List of works - Vsevolod Makeev

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

scientific article

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

scientific article

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

scientific article published on 27 July 2007

A novel model system for design of biomaterials based on recombinant analogs of spider silk proteins.

scientific article published on 7 October 2008

A promoter-level mammalian expression atlas

scientific article

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

scientific article

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

scientific article

Assessing computational tools for the discovery of transcription factor binding sites

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Empirical potentials for ion binding in proteins

scientific article published in June 2010

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

scientific article published on 04 March 2019

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

scientific article published on 6 March 2006

Evolution of transcription factor DNA binding sites

scientific article published on 17 February 2005

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

scientific article published on 10 October 2007

Exploring massive, genome scale datasets with the GenometriCorr package

scientific article

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

scientific article

From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites

scientific article

Functional annotation of human long noncoding RNAs via molecular phenotyping

scientific article published on 27 July 2020

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

article

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

article

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

scientific article

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

scientific article

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

scientific article published on 11 November 2017

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

scientific article published on 06 September 2019

Homotypic regulatory clusters in Drosophila.

scientific article

Identification of proteins associated with murine cytomegalovirus virions

scientific article

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

scientific article

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

scientific article published on 09 November 2007

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

scientific article

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

scientific article published on 30 September 2013

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

scientific article published on 01 January 2018

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

scientific article

Negative selection maintains transcription factor binding motifs in human cancer.

scientific article

Predictive biology using systems and integrative analysis and methods ⬇️

scientific article published on 01 January 2013

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

scientific article published on 26 December 2016

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

scientific article published in November 2001

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

scientific article published on 10 January 2006

Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response-What is First?

scientific article published on 14 April 2020

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

scientific article published on 10 December 2011

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

scientific article

Upstream open reading frames regulate translation of the long isoform of SLAMF1 mRNA that encodes costimulatory receptor CD150.

scientific article published on December 2014

Use of Primary Macrophages for Searching Novel Immunocorrectors

scientific article published on 25 January 2017

List of works by Vsevolod Makeev

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

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

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

A novel model system for design of biomaterials based on recombinant analogs of spider silk proteins.

A promoter-level mammalian expression atlas

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

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

Assessing computational tools for the discovery of transcription factor binding sites

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

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

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

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

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

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

Empirical potentials for ion binding in proteins

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

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

Evolution of transcription factor DNA binding sites

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

Exploring massive, genome scale datasets with the GenometriCorr package

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

From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites

Functional annotation of human long noncoding RNAs via molecular phenotyping

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

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

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

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

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

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

Homotypic regulatory clusters in Drosophila.

Identification of proteins associated with murine cytomegalovirus virions

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

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

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

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

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

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

Negative selection maintains transcription factor binding motifs in human cancer.

Predictive biology using systems and integrative analysis and methods ⬇️

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

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

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

Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response-What is First?

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

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

Upstream open reading frames regulate translation of the long isoform of SLAMF1 mRNA that encodes costimulatory receptor CD150.

Use of Primary Macrophages for Searching Novel Immunocorrectors