Yasubumi Sakakibara
Keio University
Machine learningMathematicsComputer scienceBioinformaticsBiology
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Publications 144
#1Vasanthan Jayakumar (Keio: Keio University)H-Index: 2
#2Hiromi Ishii (Keio: Keio University)
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 10 authors...
BACKGROUND: The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcriptomics. RESULTS: Here we utilize single-molecule, long-read sequence data to improve and update the existing genome assembly and report a near-complete genome of the common marmoset. The assembly is of 2.79 G...
#1Taishiro Kishimoto (Keio: Keio University)H-Index: 18
#2Akihiro Takamiya (Keio: Keio University)H-Index: 5
Last. Yoko Eguchi (Keio: Keio University)H-Index: 7
view all 23 authors...
Background: Depressive and neurocognitive disorders are debilitating conditions that account for the leading causes of years lived with disability worldwide. Overcoming these disorders is an extremely important public health problem today. However, there are no biomarkers that are objective or easy-to-obtain in daily clinical practice, which leads to difficulties in assessing treatment response and developing new drugs. Due to advances in technology, it has become possible to quantify important ...
2 CitationsSource
#1Wakako Kumita (Central Institute for Experimental Animals)H-Index: 2
#2Kenya Sato (Central Institute for Experimental Animals)H-Index: 3
Last. Erika Sasaki (Central Institute for Experimental Animals)H-Index: 21
view all 13 authors...
Genetically modified nonhuman primates (NHP) are useful models for biomedical research. Gene editing technologies have enabled production of target-gene knock-out (KO) NHP models. Target-gene-KO/knock-in (KI) efficiency of CRISPR/Cas9 has not been extensively investigated in marmosets. In this study, optimum conditions for target gene modification efficacies of CRISPR/mRNA and CRISPR/nuclease in marmoset embryos were examined. CRISPR/nuclease was more effective than CRISPR/mRNA in avoiding mosai...
1 CitationsSource
#1Vasanthan Jayakumar (Keio: Keio University)H-Index: 2
#2Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
14 CitationsSource
#1Yoshihiro Yamanishi (Kyushu Institute of Technology)H-Index: 27
#2Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
Last. Yangjun Chen (La Trobe University)H-Index: 27
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#1Le Thi Thu Hong (National Agriculture and Food Research Organization)
#2Tsuyoshi Hachiya (Keio: Keio University)H-Index: 11
Last. Keitarou Kimura (National Agriculture and Food Research Organization)H-Index: 13
view all 8 authors...
Poly-γ-glutamic acid (γPGA) production by Bacillus subtilis is regulated by the quorum sensing system where DegQ transmits the cell density signal to a DNA-binding protein DegU. A mutation suppressing the γPGA-negative phenotype of degQ gene knock-out mutant (Δ degQ ) was identified through whole genome sequencing. The mutation conferred an amino acid substitution of Ser103 to phenylalanine (S103F) in yabJ that belongs to the highly conserved YjgF/YER057c/UK114 family. Genetic experiments includ...
#1Maya Hirohara (Keio: Keio University)H-Index: 1
#2Yutaka Saito (AIST: National Institute of Advanced Industrial Science and Technology)H-Index: 7
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 5 authors...
Previous studies have suggested deep learning to be a highly effective approach for screening lead compounds for new drugs. Several deep learning models have been developed by addressing the use of various kinds of fingerprints and graph convolution architectures. However, these methods are either advantageous or disadvantageous depending on whether they (1) can distinguish structural differences including chirality of compounds, and (2) can automatically discover effective features. We develope...
3 CitationsSource
#1Manato Akiyama (Keio: Keio University)H-Index: 1
#2Kengo Sato (Keio: Keio University)H-Index: 18
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 3 authors...
A popular approach for predicting RNA secondary structure is the thermodynamic nearest-neighbor model that finds a thermodynamically most stable secondary structure with minimum free energy (MFE). ...
1 CitationsSource
#1Tatsuya Mizuguchi (Keio: Keio University)
#2Shino Ito (Keio: Keio University)H-Index: 1
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 4 authors...
#1Yoshimasa Aoto (Keio: Keio University)H-Index: 2
#2Kazuhiro OkumuraH-Index: 5
Last. Yasubumi Sakakibara (Keio: Keio University)H-Index: 29
view all 7 authors...
Recent years have witnessed substantial progress in understanding tumor heterogeneity and the process of tumor progression; however, the entire process of the transition of tumors from a benign to metastatic state remains poorly understood. In the present study, we performed a prospective cancer genome-sequencing analysis by employing an experimental carcinogenesis mouse model of squamous cell carcinoma to systematically understand the evolutionary process of tumors. We surgically collected a pa...