NATIONAL ANIMAL GENOME RESEARCH PROGRAM
Bioinformatics Coordination Program
Published Papers
( 2003 — 2010 )

  1. Oliver Couture, Keith Callenberg, Neeraj Koul, Sushain Pandit, Remy Younes, Zhi-Liang Hu, Jack Dekkers, James Reecy, Vasant Honavar, Christopher Tuggle (2009). ANEXdb: an integrated animal ANnotation and microarray EXpression database. Mamm Genome, DOI 10.1007/s00335-009-9234-1

  2. Ramos, A.M., R.P. Crooijmans, N.A. Affara, A.J. Amaral, A.L. Archibald, J.E. Beever, C. Bendixen, C. Churcher, R. Clark, P. Dehais, M.S. Hansen, J. Hedegaard, Z-L. Hu, H.H. Kerstens, A.S. Law, H-J. Megens, D. Milan, D.J. Nonneman, G.A. Rohrer, M.F. Rothschild, T.L. Smith, R.D. Schnabel, C.P. Van Tassell, J.F. Taylor, R.T. Wiedmann, L.B. Schook, M.A. M. Groenen. (2009) Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS ONE 4(8): e6524. doi:10.1371/journal.pone.0006524

  3. The Bovine Genome Sequencing and Analysis Consortium, C,G. Elsik, R.L. Tellam, K.C. Worley, et al (2009). The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science 24 April 2009: Vol.324. no.5926, pp.522-528

  4. Steibel JP, Wysocki M, Lunney JK, Ramos AM, Hu ZL, Rothschild MF, Ernst CW. (2009). Assessment of the swine protein-annotated oligonucleotide microarray. Anim Genet. 2009 Jun 8. [Epub ahead of print]

  5. James E Koltes, Zhi-Liang Hu, Eric Fritz and James M Reecy (2009). BEAP: The BLAST Extension and Alignment Program- a tool for contig construction and analysis of preliminary genome sequence. BMC Research Notes 2009, 2:11

  6. Zhi-Liang Hu, Jie Bao and James M. Reecy (2008). CateGOrizer: A Web-Based Program to Batch Analyze Gene Ontology Classification Categories". Online Journal of Bioinformatics. 9 (2):108-112.

  7. Bowen, Danielle M., Zhi-Liang Hu, Zhi-Qiang Du and M. F. Rothschild (2009) "SNP discovery in Litopenaeus vannamei with a new computational pipeline". Animal Genetics, 40, 106-109.

  8. Karlskov-Mortensen, Peter, Zhi-Liang Hu, James M. Reecy, Merete Fredholm (2008). A data resource of 838 porcine microsatellite sequences with repeat motifs of three to six bases. Animal Genetics. 39(1):85-86.

  9. Hughes L.M., Bao J., Zhi-Liang Hu, Honavar V. & Reecy J.M. (2008). Animal Trait Ontology (ATO): the importance and usefulness of a unified trait vocabulary for animal species. Journal of Animal Science, 86:1485-1491.

  10. Benjaporn Somridhivej, Shaolin Wang, Zhenxia Sha, Hong Liu, Jonas Quilang, Peng Xu, Ping Li, Zhi-Liang Hu, Zhanjiang Liu (2008). Characterization, polymorphism assessment, and database construction for microsatellites from BAC end sequences of channel catfish (Ictalurus punctatus): A resource for integration of linkage and physical maps. Aquaculture, 275 (2008) 76-80.

  11. Xiaoping Li, Zhi-Liang Hu, S-J. Moon, K-T Do, Y-K Ha, H. Kim, M. J. Byun, B-H Choi, M. F. Rothschild, J. M. Reecy and K-S. Kim (2007). Development and characterization of an in silico Coding Gene SNP map in pigs. Animal Genetics, 39(4): 446 - 450.

  12. Ting-Hua Huang, Bin Fan, Max F. Rothschild, Zhi-Liang Hu, Kui Li and Shu-Hong Zhao (2007). MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics, 8:341 doi:10.1186/1471-2105-8-341.

  13. Peter Karlskov-Mortensen, Zhi-Liang Hu, J. Gorodkin, James. M. Reecy, M. Fredholm (2007) Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences. Animal Genetics 38(4),401-405.

  14. Zhi-Liang Hu and James M. Reecy (2006). Animal QTLdb: Beyond a Repository - A Public Platform for QTL Comparisons and Integration with Diverse Types of Structural Genomic Information. Mammalian Genome, Volume 18, 1-4 (2007).

  15. Ramos, AM. Z-L. Hu, S. Humphay, J. Rogers, J. Reecy and M. F. Rothschild, (2006). Using Large Scale Porcine Genome Sequence Information to Find the Underlying Mutations Associated with Chromosome 17 QTL for Meat Quality. The 8th World Congress on Genetics Applied to Livestock Production (WCGALP), Belo Horizonte, Minas Gerais, Brazil, August 13-18, 2006.

  16. Zhi-Liang Hu, Eric Ryan Fritz and James M. Reecy (2006). AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Research, 2007, 35(Database issue):D604-D609; doi:10.1093/nar/gkl946.

  17. Bao, Jie, Zhi-Liang Hu, Doina Caragea, James Reecy, Vasant G Honavar (2006). "A Tool for Collaborative Construction of Large Biological Ontologies". The 4th International Workshop on Biological Data Management (BIDM'06) / 17th International Conference on Database and Expert Systems Applications (DEXA'06), pp. 191-195.

  18. Zhi-Liang Hu, James Reecy and Max Rothschild (2005). "A Quantitative Trait Loci Resource and Comparison Tool for Pigs: PigQTLDB". Iowa State "Animal Industry 2005 Report".

  19. Zhi-Liang Hu, Svetlana Dracheva, Wonhee Jang, Donna Maglott, John Bastiaansen, Max F. Rothschild and James M. Reecy (2005). "A QTL Resource and Comparison Tool for Pigs: PigQTLDB". Mammalian Genome. (2005) Volume 16(10):792-800.

  20. Zhi-Liang Hu, Kim Glenn, Antonio M. Ramos, Charles J. Otieno, Jim M. Reecy, and Max F. Rothschild (2005). "Expeditor: A Pipeline for Designing Primers Using Human Gene Structure and Livestock Animal EST Information". Journal of Heredity, Volume 96, Number 1, pp. 80-82.
Last updated: March 07, 2010
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Contact: NAGRP Bioinformatics Team 		March 18, 2010 (Thursday)