National Animal Genome Research Program
Bioinformatics Coordination Program
Published Papers
( 2003 — 2024 )

  1. Hamid Beiki, Brenda M Murdoch, Carissa A Park, Chandlar Kern, Denise Kontechy, Gabrielle Becker, Gonzalo Rincon, Honglin Jiang, Huaijun Zhou, Jacob Thorne, James E Koltes, Jennifer J Michal, Kimberly Davenport, Monique Rijnkels, Pablo J Ross, Rui Hu, Sarah Corum, Stephanie McKay, Timothy P L Smith, Wansheng Liu, Wenzhi Ma, Xiaohui Zhang, Xiaoqing Xu, Xuelei Han, Zhihua Jiang, Zhi-Liang Hu, James M Reecy. (2024). Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology. GigaScience, Volume 13, 2024, giae019.

  2. Zhi-Liang Hu, Carissa A Park, James M Reecy (2023). A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants. Database, Volume 2023, 2023, baad024. DOI:10.1093/database/baad024.

  3. Hamid Beiki, Brenda M. Murdoch, Carissa A. Park, Chandlar Kern, Denise Kontechy, Gabrielle Becker, Gonzalo Rincon, Honglin Jiang, View ORCID ProfileHuaijun Zhou, Jacob Thorne, James E. Koltes, Jennifer J. Michal, Kimberly Davenport, Monique Rijnkels, View ORCID ProfilePablo J. Ross, Rui Hu, Sarah Corum, Stephanie McKay, Timothy P.L. Smith, Wansheng Liu, Wenzhi Ma, Xiaohui Zhang, Xiaoqing Xu, Xuelei Han, Zhihua Jiang, Zhi-Liang Hu, James M. Reecy. (2022). Functional genomics of cattle through integration of multi-omics data. bioRxiv 2022.10.05.510963; doi: https://doi.org/10.1101/2022.10.05.510963.

  4. Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2022). A database structural improvement for efficient trait variation curation in Animal QTLdb and CorrDB. The 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, The Neatherlands, 3-8 July 2022.

  5. Surya Saha, Scott Cain, Ethalinda K. S. Cannon, Nathan Dunn, Andrew Farmer, Zhi-Liang Hu, Gareth Maslen, Sierra Moxon, Christopher J Mungall, Rex Nelson, Monica F. Poelchau (2022). Recommendations for extending the GFF3 specification for improved interoperability of genomic data. arXiv:2202.07782 [q-bio.OT].

  6. Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2022). Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services. Nucleic Acids Research, Volume 50, Issue D1, pages D956-D961.

  7. Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2019). Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB. Nucleic Acids Research, Volume 47, Issue D1, January 8, 2019, Pages D701–D710.

  8. Lisa Harper, Jacqueline Campbell, Ethalinda Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson, Bradford Condon, Laurel Cooper, Nathan Dunn, Christine G Elsik, Andrew Farmer, Stephen P Ficklin, David Grant, Emily Grau, Nic Herndon, Zhi-Liang Hu, ... (2018). AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database,1:1–32.

  9. Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2018). Development of Animal QTLdb and CorrDB: Resynthesizing Big Data to Improve Meta-analysis of Genetic and Genomic Information. The 11th World Congress on Genetics Applied to Livestock Production (WCGALP). New Zealand, February 7-16, 2018.

  10. Hamid Beiki, Ardeshir Nejati-Javaremi, Abbas Pakdel, Ali Masoudi-Nejad, Zhi-Liang Hu and James M Reecy. (2016). Large-scale gene co-expression network as a source of functional annotation for cattle genes. BMC Genomics, 2016, 17:846.

  11. Zhi-Liang Hu, Carissa A. Park and James M. Reecy (2016). Developmental progress and current status of the Animal QTLdb. Nucleic Acids Research, 44 (D1): D827-D833.

  12. Carissa A Park, Susan M Bello, Cynthia L Smith, Zhi-Liang Hu, Diane H Munzenmaier, Rajni Nigam, Jennifer R Smith, Mary Shimoyama, Janan T Eppig and James M Reecy. (2013) The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. Journal of Biomedical Semantics 2013, 4(1):13.

  13. Harry D Dawson, Jane E Loveland, Geraldine Pascal, James GR Gilbert, Hirohide Uenishi, Katherine M Mann, Yongming Sang, Jie Zhang, Denise Carvalho-Silva, Toby Hunt, Matthew Hardy, Zhi-Liang Hu, Shu-Hong Zhao, ... Claire Rogel-Gaillard* and Christopher K Tuggle (2013). Structural and functional annotation of the porcine immunome. BMC Genomics 2013, 14:332.

  14. Bouabid Badaoui, Christopher K Tuggle, Zhi-Liang Hu, James M Reecy, Tahar Ait-Ali, Anna Anselmo and Sara Botti (2013). Pig immune response to general stimulus and to porcine reproductive and respiratory syndrome virus infection: a meta-analysis approach. BMC Genomics 2013, 14:220; doi:10.1186/ 1471-2164-14-220.

  15. Zhi-Liang Hu, Carissa A. Park, Xiao-Lin Wu and James M. Reecy (2012). Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Research, 41 (D1): D871-D879.

  16. Martien Groenen, Alan Archibald, Hirohide Uenishi, Christopher Tuggle, Yasuhiro Takeuchi, Max Rothschild, Claire Rogel-Gaillard, Chankyu Park, Denis Milan, Hendrik-Jan Megens, Shengting Li, Denis Larkin, et al. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393-398 (15 November 2012).

  17. Endale Ahanda ML, Fritz ER, Estellé, Zhi-Liang Hu, Madsen O, Groenen MA, Beraldi D, Kapetanovic R, Hume DA, Rowland RR, Lunney JK, Rogel-Gaillard C, Reecy JM, Giuffra E. (2012). Prediction of Altered 3'-UTR miRNA-Binding Sites from RNA-Seq Data: The Swine Leukocyte Antigen Complex (SLA) as a Model Region. PLoS One. 2012;7(11).

  18. Marie-Laure Endale Ahanda, Eric R Fritz, Jordi Estellé, Zhi-Liang Hu, Ole Madsen, Martien AM Groenen, Dario Beraldi, Ronan Kapetanovic, David A Hume, Robert RR Rowland, Joan K Lunney, Claire Rogel-Gaillard, James M Reecy, Elisabetta Giuffra (2012). Prediction of Altered 3'-UTR miRNA-Binding Sites from RNA-Seq Data: The Swine Leukocyte Antigen Complex (SLA) as a Model Region. PLoS One. 2012; 7(11):e48607. doi: 10.1371/journal.pone.0048607. Epub 2012 Nov 6.

  19. Zhi-Liang Hu, James E Koltes, Carissa A. Park, Eric R. Fritz and James M. Reecy (2011). Review: Bioinformatics approaches to livestock animal genomics research. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 2011 6, No. 044.

  20. Zhi-Liang Hu, Antonio M. Ramos, Sean J. Humphray, Jane Rogers, James M. Reecy and Max F. Rothschild. (2011). Use of Genome Sequence Information for Meat Quality Trait QTL Mining for Causal Genes and Mutations on Pig Chromosome 17. Frontiers in Livestock Genomics, 2:43. doi: 10.3389/fgene.2011.00043.

  21. Xiao-Lin Wu, Daniel Gianola, Zhi-Liang Hu and James M. Reecy (2011). Meta-Analysis of Quantitative Trait Association and Mapping Studies using Parametric and Non-Parametric Models. Biometrics & Biostatistics, J Biomet Biostat 2011, S1. doi: 10.4172/2155-6180.S1-001.

  22. Zhi-Liang Hu, Xiao-Lin Wu and James M. Reecy (2011). Extension of Animal QTLdb: QTL Meta-analysis on the Fly. Poster paper published on ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), August 1-3, 2011, Chicago, IL, USA.

  23. Jianguo Lu, Eric Peatman, Qing Yang, Shaolin Wang, Zhi-Liang Hu, James Reecy, Huseyin Kucuktas and Zhanjiang Liu (2011). The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish. Nucleic Acids Res., 39 (supp. 1): D815-821.

  24. Gorbach, Danielle M, Zhi-Liang Hu, ZhiQiang Du, Max F. Rothschild (2010). Mining ESTs to determine the usefulness of SNPs across shrimp species. Anim Biotechnol. 2010 Apr;21 (2):100-3.

  25. Zhi-Liang Hu, Carissa A. Park, Eric R. Fritz and James M. Reecy (2010). QTLdb: A Comprehensive Database Tool Building Bridges between Genotypes and Phenotypes. Invited Lecture with full paper published electronically on The 9th World Congress on Genetics Applied to Livestock Production (WCGALP). Leipzig, Germany August 1-6, 2010.

  26. Yu Gao, Laurence Flori, Jerome Lecardonnel, Diane Esquerre, Zhi-Liang Hu, Angelique Teillaud, Gaetan Lemonnier, Francois Lefevre, Isabelle P Oswald and Claire Rogel-Gaillard (2010). Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response. BMC Genomics 2010, 11:292.

  27. 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

  28. 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

  29. 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

  30. 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]

  31. 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

  32. 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.

  33. 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.

  34. 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.

  35. 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.

  36. 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.

  37. 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.

  38. 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.

  39. 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.

  40. 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).

  41. 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.

  42. Zhi-Liang Hu, Eric Ryan Fritz and James M. Reecy (2007). AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Research, 35 (suppl 1): D604-D609.

  43. 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.

  44. 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".

  45. 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.

  46. 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: (Dec 31, 1969)


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