Stephen P. Ficklin

According to our database, Stephen P. Ficklin authored at least 27 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

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, Anne E. Thessen, Brandon Whitehead, Taner Z. Sen

Database J. Biol. Databases Curation, 2023

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

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

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

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, Sook Jung, Kelly Lager, Dorrie Main, Monica Poelchau, Risharde Ramnath, Peter Richter, Joe West, Stephen P. Ficklin

Briefings Bioinform., 2021

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, F. Alex Feltus, Stephen P. Ficklin

Database J. Biol. Databases Curation, 2020

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

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, 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

Nucleic Acids Res., 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, Jill L. Wegrzyn, F. Alex Feltus, Stephen P. Ficklin

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, Sumaira Zaman, Eliza M. Baker, Risharde Ramnath, Stephen P. Ficklin, Margaret Staton, Frank Alex Feltus, Sook Jung, Doreen Main, Jill L. Wegrzyn

Database J. Biol. Databases Curation, 2019

Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps.

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

Database J. Biol. Databases Curation, 2019

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

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

Proceedings of the Application of Semantic Technology in Biodiversity Science, 2018

Making sense of performance in in-memory computing frameworks for scientific data analysis: A case study of the spark system.

Xuechen Zhang, Ujjwal Khanal, Xinghui Zhao, Stephen P. Ficklin

J. Parallel Distributed Comput., 2018

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, Bradford Condon, Laurel Cooper, Nathan A. Dunn, Christine G. Elsik, Andrew D. Farmer, Stephen P. Ficklin, David M. 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

Database J. Biol. Databases Curation, 2018

2017

blend4php: a PHP API for galaxy.

Connor Wytko, Brian Soto, Stephen P. Ficklin

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, Jodi L. Humann, Dorrie Main

Database J. Biol. Databases Curation, 2017

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

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, Chun-Huai Cheng, Dorrie Main

Database J. Biol. Databases Curation, 2016

Understanding Software Platforms for In-Memory Scientific Data Analysis: A Case Study of the Spark System.

Xuechen Zhang, Ujjwal Khanal, Xinghui Zhao, Stephen P. Ficklin

Proceedings of the 22nd IEEE International Conference on Parallel and Distributed Systems, 2016

2014

CottonGen: a genomics, genetics and breeding database for cotton research.

Jing Yu, Sook Jung, Chun-Huai Cheng, Stephen P. Ficklin, Taein Lee, Ping Zheng, Don Jones, Richard G. Percy, Dorrie Main

Nucleic Acids Res., 2014

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, Aureliano Bombarely, Ilhyung Cho, Sushan Ru, Kate Evans, Cameron Peace, Albert G. Abbott, Lukas A. Mueller, Mercy A. Olmstead, Dorrie Main

Nucleic Acids Res., 2014

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

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

2011

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

2004

GDR (<i>G</i>enome <i>D</i>atabase for <i>R</i>osaceae): 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

2003

Interactive Dynamic Environments Using Image-Based Modeling and Rendering.

Timothy A. Davis, Stephen P. Ficklin

Proceedings of the 24th Annual Conference of the European Association for Computer Graphics, 2003