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Li Y, Fu H, Zhang F, Ren L, Tian J, Li Q, Liu S#. Insulin-Like Peptide Receptor-Mediated Signaling Pathways Orchestrate Regulation of Growth in the Pacific Oyster (Crassostrea gigas), as Revealed by Gene Expression Profiles. International Journal of Molecular Sciences, 2021, 22:5259.Ren L, Li Y, Fu H, Zhang F, Yang B, Tan C, Li Q, Liu S#. A regulatory variant of tryptophan hydroxylase gene modulates transcription activity and biases growth rate in the Pacific oyster, Crassostrea gigas. Aquaculture, 2021, 542: 736906.Fu H, Jiao Z, Li Y, Tiang J, Ren L, Zhang F, Li Q, Liu S#. Transient Receptor Potential (TRP) Channels in the Pacific Oyster (Crassostrea gigas): Genome-Wide Identification and Expression Profiling after Heat Stress between C. gigasand C. angulata. International Journal of Molecular Sciences, 2021, 22(6):3222.Wang H, Yang B, Li X, Li Q, Liu S#. Screening of bacterial pathogens associated with mass summer mortality of the Pacific Oyster, Crassostrea gigas, in China. Aquaculture Reports, 2021, 20:100672Yang B, Zhai S, Li X, Li Q, Shan H, Liu S#. Identification of Vibrio alginolyticusas a causative pathogen associated with mass summer mortality of the Pacific Oyster (Crassostrea gigas) in China. Aquaculture, 2021, 535: 736363.Zhai S, Yang B, Zhang F, Li Q, Liu S#. Estimation of genetic parameters for resistance to Vibrio alginolyticusinfection in the Pacific oyster (Crassostrea gigas). Aquaculture, 2021, 736545.Doi: j.aquaculture.2021.736545Tian J, Jiao Z, Fu H, Qi L, Li Q, Liu N, Liu S#. Identification of cytochrome P450s and their expression profiles following cadmium exposure in the Pacific oyster, Crassostrea gigas. Aquaculture Reports, 2021, 19:100582.Han Z, Li Q, Xu C, Liu S, Yu, H, Kong L.QTL mapping for orange shell color and sex in the Pacific oyster (Crassostrea gigas). Aquaculture, 2021, 530, 735781.Chi Y, Li Q, Liu S, Kong L. Genetic parameters of growth and survival in the Pacific oyster,Crassostrea gigas, Aquaculture Research, 2021, 52:282–290.Li Y, Fu H, Zhang F, Ren L, Tiang J, Li Q, Liu S#. Identification, characterization, and expression profiles of insulin-like peptides suggest their critical roles in growth regulation of the Pacific oyster, Crassostrea gigas. Gene, 2021, 769: 145244.Yue C, Li Q, Yu H, Liu S, Kong L.Restriction site-associated DNA sequencing (RAD-seq) analysis in Pacific oyster Crassostrea gigasbased on observation of individual sex changes. Scientific Reports, 2020, 9873.Han Z, Li Q, Liu S, Kong L. Crossbreeding of three different shell color lines in the Pacific oyster reveals high heterosis for survival but low heterosis for
3growth. Aquaculture, 2020, 529, 735621.Zhang F, Hu B, Fu H, Jiao Z, Li Q#, Liu S#. Comparative transcriptome analysis reveals molecular basis underlying fast-growth of the selectively bred Pacific oyster, Crassostrea gigas. Frontiers in Genetics, 2019, 10:610.Bao L, Tian C, Liu S, Zhang Y, Elaswad A, Yuan Z, Khalil K, Sun F, Yang Y, Zhou T, Li N, Tan S, Zeng Q, Liu Y, Li Y, Li Y, Gao D, Dunham R, Davis K, Waldbieser G, Liu Z. The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish. BMC Biology, 2019, 17:6.Xu C, Li Q, Yu H, Liu S, Kong L, Chong J. Inheritance of shell pigmentation in Pacific oyster Crassostrea gigas. Aquaculture, 2019, 512:734249.Han Z, Li Q, Liu S, Yu H, Kong L. Genetic variability of an orange-shell mutant line of the Pacific oyster Crassostrea gigasduring artificial selection inferred from microsatellites and mitochondrial COI sequences. Aquaculture, 2019,508:159-166.Xu H, Li Q, Han Z, Liu S, Yu H, Kong L. Fertilization, survival and growth of hybrids between Crassostrea gigasand Crassostrea nippona. Aquaculture, 2019, 507(30):91-96.Zhang J, Li Q, Liu S, Yu H, Kong L. The effect of temperature on physiological energetics of a fast-growing selective strain and a hatchery population of the Pacific oyster (Crassostrea gigas). Aquaculture Research, 2018, 49:2844–2851.Zhou T, Li N, Jin Y, Zeng Q, Prabowo W, Liu Y, Tian C, Bao L, Liu S, Yuan Z, Fu Q, Gao S, Gao D, Dunham R, Shubin N, Liu Z. Chemokine C-C motif ligand 33 is a key regulator of teleost fish barbel development. PNAS, 2018, 115(22):E5018-E5027.Li N,Bao L,Zhou T,Yuan Z,Liu S,Dunham R,Li Y,Wang K,Xu X,Jin Y,Zeng Q,Gao S,Fu Q,Liu Y,Yang Y,Li Q,Meyer A,Gao D,Liu Z.Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation. BMC Genomics, 2018, 19:952.Gao S*, Liu S*, Yao J, Li N, Yuan Z, Zhou T, Li Q, Liu Z. Genomic Organization and Evolution of Olfactory Receptors and Trace Amine-Associated Receptors in Channel Catfish. BBA -General Subjects, 2017, 1861:644-651.Gao S*, Liu S*, Yao J, Zhou T, Li N, Li Q, Dunham R, Liu Z. Taste Receptors and Gustatory Associated G proteins in Channel Catfish. CBP -Part D: Genomics and Proteomics 2017, 21:1-9.Geng X, Liu S, Yuan Z, Jiang Y, Zhi D, Liu Z. A Genome-Wide Association Study Reveals That Genes with Functions for Bone Development Are Associated with Body Conformation in Catfish. Marine Biotechnology, 2017, 19:570-578.Li Y*, Liu S*, Qin Z, Yao J, Jiang C, Song L, Dunham R, Liu Z. The serpin superfamily in channel catfish: Identification, phylogenetic analysis and expression profiling in mucosal tissues after bacterial infection. Developmental and Comparative Immunology, 2015, 49(2), 267-277.Nunes J*, Liu S*, Pértille F, Perazza C, Val V, Hilsdorf A, Liu Z, Coutinho L. Large-
4scale SNP discovery and construction of a high-density genetic map ofColossoma macropomumthough genotyping-by-sequencing. Scientific Reports. 2017, 7:46112.Wang X, Liu S, Jiang C, Geng X, Zhou T, Li N, Bao L, Li Y, Yao J, Yang Y, Jin Y, Dunham R, Liu Z. Multiple across-strain and within-strain QTLs suggest highly complex genetic architecturefor hypoxia tolerance in channel catfish. Molecular Genetics and Genomics, 2017, 292:63-76.Zhou T, Liu S, GengX, Jin Y, Jiang C, Bao L, Yao J, Zhang Y, Zhang J, Sun L, Wang X, Li N, Tan S, Liu Z. GWAS analysis of QTL for enteric septicemia of catfish and their involved genes suggest evolutionary conservation of a molecular mechanism of disease resistance. Molecular Genetics and Genomics, 2017, 292(1):231-242.Li Y, Liu S, Wang R, Qin Z and Liu Z. 2017. Bioinformatic considerations and approaches for high-density Linkage Mapping in Aquaculture. In: Bioinformatics in Aquaculture: Principles and Methods, Wiley and Blackwell Publishing, Ames, IA (Ed. Liu Z). Ch20: 356-379.Liu Sand Liu Z. 2017. Analysis of microRNAs and their target genes. In: Bioinformatics in Aquaculture: Principles and Methods, Wiley and Blackwell Publishing, Ames, IA (Ed. Liu Z). Ch13: 200-227.Liu Sand Liu Z. 2017. Introduction to Linux and command line tools for bioinformatics. In: Bioinformatics in Aquaculture: Principles and Methods, Wiley and Blackwell Publishing, Ames, IA (Ed. Liu Z). Ch1: 3-29.Liu S*, Li Y*, Qin Z, Geng X, Bao L, Kaltenboeck L, Kucuktas H, Dunham R, Liu Z. High-density interspecific genetic linkage mapping provides insights into genomic incompatibility between channel catfish and blue catfish. Animal Genetics, 2016, 47:81-90.Liu S, Zeng P and Liu Z. 2017. Gene set analysis of SNP data from genome-wide association studies. In: Bioinformatics in Aquaculture: Principles and Methods, Wiley and Blackwell Publishing, Ames, IA (Ed. Liu Z). Ch24: 434-459.Liu S, Zeng Q, Wang X and Liu Z. 2017. SNP array development, genotyping, data analysis, and applications. In: Bioinformatics in Aquaculture: Principles and Methods, Wiley and Blackwell Publishing, Ames, IA (Ed. Liu Z). Ch18: 308-337.Liu Z*, Liu S*, Yao J*, Bao L*, Zhang J*, Li Y*, Jiang C, Sun L, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, Wang R, Koren S, Jiang Y, Zimin A, Xu P, Phillippy A, Geng X, Song L, Sun F, Li C, Wang X, Chen A, Jin Y, Yuan Z, Yang Y, Tan S, Peatman E, Lu J, Qin Z, Dunham R, Li Z, Sonstegard T, Feng J, Danzmann R, Schroeder S, Scheffler B, Duke M, Ballard L, Kucuktas H, Kaltenboeck L, Liu H, Armbruster J, Xie Y, Kirby M, Tian Y, Flanagan M, Mu W, Waldbieser G. The channel catfish genome sequence provides insights into evolution of scale formation in teleosts. Nature Communications, 2016, 7:11757.Yuan Z*, Liu S*, Yao J. Zeng Q, Tan S, Liu Z. Expression of Bcl-2 genes in channel catfish after bacterial infection and hypoxia stress. Developmental
5Comparative Immunology, 2016, 69:79-90.Zeng Q*, Liu S*, Yao J*, Zhang Y, Yuan Z, Jiang C, Chen A, Fu Q, Sun B, Dunham R, Liu Z. Transcriptome Display during Testicular Differentiation of Channel Catfish (Ictalurus punctatus) as Revealed by RNA-Seq Analysis. Biology of Reproduction, 2016, 95:19, 1-17.Liu S,Yao J, Zhang J, LiuZ. Next generation sequencing yields the complete mitochondrial genome of the striped raphael catfish, Platydoras armatulus(Siluriformes: Doradidae). Mitochondrial DNA, 2016, 27(3):1963-4.Liu S,Zhang J, Yao J, LiuZ. The complete mitochondrial genome of the armored catfish, Hypostomus plecostomus(Siluriformes: Loricariidae). Mitochondrial DNA, 2016, 27(3):1908-9.Jin Y, Liu S, Yuan Z, Yang Y, Tan S, Liu Z. 2015. Catfish genomic studies: Progress and perspectives. In: Genomics in Aquaculture, Elsevier (Eds.MacKenzie S and Jentoft S). Ch 4: 73-104.Li Y*, Liu S*, Qin Z, Waldbieser G, Wang R, Sun L, Bao L, Danzmann R, Dunham R, Liu Z. Construction of high-density SNP-based genetic map and its integration with BAC-based physical map in channel catfish. DNA Research, 2015, 22 (1): 39-52.Liu S*, Wang X*, Sun F, Zhang J, Feng J, Liu H, Rajendran KV, Sun L, Zhang Y, Jiang Y, Peatman E, Kaltenboeck L, KucuktasH and Liu Z. RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding and degradation in response to heat stress in catfish. Physiological Genomics, 2013, 45 (12):462-476.Liu S, Li Q, Liu Z. Genome-wide identification and evolutionary analysis of the ATP-binding cassette (ABC) transporter superfamily in catfish. PLoS ONE, 2013, 8(5): e63895.Liu S, Zhang Y, Sun F, Jiang Y, Wang R, Li C, Zhang J, Liu Z. 2012. Functional genomics research in aquaculture: principles and general approaches. In: Functional Genomics in Aquaculture, Wiley and Blackwell Publishing, Ames, IA (Eds. Saroglia M and Liu Z). Ch1: 1-40.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 Z. Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote. BMC Genomics. 2012, 13:595.Liu S, Zhou Z, Lu J, Sun F, Wang S, Liu H, Jiang Y, Kucuktas H, Kaltenboeck L, Peatman E, Liu Z. Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics. 2011, 12:53.
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