Computational Bio Big-Data Open Innovation Laboratory

News

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. Masato 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. Masato 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. Masato 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. Masato 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. Masato 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]
2023/02/03: ”Engineering the substrate specificity of toluene degrading enzyme XylM using biosensor XylS and machine learning” by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in “ACS Synthetic Biology”. [HERE]
2023/02/02: ”An immune-suppressing protein in human endogenous retroviruses” 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]
2023/01/25: ”How to optimally sample a sequence for rapid analysis” by Dr. Martin C. Frith, a Chief Senior Researcher of the Sequence Analysis Algorithms Team, as the 1st author, was published in “Bioinformatics”. [HERE]
2023/01/22: ”Selection of target-binding proteins from the information of weakly enriched phage display libraries by deep sequencing and machine learning” by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in “mAbs”. [HERE]
2023/01/05: ”A multipoint guidance mechanism for β-barrel folding on the SAM complex” by Dr. Chie Motono, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in “Nature Structural & Molecular Biology”. [HERE]
2022/12/22: ”How to improve the production of peptidyl compounds in filamentous fungi” by Dr. Koichi Tamano, a Senior Researcher of the Single-Cell Data Analysis Team, as the corresponding author, was published in “Frontiers in Fungal Biology”. [HERE]
2022/12/12: ”Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral” by Dr. Keigo Ide, Dr. Yohei Nishikawa, Ms. Yuko Tsukada, Dr. Masato Kogawa, Mr. Ryota Wagatsuma, Associate Prof. Masato Hosokawa, Prof. Kei Yura, 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 “Microbiome”. [HERE]
2022/12/05: “EvoOpt: an MSA-guided, fully unsupervised sequence optimization pipeline for protein design” by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published at MLSB(Machine Learning in Structural Biology) Workshop. [HERE]
2022/11/20: ”Cells with stem-like properties are associated with the development of HPV18-positive cervical cancer” by Mr. Ryota Wagatsuma, an RA of the Single-Cell Data Analysis Team, Ms. Miki Yamazaki, a former RA of the Biofunction Analysis Team, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the co-authors, was published in “Cancer Science”. [HERE]
2022/11/18: ”Disruption of SMC-related genes promotes recombinant cholesterol esterase production in Burkholderia stabilis” by Dr. Yoshiaki Yasutake, a Senior Researcher of the Single-Cell Data Analysis Team, as a co-author, was published in “Applied Microbiology and Biotechnology”. [HERE]
2022/11/14: ”Reproducible and sensitive micro-tissue RNA sequencing from formalin-fixed paraffin-embedded tissues for spatial gene expression analysis” by Ms. Miki Yamazaki, a former RA of the Biofunction Analysis Team, Mr. Ryota Wagatsuma, an RA of the Single-Cell Data Analysis Team, Dr. Keigo Ide, a former RA of Single-Cell Data Analysis Team, Associate Prof. Masato Hosokawa, a member 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 “Scientific　Report”. [HERE]
2022/10/28: ”Structural basis for the substrate specificity switching of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. RD004668” by Dr. Yoshiaki Yasutake, a Senior Researcher of the Single-Cell Data Analysis Team, as a co-author, was published in “Bioscience Biotechnology and Biochemistry”. [HERE]
2022/10/19: ”Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation” by Mr. Kenta Katayama, a former RA of the Sequence Analysis Algorithms Team, Mr. Kento Kubo, a RA of the Sequence Analysis Algorithms Team, Dr. Hayato Tsuyuzaki, a former RA of the Biofunction Analysis Team, as the co-authors, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the co-corresponding authors, was published in “Nucleic Acids Research”. [HERE]
2022/10/03: “The Effect of Co-Culture of Two Coral Species on Their Bacterial Composition Under Captive Environments” by Mr. Keigo Ide, a former RA of the Single-Cell Data Analysis Team, as the 1st author, Dr. Yohei Nishijima, a member of the Single-Cell Data Analysis Team, Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the corresponding author, was published in "Marine Biotechnology". [HERE]
2022/09/29: ”Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater” by Dr. Yohei Nishikawa, a Researcher of the Single-Cell Data Analysis Team as the 1st author, Associate Prof. Masato Hosokawa, a member of the Single-Cell Data Analysis Team, Mr. Ryota Agatsuma, an RA of Single-Cell Data Analysis Team, Mr. Keigo Ide, a formor RA of Single-Cell Data Analysis Team and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the corresponding author, was published in “ ISME Communications”. [HERE]
2022/09/06: “Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort” by Dr. Suguru Nishijima, a former PD of the Biofunction Analysis Team, as the 1st author, was published in "Nature Communications". [HERE]
2022/08/22: “Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements” by Dr. Chie Motono, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, Dr. Kazuhiko Fukui, a former member of the CBBD-OIL, as the corresponding author was published in "Database". [HERE]
2022/08/05: “Exploring strain diversity of dominant human skin bacterial species using single-cell genome sequencing” by Mr. Keigo Ide, a former RA of the Single-Cell Data Analysis Team, as the 1st author, Prof. Haruko Takeyama, the Director of the CBBD-OIL, as a co-author, and Associate Prof. Masato Hosokawa, a member of the Single-Cell Data Analysis Team, as the corresponding author, was published in "Frontiers in Microbiology". [HERE]
2022/07/11: "Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts" by Dr. Chie Motono, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in "Scientific Reports". [HERE]
2022/07/08: "Bioinformatics approaches for determining the functional impact of repetitive elements on non-coding RNAs" by Dr. Chao Zeng, former PD 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 "Methods in Molecular Biology". [HERE]
2022/07/01: "Population-level metagenomics uncovers distinct effects of multiple medications on the human gut microbiome" by Dr. Suguru Nishijima, a former PD of the Biofunction Analysis Team, as a corresponding author, was published in "Gastroenterology". [HERE]
2022/06/07: The press release of a research activity, “Scientists Develop Novel Computational Model for Aptamer Generation, With Wide Applications”, involving Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, has been posted on the Waseda University’s website. [HERE]
2022/05/18: "AI and computational chemistry-accelerated development of an alotaketal analogue with conventional PKC selectivity" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in "Chemical Communications". [HERE]
2022/04/13: “Concomitant knockout of target and transporter genes in filamentous fungi by genome co-editing” by Dr. Koichi Tamano, a Senior Researcher of the Single-Cell Data Analysis Team, was published in “MicrobiologyOpen”. [HERE]
2022/04/08: "Metagenomic identification of microbial signatures predicting pancreatic cancer from a multinational study" by Dr. Suguru Nishijima, a former PD of the Biofunction Analysis Team, as a co-author, was published in "Gastroenterology". [HERE]
2022/04/04: “Scaffold size-dependent effect on the enhanced uptake of antibiotics and other compounds by Escherichia coli and Pseudomonas aeruginosa” by Dr. Yoshiaki Yasutake, a Senior Researcher of the Single-Cell Data Analysis Team, as a co-author, was published in “Scientific Reports”. [HERE]
2022/03/28: "Paleozoic protein fossils illuminate the evolution of vertebrate genomes and transposable elements" by Dr. Martin C. Frith, a Senior Researcher of the Sequence Analysis Algorithms Team, was published in "Molecular Biology and Evolution". [HERE]
2022/03/02: "Single-cell metabolite detection and genomics reveals uncultivated talented producer" by Dr. Masato Kogawa, a former member of the Biofunction Analysis Team, as the 1st author, Mr. Keigo Ide, RA of the Single-Cell Data Analysis Team, Dr. Yohei Nishikawa, the participant of the CBBD-OIL, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as the corresponding author, was published in "PNAS Nexus". [HERE]
2022/01/14: "Cytoplasmic incompatibility in the semivoltine longicorn beetle Acalolepta fraudatrix (Coleoptera: Cerambycidae) double infected with Wolbachia" by Dr. Hisashi Anbutsu, the leader of the Single-Cell Data Analysis Team, as a co-author, was published in "PLoS ONE". [HERE]

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