Zobrazeno 1 - 10
of 18
pro vyhledávání: '"Dmitry Penzar"'
Autor:
Giovanna Ambrosini, Ilya Vorontsov, Dmitry Penzar, Romain Groux, Oriol Fornes, Daria D. Nikolaeva, Benoit Ballester, Jan Grau, Ivo Grosse, Vsevolod Makeev, Ivan Kulakovskiy, Philipp Bucher
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-18 (2020)
Abstract Background Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biolog
Externí odkaz:
https://doaj.org/article/2d492ad437f8494bbf89e6f28ecd6dc1
Publikováno v:
BMC Bioinformatics, Vol 19, Iss 1, Pp 1-14 (2018)
Abstract Background Many algorithms and programs are available for phylogenetic reconstruction of families of proteins. Methods used widely at present use either a number of distance-based principles or character-based principles of maximum parsimony
Externí odkaz:
https://doaj.org/article/9475f366433645e4bbf2d6ea060fff23
Autor:
Daniil Nikitin, Dmitry Penzar, Andrew Garazha, Maxim Sorokin, Victor Tkachev, Nicolas Borisov, Alexander Poltorak, Vladimir Prassolov, Anton A. Buzdin
Publikováno v:
Frontiers in Immunology, Vol 9 (2018)
Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly
Externí odkaz:
https://doaj.org/article/6d9cc36de1164356b8f1d1e9e82516e2
Autor:
Anna A. Igolkina, Arsenii Zinkevich, Kristina O. Karandasheva, Aleksey A. Popov, Maria V. Selifanova, Daria Nikolaeva, Victor Tkachev, Dmitry Penzar, Daniil M. Nikitin, Anton Buzdin
Publikováno v:
Cells, Vol 8, Iss 9, p 1034 (2019)
Background: Transposons are selfish genetic elements that self-reproduce in host DNA. They were active during evolutionary history and now occupy almost half of mammalian genomes. Close insertions of transposons reshaped structure and regulation of m
Externí odkaz:
https://doaj.org/article/39755053ca0949cfbfd058195a4ebaa6
Autor:
Daniil Nikitin, Andrew Garazha, Maxim Sorokin, Dmitry Penzar, Victor Tkachev, Alexander Markov, Nurshat Gaifullin, Pieter Borger, Alexander Poltorak, Anton Buzdin
Publikováno v:
Cells, Vol 8, Iss 8, p 832 (2019)
In the article ‘Retroelement—Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution,’ a number of transcription factor binding sites (TFBS) mapped on all retroelement classes were incorrec
Externí odkaz:
https://doaj.org/article/13bf5973bc0a4e4680625ac8d8c736a8
Autor:
Daniil Nikitin, Andrew Garazha, Maxim Sorokin, Dmitry Penzar, Victor Tkachev, Alexander Markov, Nurshat Gaifullin, Pieter Borger, Alexander Poltorak, Anton Buzdin
Publikováno v:
Cells, Vol 8, Iss 2, p 130 (2019)
Background: Retroelements (REs) are transposable elements occupying ~40% of the human genome that can regulate genes by providing transcription factor binding sites (TFBS). RE-linked TFBS profile can serve as a marker of gene transcriptional regulati
Externí odkaz:
https://doaj.org/article/b217f050120145bebf34ae564f97d238
Motivation. Phylogenetic inference based on protein sequence alignment is a widely used procedure. Numerous phylogenetic algorithms have been developed, most of which have many parameters and options.Choosing a program, options, and parameters can be
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2a0f5794d58155fbf4aee61a2ef6c0fb
https://doi.org/10.21203/rs.3.rs-2408681/v1
https://doi.org/10.21203/rs.3.rs-2408681/v1
Autor:
Dmitry Penzar, Daria Nogina, Georgy Meshcheryakov, Andrey Lando, Abdul Muntakim Rafi, Carl de Boer, Arsenii Zinkevich, Ivan V. Kulakovskiy
Parallel reporter assays provide rich data to decipher gene regulatory regions with deep learning. Here we introduce LegNet, a convolutional network architecture that secured the first place for ourautosome.orgteam in the DREAM 2022 challenge of pred
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b021e6086b5fbea13fd59e5360ee901a
https://doi.org/10.1101/2022.12.22.521582
https://doi.org/10.1101/2022.12.22.521582
Publikováno v:
BMC Bioinformatics, Vol 19, Iss 1, Pp 1-14 (2018)
BMC Bioinformatics
BMC Bioinformatics
Background Many algorithms and programs are available for phylogenetic reconstruction of families of proteins. Methods used widely at present use either a number of distance-based principles or character-based principles of maximum parsimony or maxim
Autor:
Ilya E. Vorontsov, Romain Groux, Ivo Grosse, Ivan V. Kulakovskiy, Oriol Fornes, Daria D. Nikolaeva, Philipp Bucher, Benoit Ballester, Jan Grau, Giovanna Ambrosini, Dmitry Penzar, Vsevolod J. Makeev
Publikováno v:
Genome Biology
Genome Biology, BioMed Central, 2020, 21 (1), ⟨10.1186/s13059-020-01996-3⟩
Genome Biology, Vol 21, Iss 1, Pp 1-18 (2020)
Genome Biology, BioMed Central, 2020, 21 (1), ⟨10.1186/s13059-020-01996-3⟩
Genome Biology, Vol 21, Iss 1, Pp 1-18 (2020)
Background Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological appl
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4b5990db3e3f2a611f6878fc277b11a9
https://hal-amu.archives-ouvertes.fr/hal-02773294/document
https://hal-amu.archives-ouvertes.fr/hal-02773294/document