Zhang Yaozhong 張耀中

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ZHANG Yaozhong 張耀中

張耀中チョウヨウチュウ

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Researcher Number	60817138
Affiliation (Current)	2025: 東京大学, 医科学研究所, 准教授
Affiliation (based on the past Project Information) *help	2023: 東京大学, 医科学研究所, 准教授 2021 – 2022: 東京大学, 医科学研究所, 特任准教授 2019: 東京大学, 医科学研究所, 助教
Review Section/Research Field	Principal Investigator Basic Section 62010:Life, health and medical informatics-related Except Principal Investigator Complex systems
Keywords	Principal Investigator 深層学習 / 構造変異 / ナノポアシーケンシング / nanopore sequencing / 全ゲノム表現学習 / k-mer / 事前表現学習モデル / メチル化 / pre-training / representation learning … More / k-mer model / nanopore methylation / deep learning / nanopore / methylation … More Except Principal Investigator 人工知能 / バイオインフォマティクス / 統計的モデリング / システム生物学 / がん Less

The development of a high-performance nanopore methylation detection method with consideration of structural variationPrincipal Investigator
- Principal Investigator
  
  ZHANG Yaozhong
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  The University of Tokyo
Neodimensional exploration for cancer systems by supercomputing and innovative information technology
- Principal Investigator
  
  MIYANO SATORU
- Project Period (FY)
  2015 – 2019
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  The University of Tokyo

All 2024 2023 2022 2021 2020 2017 Other

All Journal Article Presentation Other

[Journal Article] Predicting cell types with supervised contrastive learning on cells and their types2024
- Author(s)
  Heryanto Yusri Dwi、Zhang Yao-zhong、Imoto Seiya
- Journal Title
  
  Scientific Reports
  
  Volume: 14 Issue: 1 Pages: 1-16
- DOI
  10.1038/s41598-023-50185-2
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K12104
[Journal Article] Imputing time-series microbiome abundance profiles with diffusion model2023
- Author(s)
  Seki Misato、Zhang Yao-Zhong、Imoto Seiya
- Journal Title
  
  IEEE Xplore
  
  Volume: BIBM 2023 Pages: 914-919
- DOI
  10.1109/bibm58861.2023.10385703
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K12104, KAKENHI-PROJECT-21H03538
[Journal Article] Zero-shot-capable identification of phage?host relationships with whole-genome sequence representation by contrastive learning2023
- Author(s)
  Zhang Yao-zhong、Liu Yunjie、Bai Zeheng、Fujimoto Kosuke、Uematsu Satoshi、Imoto Seiya
- Journal Title
  
  Briefings in Bioinformatics
  
  Volume: 24 Issue: 5 Pages: 1-10
- DOI
  10.1093/bib/bbad239
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K16329, KAKENHI-PROJECT-21K12104, KAKENHI-PROJECT-22H00477, KAKENHI-PROJECT-21H03538
[Journal Article] Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings2023
- Author(s)
  Zhang Yao-zhong、Bai Zeheng、Imoto Seiya
- Journal Title
  
  Bioinformatics
  
  Volume: 39 Issue: 10 Pages: 1-10
- DOI
  10.1093/bioinformatics/btad617
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K12104, KAKENHI-PROJECT-21H03538
[Journal Article] Microbial Gene Ontology informed deep neural network for microbe functionality discovery in human diseases2023
- Author(s)
  Liu Yunjie、Zhang Yao-zhong、Imoto Seiya
- Journal Title
  
  PLOS ONE
  
  Volume: 18 Issue: 8 Pages: 1-13
- DOI
  10.1371/journal.pone.0290307
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K12104, KAKENHI-PROJECT-21H03538
[Journal Article] Identification of bacteriophage genome sequences with representation learning2022
- Author(s)
  Bai Zeheng、Zhang Yao-zhong、Miyano Satoru、Yamaguchi Rui、Fujimoto Kosuke、Uematsu Satoshi、Imoto Seiya
- Journal Title
  
  Bioinformatics
  
  Volume: 38 Issue: 18 Pages: 4264-4270
- DOI
  10.1093/bioinformatics/btac509
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K12104, KAKENHI-PROJECT-22H00477, KAKENHI-PROJECT-21H03538, KAKENHI-PROJECT-21K19495
[Journal Article] Dysfunctional analysis of the pre-training model on nucleotide sequences and the evaluation of different k-mer embeddings2022
- Author(s)
  Zhang Yao-zhong、Bai Zeheng、Imoto Seiya
- Journal Title
  
  bioAxiv
  
  Volume: preprint Pages: 1-7
- DOI
  10.1101/2022.12.05.518770
- Open Access
- Data Source
  KAKENHI-PROJECT-21K12104
[Journal Article] Discovering microbe functionality in human disease with a gene-ontology-aware model2021
- Author(s)
  Liu Yunjie、Zhang Yaozhong、Imoto Seiya
- Journal Title
  
  Proceedings of 2021 IEEE International Conference on Bioinformatics and Biomedicine
  
  Pages: 1873-1880
- DOI
  10.1109/bibm52615.2021.9669492
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K12104
[Journal Article] Identification of Bacteriophages Using Deep Representation Model with Pre-training2021
- Author(s)
  Bai Zeheng、Zhang Yao-zhong、Miyano Satoru、Yamaguchi Rui、Uematsu Satoshi、Imoto Seiya
- Journal Title
  
  BioAxiv
  
  Pages: 1-7
- DOI
  10.1101/2021.09.25.461359
- Data Source
  KAKENHI-PROJECT-21K12104
[Journal Article] On the application of BERT models for nanopore methylation detection2021
- Author(s)
  Zhang Yao-Zhong、Yamaguchi Kiyoshi、Hatakeyama Sera、Furukawa Yoichi、Miyano Satoru、Yamaguchi Rui、Imoto Seiya
- Journal Title
  
  Proceedings of 2021 IEEE International Conference on Bioinformatics and Biomedicine
  
  Pages: 320-327
- DOI
  10.1109/bibm52615.2021.9669841
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K12104
[Journal Article] Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers2021
- Author(s)
  Zhang Yao-zhong、Imoto Seiya、Miyano Satoru、Yamaguchi Rui
- Journal Title
  
  PLOS Computational Biology
  
  Volume: 17 Issue: 10 Pages: 1009186-1009186
- DOI
  10.1371/journal.pcbi.1009186
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K12104
[Journal Article] Nanopore base-calling from a perspective of instance segmentation2020
- Author(s)
  Zhang Y-Z, Akdemir A, Tremmel G, Imoto S, Miyano S, Shibuya T, Yamaguchi R.
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 23;21(Suppl 3) Issue: S3 Pages: 136-136
- DOI
  10.1186/s12859-020-3459-0
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-15H05912, KAKENHI-PROJECT-17H01693, KAKENHI-PROJECT-17K20023
[Journal Article] Identification of a p53-repressed gene module in breast cancer cells2017
- Author(s)
  Miyamoto T, Tanikawa C, Yodsurang V, Zhang YZ, Imoto S, Yamaguchi R, Miyano S, Nakagawa H, Matsuda K
- Journal Title
  
  Oncotarget
  
  Volume: 8(34) Issue: 34 Pages: 55821-55836
- DOI
  10.18632/oncotarget.19608
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-15H05912, KAKENHI-PUBLICLY-16H01566
[Journal Article] The Transcriptional Landscape of p53 Signalling Pathway2017
- Author(s)
  Tanikawa C, Zhang YZ, Yamamoto R, Tsuda Y, Tanaka M, Funauchi Y, Mori J, Imoto S, Yamaguchi R, Nakamura Y, Miyano S, Nakagawa H, Matsuda K
- Journal Title
  
  EBioMedicine
  
  Volume: 20 Pages: 109-119
- DOI
  10.1016/j.ebiom.2017.05.017
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-15H05912, KAKENHI-PUBLICLY-16H01566
[Journal Article] Sequence-specific bias correction for RNA-seq data using recurrent neural networks2017
- Author(s)
  Zhang Y-Z, Yamaguchi R, Imoto S, Miyano S
- Journal Title
  
  BMC Genomics
  
  Volume: 18(Suppl 1) Issue: S1 Pages: 1044-1044
- DOI
  10.1186/s12864-016-3262-5
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PLANNED-15H05912, KAKENHI-PROJECT-16H02676
[Presentation] Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning2023
- Author(s)
  Yao-zhong Zhang
- Organizer
  International Workshop on Bioinformatics and Systems Biology (IBSB)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K12104
[Presentation] Dysfunctional analysis of the pre-training model on nucleotide sequences and the evaluation of different k-mer embeddings2023
- Author(s)
  Yao-zhong Zhang
- Organizer
  27th Annual International Conference on Research in Computational Molecular Biology
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K12104
[Presentation] Imputing time-series microbiome abundance profiles with diffusion model2023
- Author(s)
  Misato Seki, Yao-zhong Zhang, Seiya Imoto
- Organizer
  International Conference on Bioinformatics and Biomedicine (BIBM)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K12104
[Presentation] On the application of BERT models for nanopore methylation detection2021
- Author(s)
  Yao-zhong Zhang
- Organizer
  IEEE International Conference on Bioinformatics and Biomedicine
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K12104
[Presentation] Discovering microbe functionality in human disease with a gene-ontology-aware model2021
- Author(s)
  Yunjie Liu,Yao-zhong Zhang, Seiya Imoto
- Organizer
  Biological Ontologies and Knowledge Bases workshop 2021
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K12104
[]

1. MIYANO SATORU (50128104)

# of Collaborated Projects: 1 results

# of Collaborated Products: 4 results
2. 島村徹平 (00623943)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
3. 白石友一 (70516880)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. PARK HEEWON (70756642)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
5. 山口類 (90380675)

# of Collaborated Projects: 1 results

# of Collaborated Products: 4 results
6. 新井田厚司 (00772493)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
7. 片山琴絵 (40581195)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. 井元清哉 (10345027)

# of Collaborated Projects: 1 results

# of Collaborated Products: 4 results
9. 玉田嘉紀 (80435495)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
10. 藤本康介

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Zhang Yaozhong 張 耀中

ZHANG Yaozhong 張 耀中

張 耀中 チョウ ヨウチュウ

Research Projects

Research Products

Co-Researchers

The development of a high-performance nanopore methylation detection method with consideration of structural variationPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Neodimensional exploration for cancer systems by supercomputing and innovative information technology

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] Predicting cell types with supervised contrastive learning on cells and their types2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Imputing time-series microbiome abundance profiles with diffusion model2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Zero-shot-capable identification of phage?host relationships with whole-genome sequence representation by contrastive learning2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Microbial Gene Ontology informed deep neural network for microbe functionality discovery in human diseases2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Identification of bacteriophage genome sequences with representation learning2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Dysfunctional analysis of the pre-training model on nucleotide sequences and the evaluation of different k-mer embeddings2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Discovering microbe functionality in human disease with a gene-ontology-aware model2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Identification of Bacteriophages Using Deep Representation Model with Pre-training2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] On the application of BERT models for nanopore methylation detection2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Nanopore base-calling from a perspective of instance segmentation2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Identification of a p53-repressed gene module in breast cancer cells2017

Author(s)

Zhang Yaozhong 張耀中

ZHANG Yaozhong 張耀中

張耀中チョウヨウチュウ