V. Makeev

发表

Homotypic regulatory clusters in Drosophila.

Anna G. Nazina, A. Lifanov, V. Makeev, 2003, Genome research.

Assessing computational tools for the discovery of transcription factor binding sites

William Stafford Noble, Chun Jimmie Ye, Z. Weng, 2005, Nature Biotechnology.

DNA sequence motif: a jack of all trades for ChIP-Seq data.

V. Makeev, I. Kulakovskiy, Vsevolod J Makeev, 2013, Advances in protein chemistry and structural biology.

Landscape of allele-specific transcription factor binding in the human genome

Dmitry D. Penzar, V. Makeev, A. Favorov, 2020, Nature Communications.

Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers.

Anna G. Nazina, A. Lifanov, V. Makeev, 2002, Genome research.

Role of structural water for prediction of cation binding sites in apoproteins

V. Makeev, V. Tumanyan, I. Kulakovskiy, 2018, Journal of biomolecular structure & dynamics.

Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling

V. Makeev, S. V. Rakhmanov, 2007, BMC Structural Biology.

An integrated expression atlas of miRNAs and their promoters in human and mouse

Jay W. Shin, Thomas J. Ha, Louise N. Winteringham, 2017, Nature Biotechnology.

Evolution of transcription factor DNA binding sites.

M. Gelfand, V. Makeev, E. Kotelnikova, 2005, Gene.

CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation

Alexander V. Favorov, V. Makeev, A. Mironov, 2012, Nucleic acids research.

Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.

Anna G. Nazina, A. Lifanov, V. Makeev, 2003, Nucleic acids research.

Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources

V. Makeev, I. Kulakovskiy, 2009 .

The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region

M. A. Afanasyeva, V. Makeev, I. Kulakovskiy, 2017, PloS one.

What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants

Vsevolod J. Makeev, Ivan V. Kulakovskiy, Ilya E. Vorontsov, 2019, Front. Genet..

A mitochondria-specific mutational signature of aging: increased rate of A>G substitutions on a heavy chain

A. Reymond, V. Makeev, K. Khrapko, 2022, bioRxiv.

A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease

Steve D. M. Brown, S. Greenaway, A. Mallon, 2020, BMC genomics.

Functional annotation of human long noncoding RNAs using chromatin conformation data

Jay W. Shin, Jordan A. Ramilowski, C. Hon, 2021 .

Identification of self-consistent modulons from bacterial microarray expression data with the help of structured regulon gene sets

V. Makeev, Y. Medvedeva, S. Mande, 2013, Journal of biomolecular structure & dynamics.

DNA Segmentation Through the Bayesian Approach

Mikhail A. Roytberg, Vladimir G. Tumanyan, Vasily Ramensky, 2000, J. Comput. Biol..

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Boris Lenhard, Lusy Handoko, Piero Carninci, 2020, Genome research.

Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2020 .

Preservation of methylated CpG dinucleotides in human CpG islands

Alexander Y. Panchin, V. Makeev, Y. Medvedeva, 2016, Biology Direct.

Functional annotation of human long noncoding RNAs via molecular phenotyping

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2019, bioRxiv.

Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis

V. Makeev, A. Orekhov, M. Bukrinsky, 2018, Current pharmaceutical design.

Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance

V. Makeev, A. Kasianov, L. Shcherbakova, 2019, PeerJ.

Intergenic, gene terminal, and intragenic CpG islands in the human genome

E. O. Ermakova, V. Makeev, A. Heinzel, 2010, BMC Genomics.

A model of evolution with constant selective pressure for regulatory DNA sites

M. Gelfand, V. Makeev, E. Kotelnikova, 2007, BMC Evolutionary Biology.

ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs

V. Makeev, F. Kolpakov, Y. Aulchenko, 2022, Nucleic Acids Res..

Use of Primary Macrophages for Searching Novel Immunocorrectors.

V. Makeev, A. Orekhov, M. Bukrinsky, 2017, Current pharmaceutical design.

Systematic identification of cis-interacting lncRNAs and their targets

Howard Y. Chang, Jay W. Shin, Jordan A. Ramilowski, 2022, bioRxiv.

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Dmitry D. Penzar, Jan Grau, P. Bucher, 2020, Genome Biology.

A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand

A. Reymond, V. Makeev, J. Fellay, 2022, Nucleic acids research.

Complete Genome Sequence of Bifidobacterium longum GT15: Identification and Characterization of Unique and Global Regulatory Genes

V. Makeev, N. V. Zakharevich, V. Danilenko, 2015, Microbial Ecology.

Stochastic modeling of noninteracting probes in the protein structure space for construction of knowledge-based potentials for atom-atom interactions

V. Makeev, S. V. Rakhmanov, 2008 .

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

M. Gelfand, V. Makeev, M. Logacheva, 2011, BMC Genomics.

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

F. A. Kolpakov, Vladimir B. Bajic, Arturo Magana-Mora, 2017, Nucleic Acids Res..

A promoter-level mammalian expression atlas

Cesare Furlanello, Finn Drabløs, Carsten O. Daub, 2015 .

Cyclical fate restriction: a new view of neural crest cell fate specification.

R. Kelsh, V. Makeev, A. Rocco, 2021, Development.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Martin S. Taylor, Jay W. Shin, Thomas J. Ha, 2021, Nature Communications.

GTRD: an integrated view of transcription regulation

Alexander E. Kel, Vsevolod J. Makeev, Fedor A. Kolpakov, 2020, Nucleic Acids Res..

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

Vladimir B. Bajic, Haitham Ashoor, Wail Ba-alawi, 2015, Nucleic Acids Res..

The complete genome sequence of Pantoea ananatis AJ13355, an organism with great biotechnological potential

V. Makeev, N. Kadotani, L. I. Golubeva, 2011, Applied Microbiology and Biotechnology.

Jaccard index based similarity measure to compare transcription factor binding site models

Vsevolod J. Makeev, Ivan V. Kulakovskiy, Ilya E. Vorontsov, 2013, Algorithms for Molecular Biology.

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

Vladimir B. Bajic, Ulf Schaefer, Vsevolod J. Makeev, 2012, Nucleic Acids Res..

Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software

Mikhail A. Roytberg, Vladimir G. Tumanyan, Vasily Ramensky, 2001, Bioinform..

Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide Composition

Mikhail S. Gelfand, Mikhail A. Roytberg, Vladimir G. Tumanyan, 2000, JOBIM.

Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes

V. Makeev, N. V. Zakharevich, V. Danilenko, 2019, PeerJ.

G and T nucleotide contents show specie-invariant negative correlation for all three codon positions.

V. Makeev, G K Frank, V J Makeev, 1997, Journal of biomolecular structure & dynamics.

The Gene Regulation Knowledge Commons: The action area of GREEKC.

Juan M. Vaquerizas, Pedro T. Monteiro, D. Zerbino, 2021, Biochimica et biophysica acta. Gene regulatory mechanisms.

Segmentation of Heteropolymer Sequences Specifying Subsequences with Different Composition and Statistical Properties

V. Makeev, A. Khokhlov, P. Khalatur, 2003 .

In vitro selection of optimal RelB/p52 DNA-binding motifs.

V. Makeev, D. Kuprash, L. Britanova, 2008, Biochemical and biophysical research communications.

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

V. Makeev, T. Merkulova, V. Levitsky, 2014, BMC Genomics.

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

V. Makeev, T. Merkulova, V. Levitsky, 2014, BMC Genomics.

From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites

Victor G. Levitsky, Vsevolod J. Makeev, Dmitry Yu. Oshchepkov, 2013, J. Bioinform. Comput. Biol..

Deep and wide digging for binding motifs in ChIP-Seq data

Vsevolod J. Makeev, Alexander V. Favorov, Valentina Boeva, 2010, Bioinform..

A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease

Steve D. M. Brown, S. Greenaway, A. Mallon, 2020, BMC genomics.

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

Mireille Régnier, Julien Clément, Mikhail A. Roytberg, 2007, Algorithms for Molecular Biology.

Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression

Mireille Régnier, Vsevolod J. Makeev, Dmitri A. Papatsenko, 2006, Bioinform..

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

Andrey A. Mironov, Sarah J. Wheelan, Vsevolod J. Makeev, 2012, PLoS Comput. Biol..

Motif discovery and motif finding from genome-mapped DNase footprint data

Vsevolod J. Makeev, Alexander V. Favorov, Ivan V. Kulakovskiy, 2009, Bioinform..

Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes.

Andrey A Mironov, M. Gelfand, V. Makeev, 2006, Genome research.

PERFECTOS-APE - Predicting Regulatory Functional Effect of SNPs by Approximate P-value Estimation

Vsevolod J. Makeev, Ivan V. Kulakovskiy, Ilya E. Vorontsov, 2015, BIOINFORMATICS.

A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

Vsevolod J. Makeev, Natalia G. Esipova, Ivan V. Kulakovskiy, 2011, Bioinform..

Negative selection maintains transcription factor binding motifs in human cancer

V. Makeev, I. Kulakovskiy, E. Lukianova, 2015, BMC Genomics.

Heteroplasmic Variants of Mitochondrial DNA in Atherosclerotic Lesions of Human Aortic Intima

V. Makeev, A. Orekhov, A. Grechko, 2019, Biomolecules.

Phenomenon of individual difference in human monocyte activation.

V. Makeev, A. Orekhov, N. Nikiforov, 2015, Experimental and molecular pathology.

Complete Genome Sequence of Bifidobacterium longum GT15: Unique Genes for Russian Strains

V. Makeev, N. V. Zakharevich, V. Danilenko, 2014, Genome Announcements.

Positional weight matrices have sufficient prediction power for analysis of noncoding variants

V. Makeev, I. Kulakovskiy, Sergey Abramov, 2022, F1000Research.

The complete genome of the oil emulsifying strain Thalassolituus oleivorans K-188 from the Barents Sea.

T. V. Gerasimova, V. Makeev, A. Kasianov, 2017, Marine genomics.

Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

Ben D. MacArthur, Dmitri Papatsenko, Vsevolod J. Makeev, 2015, Stem cell reports.

Preferred distances between transcription factor binding sites

Vsevolod J. Makeev, Ivan V. Kulakovskiy, Artem S. Kasianov, 2011 .

Identification of Proteins Associated with Murine Cytomegalovirus Virions

Markus Wagner, Mark Borodovsky, Hidde L. Ploegh, 2004, Journal of Virology.

Assessing Ribosome Distribution Along Transcripts with Polarity Scores and Regression Slope Estimates.

V. Makeev, V. Gladyshev, I. Kulakovskiy, 2021, Methods in molecular biology.

HDL activates expression of genes stimulating cholesterol efflux in human monocyte-derived macrophages.

V. Makeev, A. Orekhov, M. Bukrinsky, 2018, Experimental and molecular pathology.

Jaccard index based similarity measure to compare transcription factor binding site models

V. Makeev, I. Kulakovskiy, I. Vorontsov, 2013, Algorithms for Molecular Biology.

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Jan Grau, P. Bucher, V. Makeev, 2020, Genome Biology.

Mitochondrial mutational spectrum is associated with mammalian longevity: a novel signature of oxidative damage

A. Reymond, V. Makeev, J. Fellay, 2021 .

Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data

V. Makeev, F. Kolpakov, I. Yevshin, 2018, BMC Research Notes.

Search of periodicities in primary structure of biopolymers: a general Fourier approach

Vladimir G. Tumanyan, Vsevolod J. Makeev, V. Makeev, 1996, Comput. Appl. Biosci..

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length

Mikhail S. Gelfand, Andrey A. Mironov, Vsevolod J. Makeev, 2005, Bioinform..

Preservation of methylated CpG dinucleotides in human CpG islands

V. Makeev, Y. Medvedeva, A. Y. Panchin, 2016, Biology Direct.

A>G substitutions on a heavy chain of mitochondrial genome marks an increased level of aerobic metabolism in warm versus cold vertebrates

V. Makeev, J. Fellay, K. Khrapko, 2023, bioRxiv.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Thomas J. Ha, L. K. Nielsen, Kelly J. Hitchens, 2021 .

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Thomas J. Ha, L. K. Nielsen, Kelly J. Hitchens, 2021 .

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping 1

Howard Y. Chang, Martin S. Taylor, Jay W. Shin, 2019 .

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Thomas J. Ha, L. K. Nielsen, Kelly J. Hitchens, 2022 .

Complete Genome Sequence of Bifidobacterium longum GT15: Identification and Characterization of Unique and Global Regulatory Genes

V. Makeev, N. V. Zakharevich, V. Danilenko, 2015, Microbial Ecology.

Functional annotation of human long noncoding RNAs using chromatin conformation data

Jay W. Shin, Jordan A. Ramilowski, C. Hon, 2021 .

The channel in transporters is formed by residues that are rare in transmembrane helices

Mikhail S. Gelfand, Vsevolod J. Makeev, Roman A. Sutormin, 2003, Silico Biol..

The complete genome sequence of Pantoea ananatis AJ13355, an organism with great biotechnological potential

V. Makeev, N. Kadotani, L. I. Golubeva, 2011, Applied Microbiology and Biotechnology.

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Silvio C. E. Tosatto, Julius O. B. Jacobsen, Nicholas A. Sinnott-Armstrong, 2024, Genome biology.

A promoter-level mammalian expression atlas

Martin S. Taylor, Jay W. Shin, Thomas J. Ha, 2014, Nature.

HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors

V. Makeev, A. Jolma, I. Yevshin, 2023, Nucleic acids research.

The Efficiency of 5-Methylcytosine Identification in DNA of Escherichia coli Cells that Carry Bacterial DNA Methyltransferase Genes Using an Oxford Nanopore Device

V. Makeev, S. Degtyarev, V. Ilinsky, 2020, Biophysics.

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Nicholas A. Sinnott-Armstrong, Jonathan M. Mudge, Hui Ting Grace Yeo, 2022, Genome biology.

Conserved sections of the transcription regulatory modules in Drosophila early genes, including homotypic transcription factor-binding sites, are arranged with an 84-nt period, which corresponds to the superhelical turn length of nucleosomal DNA

A. Lifanov, V. Makeev, N. Esipova, 2016 .

Statistical framework for calling allelic imbalance in high-throughput sequencing data

V. Makeev, I. Kulakovskiy, Sergey Abramov, 2023, bioRxiv.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Thomas J. Ha, Kelly J. Hitchens, J. Harrow, 2021 .