Collaborative works

1. Project: Visualization of genotype-tissue expression (GTEx) analysis data for expression profiling in different tissues sampled at different biological stages.
   Dates: July 8 - Dec. 27, 2022Online: Dec. 28, 2022
   Service type: Web tools, Data repository
   Collaborations:: Teng Jinyan, Lingzhao Fang

   Status: Success, online
2. Project: An inactive cytoscape tool for query/visulization of phenotypically related cattle traits by their underlining gene interactions discovered via functional genomics through integration of multi-omics data.
   Dates: Mar. 10 - Jul. 21, 2022 Online: Aug. 10, 2022
   Service type: Web tools, Data repository
   Collaborations: Hamid Beiki, James Reecy, Iowa State University, on a manuscript "Beiki et al. (2022). Functional genomics of cattle through integration of multi-omics data (Manuscript under preparation)"

   Status: Success, online
3. Project: JBrowse for cattle transcription factors alignments
   Dates: Feb. 10, 2018 - Apr. 07, 2018Online: Mar. 30, 2018
   Service type: Web tools, Data repository
   Collaborators: Marcela Maria de Souza and Luciana Correia de Almeida Regitano, Brazil
   Status: Success, online
4. Project: JBrowse for goat genome and featured track alignments
   Dates: Sep. 30, 2016 - Dec. 17, 2016Online: Oct. 10, 2016
   Service type: Web tools, Data repository
   Collaborators: Ben Rosen, USDA-ARS
   Status: Success, online
5. Project: CGCN - Discover gene connectivities using gene expression data from the NCBI GEO repository - a cattle gene data set from weighted correlation network analysis to calculate similarity between gene expression values based on "Topological Overlap Measure (TOM)".
   Dates: Feb. 10, 2016 - Nov. 10, 2016Online: Feb 23, 2016
   Service type: Web tools, Data repository
   Collaborators: Hamid Beiki, James Reecy, Iowa State University
   Status: Success, online
6. Project: Development of an EpiDB - Aims at providing gene and epigenetics expression data useful for dissecting quantitative trait data in livestock.
   Dates: Sept 23, 2012 - On-goingOnline: Feb 04, 2016
   Service type: Database/web site
   Collaborators: James Koltes, University of Arkansas
   Status: Success, online, in further progress.
7. Project: Hosting the OMIA - Online Mendelian Inheritance in Animals database
   Dates: Mar. 10, 2015 - Dec. 31, 2015 Online: Dec 27, 2016
   Service type: Database/web site, Virtual Machine host
   Collaborators: Frank Nicholas, Matthew Hobbs, Sydney University
   Status: Success, online
8. Project: Developing databases resources for the Striped Bass Genome Database
   Dates: Nov. 15, 2014 - On-going Online: April 7, 2016
   Service type: Virtual Machine
   Collaborators: Benjamin Reading and Charles H. Opperman, North Carolina State University
   Status: Success, online
9. Project: ISU Beef Project Database
   Dates: February 11, 2011. Online:July 28, 2014 - current
   Service type: Database/web site
   Collaborators: James Reecy
   Status: Completed, in service
10. Project: Cattle RH and Genome Coordinates Map Alignments
    Dates: September 2-12, 2013
    Service type: Web tool
    Collaborators: James Reecy
    Status: Success
11. Project: VCF Miner: A Platform and Tools for Collaborative Information Mining from Next-Generation Sequence Variant Data
    Dates: August 12, 2013 - Dec. 31, 2013
    Service type: Data repository / database
    Collaborators: Autumn Laughbaum, Carrie Finno, Claire Wade, Curt Van Tassell, Danika Bannasch, James Koltes, James Reecy, Jessica Petersen, Joern Wrede, Ludovic Orlando, Matthew McClure, Ottmar Distl, Robert D. Schnabel, Susan Lamont
    Status: Completed; transferred
12. Project: Blast Match of Query Sequences to Pig Genome Build 10.2 Genes by Their Map Locations -- A Pilot Analysis of 3 Pig Array Platforms
    Dates: May 12, 2012 - June 1, 2012
    Service type: Experimental data analysis
    Collaborator: Chris Tuggle, Iowa State University
    Status: Completed
13. Project: CRI-MAP Users Forum
    Dates: Ari, 16, 2013
    Collaborator: Jill Maddox, Australia
    Status: Completed, online
14. Project: Annotation comparisons between multiple arrays
    Dates: May 20, 2011 - June 15, 2011; Oct 10, 2011
    Collaborator: Chris Tuggle, Iowa State Univeristy; Bouabid Badaoui, CERSA, Italy
    Status: Completed
15. Project: Epigenetics Group: Listserv
    Dates: Jan, 26, 2013
    Collaborator: Hasan Khatib, University of Wisconsin-Madison
    Status: Completed, in service
16. Project: Oyster Scaffold Tracks for Predicted mRNA, CDS, etc.
    Dates: Feb, 13, 2013
    Collaborator: Steven Roberts of University of Washington
    Status: Success, online
17. Project: OMIA Support Group: listserv
    Dates: Jan, 19, 2013
    Collaborator: Frank Nicolas, The University of Sydney
    Status: Success: in service
18. Project: Pig Genome Database
    Dates: Apr. 2011 - 2014
    Status: Completed
19. Project: SheepModels Discussion Listserv
    Dates: Jan, 2012
    Collaborator: Jill Maddox, The University of Melbourne
    Status: Fullfilled
20. Project: Zebrafish Gbrowse
    Dates: Jan, 2011
    Collaborator: John Liu, Auburn Univeristy
    Status: Completed
21. Project: Ruminant Genome Biology Consortium
    Dates: Oct, 2010 - 2015
    Collaborator: Hutton Oddy, University of New England
    Status: Completed
22. Project: ANEXdb and AnnotDB
    Dates: Jan, 2007 - 2012
    Collaborator: Chris Tuggle, Iowa State University
    Status: Completed
23. Project: CRI-MAP Improvement website
    Dates: Sep, 2010
    Collaborator: Jill Maddox, Australia
    Status: Success, in service
24. Project: Teleost Alternative Splicing Database (TASD)
    Dates: Jun, 2010
    Collaborator: John Liu, Auburn Univeristy
    Status: Success, in service
25. Project: Catfish SNP Project (cBARBEL)
    Dates: Jan, 2010 - Dec. 2011
    Collaborator: John Liu, Auburn Univeristy
    Status: Completed
26. Project: Characterization of the rainbow trout transcriptome
    Dates: Jun, 2010
    Collaborators: Moh Salem (West Virginia University)
    Status: Success, in service
27. Project: A pig gene wish list for annotation
    Dates: Nov, 2009 - Sep, 2010
    Collaborator: The Pig Gene Annotation Consortium
    Status: Completed
28. Project: Striped Bass Ovarian Transcriptome Sequence Database
    Dates: Oct, 2009
    Collaborators: Craig Sullivan (NCSU) and Robert Chapman (DNR)
    Status: Success, in service
29. Project: Map of INRA Pig Oligo Sequence to Pig Genome
    Dates: Jan - Feb, 2009
    Collaborators: Yu Gao and Claire Rogel-Gaillard (INRA)
    Status: Success
30. Project: MSU PRP Database
    Dates: Feb - May, 2009
    Collaborator: Cathy Ernst (MSU)
    Status: Inactive
    Status: Inactive
31. Project: Linkage Maps of Rainbow Trout
    Dates: Feb - Apr, 2009
    Collaborator: Caird Rexroad (ARS, USDA)
    Status: Success, online
32. Project: Pig Oligo Array Annotations
    Dates: Aug - Nov, 2008
    Collaborators: Joan Lunney (USDA), Juan Steibel and Cathy Ernst (MSU)
    Status: Success, results published
33. Project: Berk-York QTL Project Database
    Dates: Aug - Oct, 2008
    Collaborator: Max Rothschild, Iowa State University
    Status: Complete, in service
34. Project: PRRS Host Genomic Consortium (PHGC) Database
    Dates: Jun, 2008 - On-going
    Collaborators: Joan Lunney (USDA), JP Steibel (MSU), Max Rothschild (ISU), Raymond Rowland (KSU)
    Status: Success, in service
35. Project: Compiled Pig Public SNP data (May - Jul, 2008)
    Collaborators: Pig 60K SNP Chip Consortium, Martien Groenen et al., Wageningen University
    Status: Completed
36. Project: Lush Geneticists Pedigree
    Dates: Dec, 2007 - Current
    Collaborator: Jack Dekkers, Iowa State University
    Status: Completed
37. Project: SNP Discoveries in shrimp ( Monodon, Vaname and Combined)
    Dates: Jul - Nov, 2007
    Collaborator: Max Rothschild, Iowa State University
    Status: Completed
38. Project: Automated pig genome sequencing progress track
    Dates: Jan, 2005
    Collaborator: Max Rothschild, Iowa State University
    Status: Completed