Veniamin Fishman Department: - Head: Sector of Genomic mechanisms of ontogenesis Laboratory of 3D Genomics Email: minja@bionet.nsc.ru

Publications

2024	A HGF Mutation in the Familial Case of Primary Lymphedema: A Report Galina Koksharova, Natalia Kokh, Maria Gridina, Rustam Khapaev, Vadim Nimaev, Veniamin Fishman [INT J MOL SCI]
	A germline chimeric KANK1-DMRT1 transcript derived from a complex structural variant is associated with a congenital heart defect segregating across five generations Silvia Souza da Costa, Veniamin Fishman, Mara Pinheiro, Andre Rodrigueiro, Maria Teresa Sanseverino, Paulo Zielinsky, Claudia M. B. Carvalho, Carla Rosenberg, Ana Cristina Victorino Krepischi [CHROMOSOME RES]
	Modification of the Hi-C Technology for Molecular Genetic Analysis of Formalin-Fixed Paraffin-Embedded Sections of Tumor Tissues Maria M Gridina, Yana K Stepanchuk, Miroslav A Nurridinov, Timofey A Lagunov, Nikita Yu Torgunakov, Artem A Shadsky, Anastasia I Ryabova, Nikolay V Vasiliev, Sergey V Vtorushin, Tatyana S Gerashchenko, Evgeny V Denisov, Mikhail A Travin, Maxim A Korolev, Veniamin S Fishman [BIOCHEMISTRY-MOSCOW+]
	Structural variants in the Epb41l4a locus: TAD disruption and Nrep gene misregulation as hypothetical drivers of neurodevelopmental outcomes Paul Salnikov, Alexey Korablev, Irina Serova, Polina Belokopytova, Aleksandra Yan, Yana Stepanchuk, Savelii Tikhomirov, Veniamin Fishman [SCI REP-UK]
	Towards Development of the 4C-Based Method Detecting Interactions of Plasmid DNA with Host Genome Alexandra P Yan, Paul A Salnikov, Maria M Gridina, Polina S Belokopytova, Veniamin S Fishman [BIOCHEMISTRY-MOSCOW+]
2023	Экспрессия генов биомолекул, ассоциированных с этиопатогенезом атеросклероза, в атеросклеротических бляшках коронарных артерий Семаев С.Е., Шахтшнейдер Е.В., Иванощук Д.Е., Фишман В.С., Полонская Я.В., Каштанова Е.В., Чернявский А.М., Мурашов И.С., Волков А.М., Рагино Ю.И. [КОМПЛЕКСНЫЕ ПРОБЛЕМЫ СЕРДЕЧНО-СОСУДИСТЫХ ЗАБОЛЕВАНИЙ]
	A family case of a rare autoinflammatory disease associated with mutations in the NLRP3 and TNFRSF1A genes in the practice of a rheumatologist Kurochkina Yu.D., Korolev M.A., Letyagina E.A., Fishman V.S., Gridina M.M.,Valeeva E.S. [Бюллетень сибирской медицины]
	A Cre-LoxP-based approach for combinatorial chromosome rearrangements in human HAP1 cells Anna Khabarova, Galina Koksharova, Pavel Salnikov, Polina Belokopytova, Roman Mungalov, Inna Pristyazhnuk, Artem Nurislamov, Maria Gridina, Veniamin Fishman [CHROMOSOME RES]
	Annotation of uORFs in the OMIM genes allows to reveal pathogenic variants in 5'UTRs Alexandra Filatova, Ivan Reveguk, Maria Piatkova, Daria Bessonova, Olga Kuziakova, Victoria Demakova, Alexander Romanishin, Veniamin Fishman, Yerzhan Imanmalik, Nikolay Chekanov, Rostislav Skitchenko, Yury Barbitoff, Olga Kardymon, Mikhail Skoblov [NUCLEIC ACIDS RES]
	Cell type–specific interpretation of noncoding variants using deep learning–based methods Maria Sindeeva, Nikolay Chekanov, Manvel Avetisian, Tatiana I Shashkova, Nikita Baranov, Elian Malkin, Alexander Lapin, Olga Kardymon, Veniamin Fishman [GigaScience]
	Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease Gridina Maria, Popov Andrey, Shadskiy Artem, Torgunakov Nikita, Kechin Andrey, Khrapov Evgeny, Ryzhkova Oxana, Filipenko Maxim & Fishman Veniamin [EPIGENET CHROMATIN]
	Function and Evolution of the Loop Extrusion Machinery in Animals Evelyn Kabirova, Artem Nurislamov, Artem Shadskiy, Alexander Smirnov, Andrey Popov, Pavel Salnikov, Nariman Battulin, Veniamin Fishman [INT J MOL SCI]
	Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line Maslova A, Plotnikov V, Nuriddinov M, Gridina M, Fishman V, Krasikova [BMC GENOMICS]
	Influence of human peripheral blood samples preprocessing on the quality of Hi-C libraries M M Gridina, E Vesna, M E Minzhenkova, N V Shilova, O P Ryzhkova, L P Nazarenko, E O Belyaeva, I N Lebedev, V S Fishman [Vavilov journal of genetics and breeding]
	Lampbrush chromosome studies in the post-genomic era Alla Krasikova, Veniamin Fishman, Tatiana Kulikova [BIOESSAYS]
2022	3DGenBench: a web-server to benchmark computational models for 3D Genomics Belokopytova, Emil Viesná, Mateusz Chiliński, Yifeng Qi, Hossein Salari, Marco Di Stefano, Andrea Esposito, Mattia Conte, Andrea M. Chiariello, Vladimir B. Teif, Dariusz Plewczynski, Bin Zhang, Daniel Jost, Veniamin Fishman [NUCLEIC ACIDS RES]
	ADAMTS1 Is Differentially Expressed in Human Lymphocytes with Various Frequencies of Endogenous γH2AX Foci and Radiation-Induced Micronuclei S. A. Vasilyev, R. R. Savchenko, A. A. Belenko, N. A. Skryabin, A. A. Sleptsov, V. S. Fishman, A. A. Murashkina, O. V. Gribova, Z. A. Startseva, E. S. Sukhikh, A. V. Vertinskiy, L. G. Sukhikh, O. L. Serov, I. N. Lebedev [RUSS J GENET+]
	Anopheles mosquitoes reveal new principles of 3D genome organization in insects Varvara Lukyanchikova*, Miroslav Nuriddinov*, Polina Belokopytova, Alena Taskina, Jiangtao Liang, Maarten Reijnders, Livio Ruzzante, Romain Feron, Robert Waterhouse, Yang Wu, Chunhong Mao, Zhijian Tu, Igor Sharakhov, and Veniamin Fishman * authors contributed equally [NAT COMMUN]
	Comparison and critical assessment of single-cell Hi-C protocols M Gridina, A Taskina, T Lagunov, A Nurislamov, T Kulikova, A Krasikova, V Fishman [Heliyon]
	FastContext: A tool for identification of adapters and other sequence patterns in next generation sequencing (NGS) data Е. Viesná, V. Fishman [Vavilov journal of genetics and breeding]
	Method for the Isolation of “RNA-seq-Quality” RNA from Human Intervertebral Discs after Mortar And Pestle Homogenization Artemii A. Ivanov, Olga N. Leonova, Daniil S. Wiebe, Alexsandr V. Krutko, Mariya M. Gridina, Veniamin S. Fishman, Yurii S. Aulchenko, Yakov A. Tsepilov, Tatiana S. Golubeva [Cells]
	Multilevel view on chromatin architecture alterations in cancer Maria Gridina, Veniamin Fishman [Frontiers in Genetics]
	Single-Cell DNA Methylation Analysis of Chicken Lampbrush Chromosomes Artem Nurislamov, Timofey Lagunov, Maria Gridina, Alla Krasikova, Veniamin Fishman [INT J MOL SCI]
	The role of high-order chromatin organization in gene regulation Veniamin Fishman, Alexey V Pindyurin [Frontiers in Genetics]
	Комплексные геномные перестройки в этиологии «хромосомного фенотипа» М. Е. Миньженкова, Ж. Г. Маркова, Д. А. Юрченко, А. А. Тарлычева, Т. В. Маркова, Н. А. Семенова, А. Ф. Муртазина, В. В. Кадышев, М. М. Гридина, Э. . Весна, В. С. Фишман, Н. В. Шилова [Медицинская генетика]
2021	Differential DNA Methylation of the IMMP2L Gene in Families with Maternally Inherited 7q31.1 Microdeletions is Associated with Intellectual Disability and Developmental Delay Vasilyev Stanislav A., Skryabin Nikolay, A. Kashevarova Anna A., Tolmacheva Ekaterina N., Savchenko Renata R., Vasilyeva Oksana Yu., Lopatkina Maria E., Zarubin Alexei A., Fishman Veniamin S., Belyaeva Elena O., Filippova Miroslava O., Shorina Asia R., Maslennikov Arkadiy B., Shestovskikh Olga L., Gayner Tatyana A., Culic Vida, Vulic Robert, Nazarenko Lyudmila P., Lebedev Igor N. [CYTOGENET GENOME RES]
	A cookbook for DNase Hi-C Maria Gridina, Evgeniy Mozheiko, Emil Valeev, Ludmila P. Nazarenko, Maria E. Lopatkina, Zhanna G. Markova, Maria I. Yablonskaya, Viktoria Yu Voinova, Nadezhda V. Shilova, Igor N. Lebedev, Veniamin Fishman [EPIGENET CHROMATIN]
	Derivation of Ringed Seal ( Phoca hispida) Induced Multipotent Stem Cells Violetta R Beklemisheva, Polina S Belokopytova, Veniamin S Fishman, Aleksei G Menzorov [CELL REPROGRAM]
	Erythrocytes 3D genome organization in vertebrates Anastasia Ryzhkova, Alena Taskina, Anna Khabarova, Veniamin Fishman, Nariman Battulin [SCI REP-UK]
	Here and there: the double-side transgene localization P A Salnikov, A A Khabarova, G S Koksharova, R V Mungalov, P S Belokopytova, I E Pristyazhnuk, A R Nurislamov, P Somatich, M M Gridina, V S Fishman [Vavilov journal of genetics and breeding]
	Predicting Genome Architecture: Challenges and Solutions P. Belokopytova, V. Fishman [Frontiers in Genetics]
	The Mutation Spectrum of Maturity Onset Diabetes of the Young (MODY)-Associated Genes amongWestern Siberia Patients Dinara E. Ivanoshchuk, Elena V. Shakhtshneider, Oksana D. Rymar, Alla K. Ovsyannikova, Svetlana V. Mikhailova, Veniamin S. Fishman, Emil S. Valeev, Pavel S. Orlov and Mikhail I. Voevoda [J. Pers. Med]
	Анализ дифференциальной экспрессии генов липидного обмена в атеросклеротических бляшках у пациентов с коронарным атеросклерозом Шахтшнейдер Е.В., Иванощук Д.Е., Рагино Ю.И., Фишман В.С., Полонская Я.В., Каштанова Е.В., Чернявский А.М., Мурашов И.С., Воевода М.И. [Сибирский журнал клинической и экспериментальной медицины]
	Создание библиотек баркодированных плазмид с помощью метода клонирования по Гибсону А.В. Смирнов, А.М. Юнусова, А.А. Муравьева, Э.C. Валеев, В.C. Фишман, Н.Р. Баттулин [Письма в Вавиловский журнал генетики и селекции]
2020	DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote Alexander Smirnov, Veniamin Fishman, Anastasia Yunusova, Alexey Korablev, Irina Serova, Boris V Skryabin, Timofey S Rozhdestvensky, Nariman Battulin [NUCLEIC ACIDS RES]
	Effect of the THBS1 Gene Knockout on the Radiation-Induced Cellular Response in a Model System In Vitro R. R. Savchenko, S. A. Vasilyev, V. S. Fishman, E. S. Sukhikh, L. G. Sukhikh, A. A. Murashkin, I. N. Lebedev [RUSS J GENET+]
	Postsynthetic On-Column 2' Functionalization of RNA by Convenient Versatile Method Olga A Krasheninina, Veniamin S Fishman, Alexander A Lomzov, Alexey V Ustinov, Alya G Venyaminova [INT J MOL SCI]
	Quantitative prediction of enhancer-promoter interactions Polina Belokopytova, Miroslav Nuriddinov, Evgeniy Mozheiko, Daniil Fishman, Veniamin Fishman [GENOME RES]
2019	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. [NUCLEIC ACIDS RES]
	C-InterSecture—a computational tool for interspecies comparison of genome architecture Нуриддинов Мирослав Абдурахимович Фишман Вениамин Семёнович [BIOINFORMATICS]
	Detection of Point Mutations and Chromosomal Translocations Based on Massive Parallel Sequencing of Enriched 3C Libraries Mozheiko E.A., Fishman V.S. [RUSS J GENET+]
	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 Aleksei G. Menzorov Konstantin E. Orishchenko Veniamin S. Fishman Anastasia A. Shevtsova Roman V. Mungalov Inna E. Pristyazhnyuk Elena A. Kizilova Natalia M. Matveeva Natalia Alenina Michael Bader Nikolai B. Rubtsov Oleg L. Serov [J CELL BIOCHEM]
	Time origin and structural analysis of the induced CRISPR/cas9 megabase-sized deletions and duplications involving the Cntn6 gene in mice. Inna E. Pristyazhnyuk, Julia Minina, Alexey Korablev, Irina Serova, Veniamin Fishman, Maria Gridina, Timofey S. Rozhdestvensky, Leonid Gubar, Boris V. Skryabin, and Oleg L. Serov [SCI REP-UK]
	Использование тимидинкиназы для отрицательной селекции индуцированных плюрипотентных стволовых клеток Алексей Гавриилович Мензоров, Константин Евгеньевич Орищенко, Мария Михайловна Гридина, Вениамин Семенович Фишман, Олег Леонидович Серов, Анна Александровна Кашеварова, Татьяна Владимировна Никитина, Игорь Николаевич Лебедев [Гены и клетки]
	Происхождение и судьба масштабных хромосомных перестроек, индуцированных технологией CRISPR/Cas9 у мышей: от зигот до соматических клеток Алексей Николаевич Кораблев, Инна Евгеньевна Пристяжнюк, Юлия Михайловна Минина, Ирина Александровна Серова, Вениамин Семенович Фишман, Мария Михайловна Гридина, Timofey Rozhdestvensky, Leonid Gubar, Boris Skryabin, Олег Леонидович Серов [Гены и клетки]
	Создание репортерного лентивирусного вектора Lego-REX1-EGFP для отбора индуцированных плюрипотентных стволовых клеток Артем Рустамович Нурисламов, Вениамин Семенович Фишман, Алексей Гавриилович Мензоров [Гены и клетки]
2018	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 Maria M. Gridina, Natalia M. Matveeva, Veniamin S. Fishman, Aleksei G. Menzorov, Helen A. Kizilova, Nikolay A. Beregovoy, Igor I. Kovrigin, Inna E. Pristyazhnyuk, Igor P. Oscorbin, Maxim L. Filipenko, Anna A. Kashevarova, Nikolay A. Skryabin, Tatyana V. Nikitina, Elena A. Sazhenova, Ludmila P. Nazarenko, Igor N. Lebedev, Oleg L. Serov [MOL NEUROBIOL]
	Interpreting chromosomal rearrangements in the context of 3-dimentional genome organization: a practical guide for medical genetics V.S. Fishman, P.A. Salnikov, N.R. Battulin [BIOCHEMISTRY-MOSCOW+]
	Intragenic Microduplication of LAMA1 and a Constitutional 18p11.32 Microduplication in a Patient with Keratosis Pilaris and Intellectual Disability. Anna A. Kashevarova, Lyudmila P. Nazarenko, Nikolay A. Skryabin, Tatyana V. Nikitina, Stanislav A. Vasilyev, Ekaterina N. Tolmacheva, Mariya E. Lopatkina, Olga A. Salyukova, Nataliya N. Chechetkina, Ekaterina A. Vorotelyak, Ekaterina, P. Kalabusheva, Veniamin S. Fishman, Julia Kzhyshkowska, Claudio Graziano, Pamela Magini, Giovanni Romeo, Igor N. Lebedev [AM J MED GENET A]
	АНАЛИЗ ДИФФЕРЕНЦИАЛЬНОЙ ЭКСПРЕССИИ МАТРИКСНЫХ МЕТАЛЛОПРОТЕИНАЗ В СТАБИЛЬНОЙ И НЕСТАБИЛЬНОЙ АТЕРОСКЛЕРОТИЧЕСКИХ БЛЯШКАХ МЕТОДОМ ПОЛНОГЕНОМНОГО СЕКВЕНИРОВАНИЯ РНК: ПИЛОТНОЕ ИССЛЕДОВАНИЕ Иванощук Д.Е., Рагино Ю. И. , Шахтшнейдер Е.В., Михайлова С.В. , Фишман В. С., Полонская Я.В. , Каштанова Е.В., Чернявский А.М. , Мурашов И.С., Воевода М.И. [Российский Кардиологический Журнал]
2017	5’-биспиренильные зонды типа «молекулярный маяк» для детекции РНК. Крашенинина О.А., Фишман В.С., Новопашина Д.С., Веньяминова А.Г. [Биоорганическая химия]
	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. [SCI REP-UK]
	Deterministic versus stochastic model of reprogramming: new evidence from cellular barcoding technique Anastasia M. Yunusova, Veniamin S. Fishman, Gennady V. Vasiliev, Nariman R. Battulin. [OPEN BIOL]
	Rational design and studies of excimer forming novel dual probes to target RNA Krasheninina OA, Lomzov AA, Fishman VS, Novopashina DS, Venyaminova AG. [Bioorganic & Medicinal Chemistry]
	Нарушение экспрессии аллелей гена CNTN6 в нейронах, полученных из индуцированных плюрипотентных стволовых клеток пациента с 3p26.3 микродупликацией Гридина М.М., Матвеева Н.М., Фишман В.С., Мензоров А.Г., Кизилова Е.А., Ковригин И.И., Пристяжнюк И.Е., Никитина Т.В., Кашеварова А.А., Скрябин Н.А., Назаренко Л.П., Лебедев И.Н., Серов О.Л. [Гены и клетки]
	Установление границ хромосомных перестроек у пациентов с микроделециями и микродупликациями 3p26.3 Гридина М.М., Шнайдер Т.А., Ковригин И.И., Мензоров А.Г., Фишман В.С. [Acta Naturae]
2016	Modeling of chromosomal diseases related to intellectual disability using genome editing of induced pluripotent stem cells from a patient with CNTN6 gene microdeletion Shnayder T.A., Menzorov A.G., Matveeva N.M., Fishman V.S., Pristyazhnyuk I.E., Karamysheva T.V., Kashevarova A.A., Skryabin N.A., Sazhenova E.A., Lebedev I.N., Serov O.L. [EUR J HUM GENET]
	Практическое руководство по редактированию геномов системой CRISPR/Cas9 Мензоров А.Г., Лукьянчикова В.А., Кораблев А.Н., Серова И.А., Фишман В.С. [Vavilov journal of genetics and breeding]
2015	Cell divisions are not essential for the direct conversion of fibroblasts into neuronal cells VS Fishman, TA Shnayder, KE Orishchenko, M Bader, N Alenina and OL Serov [CELL CYCLE]
	Comparison of American mink embryonic stem and induced pluripotent stem cell transcriptomes Aleksei G Menzorov, Natalia M Matveeva, Marios N Markakis, Venyamin S Fishman, Knud Christensen, Anna A Khabarova, Inna E Pristyazhnyuk, Elena A Kizilova, Susanna Cirera, Razvan Anistoroaei, Oleg L Serov [BMC GENOMICS]
	Comparison of the 3D organization of sperm and fibroblast genomes using the Hi-C approach Nariman Battulin, Veniamin S Fishman, Alexander M Mazur, Mikhail Pomaznoy, Anna A Khabarova, Dmitry A Afonnikov, Egor B Prokhortchouk, Oleg L Serov [GENOME BIOL]
	Direct Conversion of Somatic Cells to Neuronal Precursors: Problems and Outlooks I. E. Pristyazhnyuk, T. A. Shnayder, V. S. Fishman, N. M. Matveeva, and O. L. Serov [Russian Journal of Genetics: Applied Research]
2014	A Novel KCNJ5-insT149 Somatic Mutation Close to, but Outside, the Selectivity Filter Causes Resistant Hypertension by Loss of Selectivity for Potassium Kuppusamy M, Caroccia B, Stindl J, Bandulik S, Lenzini L, Gioco F, Fishman V, Zanotti G, Gomez-Sanchez C, Bader M, Warth R, Rossi GP [The Journal of Clinical Endocrinology & Metabolism]
	Reprogramming of somatic cells: problems and solutions 6. Т.А. Schneider, V.S. Fishman, M. А. Liskovykh, S.V.Ponamartsev, О.L. Serov, А.N. Tomilin, N. Alenina []
	Прямая конверсия соматических клеток в нейрональные предшественники: проблемы и перспективы. И.Е. Пристяжнюк, Т.А. Шнайдер, В.С. Фишман, Н.М. Матвеева, О.Л. Серов [Vavilov journal of genetics and breeding]
2013	INVESTIGATION OF THE SPATIAL GENOME ORGANIZATION OF MOUSE SPERM AND FIBROBLASTS BY THE Hi-C METHOD N.R. Battulin, V.S. Fishman, A.A. Khabarova, M.Yu. Pomaznoy, T.A. Shnaider, D.A. Afonnikov, O.L. Serov [Vavilov journal of genetics and breeding]
2012	3С-методы в исследованиях пространственной организации генома Н.Р. Баттулин, В.С. Фишман, Ю.Л. Орлов, А.Г. Мензоров, Д.А. Афонников, О.Л. Серов [Vavilov journal of genetics and breeding]