2020 年度


Zeng C. and Hamada M., “Detection and characterization of ribosome-associated long noncoding RNAs", Methods in Molecular Biology, 2254:179-194, 2021 [HERE]

Sugeno A, Piao W, Yamazaki M, Takahashi K, Arikawa K, Matsunaga H, Hosokawa M, Tominaga D, Goshima Y, Takeyama H, Ohshima T., “Cortical transcriptome analysis after spinal cord injury reveals the regenerative mechanism of central nervous system in CRMP2 knock-in mice", Neural Regeneration Research, 16(7):1258-1265, 2021 [HERE]

Yasutake Y., ...., Aburatani S., ...., and Tamura T., “Bacterial triacylglycerol lipase is a potential cholesterol esterase: Identification of a key determinant for sterol-binding specificity", International Journal of Biological Macromolecules, 167, 578-586, 2021 [HERE]

Kurumida Y., Saito Y. and Kameda T., “Predicting antibody affinity changes upon mutations by combining multiple predictors", Scientific Reports, 10, 19533, 2020 [HERE]

Ono Y., Asai K. and Hamada M., “PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores", Bioinformatics, btaa835, 2020 [HERE]

Matsutani T. and Hamada M., “Parallelized latent Dirichlet allocation provides a novel interpretability of mutation signatures in cancer genomes", Genes, 11(10):1127, 2020 [HERE]

Lee JH., Saito Y., Park SJ. and Nakai K., “Existence and possible roles of independent non-CpG methylation in the mammalian brain", DNA Research, dsaa020, 2020 [HERE]

Inagaki T., ...., Mori K., ...., Takeyama H., et al., “Characterization of a novel alphaherpesvirus isolated from the fruit bat Pteropus lylei in Vietnam", Journal of Virology, 94(18):e00673-20, 2020 [HERE]

Tamano K., Yasunaka Y., Kamishima M., Itoh A., Miura A., Kan E., Koyama Y. and Tamura T., “Enhancement of the productivity of free dihomo-γ-linolenic acid via co-overexpression of elongase and two desaturase genes in Aspergillus oryzae", Journal of Bioscience and Bioengineering, 2020 [HERE]

Nguyen T. D., Saito Y. and Kameda T., “CodonAdjust: a software for in silico design of a mutagenesis library with specific amino acid profiles", Protein Engineering, Design and Selection, gzaa013, 2020 [HERE]

Kosakamoto H., ...., Miyazaki R., Koto A., et al., “Local necrotic cells trigger systemic immune activation via gut microbiome dysbiosis in Drosophila", Cell reports, 32(3), 2020 [HERE]

Zeng C. and Hamada M., “RNA-Seq analysis reveals localization-associated alternative splicing across 13 cell lines", Genes, 11(7), 2020 [HERE]

Umemura M., Kuriiwa K., Tamano K. and Kawarabayasi Y., "Ustiloxin biosynthetic machinery is not compatible between Aspergillus flavus and Ustilaginoidea virens", Fungal Genetics and Biology, 143, 2020 [HERE]

Hosoda S., Nishijima S., Fukunaga T., Hattori M. and Hamada M., "Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation", Microbiome, 8, 95, 2020 [HERE]

Ishida R., Adachi T., Yokota A., Yoshihara H., Aoki K., Nakamura Y. and Hamada M., "RaptRanker: in silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information", Nucleic Acids Research, 2020 [HERE]

Ellegaard K. M., Suenami S., Miyazaki R. and Engel P., "Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species", Current Biology, 2020 [HERE]

Koto A., Nobu M.K., Miyazaki R., "Deep sequencing uncovers caste-associated diversity of symbionts in the social ant Camponotus japonicus", mBio, 2020 [HERE]


露崎隼、細川正人、竹山春子、佐藤政允, “シングルセルRNA-seq解析から明らかになった分裂酵母の目覚め機構”, バイオサイエンスとインダストリー, 78(6):507-509, 2020 [HERE]

齋藤裕, “機械学習による生体分子の機能改良”, JSBi Bioinformatics Review, 1(1):12-17, 2020 [HERE]

齋藤裕、北川 航、亀田倫史, “放線菌におけるタンパク質生産量向上のための新規コドン最適化技術”, バイオサイエンスとインダストリー, 78(5):412-413, 2020 [HERE]


Anbutsu H., and Fukatsu T., "Symbiosis for insect cuticle formation", Cellular Dialogues in the Holobiont, 2020 [HERE]

木口悠也, "ヒト腸内ファージ叢(バイローム)解析", ヒトマイクロバイオーム Vol.2 ~解析技術の進展とデータ駆動型・ターゲット機能型研究最前線~, 2020 [HERE]

2019 年度


Kikuchi Y., et al., "Burkholderia insecticola triggers midgut closure in the bean bug Riptortus pedestris to prevent secondary bacterial infections of midgut crypts", The ISME Journal, 2020 [HERE]

Umemura M., et al., "Promoter tools for further development of Aspergillus oryzae as a platform for fungal secondary metabolite production", Fungal Biology and Biotechnology, 7(3), 2020 [HERE]

Zhang Y. and Hamada M., "MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq", BMC Bioinfomatics, 21(103), 2020 [HERE]

Tsuyuzaki H., et al., "Time-lapse single-cell transcriptomics reveals modulation of histone H3 for dormancy breaking in fission yeast", Nature Communications, 11, 2020 [HERE]

Mie Y., et al., "Electrochemically boosted cytochrome P450 reaction that efficiently produces 25-hydroxyvitamin D3", Journal of Catalysis, 384, 2020 [HERE]

Usuki S., et al., "Nrp1 is activated by konjac ceramide binding-induced structural rigidification of the a1a2 domain", Cells, 9(2), 2020 [HERE]

Yasutake Y., et al., "Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine", Scientific Reports, 10(3021), 2020 [HERE]

Fujita R. et al., "Nucleosome destabilization by nuclear non-coding RNAs", Communications Biology, 3(60), 2020 [HERE]

Watanabe A., Sasaki H., et al., "Effect of dose and timing of Burdock (Arctium lappa) root intake on intestinal microbiota of mice", Microorganisms, 8(2), 2020 [HERE]

Tamura K., Sasaki H., et al., "The timing effects of soy protein intake on mice gut microbiota", Nutrients, 12(1), 2020 [HERE]

Nakato R., et al., "Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells", Epigenetics & Chromatin, 12(77), 2019 [HERE]

Sasaki H., et al., “Mice Microbiota Composition Changes by Inulin Feeding with a Long Fasting Period under a Two-Meals-Per-Day Schedule”, Nutrients, 11(11), 2019 [HERE]

Ishiya K., et al., “MitoIMP: A computational framework for imputation of missing data in low-coverage human mitochondrial genome”, Bioinformatics and Biology Insights, 13(1), 2019 [HERE]

Mori K., et al., “Cellulase productivity of Trichoderma reesei mutants developed in Japan varies with varying pH conditions”, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, 128(3), 2019 [HERE]

Suzuki Y., et al., “Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut”, Microbiome, 27(7), 2019 [HERE]

Sone J., et al., “Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease”, Nature Genetics, 51(8), 2019 [HERE]

Suenami S., et al., “Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima.”, Scientific Reports, 9(9830), 2019 [HERE]

Fukunaga T., et al., “Computational approaches for alternative and transient secondary structures of ribonucleic acids”, Brief Funct Genomics, 18(3), 2019 [HERE]

Yoshida K., et al., “Production of recombinant extracellular cholesterol esterase using consistently active promoters in Burkholderia stabilis”, Biosci Biotechnol Biochem, 83, 2019 [HERE]

Saito Y., et al., “Developing a codon optimization method for improved expression of recombinant proteins in actinobacteria”, Scientific Reports, 9(1), 2019 [HERE]

Ohbayashi T., et al., “Burkholderia gut symbionts associated with European and Japanese populations of the dock bug Coreus marginatus (Coreoidea: Coreidae)”, Microbes and Environments, 34, 2019 [HERE]

Oishi S., et al., “Morphogenesis and development of midgut symbiotic organ of the stinkbug Plautia stali (Hemiptera: Pentatomidae)”, Zoological Letters, 5(16), 2019 [HERE]

Fukunaga T., et al., “a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data”, Front Genet, 10(462), 2019 [HERE]

Tani H., et al., “Identification of RNA biomarkers for chemical safety screening in neural cells derived from mouse embryonic stem cells using RNA deep sequencing analysis.”, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 512(4), 2019 [HERE]

Matsunami M., et al., “A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology”, DNA RESEARCH, 26(3), 2019 [HERE]

Matsutani T., et al., “Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference”, Bioinformatics, 2019 [HERE]

Kutsukake M., et al., “Exaggeration and cooption of innate immunity for social defense”, PNAS, 116(18), 2019 [HERE]

Matsumura T., et al., “Sequential sensing by TLR2 and Mincle directs immature myeloid cells to afford protection against invasive group A streptococcal infection”, Cell Reports, 27(2), 2019 [HERE]

Yoshida K., et al., “Genome sequence of Rhodococcus erythropolis type strain, JCM 3201”, Microbiology Resource Announcements, 8(14), 2019 [HERE]

Tamano K., et al., “Heterologous production of free dihomo-γ-linolenic acid by Aspergillus oryzae and its extracellular release via surfactant”, J Biosci Bioeng, 127, 2019 [HERE]

Mie Y., et al., “Anodized gold surface enables mediator-free and low-overpotential electrochemical oxidation of NADH: A facile method for the development of an NAD+-dependent enzyme biosensor”, Sensor Actuat B-Chem, 288 [HERE]


岩田 大輝他, “属性ベース暗号とIntel SGXを用いた堅牢かつ柔軟なアクセス制御を実現するデータ分析プラットフォームの構築”, 研究報告数理モデル化と問題解決(MPS), 2019 [HERE]

2018 年度


Takayasu L., et al., “Circadian oscillations of microbial and functional composition in the human salivary microbiome”, DNA RESEARCH, 24(3), 2019 [HERE]

Morteza Mahmoudi Sabe, et al., “The hominoid-specific gene DSCR4 is involved in regulation of human leukocyte migration”, bioRixv, 2018 [HERE]

Kajiwara Y., et al., “Genomic Sequence of Saccharomyces cerevisiae BAW-6, a Yeast Strain Optimal for Brewing Barley Shochu.”, Microbiology Resource Announcements, 6(14), 2018 [HERE]

Tominaga D., et al., “Mathematical Model for Small Size Time Series Data of Bacterial Secondary Metabolic Pathways”, Bioinformatics and Biology Insights, 12, 2018 [HERE]

Zeng C., et al., “Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data”, BMC GENOMICS, 19(414), 2018 [HERE]

Inagaki T., et al., “Acyclovir sensitivity and neurovirulence of herpes simplex virus type 1 with amino acid substitutions in the viral thymidine kinase gene, which were detected in the patients with intractable herpes simplex encephalitis previously reported”, JAPANESE JOURNAL OF INFECTIOUS DISEASES, 71(5), 2018 [HERE]

Saito Y., et al., “Machine-learning-guided mutagenesis for directed evolution of fluorescent proteins”, ACS Synthetic Biology, 7(9), 2018 [HERE]

Takahashi M, et al., “Effects of Meal Timing on Postprandial Glucose Metabolism and Blood Metabolites in Healthy Adults”, Nutrients, 10(11), 2018 [HERE]

Ying Y., et al., “Heterologous production of asperipin-2a: proposal for sequential oxidative macrocyclization by a fungi-specific DUF3328 oxidase”, Organic & Biomolecular Chemistry, 17, 2019 [HERE]

ZHANG YIQIAN, et al., “DeepM6ASeq: Prediction and Characterization of m6A-containing Sequences using Deep Learning”, BMC BIOINFORMATICS,19, 2018 [HERE]

Zeng C., et al., “Identifying sequence features that drive ribosomal association for lncRNA”, BMC GENOMICS, 19(10), 2018 [HERE]

Hirohara M., et al., “Convolutional neural network based on SMILES representation of compounds for detecting chemical motif”, BMC Bioinformatics, 19(19), 2018 [HERE]

Yasutake Y., et al., “Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4ʹ-modified nucleoside RT inhibitors”, Biochem. Biophys. Res. Commun., 509 (4), 2019 [HERE]

Sudo H., et al., “An efficient private evaluation of a decision graph”, ICISC 2018 (LNCS), 11369, 2018 [HERE]

Victoria Shabardin, et al., “NanoPipe - a web server for nanopore MinION sequencing data analysis”, GigaScience, 8(2), 2019 [HERE]

Ohbayashi T., et al., “Comparative cytology, physiology and transcriptomics of Burkholderia insecticola in symbiosis with the bean bug Riptortus pedestris and in culture.”, The ISME Journal, 2019 [HERE]

Ito M., et al., “Enrichment of bacteria and alginate lyase genes potentially involved in brown alga degradation in the gut of marine gastropods”, Scientific Reports, 9, 2019 [HERE]

Moriyama M., et al., “Eco-physiological responses to climate change in cicadas”, Physiological Entomology, 44(2), 2019 [HERE]

Koto A., et al., “The oxytocin/vasopressin-like peptide inotocin regulates cuticular hydrocarbon synthesis and water balancing in ants”, Proceedings of the National Academy of Science of the United States of America, 116(12), 2019 [HERE]

Nagata N., et al., “Effects of bowel preparation on the human gut microbiome and metabolome”, Scientific Reports, 9, 2019 [HERE]

Mitsuhashi S., et al., “Robust detection of tandem repeat expansions from long DNA reads”, bioRixv, 2018 [HERE]

Ishiya K., et al., “Outlier detection for minor compositional variations in taxonomic abundance data”, Applied Sciences-Basel, 9(7), 2019 [HERE]


服部 正平他, “メタゲノム解析によるヒト腸内マイクロバイオームの国レベル多様性”, 最新医学, 73(4), 2018 [HERE]

山根順子, "ヒト ES 細胞を用いた高精度の化合物毒性予測システムの構築" [HERE]

安佛 尚志, “ゾウムシの硬さを支える極小ゲノムの共生細菌”, 昆虫と自然, 53(11), 2018 [HERE]

須田亙他, “大規模シークエンスデータを用いたヒトマイクロバイオーム研究”, CLINICAL CALCIUM, 28(10), 2018

2017 年度


Fukunaga T., et al., “RIblast: An ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach”, BIOINFORMATICS, 33(17), 2017 [HERE]

Iwakiri J., et al., “Computational prediction of lncRNA-mRNA interactions by integrating tissue specificity in human transcriptome”, Biology Direct, 8, 2017 [HERE]

Yoda T., et al., “Site-specific gene expression analysis using an automated tissue micro-dissection punching system”, Scientific Reports, 7, 2017 [HERE]

Takeda I., et al., “Exploration of Activated Pathways for Improving Antifungal Agent FR901469 Productivity in Fungal Species No. 11243 Using Comprehensive Pathway Model”, Journal of Biosciences and Medicines, 5(7), 2017 [HERE]

Hosokawa M., et al., “Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics”, Scientific Reports, 5199, 2017 [HERE]

Hosokawa M., et al., “Analysis of environmental bacteria at single-cell level”, IEEE Xplore, 2017 [HERE]

Frith M., et al., “A bestiary of localized sequence rearrangements in human DNA”, BioRxiv, 2017 [HERE]

Anbutsu H., et al., “Small genome symbiont underlies cuticle hardness in beetles”, PNAS, 114(40), 2017 [HERE]

Hirota B., et al., “A novel, extremely elongated, and endocellular bacterial symbiont supports cuticle formation of a grain pest beetle”, mBio, 8(5), 2017 [HERE]

Ogi A., et al., “Characterization of amylolytic enzyme overproducing mutant of Aspergillus luchuensis obtained by ion beam mutagenesis”, JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY, 63(6), 2017 [HERE]

Mori K., et al., “Genome Sequence of Saccharomyces cerevisiae Strain Kagoshima No. 2, Used for Brewing the Japanese Distilled Spirit Shōchū”, Genome Announc., 5(41), 2017 [HERE]

Mariia S. Bogacheva, et al.,“Differences in definitive endoderm induction approaches using growth factors and small molecules”, JOURNAL OF CELLULAR PHYSIOLOGY, 233(4), 2017 [HERE]

Takeda T., et al., “Beyond similarity assessment: Selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian”, BIOINFORMATICS, 34(4), 2018 [HERE]

Hamada M., “In silico approaches to RNA aptamer design”, BIOCHIMIE, 145, 2018 [HERE]

Jaeyoon Chung, et al., “Genome-wide association study of Alzheimer's disease endophenotypes at prediagnosis stages”, Alzheimers & Dementia, 1, 2017 [HERE]

Mona Alshahrani , et al., “DANNP: An efficient artificial neural network pruning tool”, PeerJ, 3(137),2017 [HERE]

Kiritani K., et al., “Module-based systematic construction of plasmids for episomal gene expression in fission yeast”, GENE, 637, 2017 [HERE]

Ivan V. Kulakovskiy, et al., “HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis”, NUCLEIC ACIDS RESEARCH, 46(D1), 2018 [HERE]

Chishima T., et al., “Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs”, Genes, 9(1), 2018 [HERE]

Ito N., et al., “Ribosome incorporation into somatic cells promotes transdifferentiation towards multipotency”, Scientific Reports, 8(1), 2018 [HERE]

Kogawa M., et al., “Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes”, Scientific Reports, 8, 2018 [HERE]

Ohta T., et al., “Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus x yedoensis 'Somei-yoshino' across the Japanese archipelago”, JOURNAL OF PLANT RESEARCH, 131(4), 2018 [HERE]

Sudo H., et al., “secure wavelet matrix: alphabet-friendly privacy-preserving”, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 2018 [HERE]


細川正人他, “環境微生物のシングルセルゲノム解析に向けた技術基盤”, BIO INDUSTRY, 34(6), 2017

大島健志郎他、“ヒト腸内マイクロバイオータのメタゲノム解析”, ファルマシア, 53(11), 2017 [HERE]

服部正平他、“日本人腸内細菌叢のユニークさと国間多様性”, 医学のあゆみ, 264(1), 2018 [HERE]

服部正平他, “日本人腸内細菌叢の特徴と国間多様性”, 糖尿病診療マスター, 15(6), 2017 [HERE]

安佛 尚志, “共生細菌が生み出すゾウムシの硬い外骨格”, 生命誌ジャーナル, 96, 2018 [HERE]

安佛 尚志, “共生細菌が生み出すゾウムシの硬い外骨格”, 季刊「生命誌」BRHカード2018春, 96, 2018 [HERE]

2016 年度


Yamagami K., et al., “Preimplantation embryo-secreted factors modulate maternal gene expression in rat uterus”, CELL AND TISSUE RESEARCH, 364(2), 2016[HERE]

Shibata M., et al., “Transcriptomic features associated with energy production in the muscles of Pacific bluefin tuna and Pacific cod”, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 80(6), 2016[HERE]

Wong PS., et al., “Elucidation of the sequential transcriptional activity in Escherichia coli using time-series RNA-seq data”, BIOINFORMATION, 13(1), 2017[HERE]

Takayama Y., et al., “Brief exposure to small molecules allows induction of mouse embryonic fibroblasts into neural crest-like precursors”, FEBS Letters, 591(4), 2017[HERE]

Maruyama T., et al., “SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions”, BMC BIOINFORMATICS, 18(152),2017[HERE]

Saito Y., et al., “Epigenetic silencing of V(D)J recombination is a major determinant for selective differentiation of mucosal-associated invariant T cells from induced pluripotent stem cells”, PLOS ONE, 12(3), 2017[HERE]

Shibata H., et al., “The habu genome reveals accelerated evolution of venom protein genes”, Scientific Reports, 8(1), 2016[HERE]