Huang S, Yoshitake K, Kinoshita S, Asakawa S. Transcriptional landscape of small non-coding RNAs reveals diversity of categories and functions in molluscs. RNA Biol. 2024 Jan;21(1):1-13. doi: 10.1080/15476286.2024.2348893. Epub 2024 May 1. PMID: 38693614; PMCID: PMC11067994.
Ueda H, Ito M, Yonezawa R, Hayashi K, Tomonou T, Kashitani M, Oyama H, Shirai K, Suo R, Yoshitake K, Kinoshita S, Asakawa S, Itoi S. Japanese Planocerid Flatworms: Difference in Composition of Tetrodotoxin and Its Analogs and the Effects of Ingestion by Toxin-Bearing Fishes in the Ryukyu Islands, Japan. Mar Biotechnol (NY). 2024 Apr 17. doi: 10.1007/s10126-024-10312-0. Epub ahead of print. PMID: 38630353.
Teber R, Asakawa S. In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes. Int J Mol Sci. 2024 Feb 22;25(5):2566. doi: 10.3390/ijms25052566. PMID: 38473813; PMCID: PMC10931772.
Lanza A, Kimura S, Hirono I, Yoshitake K, Kinoshita S, Asakawa S. Transcriptome analysis of Edwardsiella piscicida during intracellular infection reveals excludons are involved with the activation of a mitochondrion-like energy generation program. mBio. 2024 Mar 13;15(3):e0352623. doi:10.1128/mbio.03526-23. Epub 2024 Feb 13. PMID: 38349189; PMCID: PMC10936155.
Mizobata H, Tomita K, Yonezawa R, Hayashi K, Kinoshita S, Yoshitake K, Asakawa S. The highly developed symbiotic system between the solar-powered nudibranch Pteraeolidia semperi and Symbiodiniacean algae. iScience. 2023 Nov 15;26(12):108464. doi: 10.1016/j.isci.2023.108464. PMID: 38125017; PMCID: PMC10730344.
Lanza A, Mizobata H, Yonezawa R, Yoshitake K, Shigeharu K, Asakawa S. Complete genome sequence of Edwardsiella sp. NBRC12716 isolated in 1962
from the liver of diseased eel. Microbiol Resour Announc. 2023 Oct 19;12(10):e0073723. doi: 10.1128/MRA.00737-23. Epub 2023 Sep 29. PMID: 37772863; PMCID: PMC10586094.
Mizobata H, Hayashi K, Yonezawa R, Lanza A, Kinoshita S, Yoshitake K, Asakawa S. The complete mitochondrial genome of Spurilla braziliana MacFarland 1909 (Nudibranchia, Aeolidiidae). Mitochondrial DNA B Resour. 2023 Aug 9;8(8):862-866. doi: 10.1080/23802359.2023.2241693. PMID: 37576982; PMCID: PMC10413916.
Kurokochi H, Tajima N, Sato MP, Yoshitake K, Asakawa S, Isobe S, Shirasawa K. Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake). DNA Res. 2023 Apr 25;30(3):dsad006. doi: 10.1093/dnares/dsad006. Epub ahead of print. PMID: 37186136; PMCID: PMC10211490.
2022
Bhuiyan A, Asakawa S. Synthesis and cloning of long repeat sequences using single-stranded circular DNA. Front Bioeng Biotechnol. 2023 Mar 9;11:1115159. doi: 10.3389/fbioe.2023.1115159. PMID: 36970617; PMCID: PMC10033958.
Yoshitake K, Yanagisawa K, Sugimoto Y, Nakamura H, Mizusawa N, Miya M, Hamasaki K, Kobayashi T, Watabe S, Nishikiori K, Asakawa S. Pilot study of a
comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers. Funct Integr Genomics. 2023 Mar 22;23(2):96. doi: 10.1007/s10142-023-01013-3. PMID: 36947319; PMCID: PMC10033627.
Senevirathna JDM, Yonezawa R, Saka T, Hiramatsu Y, Smith AR, Igarashi Y, Yoshitake K, Kinoshita S, Funasaka N, Asakawa S. Draft genome sequencing and assembly of Risso’s dolphin, Grampus griseus. J Genomics. 2023 Jan 1;11:9-13. doi: 10.7150/jgen.78761. PMID: 36632052; PMCID: PMC9830294.
Huang S, Yoshitake K, Watabe S, Asakawa S. Environmental DNA study on aquatic ecosystem monitoring and management: Recent advances and prospects. J Environ Manage. 2022 Dec 1;323:116310. doi: 10.1016/j.jenvman.2022.116310. Epub 2022 Sep 24. PMID: 36261997.
Yusuke Kijima, WanTong Wang, Yoji Igarashi, Kazutoshi Yoshitake, Shuichi Asakawa, Yutaka, Suzuki, Shugo Watabe, Shigeharu Kinoshita. Age-Associated Different Transcriptome Profiling in Zebrafish and Rats: an Insight into the Diversity of Vertebrate Aging. Marine Biotechnology, 2022, https://doi.org/10.1007/s10126-022-10153-9
Kazutoshi Yoshitake, Asano Ishikawa, Ryo, Yonezawa,, Shigeharu Kinoshita, Jun Kitano, Shuichi Asakawa. Construction of a Chromosome-Level Japanese Stickleback Species Genome Using Ultra-Dense Linkage Analysis with Single-Cell Sperm Sequencing. NAR Genomics and Bioinformatics, 2022, 4(2), lqac026.
Abdalla Elbialy, Kaidiliayi Sulidan, Afsana Bhuiyan, Yoji Igarashi, Kazutoshi Yoshitake, Dai Yamanouchi, Junsu Kang, Shuichi Asakawa, Shugo Watabe, Shigeharu Kinoshita. Induction of Endoplasmic Reticulum Stress Markers in an Acromegaly Model. Journal of Cellular Biochemistry. 2022, 1-11.
Keisuke Shimizu, Lumi Negishi, Takumi Ito, Shogo Touma, Toshie Matsumoto, Masahiko Awaji, Hitoshi Kurumizaka, Kazutoshi Yoshitake, Shigeharu Kinoshita, Shuichi Asakawa, Michio Suzuki. Evolution of nacre- and prisms-related shell matrix proteins in the pen shell, Atrina pectinata. Comparative biochemistry and physiology. Part D, Genomics & proteomics, 2022, 44, 101025-101025.
2021
Sharmin Hasan, Shuichi Asakawa, Shugo Watabe, Shigeharu Kinoshita. Regulation of the Expression of the Myosin Heavy Chain (MYH) Gene myh14 in Zebrafish Development. Marine biotechnology (New York, N.Y.), 2021
Huang SQ, Yoshitake K, Asakawa S. A review of discovery profiling of PIWI-interacting RNAs and their diverse functions in metazoans. International Journal of Molecular Sciences, 2021, 222, 1166.
Huang SQ, Ichikawa Y, Yoshitake K, Kinoshita S, Asaduzzaman M, Omori F, Maeyama K, Nagai K, Watabe S, Asakawa S. Conserved and widespread expression of piRNA-like molecules and PIWI-like genes reveal dual functions of transposon silencing and gene regulation in Pinctada fucata (Mollusca). Frontiers in Marine Science, 2021, 8, 730556.
Jayan Duminda M Senevirathna, Ryo Yonezawa, Taiki Saka, Yoji Igarashi, Kazutoshi Yoshitake, Shigeharu Kinoshita, Noriko Funasaka, Shuichi Asakawa. Another polymorphic mitochondrial genome of Grampus griseus and phylogeny of family Delphinidae. Mitochondrial DNA. Part B, Resources, 6(9), 2569-2571, 2021
Zhongneng Xu, Shuichi Asakawa. A model explaining mRNA level fluctuations based on activity demands and RNA age. PLOS Computational Biology. 2021.https://doi.org/10.1371/journal.pcbi.1009188 .
Senevirathna, Jayan D. M. , Shuichi Asakawa. Multi-Omics Approaches and Radiation on Lipid Metabolism in Toothed Whales. Life (Basel). 2021 Apr 20;11(4):364. doi: 10.3390/life11040364.
Kazutoshi Yoshitake, Atushi Fujiwara, Aiko Matsuura, Masashi Sekino, Motoshige Yasuike, Yoji Nakamura, Reiichiro Nakamichi, Masaaki Kodama, Yumiko Takahama, Akinori Takasuka, Shuichi Asakawa, Kazuomi Nishikiori, Takanori Kobayashi & Shugo Watabe. Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA). Scientific Reports volume 11, Article number: 7031 (2021) .
Kaoru Matsumoto, Tomoko Sakami, Tsuyoshi Watanabe, Yukiko Taniuchi, Akira Kuwata, Shigeho Kakehi, Tan Engkong, Yoji Igarashi, Shigeharu Kinoshita, Shuichi Asakawa, Masahira Hattori, Shugo Watabe, Yoshizumi Ishino, Takanori Kobayashi, Takashi Gojobori, Kazuho Ikeo. Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters. PloS one, 16(10) e0257862, 2021
Songqian Huang, Kazutoshi Yoshitake, Md Asaduzzaman, Shigeharu Kinoshita, Shugo Watabe, Shuichi Asakawa. Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach. RNA biology, 1-14, 2021
2020
Huang S, Yoshitake K, Asaduzzaman M, Kinoshita S, Watabe S, Asakawa S. Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach. RNA Biology, 2021, Jan 7:1-14 , DOI:10.1080/15476286.2020.1867798.
Wong LL, Deris ZM, Igarashi Y, Huang S, Asakawa, S, Ayub Q,, Lim SY, Ikhwanuddin, Mhd, Iehata S, Okamoto, K, Mariom, Asaduzzaman, Md. Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region. BIOLOGY-BASEL, 2020, 9, 9
Ineno T, Yamada K, Tamaki K, Kodama R, Tan E, Kinoshita S, Muto K, Yada T, Kitamura S, Asakawa S, Watabe S. Determination of thermal tolerance in rainbowtrout Oncorhynchus mykiss based on effective time, and its reproducibility for a large number of fish. FISHERIES SCIENCE, 2020, 86, 5
Asaduzzaman Md, Igarashi Y, Wahab Md A, Nahiduzzaman Md, Rahman Md J, Phillips MJ, Huang S, Asakawa S, Rahman Md M, Wong LL. Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation. GENES, 2020, 11, 1
Asaduzzaman Md, Wahab Md A, Rahman Md J, Nahiduzzzaman Md, Dickson Malcom W, Igarashi Y, Asakawa S, Wong LL. Fine-scale population structure and ecotypes of anadromous Hilsa shad (Tenualosa ilisha) across complex aquatic ecosystems revealed by NextRAD genotyping. SCIENTIFIC REPORTS, 2019, 9
Tasumi S, Kobayashi K, Takanashi S, Asakawa S, Nakamura O, Kikuchi K, Suzuki Y. Expression and presentation of immune-related membrane proteins of fish by a cell surface display platform using insect cells. MOLECULAR IMMUNOLOGY, 2019, 114
Yonezawa R, Itoi S, Igarashi Y, Yoshitake K, Oyama H, Kinoshita S, Asakawa S. Characterization and phylogenetic position of two sympatric sister species of toxic flatworms Planocera multitentaculata and Planocera reticulata (Platyhelminthes: Acotylea). Mitochondrial DNA Part B Resources. 2020, 5(3), 2352-2354.
Elbialy A, Igarashi Y, Asakawa S, Watabe S, Kinoshita S. An Acromegaly Disease Zebrafish Model Reveals Decline in Body Stem Cell Number along with Signs of Premature Aging. Biology. 2020, 9(6), 120.
Kakinuma M, Yasumoto K, Suzuki M, Kasugai C, Koide M, Mitani K, Shidoji K, Kinoshita S, Hattori F, Maeyama K, Awaji M, Nagai K, Watabe S. Trivalent Iron Is Responsible for the Yellow Color Development in the Nacre of Akoya Pearl Oyster Shells. Marine Biotechnology. 2020, 22, 19-30.
2019
Asaduzzaman Md, Iehata S, Islam Md M, Kader Md A, Bolong Abol-Munafi A, Ikeda D, Kinoshita S. Sodium alginate supplementation modulates gut microbiota, health parameters, growth performance and growth-related gene expression in Malaysian Mahseer Tor tambroides. Aquaculture Nutrition. 2019, 25(6), 1300-1317.
Huang SQ, Ichikawa Y, Yoshitake K, Kinoshita S, Igarashi Y, Omori F, Maeyama K, Nagai K, Watabe S, and Asakawa S. Identification and characterization of microRNAs and their predicted functions in biomineralization in the pearl oyster (Pinctada fucata). Biology. 2019, 8(2), 47.
Ineno T, Tamaki K, Yamada K, Kodama R, Tan E, Kinoshita S, Muto K, Yada T, Kitamura S, Asakawa S, Watabe S. Evaluation of the thermal tolerances of different strains of rainbow trout Oncorhynchus mykiss by measuring the effective time required for loss of equilibrium at an approximate upper lethal temperature. Fisheries Science. 2019, 85(5), 839-845.
Shakur Ahammad AK, Asaduzzaman M, Ceyhun SB, Ceylan H, Asakawa S, Watabe S, Kinoshita S. Multiple transcription factors mediating the expressional regulation of myosin heavy chain gene involved in the indeterminate muscle growth of fish. Gene, 2019, Mar 1, 687, 308-318. doi: 10.1016/j.gene.2018.11.040.
Igarashi Y, Mori D, Mitsuyama S, Yoshitake K, Ono H, Watanabe T, Taniuchi Y, Sakami T, Kuwata A, Kobayashi T, Ishino Y, Watabe S, Gojobori T, and Asakawa S. A Preliminary Metagenome Analysis Based on a Combination of Protein Domains. Proteomes. 2019, 7(2), 19.
Kraitavin W, Yoshitake K, Igarashi Y, Mitsuyama S, Kinoshita S, Kambayashi D, Watabe S, and Asakawa S. Transcriptome analysis of yamame (Oncorhynchus masou) in normal conditions after heat stress. Biology. 2019,8:21.
Mariom, Take S, Igarashi Y, Yoshitake K, Asakawa S, Maeyama K, Nagai K, Watabe S, and Kinoshita S. Gene expression profiles at different stages for formation of pearl sac and pearl in the pearl oyster Pinctada fucata. BMC Genomics. 2019,20:240.
Huang SQ, Ichikawa Y, Igarashi Y, Yoshitake K, Kinoshita K, Omori F, Maeyama K, Nagai K, Watabe S, and Asakawa S. Piwi-interacting RNA (piRNA) expression patterns in pearl oyster (Pinctada fucata) somatic tissues. Scientific Reports. 2019,9:247.
2018
Kijima Y, Wang W, Igarashi Y, Yoshitake K, Asakawa S, Suzuki Y, Watabe S, and Kinoshita S. Age-associated different transcriptome profiling in zebrafish and rat: insight into diversity of vertebrate aging, bioRxiv, doi: https://doi.org/10.1101/478438.
Yoshitake K, Igarashi Y, Mizukoshi M, Kinoshita S, Mitsuyama S, Suzuki Y, Saito K, Watabe S, and Asakawa S. Artificially designed hybrids facilitate efficient generation of high-resolution linkage maps. Scientific Reports. 2018,8:16104.
Shinohara M, Kinoshita S, Tang E, Funabara D, Kakinuma M, Maeyama K, Nagai K, Awaji M, Watabe S, and Asakawa S. Comparison of Two Pearl Sacs Formed in the Same Recipient Oyster with Different Genetic Background Involved in Yellow Pigmentation in Pinctada fucata. Mar Biotechnol. 2018,20:594-602.
Elbialy A, Asakawa S, Watabe S, and Kinoshita S. A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways. Biology. 2018,7:4.
De Silva DPN, Tan E, Mizuno N, Hosoya S, Reza Md S, Watabe S, Kinoshita S, and Asakawa S. Transcriptomic analysis of immunoglobulin novel antigen receptor (IgNAR) heavy chain constant domains of brownbanded bamboo shark (Chiloscyllium punctatum). Fish and Shellfish Immunology. 2018,84:370-376.
Igarashi Y, Zhang H, Tan E, Sekino M, Yoshitake K, Kinoshita S, Mitsuyama S, Yoshinaga T, Chow S, Kurogi H, Shinoda A, Han Y.-S, Wakiya R, Mochioka N, Yamamoto T, Kuwada H, Kaji Y, Suzuki Y, Gojobori T, Kobayashi T, Saitoh K, Watabe S, and Asakawa S. Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation. Genes. 2018,9:474.
Xu Z, and Asakawa S. Physiological RNA dynamics in RNA-Seq analysis. Briefings in Bioinformatics. 2018,bby045.
Koyama H, Mizusawa N, Hoashi M, Tan E, Yasumoto K, Jimbo M, Ikeda D, Yokoyama T, Asakawa S, Piyapattanakorn S, Watabe S. Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimp Marsupenaeus japonicus acclimated at different salinities. J Exp Biol. 2018, jeb.168997.
Fu X, Sun J, Tan E, Shimizu K, Reza MS, Watabe S, Asakawa S. High-Throughput Sequencing of the Expressed Torafugu (Takifugu rubripes) Antibody Sequences Distinguishes IgM and IgT Repertoires and Reveals Evidence of Convergent Evolution. Front Immunol. 2018, 21;9:251.
Honein K, Jagoda SSSS, Arulkanthan A, Ushio H, Asakawa S. Draft Genome Sequence of Aeromonas hydrophila Strain Ae25, Isolated from a Septicemic Moribund Koi Carp (Cyprinus carpio) in Sri Lanka. Genome Announc. 2018, 1;6(5).
Zhang X, Mizukoshi M, Zhang H, Tan E, Igarashi Y, Suzuki Y, Mitsuyama S, Kinoshita S, Saito K, Watabe S and Asakawa A. Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population: Case Study of Torafugu (Takifugu rubripes). Genes. 2018,9(3).
Kinoshita S, Ceyhun SB, Md A, Siddique BS, Akolkar DB, Asakawa S, Watabe S. Promoter analysis of the fish gene of slow/cardiac-type myosin heavy chain implicated in specification of muscle fiber types. Fish Physiol Biochem. 2018,44(2):679-691.
Ohmori F, Kinoshita S, Funabara D, Koyama H, Nagai K, Maeyama K, Okamoto K, Asakawa S, Watabe S. Novel Isoforms of N16 and N19 Families Implicated for the Nacreous Layer Formation in the Pearl Oyster Pinctada fucata. Mar Biotechnol. 2018,20(2):155-167.
Asaduzzaman M, Sofiab E, Shakil A, Haque NF, Khan NAM, Ikeda D, Kinoshita S, Abol-Munafi AB. Host gut-derived probiotic bacteria promote hypertrophic muscle progression and upregulate growth-related gene expression of slow-growing Malaysian Mahseer Tor tambroides. Aquaculture Reports. 2018,9:37-45.
2017
Kurokochi H, Zhang S, Takeuchi Y, Tan E, Asakawa S, Lian C. Local-Level Genetic Diversity and Structure of Matsutake Mushroom (Tricholoma matsutake) Populations in Nagano Prefecture, Japan, Revealed by 15 Microsatellite Markers. J Fungi (Basel). 2017, 11;3(2).
Ikeda D, Koyama H, Mizusawa N, Kan-No N, Tan E, Asakawa S, Watabe S. Global gene expression analysis of the muscle tissues of medaka acclimated to low and high environmental temperatures., Comp Biochem Physiol Part D Genomics Proteomics. 2017, 24:19-28.
Fu X, Zhang F, Watabe S, Asakawa S. Immunoglobulin light chain (IGL) genes in torafugu: Genomic organization and identification of a third teleost IGL isotype., Sci Rep. 2017, 7:40416.
Asaduzzaman M, Ikeda D, Abol-Munafi AB, Bulbul M, Ali ME, Kinoshita S, Watabe S, Kader MA. Dietary supplementation of inosine monophosphate promotes cellular growth of muscle and upregulates growth-related gene expression in Nile tilapia Oreochromis niloticus. Aquaculture. 2017, 468:297-306.
Okita K, Tan E, Satone H, Kinoshita S, Asakawa A, Ojima D, Yamazaki H, Sakiyama K, Takatani T, Arakawa O, Hagiwara S, Sakakura Y. Transcriptome analysis of tetrodotoxin sensing and tetrodotoxin action in the central nervous system of tiger puffer Takifugu rubripes juveniles. Fisheries Science. 2017:83(3),401-412.
Kubota K, Tsuchihashi Y, Kogure T, Maeyama K, Hattori F, Kinoshita S, Sakuda S, Nagasawa H, Yoshimura E, Suzuki M. Structural and functional analyses of a TIMP and MMP in the ligament of Pinctada fucata. J Struct Biol. 2017,199:216-224.
Asaduzzaman M, Ikeda D, Kader MA, KinoshitaS, Ghaffar MA, Abol-Munafi AB. Cellular muscle growth and molecular cloning and expression of growth-related gene of Malaysian Mahseer Tor tambroides larvae fed with live and formulated feeds in indoor nursery rearing system. Aquaculture Reports. 2017,5:1-9.
Hiroki Abe, Shugo Watabe, Yoshihiro Ochiai, Shigeru Okada, Naoko Yoshikawa, Shigeharu Kinoshita, Gen Kaneko, and Shigeki Matsunaga: Chemistry of aquatic organisms and their utilization. Introduction for Fisheries and Aquatic Biology (ed. by Hisashi Kurokura and Neelam Ramaiah), Chapter IV, Terapub, Tokyo, 2011, pp. 169-232.
Shugo Watabe and Daisuke Ikeda “Diversity of the pufferfish Takifugu rubripes fast skeletal myosin heavy chain genes.” Comp. Biochem.Physiol., Part D, 1, 28-34(2006)
Shugo Watabe, Ian A. Johnson, and Greg Elgar “International symposium on functional genomics of pufferfish: recent advances and perspective.” Comp. Biochem. Physiol.,Part D, 1, 4-5 (2006).
舩津保浩、深見克哉、渡部終五 “臭気抑制菌 S. nepalensisを用いた水産発酵食品の風味改良- とくにイカ黒作りの臭気改良について” New Food Industry, 48, 22-30(2006).
2005
Daisuke Funabara, Satoshi Kanoh, Marion J. Siegman, Thomas M. Butler, David J. Hartshorne, and Shugo Watabe “Twitchin as a regulator of catch contraction in molluscan smooth muscle.” J. Muscle Res. Cell Motil., 26, 455-460 (2005).
