The Soldatov lab aims to understand molecular principles of cell fate decisions that ensure tissue homeostasis and how the distortion of these mechanisms shapes cancer evolution. We are broadly interested in questions related to the organization of normal tissues and cancer, viewing it as a dynamic ecosystem of fundamental units — cells. Why do seemingly similar stem cells manifest distinct phenotypic properties, such as proliferative capacity or regenerative potential? How does this phenotypic plasticity, which enables cancers to evolve and evade treatments, emerge? Do exposures to external insults, such as injury or pathogens, rewire cellular behaviors? How does the microenvironment shape cell fate decisions? To advance these questions, we develop computational methods to analyze cellular heterogeneity using high-throughput measurements at the level of individual cells. The lab leverages machine learning approaches, dynamic systems theory, and data science to gain insights into the evolution of tissue ecosystems in the context of basic and translational science.
View available career opportunities in the lab here.
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. 2023 Mar;41(3):417-426. doi: 10.1038/s41587-022-01468-y. Epub 2022 Sep 26. PMID: 36163550; PMCID: PMC10289836.
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. PMID: 34435732; PMCID: PMC8388041.
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. PMID: 34385354; PMCID: PMC9217108.
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. PMID: 32968047; PMCID: PMC7511944.
Soldatov R, Kaucka M, Kastriti ME, Petersen J, Chontorotzea T, Englmaier L, Akkuratova N, Yang Y, Häring M, 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, Zeisel A, Braun E, Hochgerner H, Petukhov V, Lidschreiber K, Kastriti ME, et al. RNA velocity of single cells. Nature. 2018 Aug;560(7719):494-498. doi: 10.1038/s41586-018-0414-6. Epub 2018 Aug 8. PMID: 30089906; PMCID: PMC6130801.
Mesitov MV, Soldatov RA, Zaichenko DM, Malakho SG, Klementyeva TS, Sokolovskaya AA, Kubatiev AA, Mironov AA, Moskovtsev AA. Differential processing of small RNAs during endoplasmic reticulum stress. Sci Rep. 2017 Apr 13;7:46080. doi: 10.1038/srep46080. PMID: 28452371; PMCID: PMC5408347.
Terekhanova NV, Seplyarskiy VB, Soldatov RA, Bazykin GA. Evolution of Local Mutation Rate and Its Determinants. Mol Biol Evol. 2017 May 1;34(5):1100-1109. doi: 10.1093/molbev/msx060. PMID: 28138076; PMCID: PMC5850301.
Seplyarskiy VB, Soldatov RA, Popadin KY, Antonarakis SE, Bazykin GA, Nikolaev SI. APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. Genome Res. 2016 Feb;26(2):174-82. doi: 10.1101/gr.197046.115. Epub 2016 Jan 11. PMID: 26755635; PMCID: PMC4728370.
Vinogradova SV, Sutormin RA, Mironov AA, Soldatov RA. Probing-directed identification of novel structured RNAs. RNA Biol. 2016;13(2):232-42. doi: 10.1080/15476286.2015.1132140. Erratum in: RNA Biol. 2016 Aug 2;13(8):741. PMID: 26732206; PMCID: PMC4829316.
Seplyarskiy VB, Bazykin GA, Soldatov RA. Polymerase ζ Activity Is Linked to Replication Timing in Humans: Evidence from Mutational Signatures. Mol Biol Evol. 2015 Dec;32(12):3158-72. doi: 10.1093/molbev/msv184. Epub 2015 Sep 15. PMID: 26376651.
Soldatov RA, Vinogradova SV, Mironov AA. RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments. Bioinformatics. 2014 Feb 15;30(4):457-63. doi: 10.1093/bioinformatics/btt701. Epub 2013 Nov 28. PMID: 24292360.
The projects will involve analysis of multi-omics, pooled perturbations and spatially-resolved datasets.
Please visit Dr. Soldatov’s faculty page, PubMed or Google Scholar for more publications.
