NATIONAL ANIMAL GENOME RESEARCH PROGRAM
Bioinformatics Coordination Program
Published Papers
( 2003 — 2009 )

  1. A.M. Ramos, 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

  2. 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

  3. 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]

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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).

  14. 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.

  15. 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.

  16. 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".

  17. 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.

  18. 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: November 03, 2009
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Contact: NAGRP Bioinformatics Team 		November 22, 2009 (Sunday)