Author

Yoshiaki Yasumizu

Yale UniversityORCID 0000-0002-9872-4909Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Organism:human· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Approach:deep learning· 1

Frequent Co-Authors

David A. HafleriD· 2 shared Anthony RussoiD· 1 shared Atsushi Hara· 1 shared Biqing ZhuiD· 1 shared David A PosneriD· 1 shared Erin E. LongbrakeiD· 1 shared Étienne CaroniD· 1 shared Gia-Bao Dam· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersBioinformatics

David A. HaflerORCID

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3 papers

Recent·Most cited

Benchmarking generative scaffold design methods for peptide engineering in TCR-MHC complexes

Linhui Xie, Gia-Bao Dam, Yashvi Patel, Lilian Denzler, Yanjun Shao, Ruimin Wang, Étienne Caron, Yoshiaki Yasumizu, David A. Hafler, María Rodríguez Martínez

The paper benchmarks generative methods for designing peptides in TCR-pMHC complexes, revealing method-dependent differences in backbone generation and conformational diversity.

bioRxiv · Jan 23, 2026 · PreprintBioinformatics

Myeloid-Driven Inflammation in Prodromal Parkinson's Disease

Yoshiaki Yasumizu, M. Elizabeth Deerhake, Jeonghyeon Moon, Nicholas Buitrago-Pocasangre, Anthony Russo, Haowei Wang, Biqing Zhu, John Peter Seibyl, Vijaya Reddy, Qianchang Wang, Karen J Neish, Maria Grazia Spillantini, David A Posner, Menna Ruth Clatworthy, Tomokazu S. Sumida, , David A. Hafler

The paper identifies increased myeloid-driven inflammation in the CNS of prodromal Parkinson's Disease patients, linking gut and CNS immune responses through shared T cell clones.

bioRxiv · May 16, 2025 · PreprintImmunology

VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data

Yoshiaki Yasumizu, Atsushi Hara, Shimon Sakaguchi, Naganari Ohkura

VIRTUS detects and quantifies viral transcripts in RNA-seq data, enabling identification of infected cells and viral composition.

Bioinformatics · Sep 21, 2020Peer-reviewedBioinformatics