Author

David M. Umbach

National Institutes of HealthORCID 0000-0002-7142-2812Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 3 Approach:statistical model· 3 Research Focus:deconvolution· 2 Organism:human· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:drug response / drug discovery· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Leping LiiD· 3 shared Igor ShatsiD· 2 shared Kai KangiD· 2 shared Xiaoling LiiD· 2 shared Yuanyuan LiiD· 2 shared Caizhi David HuangiD· 1 shared J.M. KrahniD· 1 shared Melissa LiiD· 1 shared

Activity by Year

2018-2021 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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3 shared papersBioinformatics

Leping LiORCID

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3 papers

Recent·Most cited

CDSeqR: fast complete deconvolution for gene expression data from bulk tissues

Kai Kang, Caizhi David Huang, Yuanyuan Li, David M. Umbach, Leping Li

CDSeqR improves computational efficiency of CDSeq for bulk RNA-seq deconvolution and adds a function for cell type annotation using scRNA-seq data.

BMC Bioinformatics · May 24, 2021Peer-reviewedBioinformatics

Predicting Tumor Response to Drugs based on Gene-Expression Biomarkers of Sensitivity Learned from Cancer Cell Lines

Yuanyuan Li, David M. Umbach, J.M. Krahn, Igor Shats, Xiaoling Li, Leping Li

The paper builds predictive models for drug sensitivity using gene expression data from cancer cell lines and applies them to predict drug responses in tumor and normal tissues.

BMC Genomics · Apr 15, 2021Peer-reviewedBioinformatics

A novel computational complete deconvolution method using RNA-seq data

Kai Kang, Qian Meng, Igor Shats, David M. Umbach, Melissa Li, Yuanyuan Li, Xiaoling Li, Leping Li

This paper introduces CDSeq, a computational method that estimates both cell type proportions and gene expression profiles from bulk RNA-seq data, outperforming existing methods in accuracy.

bioRxiv · Dec 14, 2018 · PreprintBioinformatics