Publications

Selected publications

Patterns of Transposable Element Distribution Around Chromatin Ligation Points Revealed by Micro-C Data Analysis
Vikhorev AV, Rempel MM, Polesskaya OO, Savelev IV, Myakishev-Rempel M. arXiv preprint arXiv:2408.11079 (2024).
→ High-resolution chromatin contact analysis showing Alu and LINE1 enrichment near loop anchors.

The Avoidance of Purine Stretches by Cancer Mutations
Vikhorev AV, Savelev IV, Polesskaya OO, Rempel MM, Miller RA, Myakishev-Rempel M. International Journal of Molecular Sciences 25(20):11050 (2024).
→ Computational analysis showing that cancer mutations avoid purine-rich regions.
High-molecular-mass hyaluronan mediates the cancer resistance of the naked mole rat
Tian X, Azpurua J, Hine C, Vaidya A, Myakishev-Rempel M, et al. Nature 499(7458):346-349 (2013).
→ Discovery of extracellular matrix mechanism explaining cancer resistance and longevity in naked mole rat.

Optogenetic regulation of transcription
Polesskaya O, Baranova A, Bui S, Kondratev N, Kananykhina E, Nazarenko O, Myagkova E, For AV, Kulemzin SV, Gornostaeva A, Roy-Engel AM, Petrenko V, Baranova TI, Muravenko OV, Varnavsky A, Myakishev-Rempel M. BMC Neuroscience 19(Suppl 1):12 (2018).
→ Demonstration of light-activated transcription control for studying chromatin regulation.
All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues
Rozenberg JM, Shlyakhtenko A, Glass K, Rishi V, Myakishev MV, FitzGerald PC, Vinson C. BMC Genomics 9(1):67 (2008).
→ Genome-wide finding that CpG content predicts RNA Pol II promoter binding.
Classification of human B-ZIP proteins based on dimerization properties
Vinson C, Myakishev M, Acharya A, Mir AA, Moll JR, Bonovich M. Molecular and Cellular Biology 22(18):6321-6335 (2002).
→ Systematic classification of transcription factor dimerization specificity.

Genetic variation in the 6p22.3 gene DTNBP1 … is associated with schizophrenia
Straub RE, Jiang Y, MacLean CJ, Ma Y, Webb BT, Myakishev MV, et al. American Journal of Human Genetics 71(2):337-348 (2002).
→ Landmark discovery linking DTNBP1 to schizophrenia susceptibility.
High-throughput SNP genotyping by allele-specific PCR with universal energy-transfer-labeled primers
Myakishev MV, Khripin Y, Hu S, Hamer DH. Genome Research 11(1):163-169 (2001).
→ Development of a widely used high-throughput SNP genotyping method.
Centrifugal method and apparatus for isolating a substance from a mixture of substances in a sample liquid
Beritashvili DR, Myakishev MV, Ershov GM, Georgiev GP, Kapanadze GI. US Patent 5,610,074 (1997).
→ Early patent on centrifugal separation technology.

Evidence for DNA resonance signaling via longitudinal hydrogen bonds
Savelev I, Myakishev-Rempel M. Progress in Biophysics and Molecular Biology 156:14–19 (2020).
→ Theoretical framework suggesting that DNA information may propagate through mechanical vibrations along hydrogen bonds, influencing chromatin dynamics.
Possible traces of resonance signaling in the genome
Savelev I, Myakishev-Rempel M. Progress in Biophysics and Molecular Biology 151:23–31 (2020).
→ Computational study identifying motifs and repetitive element distributions reflecting possible resonance constraints.
On possible role of DNA electrodynamics in chromatin regulation
Polesskaya O, Guschin V, Kondratev N, Garanina I, Nazarenko O, Baranova A, Myakishev-Rempel M. Progress in Biophysics and Molecular Biology 134:50–54 (2018).
→ Review of evidence for DNA’s electrical properties affecting chromatin folding.
Prediction of oscillation patterns of charges in a DNA sequence
Myakishev-Rempel M, Savelev I. US Patent App. 17/529,253 (2022).
→ Patent describing algorithmic prediction of charge oscillations along DNA.

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