Liu S, Zhang Y, Zhou Z, Waldbieser G, Sun F, Lu J, Zhang J, Jiang Y, Zhang H, Wang X, Rajendran KV, Kucuktas H, Peatman E, Liu ZJ. (2013). Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote. BMC Genomics, in press.

Preziosa E, Liu S, Terova G, Gao X, Liu H, Kucuktas H, Terhune J, and Liu ZJ. (2013). Effect of Nutrient Restriction and Re-feeding on Calpain Family Genes in Skeletal Muscle of Channel Catfish (Ictalurus punctatus). PLoS One, in press.

Ninwichian P, Peatman E, Liu H, Kucuktas H, Somridhivej B, Liu S, Li P, Jiang Y, Sha Z, Kaltenboeck M, Abernathy J, Wang W, Chen F, Lee Y, Wong L, Wang S, Lu J, Liu ZJ. (2012). Second generation genetic linkage map and its integration with the BAC-based physical map in channel catfish. G3.2:1233-1241.

Sun F, Peatman E, Li C, Liu S, Jiang Y, Zhou Z, Liu ZJ. (2012). Transcriptomic signatures of attachment, NF-kB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection. Developmental and Comparative Immunology, 38:169-180.

Wang R, Li C, Stoeckel J, Moyer G, Liu ZJ, and Peatman E. (2012) . Rapid development of molecular resources for a freshwater mussel, Villosa lienosa (Bivalvia: Unionidae) using a RNA-seq-based approach. Freshwater Science 31(3):695-708.

Lu J, Peatman E, Tang H, Lewis J, Liu ZJ. (2012). Profiling of gene duplication patterns of teleost genomes: Evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications. BMC Genomics, 13:246.

Li C, Zhang Y, Wang R, Lu J, Nandi S, Mohanty S, Terhune J, Liu ZJ, Peatman E. (2012). RNA-Seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish & Shellfish Immunology, 32:816-827.

Rajendran KV, Zhang J, Liu S, Kucuktas H, Wang X, Liu H, Wood T, Terhune J, Peatman E, Liu ZJ. (2012). Pathogen recognition receptors in channel catfish: II. Identification, phylogeny and expression of retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), Developmental and Comparative Immunology, 37:381-389.

Browdy, C.L., Hulata, G., Liu, Z., Allan, G.L., Sommerville, C., Passos de Andrade, T., Pereira, R., Yarish, C., Shpigel, M., Chopin, T., Robinson, S., Avnimelech, Y. & Lovatelli, A. (2012). Novel and emerging technologies: can they contribute to improving aquaculture sustainability? In R.P. Subasinghe, J.R. Arthur, D.M. Bartley, S.S. De Silva, M. Halwart, N. Hishamunda, C.V. Mohan & P. Sorgeloos, eds. Farming the Waters for People and Food. Proceedings of the Global Conference on Aquaculture 2010, Phuket, Thailand. 22–25 September 2010. pp. 149–191. FAO, Rome and NACA, Bangkok.

Zhang H, Peatman E, Liu H, Feng T, Chen L, Liu ZJ. (2012). Molecular characterization of three L-type lectin genes from channel catfish, Ictalurus punctatus and their responses to Edwardsiella ictaluri challenge. Fish and Shellfish Immunology 32:598-608. doi: 10.1016/j.fsi.2011.12.009.

Rajendran KV, Zhang J, Liu Shikai, Kucuktas H, Wang X, Liu H, Sha Z, Terhune J, Peatman E, Liu ZJ. (2012). Pathogen recognition receptors in channel catfish: I. Identification, phylogeny and expression of NOD-like receptors. Developmental and Comparative Immunology 37:77-86.

Liu, S, Zhang Y, Sun F, Jiang Y, Wang R, Li C, Zhang J, Liu ZJ. (2012). Approaches for Functional Genomics in aquaculture. pp. 1-40. In: Functional Genomics in Aquaculture, Wiley and Blackwell Publishing, Ames, IA.

Zhang J, Jiang Y, Wang R, Li C, Zhang Y, Sun F, Liu, S, Liu ZJ. (2012). Chapter 2, Genomic resources for aquaculture functional genomics. pp. 41-77. In: Functional Genomics in Aquaculture, Wiley and Blackwell Publishing, Ames, IA..

Zhou Z, Liu H, Liu S, Sun F, Peatman E, Kucuktas H, Kaltenboeck L, Feng T, Zhang H, Niu D, Lu J, Waldbieser G, Liu ZJ. (2012). Alternative complement pathway of channel catfish (Ictalurus punctatus): molecular characterization, mapping and expression analysis of factors Bf/C2 and Df. Fish and Shellfish Immunology 32:186-195. doi:10.1016/j.fsi.2011.11.012.

Zhang H, Peatman E, Liu H, Niu D, Feng T, Kucuktas H, Waldbieser G, Chen L, Liu ZJ. (2012). Characterization of mannose-binding lectin from channel catfish (Ictalurus punctatus). Research in Veterinary Science 92:408-413.

Jiang Y, Lu J, Peatman E, Kucuktas H, Liu S, Wang S, Sun F, Liu ZJ. (2011). A Pilot study for channel catfish whole genome sequencing and de novo assembly. BMC Genomics, 12:629 doi:10.1186/1471-2164-12-629.

Ninwichian P, Peatman E, Perera D, Liu S, Kucuktas H, Dunham R, and Liu Z.J. (2011). Identification of a sex-linked marker for channel catfish. Animal Genetics, 43(4):476-477.

Feng T, Zhang H, Liu H, Zhou Z, Niu D, Wong L, Kucuktas H, Liu X, Peatman E, Liu ZJ. (2011). Molecular characterization and expression analysis of the channel catfish cathepsin D genes. Fish and Shellfish Immunology 31:164-169.

Niu D, 1, Peatman E, Liu H, Lu J, Kucuktas H, Liu S, Sun F, Zhang H, Feng T, Zhou Z, Terhune J, Waldbieser G, Li J, Liu ZJ. (2011). Microfibrillar-associated protein 4 (MFAP4) genes in catfish play a novel role in innate immune responses. Developmental and Comparative Immunology 35:568-579.

Feng T, Zhang H, Liu H, Zhou Z, Niu D, Wong L, Kucuktas H, Liu X, Peatman E, Liu Z. (2011) Molecular characterization and expression analysis of the channel catfish cathepsin D genes. Fish Shellfish Immunol., 31:164-169.

Zhang H, Peatman E, Liu H, Niu D, Feng T, Kucuktas H, Waldbieser G, Chen L, Liu Z. (2011) Characterization of a mannose-binding lectin from channel catfish (Ictalurus punctatus). Res Vet Sci. 92:408-413.

Wong LL, Peatman E, Lu J, Kucuktas H, He S, Zhou C, Na-nakorn U, Liu Z. (2011) DNA barcoding of catfish: species authentication and phylogenetic assessment. PLoS One. 6(3):e17812.

Liu S, Zhou Z, Lu J, Sun F, Wang S, Liu H, Jiang Y, Kucuktas H, Kaltenboeck L, Peatman E, Liu Z. (2011) Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics. 12:53.

Niu D, Peatman E, Liu H, Lu J, Kucuktas H, Liu S, Sun F, Zhang H, Feng T, Zhou Z, Terhune J, Waldbieser G, Li J, Liu Z. (2011) Microfibrillar-associated protein 4
(MFAP4) genes in catfish play a novel role in innate immune responses. Dev Comp Immunol. 35(5):568-79.

Liu H, Peatman E, Wang W, Abernathy J, Liu S, Kucuktas H, Terhune J, Xu DH, Klesius P, Liu Z. (2011) Molecular responses of ceruloplasmin to Edwardsiella ictaluri infection and iron overload in channel catfish (Ictalurus punctatus). Fish Shellfish Immunol. (3):992-7.

Liu H, Peatman E, Wang W, Abernathy J, Liu S, Kucuktas H, Lu J, Xu DH, Klesius P, Waldbieser G, Liu Z. (2011) Molecular responses of calreticulin genes to iron overload and bacterial challenge in channel catfish (Ictalurus punctatus). Dev Comp Immunol. 35(3):267-72.

Lu J, Peatman E, Yang Q, Wang S, Hu Z, Reecy J, Kucuktas H, Liu Z. (2011) The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish. Nucleic Acids Res. 2011 39 (Database issue): D815-21.

Liu W, Li H, Bao X, Gao X, Li Y, He C, and Liu ZJ. (2010). Genetic differentiation between natural and hatchery stocks of Japanese scallop (Mizuhopecten yessoensis) as revealed by AFLP analysis. International Journal of Molecular Sciences 11: 3933-3941. doi:10.3390/ijms11103933.

Liu ZJ. (2010). Genomic variations, marker technologies and their usefulness for genome-based selection. In: Next Generation Sequencing, SNPs, and Whole Genome Selection, Wiley and Blackwell Publishing, Ames, IA.

Lu J and Liu ZJ. (2010). Copy number variations (CNV) and whole genome selection. In: Next Generation Sequencing, SNPs, and Whole Genome Selection, Wiley and Blackwell Publishing, Ames, IA.

Kucuktas H and Liu ZJ. (2010). Construction of libraries for next generation sequencing. In: Next Generation Sequencing, SNPs, and Whole Genome Selection, Wiley and Blackwell Publishing, Ames, IA.

Wang S and Liu ZJ. (2010). SNP discovery through EST data mining. In: Next Generation Sequencing, SNPs, and Whole Genome Selection, Wiley and Blackwell Publishing, Ames, IA.

Wang S, Liu H, and Liu ZJ. (2010). SNP quality assessment. In: Next Generation Sequencing, SNPs, and Whole Genome Selection, Wiley and Blackwell Publishing, Ames, IA.

Wang S, Liu H, Bushek D, Ford S, Peatman E, Kucuktas H, Quilang J, Li P, Wallace R, Wang Y, Guo X, and Liu ZJ. (2010). Microarray analysis of gene expression in eastern oyster (Crassostrea virginica) reveals a novel combination of antimicrobial and oxidative stress host responses after dermo (Perkinsus marinus) challenge. Fish and Shellfish Immunology 29: 921-929.

Lu J, Peatman E, Yang Q, Wang S, Hu Z, Kucuktas H, Liu ZJ. (2010). Catfish Genome Database cBARBEL: A informatic platform for genome biology of ictalurid catfish. Nucleic Acids Research : 1-7, doi:10.1093/nar/gkq765.

Xu B, Wang S, Jiang Y, Yang L, Li P, Xie C, Xing J, Ke Z, Li J, Gai J, Yang G, Bao B, and Liu ZJ. (2010). Generation and analysis of ESTs from the grass carp, Ctenopharyngodon idellus. Animal Biotechnology 21: 1-9.

Chen F, Lee Y, Jiang Y, Wang S, Peatman E, Abernathy J, Liu H, Liu S, Kucuktas H, Ke C, Liu ZJ. (2010). Identification and characterization of full-length cDNAs in catfish (Ictalurus spp.). PLoS One 12, e11546.

Lu J, Peatman E, Wang W, Yang Q, Abernathy J, Wang S, Kucuktas H, Liu ZJ. (2010). Alternative splicing in teleost fish genomes: Same-species and cross-species analysis and comparisons. Molecular Genetics and Genomics 283:531–539.

Browdy C, Hulata G, Liu ZJ, Allan GL., Sommerville C, Passos de Andrade T, Pereira R, Yarish C, Shpigel M, Chopin T, Robinson S, Avnimelech Y. (2010). Novel and emerging technologies: can they contribute to improving aquaculture sustainability? UN FAO Expert paper, in press.

Liu ZJ. (2010). Development of genomic resources in support of sequencing, assembly, and annotation of the catfish genome. Comparative Biochemistry and Physiology, Part D, Genomics and Proteomics, in press. doi:10.1016/j.cbd.(2010).03.001.

Liu ZJ, Peatman E. (2010). Whole Genome Sequencing of Aquaculture Species: Identifying the Genotypes behind Production Phenotypes. Global Aquaculture Advocate, March/April (2010):68-70.

Liu H, Takano T, Peatman E, Abernathy J, Wang S, Sha Z, Kucuktas H, Liu ZJ. (2010). Molecular characterization and gene expression of the channel catfish ferritin H subunit after bacterial infection and iron treatment. Journal of Experimental Zoology, Part A: Ecological Genetics and Physiology 313:359-368.

Jiang Y, Abernathy J, Peatman E, Liu H, Wang S, Xu D-H, Kucuktas H, Klesius P, Liu Z.J. (2010). Identification and characterization of matrix metalloproteinase-13 sequence structure and expression during embryogenesis and infection in channel catfish (Ictalurus punctatus). Developmental and Comparative Immunology 34:590-597.

Sha Z, Wang S, Zhuang Z, Wang Q, Wang Q, Li P, Ding H, Wang N, Liu ZJ, Chen S. (2010). Generation and analysis of 10,000 ESTs from the half smooth tongue sole, Cynoglossus semilaevis and identification of microsatellite and SNP markers. Journal of Fish Biology 76:1190–1204.

Wang S, Abernathy J, Waldbieser G, Lindquist E, Richardson P, Lucas S, Wang M, Li P, Thimmapuram J, Liu L, Vullaganti D, Kucuktas H, Murdock C, Small B, Wilson M, Liu H, Jiang Y, Lee Y, Chen F, Lu J, Wang W, Peatman E, Xu P, Somridhivej B, Baoprasertkul P, Quilang J, Sha Z, Bao B, Wang Y, Wang Q, Takano T, Nandi S, Liu S, Wong L, Kaltenboeck L, Quiniou S, Bengten E, Miller N, Trant J, Rokhsar D, Liu ZJ., and Catfish Genome Consortium. (2010). Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biology 11 (1):R8.

Wang S, Zhang L, Hu J, Bao Z, Liu ZJ. (2010). Molecular and cellular evidence for biased mitotic gene conversion in hybrid scallop. BMC Evolutionary Biology 10:6. doi:10.1186/1471-2148-10-6.

Abernathy J, Peatman E, Liu ZJ. (2010). Basic Aquaculture Genetics, SRAC Publication No. 5001, 1-14.

Liu H, Takano T, Abernathy J, Wang S, Sha Z, Jiang Y, Terhune J, Kucuktas H, Peatman E, Liu ZJ. (2010) Structure and expression of transferrin gene of channel catfish, Ictalurus punctatus. Fish and Shellfish Immunity. 28:159-166.

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