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Büttner, M. ; Miao, Z.* ; Wolf, F.A. ; Teichmann, S.A.* & Theis, F.J.: A test metric for assessing single-cell RNA-seq batch correction. Nat. Methods 16, 43-49 (2019)
Wolf, F.A. et al.: PAGA: Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol. 20:59 (2019)
Plass, M.* et al.: Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics. Science 360:eaaq1723 (2018)
Wolf, F.A. ; Angerer, P. & Theis, F.J.: SCANPY: Large-scale single-cell gene expression data analysis. Genome Biol. 19:15 (2018)
Angerer, P. et al.: Single cells make big data: New challenges and opportunities in transcriptomics. Curr. Opin. Syst. Biol. 4, 85-91 (2017)
Chlis, N.-K. ; Wolf, F.A. & Theis, F.J.: Model-based branching point detection in single-cell data by K-Branches clustering. Bioinformatics 33, 3211-3219 (2017)
Eulenberg, P. et al.: Reconstructing cell cycle and disease progression using deep learning. Nat. Commun. 8:463 (2017)
Haghverdi, L. ; Büttner, M. ; Wolf, F.A. ; Buettner, F. & Theis, F.J.: Diffusion pseudotime robustly reconstructs lineage branching. Nat. Methods 13, 845-848 (2016)