Assessment of computational methods for the analysis of single-cell ATAC-seq data

Huidong Chen, Caleb A. Lareau, Tommaso Andreani, +6

Genome biology

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index

Lan Jiang, Huidong Chen, Luca Pinello, +1

Genome biology

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

Huidong Chen, Luca Albergante, Jonathan Y. Hsu, +12

Nature Communications

Three subtypes of lung cancer fibroblasts define distinct therapeutic paradigms

Haichuan Hu, Zofia Piotrowska, Patricia J. Hare, +25

Cancer Cell

Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing

Qin Tang, Sowmya Iyer, Riadh Lobbardi, +13

The Journal of Experimental Medicine

Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing

Carman Man-Chung Li, Hana Shapiro, Christina Tsiobikas, +12

Cell Reports

Systems BiologyDevelopmental BiologySingle-cell Rna SequencingSingle Cell SequencingMedicine +13

Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

Xiaoping Han, Haide Chen, Daosheng Huang, +6

Genome biology

Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph

Luca Albergante, Evgeny M. Mirkes, Jonathan Bac, +7

Entropy

Cluster ComputingGeometric LearningEngineeringMachine LearningScalable Learning +23

Decreased Expression of Semaphorin-3A, a Neurite-Collapsing Factor, is Associated With Itch in Psoriatic Skin

Kenzen Kou, Fumio Nakamura, Michiko Aihara, +7

Acta Dermato Venereologica

InflammationSensory C-fibresHealthy SkinPsoriatic SkinSignal Transduction +13

SIMBA: single-cell embedding along with features

Huidong Chen, Jayoung Ryu, Michael Vinyard, +2

Nature Methods