Computational Bio Big-Data Open Innovation Laboratory

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2024/10/24: ”Targeted nanopore sequencing using the Flongle device to identify mitochondrial DNA variant” by Dr. Martin C. Frith, a Chief Senior Researcher of the Sequence Analysis Algorithms Team, as the co-author, was published in “Scientific Reports“. [HERE] New!
2024/10/17: ”The MTR4/hnRNPK complex surveils aberrant polyadenylated RNAs with multiple exons” by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the co-author, was published in “Nature Communications“. [HERE]
2024/10/07: ”Landscape of evolutionary arms races between transposable elements and KRAB-ZFP family” by Mr. Masato Kosuge, an RA of the Sequence Analysis Algorithms Team, as the 1st author, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the corresponding author, was published in “Scientific Reports“. [HERE]
2024/09/10: ”Prediction of antibiotic resistance mechanisms using a protein language model” by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the corresponding author, was published in “Bioinformatics“. [HERE]
2024/08/31: ”In situ Raman hyperspectral analysis of microbial colonies for secondary metabolites screening” by Mr. Shunnosuke Suwa, an RA of the Single-Cell Data Analysis Team, as the 1st author, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the corresponding author, was published in “Analytical Chemistry“. [HERE]
2024/08/16: ”A simple method for finding related sequences by adding probabilities of alternative alignments” by Dr. Martin C. Frith, a Chief Senior Researcher of the Sequence Analysis Algorithms Team, as the 1st author, was published in “Genome Research“. [HERE] New!
2024/07/30: ”Evolution and subfamilies of HERVL human endogenous retrovirus” by Dr. Martin C. Frith, a Chief Senior Researcher of the Sequence Analysis Algorithms Team, as the corresponding author, was published in “Bioinformatics Advances“. [HERE]
2024/07/08: ”Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations” by Dr. Yoshiaki Yasutake, a Senior Researcher of the Single-Cell Data Analysis Team, as the 1st author, was published in “Scientific Reports". [HERE]
2024/07/08: ”Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles” by Dr. Yohei Nishikawa, a Researcher of the Single-Cell Data Analysis Team, Mr. Ryota Wagatsuma, an RA of the Team, both as the co-1st author, Associate Prof. Masahito Hosokawa, a member of the Team, as a co-author, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the co-corresponding author, was published in “The ISME Journal”. [HERE]
2024/07/08: ”Functional redundancy of ubiquitin-like sulfur-carrier proteins facilitates flexible, efficient sulfur utilization in the primordial archaeon Thermococcus kodakarensis” by Dr. Naoki Shigi, the Deputy Director of the CBBD-OIL, as the co-corresponding author, is now available online in “mBio". [HERE]
2024/07/02: ”Inflammation primes the kidney for recovery by activating AZIN1 adenosine-to-inosine editing” by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as a co-author, is now available online in “The Journal of Clinical Investigation". [HERE]
2024/06/13: ”The origin of esterase activity of Parkinson's disease causative factor DJ-1 implied by evolutionary trace analysis of its prokaryotic homolog HchA” by Dr. Chie Motono, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was available online in “Journal of Biological Chemistry”. [HERE]
2024/04/23: ”Individual Atg8 paralogs and a bacterial metabolite sequentially promote hierarchical CASM-xenophagy induction and transition” by Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the co-author, was published in “Cell Reports”. [HERE]
2024/04/23: ”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 oryzae” by Dr. Koichi Tamano, a Senior Researcher of the Single-Cell Data Analysis Team, as the 1st author, was published in “Journal of Bioscience and Bioengineering”. [HERE]
2024/04/15: ”Identification of a novel noncoding RNA transcript TISPL upregulated by stressors that stimulate ATF4” by Dr. Yutaro Wakabayashi, a former RA of the Sequence Analysis Algorithms Team, as the 1st author, and Dr. Chao Zeng, a member of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the co-authors, was published in “Gene”. [HERE]
2024/04/04: ”Analysis of microbial dynamics in the soybean root-associated environments from community to single-cell levels” by Ms. Masako Kifushi, Dr. Yohei Nishikawa, Associate Prof. Masahito Hosokawa, Dr.Keigo Ide, former and current CBBD-OIL members, as the 1st and co-authors, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the corresponding author, was published in “Journal of Bioscience and Bioengineering”. [HERE]
2024/03/08: ”RaptGen-Assisted generation of an RNA/DNA hybrid aptamer against SARS-CoV-2 spike protein” by Mr. Akiya Michishita, an RA of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the co-authors, was published in “Biochemistry”. [HERE]
2024/03/07: ”Gustatory responsiveness of honey bees colonized with a defined or conventional gut microbiota” by Dr. Ryo Miyazaki, a Senior Researcher of the Single-Cell Data Analysis Team, as the corresponding author, was published in “Microbes and Environments”. [HERE]
2024/01/18: ”Deep generative design of RNA family sequences” by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the corresponding author, was published in “Nature Methods”. [HERE]
2024/01/03: ”Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere” by Ms. Kana Jitsuno, an RA of the Single-Cell Data Analysis Team, as the 1st author, Dr. Yohei Nishikawa, a Researcher of the Single-Cell Data Analysis Team, Prof. Katsuhiko Mineta, a member of the Single-Cell Data Analysis Team, as co-authors, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the corresponding author, was published in “mSphere”. [HERE]
2023/12/19: ”Atg15 is a vacuolar phospholipase that disintegrates organelle membranes” by Dr. Chie Motono, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in “Cell Reports”. [HERE]
2023/12/12: ”DNA conserved in diverse animals since the Precambrian controls genes for embryonic development” by Dr. Martin C. Frith, a Chief Senior Researcher of the Sequence Analysis Algorithms Team, as the 1st author, was published in “Molecular Biology and Evolution”. [HERE]
2023/11/24: ”Cost-effective Cas9-mediated targeted sequencing of Spinocerebellar ataxia repeat expansions” by Dr. Martin C. Frith, a Chief Senior Researcher of the Sequence Analysis Algorithms Team, as the co-author, was published in “Journal of Molecular Diagnostics”. [HERE]
2023/11/23: ”Identification of target cells of human papillomavirus 18 using squamocolumnar junction organoids” by Dr. Miki Yamazaki, a former member of the Single-Cell Data Analysis Team, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the co-authors, was published in “Cancer Science”. [HERE]
2023/11/11: ”Glutamate-sensing genes are conserved among populations compared to glutamate metabolism genes” by Prof. Katsuhiko Mineta, a member of the Single-Cell Data Analysis Team, as the corresponding author, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as a co-author, was published in “Annals of Nutrition and Metabolism”. [HERE]
2023/10/26: ”Probiotic responder identification in cross-over trials for constipation using a Bayesian statistical model considering lags between intake and effect periods” by Dr. Shion Hosoda , a former RA of the Sequence Analysis Algorithms Team, as the 1st author, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the corresponding author, was published in “Computational and Structural Biotechnology Journal". [HERE]
2023/10/10: ”DeepRaccess: high-speed RNA accessibility prediction using deep learning” by Mr. Kaisei Hara , a former RA of the Sequence Analysis Algorithms Team, as the 1st author, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the corresponding author, was published in “Frontiers in Bioinformatics". [HERE]
2023/09/27: ”Social isolation shortens lifespan through oxidative stress in ants” by Dr. AKiko Koto, a Senior Researcher of the Single-Cell Data Analysis Team, as the 1st and the corresponding authors, Dr. Pui Shan Won, a former PD of the CBBD-OIL, and Dr. Sachiyo Aburatani, the former Deputy Director of the CBBD-OIL, as the co-authors, was published in “Nature communications”. [HERE]
2023/09/12: ”Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics” by Associate Prof. Masahito Hosokawa, a member of the Single-Cell Data Analysis Team, as the corresponding author, was published in “Computational and Structural Biotechnology Journal”. [HERE]
2023/09/08: ”Tools for microbial single-cell genomics for obtaining uncultured microbial genomes” by Associate Prof. Masahito Hosokawa, a member of the Single-Cell Data Analysis Team, as the 1st and the corresponding author, and Dr. Yohei Nishikawa, a Researcher of the Single-Cell Data Analysis Team, as a co-author, was published in “Biophysical Reviews”. [HERE]
2023/08/24: ”The architecture of metabolic networks constrains the evolution of microbial resource hierarchies” by Dr. Ryo Miyazaki, a Senior Researcher of the Single-Cell Data Analysis Team, as a co-author, was published in “Molecular Biology and Evolution”. [HERE]
2023/08/09: ”Structural basis for cross-group recognition of an influenza virus hemagglutinin antibody that targets postfusion stabilized epitope” by Prof. Haruko Takeyama, the Director of the CBBD-OIL, as a co-author, was published in “PLoS Pathogens”. [HERE]
2023/08/08: ”Neat1 lncRNA organizes the inflammatory gene expressions in the dorsal root ganglion in neuropathic pain caused by nerve injury” by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as a co-author, was published in “Frontiers in Immunology”. [HERE]
2023/07/19: ”Landscape of semi-extractable RNAs across five human cell lines” by Dr. Chao Zeng, a member of the Sequence Analysis Algorithms Team, as the 1st author, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the corresponding author, was published in “Nucleic Acids Research”. [HERE]
The press release of the research activity, “Unraveling the mystery of semi-extractable RNAs from human cell lines,” has been posted on the Waseda University’s website[HERE] and cited on “EurekAlert!” by AAAS.[HERE]
2023/06/11: ”Enhancing the sensitivity of bacterial single-cell RNA sequencing using RamDA-seq and Cas9-based rRNA depletion” by Prof. Haruko Takeyama, the Director of the CBBD-OIL, as a co-author, Associate Prof. Masahito Hosokawa, a member of the Single-Cell Data Analysis Team, as the corresponding author, was published in “Journal of Bioscience and Bioengineering”. [HERE]
2023/06/10: ”Transposons contribute to the acquisition of cell type-specific cis-elements in the brain” by Mr. Kotaro Sekine, a former RA of the Sequence Analysis Algorithms Team, as the 1st author, Dr. Masahiro Onoguchi, a former PD of the Sequence Analysis Algorithms Team, Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, both as the corresponding authors, was published in “Communications Biology”. [HERE]
2023/06/07: ”Biallelic structural variations within FGF12 detected by long-read sequencing in epilepsy” by Dr. Martin C. Frith, a Chief Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in “Life Science Alliance”. [HERE]
2023/05/27: ”Single-cell level Raman molecular profiling reveals the classification of growth phases of Chaetoceros tenuissimus” by Mr. Koya Kubo, Dr. Shunpei Horii, former RAs of the Single-Cell Data Analysis Team, as the co-authors and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the corresponding author, was published in “Journal of Physical Chemistry B”. [HERE]
2023/05/25: ”Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery” by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as a co-author, was published in “Briefings in Bioinformatics”. [HERE]
2023/05/20: ”White spot syndrome virus (WSSV) modulates lipid metabolism in white shrimp” by Prof. Haruko Takeyama, the Director of the CBBD-OIL, as a co-author, was published in “Communications Biology”. [HERE]
2023/05/13: ”Target enrichment of uncultured human oral bacteria with phage-derived molecules found by single-cell genomics” by Associate Prof. Masahito Hosokawa, a member of the Single-Cell Data Analysis Team, as the 1st and the corresponding author, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as a co-author, was published in “Journal of Bioscience and Bioengineering”. [HERE]
2023/05/11: ”Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk ” by Mr. Atsushi Takeda, a RA of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the co-authors, was published in “Nature Genetics”. [HERE]
2023/05/11: ”Alzheimer's disease heterogeneity explained by polygenic risk scores derived from brain transcriptomic profiles ” by Prof. Haruko Takeyama, the Director of the CBBD-OIL, as a co-author, was published in “Alzheimers & Dementia”. [HERE]
2023/05/10: ”Combined actions of bacteriophage-encoded genes in Wolbachia-induced male lethality” by Dr. Hisashi Anbutsu, the Deputy Director of the CBBD-OIL, Dr. Yohei Nishikawa, a Researcher of the Single-Cell Data Analysis Team, both as the co-1st authors, Associate Prof. Masahito Hosokawa, a member of the Single-Cell Data Analysis Team, as a co-author, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the co-corresponding author, was published in “iScience”. [HERE]
2023/05/08: ”Basic structures of gut bacterial communities in eusocial insects” by Dr. AKiko Koto, a Senior Researcher of the Single-Cell Data Analysis Team, as a co-author and Dr. Ryo Miyazaki, a Senior Researcher of the Single-Cell Data Analysis Team, as the corresponding author, was published in “Insects”. [HERE]
2023/04/21: ”Editorial: The use of metabolic engineering techniques to increase the productivity of primary and secondary metabolites within filamentous fungi” by Dr. Koichi Tamano, a Senior Researcher of the Single-Cell Data Analysis Team, as the 1st and corresponding author, was published in “Frontiers in Fungal Biology”. [HERE]
2023/04/21: ”A multiomics atlas of brown adipose tissue development over time” by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in “Endocrinology”. [HERE]
2023/04/06: ”Inference of transcriptome signatures of Escherichia coli in long-term stationary phase” by Dr. Ryo Miyazaki, a Senior Researcher of the Single-Cell Data Analysis Team, as a co-author, was published in “Scientific Reports”. [HERE]
2023/04/01: ”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” by Dr. Koichi Tamano, a Senior Researcher of the Single-Cell Data Analysis Team, as the 1st author, was published in “Bioscience, Biotechnology & Biochemistry”. [HERE]

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