Robert Foreman
University of California, Los Angeles
7 Papers
4 Citations
Robert Foreman is an academic researcher from University of California, Los Angeles. The author has contributed to research in topics: Gene expression & Transcriptional bursting. The author has an hindex of 3, co-authored 7 publications. Previous affiliations of Robert Foreman include University of California, San Diego.
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Papers
Joint cell segmentation and cell type annotation for spatial transcriptomics
Russell Littman,Zachary Hemminger,Robert Foreman,Douglas Arneson,Guanglin Zhang,Fernando Gomez-Pinilla,Xia Yang,Roy Wollman +7 more
TL;DR: In this paper, a computational framework for joint cell segmentation and cell type annotation that utilizes prior knowledge of cell type-specific gene expression was developed, which can be leveraged to improve the accuracy of RNA hybridization-based spatial transcriptomics while providing highly granular cell (sub)type information.
Mammalian gene expression variability is explained by underlying cell state
Robert Foreman,Roy Wollman +1 more
TL;DR: It is demonstrated that the majority of expression variability results from cell state differences and that the contribution of transcriptional bursting is relatively minimal, with the remaining variability effectively at the Poisson limit for most genes.
71
An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF-induced necroptosis decisions
Marie Oliver Metzig,Ying Tang,Simon Mitchell,Brooks Taylor,Robert Foreman,Roy Wollman,Alexander Hoffmann +6 more
TL;DR: TNF's dual roles in either coordinating cellular responses to inflammation, or further amplifying inflammation are determined by a dynamic NFκB‐A20‐RIPK3 circuit, that could be targeted to treat inflammation and cancer.
JSTA: joint cell segmentation and cell type annotation for spatial transcriptomics
Russell Littman,Zachary Hemminger,Robert Foreman,Douglas Arneson,Douglas Arneson,Guanglin Zhang,Fernando Gomez-Pinilla,Xia Yang,Roy Wollman +8 more
TL;DR: JSTA, a computational framework for Joint cell Segmentation and cell Type Annotation that utilizes prior knowledge of cell-type specific gene expression to improve the accuracy of RNA hybridization based spatial transcriptomics while providing highly granular cell (sub)type information.
6
Identifying chromatin features that regulate gene expression distribution.
TL;DR: By mapping the measurements of reporter expression at different genomic loci with multiple epigenetic profiles including the enrichment of transcription factors and the distance to different chromatin states, this work identified new factors that impact the regulation of gene expression distributions.