Clarence K. Mah
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Author Swipe
View article: Aberrant host mRNA partitioning in Ebola virus condensates driven by RNA folding perpetuates species-dependent interferon response
Aberrant host mRNA partitioning in Ebola virus condensates driven by RNA folding perpetuates species-dependent interferon response Open
RNA viruses form membraneless condensates in host cells to drive replication, but whether these compartments also regulate host RNAs remains unclear. Using MERFISH-based subcellular transcriptomics, we quantified cellular mRNA recruitment …
View article: Correction: Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma
Correction: Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma Open
View article: Bento: a toolkit for subcellular analysis of spatial transcriptomics data
Bento: a toolkit for subcellular analysis of spatial transcriptomics data Open
The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell–cell interactions, and spatial expression patterns, they are limited to the multicellular…
View article: Computational cell–cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment
Computational cell–cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment Open
View article: Bento: A toolkit for subcellular analysis of spatial transcriptomics data
Bento: A toolkit for subcellular analysis of spatial transcriptomics data Open
The spatial organization of molecules in a cell is essential for performing their functions. Spatial transcriptomics technologies have opened the door to characterization of cellular and subcellular organization. While current computationa…
View article: Automated, Miniaturized, and Scalable Screening of Healthcare Workers, First Responders, and Students for SARS-Cov-2 in San Diego County
Automated, Miniaturized, and Scalable Screening of Healthcare Workers, First Responders, and Students for SARS-Cov-2 in San Diego County Open
View article: INSPECT sample tracking system v1
INSPECT sample tracking system v1 Open
A specimen to data tracking tool for SEARCH SARS-CoV-2 tests. The application is used by SEARCH technicians to track samples as they proceed through each step within the RT-qPCR testing workflow. The app is currently hosted here: http://in…
View article: An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data Open
Single-cell RNA sequencing (scRNA-seq) has emerged as a popular method to profile gene expression at the resolution of individual cells. While there have been methods and software specifically developed to analyze scRNA-seq data, they are …
View article: genepattern/single_cell_clustering_notebook: Response to reviewers + Binder fix
genepattern/single_cell_clustering_notebook: Response to reviewers + Binder fix Open
Notebook has been updated based on feedback from reviewers from v1 (https://f1000research.com/articles/7-1306/v1) + updated requirements so binder runs the notebook correctly.
View article: An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays
An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays Open
Illumina Infinium DNA methylation arrays are a cost-effective technology to measure DNA methylation at CpG sites genome-wide and across cohorts of normal and cancer samples. While copy number alterations are commonly inferred from array-CG…
View article: Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups
Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups Open
View article: An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data Open
Single-cell RNA sequencing (scRNA-seq) has emerged as a popular method to profile gene expression at the resolution of individual cells. While there have been methods and software specifically developed to analyze scRNA-seq data, they are …
View article: genepattern/single_cell_clustering_notebook: v1.0.2
genepattern/single_cell_clustering_notebook: v1.0.2 Open
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View article: Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States
Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States Open