Monica Poelchau
Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata. Database J. Biol. Databases Curation 2020 (2020)
Benjamin T. Shealy, Josh J. R. Burns, Melissa C. Smith, F. Alex Feltus, Stephen P. Ficklin
GPU Implementation of Pairwise Gaussian Mixture Models for Multi-Modal Gene Co-Expression Networks. IEEE Access 7 (2019)
Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi L. Humann, Stephen P. Ficklin, Ksenija Gasic, Kristin Scott, Morgan Frank, Sushan Ru, Heidi Hough, Kate Evans, Cameron Peace, Mercy A. Olmstead, Lisa W. DeVetter, James McFerson, Michael Coe, Jill L. Wegrzyn, Margaret E. Staton, Albert G. Abbott, Dorrie Main
15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Res. 47 (Database-Issue) (2019)
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, Jill L. Wegrzyn, F. Alex Feltus, Stephen P. Ficklin
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. Database J. Biol. Databases Curation 2019 (2019)
Taylor Falk, Nic Herndon, Emily S. Grau, Sean Buehler, Peter Richter, Sumaira Zaman, Eliza M. Baker, Risharde Ramnath, Stephen P. Ficklin, Margaret Staton, Frank Alex Feltus, Sook Jung, Doreen Main, Jill L. Wegrzyn
Growing and cultivating the forest genomics database, TreeGenes. Database J. Biol. Databases Curation 2019 (2019)
Katheryn Buble, Sook Jung, Jodi L. Humann, Jing Yu, Chun-Huai Cheng, Taein Lee, Stephen P. Ficklin, Heidi Hough, Bradford Condon, Margaret E. Staton, Jill L. Wegrzyn, Dorrie Main
Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps. Database J. Biol. Databases Curation 2019 (2019)
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, Bradford Condon, Laurel Cooper, Nathan A. Dunn, Christine G. Elsik, Andrew Farmer, Stephen P. Ficklin, David Grant, Emily S. Grau, Nic Herndon, Zhi-Liang Hu, Jodi L. Humann, Pankaj Jaiswal, Clément Jonquet, Marie-Angélique Laporte, Pierre Larmande, Gerard R. Lazo, Fiona McCarthy, Naama Menda, Christopher J. Mungall, Monica C. Munoz-Torres, Sushma Naithani, Rex T. Nelson, Daureen Nesdill, Carissa A. Park, James M. Reecy, Leonore Reiser, Lacey-Anne Sanderson, Taner Z. Sen, Margaret Staton, Sabarinath Subramaniam, Marcela Karey Tello-Ruiz, Victor Unda, Deepak R. Unni, Liya Wang, Doreen Ware, Jill L. Wegrzyn, Jason Williams, Margaret Woodhouse, Jing Yu, Doreen Main
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database J. Biol. Databases Curation 2018 (2018)
Xuechen Zhang, Ujjwal Khanal, Xinghui Zhao, Stephen P. Ficklin
Making sense of performance in in-memory computing frameworks for scientific data analysis: A case study of the spark system. J. Parallel Distributed Comput. 120 (2018)
Taylor Falk, Nic Herndon, Emily S. Grau, Sean Buehler, Peter Richter, Sumaira Zaman, Eliza M. Baker, Risharde Ramnath, Stephen P. Ficklin, Margaret Staton, Frank Alex Feltus, Sook Jung, Doreen Main, Jill L. Wegrzyn
Growing and cultivating the forest genomics database, TreeGenes. Database J. Biol. Databases Curation 2018 (2018)
Connor Wytko, Brian Soto, Stephen P. Ficklin
blend4php: a PHP API for galaxy. Database J. Biol. Databases Curation 2017 (2017)
Ming Chen, Nathan Henry, Abdullah Almsaeed, Xiao Zhou, Jill L. Wegrzyn, Stephen P. Ficklin, Margaret Staton
New extension software modules to enhance searching and display of transcriptome data in Tripal databases. Database J. Biol. Databases Curation 2017 (2017)
Sook Jung, Taein Lee, Chun-Huai Cheng, Stephen P. Ficklin, Jing Yu, Jodi L. Humann, Dorrie Main
Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases. Database J. Biol. Databases Curation 2017 (2017)
Xuechen Zhang, Ujjwal Khanal, Xinghui Zhao, Stephen P. Ficklin
Understanding Software Platforms for In-Memory Scientific Data Analysis: A Case Study of the Spark System. ICPADS (2016)
Sook Jung, Taein Lee, Stephen P. Ficklin, Jing Yu, Chun-Huai Cheng, Dorrie Main
Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. Database J. Biol. Databases Curation 2016 (2016)
Sook Jung, Taein Lee, Stephen P. Ficklin, Jing Yu, Chun-Huai Cheng, Dorrie Main
Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. Database J. Biol. Databases Curation 2016 (2016)
Jing Yu, Sook Jung, Chun-Huai Cheng, Stephen P. Ficklin, Taein Lee, Ping Zheng, Don Jones, Richard G. Percy, Dorrie Main
CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Res. 42 (Database-Issue) (2014)
Sook Jung, Stephen P. Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Ping Zheng, Jing Yu, Aureliano Bombarely, Ilhyung Cho, Sushan Ru, Kate Evans, Cameron Peace, Albert G. Abbott, Lukas A. Mueller, Mercy A. Olmstead, Dorrie Main
The Genome Database for Rosaceae (GDR): year 10 update. Nucleic Acids Res. 42 (Database-Issue) (2014)
F. Alex Feltus, Stephen P. Ficklin, Scott M. Gibson, Melissa C. Smith
Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. BMC Syst. Biol. 7 (2013)
Lacey-Anne Sanderson, Stephen P. Ficklin, Chun-Huai Cheng, Sook Jung, F. Alex Feltus, Kirstin E. Bett, Dorrie Main
Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. Database J. Biol. Databases Curation 2013 (2013)
Stephen P. Ficklin, Lacey-Anne Sanderson, Chun-Huai Cheng, Margaret Staton, Taein Lee, Ilhyung Cho, Sook Jung, Kirstin E. Bett, Doreen Main
Tripal: a construction toolkit for online genome databases. Database J. Biol. Databases Curation 2011 (2011)
Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen P. Ficklin, Ilhyung Cho, Albert G. Abbott, Jeffrey Tomkins, Dorrie Main
osaceae): integrated web resources for Rosaceae genomics and genetics research. BMC Bioinform. 5 (2004)
Timothy A. Davis, Stephen P. Ficklin
Interactive Dynamic Environments Using Image-Based Modeling and Rendering. Eurographics (Short Presentations) (2003)