Faure L, Soldatov R, Kharchenko PV, Adameyko I. scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data. Bioinformatics. 2023 Jan 1;39(1):btac746. doi: 10.1093/bioinformatics/btac746. PMID: 36394263; PMCID: PMC9805561.
Gao T, Soldatov R, Sarkar H, Kurkiewicz A, Biederstedt E, Loh PR, Kharchenko PV. Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes. Nat Biotechnol. 2022 Sep 26. doi: 10.1038/s41587-022-01468-y. Epub ahead of print. PMID: 36163550
Petukhov V, Xu RJ, Soldatov RA, Cadinu P, Khodosevich K, Moffitt JR, Kharchenko PV. Cell segmentation in imaging-based spatial transcriptomics. Nat Biotechnol. 2022 Mar;40(3):345-354. doi: 10.1038/s41587-021-01044-w. Epub 2021 Oct 14. PMID: 34650268
Bergen V, Soldatov RA, Kharchenko PV, Theis FJ. RNA velocity-current challenges and future perspectives. Mol Syst Biol. 2021 Aug;17(8):e10282. doi: 10.15252/msb.202110282. PMCID: PMC8388041. PMID: 34435732
Seplyarskiy VB, Soldatov* RA, et al; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Population Genetics Working Group, Gilissen C, Wong WSW, Kharchenko PV, Sunyaev S. Population sequencing data reveal a compendium of mutational processes in the human germ line. Science. 2021 Aug 27;373(6558):1030-1035. doi: 10.1126/science.aba7408. Epub 2021 Aug 12. PMCID: PMC9217108. PMID: 34385354
Krivanek J, Soldatov* RA, Kastriti ME, Chontorotzea T, Herdina AN, Petersen J, Szarowska B, Landova M, Matejova VK, Holla LI, Kuchler U, Zdrilic IV, Vijaykumar A, Balic A, Marangoni P, Klein OD, et al. Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth. Nat Commun. 2020 Sep 23;11(1):4816. doi: 10.1038/s41467-020-18512-7. PMCID: PMC7511944. PMID: 32968047
Soldatov* R, Kaucka* M, Kastriti* ME, et al. Spatiotemporal structure of cell fate decisions in murine neural crest. Science. 2019 Jun 7;364(6444):eaas9536. doi: 10.1126/science.aas9536. PMID: 31171666
La Manno G, Soldatov R, et al. Nature. 2018 Aug;560(7719):494-498. doi: 10.1038/s41586-018-0414-6. Epub 2018 Aug 8. PMCID: PMC6130801. PMID: 30089906