Ruslan Soldatov, PhD

Assistant Member
Contact
Tiffany Cordero 646.608.7670

About

Dr. Soldatov joined the Computational Oncology Service in 2022 as an Assistant Attending. Dr. Soldatov’s research aims to characterize mechanisms of cell fate decisions that coordinate tissue function and quantify how distortions of these mechanisms shape the course of cancer evolution. He develops computational methods to analyze high-throughput measurements at the single-cell resolution, including multi-omics and lineage data. Dr. Soldatov received a PhD in computational biology from the Institute for Information Transmission Problems, Moscow and trained as a postdoctoral fellow at Harvard Medical School with Dr. Peter Kharchenko. Before joining MSKCC, he was an Instructor in Biomedical Informatics at Harvard Medical School. Dr. Soldatov authored many publications in high-ranking journals.
The Soldatov Lab

Education

PhD

The Institute for Information Transmission Problems in Moscow, Russia

Appointments

Computational Oncology, Department of Epidemiology & Biostatistics

Selected Publications

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.

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