Author

Joe Shuga

10X Genomics (United States)

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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Genomics· 2 Bioinformatics· 1 Developmental Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 3 Organism:human· 3 Assay:scRNA-seq· 3 Research Focus:cell type annotation· 2 Research Focus:clustering· 2 Approach:experimental assay· 2 Approach:statistical model· 2 Assay:whole-genome sequencing· 2

Frequent Co-Authors

Claudia Catalanotti· 2 shared Michael Schnall-Levin· 2 shared Rajiv Bharadwaj· 2 shared Shamoni MaheshwariiD· 2 shared Tobias D. Wheeler· 2 shared Zachary Bent· 2 shared Adam Weinstein· 1 shared Alex A. PolleniD· 1 shared

Activity by Year

2017-2021 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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2 shared papersBioinformatics

Claudia Catalanotti

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Author profile →

4 papers

Recent·Most cited

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

Joint single cell DNA-Seq and RNA-Seq of gastric cancer reveals subclonal signatures of genomic instability and gene expression

Noemi Andor, Billy T. Lau, Claudia Catalanotti, Vijay Kumar, Anuja Sathe, Kamila Belhocine, Tobias D. Wheeler, Andrew D. Price, Maengseok Song, Željko Džakula, Jon M. Sorenson, David A. Stafford, Zachary Bent, Laura E. DeMare, Lance Hepler, , Hanlee P. Ji

The paper combines single cell DNA-Seq and RNA-Seq in gastric cancer to reveal subclonal genomic instability and gene expression patterns, showing evidence of tumor evolution.

bioRxiv · Jun 21, 2020 · PreprintGenomics

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

Alex A. Pollen, Aparna Bhaduri, Madeline G. Andrews, Tomasz Jan Nowakowski, Olivia S. Meyerson, Mohammed A. Mostajo-Radji, Elizabeth Di Lullo, Beatriz Alvarado, Melanie A. Bedolli, Max L. Dougherty, Ian T. Fiddes, Zev N. Kronenberg, Joe Shuga, Anne A. Leyrat, Jay A. A. West, , Arnold R. Kriegstein

The paper uses chimpanzee cerebral organoids to identify human-specific genes in cortical development and finds increased PI3K/AKT/mTOR activation in human outer radial glia.

Cell · Feb 1, 2019Peer-reviewedDevelopmental Biology

Massively parallel digital transcriptional profiling of single cells

Grace X. Y. Zheng, Jessica M. Terry, Phillip Belgrader, Paul Ryvkin, Zachary Bent, Ryan Wilson, Solongo B. Ziraldo, Tobias D. Wheeler, Geoff P. McDermott, Junjie Zhu, Mark Gregory, Joe Shuga, Luz Montesclaros, Jason G. Underwood, Don A. Masquelier, , Jason H. Bielas

8-channel GemCode droplet barcoding captures ∼50% of loaded cells for 3′ mRNA counting, profiling 68k peripheral blood mononuclear cells and calling transplant chimerism from transcript variants.

Nature Communications · Jan 16, 2017Peer-reviewedGenomics✦ In-depth digest