Search Results - "Mironov, Andrey A"

Tissue-specific regulation of gene expression via unproductive splicing by Mironov, Alexei, Petrova, Marina, Margasyuk, Sergey, Vlasenok, Maria, Mironov, Andrey A, Skvortsov, Dmitry, Pervouchine, Dmitri D

“…Abstract Eukaryotic gene expression is regulated post-transcriptionally by a mechanism called unproductive splicing, in which mRNA is triggered to degrade by…”
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Replicate sequencing libraries are important for quantification of allelic imbalance by Mendelevich, Asia, Vinogradova, Svetlana, Gupta, Saumya, Mironov, Andrey A., Sunyaev, Shamil R., Gimelbrant, Alexander A.

“…A sensitive approach to quantitative analysis of transcriptional regulation in diploid organisms is analysis of allelic imbalance (AI) in RNA sequencing…”
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Exploring massive, genome scale datasets with the GenometriCorr package by Favorov, Alexander, Mularoni, Loris, Cope, Leslie M, Medvedeva, Yulia, Mironov, Andrey A, Makeev, Vsevolod J, Wheelan, Sarah J

“…We have created a statistically grounded tool for determining the correlation of genomewide data with other datasets or known biological features, intended to…”
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Inter-chromosomal contact networks provide insights into Mammalian chromatin organization by Kaufmann, Stefanie, Fuchs, Christiane, Gonik, Mariya, Khrameeva, Ekaterina E, Mironov, Andrey A, Frishman, Dmitrij

“…The recent advent of conformation capture techniques has provided unprecedented insights into the spatial organization of chromatin. We present a large-scale…”
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Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes by Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.

“…Using comparative analysis of genes, operons, and regulatory elements, we describe the cobalamin (vitamin B12) biosynthetic pathway in available prokaryotic…”
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BaRDIC: robust peak calling for RNA–DNA interaction data by Mylarshchikov, Dmitry E, Nikolskaya, Arina I, Bogomaz, Olesja D, Zharikova, Anastasia A, Mironov, Andrey A

“…Abstract Chromatin-associated non-coding RNAs play important roles in various cellular processes by targeting genomic loci. Two types of genome-wide NGS…”
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Origin of the nuclear proteome on the basis of pre-existing nuclear localization signals in prokaryotic proteins by Lisitsyna, Olga M, Kurnaeva, Margarita A, Arifulin, Eugene A, Shubina, Maria Y, Musinova, Yana R, Mironov, Andrey A, Sheval, Eugene V

“…The origin of the selective nuclear protein import machinery, which consists of nuclear pore complexes and adaptor molecules interacting with the nuclear…”
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Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors by Korostelev, Yuriy D, Zharov, Ilya A, Mironov, Andrey A, Rakhmaininova, Alexandra B, Gelfand, Mikhail S

“…The large and increasing volume of genomic data analyzed by comparative methods provides information about transcription factors and their binding sites that,…”
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Comparative Genomics of Bacterial Zinc Regulons: Enhanced Ion Transport, Pathogenesis, and Rearrangement of Ribosomal Proteins by Panina, Ekaterina M., Mironov, Andrey A., Gelfand, Mikhail S.

“…Zinc is an important component of many proteins, but in large concentrations it is poisonous to the cell. Thus its transport is regulated by zinc repressors…”
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Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients by Valyaeva, Anna A, Tikhomirova, Maria A, Potashnikova, Daria M, Bogomazova, Alexandra N, Snigiryova, Galina P, Penin, Aleksey A, Logacheva, Maria D, Arifulin, Eugene A, Shmakova, Anna A, Germini, Diego, Kachalova, Anastasia I, Saidova, Aleena A, Zharikova, Anastasia A, Musinova, Yana R, Mironov, Andrey A, Vassetzky, Yegor S, Sheval, Eugene V

“…An increased frequency of B-cell lymphomas is observed in human immunodeficiency virus-1 (HIV-1)-infected patients, although HIV-1 does not infect B cells…”
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Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function by Samborskaia, Margarita D, Galitsyna, Aleksandra, Pletenev, Ilya, Trofimova, Anna, Mironov, Andrey A, Gelfand, Mikhail S, Khrameeva, Ekaterina E

“…Regulation of gene transcription is a complex process controlled by many factors, including the conformation of chromatin in the nucleus. Insights into…”
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A Metabolic Network in the Evolutionary Context: Multiscale Structure and Modularity by Spirin, Victor, Gelfand, Mikhail S., Mironov, Andrey A., Mirny, Leonid A.

“…The enormous complexity of biological networks has led to the suggestion that networks are built of modules that perform particular functions and are "reused"…”
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Hidden Markov models for evolution and comparative genomics analysis by Bykova, Nadezda A, Favorov, Alexander V, Mironov, Andrey A

“…The problem of reconstruction of ancestral states given a phylogeny and data from extant species arises in a wide range of biological studies. The…”
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Evolution of Prokaryotic Genes by Shift of Stop Codons by Vakhrusheva, Anna A., Kazanov, Marat D., Mironov, Andrey A., Bazykin, Georgii A.

“…De novo origin of coding sequence remains an obscure issue in molecular evolution. One of the possible paths for addition (subtraction) of DNA segments to…”
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Spatial proximity and similarity of the epigenetic state of genome domains by Khrameeva, Ekaterina E, Mironov, Andrey A, Fedonin, Gennady G, Khaitovich, Philipp, Gelfand, Mikhail S

“…Recent studies demonstrate that the organization of the chromatin within the nuclear space might play a crucial role in the regulation of gene expression. The…”
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Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families by Kalinina, Olga V., Mironov, Andrey A., Gelfand, Mikhail S., Rakhmaninova, Aleksandra B.

“…The increasing volume of genomic data opens new possibilities for analysis of protein function. We introduce a method for automated selection of residues that…”
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Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale by Mendelevich, Asia, Gupta, Saumya, Pakharev, Aleksei, Teodosiadis, Athanasios, Mironov, Andrey A, Gimelbrant, Alexander A

“…Abstract Motivation Analysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed…”
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An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies by Mazin, Pavel V, Gelfand, Mikhail S, Mironov, Andrey A, Rakhmaninova, Aleksandra B, Rubinov, Anatoly R, Russell, Robert B, Kalinina, Olga V

“…Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins,…”
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Weak Negative and Positive Selection and the Drift Load at Splice Sites by Denisov, Stepan V., Bazykin, Georgii A., Sutormin, Roman, Favorov, Alexander V., Mironov, Andrey A., Gelfand, Mikhail S., Kondrashov, Alexey S.

“…Splice sites (SSs) are short sequences that are crucial for proper mRNA splicing in eukaryotic cells, and therefore can be expected to be shaped by strong…”
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OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins by Ilnitskiy, Ivan S, Zharikova, Anastasia A, Mironov, Andrey A

“…Abstract Extensive amounts of data from next-generation sequencing and omics studies have led to the accumulation of information that provides insight into the…”
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