Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures. - Dmitri D. Pervouchine; Ekaterina Khrameeva; Marina Pichugina; Olexii Nikolaienko; Mikhail S. Gelfand; Petr Rubtsov; Andrey A. Mironov (RECOMB, 2012)

Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. - Ekaterina Khrameeva; Mikhail S. Gelfand (BMC Bioinform., 2012)

History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. - Ekaterina Khrameeva; Geoffrey Fudenberg; Mikhail S. Gelfand; Leonid A. Mirny (J. Bioinform. Comput. Biol., 2016)

Prediction of 3D Chromatin Structure Using Recurrent Neural Networks. - Michal Rozenwald; Ekaterina Khrameeva; Grigory V. Sapunov; Mikhail S. Gelfand (BIBM, 2018)

Prediction of chromatin spatial structure characteristics using machine learning methods. - Sergei Starikov; Ekaterina Khrameeva; Mikhail S. Gelfand (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)

Neanderthal and Denisovan ancestry in Papuans: A functional study. - Evgeny E. Akkuratov; Mikhail S. Gelfand; Ekaterina Khrameeva (J. Bioinform. Comput. Biol., 2018)

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)

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)

A hierarchical algorithm with randomized learning for robust tissue segmentation and classification in digital pathology. - Svetlana Illarionova; Rifat A. Hamoudi; M. Zapevalina; I. Fedin; Nadezhda Alsahanova; Alexander Bernstein; Evgeny Burnaev; V. Alferova; Ekaterina Khrameeva; D. Shadrin; I. Talaat; Ahmed Bouridane; et al. (Inf. Sci., 2025)