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Publications
| 2024 |
Analysis of auxin responses in the fern Ceratopteris richardii identifies the developmental phase as a major determinant for response properties
Sjoerd Woudenberg, Melissa Dipp Alvarez, Juriaan Rienstra, Victor Levitsky, Victoria Mironova, Enrico Scarpella, Andre Kuhn, Dolf Weijers
[DEVELOPMENT]
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Developmental and housekeeping genes: two types of genetic organization in the Drosophila genome
Igor Zhimulev, Tatyana Vatolina, Victor Levitsky, Anton Tsukanov
[INT J MOL SCI]
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Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data
Vladimir V. Raditsa,
Anton V. Tsukanov,
Anton G. Bogomolov,
Victor G. Levitsky
[NAR Genomics and Bioinformatics]
|
| 2023 |
РАЗВИТИЕ ИДЕИ Н.К. КОЛЬЦОВА О ГЕНЕТИЧЕСКОЙ ОРГАНИЗАЦИИ
МЕЖДИСКОВ ПОЛИТЕННЫХ ХРОМОСОМ DROSOPHILA MELANOGASTER
И. Ф. Жимулев, Т. Ю. Ватолина, В. Г. Левицкий,
Т. Д. Колесникова, А. В. Цуканов
[Онтогенез]
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| 2022 |
CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana
Lavrekha VV, Levitsky VG, Tsukanov AV, Bogomolov AG, Grigorovich DA, Omelyanchuk N, Ubogoeva EV, Zemlyanskaya EV, Mironova V
[Frontiers in Plant Science]
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Motif models proposing independent and interdependent impacts of nucleotides are related to high and low affinity transcription factor binding sites in Arabidopsis
Tsukanov, A. V., Mironova V. V., Levitsky V. G.
[Frontiers in Plant Science]
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Transcription Factors as Important Regulators of Changes in Behavior through Domestication of Gray Rats: Quantitative Data from RNA Sequencing
Oshchepkov, D., Chadaeva I., Kozhemyakina R., Shikhevich S., Sharypova E., Savinkova L., Klimova N.V., Tsukanov A., Levitsky V.G., Markel A.L.
[INT J MOL SCI]
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Web-MCOT Server for Motif Co-Occurrence Search in ChIP-Seq Data
Victor G. Levitsky, Alexey M. Mukhin, Dmitry Yu. Oshchepkov, Elena V. Zemlyanskaya, Sergey A. Lashin
[INT J MOL SCI]
|
| 2021 |
Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures
Dongbo Shi, Virginie Jouannet, Javier Agustí, Verena Kaul, Victor Levitsky, Pablo Sanchez, Victoria V Mironova, Thomas Greb
[PLANT CELL]
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Transcriptional regulation in plants: Using omics data to crack the cis-regulatory code
Elena V. Zemlyanskaya, Vladislav A. Dolgikh, Victor G. Levitsky, Victoria Mironova
[CURR OPIN PLANT BIOL]
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Метод поиска структурной гетерогенности сайтов связывания транскрипционных факторов с использованием альтернативных de novo моделей на примере FOXA2
А.В. Цуканов , В.Г. Левицкий, Т.И. Меркулова
[Vavilov journal of genetics and breeding]
|
| 2020 |
Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis
Alejandra Freire-Rios, Keita Tanaka, Isidro Crespo, Elmar van der Wijk, Yana Sizentsova, Victor Levitsky, Simon Lindhoud, Mattia Fontana, Johannes Hohlbein, D. Roeland Boer, Victoria Mironova, and Dolf Weijers
[P NATL ACAD SCI USA]
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Asymmetric conservation within pairs of co-occurred motifs mediates weak direct binding of transcription factors in ChIP-seq data
Victor Levitsky, Dmitry Oshchepkov, Elena Zemlyanskaya, Tatyana Merkulova
[INT J MOL SCI]
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Faint gray bands in Drosophila melanogaster polytene chromosomes are formed by coding sequences of housekeeping genes
Olga V. Demakova, Sergey A. Demakov, Lidiya V. Boldyreva, Tatyana Yu. Zykova, Victor G. Levitsky, Valeriy F. Semeshin, Galina V. Pokholkova, Darya S. Sidorenko, Fedor P. Goncharov, Elena S. Belyaeva, Igor F. Zhimulev
[CHROMOSOMA]
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Genes Containing Long Introns Occupy Series of Bands and Interbands In Drosophila melanogaster polytene Chromosomes
Varvara A. Khoroshko, Galina V. Pokholkova, Victor G. Levitsky, Tatyana Yu. Zykova, Oksana V. Antonenko, Elena S. Belyaeva, and Igor F. Zhimulev
[Genes]
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Nucleosome positioning around transcription start site correlates with gene expression only for active chromatin state in Drosophila interphase chromosomes
Victor G. Levitsky, Tatyana Yu. Zykova, Yuri M. Moshkin, Igor F. Zhimulev
[INT J MOL SCI]
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Specification and regulation of vascular tissue identity in the Arabidopsis embryo
Margot E. Smit, Cristina I. Llavata-Peris, Mark Roosjen, Henriette van Beijnum, Daria Novikova, Victor Levitsky, Iris Sevilem, Pawel Roszak, Daniel Slane, Gerd Jürgens, Victoria Mironova, Siobhan M. Brady, Dolf Weijers
[DEVELOPMENT]
|
| 2019 |
A single ChIP-seq dataset is sufficient for comprehensive
analysis of motifs co-occurrence with MCOT package
Levitsky V., Zemlyanskaya E., Oshchepkov D., Podkolodnaya O., Ignatieva E.,
Grosse I., Mironova V., Merkulova T.
[NUCLEIC ACIDS RES]
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Architecture of promoters of house-keeping genes in polytene chromosome interbands of Drosophila melanogaster
Zykova TY, Levitsky VG, Zhimulev IF
[Doklady Biochemistry and Biophysics]
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Разработка программного комплекса WebMCOT для поиска совместно встречаемых ДНК-мотивов сайтов связывания транскрипционных факторов
Мухин Алексей Максимович, Левицкий Виктор Георгиевич, Лашин Сергей Александрович
[Вестник НГУ. Серия: Информационные технологии]
|
| 2018 |
Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana
Pavel Cherenkov, Daria Novikova, Nadya Omelyanchuk, Victor Levitsky, Ivo Grosse, Dolf Weijers, Victoria Mironova
[J EXP BOT]
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Genetic Organization of Open Chromatin Domains Situated in Polytene Chromosome Interbands in Drosophila
Zykova TY, Popova OO, Khoroshko VA, Levitsky VG, Lavrov SA, Zhimulev IF
[Doklady Biochemistry and Biophysics]
|
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Polytene Chromosomes – A Portrait of Functional Organization of the Drosophila Genome
Tatyana Yu Zykova, Victor G. Levitsky , Elena S. Belyaeva, Igor F. Zhimulev
[CURR GENOMICS]
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Spatial specificity of auxin responses coordinates
wood formation
Klaus Brackmann, Jiyan Qi, Michael Gebert, Virginie Jouannet, Theresa Schlamp, Karin Grünwald, Eva-Sophie Wallner, Daria D. Novikova, Victor G. Levitsky, Javier Agustí, Pablo Sanchez, Jan U. Lohmann, Thomas Greb
[NAT COMMUN]
|
| 2017 |
Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots
N. A. Omelyanchuk, D. S. Wiebe, D. D. Novikova, V. G. Levitsky, N. Klimova, V. Gorelova, C. Weinholdt, G. V. Vasiliev, E. V. Zemlyanskaya, N. A. Kolchanov, A. V. Kochetov, I. Grosse, V. V. Mironova
[SCI REP-UK]
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Protein and genetic composition of four chromatin types in Drosophila melanogaster cell lines
Boldyreva L.V., Goncharov F.P., Demakova O.V., Zykova T.Y., Levitsky V.G., Kolesnikov N.N., Pindyurin A.V., Semeshin V.F., Zhimulev I.F.
[CURR GENOMICS]
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The Interplay of Chromatin Landscape and DNA-Binding Context Suggests Distinct Modes of EIN3 Regulation in Arabidopsis thaliana
Zemlyanskaya EV, Levitsky VG, Oshchepkov DY, Grosse I, Mironova VV
[Frontiers in Plant Science]
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The computational analysis of whole-genome data predicts a role of chromatin landscape in regulation of primary ethylene response in Arabidopsis thaliana
Zemlyanskaya E.V., Levitsky V.G., Oshchepkov D.Y.
[Acta Naturae]
|
| 2016 |
Chromatin heterogeneity and distribution of regulatory elements in the latereplicating regions of Drosophila melanogaster chromosomes
Khoroshko V.A., Levitsky V.G., Zykova T.Y., Antonenko O.V., Belyaeva E.S., Zhimulev I.F.
[PloS One]
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Estimation of the Role of Single Nucleotide Polymorphism in Lymphotoxin Beta Gene during Pig Domestication Based on the Bioinformatic and Experimental Approaches
R. B. Aitnazarov, E. V. Ignatieva, N. E. Bazarova, V. G. Levitsky, S. P. Knyazevd, Y. Gon, and N. S. Yudin
[Russian Journal of Genetics: Applied Research]
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Hidden Heterogeneity of Transcription Factor Binding Sites: A Case Study of SF-1
V.G. Levitsky, D.Yu. Oshchepkov, N.V. Klimova, E.V Ignatieva, G.V. Vasiliev, V.M. Merkulov, T.I. Merkulova
[COMPUT BIOL CHEM]
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Meta-analysis of transcriptome data identified TGTCNN motif variants associated with the response to plant hormone auxin in Arabidopsis thaliana L.
Zemlyanskaya EV, Wiebe DS, Omelyanchuk NA, Levitsky VG, Mironova VV.
[Journal of Bioinformatics and Computational Biology]
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The Molecular Mechanisms of Heterochromatin Expansion in Rye Chromosomes
Evtushenko EV, Levitsky VG, Elisafenko EA, Gunbin KV, Belousov AI, Safar J, Dolezel J, Vershinin AV
[CYTOGENET GENOME RES]
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The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements.
Evtushenko EV, Levitsky VG, Elisafenko EA, Gunbin KV, Belousov AI, Šafář J, Doležel J, Vershinin AV.
[BMC GENOMICS]
|
| 2015 |
Effect of flanking sequences on the accuracy of the recognition of transcription factor binding sites.
Khlebodarova T. M., Oshchepkov D. Yu., Levitsky V. G., Podkolodnaya O. A., Ignatieva E. V., Ananko E. A., Stepanenko I. L., Kolchanov N. A.
[Russian Journal of Genetics: Applied Research]
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Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster.
Zhimulev IF, Zykova TYu, Goncharov FP, Khoroshko VA, Demakova OV, Semeshin VF, Pokholkova GV, Boldyreva LV, Demidova DS, Levitsky VG, Demakov SA, Belyaeva ES
[CHROMOSOME RES]
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Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data
Ignatieva EV, Levitsky VG, Kolchanov NA
[International Journal of Genomics]
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Оценка роли однонуклеотидного полиморфизма в гене лимфотоксина бета при доместикации свиньи на основе биоинформационного и экспериментального подходов
Р.Б. Айтназаров, Е.В. Игнатьева, Н.Э. Базарова, В.Г.Левицкий, С.П. Князев, Я. Гон, Н.С. Юдин
[Vavilov journal of genetics and breeding]
|
| 2014 |
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data
Victor G Levitsky, Ivan V Kulakovskiy, Nikita I Ershov, Dmitry Yu Oschepkov, Vsevolod J Makeev, T C Hodgman, Tatyana I Merkulova
[BMC GENOMICS]
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Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome
Mironova VV, Omelyanchuk NA, Wiebe DS, Levitsky VG
[BMC GENOMICS]
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Genetic basis of olfactory cognition: extremely high level of DNA sequence polymorphism in promoter regions of the human olfactory receptor genes revealed using the 1000 Genomes Project dataset
Ignatieva E.V., Levitsky V.G., Yudin N.S., Moshkin M.P., Kolchanov N.A.
[Front Psychol]
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The roles of the monomer length and nucleotide context of plant tandem repeats in nucleosome positioning
Levitsky VG, Babenko VN, Vershinin AV
[Journal Of Biomolecular Structure & Dynamics]
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Влияние фланкирующих последовательностей на точность распознавания сайтов связывания транскрипционных факторов.
Хлебодарова Т.М., Ощепков Д.Ю., Левицкий В.Г., Подколодная О.А., Игнатьева Е.В., Ананько Е.А., Степаненко И.Л., Колчанов Н. А.
[Vavilov journal of genetics and breeding]
|
| 2013 |
From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites.
Kulakovskiy I, Levitsky V, Oshchepkov D, Bryzgalov L, Vorontsov I, Makeev V.
[Journal of Bioinformatics and Computational Biology]
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Translation efficiency in yeasts correlates with nucleosome formation in promoters
Matushkin YG, Levitsky VG, Orlov YL, Likhoshvai VA, Kolchanov NA.
[Journal Of Biomolecular Structure & Dynamics]
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Эффективность элонгации генов дрожжей кореллирует с плотностью нуклеосомной упаковки в 5’-нетранслируемом районе.
Матушкин Ю.Г., Левицкий В.Г., Соколов В.С., Лихошвай В.А., Орлов Ю.Л.
[Mathematical Biology & Bioinformatics]
|
| 2012 |
ICGenomics: программный комплекс анализа символьных последовательностей геномики
Ю.Л. Орлов, А.О. Брагин, И.В. Медведева, К.В. Гунбин, П.С. Деменков, О.В. Вишневский, В.Г. Левицкий, Д.Ю. Ощепков, Н.Л. Подколодный, Д.А. Афонников, И. Гроссе, Н.А. Колчанов
[Vavilov journal of genetics and breeding]
|
| 2011 |
Analysis of Data on Large Scale Chromatin Immunoprecipitation by Recognition of Transcription Factor Binding Sites
VG Levitskii, GV Vasil’ev, DYu Oshchepkov, NI Ershov, and TI Merkulova
[Russian Journal of Genetics: Applied Research]
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In silico prediction of transcriptional factor-binding sites.
Oshchepkov DY, Levitsky VG
[Methods in Molecular Biology]
|
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Разработка методов распознования сайтов связывания транскрипционных факторов FoxA, их экспериментальная верификация и использование для анализа данных массовой иммунопреципитации хроматина
Левицкий В. Г., Ощепков Д. Ю., Ершов Н. И., Брызгалов Л. О., Антонцева Е. В., Васильев Г. В., Меркулова Т. И., Колчанов Н. А.
[Doklady Akademii Nauk]
|
| 2010 |
Анализ результатов эксперимента по массовой иммунопреципитации хроматина с помощью методов распознавания сайтов связывания транскрипционных факторов
Левицкий В.Г., Васильев Г.В., Ощепков Д.Ю., Ершов Н.И., Меркулова Т.И.
[Информационный вестник ВОГИС]
|
| 2009 |
Изменения транскриптома печени крысы под действием гепатоканцерогенного для этих животных 3МЕДАБ и неканцерогенного ОАТ
Н.И. Ершов, В.Г. Левицкий, Д.Ю. Ощепков, О.В. Вишневский, Л.О. Брызгалов, Е.В. Антонцева, Т.И. Меркулова.
[Информационный вестник ВОГИС]
|
| 2008 |
ExpertDiscovery system application for the hierarchical analysis of eukaryotic transcription regulatory regions based on DNA codes of transcription
Khomicheva IV, Vityaev EE, Ananko EA, Shipilov TI, Levitsky VG.
[INTELL DATA ANAL]
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Genetic algorithm and optimized weight matrix application for peroxisome proliferator response elements recognition: Prerequisites of accuracy growth for wide genome research
Victor G. Levitsky, Elena V. Ignatieva, Eugenia Aman, Tatyana I. Merkulova, Nikolay A. Kolchanov, T. Charles Hodgman
[INTELL DATA ANAL]
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| 2007 |
Bioinformatical and experimental approaches to investigation of transcription factor binding sites in vertebrate gene
Merkulova T. I., Oshchepkov D. Yu., Ignatieva E. V., Ananko E. A., Levitsky V. G., Vasiliev G. V., Klimova N. V. , Merkulov V. M., Kolchanov N. A.
[BIOCHEMISTRY-MOSCOW+]
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Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes
Kolchanov NA, Merkulova TI, Ignatieva EV, Ananko EA, Oshchepkov DY, Levitsky VG, Vasiliev GV, Klimova NV, Merkulov VM, Hodgman TC
[BRIEF BIOINFORM]
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Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
Levitsky V.G., Ignatieva E.V., Ananko E.A., Turnaev I.I., Merkulova T.I., Kolchanov N.A., Hodgman T.C.
[BMC BIOINFORMATICS]
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Экспериментальные и компьютерные подходы к изучению регуляторных элементов в эукариотических генах
Меркулова Т. И., Ощепков Д. Ю., Игнатьева Е. В., Ананько Е.В., Левицкий В.Г., Васильев Г. В., Климова Н. В., Меркулов В.М., Колчанов Н.А.
[BIOCHEMISTRY-MOSCOW+]
|
| 2006 |
Method SiteGA for transcription factor binding sites recognition
Levitsky, V.G., Ignatieva E.V., Ananko E.A., Merkulova T.I., Kolchanov N.A., Hodgman T.C.
[BIOPHYSICS]
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Pattern of locally positioned dinucleotides correlates with microRNA abundance in plants
Khomicheva I.V., Levitsky V.G., Omelyanchuk N.A., Kolchanov N.A., Savinskaya S.A.
[BIOPHYSICS]
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Potential binding sites for SF-1: Recognition by the SiteGA method, experimental verification, and search for new target genes
Klimova NV, Levitsky VG, Ignatieva EV, Vasiliev GV, Kobzev VF, Busygina TV, Merkulova TI, Kolchanov NA
[Molecular Biology]
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Statistical analysis of nucleosome formation sites
Orlov IuL, Levitskii VG, Smirnova OG, Podkolodnaia OA, Khlebodarova TM, Kolchanov NA.
[BIOPHYSICS]
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Паттерн определенных динуклеотидов микроРНК арабидопсиса связан с уровнем их содержания в растении.
Левицкий В.Г., Хомичева И.В., Омельянчук Н.А., Пономаренко М.П., Колчанов Н.А.
[Информационный вестник ВОГИС]
|
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Распознавание сайтов связывания транскрипционных факторов с помощью метода SiteGA
Левицкий В.Г., Игнатьева Е.В.,Ананько Е.А.,Меркулова Т.И., Колчанов Н.А.,Ходжман Ч.
[BIOPHYSICS]
|
| 2004 |
Интегрированная компьютерная система по регуляции экспрессии генов эукариот.
Н. А. Колчанов, О. А Подколодная, Е. А. Ананько, Д. А. Афонников, О. В. Вишневский, Д. В. Воробьев, Е. В. Игнатьева, В. Г. Левицкий, В. А. Лихошвай, Н.А.Омельянчук, Н.Л. Подколодный, А. В. Ратушный
[Molecular Biology]
|
| 1999 |
Investigating extended regulatory regions of genomic DNA sequences
Babenko VN, Kosarev PS, Vishnevsky OV, Levitsky VG, Basin VV, Frolov AS
[BIOINFORMATICS]
|
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Nucleosomal DNA property database.
Levitsky V.G., Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Kolchanov N.A.
[BIOINFORMATICS]
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