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Sara Aibar on Muck Rack

Sara Aibar

As seen in: Nature
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Articles

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

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By Sara Aibar, Carmen Bravo González-Blas, Liesbeth Minnoye, Dafni Papasokrati
| Nature Verified
Abstract We present cisTopic, a probabilistic framework used to simultaneously discover coaccessible enhancers and stable cell states from sparse single-cell epigenomics data (http://github.com/aertslab/cistopic). Using a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain and transcription factor perturbations, we demonstrate that topic modeling can be exploited for robust identification of cell types, enhancers and relevant transcription factors.
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Phenotype molding of stromal cells in the lung tumor microenvironment

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By Diether Lambrechts, Els Wauters, Bram Boeckx, Sara Aibar
| Nature Verified
Cancer cells are embedded in the tumor microenvironment (TME), a complex ecosystem of stromal cells. Here, we present a 52,698-cell catalog of the TME transcriptome in human lung tumors at single-cell resolution, validated in independent samples where 40,250 additional cells were sequenced. By comparing with matching non-malignant lung samples, we reveal a highly complex TME that profoundly molds stromal cells.
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