Author

Yuko Koike

Institute for Systems Biology

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Bioinformatics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:differential expression· 1 Research Focus:dimensionality reduction· 1 Research Focus:gene regulatory network inference· 1 Approach:graph neural network· 1 Organism:human· 1 Assay:metabolomics· 1

Frequent Co-Authors

Adelina ChauiD· 1 shared Allon WagneriD· 1 shared Bernhard Ørn PalssoniD· 1 shared Daniel Craig ZielinskiiD· 1 shared Daniel P. LewinsohniD· 1 shared James T. YurkovichiD· 1 shared Nicolas DiasiD· 1 shared Nilah M. IoannidisiD· 1 shared

Activity by Year

2021-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

1 shared paperBioinformatics

Adelina ChauORCID

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

Extracting interpretable single-cell metabolic states with graph-guided representation learning

Daniel P. Lewinsohn, Nicolas Dias, Adelina Chau, Yuko Koike, Zachary D. Smith, Nilah M. Ioannidis, Allon Wagner

The paper introduces MeRN, a graph-guided variational autoencoder for learning single-cell metabolic states from transcriptomes, and identifies metabolic drivers in various biological contexts.

bioRxiv · Sep 24, 2026 · PreprintBioinformatics

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

Zachary B. Haiman, Daniel Craig Zielinski, Yuko Koike, James T. Yurkovich, Bernhard Ørn Palsson

MASSpy provides a framework for dynamic metabolic modeling using mass action kinetics, integrating with existing tools and supporting simulation and uncertainty quantification.

PLoS Computational Biology · Jan 28, 2021Peer-reviewedSystems Biology