Author

Ben Ernest

National Institutes of Health

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

Biology Disciplines

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Bioinformatics· 2 Genomics· 2 Developmental Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Organism:human· 3 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Bao Quoc TraniD· 3 shared Charles WangiD· 3 shared Malcolm C. MoosiD· 3 shared Wanqiu CheniD· 3 shared Wenming XiaoiD· 3 shared Yongmei ZhaoiD· 3 shared Andreas SchereriD· 2 shared Baitang NingiD· 2 shared

Activity by Year

2020-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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3 shared papersGenomics

Bao Quoc TranORCID

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Author profile →

5 papers

Recent·Most cited

Enhancing the Fitness of Embryoid Bodies and Organoids by Chemical Cytoprotection

Seungmi Ryu, Claire Weber, Pei‐Hsuan Chu, Carlos A. Tristan, Ben Ernest, Vukasin M. Jovanovic, Tao Deng, J. Slámečka, Hyenjong Hong, John C. Braisted, Marissa B. Hirst, Anton M. Simeonov, Ty C. Voss, Ilyas Singeç

This paper shows that using a small molecule cocktail called CEPT during cell aggregation improves the survival and quality of embryoid bodies and organoids derived from human pluripotent stem cells.

bioRxiv · Mar 21, 2022 · PreprintDevelopmental Biology

SEQUIN: rapid and reproducible analysis of RNA-seq data in R/Shiny

Claire Weber, Marissa B. Hirst, Ben Ernest, Hannah M. Baskir, Carlos A. Tristan, Pei‐Hsuan Chu, Ilyas Singeç

SEQUIN provides a web-based RNA-seq analysis tool with quality control, visualization, and differential expression analysis for various biological contexts.

bioRxiv · Feb 23, 2022 · PreprintBioinformatics

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies

Li Tai Fang, Bin Zhu, Yongmei Zhao, Wanqiu Chen, Zhaowei Yang, Liz Kerrigan, Kurt J. Langenbach, Maryellen de Mars, Charles Lu, Kenneth B. Idler, Howard J. Jacob, Yuanting Zheng, Luyao Ren, Ying Yu, Erich B. Jaeger, , Paul G. Giresi

The paper establishes reference samples with high-coverage whole-genome sequencing to create truth sets for somatic mutation and germline variant detection using NGS technologies.

Nature Biotechnology · Sep 1, 2021Peer-reviewedBioinformatics

Achieving reproducibility and accuracy in cancer mutation detection with whole-genome and whole-exome sequencing

Wenming Xiao, Luyao Ren, Zhong Chen, Li Tai Fang, Yongmei Zhao, Justin Lack, Meijian Guan, Bin Zhu, Erich B. Jaeger, Liz Kerrigan, Thomas M. Blomquist, Tiffany Hung, Marc Sultan, Kenneth B. Idler, Charles Lu, , Leming M. Shi

This study evaluates reproducibility and accuracy of cancer mutation detection using whole-genome and whole-exome sequencing across multiple sequencing centers and bioinformatics pipelines.

Nature Biotechnology · Sep 1, 2021Peer-reviewedGenomics

A Comprehensive Multi-Center Cross-platform Benchmarking Study of Single-cell RNA Sequencing Using Reference Samples

Wanqiu Chen, Yongmei Zhao, Xin Chen, Zhaowei Yang, Xiaojiang Xu, Yingtao Bi, Vicky Chen, Jing Li, Hannah Choi, Ben Ernest, Bao Quoc Tran, Monika Mehta, Parimal Kumar, Andrew A. Farmer, Alain A. Mir, , Charles Wang

This study benchmarks scRNA-seq reproducibility across platforms and pipelines, finding that batch correction methods significantly affect results.

Nature Biotechnology · Dec 21, 2020Peer-reviewedGenomics