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Taniue K., …., Hamada M., et al., “The MTR4/hnRNPK complex surveils aberrant polyadenylated RNAs with multiple exons”, Nature Communications, 2024 [HERE]
Kosuge M., Ito J., Hamada M., “Landscape of evolutionary arms races between transposable elements and KRAB-ZFP family”, Scientific Reports, 2024 [HERE]
Yagimoto K., …., Hamada M., “Prediction of antibiotic resistance mechanisms using a protein language model", Bioinformatics, 2024 [HERE]
Suwa S., …., Takeyama H., “In situ Raman hyperspectral analysis of microbial colonies for secondary metabolites screening, Analytical Chemistry, 2024 [HERE]
Frith M. C., “A simple method for finding related sequences by adding probabilities of alternative alignments”, Genome Research, 2024 [HERE]
Zang H., Frith M. C., “Evolution and subfamilies of HERVL human endogenous retrovirus”, Bioinformatics Advances, 2024 [HERE]
Yasutake Y., et al., “Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations”, Scientific Reports, 2024 [HERE]
Nishikawa Y., Wagatsuma R., …., Hosokawa M., Takeyama H., “Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles”, The ISME Journal, 2024 [HERE]
Hidese R., …., Shigi N., et al., “Functional redundancy of ubiquitin-like sulfur-carrier proteins facilitates flexible, efficient sulfur utilization in the primordial archaeon Thermococcus kodakarensis”, mBio, 2024 [HERE]
Heruye S. H., …., Hamada M., et al., “Inflammation primes the kidney for recovery by activating AZIN1 adenosine-to-inosine editing”, The Journal of Clinical Investigation, 2024 [HERE]
Watanabe A., …., Motono C., et al., “The origin of esterase activity of Parkinson's disease causative factor DJ-1 implied by evolutionary trace analysis of its prokaryotic homolog HchA”, Journal of Biological Chemistry, 2024 [HERE]
Sakuma C., …., Takeyama H., et al., “Individual Atg8 paralogs and a bacterial metabolite sequentially promote hierarchical CASM-xenophagy induction and transition”, Cell Reports, 2024 [HERE]
Tamano K., Takayama H., “Double knockout of two target genes via genome co-editing using a nitrate transporter gene nrtA and a putative thiamine transporter gene thiI as selectable markers in Aspergillus oryza”, Journal of Bioscience and Bioengineering, 2024 [HERE]
Wakabayashi Y., ...., Zeng C., Hamada M., et al., “Identification of a novel noncoding RNA transcript TISPL upregulated by stressors that stimulate ATF4”, Gene, 2024 [HERE]
Kifushi M., Nishikawa Y., Hosokawa M., Ide K., ...., Takeyama H., “Analysis of microbial dynamics in the soybean root-associated environments from community to single-cell levels”, Journal of Bioscience and Bioengineering, 2024 [HERE]
安佛 尚志, “技術で未来拓く 産総研の挑戦（318）早大と共同ラボ”, 日刊工業新聞, 7/4, 2024 [HERE]
Adachi T., …., Michishita A., …., Hamada M., et al., “RaptGen-Assisted generation of an RNA/DNA hybrid aptamer against SARS-CoV-2 spike protein”, Biochemistry, 2024 [HERE]
Suenami S,. Sato M., Miyazaki R., “Gustatory responsiveness of honey bees colonized with a defined or conventional gut microbiota”, Microbes and Environments, 39(1), 2024 [HERE]
Sumi S., Hamada M., Saito H., “Deep generative design of RNA family sequences”, Nature Methods, 2024 [HERE]
Jitsuno K., …., Nishikawa Y., …., Mineta K., ...., Takeyama H., et al., “Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere”, mSphere, 2024 [HERE]
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Frith M. C., Ni S., “DNA conserved in diverse animals since the Precambrian controls genes for embryonic development”, Molecular Biology and Evolution, msad275, 2023 [HERE]
Tachikawa K., ...., Frith M. C., et al., “Cost-effective Cas9-mediated targeted sequencing of Spinocerebellar ataxia repeat expansions”, Journal of Molecular Diagnostics, 2023 [HERE]
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Goto K., ...., Takeyama H., ...., Mineta K., “Glutamate-sensing genes are conserved among populations compared to glutamate metabolism genes”, Annals of Nutrition and Metabolism, 2023 [HERE]
Hosoda S., ...., Hamada M., “Probiotic responder identification in cross-over trials for constipation using a Bayesian statistical model considering lags between intake and effect periods”, Computational and Structural Biotechnology Journal, 21:5350-5357, 2023 [HERE]
Hara K., ...., Hamada M., “DeepRaccess: high-speed RNA accessibility prediction using deep learning”, Frontiers in Bioinformatics, 3:1275787, 2023 [HERE]
Koto A., ...., Wong P.S., Aburatani S., et al., “Social isolation shortens lifespan through oxidative stress in ants”, Nature communications, 14, 5493, 2023 [HERE]
Arikawa K., Hosokawa M., “Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics”, Computational and Structural Biotechnology Journal, 2023 [HERE]
Hosokawa M., Nishikawa Y., “Tools for microbial single-cell genomics for obtaining uncultured microbial genomes”, Biophysical Reviews, 2023 [HERE]
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Tonouchi K., ...., Takeyama H., et al., “Structural basis for cross-group recognition of an influenza virus hemagglutinin antibody that targets postfusion stabilized epitope”, PLoS Pathogens, 19(8):e1011554, 2023 [HERE]
Maruyama M., ...., Hamada M., et al., “Neat1 lncRNA organizes the inflammatory gene expressions in the dorsal root ganglion in neuropathic pain caused by nerve injury”, Frontiers in Immunology, 14:1185322, 2023 [HERE]
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Nishimura M., Takeyama H., Hosokawa M., “Enhancing the sensitivity of bacterial single-cell RNA sequencing using RamDA-seq and Cas9-based rRNA depletion”, Journal of Bioscience and Bioengineering, 2023 [HERE]
Sekine K., Onoguchi K., Hamada M., “Transposons contribute to the acquisition of cell type-specific cis-elements in the brain”, Communications Biology, 6:631, 2023 [HERE]
Ohori S., ...., Frith M., et al., “Biallelic structural variations within FGF12 detected by long-read sequencing in epilepsy”, Life Science Alliance, 6(8):e202302025, 2023 [HERE]
Sato K., Hamada M., “Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery”, Briefings in Bioinformatics, 1bbad186, 2023 [HERE]
Ando M., ...., Kubo K., Horii S., ...., Takeyama H., “Single-cell level Raman molecular profiling reveals the classification of growth phases of Chaetoceros tenuissimus”, Journal of Physical Chemistry B, 127(22):5027–5033, 2023 [HERE]
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Hosokawa M., ...., Takeyama H., “Target enrichment of uncultured human oral bacteria with phage-derived molecules found by single-cell genomics”, Journal of Bioscience and Bioengineering, 2023 [HERE]
Kojima S., ...., Takeda A., ...., Hamada M., et al., “Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk”, Nature Genetics, 5:939–951, 2023 [HERE]
Jaeyoon C., ...., Takeyama H., et al., “Alzheimer's disease heterogeneity explained by polygenic risk scores derived from brain transcriptomic profiles”, Alzheimers & Dementia, 2023 [HERE]
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Suenami S., Koto A., Miyazaki R., “Basic structures of gut bacterial communities in eusocial insects”, Insects, 14(5):444, 2023 [HERE]
Tamano K., et al., “Editorial: The use of metabolic engineering techniques to increase the productivity of primary and secondary metabolites within filamentous fungi”, Frontiers in Fungal Biology, 4:1178290, 2023 [HERE]
Kumagai Y., Saito Y., et al., “A multiomics atlas of brown adipose tissue development over time”, Endocrinology, 164(6):bqad064, 2023 [HERE]
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Tamano K., et al., “Overexpression of a predicted transketolase gene and disruption of an α-1,3-glucan synthase gene in Aspergillus oryzae DGLA3 strain enhances the yield of free dihomo-γ-linolenic acid”, Bioscience, Biotechnology & Biochemistry, 87(4), 448–457, 2023 [HERE]
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Yamaguchi H., Saito Y., “EvoOpt: an MSA-guided, fully unsupervised sequence optimization pipeline for protein design.” Machine Learning in Structural Biology Workshop, The 36th Conference on Neural Information Processing Systems (NeurIPS), 2022 [HERE]
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Konishi K., Yasutake Y., et al., “Structural basis for the substrate specificity switching of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. RD004668”, Bioscience Biotechnology and Biochemistry, 87(1):74–81, 2022 [HERE]
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Nishijima S., et al., “Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort”, Nature Communications,13:5252, 2022 [HERE]
Kagiwada H., Motono C., ...., Fukui K., “Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements”, Database, 2022 [HERE]
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Nagata N., Nishijima S., et al., "Population-level metagenomics uncovers distinct effects of multiple medications on the human gut microbiome", Gastroenterology, 2022 [HERE]
Iwao N., ...., Hamada M., "Generative aptamer discovery using RaptGen", Nature Computational Science, 2:378–386, 2022 [HERE]
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Tamano K., "Concomitant knockout of target and transporter genes in filamentous fungi by genome co-editing", MicrobiologyOpen, 2022 [HERE]
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M. C. Frith, "Paleozoic protein fossils illuminate the evolution of vertebrate genomes and transposable elements", Molecular Biology and Evolution, msac068, 2022 [HERE]
Kogawa M., ...., Ide K., Nishikawa Y., ...., Takeyama H., "Single-cell metabolite detection and genomics reveals uncultivated talented producer", PNAS Nexus, 1(1):pgab007, 2022 [HERE]
Aikawa T., ...., Anbutsu H., "Cytoplasmic incompatibility in the semivoltine longicorn beetle Acalolepta fraudatrix (Coleoptera: Cerambycidae) double infected with Wolbachia", PLoS ONE, 17(1):e0261928, 2022 [HERE]
Tamano K., et al., "Major involvement of two laccase genes in conidial pigment biosynthesis in Aspergillus oryzae", Applied Microbiology and Biotechnology, 106:287–300, 2022 [HERE]
Tamano K., Yoshimi A., "Metabolic engineering techniques to increase the productivity of primary and secondary metabolites within filamentous fungi", Frontiers in Fungal Biology, 2:743070, 2021 [HERE]
Saito Y., et al., "Machine-learning-guided library design cycle for directed evolution of enzymes: The effects of training data composition on sequence space exploration", ACS Catalysis, 11, 14615-14624, 2021 [HERE]
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Hamaguchi Y., Zeng C., Hamada M., "Impact of human gene annotations on RNA-seq differential expression analysis", BMC Genomics, 22:730, 2021 [HERE]
Kiguchi Y., Nishijima S., et al., "Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads", DNA Research, 28(6):dsab019, 2021 [HERE]
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Suzuki G., Saito Y., Seki M. et al., "Machine learning approach for discrimination of genotypes based on bright-field cellular images", npj Systems Biology and Applications, 7, 31, 2021 [HERE]
Onoguchi M., Zeng C., Matsumaru A. and Hamada M., “Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements”, NAR Genomics and Bioinformatics, 3(3), 2021 [HERE]
Yamaguchi H. and Saito Y., “Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins", Briefings in Bioinformatics, bbab234, 2021 [HERE]
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Iuchi H., Matsutani T., Yamada K., Iwano N., Sumi S., Hosoda S., Zhao S., Fukunaga T. and Hamada M., “Representation learning applications in biological sequence analysis", Computational and Structural Biotechnology Journal, 19:3198-3208, 2021 [HERE]
Takahashi S., ....,Zeng C., ...., Hamada M. et al., “Long non-coding RNA CRNDE is involved in resistance to EGFR tyrosine kinase inhibitor in EGFR-mutant lung cancer via eIF4A3/MUC1/EGFR signaling", International Journal of Molecular Sciences, 22(8):4005, 2021 [HERE]
Wong P. S., Tamano K. and Aburatani S., “Improvement of free fatty acid secretory productivity in Aspergillus oryzae by comprehensive analysis on time-series gene expression", Frontiers in Microbiology, 12:605095, 2021 [HERE]
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Tsuyuzaki H., Ujiie R. and Sato M., “Wake-up alarm: virtual time-lapse gene expression landscape illuminates mechanisms underlying dormancy breaking of germinating spores", Current Genetics, 2021 [HERE]
Saber M., Karimiavargani M., Uzawa T., Hettiarachchi N., Hamada M., Ito Y. and Saitou N., "Possible roles for the hominoid-specific DSCR4 gene in human cells", Genes & Genetic Systems, 96(1):1-11, 2021 [HERE]
Iuchi H. and Hamada M., “Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression", NAR Genomics and Bioinformatics, 3(1), 2021 [HERE]
Zhang Y. and Hamada M., “Identification of m6A-associated RNA binding proteins using an integrative computational framework", Frontiers in Genetics, 12:625797, 2021 [HERE]
Miyazaki Y., ...., Saito Y. et al., “Adipose-derived mesenchymal stem cells differentiate into heterogeneous cancer-associated fibroblasts in a stroma-rich xenograft model", Scientific Reports, 11, 4690, 2021 [HERE]
Wolter L. A., Suenami S. and Miyazaki R., “Frischella japonica sp. nov., an anaerobic member of the Orbales in the Gammaproteobacteria, isolated from the gut of the eastern honey bee, Apis cerana japonica Fabricius", International Journal of Systematic and Evolutionary Microbiology, 2021 [HERE]
Zeng C., Onoguchi M. and Hamada M., “Association analysis of repetitive elements and R-loop formation across species", Mobile DNA, 12, 3, 2021 [HERE]
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Sugeno A., Piao W., Yamazaki M., Takahashi K., Arikawa K., Matsunaga H., Hosokawa M., Tominaga D., Goshima Y., Takeyama H. and 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]
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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]
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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]
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齋藤 裕, “ゲノムは遺伝子を単語とする文章である（か？）”, バイオサイエンスとインダストリー, 79(1):49, 2021 [HERE]
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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]
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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]
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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]
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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]
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