Publications

Wang F, Ren J, Zhou Y, Huo W, Liu H, Qin M, et al (2026). Cross-species comparison of amniote single-cell transcriptomes reveals evolutionary conservation and divergence in the chicken immune system. NAT COMMUN, 10-1038.

Li Z, Sun Y, Sun D, Yang N, Yin Z, Hou Z (2026). Comprehensive multi-omics reveals dynamic chromatin changes and gene regulatory networks during duck folliculogenesis. J ANIM SCI BIOTECHNO, 17(1), 79.

Sun Y, Li Z, Jie Y, Yang N, Yin Z, Hou Z (2026). Single-cell transcriptomics reveal mechanisms of skeletal muscle differentiation across duck embryonic development. COMMUN BIOL, 9(1), 404.

You G, Jiang T, Li H, Dong W, Zhao X, Zhang S, et al (2025). Genetic Basis of Egg Production in Baicheng-You Chickens: A Genome-Wide Association Study. Animals, 15(23), 3360.

Yan D, Zhu F, Wang H, Yin Z, Hou Z (2025). Comprehensive duck DNA fingerprinting based on machine learning for breed identification. POULTRY SCI, 104(8), 105359.

Fang L, Teng J, Lin Q, Bai Z, Liu S, Guan D, et al (2025). The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project. NAT GENET, 57(4), 786-96.

Zhao Q, Zhu F, Hou Z (2025). Reply to: The genomic structure of complex chromosomal rearrangement at the Fm locus in black-bone Silkie chicken. COMMUN BIOL, 8(1), 536.

Zhao Q, Yin Z, Hou Z (2025). Near telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and missing genes in birds. J ANIM SCI BIOTECHNO, 16(1), 9.

Gu Y, Wu K, Niu B, Wang Z, Jie Y, Fan Z, et al (2025). Hyperthermia suppresses the biological characteristics and migration of chicken primordial germ cells. Frontiers in genome editing, 6, 1512108.

Yang Y, Yin Z, Lin X, Zhao C, Yang F, Chen F, et al (2025). Research note: Whole-genome sequencing revealed genomic diversity dynamics in duck conserved populations. POULTRY SCI, 104(1), 104509.

Ren J, Kou W, Xu Y, Lu M, Gong M, Zhang X, et al (2025). Pan-genome analyses add ∼1000 genes to the complete genome assembly of chicken. Journal of genetics and genomics, 52(1), 116-9.

Gu S, Gao J, Li Z, Zhang S, Wen C, Sun C, et al (2024). Comparative Analysis of Myofiber Characteristics, Shear Force, and Amino Acid Contents in Slow- and Fast-Growing Broilers. Foods (Basel, Switzerland), 13(24), 3997.

Sun D, Liu Y, Li X, Ge M, Zhu M, He Y, et al (2024). Transcriptional activity and variation analysis of genes critical for long-chain fatty acid (C≥16) elongation and desaturation in Pekin ducks. POULTRY SCI, 103(12), 104437.

Yu J, Zhou J, Yang F, Hao J, Hou Z, Zhu F (2024). Genome-wide association analysis identifies candidate genes for carcass yields in Peking ducks. ANIM GENET, 55(6), 833-7.

Sun D, Li X, Liu Y, Ge M, Hou Z (2024). The Application of Duck Embryonic Fibroblasts CCL-141 as a Cell Model for Adipogenesis. Animals : an open access journal from MDPI, 14(20), 2973.

Wang Z, Zhao M, Su Y, Zhao Q, Ma Z, Yue Q, et al (2024). The impact of NUMB on chicken abdominal adipogenesis: A comprehensive analysis. INT J BIOL MACROMOL, 278(Pt 3), 134904.

Yu J, Zhou J, Yang F, Hao J, Hou Z, Zhu F (2024). Genome-Wide Association Analysis Identifies Important Haplotypes and Candidate Gene XKR4 for Body Size Traits in Pekin Ducks. Animals : an open access journal from MDPI, 14(16), 2349.

Guo B, Yan L, Tang Y, Du J, Dai Z, Liu J, et al (2024). Green Light Mitigates Cyclic Chronic Heat-Stress-Induced Liver Oxidative Stress and Inflammation via NF-κB Pathway Inhibition in Geese. Antioxidants (Basel, Switzerland), 13(7), 772.

Zhou J, Yu J, Zhu M, Yang F, Hao J, He Y, et al (2024). Genome-Wide Association Analysis and Genetic Parameters for Egg Production Traits in Peking Ducks. Animals : an open access journal from MDPI, 14(13), 1891.

Li X, Sun D, Wang Z, Zhao Q, Liu Y, Hou Z (2024). Transcriptional regulatory mechanism of NR2F2 and ZNF423 in avian preadipocyte differentiation. GENE, 897, 148106.

Wang Z, Su Y, Zhao M, Ma Z, Li J, Hou Z, et al (2024). NOTCH1 as a Negative Regulator of Avian Adipocyte Differentiation: Implications for Fat Deposition. Animals : an open access journal from MDPI, 14(4), 585.

Sun C, Lan F, Zhou Q, Guo X, Jin J, Wen C, et al (2024). Mechanisms of hepatic steatosis in chickens: integrated analysis of the host genome, molecular phenomics and gut microbiome. GIGASCIENCE, 13, giae23.

Sun C, Lan F, Zhou Q, Guo X, Jin J, Wen C, et al (2024). Correction to: mechanisms of hepatic steatosis in chickens: integrated analysis of the host genome, molecular phenomics and gut microbiome. GIGASCIENCE, 13, giae69.

Yin Z, Li X, Sun Y, Smith J, Hincke M, Yang N, et al (2023). Selection on the promoter regions plays an important role in complex traits during duck domestication. BMC BIOL, 21(1), 303.

Zhu F, Yin Z, Zhao Q, Sun Y, Jie Y, Smith J, et al (2023). A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes. COMMUN BIOL, 6(1), 1233.

Liu Y, Sun D, Li X, Ge M, Hou Z (2023). Research Note: Identification of core promoter region of the polyunsaturated fatty acid synthesis-related gene family in chicken. POULTRY SCI, 102(9), 102857.

Li X, Zhang F, Sun Y, Sun D, Yang F, Liu Y, et al (2023). A novel candidate gene CLN8 regulates fat deposition in avian. J ANIM SCI BIOTECHNO, 14(1), 70.

Sun Y, Sang Q, Yin Z, Zhang F, Zhu F, Hou Z (2023). Genome-wide association study identified the candidate genes associated with angel wing trait in Pekin duck. ANIM GENET, 54(2), 211-5.

Li Z, Sang Q, Sun Y, Liu Y, Hou Z (2023). Exploring the effect of the microbiota on the production of duck striped eggs. POULTRY SCI, 102(3), 102436.

Xu M, Gu L, Lv W, Duan S, Li L, Du Y, et al (2022). Chromosome-level genome assembly of the Muscovy duck provides insight into fatty liver susceptibility. GENOMICS, 114(6), 110518.

Lv H, Wang T, Zhai S, Hou Z, Chen S (2022). Dynamic transcriptome changes during osteogenic differentiation of bone marrow-derived mesenchymal stem cells isolated from chicken. FRONT CELL DEV BIOL, 10, 940248.

Yue Y, Ren L, Zhang C, Miao K, Tan K, Yang Q, et al (2022). Mitochondrial genome undergoes de novo DNA methylation that protects mtDNA against oxidative damage during the peri-implantation window. P NATL ACAD SCI USA, 119(30), e2093799177.

Smith J, Alfieri JM, Anthony N, Arensburger P, Athrey GN, Balacco J, et al (2022). Fourth Report on Chicken Genes and Chromosomes 2022. CYTOGENET GENOME RES, 162(8-9), 405-528.

Sun D, Li X, Yin Z, Hou Z (2021). The Full-Length Transcriptome Provides New Insights Into the Transcript Complexity of Abdominal Adipose and Subcutaneous Adipose in Pekin Ducks. FRONT PHYSIOL, 12, 767739.

Zhu F, Yin Z, Wang Z, Smith J, Zhang F, Martin F, et al (2021). Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. NAT COMMUN, 12(1), 5932.

Zhao P, Zheng X, Yu Y, Hou Z, Diao C, Wang H, et al (2021). Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation. Genomics, proteomics & bioinformatics, 19(5), 772-86.

Qin F, Wang X, Ding S, Li G, Hou Z (2021). Prediction of Peking duck intramuscle fat content by near-infrared spectroscopy. POULTRY SCI, 100(8), 101281.

Lv H, Huang Y, Wang T, Zhai S, Hou Z, Chen S (2021). Microbial Composition in the Duodenum and Ileum of Yellow Broilers With High and Low Feed Efficiency. FRONT MICROBIOL, 12, 689653.

Ding S, Li G, Chen S, Zhu F, Hao J, Yang F, et al (2021). Comparison of carcass and meat quality traits between lean and fat Pekin ducks. ANIM BIOSCI, 34(7), 1193-201.

Li G, Zhu F, Zhang F, Yang F, Hao J, Hou Z (2021). Genome-wide association study reveals novel loci associated with feeding behavior in Pekin ducks. BMC GENOMICS, 22(1), 334.

Wang Z, Zhao Q, Li X, Yin Z, Chen S, Wu S, et al (2021). MYOD1 inhibits avian adipocyte differentiation via miRNA-206/KLF4 axis. J ANIM SCI BIOTECHNO, 12(1), 55.

Li G, Liu W, Zhang F, Zhu F, Yang F, Hao J, et al (2020). Genome-wide association study of bone quality and feed efficiency-related traits in Pekin ducks. GENOMICS, 112(6), 5021-8.

Zhang F, Yin Z, Zhang J, Zhu F, Hincke M, Yang N, et al (2020). Integrating transcriptome, proteome and QTL data to discover functionally important genes for duck eggshell and albumen formation. GENOMICS, 112(5), 3687-95.

Li G, Zhu F, Yang F, Hao J, Hou Z (2020). Selection response and genetic parameter estimation of feeding behavior traits in Pekin ducks. POULTRY SCI, 99(5), 2375-84.

Yin Z, Lian L, Zhu F, Zhang Z, Hincke M, Yang N, et al (2020). The transcriptome landscapes of ovary and three oviduct segments during chicken (Gallus gallus) egg formation. GENOMICS, 112(1), 243-51.

Zhu F, Cui Q, Yang Y, Hao J, Yang F, Hou Z (2020). Genome-wide association study of the level of blood components in Pekin ducks. GENOMICS, 112(1), 379-87.

Yin Z, Zhang F, Smith J, Kuo R, Hou Z (2019). Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos. SCI DATA, 6(1), 275.

Xing K, Zhao X, Ao H, Chen S, Yang T, Tan Z, et al (2019). Transcriptome analysis of miRNA and mRNA in the livers of pigs with highly diverged backfat thickness. SCI REP-UK, 9(1), 16740.

Yan W, Sun C, Zheng J, Wen C, Ji C, Zhang D, et al (2019). Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota. FRONT MICROBIOL, 10, 2126.

Wang Z, Yin Z, Zhang F, Li X, Chen S, Yang N, et al (2019). Dynamics of transcriptome changes during subcutaneous preadipocyte differentiation in ducks. BMC GENOMICS, 20(1), 688.

Zhu F, Cheng S, Yang Y, Hao J, Yang F, Hou Z (2019). Genome-Wide Association Study of Growth and Feeding Traits in Pekin Ducks. FRONT GENET, 10, 702.

Chen X, Li X, He Z, Hou Z, Xu G, Yang N, et al (2019). Comparative study of eggshell antibacterial effectivity in precocial and altricial birds using Escherichia coli. PLOS ONE, 14(7), e220054.

Zhu F, Zhang F, Hincke M, Yin Z, Chen S, Yang N, et al (2019). iTRAQ-Based Quantitative Proteomic Analysis of Duck Eggshell During Biomineralization. PROTEOMICS, 19(11), e1900011.

Yin Z, Zhu F, Lin F, Jia T, Wang Z, Sun D, et al (2019). Revisiting avian 'missing' genes from de novo assembled transcripts. BMC GENOMICS, 20(1), 4.

Deng M, Zhu F, Yang Y, Yang F, Hao J, Chen S, et al (2019). Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks. BMC GENOMICS, 20(1), 1.

Hou Z, An L, Han J, Yuan Y, Chen D, Tian J (2018). Revolutionize livestock breeding in the future: an animal embryo-stem cell breeding system in a dish. J ANIM SCI BIOTECHNO, 9, 90.

Gao Y, Li X, Wang D, Zheng C, Hou Z, Ning Z (2018). Genetic parameters and characterization of egg content spreading area in White Leghorn chickens. POULTRY SCI, 97(10), 3429-34.

Lin F, Zhu F, Hao J, Yang F, Hou Z (2018). In vivo prediction of the carcass fatness using live body measurements in Pekin ducks. POULTRY SCI, 97(7), 2365-71.

Wu Y, Zhang Y, Hou Z, Fan G, Pi J, Sun S, et al (2018). Population genomic data reveal genes related to important traits of quail. GIGASCIENCE, 7(5), giy49.

Xie S, Yang X, Wang D, Zhu F, Yang N, Hou Z, et al (2018). Thyroid transcriptome analysis reveals different adaptive responses to cold environmental conditions between two chicken breeds. PLOS ONE, 13(1), e191096.

Weckle A, McGowen MR, Xing J, Chen C, Sterner KN, Hou Z, et al (2017). Ancestral resurrection of anthropoid estrogen receptor β demonstrates functional consequences of positive selection. MOL PHYLOGENET EVOL, 117, 2-9.

Zhu F, Gao Y, Lin F, Hao J, Yang F, Hou Z (2017). Systematic analysis of feeding behaviors and their effects on feed efficiency in Pekin ducks. J ANIM SCI BIOTECHNO, 8, 81.

Shi S, Shen Y, Zhang S, Zhao Z, Hou Z, Zhou H, et al (2017). Combinatory Evaluation of Transcriptome and Metabolome Profiles of Low Temperature-induced Resistant Ascites Syndrome in Broiler Chickens. SCI REP-UK, 7(1), 2389.

Wang D, Li Y, Liu L, Liu J, Bao M, Yang N, et al (2017). Traits of eggshells and shell membranes of translucent eggs. POULTRY SCI, 96(5), 1514.

Wang D, Li Y, Liu L, Liu J, Bao M, Yang N, et al (2017). Traits of eggshells and shell membranes of translucent eggs. POULTRY SCI, 96(2), 351-8.

Liu L, Fan Y, Zhang Z, Yang C, Geng T, Gong D, et al (2017). Analysis of gene expression and regulation implicates C2H9orf152 has an important role in calcium metabolism and chicken reproduction. ANIM REPROD SCI, 176, 1-10.

Zhu F, Cui Q, Hou Z (2016). SNP discovery and genotyping using Genotyping-by-Sequencing in Pekin ducks. SCI REP-UK, 6, 36223.

Jin S, Zhu F, Wang Y, Yi G, Li J, Lian L, et al (2016). Deletion of Indian hedgehog gene causes dominant semi-lethal Creeper trait in chicken. SCI REP-UK, 6, 30172.

Tan K, An L, Miao K, Ren L, Hou Z, Tao L, et al (2016). Impaired imprinted X chromosome inactivation is responsible for the skewed sex ratio following in vitro fertilization. P NATL ACAD SCI USA, 113(12), 3197-202.

Xing K, Zhu F, Zhai L, Chen S, Tan Z, Sun Y, et al (2016). Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data. SCI REP-UK, 6, 23219.

Lipovich L, Hou Z, Jia H, Sinkler C, McGowen M, Sterner KN, et al (2016). High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. The Journal of comparative neurology, 524(2), 288-308.

Zhu F, Yuan J, Zhang Z, Hao J, Yang Y, Hu S, et al (2015). De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks. ANIM GENET, 46(6), 636-45.

Zhao H, Sui L, Miao K, An L, Wang D, Hou Z, et al (2015). Comparative analysis between endometrial proteomes of pregnant and non-pregnant ewes during the peri-implantation period. J ANIM SCI BIOTECHNO, 6(1), 18.

Xing K, Zhu F, Zhai L, Liu H, Wang Y, Wang Z, et al (2015). Integration of transcriptome and whole genomic resequencing data to identify key genes affecting swine fat deposition. PLOS ONE, 10(4), e122396.

Sui L, An L, Tan K, Wang Z, Wang S, Miao K, et al (2014). Dynamic proteomic profiles of in vivo- and in vitro-produced mouse postimplantation extraembryonic tissues and placentas. BIOL REPROD, 91(6), 155.

Li G, Li D, Yang N, Qu L, Hou Z, Zheng J, et al (2014). A genome-wide association study identifies novel single nucleotide polymorphisms associated with dermal shank pigmentation in chickens. POULTRY SCI, 93(12), 2983-7.

Shi S, Shen Y, Zhao Z, Hou Z, Yang Y, Zhou H, et al (2014). Integrative analysis of transcriptomic and metabolomic profiling of ascites syndrome in broiler chickens induced by low temperature. Molecular bioSystems, 10(11), 2984-93.

Xing K, Zhu F, Zhai L, Liu H, Wang Z, Hou Z, et al (2014). The liver transcriptome of two full-sibling Songliao black pigs with extreme differences in backfat thickness. J ANIM SCI BIOTECHNO, 5(1), 32.

Zhang Q, Liu L, Zhu F, Ning Z, Hincke MT, Yang N, et al (2014). Integrating de novo transcriptome assembly and cloning to obtain chicken Ovocleidin-17 full-length cDNA. PLOS ONE, 9(3), e93452.

Wang Y, Wang C, Hou Z, Miao K, Zhao H, Wang R, et al (2013). Comparative analysis of proteomic profiles between endometrial caruncular and intercaruncular areas in ewes during the peri-implantation period. J ANIM SCI BIOTECHNO, 4(1), 39.

Fan Y, Hou Z, Yi G, Xu G, Yang N (2013). The sodium channel gene family is specifically expressed in hen uterus and associated with eggshell quality traits. BMC GENET, 14, 90.

Nie J, An L, Miao K, Hou Z, Yu Y, Tan K, et al (2013). Comparative analysis of dynamic proteomic profiles between in vivo and in vitro produced mouse embryos during postimplantation period. J PROTEOME RES, 12(9), 3843-56.

Yang Y, Hou Z, Qian Y, Kang H, Zeng Q (2012). Increasing the data size to accurately reconstruct the phylogenetic relationships between nine subgroups of the Drosophila melanogaster species group (Drosophilidae, Diptera). MOL PHYLOGENET EVOL, 62(1), 214-23.

Hou Z, Sterner KN, Romero R, Than NG, Gonzalez JM, Weckle A, et al (2012). Elephant transcriptome provides insights into the evolution of eutherian placentation. GENOME BIOL EVOL, 4(5), 713-25.

Jameson NM, Hou Z, Sterner KN, Weckle A, Goodman M, Steiper ME, et al (2011). Genomic data reject the hypothesis of a prosimian primate clade. J HUM EVOL, 61(3), 295-305.

Wildman DE, Uddin M, Romero R, Gonzalez JM, Than NG, Murphy J, et al (2011). Spontaneous abortion and preterm labor and delivery in nonhuman primates: evidence from a captive colony of chimpanzees (Pan troglodytes). PLOS ONE, 6(9), e24509.

Goodman M, Sterner KN, Islam M, Uddin M, Sherwood CC, Hof PR, et al (2009). Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries. P NATL ACAD SCI USA, 106(49), 20824-9.

Qu L, Liu W, Yang F, Hou Z, Zheng J, Xu G, et al (2009). Origin and domestication history of Peking ducks deltermined through microsatellite and mitochondrial marker analysis. Science in China. Series C, Life sciences, 52(11), 1030-5.

Hou Z, Romero R, Wildman DE (2009). Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data. MOL PHYLOGENET EVOL, 52(3), 660-4.

Hou Z, Yang N, Li J, Xu G (2009). Egg quality prediction by using Fourier transform near infrared reflectance spectroscopy (FT-NIR). Guang pu xue yu guang pu fen xi = Guang pu, 29(8), 2063-6.

Than NG, Romero R, Goodman M, Weckle A, Xing J, Dong Z, et al (2009). A primate subfamily of galectins expressed at the maternal-fetal interface that promote immune cell death. P NATL ACAD SCI USA, 106(24), 9731-6.

Hou Z, Romero R, Uddin M, Than NG, Wildman DE (2009). Adaptive history of single copy genes highly expressed in the term human placenta. GENOMICS, 93(1), 33-41.

Than NG, Romero R, Erez O, Weckle A, Tarca AL, Hotra J, et al (2008). Emergence of hormonal and redox regulation of galectin-1 in placental mammals: implication in maternal-fetal immune tolerance. P NATL ACAD SCI USA, 105(41), 15819-24.

Hou Z, Xu G, Su Z, Yang N (2007). Purifying selection and positive selection on the myxovirus resistance gene in mammals and chickens. GENE, 396(1), 188-95.

Qu L, Li X, Xu G, Chen K, Yang H, Zhang L, et al (2006). Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers. Science in China. Series C, Life sciences, 49(4), 332-41.

Hou Z, Yang N (2003). Factors affecting codon usage in Yersinia pestis. Sheng wu hua xue yu sheng wu wu li xue bao Acta biochimica et biophysica Sinica, 35(6), 580-6.

Hou Z, Yang N (2002). Analysis of factors shaping S. pneumoniae codon usage. Yi chuan xue bao = Acta genetica Sinica, 29(8), 747-52.

Hou Z, Yang N (2002). Advances in major histocompatibility complex research in poultry. Yi chuan = Hereditas, 24(1), 72-6.