A multiresolution framework to characterize single-cell state landscapes.
A multiresolution framework to characterize single-cell state landscapes.
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一个多分辨率框架，以表征单细胞状态景观。
DOI：
10.1038/s41467-020-18416-6
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发表时间：
2020-10-26
影响因子：
16.6
通讯作者：
Kellis M
中科院分区：
文献类型：
--
作者：
Mohammadi S;Davila-Velderrain J;Kellis M
Dissecting the cellular heterogeneity embedded in single-cell transcriptomic data is challenging. Although many methods and approaches exist, identifying cell states and their underlying topology is still a major challenge. Here, we introduce the concept of multiresolution cell-state decomposition as a practical approach to simultaneously capture both fine- and coarse-grain patterns of variability. We implement this concept in ACTIONet, a comprehensive framework that combines archetypal analysis and manifold learning to provide a ready-to-use analytical approach for multiresolution single-cell state characterization. ACTIONet provides a robust, reproducible, and highly interpretable single-cell analysis platform that couples dominant pattern discovery with a corresponding structural representation of the cell state landscape. Using multiple synthetic and real data sets, we demonstrate ACTIONet’s superior performance relative to existing alternatives. We use ACTIONet to integrate and annotate cells across three human cortex data sets. Through integrative comparative analysis, we define a consensus vocabulary and a consistent set of gene signatures discriminating against the transcriptomic cell types and subtypes of the human prefrontal cortex. Dissecting the cellular heterogeneity embedded in single-cell transcriptomic data is challenging. Here, the authors introduce the concept of multiresolution cell-state decomposition as a practical approach to simultaneously capture both fine- and coarse-grain patterns of variability.
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影响因子：
46.9
作者：
Becht, Etienne;McInnes, Leland;Newell, Evan W.
通讯作者：
Newell, Evan W.
影响因子：
64.5
作者：
Davie K;Janssens J;Koldere D;De Waegeneer M;Pech U;Kreft Ł;Aibar S;Makhzami S;Christiaens V;Bravo González-Blas C;Poovathingal S;Hulselmans G;Spanier KI;Moerman T;Vanspauwen B;Geurs S;Voet T;Lammertyn J;Thienpont B;Liu S;Konstantinides N;Fiers M;Verstreken P;Aerts S
通讯作者：
Aerts S
影响因子：
4.6
作者：
Gaiteri C;Chen M;Szymanski B;Kuzmin K;Xie J;Lee C;Blanche T;Chaibub Neto E;Huang SC;Grabowski T;Madhyastha T;Komashko V
通讯作者：
Komashko V
DOI：
10.1109/tpami.2013.226
发表时间：
2014-04-01
影响因子：
23.6
作者：
Gillis, Nicolas;Vavasis, Stephen A.
通讯作者：
Vavasis, Stephen A.
影响因子：
48
作者：
Korsunsky, Ilya;Millard, Nghia;Raychaudhuri, Soumya
通讯作者：
Raychaudhuri, Soumya