2024
Shinya Nakata, Kanako Iwasaki, Hiromasa Funato, Masashi Yanagisawa, Haruka Ozaki. Neuronal subtype-specific transcriptomic changes in the cerebral neocortex associated with sleep pressure. Neuroscience Research (2024)
2023
Maehara, Hideki, Toshiya Kokaji, Atsushi Hatano, Yutaka Suzuki, Masaki Matsumoto, Keiichi I. Nakayama, Riku Egami, et al. 2023. “DNA Hypomethylation Characterizes Genes Encoding Tissue-Dominant Functional Proteins in Liver and Skeletal Muscle.” Scientific Reports 13 (1): 19118.
Tahara, Saeko, Takaho Tsuchiya, Hirotaka Matsumoto, and Haruka Ozaki. 2023. “Transcription Factor-Binding K-Mer Analysis Clarifies the Cell Type Dependency of Binding Specificities and Cis-Regulatory SNPs in Humans.” BMC Genomics 24 (1): 597.
Inagaki, Takashi, Akari Kato, Koichi Takahashi, Haruka Ozaki, and Genki N. Kanda. 2023. “LLMs Can Generate Robotic Scripts from Goal-Oriented Instructions in Biological Laboratory Automation.” arXiv Preprint arXiv:2304. 10267.
Taguchi, Shodai, Yasuyuki Suda, Kenji Irie, and Haruka Ozaki. 2023. “Automation of Yeast Spot Assays Using an Affordable Liquid Handling Robot.” SLAS Technology 28 (2): 55–62.
Arai, Yuya, Ko Takahashi, Takaaki Horinouchi, Koichi Takahashi, and Haruka Ozaki. 2023. “SAGAS: Simulated Annealing and Greedy Algorithm Scheduler for Laboratory Automation.” SLAS Technology 28 (4): 264–77.
Aso, Hirofumi, Jumpei Ito, Haruka Ozaki, Yukie Kashima, Yutaka Suzuki, Yoshio Koyanagi, and Kei Sato. 2023. “Single-Cell Transcriptome Analysis Illuminating the Characteristics of Species-Specific Innate Immune Responses against Viral Infections.” GigaScience 12: giad086.
2022
Nishino, Teppei, Masaharu Yoshihara, Takahiro Nakayama, Takaho Tsuchiya, Saeko Tahara, Haruka Ozaki, and Satoru Takahashi. 2022. “Identifying Potential Regulators of JAGGED1 Expression in Portal Mesenchymal Cells.” BMC Research Notes 15 (1): 1–6.
Tsuchiya, Takaho, Hiroki Hori, and Haruka Ozaki. 2022. “CCPLS Reveals Cell-Type-Specific Spatial Dependence of Transcriptomes in Single Cells.” Bioinformatics 38 (21): 4868–77.
Kokaji, Toshiya, Miki Eto, Atsushi Hatano, Katsuyuki Yugi, Keigo Morita, Satoshi Ohno, Masashi Fujii, et al. 2022. “In Vivo Transomic Analyses of Glucose-Responsive Metabolism in Skeletal Muscle Reveal Core Differences between the Healthy and Obese States.” Scientific Reports 12 (1): 13719.
Odaka, Haruki, Haruka Ozaki, and Hiroaki Tateno. 2022. “scGR-Seq: Integrated Analysis of Glycan and RNA in Single Cells.” STAR Protocols 3 (1): 101179.
2021
Suzuki, Sayaka R., Akihiro Kuno, and Haruka Ozaki. 2021. “Cell-to-Cell Interaction Analysis of Prognostic Ligand-Receptor Pairs in Human Pancreatic Ductal Adenocarcinoma.” Biochemistry and Biophysics Reports 28: 101126.
Itoh, Takeshi D., Takaaki Horinouchi, Hiroki Uchida, Koichi Takahashi, and Haruka Ozaki. 2021. “Optimal Scheduling for Laboratory Automation of Life Science Experiments with Time Constraints.” SLAS Technology 26 (6): 650–59.
Minoshima, Fumi, Haruka Ozaki, Haruki Odaka, and Hiroaki Tateno. 2021. “Integrated Analysis of Glycan and RNA in Single Cells.” iScience 24 (8): 102882.
Egami, Riku, Toshiya Kokaji, Atsushi Hatano, Katsuyuki Yugi, Miki Eto, Keigo Morita, Satoshi Ohno, et al. 2021. “Trans-Omic Analysis Reveals Obesity-Associated Dysregulation of Inter-Organ Metabolic Cycles between the Liver and Skeletal Muscle.” iScience 24 (3): 102217.
2020
Mori, Koichi, Haruka Ozaki, and Tsukasa Fukunaga. 2020. “MotiMul: A Significant Discriminative Sequence Motif Discovery Algorithm with Multiple Testing Correction.” In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 186–93. IEEE.
Kokaji, Toshiya, Atsushi Hatano, Yuki Ito, Katsuyuki Yugi, Miki Eto, Keigo Morita, Satoshi Ohno, et al. 2020. “Transomics Analysis Reveals Allosteric and Gene Regulation Axes for Altered Hepatic Glucose-Responsive Metabolism in Obesity.” Science Signaling 13 (660): eaaz1236.
Wakida, Hiroyasu, Kentaro Kawata, Yuta Yamaji, Emi Hattori, Takaho Tsuchiya, Youichiro Wada, Haruka Ozaki, and Nobuyoshi Akimitsu. 2020. “Stability of RNA Sequences Derived from the Coronavirus Genome in Human Cells.” Biochemical and Biophysical Research Communications 527 (4): 993–99.
Ozaki, Haruka, Tetsutaro Hayashi, Mana Umeda, and Itoshi Nikaido. 2020. “Millefy: Visualizing Cell-to-Cell Heterogeneity in Read Coverage of Single-Cell RNA Sequencing Datasets.” BMC Genomics 21 (1): 177.
Kaminuma, Eli, Yukino Baba, Masahiro Mochizuki, Hirotaka Matsumoto, Haruka Ozaki, Toshitsugu Okayama, Takuya Kato, et al. 2020. “DDBJ Data Analysis Challenge: A Machine Learning Competition to Predict Arabidopsis Chromatin Feature Annotations from DNA Sequences.” Genes & Genetic Systems 95 (1): 43–50.
2019
Matsumoto, Hirotaka, Tetsutaro Hayashi, Haruka Ozaki, Koki Tsuyuzaki, Mana Umeda, Tsuyoshi Iida, Masaya Nakamura, Hideyuki Okano, and Itoshi Nikaido. 2020. “An NMF-Based Approach to Discover Overlooked Differentially Expressed Gene Regions from Single-Cell RNA-Seq Data.” NAR Genomics and Bioinformatics 2 (1): lqz020.
Yoshitane, Hikari, Yoshimasa Asano, Aya Sagami, Seinosuke Sakai, Yutaka Suzuki, Hitoshi Okamura, Wataru Iwasaki, Haruka Ozaki, and Yoshitaka Fukada. 2019. “Functional D-Box Sequences Reset the Circadian Clock and Drive mRNA Rhythms.” Communications Biology 2 (1): 300.
Takeuchi, Mio, Haruka Ozaki, Satoshi Hiraoka, Yoichi Kamagata, Susumu Sakata, Hideyoshi Yoshioka, and Wataru Iwasaki. 2019. “Possible Cross-Feeding Pathway of Facultative Methylotroph Methyloceanibacter Caenitepidi Gela4 on Methanotroph Methylocaldum Marinum S8.” PloS One 14 (3): e0213535.
2018
Hayashi, Tetsutaro, Haruka Ozaki, Yohei Sasagawa, Mana Umeda, Hiroki Danno, and Itoshi Nikaido. 2018. “Single-Cell Full-Length Total RNA Sequencing Uncovers Dynamics of Recursive Splicing and Enhancer RNAs.” Nature Communications 9 (1): 619.
Until 2017
Wong, Marty Kwok Shing, Takehiro Tsukada, Nobuhiro Ogawa, Supriya Pipil, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki, and Yoshio Takei. 2017. “A Sodium Binding System Alleviates Acute Salt Stress during Seawater Acclimation in Eels.” Zoological Letters 3 (1): 22.
Takei, Yoshio, Marty K-S Wong, Supriya Pipil, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki, and Makoto Kusakabe. 2017. “Molecular Mechanisms Underlying Active Desalination and Low Water Permeability in the Esophagus of Eels Acclimated to Seawater.” American Journal of Physiology. Regulatory, Integrative and Comparative Physiology 312 (2): R231–44.
Terajima, Hideki, Hikari Yoshitane, Haruka Ozaki, Yutaka Suzuki, Shigeki Shimba, Shinya Kuroda, Wataru Iwasaki, and Yoshitaka Fukada. 2017. “ADARB1 Catalyzes Circadian A-to-I Editing and Regulates RNA Rhythm.” Nature Genetics 49 (1): 146–51.
Wong, Marty Kwok-Shing, Supriya Pipil, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki, and Yoshio Takei. 2016. “Flexible Selection of Diversified Na+/K+-ATPase α-Subunit Isoforms for Osmoregulation in Teleosts.” Zoological Letters 2 (1): 1–22.
Ozaki, Haruka, and Wataru Iwasaki. 2016. “MOCCS: Clarifying DNA-Binding Motif Ambiguity Using ChIP-Seq Data.” Computational Biology and Chemistry 63 (August): 62–72.
Ishizu, Hirotsugu, Yuka W. Iwasaki, Shigeki Hirakata, Haruka Ozaki, Wataru Iwasaki, Haruhiko Siomi, and Mikiko C. Siomi. 2015. “Somatic Primary piRNA Biogenesis Driven by Cis-Acting RNA Elements and Trans-Acting Yb.” Cell Reports 12 (3): 429–40.
Wong, Marty Kwok-Shing, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki, and Yoshio Takei. 2014. “Discovery of Osmotic Sensitive Transcription Factors in Fish Intestine via a Transcriptomic Approach.” BMC Genomics 15 (1): 1134.
Hirase, Shotaro, Haruka Ozaki, and Wataru Iwasaki. 2014. “Parallel Selection on Gene Copy Number Variations through Evolution of Three-Spined Stickleback Genomes.” BMC Genomics 15 (1): 735.
Yoshitane, Hikari, Haruka Ozaki, Hideki Terajima, Ngoc-Hien Du, Yutaka Suzuki, Taihei Fujimori, Naoki Kosaka, et al. 2014. “CLOCK-Controlled Polyphonic Regulation of Circadian Rhythms through Canonical and Noncanonical E-Boxes.” Molecular and Cellular Biology 34 (10): 1776–87.
Fukunaga, Tsukasa, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki, and Hisanori Kiryu. 2014. “CapR: Revealing Structural Specificities of RNA-Binding Protein Target Recognition Using CLIP-Seq Data.” Genome Biology 15: 1–15.