Maiia Shulman

dblp:424/4641 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2025
0009-0006-6308-1997ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 1 heaviest of 1, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › omics data analysis
spatial omics
0.912025
Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data · Bioinform. 2025

Methods — techniques the papers use, named apart from their topics

simulation · 0.9benchmarking · 0.9
YearPublicationVenuePosition
2025 Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
abstract
MOTIVATION: Spatially resolved chromatin accessibility profiling offers the potential to investigate gene regulatory processes within the spatial context of tissues. However, current methods typically work at spot resolution, aggregating measurements from multiple cells, thereby obscuring cell-type-specific spatial patterns of accessibility. Spot deconvolution methods have been developed and extensively benchmarked for spatial transcriptomics, yet no dedicated methods exist for spatial chromatin accessibility, and it is unclear if RNA-based approaches are applicable to that modality. RESULTS: Here, we demonstrate that these RNA-based approaches can be applied to spot-based chromatin accessibility data by a systematic evaluation of five top-performing spatial transcriptomics deconvolution methods. To assess performance, we developed a simulation framework that generates both transcriptomic and accessibility spot data from dissociated single-cell and targeted multiomic datasets, enabling direct comparisons across both data modalities. Our results show that Cell2location and RCTD, in contrast to other methods, exhibit robust performance on spatial chromatin accessibility data, achieving accuracy comparable to RNA-based deconvolution. Generally, we observed that RNA-based deconvolution exhibited slightly better performance compared to chromatin accessibility-based deconvolution, especially for resolving rare cell types, indicating room for future development of specialized methods. In conclusion, our findings demonstrate that existing deconvolution methods can be readily applied to chromatin accessibility-based spatial data. Our work provides a simulation framework and establishes a performance baseline to guide the development and evaluation of methods optimized for spatial epigenomics. AVAILABILITY AND IMPLEMENTATION: All methods, simulation frameworks, peak selection strategies, analysis notebooks and scripts are available at https://github.com/theislab/deconvATAC.
Sarah Ouologuem, Laura D. Martens, Anna C. Schaar, Maiia Shulman, Julien Gagneur, Fabian J. Theis
Bioinform.4