Author

Yusuke Koga

Boston UniversityORCID 0000-0003-4875-6598Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:scRNA-seq· 5 Research Focus:clustering· 4 Research Focus:benchmarking· 3 Approach:statistical model· 3 Research Focus:batch correction / integration· 2 Research Focus:dimensionality reduction· 2 Organism:human· 2 Research Focus:software / tool· 2

Frequent Co-Authors

Joshua David CampbelliD· 5 shared Masanao YajimaiD· 4 shared William Evan JohnsoniD· 4 shared Zhe WangiD· 4 shared Frederick Jansen· 2 shared Irzam SarfraziD· 2 shared Rui HongiD· 2 shared Salam Al AbdullatifiD· 2 shared

Activity by Year

2019-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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5 shared papersBioinformatics

Joshua David CampbellORCID

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Author profile →

5 papers

Recent·Most cited

Interactive analysis of single-cell data using flexible workflows with SCTK2.0

Yichen Wang, Irzam Sarfraz, Nida Pervaiz, Rui Hong, Yusuke Koga, Vidya Prasad Akavoor, Xinyun Cao, Salam Al Abdullatif, Syed Ali Zaib, Zhe Wang, Frederick Jansen, Masanao Yajima, William Evan Johnson, Joshua David Campbell

SCTK2.0 provides an integrated toolkit for scRNA-seq analysis with a graphical interface, enabling non-programmers to perform end-to-end workflows and generate reproducible reports.

Patterns · Aug 1, 2023Peer-reviewedBioinformatics

Celda: A Bayesian model to perform co-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data

Zhe Wang, Shiyi Yang, Yusuke Koga, Sean E. Corbett, Conor V. Shea, William Evan Johnson, Masanao Yajima, Joshua David Campbell

Celda identifies transcriptional modules and cell subpopulations in scRNA-seq data, outperforming existing methods in detecting biological programs and cell types.

NAR Genomics and Bioinformatics · Jul 9, 2022Peer-reviewedBioinformatics

Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data

Rui Hong, Yusuke Koga, Shruthi Bandyadka, Anastasia Leshchyk, Yichen Wang, Vidya Prasad Akavoor, Xinyun Cao, Irzam Sarfraz, Zhe Wang, Salam Al Abdullatif, Frederick Jansen, Masanao Yajima, William Evan Johnson, Joshua David Campbell

The paper introduces a pipeline for generating, visualizing, and reporting quality control metrics for scRNA-seq data, improving standardization across platforms.

Nature Communications · Mar 30, 2022Peer-reviewedBioinformatics

Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Shiyi Yang, Sean E. Corbett, Yusuke Koga, Zhe Wang, William Evan Johnson, Masanao Yajima, Joshua David Campbell

DecontX is a Bayesian method to remove ambient RNA contamination in scRNA-seq data, improving cell cluster separation and marker gene accuracy.

Genome biology · Mar 5, 2020Peer-reviewedBioinformatics

Pipeliner: A Nextflow-based framework for the definition of sequencing data processing pipelines

Anthony N. Federico, Tanya T. Karagiannis, Kritika Karri, Dileep Kishore, Yusuke Koga, Joshua David Campbell, Stefano Monti

Pipeliner provides a Nextflow-based framework for creating flexible and reproducible sequencing data processing pipelines, supporting bulk RNA-seq, scRNA-seq, and DGE data.

Frontiers in Genetics · Jun 28, 2019Peer-reviewedBioinformatics