Large-scale analysis of RNA-DNA interactions. - Aleksandra A. Galitsyna; Anastasia Zharikova; Maria Logacheva; Sergey V. Razin; Andrey Mironov; Alexey Gavrilov (BIBM, 2018)

Reconstruction of the chromatin 3D conformation from single cell Hi-C data. - Pavel I. Kos; Aleksandra A. Galitsyna; Sergey V. Ulianov; Mikhail S. Gelfand; Sergey V. Razin; Alexander V. Chertovich (BIBM, 2018)

The chromatin structure of Dictyostelium discoideum. - Olga Tsoy; Aleksandra A. Galitsyna; Ekaterina Khrameeva; Sergey V. Ulianov; Mikhail S. Gelfand; Sergey V. Razin (BIBM, 2018)

Nuclear lamina maintains global spatial organization of chromatin in Drosophila cultured cells. - Sergey V. Ulianov; Semen A. Doronin; Ekaterina E. Khrameeva; Pavel I. Kos; Sergey S. Starikov; Aleksandra A. Galitsyna; Artem Luzhin; Mikhail S. Gelfand; Alexander V. Chertovich; Sergey V. Razin; Yuri Y. Shevelyov (BIBM, 2018)

Single-cell Hi-C demonstrates that TADs are stable units of Drosophila genome folding that persist in individual cells. - Vlada S. Zakharova; Aleksandra A. Galitsyna; Kirill E. Polovnikov; Ekaterina E. Khrameeva; Mariya D. Logacheva; Elena A. Mikhaleva; Egor S. Vassetzky; Aleksey A. Gavrilov; Yuri Y. Shevelev; Sergey K. Nechaev; Sergey V. Ulianov; Sergey V. Razin (BIBM, 2018)

HiChew: a Tool for TAD Clustering in Embryogenesis. - Nikolai S. Bykov; Olga M. Sigalova; Mikhail S. Gelfand; Aleksandra A. Galitsyna (ISBRA, 2020)

A machine learning framework for the prediction of chromatin folding in Drosophila using epigenetic features. - Michal Rozenwald; Aleksandra A. Galitsyna; Grigory V. Sapunov; Ekaterina E. Khrameeva; Mikhail S. Gelfand (PeerJ Comput. Sci., 2020)

Single-cell Hi-C data analysis: safety in numbers. - Aleksandra A. Galitsyna; Mikhail S. Gelfand (Briefings Bioinform., 2021)

Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data. - Pavel I. Kos; Aleksandra A. Galitsyna; Sergey V. Ulianov; Mikhail S. Gelfand; Sergey V. Razin; Alexander V. Chertovich (PLoS Comput. Biol., 2021)

HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases. - Victoria A Kobets; Sergey V. Ulianov; Aleksandra A. Galitsyna; Semen A. Doronin; Elena A. Mikhaleva; Mikhail S. Gelfand; Yuri Y. Shevelyov; Sergey V. Razin; Ekaterina E. Khrameeva (Briefings Bioinform., 2023)

Cooltools: Enabling high-resolution Hi-C analysis in Python. - Nezar Abdennur; Sameer Abraham; Geoffrey Fudenberg; Ilya M. Flyamer; Aleksandra A. Galitsyna; Anton Goloborodko; Maxim Imakaev; Betul A. Oksuz; Sergey Venev; Yao Xiao (PLoS Comput. Biol., 2024)

Pairtools: From sequencing data to chromosome contacts. - Nezar Abdennur; Geoffrey Fudenberg; Ilya M. Flyamer; Aleksandra A. Galitsyna; Anton Goloborodko; Maxim Imakaev; Sergey Venev (PLoS Comput. Biol., 2024)

Bioframe: operations on genomic intervals in Pandas dataframes. - Nezar Abdennur; Geoffrey Fudenberg; Ilya M. Flyamer; Aleksandra A. Galitsyna; Anton Goloborodko; Maxim Imakaev; Sergey Venev (Bioinform., 2024)