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  1. 2025

  2. Chromatin landscape, transcriptomic and ChIP-seq profiling of Anopheles stephensi MSQ43 cell line

    Lukyanchikova, V., Nuriddinov, M., Khabarova, A., Gridina, M., Popov, A., Belokopytova, P., Sharakhov, I. V. & Fishman, V., 26 Sept 2025, In: Scientific Data. 12, 1, p. 1566

    Research output: Contribution to journal › Article › peer-review

  3. Direction and modality of transcription changes caused by TAD boundary disruption in Slc29a3/Unc5b locus depends on tissue-specific epigenetic context

    Salnikov, P., Belokopytova, P., Yan, A., Viesná, E., Korablev, A., Serova, I., Lukyanchikova, V., Stepanchuk, Y., Torgunakov, N., Tikhomirov, S. & Fishman, V., 12 Aug 2025, In: Epigenetics & chromatin. 18, 1, 55.

    Research output: Contribution to journal › Article › peer-review

  4. DNA and Histone Modifications Identify a Putative Controlling Element (CE) on the X Chromosome of Sciara coprophila

    Posukh, O. V., Shloma, V. V., Skrypnik, P. A., Maksimov, D. A., Antoshina, P. A., Kalashnikova, D. A., Nurislamov, A., Lukyanchikova, V. A., Torgunakov, N., Battulin, N. R., Fishman, V. S., Vyatkin, Y. V., Smelova, A. A., Romanov, S. E., Laktionov, P. P., Valishayev, D., Belyakin, S. N. & Singh, P. B., 12 Aug 2025, In: Cells. 14, 16, 16 p., 1243.

    Research output: Contribution to journal › Article › peer-review

  5. Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data

    Nuriddinov, M., Belokopytova, P. & Fishman, V., Jun 2025, In: NAR Genomics and Bioinformatics. 7, 2, p. lqaf081 10 p., lqaf081.

    Research output: Contribution to journal › Article › peer-review

  6. Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants

    Gridina, M., Lagunov, T., Belokopytova, P., Torgunakov, N., Nuriddinov, M., Nurislamov, A., Nazarenko, L. P., Kashevarova, A. A., Lopatkina, M. E., Vasilyev, S., Zuev, A., Belyaeva, E. O., Salyukova, O. A., Cheremnykh, A. D., Sukhanova, N. N., Minzhenkova, M. E., Markova, Z. G., Demina, N. A., Stepanchuk, Y., Khabarova, A., & 22 othersYan, A., Valeev, E., Koksharova, G., Grigor’eva, E. V., Kokh, N., Lukjanova, T., Maximova, Y., Musatova, E., Shabanova, E., Kechin, A., Khrapov, E., Boyarskih, U., Ryzhkova, O., Suntsova, M., Matrosova, A., Karoli, M., Manakhov, A., Filipenko, M., Rogaev, E., Shilova, N. V., Lebedev, I. N. & Fishman, V., 7 May 2025, In: Genome Medicine. 17, 1, p. 47 47.

    Research output: Contribution to journal › Article › peer-review

  7. 2024

  8. Кандидатные прогностические и предиктивные транслокации высоко агрессивных форм мозговых опухолей

    Фишман, В. С. & Гридина, М. М., 10 Dec 2024, Редакционно-издательский центр НГУ, Patent No. 118, 10 Dec 2024, Priority date 10 Dec 2024

    Research output: Patent › Know-how registration

  9. Structural variants in the Epb41l4a locus: TAD disruption and Nrep gene misregulation as hypothetical drivers of neurodevelopmental outcomes

    Salnikov, P., Korablev, A., Serova, I., Belokopytova, P., Yan, A., Stepanchuk, Y., Tikhomirov, S. & Fishman, V., Dec 2024, In: Scientific Reports. 14, 1, 8 p., 5288.

    Research output: Contribution to journal › Article › peer-review

  10. Сравнительный анализ первичной структуры и получение рекомбинантной поли(ADP-рибоза)полимеразы 1 долгоживущего Heterocephalus glaber

    Naumenko, K. N., Nurislamov, A. R., Nazarov, K. D., Fishman, V. S., Popov, A. A., Petruseva, I. O., Evdokimov, A. N. & Lavrik, O. I., Nov 2024, In: Vavilovskii Zhurnal Genetiki i Selektsii. 28, 7, p. 688-695 8 p., 2.

    Research output: Contribution to journal › Article › peer-review

  11. A HGF Mutation in the Familial Case of Primary Lymphedema: A Report

    Koksharova, G., Kokh, N., Gridina, M., Khapaev, R., Nimaev, V. & Fishman, V., May 2024, In: International Journal of Molecular Sciences. 25, 10, 5464.

    Research output: Contribution to journal › Article › peer-review

  12. Modification of the Hi-C Technology for Molecular Genetic Analysis of Formalin-Fixed Paraffin-Embedded Sections of Tumor Tissues

    Gridina, M. M., Stepanchuk, Y. K., Nurridinov, M. A., Lagunov, T. A., Torgunakov, N. Y., Shadsky, A. A., Ryabova, A. I., Vasiliev, N. V., Vtorushin, S. V., Gerashchenko, T. S., Denisov, E. V., Travin, M. A., Korolev, M. A. & Fishman, V. S., Apr 2024, In: Biochemistry (Moscow). 89, 4, p. 637-652 16 p.

    Research output: Contribution to journal › Article › peer-review

  13. Towards Development of the 4C-Based Method Detecting Interactions of Plasmid DNA with Host Genome

    Yan, A. P., Salnikov, P. A., Gridina, M. M., Belokopytova, P. S. & Fishman, V. S., Apr 2024, In: Biochemistry (Moscow). 89, 4, p. 653-662 10 p.

    Research output: Contribution to journal › Article › peer-review

  14. Differential gene expression in degenerative lumbar discs from the Russian disc degeneration study (RuDDS) biobank

    Тяпкин, А. В., Иванов, А. А., Леонова, О. Н., Krutko, A. V., Peleganchuk, A. V., Фишман, В. С., Елгаева, Е. Е. & Цепилов, Я. А., 2024, In: European journal of human genetics. 32, S2, p. 996-997 2 p., EP06.052.

    Research output: Contribution to journal › Article › peer-review

  15. 2023

  16. Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease

    Maria, G., Andrey, P., Artem, S., Nikita, T., Andrey, K., Evgeny, K., Oxana, R., Maxim, F. & Veniamin, F., 11 Dec 2023, In: Epigenetics & chromatin. 16, 1, 13 p., 48.

    Research output: Contribution to journal › Article › peer-review

  17. Lampbrush chromosome studies in the post-genomic era

    Krasikova, A., Fishman, V. & Kulikova, T., May 2023, In: BioEssays. 45, 5, 7 p., e2200250.

    Research output: Contribution to journal › Article › peer-review

  18. Cell type-specific interpretation of noncoding variants using deep learning-based methods

    Sindeeva, M., Chekanov, N., Avetisian, M., Shashkova, T. I., Baranov, N., Malkin, E., Lapin, A., Kardymon, O. & Fishman, V., 20 Mar 2023, In: GigaScience. 12, p. 1-11 11 p., giad015.

    Research output: Contribution to journal › Article › peer-review

  19. Function and Evolution of the Loop Extrusion Machinery in Animals

    Kabirova, E., Nurislamov, A., Shadskiy, A., Smirnov, A., Popov, A., Salnikov, P., Battulin, N. & Fishman, V., 6 Mar 2023, In: International Journal of Molecular Sciences. 24, 5, 5017.

    Research output: Contribution to journal › Review article › peer-review

  20. A Cre-LoxP-based approach for combinatorial chromosome rearrangements in human HAP1 cells

    Khabarova, A., Koksharova, G., Salnikov, P., Belokopytova, P., Mungalov, R., Pristyazhnuk, I., Nurislamov, A., Gridina, M. & Fishman, V., 26 Feb 2023, In: Chromosome Research. 31, 1, 15 p., 11.

    Research output: Contribution to journal › Article › peer-review

  21. Benefits of NGS for Genetic Testing of Primary Lymphedema

    Kokh, N. V., Sergeevna, K. G., Gridina, M., Ivanoshchuk, D., Fishman, V. & Nimaev, V., 2023, 2023 IEEE Ural-Siberian Conference on Computational Technologies in Cognitive Science, Genomics and Biomedicine, CSGB 2023 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 133-136 4 p. (2023 IEEE Ural-Siberian Conference on Computational Technologies in Cognitive Science, Genomics and Biomedicine, CSGB 2023 - Proceedings).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Research › peer-review

  22. 2022

  23. Anopheles mosquitoes reveal new principles of 3D genome organization in insects

    Lukyanchikova, V., Nuriddinov, M., Belokopytova, P., Taskina, A., Liang, J., Reijnders, M. J. M. F., Ruzzante, L., Feron, R., Waterhouse, R. M., Wu, Y., Mao, C., Tu, Z., Sharakhov, I. V. & Fishman, V., Dec 2022, In: Nature Communications. 13, 1, 1960.

    Research output: Contribution to journal › Article › peer-review

  24. FastContext: A tool for identification of adapters and other sequence patterns in next generation sequencing (NGS) data

    Viesná, Е. & Fishman, V., Dec 2022, In: Vavilovskii Zhurnal Genetiki i Selektsii. 26, 8, p. 806-809 4 p., 10.

    Research output: Contribution to journal › Article › peer-review

  25. Method for the Isolation of “RNA-seq-Quality” RNA from Human Intervertebral Discs after Mortar and Pestle Homogenization

    Ivanov, A. A., Leonova, O. N., Wiebe, D. S., Krutko, A. V., Gridina, M. M., Fishman, V. S., Aulchenko, Y. S., Tsepilov, Y. A. & Golubeva, T. S., Nov 2022, In: Cells. 11, 22, 3578.

    Research output: Contribution to journal › Article › peer-review

  26. Single-Cell DNA Methylation Analysis of Chicken Lampbrush Chromosomes

    Nurislamov, A., Lagunov, T., Gridina, M., Krasikova, A. & Fishman, V., 20 Oct 2022, In: International Journal of Molecular Sciences. 23, 20, 12601.

    Research output: Contribution to journal › Article › peer-review

  27. Editorial: The role of high-order chromatin organization in gene regulation

    Fishman, V. & Pindyurin, A. V., 3 Oct 2022, In: Frontiers in Genetics. 13, 1045787.

    Research output: Contribution to journal › Editorial › peer-review

  28. Comparison and critical assessment of single-cell Hi-C protocols

    Gridina, M., Taskina, A., Lagunov, T., Nurislamov, A., Kulikova, T., Krasikova, A. & Fishman, V., Oct 2022, In: Heliyon. 8, 10, 6 p., e11023.

    Research output: Contribution to journal › Article › peer-review

  29. 3DGenBench: a web-server to benchmark computational models for 3D Genomics

    Belokopytova, P., Viesná, E., Chiliński, M., Qi, Y., Salari, H., Di Stefano, M., Esposito, A., Conte, M., Chiariello, A. M., Teif, V. B., Plewczynski, D., Zhang, B., Jost, D. & Fishman, V., 5 Jul 2022, In: Nucleic Acids Research. 50, W1, p. W4-W12

    Research output: Contribution to journal › Article › peer-review

  30. 2021

  31. Derivation of Ringed Seal (Phoca hispida) Induced Multipotent Stem Cells

    Beklemisheva, V. R., Belokopytova, P. S., Fishman, V. S. & Menzorov, A. G., 1 Dec 2021, In: Cellular reprogramming. 23, 6, p. 326-335 10 p.

    Research output: Contribution to journal › Article › peer-review

  32. Здесь и там: двусторонняя локализация интеграций трансгена: the double-side transgene localization

    Salnikov, P. A., Khabarova, A. A., Koksharova, G. S., Mungalov, R., Belokopytova, P. S., Pristyazhnuk, I. E., Nurislamov, A. R., Somatich, P., Gridina, M. M. & Fishman, V. S., Oct 2021, In: Vavilovskii Zhurnal Genetiki i Selektsii. 25, 6, p. 607-612 6 p., 1.

    Research output: Contribution to journal › Article › peer-review

  33. A cookbook for DNase Hi-C

    Gridina, M., Mozheiko, E., Valeev, E., Nazarenko, L. P., Lopatkina, M. E., Markova, Z. G., Yablonskaya, M. I., Voinova, V. Y., Shilova, N. V., Lebedev, I. N. & Fishman, V., 20 Mar 2021, In: Epigenetics and Chromatin. 14, 1, 15.

    Research output: Contribution to journal › Article › peer-review

  34. Erythrocytes 3D genome organization in vertebrates

    Ryzhkova, A., Taskina, A., Khabarova, A., Fishman, V. & Battulin, N., Feb 2021, In: Scientific Reports. 11, 1, 4414.

    Research output: Contribution to journal › Article › peer-review

  35. Predicting Genome Architecture: Challenges and Solutions

    Belokopytova, P. & Fishman, V., 22 Jan 2021, In: Frontiers in Genetics. 11, 15 p., 617202.

    Research output: Contribution to journal › Review article › peer-review

  36. Естественно-научные предметы. Практическая молекулярная генетика для начинающих: 8-9ые классы

    Аульченко, Ю. С., Баттулин, Н. Р., Бородин, П. М., Воронина, Е. Н., Карташов, М. Ю., Колесникова, Т. Д., Нижников, А. А., Пилипенко, А. С., Посух, О. В., Седых, С. Е., Соловьев, В. И., Торгашева, Н. А., Фишман, В. С., Хлесткина, Е. К., Цыбко, А. С., Шнайдер, Т. А. & Юнусова, А. М., 2021, Москва : Просвещение. 272 p.

    Research output: Book/Report › Teaching manual › peer-review

  37. 2020

  38. DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote

    Smirnov, A., Fishman, V., Yunusova, A., Korablev, A., Serova, I., Skryabin, B. V., Rozhdestvensky, T. S. & Battulin, N., 24 Jan 2020, In: Nucleic Acids Research. 48, 2, p. 719-735 17 p.

    Research output: Contribution to journal › Article › peer-review

  39. Quantitative prediction of enhancer-promoter interactions

    Belokopytova, P. S., Nuriddinov, M. A., Mozheiko, E. A., Fishman, D. & Fishman, V., 1 Jan 2020, In: Genome Research. 30, 1, p. 72-84 13 p.

    Research output: Contribution to journal › Article › peer-review

  40. 2019

  41. C-InterSecture-a computational tool for interspecies comparison of genome architecture

    Nuriddinov, M. & Fishman, V., 1 Dec 2019, In: Bioinformatics (Oxford, England). 35, 23, p. 4912-4921 10 p.

    Research output: Contribution to journal › Article › peer-review

  42. Time origin and structural analysis of the induced CRISPR/cas9 megabase-sized deletions and duplications involving the Cntn6 gene in mice

    Pristyazhnyuk, I. E., Minina, J., Korablev, A., Serova, I., Fishman, V., Gridina, M., Rozhdestvensky, T. S., Gubar, L., Skryabin, B. V. & Serov, O. L., 2 Oct 2019, In: Scientific Reports. 9, 1, 1 p., 14161.

    Research output: Contribution to journal › Article › peer-review

  43. Detection of Point Mutations and Chromosomal Translocations Based on Massive Parallel Sequencing of Enriched 3C Libraries

    Mozheiko, E. A. & Fishman, V. S., 1 Oct 2019, In: Russian Journal of Genetics. 55, 10, p. 1273-1281 9 p.

    Research output: Contribution to journal › Article › peer-review

  44. Targeted genomic integration of EGFP under tubulin beta 3 class III promoter and mEos2 under tryptophan hydroxylase 2 promoter does not produce sufficient levels of reporter gene expression

    Menzorov, A. G., Orishchenko, K. E., Fishman, V. S., Shevtsova, A. A., Mungalov, R. V., Pristyazhnyuk, I. E., Kizilova, E. A., Matveeva, N. M., Alenina, N., Bader, M., Rubtsov, N. B. & Serov, O. L., Oct 2019, In: Journal of Cellular Biochemistry. 120, 10, p. 17208-17218 11 p.

    Research output: Contribution to journal › Article › peer-review

  45. 3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes' chromatin

    Fishman, V., Battulin, N., Nuriddinov, M., Maslova, A., Zlotina, A., Strunov, A., Chervyakova, D., Korablev, A., Serov, O. & Krasikova, A., 25 Jan 2019, In: Nucleic Acids Research. 47, 2, p. 648-665 18 p.

    Research output: Contribution to journal › Article › peer-review

  46. 2018

  47. A mosaic intragenic microduplication of LAMA1 and a constitutional 18p11.32 microduplication in a patient with keratosis pilaris and intellectual disability

    Kashevarova, A. A., Nazarenko, L. P., Skryabin, N. A., Nikitina, T. V., Vasilyev, S. A., Tolmacheva, E. N., Lopatkina, M. E., Salyukova, O. A., Chechetkina, N. N., Vorotelyak, E. A., Kalabusheva, E. P., Fishman, V. S., Kzhyshkowska, J., Graziano, C., Magini, P., Romeo, G. & Lebedev, I. N., 1 Nov 2018, In: American Journal of Medical Genetics, Part A. 176, 11, p. 2395-2403 9 p.

    Research output: Contribution to journal › Article › peer-review

  48. Allele-Specific Biased Expression of the CNTN6 Gene in iPS Cell-Derived Neurons from a Patient with Intellectual Disability and 3p26.3 Microduplication Involving the CNTN6 Gene

    Gridina, M. M., Matveeva, N. M., Fishman, V. S., Menzorov, A. G., Kizilova, H. A., Beregovoy, N. A., Kovrigin, I. I., Pristyazhnyuk, I. E., Oscorbin, I. P., Filipenko, M. L., Kashevarova, A. A., Skryabin, N. A., Nikitina, T. V., Sazhenova, E. A., Nazarenko, L. P., Lebedev, I. N. & Serov, O. L., 1 Aug 2018, In: Molecular Neurobiology. 55, 8, p. 6533-6546 14 p.

    Research output: Contribution to journal › Article › peer-review

  49. Interpreting Chromosomal Rearrangements in the Context of 3-Dimentional Genome Organization: A Practical Guide for Medical Genetics

    Fishman, V. S., Salnikov, P. A. & Battulin, N. R., 1 Apr 2018, In: Biochemistry (Moscow). 83, 4, p. 393-401 9 p.

    Research output: Contribution to journal › Review article › peer-review

  50. Analysis of differential expression of matrix metalloproteases in stable and unstable atherosclerotic lesions by a method of full genome sequencing of RNA: Pilot study

    Ivanoschuk, D. E., Ragino, Y. I., Shakhtshneider, E. V., Mikhailova, S. V., Fishman, V. S., Polonskaya, Y. V., Kashtanova, E. V., Chernyavsky, A. M., Murashov, I. S. & Voevoda, M. I., 1 Jan 2018, In: Russian Journal of Cardiology. 23, 8, p. 52-58 7 p.

    Research output: Contribution to journal › Article › peer-review

  51. 2017

  52. Alternative dominance of the parental genomes in hybrid cells generated through the fusion of mouse embryonic stem cells with fibroblasts

    Matveeva, N. M., Fishman, V. S., Zakharova, I. S., Shevchenko, A. I., Pristyazhnyuk, I. E., Menzorov, A. G. & Serov, O. L., 22 Dec 2017, In: Scientific Reports. 7, 1, p. 18094 14 p., 18094.

    Research output: Contribution to journal › Article › peer-review

  53. Deterministic versus stochastic model of reprogramming: New evidence from cellular barcoding technique

    Yunusova, A. M., Fishman, V. S., Vasiliev, G. V. & Battulin, N. R., Apr 2017, In: Open Biology. 7, 4, 13 p., 160311.

    Research output: Contribution to journal › Article › peer-review

ID: 3445187