Publications

(^=contributed equally, *=corresponding author) (last updated 20Feb2025)

•  ^Law ST, ^Nong WY, Au MF, Cheung LH, Shum CW, Lee SY*, Cheung SG*, Hui JHL*. (accept). Genomes of two indigenous clams Anomalocardia flexuosa (Linnaeus, 1767) and Meretrix petechialis (Lamarck, 1818). Scientific Data. 
• Hong Kong Biodiversity Genomics Consortium. (2024). Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor. GigaByte. (Link) Data Links:NCBI, CUHK Research Data Repository.
• ^Law ST, ^Nong WY, ^Li C, ^Chong TK, Yip HY, Swale T, Chiu SW, Chung RY, Lam HM, Wong SY, Wong H, Hui JHL*. (2024). Genome of tropical bed bug Cimex hemipterus (Cimicidae, Hemiptera) reveals tetraspanin expanded in bed bug ancestor. Insect Science. (Link)
• Hong Kong Biodiversity Genomics Consortium. (2024). Genome assembly of the rare and endangered Grantham’s camellia, Camellia granthamiana. GigaByte. (Link) Data Links: NCBI, CUHK Research Data Repository.
• Hong Kong Biodiversity Genomics Consortium. (2024). Genome assembly of the milky mangrove Excoecaria agallocha. GigaByte. (Link) (Story also covered in: EurekAlert, GIGABlog, Mirage, Scienmag)  Data Links: NCBI, CUHK Research Data Repository.
• Hong Kong Biodiversity Genomics Consortium. (2024). Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860). GigaByte. (Link) (Story also covered in: EurekAlert, GIGABlog, Mirage, Scienmag)  Data Links: NCBI, CUHK Research Data Repository.
• Hong Kong Biodiversity Genomics Consortium (2024). Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae). GigaByte. (Link) (Story also covered in: EurekAlert, GIGABlog, Mirage, Scienmag) Data Links: NCBI, CUHK Research Data Repository.
• Hong Kong Biodiversity Genomics Consortium (2024). Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873). GigaByte. (Link) (Story also covered in: EurekAlert, GIGABlog, Mirage, Scienmag) Data Links: NCBI, CUHK Research Data Repository.
• Hong Kong Biodiversity Genomics Consortium (2024). Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778). GigaByte. (Link) (Story also covered in: EurekAlert, GIGABlog, Mirage, Scienmag) Data Links: NCBI, CUHK Research Data Repository.
• ^Li C, ^Nong WY, ^Boncan D,  So WL, Yip HY, Swale T, Jia Q, Vicentin IG, Chung G, Bendena WG, Ngo JC*, Chan TF*, Lam HM*, Hui JHL*. (2024). Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis. BMC Genomics, 25, 327. (Link)
• ^Law ST, ^Yu Y, ^Nong WN, So WL, Li Y, Swale T, Ferrier DE*, Qiu JW*, Qian PY*, Hui JHL*. (2023). The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes.  Proceedings of the Royal Society B, 290, 20231563. (Link)
• ^Lee IH, ^Nong WY, ^So WL, Cheung CK, Xie Y, Baril T,  Yip HY, Swale T, Chan SK, Wei YY, Lo N, Hayward A, Chan TF, Lam HM, Hui JHL*. (2023). The genome and sex-dependent responses to temperature in the common yellow butterfly Eurema hecabe. BMC Biology, 21, 200.(Link)
• ^Law ST, ^Nong WY, Yip HY, Liu EK, Ng TP, Tsang RH, Xia N, Shaw PC, Lam HM, Lau TW, Hui JHL*. (2023). Population genomic analyses of protected incense trees Aquilaria sinensis reveals the existence of genetically distinct subpopulations. Frontiers in Ecology and Evolution, 11, 1216370. (Link)
• Au MF, Williams GA*, Hui JHL*. (2023). Status Quo and Future Perspectives of Molecular and Genomic Studies on the Genus Biomphalaria—The Intermediate Snail Host of Schistosoma mansoni.   International Journal  of Molecular Sciences, 24(5), 4895. (Link)
• ^So WL, ^Nong WY, ^Xie Y, ^Baril T, Ma HY, Qu Z, Haimovitz J, Swale T, Gaitan-Espitia JD, Lau KF, Tobe SS, Bendena WG, Kai ZP, Hayward A*, Hui JHL*. (2022). Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes. Nature Communications, 13, 3010. (Link) Story also covered in: CUHK, OAL, Croucher, ResearchNews
• ^Nong WY, ^Yu Y, ^Aase-Remedios M, Xie Y, So WL, Li Y, Wong CF, Baril T, Law ST, Lai SY, Haimovitz J, Swale T, Chen SS, Kai ZP, Sun X, Wu Z, Hayward A, Ferrier DE*, Hui JHL*. (2022). Genome of the ramshorn snail Biomphalaria staminea – an obligate intermediate host of schistosomiasis. GigaScience, 11, giac012. (Link)
• ^Shum CW, ^Nong WY, ^So WL, ^Li Y, Qu Z, Yip HY, Swale T, Ang PO, Chan KM, Chan TF, Chu KH, Chui AP, Lau KF, Ngai SM, Xu F, Hui JHL*.(2022). Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration. Frontiers in Cell and Developmental Biology. (Link)
• ^Law ST, ^Nong WY, So WL, Baril T, Swale T, Chan CB, Tobe SS, Kai ZP. Bendena WG, Hayward A, Hui JHL*. (2022). Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees.Genomics, 114(4), 110440. (Link)
• ^So WL*, ^Ting KW, ^Lai SY, ^Huang EY, Ma Y, Chong TK, Yip HY, Lee HT, Cheung BC, Chan MK, Hong Kong Soil Biodiversity Consortium, Nong WY, Law MM*, Lai DY*, Hui JHL*. (2022). Revealing the millipede and other soil-macrofaunal biodiversity in Hong Kong using a citizen science approach. Biodiversity Data Journal.
• Huang EY, Law ST, Nong WN, Yin HY, Uea-Anuwong T, Magouras I, Hui JHL*. (2022). The screening for anticoagulant rodenticide gene VKORC1 polymorphism in the rat Rattus norvegicus, Rattus tanezumi and Rattus losea in Hong Kong. Scientific Reports, 12, 12545. (Link)
• ^So WL, ^Kai ZP, Qu Z, Bendena WG*, Hui JHL*. (2022). Rethinking sesquiterpenoids: A widespread hormone in animals. International Journal of Molecular Sciences, 23(11), 5998. (Link)
• ^Xie Y, ^Huang EY, ^Nong WY, ^Law ST, ^Yu YF, ^Cheung K, Li Y, Wong CF, Yip HY, Joyce P, Chan KM, Chu KH, Russell B*, Falkenberg L*, Hui JHL*. (2022). Population genomics, transcriptional response to heat shock, and gut microbiota of the Hong Kong oyster Magallana hongkongensis. Journal of Marine Science and Engineering, 10(2), 237. (Link)
• ^Yu Y, ^Nong WY, So WL, Xie Y, Yip HY, Haimovitz J, Swale T, Baker DM, Bendena WG, Chan TF, Chui AP, Lau KF, Qian PY, Qiu JW, Fei X, Hui JHL*. (2022). Genome of elegance coral Catalaphyllia jardinei (Euphylliidae). Frontiers in Marine Science. (Link)
• ^Nong WY, ^Qu Z, ^Li YQ, ^Barton-Owen T, ^Wong AY, Yip HY, Lee HT, Narayana S, Baril T, Swale T, Cao J, Chan TF, Kwan HS, Ngai SM, Panagiotou G, Qian PY, Qiu JW, Yip KY, Ismail N, Pati S, John A, Tobe SS, Bendena WG, Cheung SG, Hayward A, Hui JHL*. (2021). Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication. Communications Biology, 4, 83. (Link)
• ^Qu Z, ^Nong WY, ^So WL, ^Barton-Owen T, ^Li YQ, Leung TC, Li C, Baril T, Wong AY, Swale T, Chan TF, Hayward A, Ngai SM, Hui JHL*. (2020). Millipede genomes reveal unique adaptation of genes and microRNAs during myriapod evolution. PLOS Biology, 18(9), e3000636. (Link) (Story also covered in: Earth.com, EurekAlert, ScienceDaily, SCINEWS) 
• ^Qu Z, ^Yiu WC, ^Yip HY, ^Nong WY, Yu CW, Lee IH, Wong AY, Wong NW, Cheung FK, Chan TF, Lau KF, Zhong S, Chu KH, Tobe SS, Ferrier DE, Bendena WG, Hui JHL*. (2020). MicroRNA clusters integrate evolutionary constraints on expression and target affinities: the miR-6/5/4/286/3/309 cluster in Drosophila. Molecular Biology and Evolution, 37(10), 2955-2965. (Link)
•  ^Nong WY, ^Cao JQ, ^Li YQ, ^Qu Z, Sun J, Swale T, Yip HY, Qian PY, Qiu JW, Kwan HS, Bendena WG, Tobe SS, Chan TF, Yip KY, Chu KH, Ngai SM, Tsim KY, Holland PW*, Hui JHL* . (2020). Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing . Nature Communications, 11, 3051. (Link) (Feature image selected by the journal) (Recommended by F1000) (Story also covered in: CUHK, AM730, Asia Today, COSMOS, Headline Daily, HKET, Lion Rock Daily, Oriental Daily, PHYS, Singtao,  SkyPost, Yahoo)
• ^Nong WY, ^Law ST,  Wong AY, Baril T, Swale T,  Chu LM, Hayward A, Lau DT, Hui JHL*. (2020). Chromosomal-level reference genome of the incense tree Aquilaria sinensis. Molecular Ecology Resources, 20(4), 971-979. (Link)
• ^Qu Z, ^Nong WY, ^Yu YF, ^Baril T, Hayward A*, Hui JHL*. (2020). Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae). BMC Genomics, 21, 726. (Link)
• ^Li YQ, ^Nong WY, ^Baril T, Yip HY, Swale T, Hayward A*, Ferrier DE*, Hui JHL* . (2020). Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome. BMC Genomics, 21, 713. (Link)
•  Nong WY, Chai ZY, Jiang X, Qin J, Ma KY, Chan KM, Chan TF, Chow BK, Kwan HS, Wong CK, Qiu JW, Hui JHL*, Chu KH. (2020). A crustacean annotated transcriptome (CAT) database. BMC Genomics, 21, 32.  (Link)
• ^Kenny NJ, ^Chan KW, Nong WY, Qu Z, Maeso I, Yip HY, Chan TF, Kwan HS, Holland PWH, Chu KH, Hui JHL*. (2016). Ancestral whole  genome duplication in the marine chelicerate horseshoe crabs. Heredity (Edinb), 116, 190-199. (Link) (One of the most cited papers of the journal from 2016)(Readers’ Choice: The best of Heredity 2016-17) (Story also covered in: CUHK, Sing Tao, Sina, Wen Wei Po, Yahoo)
• Kenny NJ, Shen X, Chan TT, Wong NW, Chan TF, Chu KH, Lam HM, Hui JHL* (2015). Genome of the rusty millipede, Trigoniulus corallinus, illuminates diplopod, myriapod and arthropod evolution. Genome Biology and Evolution, 7(5), pp. 1280-1295. (Link) (Cover story of the journal)
• ^Kenny NJ, ^Namigai EKO, Marletaz F, Hui JHL*, Shimeld SM*. (2015). Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). Marine Genomics, 24(2), pp. 139-146. (Link)     
• Centipede Genome Consortium (Chipman AD, Ferrier DEK … Hui JHL (43rd author) … Kenny NJ … Gibbs RA, Akam M, Richards S)(2014). The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. PLoS Biology, 12(11), e1002005. (Link) (Cover story of the journal) (Story also covered in: PLoS Biology, NBC News, Tech Times,  International Business Times, Astrobiology Magazine, Sci-News, Genome  Web, UK Daily Mail, Nature World News, Reuters)  

Database:

Biodiversity of Medusozoa: http://biodiversity.sls.cuhk.edu.hk/Jellyfish_db/

Myriapod database: http://biodiversity.sls.cuhk.edu.hk/Myriapod_db/

Bidirectional miRNAs database: http://biodiversity.sls.cuhk.edu.hk/Bidirectional_db/

Our published genomes: