T. Ohta

Most-cited papers

1. ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data

   Shinya Oki, T. Ohta, Go Shioi, H. Hatanaka +6 more

   2018EMBO Reports679 citations Open access

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2. ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data

   Zhao-Nan Zou, T. Ohta, F. Miura, Shinya Oki

   2022Nucleic Acids Res.231 citations Open access

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3. ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data

   Zhao-Nan Zou, T. Ohta, Shinya Oki

   2024Nucleic Acids Research205 citations Open access

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4. Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements

   T. Amariuta, K. Ishigaki, Hiroki Sugishita, T. Ohta +8 more

   2020Nature Genetics162 citations Open access

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5. GWAS of mosaic loss of chromosome Y highlights genetic effects on blood cell differentiation

   C. Terao, Y. Momozawa, K. Ishigaki, Eiryo Kawakami +11 more

   2019Nature Communications81 citations Open access

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6. Recording provenance of workflow runs with RO-Crate

   Simone Leo, M. Crusoe, Laura Rodríguez-Navas, Raül Sirvent +14 more

   2023PLoS ONE70 citations Open access

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7. Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

   Takeru Nakazato, T. Ohta, H. Bono

   2013PLoS ONE38 citations Open access

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8. Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data

   Eiryo Kawakami, S. Nakaoka, T. Ohta, H. Kitano

   2016Nucleic Acids Research32 citations Open access

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9. Squalomix: shark and ray genome analysis consortium and its data sharing platform

   Osamu Nishimura, J. Rozewicki, Kazuaki Yamaguchi, Kaori Tatsumi +36 more

   2022F1000Research25 citations Open access

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10. Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive

    T. Ohta, Takeru Nakazato, H. Bono

    2017GigaScience17 citations Open access

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11. Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database

    Shuya Ikeda, Zhao-Nan Zou, H. Bono, Yuki Moriya +4 more

    2025bioRxiv16 citations Open access

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12. TogoID: an exploratory ID converter to bridge biological datasets

    Shuya Ikeda, Hiromasa ONO, T. Ohta, Hirokazu Chiba +7 more

    2022Bioinform.16 citations Open access

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13. Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions

    Shinya Oki, T. Ohta, Go Shioi, H. Hatanaka +6 more

    2017bioRxiv15 citations Open access

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14. Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics

    Hirotaka Suetake, Tomoya Tanjo, Manabu Ishii, Bruno P. Kinoshita +10 more

    2022F1000Research13 citations Open access

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15. Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection

    T. Ohta, Tomoya Tanjo, O. Ogasawara

    2018bioRxiv13 citations Open access

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16. A workflow reproducibility scale for automatic validation of biological interpretation results

    Hirotaka Suetake, Tsukasa Fukusato, T. Igarashi, T. Ohta

    2022bioRxiv10 citations Open access

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17. Best practices for multimodal clinical data management and integration: An atopic dermatitis research case.

    T. Ohta, Ayaka Hananoe, Ayano Fukushima-Nomura, K. Ashizaki +7 more

    2023Allergology International8 citations Open access

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18. ChIP-Atlas

    Shinya Oki, T. Ohta

    2021Practical Guide to Life Science Databases6 citations

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19. Reproducible Scientific Computing Environment with Overlay Cloud Architecture

    Shigetoshi Yokoyama, Yoshinobu Masatani, T. Ohta, O. Ogasawara +3 more

    2016IEEE International Conference on Cloud Computing6 citations

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20. BioHackathon 2015: Semantics of data for life sciences and reproducible research

    R. Vos, Toshiaki Katayama, H. Mishima, S. Kawano +73 more

    2020F1000Research5 citations Open access

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21. Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows

    Hirotaka Suetake, Tsukasa Fukusato, T. Igarashi, T. Ohta

    2022bioRxiv4 citations Open access

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22. In silico integration of thousands of epigenetic datasets into 707 cell type regulatory annotations improves the trans-ethnic portability of polygenic risk scores

    T. Amariuta, K. Ishigaki, Hiroki Sugishita, T. Ohta +6 more

    2020bioRxiv4 citations Open access

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23. 2016 Ieee International Conference on Big Data (big Data) Intercloud Brokerages Based on Pls Method for Deploying Infrastructures for Big Data Analytics

    Katsunori Miura, T. Ohta, Courtney Powell, Masaharu Munetomo

    3 citations

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24. Chromosome-scale genomes of two wild flowering cherries (Cerasus itosakura and Cerasus jamasakura) provide insights into structural evolution in Cerasus

    Kazumichi Fujiwara, A. Toyoda, Toshio Katsuki, Yutaka Sato +14 more

    2025bioRxiv2 citations Open access

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25. Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features

    Shuya Ikeda, K. Aoki-Kinoshita, Hirokazu Chiba, S. Goto +9 more

    2025Journal of Biomedical Semantics2 citations Open access

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26. Differences in the human gut microbiota with varying depressive symptom severity scores

    Yuka Masamura, Ryuichi Kubo, Yuki Midorikawa, Natsuko O. Shinozaki +4 more

    2024Bioscience of Microbiota Food and Health2 citations Open access

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27. Data validation and schema interoperability

    L. García-Castro, Jerven T. Bolleman, M. Dumontier, S. Jupp +5 more

    20202 citations Open access

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28. DNApod: DNA polymorphism annotation database from next-generation sequence read archives

    T. Mochizuki, Yasuhiro Tanizawa, Takatomo Fujisawa, T. Ohta +8 more

    2017PLoS ONE2 citations Open access

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29. Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago

    T. Ohta, T. Kawashima, Natsuko O. Shinozaki, Akito Dobashi +19 more

    2017Journal of plant research2 citations Open access

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30. AI-assisted pre-review of open-source software submissions: an experience report from BOSC 2026

    T. Ohta, N. Harris, S. Carbon

    2026arXiv.org1 citations

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31. ChIP-Atlas 2025 update: 10-year anniversary of a data-mining platform for exploring epigenomic landscape

    Zhao-Nan Zou, T. Ohta, T. Kasukawa, Shinya Oki

    2026Nucleic Acids Research1 citations Open access

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32. A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa

    Kazumichi Fujiwara, A. Toyoda, Bhim B. Biswa, Takushi Kishida +14 more

    2025Scientific Data1 citations Open access

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33. Accumulating computational resource usage of data analysis workflow to select suitable cloud instance

    T. Ohta, Tomoya Tanjo, O. Ogasawara

    20181 citations Open access

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34. DBCLS SRA: Functional mining and characterization of public NGS data

    Takeru Nakazato, T. Ohta, H. Bono

    20141 citations

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35. Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics [version 1; peer review: 2 approved with reservations]

    Hirotaka Suetake, Tomoya Tanjo, Manabu Ishii, B. Kinoshita +12 more

    1 citations

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36. Unlocking the potential of Asian genomic data: a collaborative framework for precision medicine innovation

    Wasin Naravut Tazro Shih Wee Yuko Yosuke Toshiaki Mayumi Poncheewin Suvannang Ohta Seow Kitano Afiahayati K, Wasin Poncheewin, Naravut Suvannang, T. Ohta +48 more

    2026GigaScience0 citations Open access

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37. CATaN maps gene regulatory programs that shape genetic risk across complex diseases

    Haruka Takahashi, H. Hatano, M. Kono, Koma Haruta +22 more

    2026bioRxiv0 citations Open access

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38. A transcription factor regulatory atlas for activity inference and perturbation prediction

    Hikaru Sugimoto, Koki Tsuyuzaki, Zhao-Nan Zou, Shinya Oki +2 more

    2026Nucleic Acids Research0 citations Open access

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39. Uncertainty-aware transcription factor activity and perturbation inference without additional training

    Hikaru Sugimoto, Koki Tsuyuzaki, Zhao-Nan Zou, Shinya Oki +2 more

    2025bioRxiv0 citations Open access

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40. Hybrid Genome Assembly of Short and Long Reads in Galaxy.

    T. Ohta, Yuh Shiwa

    2023Methods in molecular biology0 citations

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41. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

    Toshiaki Katayama, Shuichi Kawashima, G. Micklem, S. Kawano +72 more

    2019F1000Research0 citations Open access

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42. Collecting runtime metrics of genome analysis workflows by CWL-metrics

    T. Ohta, Tomoya Tanjo, O. Ogasawara

    20190 citations Open access

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43. The Sequence Read Archive search system to make use of public high-throughput sequencing data

    T. Ohta, Takeru Nakazato, H. Bono

    20180 citations

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44. Peer Review #2 of "Staphylococcus aureus viewed from the perspective of 40,000+ genomes (v0.1)"

    Robert A. Petit, Timothy D. Read, D. Antipov, N. Hartwick +364 more

    20180 citations Open access

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45. Methods for analyzing next-generation sequencing data XII.Galaxy - Sharing histories and workflows

    Tomoko Terada, T. Ohta, K. Shimizu, K. Kadota

    2018Japanese Journal of Lactic Acid Bacteria0 citations Open access

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46. Databases to support reanalysis of public high-throughput DNA sequencing data

    T. Ohta

    20170 citations Open access

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47. 次世代シーケンサーデータの解析手法 第 11 回 統合データ解析環境 Galaxy

    T. Ohta, Tomoko Terada, Kentaro Shimizu, Koji Kadota

    20170 citations Open access

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48. HFST: Multi omics analysis with public high-throughput sequencing

    T. Ohta, Eiryo Kawakami, Shinya Oki, Hiromasa ONO +3 more

    20160 citations

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49. Comprehensive and integrative analyses with a novel ChIP-seq and DNase-seq database

    Shinya Oki, T. Ohta, Go Shioi, H. Hatanaka +6 more

    20160 citations

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50. Annotating the SIRO model and discovering experimental protocols

    Olga Giraldo, Alexander Garcia, T. Ohta, Federico López

    20160 citations

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