Publications by authors named "Kozo Nishida"

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Shedding Light on PFAS Dark Matter Using a Novel GC-HRMS Approach.
Jeremy P Koelmel, Elizabeth Z Lin, Parker Chang, Emily Johnson, Paul Stelben, Kozo Nishida

Environ Sci Technol· December 2025

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Author Correction: A universal language for finding mass spectrometry data patterns.
Tito Damiani, Alan K Jarmusch, Allegra T Aron, Daniel Petras, Vanessa V Phelan, Kozo Nishida

Nat Methods· September 2025

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A universal language for finding mass spectrometry data patterns.
Tito Damiani, Alan K Jarmusch, Allegra T Aron, Daniel Petras, Vanessa V Phelan, Kozo Nishida

Nat Methods· June 2025

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Learning and teaching biological data science in the Bioconductor community.
Jenny Drnevich, Frederick J Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C Culhane, Kozo Nishida

PLoS Comput Biol· April 2025

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Learning and teaching biological data science in the Bioconductor community.
Jenny Drnevich, Frederick J Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C Culhane, Kozo Nishida

ArXiv· March 2025

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MS2Lipid: A Lipid Subclass Prediction Program Using Machine Learning and Curated Tandem Mass Spectral Data.
Nami Sakamoto, Takaki Oka, Yuki Matsuzawa, Kozo Nishida, Jayashankar Jayaprakash

Metabolites· November 2024

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MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities.
Hiroaki Takeda, Yuki Matsuzawa, Manami Takeuchi, Mikiko Takahashi, Kozo Nishida

Nat Commun· November 2024

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Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks.
Kozo Nishida, Junichi Maruyama, Kazunari Kaizu, Koichi Takahashi, Katsuyuki Yugi

NPJ Syst Biol Appl· February 2024

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WikiPathways 2024: next generation pathway database.
Ayushi Agrawal, Hasan Balcı, Kristina Hanspers, Susan L Coort, Marvin Martens, Kozo Nishida

Nucleic Acids Res· January 2024

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An architecture for collaboration in systems biology at the age of the Metaverse.
Eliott Jacopin, Yuki Sakamoto, Kozo Nishida, Kazunari Kaizu, Koichi Takahashi

NPJ Syst Biol Appl· January 2024

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BioHackathon 2015: Semantics of data for life sciences and reproducible research.
Rutger A Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Kozo Nishida, Naoki Nishida

F1000Res· February 2021

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WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.
Denise N Slenter, Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Kozo Nishida

Nucleic Acids Res· January 2018

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Integrated network analysis and effective tools in plant systems biology.
Atsushi Fukushima, Shigehiko Kanaya, Kozo Nishida

Front Plant Sci· November 2014

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KEGGscape: a Cytoscape app for pathway data integration.
Kozo Nishida, Keiichiro Ono, Shigehiko Kanaya, Koichi Takahashi

F1000Res· September 2014

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The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.
Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Kozo Nishida

J Biomed Semantics· February 2013

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The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.
Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Kozo Nishida

J Biomed Semantics· August 2011

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ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.
Takeshi Obayashi, Kozo Nishida, Kota Kasahara, Kengo Kinoshita

Plant Cell Physiol· February 2011

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