J
José L. McFaline-Figueroa
Researcher at University of Washington
Publications - 34
Citations - 2730
José L. McFaline-Figueroa is an academic researcher from University of Washington. The author has contributed to research in topics: Biology & Medicine. The author has an hindex of 16, co-authored 25 publications receiving 1621 citations. Previous affiliations of José L. McFaline-Figueroa include Massachusetts Institute of Technology.
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Journal ArticleDOI
Joint profiling of chromatin accessibility and gene expression in thousands of single cells
Junyue Cao,Darren A. Cusanovich,Vijay Ramani,Delasa Aghamirzaie,Hannah A. Pliner,Andrew J. Hill,Riza M. Daza,José L. McFaline-Figueroa,Jonathan S. Packer,Lena Christiansen,Frank J. Steemers,Andrew Adey,Andrew Adey,Cole Trapnell,Jay Shendure +14 more
TL;DR: By applying sci-CAR to lung adenocarcinoma cells and mouse kidney tissue, the authors demonstrate precision in assessing expression and genome accessibility at a genome-wide scale and provide an improvement over bulk analysis, which can be confounded by differing cellular subgroups.
Journal ArticleDOI
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.
Hannah A. Pliner,Jonathan S. Packer,José L. McFaline-Figueroa,Darren A. Cusanovich,Riza M. Daza,Delasa Aghamirzaie,Sanjay Srivatsan,Xiaojie Qiu,Dana Jackson,Anna Minkina,Andrew Adey,Frank J. Steemers,Jay Shendure,Jay Shendure,Cole Trapnell +14 more
TL;DR: Cicero is introduced, an algorithm that identifies co-accessible pairs of DNA elements using single-cell chromatin accessibility data and so connects regulatory elements to their putative target genes and is applied to investigate how dynamically accessible elements orchestrate gene regulation in differentiating myoblasts.
Journal ArticleDOI
A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.
Molly Gasperini,Andrew J. Hill,José L. McFaline-Figueroa,Beth Martin,Seungsoo Kim,Melissa D. Zhang,Dana Jackson,Anh Leith,Jacob Schreiber,William Stafford Noble,Cole Trapnell,Nadav Ahituv,Jay Shendure,Jay Shendure +13 more
TL;DR: A multiplex, expression quantitative trait locus (eQTL)-inspired framework for mapping enhancer-gene pairs by introducing random combinations of CRISPR/Cas9-mediated perturbations to each of many cells, followed by single-cell RNA sequencing (RNA-seq).
Journal ArticleDOI
Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana
Ken Jean-Baptiste,José L. McFaline-Figueroa,Cristina M. Alexandre,Michael W. Dorrity,Lauren M. Saunders,Kerry L. Bubb,Cole Trapnell,Stanley Fields,Christine Queitsch,Josh T. Cuperus +9 more
TL;DR: The results demonstrate that single cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution and address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress.
Journal ArticleDOI
Massively multiplex chemical transcriptomics at single-cell resolution
Sanjay Srivatsan,José L. McFaline-Figueroa,Vijay Ramani,Vijay Ramani,Lauren M. Saunders,Junyue Cao,Jonathan S. Packer,Hannah A. Pliner,Dana Jackson,Riza M. Daza,Lena Christiansen,Fan Zhang,Frank J. Steemers,Jay Shendure,Cole Trapnell +14 more
TL;DR: The results with histone deacetylase inhibitors support the view that chromatin acts as an important reservoir of acetate in cancer cells, and reveal substantial intercellular heterogeneity in response to specific compounds, commonalities inresponse to families of compounds, and insight into differential properties within families.