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List of works by Mikhail Gelfand

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

scientific article

A machine learning framework for the prediction of chromatin folding in using epigenetic features

scientific article

A metabolic network in the evolutionary context: multiscale structure and modularity

scientific article

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

scientific article

A novel class of modular transporters for vitamins in prokaryotes.

scientific article

A novel intra-U1 snRNP cross-regulation mechanism: alternative splicing switch links U1C and U1-70K expression.

scientific article

A polar mechanism coordinates different regions of alternative splicing within a single gene.

scientific article

A transporter of Escherichia coli specific for L- and D-methionine is the prototype for a new family within the ABC superfamily

scientific article

APOBEC mutagenesis is low in most types of non-B DNA structures

scientific article published in 2022

ASDB: database of alternatively spliced genes

scientific article published on 01 January 1999

Abundance and functional diversity of riboswitches in microbial communities

scientific article

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure.

scientific article published on 11 July 2017

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

scientific article

Adaptive evolution at mRNA editing sites in soft-bodied cephalopods

scientific article published on 27 November 2020

Algorithms and software for support of gene identification experiments ⬇️

scientific article published on January 1, 1998

Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenases.

scientific article

An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation.

scientific article published on 14 April 2003

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.

scientific article

Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli

scientific article

Asymmetric and non-uniform evolution of recently duplicated human genes

scientific article

Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis.

scientific article

Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families.

scientific article published in February 2004

BATMAS30: amino acid substitution matrix for alignment of bacterial transporters.

scientific article published in April 2003

Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments.

scientific article

Bioinformatics classification and functional analysis of PhoH homologs

scientific article published on 30 December 2002

Changes in segmentation and setation along the anterior/posterior axis of the homonomous trunk limbs of a remipede (Crustacea, Arthropoda)

scientific article

Changes in snoRNA and snRNA Abundance in the Human, Chimpanzee, Macaque, and Mouse Brain

scientific article published on 28 February 2016

Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction

scientific article published on 12 September 2019

Combining diverse evidence for gene recognition in completely sequenced bacterial genomes.

scientific article

Combining specificity determining and conserved residues improves functional site prediction

scientific article

Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications

scientific article

Comparative Genomic Analysis of Holospora spp., Intranuclear Symbionts of Paramecia.

scientific article published on 16 April 2018

Comparative Genomic Analysis of the Regulation of Aromatic Metabolism in Betaproteobacteria

scientific article published in 2019

Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs

scientific article

Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria

scientific article

Comparative analysis of regulatory patterns in bacterial genomes.

scientific article

Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters

scientific journal article

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization

scientific article

Comparative genomic analysis of T-box regulatory systems in bacteria

scientific article published on April 2008

Comparative genomic analysis of fungal TPP-riboswitches.

scientific article published on 13 March 2018

Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae).

scientific article

Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria.

scientific article published on 27 May 2011

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

scientific article

Comparative genomics and evolution of alternative splicing: the pessimists' science.

scientific article published on 24 July 2007

Comparative genomics and evolution of regulons of the LacI-family transcription factors

scientific article

Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis

scientific article published on 20 July 2006

Comparative genomics of CytR, an unusual member of the LacI family of transcription factors

scientific article

Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins

scientific article published on 6 August 2003

Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria.

scientific article published on 26 September 2008

Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria.

scientific article published on November 2004

Comparative genomics of the dormancy regulons in mycobacteria

scientific article

Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems.

scientific article published on 23 June 2004

Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes.

scientific article

Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms

scientific article (publication date: 13 December 2002)

Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter.

scientific article published in October 2006

Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria

scientific article

Comparison of genome architecture at two stages of male germline cell differentiation in Drosophila

scientific article published on 01 April 2022

Complete Genome and Proteome of Acholeplasma laidlawii ⬇️

scientific article published on July 22, 2011

Computational analysis of splicing errors and mutations in human transcripts

scientific article

Computational identification of BioR, a transcriptional regulator of biotin metabolism in Alphaproteobacteria, and of its binding signal.

scientific article published in February 2006

Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria

scientific article

Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria

scientific article published on 19 October 2006

Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea.

scientific article published on October 2002

Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees and macaques.

scientific article

Conserved and species-specific alternative splicing in mammalian genomes.

scientific article

Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki

scientific article published on 20 February 2018

Correction to: Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches

scientific article published on 22 July 2020

Correlated Evolution of Nucleotide Positions within Splice Sites in Mammals.

scientific article published on 7 December 2015

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L.

scientific article published on 07 February 2014

Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function

scientific article published on 10 August 2020

Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements.

scientific article

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

scientific article

Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks

scientific article

Detection of homologous recombination in closely related strains.

scientific article published on 14 January 2016

Differential Impact of Hexuronate Regulators ExuR and UxuR on the Escherichia coli Proteome

scientific article published in 2022

Dissernet

volunteer community network working to clean Russian science of plagiarism

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks

scientific article

Doing science in uncertain times

scientific article

Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches

scientific article published on 29 April 2020

Dynasty Foundation: Russian science loses to politics

scientific article published on 01 June 2015

Engineering transcription factors with novel DNA-binding specificity using comparative genomics

scientific article published on 05 March 2009

Evaluation and comparison of current fetal ultrasound image segmentation methods for biometric measurements: a grand challenge

scientific article published on 6 August 2013

Evidence for widespread association of mammalian splicing and conserved long-range RNA structures

scientific article (publication date: 2012)

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

scientific article published on 6 March 2006

Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica

scientific article published on 12 April 2013

Evolution of regulatory motifs of bacterial transcription factors.

scientific article published in January 2010

Evolution of the Exon-Intron Structure in Ciliate Genomes.

scientific article

Evolution of the NadR regulon in Enterobacteriaceae

scientific journal article

Evolution of the exon-intron structure and alternative splicing of the MAGE-A family of cancer/testis antigens.

scientific article

Evolution of transcription factor DNA binding sites

scientific article published on 17 February 2005

Evolution of transcriptional regulation in closely related bacteria

scientific article

Evolution of transcriptional regulatory networks in microbial genomes

scientific article

Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome.

scientific article

Evolutionary patterns of phosphorylated serines

scientific article

Exact mapping of prokaryotic gene starts.

scientific article

Extendable words in nucleotide sequences ⬇️

scientific article published on April 1, 1992

Fast rate of evolution in alternatively spliced coding regions of mammalian genes.

scientific article published on 18 April 2006

Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.

scientific article published on 2 December 2012

Functional implications of splicing polymorphisms in the human genome.

scientific article published on 2 May 2013

Gene cloning, expression and characterization of novel phytase from Obesumbacterium proteus

scientific article published in July 2004

Gene recognition in eukaryotic DNA by comparison of genomic sequences ⬇️

scientific article published on November 1, 2001

Gene recognition via spliced sequence alignment.

scientific article published on August 1996

Genetic language: metaphore or analogy?

scientific article

Genome analysis of E. coli isolated from Crohn's disease patients

scientific article

Genome rearrangements and phylogeny reconstruction in Yersinia pestis

scientific article published on 27 March 2018

Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp

scientific article published on 27 December 2018

Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile

scientific article published on 13 August 2020

Genome-wide analysis of bacterial promoter regions

scientific article published on 01 January 2003

Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile.

scientific article

Genome-wide molecular clock and horizontal gene transfer in bacterial evolution

scientific article

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation

scientific article

Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

scientific article published on 20 February 2017

Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry

scientific article

Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry

Genomics of sponge-associated Streptomyces spp. closely related to Streptomyces albus J1074: insights into marine adaptation and secondary metabolite biosynthesis potential

scientific article

Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane.

scientific article published on 16 March 2007

Glutamine versus ammonia utilization in the NAD synthetase family

scientific article

GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution.

scientific article published on 7 July 2015

High Rates of Genome Rearrangements and Pathogenicity of <i>Shigella</i> spp

scientific article published on 12 April 2021

History of chromosome rearrangements reflects the spatial organization of yeast chromosomes

scientific article

Horizontal gene transfer and genome evolution in Methanosarcina.

scientific article published on 5 June 2015

How gene order is influenced by the biophysics of transcription regulation

scholarly article

Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors

scientific article

Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling.

scientific article published in July 2005

Identification of replication origins in prokaryotic genomes.

scientific article published on 26 July 2008

Increase of functional diversity by alternative splicing

scientific article

Influence of the spacer region between the Shine-Dalgarno box and the start codon for fine-tuning of the translation efficiency in Escherichia coli

scientific article published on 23 March 2020

Introduction to Papers Selected from MCCMB'17

scientific article published on 01 April 2018

Introduction: 4th International Moscow Conference on Computational Molecular Biology MCCMB'09.

scientific article published in June 2010

Korchevatel'

'the rooter'. social action against unconscionable scientific publications in Russia

Large-Scale Identification and Analysis of C-Proteins ⬇️

scientific article published on 01 January 2010

Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria

scientific article published on 20 February 2007

Low conservation of alternative splicing patterns in the human and mouse genomes.

scientific article

Low-molecular-weight post-translationally modified microcins.

scientific article published on 17 August 2007

Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow

article

Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea)

scientific article published in Scientific Reports

Mining sequence annotation databanks for association patterns.

scientific article

Modulation of alternative splicing by long-range RNA structures in Drosophila

scientific article published on 22 May 2009

Natural variation of gene models in Drosophila melanogaster.

scientific article

Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans

scientific article published on April 2014

Neanderthal and Denisovan ancestry in Papuans: A functional study

scientific article published on 01 April 2018

New Intranuclear Symbiotic Bacteria from Macronucleus of Paramecium putrinum—“Candidatus Gortzia Yakutica”

Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria.

scientific article published on 26 August 2016

No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions

scientific article

Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila

scientific article published on 12 March 2019

Order and stochasticity in the folding of individual Drosophila genomes

scientific article published on 04 January 2021

Overlapping alternative donor splice sites in the human genome

scientific article

Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.

scientific article published on 12 March 2018

Performance-guarantee gene predictions via spliced alignment.

scientific article published in August 1998

Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data

scientific article published on 18 November 2021

Phospho-islands and the evolution of phosphorylated amino acids in mammals

scientific article published on 02 December 2020

Positive selection in alternatively spliced exons of human genes

scientific article published on 19 June 2008

Predictive models of protease specificity based on quantitative protease-activity profiling data

scientific article published on 19 July 2019

Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors.

scientific article published in January 2001

Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria.

scientific article

Recapitulation of the embryonic transcriptional program in holometabolous insect pupae

scientific article published in 2022

Recognition of genes in human DNA sequences.

scientific article published in January 1996

Recognition of regulatory sites by genomic comparison.

scientific article

Recognition of transmembrane segments in proteins: review and consistency-based benchmarking of internet servers.

scientific article published on October 2006

Recombination Processes and Nonlinear Markov Chains.

scientific article

Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria

scientific article

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

scientific article

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

scientific article

RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

scientific article

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

scientific article

Regulation and evolution of malonate and propionate catabolism in proteobacteria.

scientific article

Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria.

scientific article

Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?

scientific article

Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation

scientific article

Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element

scientific article

Research funds: Rid Russian science of corruption

scientific article published on 19 October 2011

Restriction-modification systems and bacteriophage invasion: who wins?

scientific article published on 13 July 2010

Riboswitches: the oldest mechanism for the regulation of gene expression?

scientific article

Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs

scientific article published on 26 June 2009

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins.

scientific article published on July 2004

SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data ⬇️

scientific article published on January 1, 2002

Sequence-derived structural features driving proteolytic processing.

scientific article published on 11 December 2013

Sequencing potential of nested strand hybridization

scientific article published on 01 January 1995

Simplification of ribosomes in bacteria with tiny genomes

scientific article published on 18 July 2020

Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110.

scientific article

Some alphabets easily beat Russian letter count

scientific article published on 01 August 2008

Spatial proximity and similarity of the epigenetic state of genome domains.

scientific article

Statistical analysis and prediction of the exonic structure of human genes

scientific article published on September 1, 1992

Statistical analysis of the exon-intron structure of higher and lower eukaryote genes.

scientific article

Structural analysis of conserved base pairs in protein-DNA complexes ⬇️

scientific article published on April 2002

Structure and Function of an ADP-Ribose-Dependent Transcriptional Regulator of NAD Metabolism

scientific article

Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci

scientific article

Systematic prediction of control proteins and their DNA binding sites.

scientific article published on 04 December 2008

Temporal regulation of gene expression of the Escherichia coli bacteriophage phiEco32.

scientific article published on 10 January 2012

Temporal regulation of viral transcription during development of Thermus thermophilus bacteriophage phiYS40.

scientific article published on 18 November 2006

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

scientific article published on January 1, 2003

The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation

scientific article published on 16 February 2018

The presence of the transposable element ISBsu2 from a cryptic plasmid in chromosomes of some Bacillus subtilis strains

scientific article published on 01 September 2002

The view from Russia

scientific article published in Nature

Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon.

scientific article published on 14 February 2008

Transcriptional regulation of the methionine and cysteine transport and metabolism in streptococci.

scientific article published in November 2007

Translation at first sight: the influence of leading codons

scientific article published on 19 May 2020

Use of the flux model of amino acid metabolism of Escherichia coli.

scientific article published in November 2006

Using orthologous and paralogous proteins to identify specificity determining residues

scientific article published on 19 February 2002

Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.

scientific article

Weak negative and positive selection and the drift load at splice sites

scientific article

What is to be done about Russian science? ⬇️

scientific article published on August 22, 2013

Widespread splicing changes in human brain development and aging

scientific article published on January 2013

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