2024

1. Yu H^#, Li Y ^#*, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S^*. (2024) Pan-evolutionary and regulatory genome architecture delineated by integrated macro- and microsynteny approach. Nature Protocols.  https://doi.org/10.1038/s41596-024-00966-4. (Behind the Paper: PanSyn: Elucidation of Pan-evolutionary and Regulatory Genome Architecture)

2. Wei J^#, Zhang W^#, Jiang A^#, Peng H^#, Zhang Q^#, Li Y, Bi J, Wang L, Liu P, Wang J, Ge Y, Zhang L, Yu H, Li L, Wang S, Leng L^*, Chen K^*, Dong B^*. (2024) Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids. Nature Communications. 15: 2395.

3. Jiang A^#, Han K^#, Wei J^#, Su X^#, Wang R, Zhang W, Liu X, Qiao J, Liu P, Liu Q, Zhang J, Zhang N, Ge Y, Zhuang Y, Yu H, Wang S, Chen K, Lu W, Xu X, Yang H, Fan G^*, Dong B^*. (2024) Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs. Science Advances. 10(13): eadi9035.

4. Cai Y^#, Lv J^#, Li R^#, Huang X, Wang S, Bao Z, Zeng Q*.(2024) Deqformer: High-definition and scalable deep learning probe design method. Briefings in Bioinformatics. 25(2): 1–9.
5. Ren L, Li S, Ye W, Lv Q, Sun Y, Zhou X, Lian S, Lv J, Wang S, Guo J, Tian Y, Zheng R, Lu Y*.(2024) Tracking organic matrix in the seashell by elemental mapping under laser-induced breakdown spectroscopy.Talanta. 271: 125658.
6. He X, Liao Y, Yang Z, Liu H, Wang S, Bao Y*.(2024) A genome-wide association study to identify the genes associated with growth-related traits in Tegillarca granosa. Aquaculture. 578: 740127.

2023

1. Wei J^#, Liu P^#, Liu F^#, Jiang A, Qiao J, Pu Z, Wang B, Zhang J, Jia D, Li Y*, Wang S*, Dong B*. (2023) EDomics: a comprehensive and comparative multi-omics database for animal evo-devo. Nucleic Acids Research. 51(D1): D913–D923.

2. Zhu X, Zhang J, Li M, Hou X, Liu A, Dong X, Wang W, Xing Q*, Huang X, Wang S, Hu J, Bao Z.(2023) Cardiac performance and heart gene network provide dynamic responses of bay scallop Argopecten irradians irradians exposure to marine heatwaves. Science of The Total Environment. 882: 163594.

3. Zhang W, Zhang Y, Shi X, Wang S, Bao Y*. (2023) Hemoglobin wonders: A fascinating gas transporter diving into molluscs. Critical Reviews in Biochemistry and Molecular Biology. 58(2–6): 132–157.

4. Liu T, Wei H, Zhang L, Liu L, Li Y, Shu Y, Yang Y, Zhao B, Xing Q, Zeng Q, Wang C, Wang S, Bao Z, Zhang L*.(2023) K252a inhibition of sperm viability for efficient crossbreeding of hermaphroditic bivalves. Aquaculture. 577: 739930.

5. Lu M^#, Hayat R^#, Zhang X^#, Jiao Y, Huang J, Huangfu Y, Jiang M, Fu J, Jiang Q, Gu Y, Wang S, Akerberg A A, Su Y*, Zhao L*.(2023) Comparative analysis of the cardiac structure and transcriptome of scallop and snail, perspectives on heart chamber evolution. Marine Life Science & Technology.5(4): 478–491. 

6. Li Y, Wang Y, Wang S, Zheng R, Bao Z, Lu Y*. (2023) Preliminary study of laser-induced breakdown spectroscopy for Mg/Ca investigation in cultured scallop shells. Journal of Laser Applications. 35: 022018.

2022

1. Han W^#, Liu L^#, Wang J^#, Wei H^#, Li Y^#, Zhang L^#, Guo Z, Li Y, Liu T, Zeng Q, Xing Q, Shu Y, Wang T, Yang Y, Zhang M, Li R, Yu J, Pu Z, Lv J, Lian S, Hu J, Hu X, Bao Z, Bao L^*, Zhang L^*, Wang S^*. (2022) Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation. Nature Ecology & Evolution. 6: 1891-1906. (Cover Story; Behind the Paper: The 'forever-young' secret of scallop sex chromosomes: exceptions to the 'general' rules)
2. Thimmappa R*, Wang S^#, Zheng M^#, Misra RC, Huang AC, Saalbach G, Chang Y, Zhou Z, Hinman V, Bao Z, Osbourn A^*. (2022) Biosynthesis of saponin defensive compounds in sea cucumbers. Nature Chemical Biology. 18:774-781.(AAAS EurekAlert News)
3. Sun Z^#, Huang S^#,*, Zhu P, Tzehau L, Zhao H, Lv J, Zhang R, Zhou L, Niu Q, Wang X, Zhang M, Jing G, Bao Z, Liu J, Wang S^*, Xu J^*. (2022) Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M. Genome Biology. 23: 36. (AAAS EurekAlert News)
4. Liu P^#, Lv J^#,*, Ma C, Zhang T, Huang X, Yang Z, Zhang L, Hu J, Wang S, Bao Z^*. (2022) Targeted genotyping of a whole-gene repertoire by an ultrahigh-multiplex and flexible HD-Marker approach. Engineering. 13:186-196.
5. Li Y^#, Liu Y^#, Yu H, Liu F, Han W, Zeng Q, Zhang Y, Zhang L, Hu J, Bao Z, Wang S^*. (2022) Adaptive bird-like genome miniaturization during the evolution of scallop swimming lifestyle. Genomics Proteomics & Bioinformatics. 20: 1066-1077. (Cover Story)
6. Li Y, Liu L, Zhang L, Wei H, Wu S, Liu T, Shu Y, Yang Y, Yang Z, Wang S, Bao Z, Zhang L*. (2022) Dynamic transcriptome analysis reveals the gene network of gonadal development from the early history life stages in dwarf surfclam Mulinia lateralis. Biology of Sex Differences. 13: 69.
7. Lv J^#, Wang Y^#,*, Ni P, Lin P, Hou H, Ding J*, Chang Y*, Hu J*, Wang S, Bao Z. (2022) Development of a high-throughput SNP array for sea cucumber (Apostichopus japonicus) and its application in genomic selection with MCP regularized deep neural networks. Genomics. 114: 110426.
8. Dai X^#, Zhu X^#, Bao L^#, Chen X, Miao Y, Li Y, Li Y, Lv J, Zhang L, Huang X, Bao Z, Wang S*, Wang J*. (2022) Decoding the byssus fabrication by spatiotemporal secretome analysis of scallop foot. Computational and Structural Biotechnology Journal. 20: 2713-2722.
9. Liu T, Li R, Liu L, Wu S, Zhang L, Li Y, Wei H, Shu Y, Yang Y, Wang S, Xing Q, Zhang L^*, Bao Z. (2022) The effect of temperature on gonadal sex differentiation of Yesso scallop Patinopecten yessoensis. Frontiers in Cell and Developmental Biology. 9: 803046.
10. Wang Y^#, Zhu X^#, Lian S^*, Li Y, Hu N, Hu X, Bao Z, Wang S. (2022) Functional characterization of Cfap206 for bivalve ciliogenesis by RNAi and CRISPR/Cas9 technologies. Frontiers in Marine Science. 9:864037.
11. Liu L, Liu T, Wu S, Li Y, Wei H, Zhang L, Shu Y, Yang Y, Xing Q, Wang S, Zhang L^*. (2022) Discovery of Nanos1 and Nanos2/3 as germ cell markers during scallop gonadal development. Marine Biotechnology. 24: 408-416.
12. 吴立新^*, 荆钊, 陈显尧, 李才文, 张国良, 王师, 董波, 庄光超. (2022) 我国海洋科学发展现状与未来展望. 地学前缘. 29: 1-12.

2021

1. Liu F, Li Y^*, Yu H, Zhang L, Hu J, Bao Z, Wang S^*. (2021) MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. Nucleic Acids Research. 49: D988-D997.
2. Bao Y^#, Zeng Q^#, Wang J^#, Zhang Z^#, Zhang Y^#, Wang S^#, Wong N^#, Yuan W, Huang Y, Zhang W, Liu J, Lv L, Xue Q, Zha S, Peng Z, Yao H, Bao Z, Wang S^*, Lin Z^*. (2021) Genomic insights into the origin and evolution of molluscan red-bloodedness in the blood clam Tegillarca granosa. Molecular Biology and Evolution. 38: 2351-2365.
3. Zeng Q^#, Liu J^#, Wang C^#, Wang H, Zhang L, Hu J, Bao L^* & Wang S^*. (2021) High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance. Computational and Structural Biotechnology Journal. 19: 4954-4960
4. Wei H, Li W, Liu T, Li Y, Liu L, Shu Y, Zhang L, Wang S, Xing Q, Zhang L^*, Bao Z. (2021) Sexual development of the hermaphroditic scallop Argopecten irradians revealed by morphological, endocrine and molecular analysis. Frontiers in Cell and Developmental Biology. 9: 646754.
5. Liu P^#, Zhang T^#, Lv J^*, Ma C, Yang Z, Huang X, Zhang L, Bao Z, Wang S^*. (2021) An efficient integrated approach for nonlethal DNA sampling and genome-wide genotyping in bivalve molluscs. Aquaculture. 536: 736489.

2020

1. Wang J^#, Zhang L^#, Lian S^#, Qin Z^#, Zhu X^#, Dai X, Huang Z, Ke C, Zhou Z, Wei J, Liu P, Hu N, Zeng Q, Dong B, Dong Y, Kong D, Zhang Z, Liu S, Xia Y, Li Y, Zhao L, Xing Q, Huang X, Hu X, Bao Z, Wang S^*. (2020) Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae. Nature Ecology & Evolution. 4: 725-736. (NEE News & Views: The origin of metazoan larvae; Behind the Paper: The mysterious origin of metazoan larvae: Larva-first or Adult-first?)
2. Yang Z, Zhang L, Hu J, Wang J, Bao Z, Wang S^*. (2020) The evo-devo of molluscs: insights from a genomic perspective. Evolution & Development. 22: 409-424. (Invited Review)
3. Wang J^#, Yu H^#, Yao L^#, Li Y^*, Liu F, Han W, Cui C, Hu J, Bao Z, Wang S^*. (2020) Genomic and transcriptomic landscapes and evolutionary dynamics of molluscan glycoside hydrolase families with implications for algae-feeding biology. Computational and Structural Biotechnology Journal. 18: 2744-2756.
4. Dong Y^#, Zeng Q^#, Ren J^#, Yao H, Lv L, He L, Ruan W, Xue Q, Bao Z, Wang S^*, Lin Z^*. (2020) The chromosomal-level genome assembly and comprehensive transcriptomes of the razor clam (Sinonovacula constricta). Frontiers in Genetics. 11: 664.
5. Zhang M^#, Wei H^#, Liu T, Li W, Li Y, Wang S, Xing Q, Hu X, Zhang L^*, Bao Z. (2020) Potential GnRH and steroidogenesis pathways in the scallop. Journal of Steroid Biochemistry and Molecular Biology. 204: 105756.
6. Wei J, Zhang J, Lu Q, Ren P, Guo X, Wang J, Li X, Chang Y, Duan S, Wang S, Yu H, Zhang X, Yang X, Gao H, Dong B^*. (2020) Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava). Molecular Ecology Resources. 20: 1414-1431.

2019

1. Lian S^#, Wang J^#, Zhang L, Xing Q, Hu N, Liu S, Dai X, Zhang F, Hu X, Bao Z & Wang S^*. (2019) Integration of biochemical, cellular and genic indicators for understanding the ageing process in a bivalve mollusc Chlamys farreri. Marine Biotechnology. 21: 718-730.

2018

1. Lv J^#, Jiao W^#, Guo H^#, Liu P, Wang R, Zhang L, Zeng Q, Hu X, Bao Z, Wang S^*. (2018) HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay. Genome Research. 28: 1919-1930.
2. Li Y^#, Wang R^#, Xun X^#, Wang J^#, Bao L^#, Thimmappa R^#, Ding J^#, Jiang J^#, Zhang L, Li T, Lv J, Mu C, Hu X, Zhang L, Liu J, Li Y, Yao L, Jiao W, Wang Y, Lian S, Zhao Z, Zhan Y, Huang X, Liao H, Wang J, Sun H, Mi X, Xia Y, Xing Q, Lu W, Osbourn A, Zhou Z^*, Chang Y^*, Bao Z^*, Wang S^*. (2018) Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation. Cell Discovery. 4: 29.
3. Li R^#, Zhang L^#,*, Li W, Zhang Y, Li Y, Zhang M, Zhao L, Hu X, Wang S, Bao Z. (2018) FOXL2 and DMRT1L are Yin and Yang genes for determining timing of sex differentiation in a bivalve mollusc Patinopecten yessoensis. Frontiers in Physiology. 9: 1166.
4. Zhang M, Wang Y, Li Y, Li W, Li R, Xie X, Wang S, Hu X, Zhang L^*, Bao Z. (2018) Identification and characterization of neuropeptides by transcriptome and proteome analyses in a bivalve mollusc Patinopecten yessoensis. Frontiers in Genetics. 9: 197.
5. Xu T, Sun J, Watanabe HK, Chen C, Nakamura M, Ji R, Feng D, Lv J, Wang S, Bao Z, Qian PY, Qiu JW^*. (2018) Population genetic structure of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) in the Northwest Pacific. Evolutionary Applications. 11: 1915-1930.
6. Xu P^#, Dai X^#, Wang D, Miao Y, Zhang X, Wang S, Teng L, Dong B, Bao Z, Wang S, Lyu Q^*, Liu W^*. (2018) The discovered chimeric protein plays the cohesive role to maintain scallop byssal root structural integrity. Scientific Reports. 8: 17082.

2017

1. Wang S^#, Zhang J^#, Jiao W^#, Li J^#, Xun X^#, Sun Y^#, Guo X^#, Huan P^#, Dong B, Zhang L, Hu X, Sun X, Wang J, Zhao C, Wang Y, Wang D, Huang X, Wang R, Lv J, Li Y, Zhang Z, Liu B, Lu W, Hui Y, Liang J, Zhou Z, Hou R, Li X, Liu Y, Li H, Ning X, Lin Y, Zhao L, Xing Q, Dou J, Li Y, Mao J, Guo H, Dou H, Li T, Mu C, Jiang W, Fu Q, Fu X, Miao Y, Liu J, Yu Q, Li R, Liao H, Li X, Kong Y, Jiang Z, Chourrout D^*, Li R^*, Bao Z^*. (2017) Scallop genome provides insights into evolution of bilaterian karyotype and development. Nature Ecology & Evolution. 1: 0120. (Cover Story; NEE News & Views: Genome evolution: Shellfish genes; Behind the Paper: The “fossil” genome of scallop Patinopecten yessoensis; ESI highly cited paper)
2. Li Y^#, Sun X^#, Hu X^#, Xun X^#, Zhang J^#, Guo X^#, Jiao W, Zhang L, Liu W, Wang J, Li J, Sun Y, Miao Y, Zhang X, Cheng T, Xu G, Fu X, Wang Y, Yu X, Huang X, Lu W, Lv J, Mu C, Wang D, Li X, Xia Y, Li Y, Yang Z, Wang F, Zhang L, Xing Q, Dou H, Ning X, Dou J, Li Y, Kong D, Liu Y, Jiang Z, Li R, Wang S^*, Bao Z^*. (2017) Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins. Nature Communications. 8: 1721. (Toxicon highlight: Neurotoxin stress-driven evolution in scallop genome)
3. Dou J^#, Dou H^#, Mu C, Zhang L, Li Y, Wang J, Li T, Li Y, Hu X, Wang S^*, Bao Z^*. (2017) Whole-genome restriction mapping by “subhaploid”-based RAD sequencing: an efficient and flexible approach for physical mapping and genome scaffolding. Genetics. 206: 1237-1250.
4. Xing Q^#, Wei T^#, Chen Z, Wang Y^*, Lu Y, Wang S, Zhang L, Bao Z. (2017) Using a multiscale image processing method to characterize the periodic growth patterns on scallop shells. Ecology and Evolution. 7: 1616-1626.
5. Xu T^#, Sun J^#, Lv J, Watanabe H, Li T, Zou W, Rouse GW, Wang S, Qian PY^*, Bao Z^*, Qiu JW^*. (2017) Genome-wide discovery of single nucleotide polymorphisms (SNPs) and single nucleotide variants (SNVs) in deep-sea mussels: Potential use in population genomics and cross-species application. Deep-Sea Research II. 137: 318-326.

2016

1. Wang S^*,#, Liu P^#, Lv J, Li Y, Cheng T, Zhang L, Xia Y, Sun H, Hu X, Bao Z^*. (2016) Serial sequencing of isolength RAD tags for cost-efficient genome-wide profiling of genetic and epigenetic variations. Nature Protocols. 11: 2189-2200.
2. Xing Q, Li Y, Guo H, Yu Q, Huang X, Wang S, Hu X, Zhang L^*, Bao Z. (2016) Cardiac performance: a thermal tolerance indicator in scallops. Marine Biology. 163: 244-252.

Early

1. Wang S^#, Lv J^#, Zhang L^#, Dou J, Sun Y, Li X, Fu X, Dou H, Mao J, Hu X, Bao Z^*. (2015) MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes. Open Biology. 5: 150130.
2. Cui Z^#,*, Hui M^#, Liu Y^#, Song C, Li X, Li Y, Liu L, Shi G, Wang S, Li F, Zhang X, Liu C, Xiang J^*, Chu KH^*. (2015) High density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis. Heredity. 115: 206-215.
3. Jiao W^#, Fu X^#, Dou J^#, Li H, Su H, Mao J, Yu Q, Zhang L, Hu X, Huang X, Wang Y, Wang S^*, Bao Z^*. (2014) High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc. DNA Research. 21: 85-101. (Editor's Choice)
4. Jiao W^#, Fu X^#, Li J^#, Li L, Feng L, Lv J, Zhang L, Wang X, Li Y, Hou R, Zhang L, Hu X, Wang S^*, Bao Z^*. (2014) Large-scale development of gene-associated single-nucleotide polymorphism markers for molluscan population genomic, comparative genomic and genome-wide association studies. DNA Research. 21: 183-193.
5. Fu X^#, Sun Y^#, Wang J, Xing Q, Zou J, Li R, Wang Z, Wang S, Hu X, Zhang L^*, Bao Z^*. (2014) Sequencing-based gene network analysis provides a core set of gene resource for understanding thermal adaptation in Zhikong scallop Chlamys farreri. Molecular Ecology Resources. 14: 184-198.
6. Fu X^#, Dou J^#, Mao J, Su H, Jiao W, Zhang L, Hu X, Huang X, Wang S^*, Bao Z^*. (2013) RADtyping: an integrated package for accurate de novo codominant and dominant RAD genotyping in mapping populations. PLoS ONE. 8: e79960.
7. Wang S^*,#, Meyer E^*,#, McKay JK, Matz MV. (2012) 2b-RAD: a simple and flexible method for genome-wide genotyping. Nature Methods. 9: 808-810. (ESI highly cited paper)
8. Ponomarev I^*,#, Wang S^#, Zhang L, Harris RA, Mayfield RD^*. (2012) Gene co-expression networks in human brain identify epigenetic modifications in alcohol dependence. Journal of Neuroscience. 32: 1884-1897.
9. Dou J, Zhao X, Fu X, Jiao W, Wang N, Zhang L, Hu X, Wang S^*, Bao Z^*. (2012) Reference-free SNP calling: Improved accuracy by preventing incorrect calls from repetitive genomic regions. Biology Direct. 7: 17.
10. Hou R, Bao Z, Wang S, Su H, Li Y, Du H, Hu J, Wang S^*, Hu X^*. (2011) Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PLoS ONE. 6: e21560.
11. Wang S, Zhang L, Hu J, Bao Z^*, Liu Z^*. (2010) Molecular and cellular evidence for biased mitotic gene conversion in hybrid scallop. BMC Evolutionary Biology. 10: 6.
12. Wang S^*, Zhang L, Meyer E, Bao Z^*. (2010) Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome. Biology Direct. 5: 18.
13. Wang S^*, Zhang L, Meyer E, Matz MV. (2010) Characterization of a group of MITEs with unusual features from two coral genomes. PLoS ONE. 5: e10700.
14. Wang S^#*, Zhang L^#, Meyer E, Matz MV. (2009) Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora. Genome Biology. 10: R126.
15. Wang S^*, Zhang L, Matz MV. (2009) Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia). Journal of Heredity. 100: 329-337.
16. Wang S, Bao Z^*, Hu X, Shao M, Zhang L, Hu J. (2008) Two novel elements (CFG1 and PYG1) of Mag lineage of Ty3/Gypsy retrotransposons from Zhikong scallop (Chlamys farreri) and Japanese scallop (Patinopecten yessoensis). Genetica. 133: 37-46.
17. Wang S, Zhang L, Zhan A., Wang X, Liu Z, Hu J, Bao Z^*. (2007) Patterns of concerted evolution of the rDNA family in a natural population of Zhikong scallop, Chlamys farreri. Journal of Molecular Evolution. 65: 660-667.
18. Wang S, Bao Z^*, Li N, Zhang L, Hu J. (2007) Analysis of the secondary structure of ITS1 in Pectinidae: implications for phylogenetic reconstruction and structural evolution. Marine Biotechnology. 9: 231-242.
19. Wang S, Bao Z^*, Zhang L, Li N, Zhan A, Guo W, Wang X, Hu J. (2006) A new strategy for species identification of planktonic larvae: PCR-RFLP analysis of the internal transcribed spacer region of ribosomal DNA detected by agarose gel electrophoresis or DHPLC. Journal of Plankton Research. 28: 375-384.
20. Wang S, Bao Z^*, Pan J, Zhang L, Yao B, Zhan A, Bi K, Zhang Q. (2004) AFLP linkage map of an intraspecific cross in Chlamys farreri. Journal of Shellfish Research. 23: 491-499.