Japanese

The aim of CBBD-OIL is to elucidate mechanisms of biological phenomena in a collaborative effort between Waseda University and National Institute of Advanced Industrial Science and Technology (AIST). Waseda University accumulates huge biological data depending on the latest experimental technologies, and has advanced mathematical methods. AIST has several types of bioinformatics techniques and theoretical biology methods for biological data. By combining the strengths of both organizations, we try to reveal the systems behind cellular biology and living organisms. We focus on the research and development of advanced computational methods that include but are not limited to:

Furthermore, by building up an intensive industry-academic-government network, CBBD-OIL provides opportunities to strengthen goal-oriented fundamental research, which leads to “bridging” the gap between researchers and private sectors, with our cutting-edge technologies of life information analysis that is soon to become the global standard.

Furthermore

News

2021/07/21
"Machine learning approach for discrimination of genotypes based on bright-field cellular images" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in "npj Systems Biology and Applications". [HERE]
2021/07/02
"Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements" by Dr. Masahiro Onoguchi, former PD of the Sequence Analysis Algorithms Team, as the 1st author, Dr. Chao Zeng, former PD of the Sequence Analysis Algorithms Team, as a co-author, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the corresponding author, was published in "NAR Genomics and Bioinformatics". [HERE]
2021/06/26
"Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as the corresponding author, was published in "Briefings in Bioinformatics". [HERE]
2021/06/02
"Biochemical and structural properties of entecavir-resistant hepatitis B virus polymerase with L180M/M204V mutations" by Dr. Yoshiaki Yasutake, a Senior Researcher of the Biofunction Analysis Team, as a co-author, was published in "Journal of Virology". [HERE]
2021/05/28
"Comparative analysis of the relationship between translation efficiency and sequence features of endogenous proteins in multiple organisms" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in "Genomics". [HERE]
2021/05/23
"Representation learning applications in biological sequence analysis" by Dr. Hitoshi Iuchi, a former PD of the Sequence Analysis Algorithms Team, as the 1st & corresponding author, Mr. Taro Matsutani, Mr. Shion Hosoda, RAs of the Sequence Analysis Algorithms Team, as co-authors, 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]
2021/04/13
"Long non-coding RNA CRNDE is involved in resistance to EGFR tyrosine kinase inhibitor in EGFR-mutant lung cancer via eIF4A3/MUC1/EGFR signaling" by Dr. Chao Zeng, a former PD of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as co-authors, was published in "International Journal of Molecular Sciences". [HERE]
2021/04/12
"Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model" by Mr. Shion Hosoda, RA of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, was adopted for an oral presentation at the ISMB/ECCB2021. [HERE]
2021/04/09
"Improvement of free fatty acid secretory productivity in Aspergillus oryzae by comprehensive analysis on time-series gene expression" by Dr. Koichi Tamano, a Senior Researcher of the Biofunction Analysis Team, and Dr. Sachiyo Aburatani, the Deputy Director of CBBD-OIL, both as the corresponding authors, was published in "Frontiers in Microbiology". [HERE]
2021/04/06
"Rational thermostabilisation of four-helix bundle dimeric de novo proteins" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in "Scientific Reports". [HERE]
2021/03/29
"Wake-up alarm: virtual time-lapse gene expression landscape illuminates mechanisms underlying dormancy breaking of germinating spores" by Dr. Hayato Tsuyuzaki, RA of the Biofunction Analysis Team, as the first-author, was published in "Current Genetics". [HERE]
2021/03/24
"Possible roles for the hominoid-specific DSCR4 gene in human cells" by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as a co-author, was published in "Genes & Genetic Systems". [HERE]
2021/03/24
"Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression" by Dr. Hitoshi Iuchi , PD of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, was published in "NAR Genomics and Bioinformatics". [HERE]
2021/03/01
"Identification of m6A-associated RNA binding proteins using an integrative computational framework" by Dr. Yiqian Zhang , a former RA of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, both as the corresponding authors, was published in "Frontiers in Genetics". [HERE]
2021/02/25
"Adipose-derived mesenchymal stem cells differentiate into heterogeneous cancer-associated fibroblasts in a stroma-rich xenograft model" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in "Scientific Reports". [HERE]
2021/02/22
"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" by Dr. Ryo Miyazaki, a Senior Researcher of the Biofunction Analysis Team, as the corresponding author, was published in "International Journal of Systematic and Evolutionary Microbiology". [HERE]
2021/01/21
"Association analysis of repetitive elements and R-loop formation across species" by Dr. Chao Zeng, Dr. Masahiro Onoguchi, PDs of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, was published in "Mobile DNA". [HERE]
2020/12/28
A preprint "Association analysis of repetitive elements and R-loop formation across species" by Dr. Chao Zeng, Dr. Masahiro Onoguchi, PDs of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, was introduced on the website "preLights". [HERE]
2020/12/17
"Detection and characterization of ribosome-associated long noncoding RNAs" by Dr. Chao Zeng, PD of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, was published in "Methods in Molecular Biology". [HERE]
2020/12/12
"Cortical transcriptome analysis after spinal cord injury reveals the regenerative mechanism of central nervous system in CRMP2 knock-in mice" by Ms. Ayaka Sugeno, a former RA of the Biofunction Analysis Team, as the 1st author, Ms. Miki Yamazaki, a former RA of the Biofunction Analysis Team, Dr. Daisuke Tominaga, a Senior Researcher of the Biofunction Analysis Team, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as co-authors, was published in "Neural Regeneration Research". [HERE]
2020/12/03
"Bacterial triacylglycerol lipase is a potential cholesterol esterase: Identification of a key determinant for sterol-binding specificity" by Dr. Yoshiaki Yasutake, a Senior Researcher of the Biofunction Analysis Team, as the 1st author, Dr. Sachiyo Aburatani, the Deputy Director of CBBD-OIL, as a co-author, and Dr. Tomohiro Tamura, a former Supervisor of CBBD-OIL, as the corresponding author, was published online in "International Journal of Biological Macromolecules". [HERE]
2020/11/11
"Predicting antibody affinity changes upon mutations by combining multiple predictors" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in "Scientific Reports". [HERE]
2020/09/25
"PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores" by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the corresponding author, was published in "Bioinformatics". [HERE]
2020/09/25
"Parallelized latent Dirichlet allocation provides a novel interpretability of mutation signatures in cancer genomes" by Mr. Taro Matsutani, a former RA of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, was published in "Genes". [HERE]
2020/09/24
"Existence and possible roles of independent non-CpG methylation in the mammalian brain" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in "DNA Research". [HERE]
2020/08/31
"Characterization of a novel alphaherpesvirus isolated from the fruit bat Pteropus lylei in Vietnam" by Mr. Takuya Inagaki, a former RA of the Biofunction Analysis Team, as the 1st author, Dr. Kazuki Mori, a former member of the Systems Biology Team, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as co-authors, was published in "Journal of Virology". [HERE]
2020/08/23
The book, "Cellular Dialogues in the Holobiont", a chapter of which was written by Dr. Hisashi Anbutsu, the leader of the Biofunction Analysis Team, was published. [HERE]
2020/08/14
"Enhancement of the productivity of free dihomo-γ-linolenic acid via co-overexpression of elongase and two desaturase genes in Aspergillus oryzae" by Dr. Koichi Tamano, a Senior Researcher of the Biofunction Analysis Team, as the 1st author, and Dr. Tomohiro Tamura, a former Supervisor of CBBD-OIL, as the last author, was published online in "Journal of Bioscience and Bioengineering". [HERE]
2020/07/24
"CodonAdjust: a software for in silico design of a mutagenesis library with specific amino acid profiles" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in "Protein Engineering, Design and Selection". [HERE]
2020/07/21
"Local necrotic cells trigger systemic immune activation via gut microbiome dysbiosis in Drosophila" by Dr. Akiko Koto, a Senior Researcher of the Biofunction Analysis Team, and Dr. Ryo Miyazaki, a Senior Researcher of the Biofunction Analysis Team, as co-authors, was published in "Cell reports". [HERE]
2020/07/18
"RNA-Seq analysis reveals localization-associated alternative splicing across 13 cell lines" by Dr. Chao Zeng, PD of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, was published in "Genes". [HERE]
2020/07/15
"Ustiloxin biosynthetic machinery is not compatible between Aspergillus flavus and Ustilaginoidea virens" by Dr. Koichi Tamano, a Senior Researcher of the Biofunction Analysis Team, as a co-author, was published online in "Fungal Genetics and Biology". [HERE]
2020/06/30
"Members" page is updated.
2020/06/24
"Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation" by Mr. Shion Hosoda, a former RA of the Sequence Analysis Algorithms Team, Dr. Suguru Nishijima, a former PD of the Biofunction Analysis Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, was published in "Microbiome". [HERE]
2020/06/15
"RaptRanker: in silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information" by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as the corresponding author, was published in "Nucleic Acids Research". [HERE]
2020/06/11
"Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species" by Dr. Ryo Miyazaki, a Senior Researcher of the Biofunction Analysis Team, as the co-senior author, was published in "Current Biology". [HERE]
2020/06/01
The Japanese book on the human microbiome, a section of which was written by Dr. Yuya Kiguchi, a former RA of the Biofunction Analysis Team, was published. [HERE]
2020/05/07
The paper that describes the privacy-preserving personal genome analysis system based on Intel SGX by Mr. Daiki Iwata, a former RA of the Sequence Analysis Algorithms Team, won the SCIS paper award at the "2020 Symposium on Cryptography and Information Security". [HERE]
2020/04/21
"Deep sequencing uncovers caste-associated diversity of symbionts in the social ant Camponotus japonicus" by Dr. Akiko Koto, a Senior Researcher of the Biofunction Analysis Team, as the first-author, and Dr. Ryo Miyazaki, a Senior Researcher of the Biofunction Analysis Team, as the corresponding author, was published in "mBio". [HERE]
2020/03/23
"Burkholderia insecticola triggers midgut closure in the bean bug Riptortus pedestris to prevent secondary bacterial infections of midgut crypts" by Dr. Yoshitomo Kikuchi, a Senior Researcher of the Biofunction Analysis Team, was published in "The ISME Journal". [HERE]
2020/03/23
"Promoter tools for further development of Aspergillus oryzae as a platform for fungal secondary metabolite production" by Dr. Maiko Umemura, a Senior Researcher of the Microbiology Data Analysis Team, was published in "Fungal Biology and Biotechnology". [HERE]
2020/03/14
"MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq" by Ms. Yiqian Zhang, RA of the Sequence Analysis Algorithms Team, and Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, was published in "BMC Bioinformatics". [HERE]
2020/03/09
"Time-lapse single-cell transcriptomics reveals modulation of histone H3 for dormancy breaking in fission yeast" by Mr. Hayato Tsuyuzaki, RA of the Biofunction Analysis Team, as the first-author, Dr. Koji Arikawa, a former TS of the Systems Biology Team, and Prof. Haruko Takeyama, the Director of the CBBD-OIL, as co-authors, was published in "Nature Communications". [HERE]
2020/02/28
"Electrochemically boosted cytochrome P450 reaction that efficiently produces 25-hydroxyvitamin D3" by Dr. Yoshiaki Yasutake, a Senior Researcher of the Microbiology Data Analysis Team, and Dr. Tomohiro Tamura, a Supervisor of CBBD-OIL, as co-authors, was published online in "Journal of Catalysis". [HERE]
2020/02/24
"Nrp1 is activated by konjac ceramide binding-induced structural rigidification of the a1a2 domain" by Dr. Yoshiaki Yasutake, a Senior Researcher of the Microbiology Data Analysis Team, and Dr. Tomohiro Tamura, a Supervisor of CBBD-OIL, as co-authors, was published in "Cells". [HERE]
2020/02/20
"Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine" by Dr. Yoshiaki Yasutake, a Senior Researcher of the Microbiology Data Analysis Team, was published in "Scientific Reports". [HERE]
2020/02/11
"Nucleosome destabilization by nuclear non-coding RNAs" by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, as a co-author, was published in "Communications Biology". [HERE]
2020/02/06
"Effect of dose and timing of Burdock (Arctium lappa) root intake on intestinal microbiota of mice" by Mr. Hiroyuki Sasaki, RA of the Biofunction Analysis Team, was published in "Microorganisms". [HERE]
2019/12/27
"The timing effects of soy protein intake on mice gut microbiota" by Mr. Hiroyuki Sasaki, RA of the Biofunction Analysis Team, was published in "Nutrients". [HERE]
2019/12/19
"Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, as a co-author, was published in "Epigenetics & Chromatin". [HERE]
2019/11/16
”Mice Microbiota Composition Changes by Inulin Feeding with a Long Fasting Period under a Two-Meals-Per-Day Schedule” by Mr. Hiroyuki Sasaki, RA of the Biofunction Analysis Team, was posted on “Nutrients”. [HERE]
2019/10/24
"Publications" page is added.
2019/09/06
”MitoIMP: A computational framework for imputation of missing data in low-coverage human mitochondrial genome” by Dr. Koji Ishiya, PD of the Systems Biology Team, was posted on “Bioinformatics and Biology Insight”. [HERE]
2019/09/06
”MitoIMP: A computational framework for imputation of missing data in low-coverage human mitochondrial genome” by Dr. Koji Ishiya, PD of the Systems Biology Team, was posted on “Bioinformatics and Biology Insight”. [HERE]
2019/09/03
”Cellulase productivity of Trichoderma reesei mutants developed in Japan varies with varying pH conditions” by Dr. Kazuki Mori and Dr. Sachiyo Aburatani as co-authors, a former member of the Systems Biology Team and the Deputy Director of CBBD-OIL, was posted on “Journal of Bioscience and Bioengineering”. [HERE]
2018/08/27
”Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut” by Dr. Suguru Nishijima as a co-author, a former member of the Biofunction Analysis Team, was posted on an online journal “Microbiome". [HERE]
2019/07/22
”Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease” by Dr. Martin Frith as a co-author, Chief Senior Researcher of the Sequence Analysis Algorithms Team, was posted on “Nature Genetics”. [HERE]
2019/07/08
”Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima.” by Dr. Ryo Miyazaki as the corresponding author, Senior Researcher of the Biofunction Analysis Team, was posted on “Scientific Reports”. [HERE]
2019/06/20
”Computational approaches for alternative and transient secondary structures of ribonucleic acids” by Prof. Michiaki Hamada as the corresponding author, the leader of the Sequence Analysis Algorithms Team, was posted on “Briefings in Functional Genomics”. [HERE]
2019/06/19
”Production of recombinant extracellular cholesterol esterase using consistently active promoters in Burkholderia stabilis” by Dr. Arturo Magana-Mora as a co-author, Dr. Yoshiaki Yasutake as a co-author, Dr. Sachiyo Aburatani as a co-author and Dr. Tomohiro Tamura as the corresponding author, a former member of the Systems Biology Team, a Senior Researcher of the Microbiology Data Analysis Team, the Deputy Director of CBBD-OIL and Supervisor of CBBD-OIL, was posted on “Biosci Biotechnol Biochem”. [HERE]
2019/06/06
"Developing a codon optimization method for improved expression of recombinant proteins in actinobacteria" by Dr. Yutaka Saito, a Senior Researcher of the Sequence Analysis Algorithms Team, was posted on “Scientific Reports”. [HERE]
2019/06/06
"Burkholderia gut symbionts associated with European and Japanese populations of the dock bug Coreus marginatus (Coreoidea: Coreidae)" by Dr. Yoshitomo Kikuchi as a co-auther, a Senior Researcher of the Biofunction Analysis Team, was posted on “Microbes and Environments”. [HERE]
2019/05/31
"Morphogenesis and development of midgut symbiotic organ of the stinkbug Plautia stali (Hemiptera: Pentatomidae)" by Dr. Minoru Moriyama, a Senior Researcher of the Biofunction Analysis Team, was posted on “Zoological Letters". [HERE]
2019/05/28
"a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data” by Prof. Michiaki Hamada as the corresponding author, the leader of the Sequence Analysis Algorithms Team, was posted on "Frontiers in Genetics". [HERE]
2019/05/18
"LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data" by Prof. Michiaki Hamada, the leader of the Sequence Analysis Algorithms Team, was posted on “Frontiers in Genetics”. [HERE]
2018/04/22
”A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology” by Dr. Kazuki Mori, TS of the Systems Biology Team, was posted on “DNA RESEARCH” run by OXFORD UNIV PRESS. [HERE]
2019/04/16
"Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference" by Prof. Michiaki Hamada and Mr. Taro Matsutani, the leader and a member of the Sequence Analysis Algorithms Team, was posted on “Bioinformatics”. [HERE]
2019/03/05
We exhibited at Waseda Open Innovation Forum 2019 held in Bellsar Shiodome.
2019/02/25
5th Core-to-core International Symposium "3D Lab Exchange Program" was held at the Okinawa Institute of Science and Technology Graduate University, Japan (Co-sponsored by the Waseda University (TWIns), Waseda BioScience Research Institute in Singapore (WABIOS), Okinawa Institute of Science and Technology Graduate University (OIST), University of Bonn (LIMES), Istituto Italiano di Tecnologia (IIT), AIST-Waseda University Comptational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), and Waseda University Research Branding Project).
2018/10/25
2018 Core-to-Core Symposium "Biotechnology Toward Next Generation Single Cell Analysis” was held at the University of Bonn, Germany (Co-sponsored by WASEDA Bioscience Research Institute in Singapore, Singapore Polytechnic and Waseda University).
2018/10/01
“Small genome symbiont underlies cuticle hardness in weevils” by Dr. Hisashi Anbutsu, the leader of the Biofunction Analysis Team, was published on “The Nature and Insects” 53(11): 19-22 issued by NEW SCIENCE co., ltd.

FOR INDUSTRY: CBBD-OIL FORUM

One of our important missions is to “supply advanced technologies to industries in need”. As we work on understanding industrial needs, we develop suitable and advanced technologies for them. Our technologies are applied to all biological fields, such as pharmaceutical, food and health industries, and so on. We aim to build a bridge between academic researchers and private companies by providing them with the latest knowledge through informatics analysis using different types of biological data, such as large omics data (genomics, proteomics, metagenomics, etc. measured in biosphere), clinical data, and various types of life and health information, in an integrative way.

In the bioinformatics field, there are many types of techniques depending on the data type. When you apply bioinformatics techniques to your data, the most suitable method should be selected. Subsequently, we use an appropriate amount of time for consultation on technologies and research that your company is interested in, before we move on to conclude an NDA (non-disclosure agreement) if necessary. After clarifying your specific needs, we provide technical guidance and proper support by experts of the relevant fields on demand.