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2024

Pan-evolutionary and regulatory genome architecture delineated by integrated macro- and microsynteny approach

Yu H#, Li Y #*, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S*

Nature Protocols.  2024, 19: 1623–1678.

Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids

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*.

Nature Communications.  2024, 15: 2395.

Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs

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*

Science Advances.  10(13): eadi9035.

Deqformer: High-definition and scalable deep learning probe design method

Cai Y#, Lv J#, Li R#, Huang X., Wang S, Bao Z, Zeng Q*.

Briefings in Bioinformatics.  2024, 25(2): 1–9.

Tracking organic matrix in the seashell by elemental mapping under laser-induced breakdown spectroscopy

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*.

Talanta.  2024, 271: 125658.

A genome-wide association study to identify the genes associated with growth-related traits in Tegillarca granosa

He X, Liao Y, Yang Z, Liu H, Wang S, Bao Y*.

Aquaculture.  2024, 578: 740127.

2023

EDomics: a comprehensive and comparative multi-omics database for animal evo-devo

Wei J#, Liu P#, Liu F#, Jiang A, Qiao J, Pu Z, Wang B, Zhang J, Jia D, Li Y*, Wang S*, Dong B*.

Nucleic Acids Research.  2023, 51: D913-D923.

Cardiac performance and heart gene network provide dynamic responses of bay scallop Argopecten irradians irradians exposure to marine heatwaves

Zhu X, Zhang J, Li M, Hou X, Liu A, Dong X, Wang W, Xing Q*

Science of The Total Environment.  882: 163594.

Hemoglobin wonders: A fascinating gas transporter diving into molluscs

Zhang W, Zhang Y, Shi X, Wang S, Bao Y*.

Critical Reviews in Biochemistry and Molecular Biology.  2024, 58(2–6): 132–157.

K252a inhibition of sperm viability for efficient crossbreeding of hermaphroditic bivalves

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*

Aquaculture.  2023, 577: 739930.

Comparative analysis of the cardiac structure and transcriptome of scallop and snail, perspectives on heart chamber evolution

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*.

Marine Life Science & Technology.  5(4): 478–491.

Preliminary study of laser-induced breakdown spectroscopy for Mg/Ca investigation in cultured scallop shells

Li Y, Wang Y, Wang S, Zheng R, Bao Z, Lu Y*.

Journal of Laser Applications.  2023, 35: 022018.

2022

Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation

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*.

Nature Ecology & Evolution.  2022, 6: 1891-1906.

Biosynthesis of saponin defensive compounds in sea cucumbers

Thimmappa R*, Wang S#, Zheng M#, Misra RC, Huang AC, Saalbach G, Chang Y, Zhou Z, Hinman V, Bao Z, Osbourn A*.

Nature Chemical Biology.  2022, 18: 774-781.

Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M

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*.

Genome Biology.  2022, 23: 36.

Targeted genotyping of a whole-gene repertoire by an ultrahigh-multiplex and flexible HD-Marker approach

Liu P#, Lv J#,*, Ma C, Zhang T, Huang X, Yang Z, Zhang L, Hu J, Wang S, Bao Z*.

Engineering.  2022, 13: 186-196.

Adaptive bird-like genome miniaturization during the evolution of scallop swimming lifestyle

Li Y#, Liu Y#, Yu H, Liu F, Han W, Zeng Q, Zhang Y, Zhang L, Hu J, Bao Z, Wang S*.

Genomics Proteomics & Bioinformatics.  2022, 20: 1066-1077.

Dynamic transcriptome analysis reveals the gene network of gonadal development from the early history life stages in dwarf surfclam Mulinia lateralis

Li Y, Liu L, Zhang L, Wei H, Wu S, Liu T, Shu Y, Yang Y, Yang Z, Wang S, Bao Z, Zhang L*.

Biology of Sex Differences.  2022, 13: 69.

Development of a high-throughput SNP array for sea cucumber (Apostichopus japonicus) and its application in genomic selection with MCP regularized deep neural networks

Lv J#, Wang Y#,*, Ni P, Lin P, Hou H, Ding J*, Chang Y*, Hu J*, Wang S, Bao Z.

Genomics.  2022, 114: 110426.

Decoding the byssus fabrication by spatiotemporal secretome analysis of scallop foot

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*.

Computational and Structural Biotechnology Journal.  2022, 20: 2713-2722.

The effect of temperature on gonadal sex differentiation of Yesso scallop Patinopecten yessoensis

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.

Frontiers in Cell and Developmental Biology.  2022, 9: 803046.

Functional characterization of Cfap206 for bivalve ciliogenesis by RNAi and CRISPR/Cas9 technologies

Wang Y#, Zhu X#, Lian S*, Li Y, Hu N, Hu X, Bao Z, Wang S.

Frontiers in Marine Science.  2022, 9: 864037.

Discovery of Nanos1 and Nanos2/3 as germ cell markers during scallop gonadal development

Liu L, Liu T, Wu S, Li Y, Wei H, Zhang L, Shu Y, Yang Y, Xing Q, Wang S, Zhang L*.

Marine Biotechnology.  2022, 24: 408-416.

2021

MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca

Liu F, Li Y*, Yu H, Zhang L, Hu J, Bao Z, Wang S*.

Nucleic Acids Research.  2021, 49: D988-D997.

Genomic insights into the origin and evolution of molluscan red-bloodedness in the blood clam Tegillarca granosa

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*.

Molecular Biology and Evolution.  2021, 38: 2351-2365.

High-quality reannotation of the king scallop genome reveals no ‘gene-rich’ feature and evolution of toxin resistance

Zeng Q#, Liu J#, Wang C#, Wang H, Zhang L, Hu J, Bao L* & Wang S*.

Computational and Structural Biotechnology Journal.  2021, 19: 4954-4960.

Sexual development of the hermaphroditic scallop Argopecten irradians revealed by morphological, endocrine and molecular analysis

Wei H, Li W, Liu T, Li Y, Liu L, Shu Y, Zhang L, Wang S, Xing Q, Zhang L*, Bao Z.

Frontiers in Cell and Developmental Biology.  2021, 9: 646754.

An efficient integrated approach for nonlethal DNA sampling and genome-wide genotyping in bivalve molluscs

Liu P#, Zhang T#, Lv J*, Ma C, Yang Z, Huang X, Zhang L, Bao Z, Wang S*.

Aquaculture.  2021, 536: 736489.

2020

Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae

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*.

Nature Ecology & Evolution.  2020, 4: 725-736.

The evo-devo of molluscs: insights from a genomic perspective

Yang Z, Zhang L, Hu J, Wang J, Bao Z, Wang S*. Evolution & Development. 2020, 22: 409-424.

Evolution & Development.  2020, 22: 409-424.

Genomic and transcriptomic landscapes and evolutionary dynamics of molluscan glycoside hydrolase families with implications for algae-feeding biology

Wang J#, Yu H#, Yao L#, Li Y*, Liu F, Han W, Cui C, Hu J, Bao Z, Wang S*.

Computational and Structural Biotechnology Journal.  2020, 18: 2744-2756.

The chromosomal-level genome assembly and comprehensive transcriptomes of the razor clam (Sinonovacula constricta)

Dong Y#, Zeng Q#, Ren J#, Yao H, Lv L, He L, Ruan W, Xue Q, Bao Z, Wang S*, Lin Z*.

Frontiers in Genetics.  2020, 11: 664.

Potential GnRH and steroidogenesis pathways in the scallop

Zhang M#, Wei H#, Liu T, Li W, Li Y, Wang S, Xing Q, Hu X, Zhang L*, Bao Z.

Journal of Steroid Biochemistry and Molecular Biology.  2020, 204: 105756.

Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava)

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*.

Molecular Ecology Resources.  2020, 20: 1414-1431.

2019

Integration of biochemical, cellular and genic indicators for understanding the ageing process in a bivalve mollusc Chlamys farreri.

Lian S#, Wang J#, Zhang L, Xing Q, Hu N, Liu S, Dai X, Zhang F, Hu X, Bao Z & Wang S*.

Marine Biotechnology.  2019, 21: 718-730.

2018

HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay

Lv J#, Jiao W#, Guo H#, Liu P, Wang R, Zhang L, Zeng Q, Hu X, Bao Z, Wang S*.

Genome Research.  2018, 28: 1919-1930.

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation

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*.

Cell Discovery.  2018, 4: 29.

FOXL2 and DMRT1L are Yin and Yang genes for determining timing of sex differentiation in a bivalve mollusc Patinopecten yessoensis

Li R#, Zhang L#,*, Li W, Zhang Y, Li Y, Zhang M, Zhao L, Hu X, Wang S, Bao Z.

Frontiers in Physiology.  2018, 9: 1166.

Identification and characterization of neuropeptides by transcriptome and proteome analyses in a bivalve mollusc Patinopecten yessoensis

Zhang M, Wang Y, Li Y, Li W, Li R, Xie X, Wang S, Hu X, Zhang L*, Bao Z.

Frontiers in Genetics.  2018, 9: 197.

Population genetic structure of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) in the Northwest Pacific

Xu T, Sun J, Watanabe HK, Chen C, Nakamura M, Ji R, Feng D, Lv J, Wang S, Bao Z, Qian PY, Qiu JW*.

Evolutionary Applications.  2018, 11: 1915-1930.

The discovered chimeric protein plays the cohesive role to maintain scallop byssal root structural integrity

Xu P#, Dai X#, Wang D, Miao Y, Zhang X, Wang S, Teng L, Dong B, Bao Z, Wang S, Lyu Q*, Liu W*.

Scientific Reports.  2018, 8: 17082.

2017

Scallop genome provides insights into evolution of bilaterian karyotype and development

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*.

Nature Ecology & Evolution.  2017, 1: 0120.

Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins

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*.

Nature Communications.  2017, 8: 1721.

Whole-genome restriction mapping by “subhaploid”-based RAD sequencing: an efficient and flexible approach for physical mapping and genome scaffolding

Dou J#, Dou H#, Mu C, Zhang L, Li Y, Wang J, Li T, Li Y, Hu X, Wang S*, Bao Z*.

Genetics.  2017, 206: 1237-1250.

Using a multiscale image processing method to characterize the periodic growth patterns on scallop shells

Xing Q#, Wei T#, Chen Z, Wang Y*, Lu Y, Wang S, Zhang L, Bao Z.

Ecology and Evolution.  2017, 7: 1616-1626.

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

Xu T#, Sun J#, Lv J, Watanabe H, Li T, Zou W, Rouse GW, Wang S, Qian PY*, Bao Z*, Qiu JW*.

Deep-Sea Research II.  2017, 137: 318-326.

2016

Serial sequencing of isolength RAD tags for cost-efficient genome-wide profiling of genetic and epigenetic variations

Wang S*,#, Liu P#, Lv J, Li Y, Cheng T, Zhang L, Xia Y, Sun H, Hu X, Bao Z*.

Nature Protocols.  2016, 11: 2189-2200.

Cardiac performance: a thermal tolerance indicator in scallops

Xing Q, Li Y, Guo H, Yu Q, Huang X, Wang S, Hu X, Zhang L*, Bao Z.

Marine Biology.  2016, 163: 244-252.

Early

MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes

Wang S#, Lv J#, Zhang L#, Dou J, Sun Y, Li X, Fu X, Dou H, Mao J, Hu X, Bao Z*.

Open Biology.  2015, 5: 150130.

High density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

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*.

Heredity.  2015, 115: 206-215.

High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc

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*.

DNA Research.  2014, 21: 85-101.

Large-scale development of gene-associated single-nucleotide polymorphism markers for molluscan population genomic, comparative genomic and genome-wide association studies

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*.

DNA Research.  2014, 21: 183-193.

Sequencing-based gene network analysis provides a core set of gene resource for understanding thermal adaptation in Zhikong scallop Chlamys farreri

Fu X#, Sun Y#, Wang J, Xing Q, Zou J, Li R, Wang Z, Wang S, Hu X, Zhang L*, Bao Z*.

Molecular Ecology Resources.  2014, 14: 184-198.

RAD typing: an integrated package for accurate de novo codominant and dominant RAD genotyping in mapping populations

Fu X#, Dou J#, Mao J, Su H, Jiao W, Zhang L, Hu X, Huang X, Wang S*, Bao Z*.

PLoS ONE.  2013, 8: e79960.

2b-RAD: a simple and flexible method for genome-wide genotyping

Wang S*,#, Meyer E*,#, McKay JK, Matz MV.

Nature Methods.  2012, 9: 808-810.

Gene co-expression networks in human brain identify epigenetic modifications in alcohol dependence

Ponomarev I*,#, Wang S#, Zhang L, Harris RA, Mayfield RD*.

Journal of Neuroscience.  2012, 32: 1884-1897.

Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora

Wang S*, Zhang L, Meyer E, Matz MV.

Genome Biology.  2009, 10: R126.

Reference-free SNP calling: Improved accuracy by preventing incorrect calls from repetitive genomic regions

Dou J, Zhao X, Fu X, Jiao W, Wang N, Zhang L, Hu X, Wang S*, Bao Z*.

Biology Direct.  2012, 7: 17.

Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX

Hou R, Bao Z, Wang S, Su H, Li Y, Du H, Hu J, Wang S*, Hu X*.

PLoS ONE.  2011, 6: e21560.

Molecular and cellular evidence for biased mitotic gene conversion in hybrid scallop

Wang S, Zhang L, Hu J, Bao Z*, Liu Z*.

BMC Evolutionary Biology.  2010, 10: 6.

Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome

Wang S*, Zhang L, Meyer E, Bao Z*.

Biology Direct.  2010, 5: 18.

Characterization of a group of MITEs with unusual features from two coral genomes

Wang S*, Zhang L, Meyer E, Matz MV.

PLoS ONE.  2009, 5: e10700.

Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia)

Wang S#*, Zhang L#, Matz MV.

Journal of Heredity.  2009, 100: 329-337.

Two novel elements (CFG1 and PYG1) of Mag lineage of Ty3/Gypsy retrotransposons from Zhikong scallop (Chlamys farreri) and Japanese scallop (Patinopecten yessoensis)

Wang S, Bao Z*, Hu X, Shao M, Zhang L, Hu J.

Genetica.  2008, 133: 37-46.

Patterns of concerted evolution of the rDNA family in a natural population of Zhikong scallop, Chlamys farreri

Wang S, Zhang L, Zhan A., Wang X, Liu Z, Hu J, Bao Z*.

Journal of Molecular Evolution.  2007, 65: 660-667.

Analysis of the secondary structure of ITS1 in Pectinidae: implications for phylogenetic reconstruction and structural evolution

Wang S, Bao Z*, Li N, Zhang L, Hu J.

Marine Biotechnology.  2007, 9: 231-242.

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

Wang S, Bao Z*, Zhang L, Li N, Zhan A, Guo W, Wang X, Hu J.

Journal of Plankton Research.  2006, 28: 375-384.

AFLP linkage map of an intraspecific cross in Chlamys farreri

Wang S, Bao Z*, Pan J, Zhang L, Yao B, Zhan A, Bi K, Zhang Q.

Journal of Shellfish Research.  2004, 23: 491-499.

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