Akamatsu S., …., Frith M. C., Yamamoto Y., “Targeted nanopore sequencing using the Flongle device to identify mitochondrial DNA variant”, Scientific Reports, 2024 [HERE]
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]
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]
Watanabe Y., ...., Motono C., et al., “Atg15 is a vacuolar phospholipase that disintegrates organelle membranes”, Cell Reports, 113567, 2023 [HERE]
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]
Toyohara Y., ...., Yamazaki M., ...., Takeyama H., et al., “Identification of target cells of human papillomavirus 18 using squamocolumnar junction organoids”, Cancer Science, 2023 [HERE]
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]
Sato T., ...., Miyazaki R., et al., “The architecture of metabolic networks constrains the evolution of microbial resource hierarchies”, Molecular Biology and Evolution, msad187, 2023 [HERE]
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]
Zeng C., ...., Hamada M., “Landscape of semi-extractable RNAs across five human cell lines”, Nucleic Acids Research, gkad567, 2023 [HERE]
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]
Ng YS., ...., Takeyama H., et al., “White spot syndrome virus (WSSV) modulates lipid metabolism in white shrimp”, Communications Biology, 6:546, 2023 [HERE]
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]
Arai H., Anbutsu H., Nishikawa Y., ...., Hosokawa M., ...., Takeyama H., et al., “Combined actions of bacteriophage-encoded genes in Wolbachia-induced male lethality”, iScience, 26(6):106842, 2023 [HERE]
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]
Takano S., ...., Miyazaki R., et al., “Inference of transcriptome signatures of Escherichia coli in long-term stationary phase”, Scientific Reports, 13: 5647, 2023 [HERE]
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]
Ogawa Y., ...., Saito Y., et al., “Engineering the substrate specificity of toluene degrading enzyme XylM using biosensor XylS and machine learning”, ACS Synthetic Biology, 2023 [HERE]
Zhang H., ...., Frith M. C., “An immune-suppressing protein in human endogenous retroviruses”, Bioinformatics Advances, 3(1):vbad013, 2023 [HERE]
Frith M. C., et al., “How to optimally sample a sequence for rapid analysis”, Bioinformatics, 39(2):btad057, 2023 [HERE]
Ito T., ...., Saito Y., et al., “Selection of target-binding proteins from the information of weakly enriched phage display libraries by deep sequencing and machine learning”, mAbs, 15(1), 2023 [HERE]
Takeda H., ...., Motono C., et al., “A multipoint guidance mechanism for β-barrel folding on the SAM complex”, Nature Structural & Molecular Biology, 30:176–187, 2023 [HERE]
Umemura M., Tamano K., “How to improve the production of peptidyl compounds in filamentous fungi”, Frontiers in Fungal Biology, 2022 [HERE]
Ide K., Nishikawa Y., ...., Tsukada Y., Kogawa M., Wagatsuma R., ...., Hosokawa M., ...., Yura K., …, Takeyama H., “Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral”, Microbiome, 10:220, 2022 [HERE]
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]
Kusakabe M., ...., Wagatsuma R., Yamazaki M., ...., Takeyama H., et al., “Cells with stem-like properties are associated with the development of HPV18-positive cervical cancer”, Cancer Science, 2022 [HERE]
Hamana H., Yasutake Y., et al., “Disruption of SMC-related genes promotes recombinant cholesterol esterase production in Burkholderia stabilis”, Applied Microbiology and Biotechnology, 106:8093–8110, 2022 [HERE]
Matsunaga H., Yamazaki M., Wagatsuma R., Ide K., ...., Hosokawa M., ...., Takeyama H., “Reproducible and sensitive micro-tissue RNA sequencing from formalin-fixed paraffin-embedded tissues for spatial gene expression analysis”, Scientific Report, 19511, 2022 [HERE]
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]
Nishikawa Y., Kogawa M., Hosokawa M., Wagatsuma R., ...., Ide K., ...., Takeyama H., “Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater”, ISME Communications, 92, 2022 [HERE]
Ide K., ...., Nishikawa Y., ...., Takeyama H., “The Effect of Co-Culture of Two Coral Species on Their Bacterial Composition Under Captive Environments”, Marine Biotechnology, 24:871–881, 2022 [HERE]
Ono Y., Katayama K., ...., Kubo K., Tsuyuzaki H., Hamada M., Sato M., “Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation”, Nucleic Acids Research, 2022 [HERE]
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]
Ide K., ...., Takeyama H., Hosokawa M., “Exploring strain diversity of dominant human skin bacterial species using single-cell genome sequencing”, Frontiers in Microbiology, 13:955404, 2022 [HERE]
Hirata Y., ...., Motono C., et al., "Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts", Scientific Reports, 2022 [HERE]
Zeng C., ...., Hamada M., "Bioinformatics approaches for determining the functional impact of repetitive elements on non-coding RNAs", Methods in Molecular Biology, 2509:315-340, 2022 [HERE]
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]
Maki J., ....,Saito Y., et al., "AI and computational chemistry-accelerated development of an alotaketal analogue with conventional PKC selectivity", Chemical Communications, 2022 [HERE]
Tamano K., "Concomitant knockout of target and transporter genes in filamentous fungi by genome co-editing", MicrobiologyOpen, 2022 [HERE]
Nagata N., Nishijima S, et al., "Metagenomic identification of microbial signatures predicting pancreatic cancer from a multinational study", Gastroenterology, 2022 [HERE]
Yamamoto K., ...., Yasutake Y., et al., "Scaffold size-dependent effect on the enhanced uptake of antibiotics and other compounds by Escherichia coli and Pseudomonas aeruginosa", Scientific Reports, 2022 [HERE]
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]
Arikawa K., Ide K., ...., Takeyama H., et al., "Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics", Microbiome, 9, 202, 2021 [HERE]
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]
Sanno R., ...., Ide K., ....,Takeyama H., et al., "Comparative analysis of mitochondrial genomes in Gryllidea (Insecta: Orthoptera): Implications for adaptive evolution in ant-loving crickets", Genome Biology and Evolution, 13(10):evab222, 2021 [HERE]
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]
Nakajima S., ...., Yasutake Y., et al., “Biochemical and structural properties of entecavir-resistant hepatitis B virus polymerase with L180M/M204V mutations", Journal of Virology, 2021 [HERE]
Tajima N., Kumagai T., Saito Y. and Kameda T., “Comparative analysis of the relationship between translation efficiency and sequence features of endogenous proteins in multiple organisms", Genomics, 2021 [HERE]
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]
Irumagawa S., Kobayashi K., Saito Y. et al., “Rational thermostabilisation of four-helix bundle dimeric de novo proteins", Scientific Reports, 11, 7526, 2021 [HERE]
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]
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. 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]
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]
Anbutsu H. and Fukatsu T., "Symbiosis for insect cuticle formation", in "Cellular Dialogues in the Holobiont", 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. and Miyazaki R., "Deep sequencing uncovers caste-associated diversity of symbionts in the social ant Camponotus japonicus", mBio, 2020 [HERE]
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]
Zeng C. and Hamada M., “The impact of alternative splicing on RNA sub cellular localization", bioRxiv, doi: https://doi.org/10.1101/860783, 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]
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]
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]
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]