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Artem A Ilyin Anna D Kononkova Anastasia V Golova Viktor V Shloma Oxana
M Olenkina Valentina
V Nenasheva Yuri
A Abramov Alexei A Kotov Daniil
A Maksimov Petr
P Laktionov Alexey
V Pindyurin Aleksandra
A Galitsyna Sergey
V Ulianov Ekaterina
E Khrameeva Mikhail
S Gelfand Stepan
N Belyakin Sergey
V Razin Yuri
Y Shevelyov 《Nucleic acids research》2022,50(6):3203
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Pavel I. Kos Aleksandra A. Galitsyna Sergey V. Ulianov Mikhail S. Gelfand Sergey V. Razin Alexander V. Chertovich 《PLoS computational biology》2021,17(11)
Construction of chromosomes 3D models based on single cell Hi-C data constitute an important challenge. We present a reconstruction approach, DPDchrom, that incorporates basic knowledge whether the reconstructed conformation should be coil-like or globular and spring relaxation at contact sites. In contrast to previously published protocols, DPDchrom can naturally form globular conformation due to the presence of explicit solvent. Benchmarking of this and several other methods on artificial polymer models reveals similar reconstruction accuracy at high contact density and DPDchrom advantage at low contact density. To compare 3D structures insensitively to spatial orientation and scale, we propose the Modified Jaccard Index. We analyzed two sources of the contact dropout: contact radius change and random contact sampling. We found that the reconstruction accuracy exponentially depends on the number of contacts per genomic bin allowing to estimate the reconstruction accuracy in advance. We applied DPDchrom to model chromosome configurations based on single-cell Hi-C data of mouse oocytes and found that these configurations differ significantly from a random one, that is consistent with other studies. 相似文献
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Galitsyna E. V. Bukharova T. B. Buianova A. A. Davygora K. S. Goldshtein D. V. 《Applied Biochemistry and Microbiology》2021,57(7):823-827
Applied Biochemistry and Microbiology - Multipotent mesenchymal stromal cells (MSCs) can be used as a model for the development of gene and cell technologies and as a means of the delivery of... 相似文献
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