Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs (2009)
Nurtdinov, Ramil N, Mironov, Andrey A, Gelfand, Mikhail S
Abstract Background Alternative splicing is an important mechanism for generating functional and evolutionary diversity of proteins in eukaryotes. Here, we studied the frequency and functionality of...
Combining specificity determining and conserved residues improves functional site prediction (2009)
Kalinina, Olga V, Gelfand, Mikhail S, Russell, Robert B
Abstract Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make...
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization (2009)
Zhang, Yan, Rodionov, Dmitry A, Gelfand, Mikhail S, Gladyshev, Vadim N
Abstract Background Nickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of...
A Novel Class of Modular Transporters for Vitamins in Prokaryotes (2009)
Rodionov, Dmitry A., Hebbeln, Peter, Eudes, Aymerick, Beek, Josy Ter, Rodionova, Irina A., Erkens, Guus B., ...
The specific and tightly controlled transport of numerous nutrients and metabolites across cellular membranes is crucial to all forms of life. However, many of the transporter proteins involved have...
Desai, Tasha A., Rodionov, Dmitry A., Gelfand, Mikhail S., Alm, Eric J., Rao, Christopher V.
The transcriptional program for a gene consists of the promoter necessary for recruiting RNA polymerase along with neighboring operator sites that bind different activators and repressors. From a...
Modulation of alternative splicing by long-range RNA structures in Drosophila (2009)
Raker, Veronica A., Mironov, Andrei A., Gelfand, Mikhail S., Pervouchine, Dmitri D.
Accurate and efficient recognition of splice sites during pre-mRNA splicing is essential for proper transcriptome expression. Splice site usage can be modulated by secondary structures, but it is...
Systematic prediction of control proteins and their DNA binding sites (2009)
Sorokin, Valeriy, Severinov, Konstantin, Gelfand, Mikhail S.
We present here the results of a systematic bioinformatics analysis of control (C) proteins, a class of DNA-binding regulators that control time-delayed transcription of their own genes as well as...
Computational analysis of splicing errors and mutations in human transcripts (2008)
Kurmangaliyev, Yerbol Z, Gelfand, Mikhail S
Abstract Background Most retained introns found in human cDNAs generated by high-throughput sequencing projects seem to result from underspliced transcripts, and thus they capture intermediate steps...
Identification of replication origins in prokaryotic genomes (2008)
Sernova, Natalia V., Gelfand, Mikhail S.
The availability of hundreds of complete bacterial genomes has created new challenges and simultaneously opportunities for bioinformatics. In the area of statistical analysis of genomic sequences,...
Rodionov, Dmitry A., Li, Xiaoqing, Rodionova, Irina A., Yang, Chen, Sorci, Leonardo, Dervyn, Etienne, ...
A comparative genomic approach was used to reconstruct transcriptional regulation of NAD biosynthesis in bacteria containing orthologs of Bacillus subtilis gene yrxA, a previously identified...
Comparative genomic analysis of T-box regulatory systems in bacteria (2008)
Vitreschak, Alexey G., Mironov, Andrei A., Lyubetsky, Vassily A., Gelfand, Mikhail S.
T-box antitermination is one of the main mechanisms of regulation of genes involved in amino acid metabolism in Gram-positive bacteria. T-box regulatory sites consist of conserved sequence and RNA...
Conserved and species-specific alternative splicing in mammalian genomes (2007)
Nurtdinov, Ramil N, Neverov, Alexey D, Favorov, Alexander V, Mironov, Andrey A, Gelfand, Mikhail S
Abstract Background Alternative splicing has been shown to be one of the major evolutionary mechanisms for protein diversification and proteome expansion, since a considerable fraction of alternative...
Abundance and functional diversity of riboswitches in microbial communities (2007)
Kazanov, Marat D, Vitreschak, Alexey G, Gelfand, Mikhail S
Abstract Background Several recently completed large-scale enviromental sequencing projects produced a large amount of genetic information about microbial communities ('metagenomes') which is not...
A model of evolution with constant selective pressure for regulatory DNA sites (2007)
Enikeeva, Farida N, Kotelnikova, Ekaterina A, Gelfand, Mikhail S, Makeev, Vsevolod J
Abstract Background Molecular evolution is usually described assuming a neutral or weakly non-neutral substitution model. Recently, new data have become available on evolution of sequence regions...
Ravcheev, Dmitry A, Gerasimova, Anna V, Mironov, Andrey A, Gelfand, Mikhail S
Abstract Background Gamma-proteobacteria, such as Escherichia coli , can use a variety of respiratory substrates employing numerous aerobic and anaerobic respiratory systems controlled by multiple...
Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria (2007)
Mamirova, Leila, Popadin, Konstantin, Gelfand, Mikhail S
Abstract Background The effectiveness of elimination of slightly deleterious mutations depends mainly on drift and recombination frequency. Here we analyze the influence of these two factors on the...
Kazakov, Alexei E., Cipriano, Michael J., Novichkov, Pavel S., Minovitsky, Simon, Vinogradov, Dmitry V., Arkin, Adam, ...
RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several...
Dmitry A. Rodionov, Mikhail S. Gelfand, Jonathan D. Todd
We used comparative genomics to investigate the distribution of conserved DNA-binding motifs in the regulatory regions of genes involved in iron and manganese homeostasis in alpha-proteobacteria....
Dmitry A Rodionov, Mikhail S Gelfand, Jonathan D. Todd
We used comparative genomics to investigate the distribution of conserved DNA-binding motifs in the regulatory regions of genes involved in iron and manganese homeostasis in alpha-proteobacteria....
Kazakov, Alexei E., Cipriano, Michael J., Novichkov, Pavel S., Minovitsky, Simon, Vinogradov, Dmitry V., Arkin, Adam, ...
RegTransBase, a manually curated database of regulatory interactions in prokaryotes, captures the knowledge in published scientific literature using a controlled vocabulary. Although a number of...
Fast rate of evolution in alternatively spliced coding regions of mammalian genes (2006)
Ermakova, Ekaterina O, Nurtdinov, Ramil N, Gelfand, Mikhail S
Abstract Background At least half of mammalian genes are alternatively spliced. Alternative isoforms are often genome-specific and it has been suggested that alternative splicing is one of the major...
Malko, Dmitry B., Makeev, Vsevolod J., Mironov, Andrey A., Gelfand, Mikhail S.
Comparative analysis of alternative splicing of orthologous genes from fruit flies (Drosophila melanogaster and Drosophila pseudoobscura) and mosquito (Anopheles gambiae) demonstrated that both in...
Malko, Dmitry B., Makeev, Vsevolod J., Mironov, Andrey A., Gelfand, Mikhail S.
Comparative analysis of alternative splicing of orthologous genes from fruit flies (Drosophila melanogaster and Drosophila pseudoobscura) and mosquito (Anopheles gambiae) demonstrated that both in...
Seliverstov, Alexander V, Putzer, Harald, Gelfand, Mikhail S, Lyubetsky, Vassily A
Abstract Background Formation of alternative structures in mRNA in response to external stimuli, either direct or mediated by proteins or other RNAs, is a major mechanism of regulation of gene...
Dmitry A. Rodionov, Inna L. Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand
Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism...
Rodionov, Dmitry A., Dubchak, Inna L., Arkin, Adam P., Alm, Eric J., Gelfand, Mikhail S.
Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism...
Dmitry A Rodionov, Inna L Dubchak, Adam P Arkin, Eric J Alm, Mikhail S Gelfand
Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism...
Mining sequence annotation databanks for association patterns (2005)
Irena I. Artamonova, Goar Frishman, Mikhail S. Gelfand, Dmitrij Frishman
Data and text mining Vol. 21 Suppl. 3 2005, pages iii49–iii57 doi:10.1093/bioinformatics/bti1206 Mining sequence annotation databanks for association patterns
EVOLUTION OF THE NADR REGULON IN (2005)
St Reading, Mikhail S. Gelfand
The NAD biosynthetic pathway and NAD transformations in E. coli and S. typhi are well characterized. Using comparative genomics methods we describe the NadR regulon in other Enterobacteriaceae,...
Oparina, Nina J., Kalinina, Olga V., Gelfand, Mikhail S., Kisselev, Lev L.
Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon...
Mining sequence annotation databanks for association patterns (2005)
Artamonova, Irena I., Frishman, Goar, Gelfand, Mikhail S., Frishman, Dmitrij
Motivation: Millions of protein sequences currently being deposited to sequence databanks will never be annotated manually. Similarity-based annotation generated by automatic software pipelines...
Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria (2004)
Rodionov, Dmitry A, Dubchak, Inna, Arkin, Adam, Alm, Eric, Gelfand, Mikhail S
Abstract Background Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of...
Reconstruction Of Regulatory And Metabolic Pathways In Metal-Reducing delta-Proteobacteria (2004)
Rodionov, Dmitry A., Dubchak, Inna, Arkin, Adam, Alm, Eric, Gelfand, Mikhail S.
Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of complete finished or...
Offman, Marc N, Nurtdinov, Ramil N, Gelfand, Mikhail S, Frishman, Dmitrij
Abstract Background Alternative splicing is an efficient mechanism for increasing the variety of functions fulfilled by proteins in a living cell. It has been previously demonstrated that...
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 determine the functional specificity of...
Kalinina, Olga V., Novichkov, Pavel S., Mironov, Andrey A., Gelfand, Mikhail S., Rakhmaninova, Aleksandra B.
SDPpred (Specificity Determining Position prediction) is a tool for prediction of residues in protein sequences that determine the proteins' functional specificity. It is designed for analysis of...
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Regulation of the methionine biosynthesis and transport genes in bacteria is rather diverse and involves two RNA-level regulatory systems and at least three DNA-level systems. In particular, the...
Increase of functional diversity by alternative splicing (2003)
Kriventseva,Evgenia V., Koch,Ina, Apweiler,Rolf, Vingron,Martin, Bork,Peer, Gelfand,Mikhail S., ...
A large-scale analysis of protein isoforms arising from alternative splicing shows that alternative splicing tends to insert or delete complete protein domains more frequently than expected by...
Increase of functional diversity by alternative splicing (2003)
Kriventseva, Evgenia V., Koch, Ina, Apweiler, Rolf, Vingron, Martin, Bork, Peer, Gelfand, Mikhail S., ...
A large-scale analysis of protein isoforms arising from alternative splicing shows that alternative splicing tends to insert or delete complete protein domains more frequently than expected by...
Low conservation of alternative splicing patterns in the human and mouse genomes (2003)
Nurtdinov, Ramil N., Artamonova, Irena I., Mironov, Andrei A., Gelfand, Mikhail S.
Alternative splicing has recently emerged as a major mechanism of generating protein diversity in higher eukaryotes. We compared alternative splicing isoforms of 166 pairs of orthologous human and...
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Comparative analysis of genes, operons and regulatory elements was applied to the lysine biosynthetic pathway in available bacterial genomes. We report identification of a lysine‐specific RNA...
VITRESCHAK, ALEXEY G., RODIONOV, DMITRY A., MIRONOV, ANDREY A., GELFAND, MIKHAIL S.
Cobalamin in the form of adenosylcobalamin (Ado-CBL) is known to repress expression of genes for vitamin B12 biosynthesis and be transported by a posttranscriptional regulatory mechanism, which...
Using orthologous and paralogous proteins to identify specificity determining residues (2002)
Mirny, Leonid A, Gelfand, Mikhail S
Abstract Background Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins...
Ponomarenko, Julia V., Orlova, Galina V., Frolov, Anatoly S., Gelfand, Mikhail S., Ponomarenko, Mikhail P.
SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for recognition of these oligomers. Since in vitro...
Exact mapping of prokaryotic gene starts (2002)
Baytaluk, Mikhail V., Gelfand, Mikhail S., Mironov, Andrey A.
It is known that while the programs used to find genes in prokaryotic genomes reliably map protein-coding regions, they often fail in the exact determination of gene starts. This problem is further...
Vitreschak, Alexey G., Rodionov, Dmitry A., Mironov, Andrey A., Gelfand, Mikhail S.
The riboflavin biosynthesis in bacteria was analyzed using comparative analysis of genes, operons and regulatory elements. A model for regulation based on formation of alternative RNA structures...
Conservation of the Biotin Regulon and the BirA Regulatory Signal in Eubacteria and Archaea (2002)
Rodionov, Dmitry A., Mironov, Andrei A., Gelfand, Mikhail S.
Structural analysis of conserved base pairs in protein-DNA complexes (2002)
Mirny, Leonid A., Gelfand, Mikhail S.
Understanding of protein–DNA interactions is crucial for prediction of DNA-binding specificity of transcription factors and design of novel DNA-binding proteins. In this paper we develop a novel...
Conservation of the binding site for the arginine repressor in all bacterial lineages (2001)
Makarova, Kira S, Mironov, Andrey A, Gelfand, Mikhail S
Abstract Background The arginine repressor ArgR/AhrC is a transcription factor universally conserved in bacterial genomes. Its recognition signal (the ARG box), a weak palindrome, is also conserved...
Brudno, Michael, Gelfand, Mikhail S., Spengler, Sylvia, Zorn, Manfred, Dubchak, Inna, Conboy, John G.
Alternative pre-mRNA splicing is a major cellular process by which functionally diverse proteins can be generated from the primary transcript of a single gene, often in tissue-specific patterns. The...
Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors (2001)
Mironov, Andrey A., Novichkov, Pavel S., Gelfand, Mikhail S.
Summary: Performance of existing algorithms for similarity-based gene recognition in eukaryotes drops when the genomic DNA has been sequenced with errors. A modification of the spliced alignment...
Genome regulation in the (so-called) post-genomic era (2000)
A report on the Second International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, 7-11 August, 2000.
Comparative analysis of regulatory patterns in bacterial genomes (2000)
Gelfand, Mikhail S., Novichkov, Pavel S., Novichkov, Elena S., Mironov, Andrey A.
Recognition of transcription regulatory sites in bacterial genomes is a notoriously difficult problem. There are no algorithms capable of making reliable predictions even for well-studied sites such...
Segmentation of yeast DNA using hidden Markov models (1999)
Leonid Peshkin, Mikhail S. Gelfand, Biotechnology Niigenetika
Motivation: Compositionally homogeneous segments of genomic DNA often correspond to meaningful biological units. Simple sliding window analysis is usually insucient for compositional segmentation of...
Frequent Alternative Splicing of Human Genes (1999)
Mironov, Andrey A., Fickett, James Wildon, Gelfand, Mikhail S.
Brudno, Michael, Gelfand, Mikhail S., Spengler, Sylvia, Zorn, Manfred, Dubchak, Inna, Conboy, John G.
Alternative pre-mRNA splicing is a major cellular process by which functionally diverse proteins can be generated from the primary transcript of a single gene, often in tissue-specific patterns. The...
Ponomarenko, Julia V., Orlova, Galina V., Frolov, Anatoly S., Gelfand, Mikhail S., Ponomarenko, Mikhail P.
SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for recognition of these oligomers. Since in vitro experimental...
Structural analysis of conserved base pairs in protein–DNA complexes
Mirny, Leonid A., Gelfand, Mikhail S.
Understanding of protein–DNA interactions is crucial for prediction of DNA-binding specificity of transcription factors and design of novel DNA-binding proteins. In this paper we develop a novel...
Vitreschak, Alexey G., Rodionov, Dmitry A., Mironov, Andrey A., Gelfand, Mikhail S.
The riboflavin biosynthesis in bacteria was analyzed using comparative analysis of genes, operons and regulatory elements. A model for regulation based on formation of alternative RNA structures...
Genome regulation in the (so-called) post-genomic era
A report on the Second International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, 7-11 August, 2000.
Conservation of the Biotin Regulon and the BirA Regulatory Signal in Eubacteria and Archaea
Rodionov, Dmitry A., Mironov, Andrei A., Gelfand, Mikhail S.
Biotin is a necessary cofactor of numerous biotin-dependent carboxylases in a variety of microorganisms. The strict control of biotin biosynthesis in Escherichia coli is mediated by the bifunctional...
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 ZUR of proteobacteria and Gram-positive...
Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Comparative analysis of genes, operons and regulatory elements was applied to the lysine biosynthetic pathway in available bacterial genomes. We report identification of a lysine-specific RNA...
Frequent Alternative Splicing of Human Genes
Mironov, Andrey A., Fickett, James Wildon, Gelfand, Mikhail S.
Alternative splicing can produce variant proteins and expression patterns as different as the products of different genes, yet the prevalence of alternative splicing has not been quantified. Here the...
Kalinina, Olga V., Novichkov, Pavel S., Mironov, Andrey A., Gelfand, Mikhail S., Rakhmaninova, Aleksandra B.
SDPpred (Specificity Determining Position prediction) is a tool for prediction of residues in protein sequences that determine the proteins' functional specificity. It is designed for analysis of...
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Regulation of the methionine biosynthesis and transport genes in bacteria is rather diverse and involves two RNA-level regulatory systems and at least three DNA-level systems. In particular, the...
Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution
Novichkov, Pavel S., Omelchenko, Marina V., Gelfand, Mikhail S., Mironov, Andrei A., Wolf, Yuri I., Koonin, Eugene V.
We describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. The approach used is based on comparing the evolutionary...
Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria
Rodionov, Dmitry A, Dubchak, Inna, Arkin, Adam, Alm, Eric, Gelfand, Mikhail S
A study of the genetic and regulatory factors in several biosynthesis, metal ion homeostasis, stress response, and energy metabolism pathways suggests that phylogenetically diverse δ-proteobacteria...
Oparina, Nina J., Kalinina, Olga V., Gelfand, Mikhail S., Kisselev, Lev L.
Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon...
Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria
Seliverstov, Alexander V, Putzer, Harald, Gelfand, Mikhail S, Lyubetsky, Vassily A
Rodionov, Dmitry A, Dubchak, Inna L, Arkin, Adam P, Alm, Eric J, Gelfand, Mikhail S
Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism...
Rodionov, Dmitry A., Hebbeln, Peter, Gelfand, Mikhail S., Eitinger, Thomas
The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for...
VITRESCHAK, ALEXEY G., RODIONOV, DMITRY A., MIRONOV, ANDREY A., GELFAND, MIKHAIL S.
Cobalamin in the form of adenosylcobalamin (Ado-CBL) is known to repress expression of genes for vitamin B12 biosynthesis and be transported by a posttranscriptional regulatory mechanism, which...
Fast rate of evolution in alternatively spliced coding regions of mammalian genes
Ermakova, Ekaterina O, Nurtdinov, Ramil N, Gelfand, Mikhail S
Malko, Dmitry B., Makeev, Vsevolod J., Mironov, Andrey A., Gelfand, Mikhail S.
Comparative analysis of alternative splicing of orthologous genes from fruit flies (Drosophila melanogaster and Drosophila pseudoobscura) and mosquito (Anopheles gambiae) demonstrated that both in...
A metabolic network in the evolutionary context: Multiscale structure and modularity
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” in evolution in a manner similar to...
Brudno, Michael, Gelfand, Mikhail S., Spengler, Sylvia, Zorn, Manfred, Dubchak, Inna, Conboy, John G.
Alternative pre-mRNA splicing is a major cellular process by which functionally diverse proteins can be generated from the primary transcript of a single gene, often in tissue-specific patterns. The...
Ponomarenko, Julia V., Orlova, Galina V., Frolov, Anatoly S., Gelfand, Mikhail S., Ponomarenko, Mikhail P.
SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for recognition of these oligomers. Since in vitro experimental...
Structural analysis of conserved base pairs in protein–DNA complexes
Mirny, Leonid A., Gelfand, Mikhail S.
Understanding of protein–DNA interactions is crucial for prediction of DNA-binding specificity of transcription factors and design of novel DNA-binding proteins. In this paper we develop a novel...
Vitreschak, Alexey G., Rodionov, Dmitry A., Mironov, Andrey A., Gelfand, Mikhail S.
The riboflavin biosynthesis in bacteria was analyzed using comparative analysis of genes, operons and regulatory elements. A model for regulation based on formation of alternative RNA structures...
Genome regulation in the (so-called) post-genomic era
A report on the Second International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, 7-11 August, 2000.
Conservation of the Biotin Regulon and the BirA Regulatory Signal in Eubacteria and Archaea
Rodionov, Dmitry A., Mironov, Andrei A., Gelfand, Mikhail S.
Biotin is a necessary cofactor of numerous biotin-dependent carboxylases in a variety of microorganisms. The strict control of biotin biosynthesis in Escherichia coli is mediated by the bifunctional...
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 ZUR of proteobacteria and Gram-positive...
Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Comparative analysis of genes, operons and regulatory elements was applied to the lysine biosynthetic pathway in available bacterial genomes. We report identification of a lysine-specific RNA...
Frequent Alternative Splicing of Human Genes
Mironov, Andrey A., Fickett, James Wildon, Gelfand, Mikhail S.
Alternative splicing can produce variant proteins and expression patterns as different as the products of different genes, yet the prevalence of alternative splicing has not been quantified. Here the...
Kalinina, Olga V., Novichkov, Pavel S., Mironov, Andrey A., Gelfand, Mikhail S., Rakhmaninova, Aleksandra B.
SDPpred (Specificity Determining Position prediction) is a tool for prediction of residues in protein sequences that determine the proteins' functional specificity. It is designed for analysis of...
Rodionov, Dmitry A., Vitreschak, Alexey G., Mironov, Andrey A., Gelfand, Mikhail S.
Regulation of the methionine biosynthesis and transport genes in bacteria is rather diverse and involves two RNA-level regulatory systems and at least three DNA-level systems. In particular, the...
Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution
Novichkov, Pavel S., Omelchenko, Marina V., Gelfand, Mikhail S., Mironov, Andrei A., Wolf, Yuri I., Koonin, Eugene V.
We describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. The approach used is based on comparing the evolutionary...
Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria
Rodionov, Dmitry A, Dubchak, Inna, Arkin, Adam, Alm, Eric, Gelfand, Mikhail S
A study of the genetic and regulatory factors in several biosynthesis, metal ion homeostasis, stress response, and energy metabolism pathways suggests that phylogenetically diverse δ-proteobacteria...
Oparina, Nina J., Kalinina, Olga V., Gelfand, Mikhail S., Kisselev, Lev L.
Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon...
Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria
Seliverstov, Alexander V, Putzer, Harald, Gelfand, Mikhail S, Lyubetsky, Vassily A
Rodionov, Dmitry A, Dubchak, Inna L, Arkin, Adam P, Alm, Eric J, Gelfand, Mikhail S
Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism...
Rodionov, Dmitry A., Hebbeln, Peter, Gelfand, Mikhail S., Eitinger, Thomas
The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for...
VITRESCHAK, ALEXEY G., RODIONOV, DMITRY A., MIRONOV, ANDREY A., GELFAND, MIKHAIL S.
Cobalamin in the form of adenosylcobalamin (Ado-CBL) is known to repress expression of genes for vitamin B12 biosynthesis and be transported by a posttranscriptional regulatory mechanism, which...
Malko, Dmitry B., Makeev, Vsevolod J., Mironov, Andrey A., Gelfand, Mikhail S.
Comparative analysis of alternative splicing of orthologous genes from fruit flies (Drosophila melanogaster and Drosophila pseudoobscura) and mosquito (Anopheles gambiae) demonstrated that both in...
Fast rate of evolution in alternatively spliced coding regions of mammalian genes
Ermakova, Ekaterina O, Nurtdinov, Ramil N, Gelfand, Mikhail S
A metabolic network in the evolutionary context: Multiscale structure and modularity
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” in evolution in a manner similar to...
Rodionov, Dmitry A, Gelfand, Mikhail S, Todd, Jonathan D, Curson, Andrew R. J, Johnston, Andrew W. B
We used comparative genomics to investigate the distribution of conserved DNA-binding motifs in the regulatory regions of genes involved in iron and manganese homeostasis in alpha-proteobacteria....
Kazakov, Alexei E., Cipriano, Michael J., Novichkov, Pavel S., Minovitsky, Simon, Vinogradov, Dmitry V., Arkin, Adam, ...
RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several...
Global Transcriptional Response of Nitrosomonas europaea to Chloroform and Chloromethane▿ †
Gvakharia, Barbara O., Permina, Elizabeth A., Gelfand, Mikhail S., Bottomley, Peter J., Sayavedra-Soto, Luis A., Arp, Daniel J.
Upon exposure of Nitrosomonas europaea to chloroform (7 μM, 1 h), transcripts for 175 of 2,460 genes were found at higher levels in treated cells than in untreated cells and transcripts for 501...
A model of evolution with constant selective pressure for regulatory DNA sites
Enikeeva, Farida N, Kotelnikova, Ekaterina A, Gelfand, Mikhail S, Makeev, Vsevolod J
Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks
Makarova, Kira S., Omelchenko, Marina V., Gaidamakova, Elena K., Matrosova, Vera Y., Vasilenko, Alexander, Zhai, Min, ...
Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group...
Conserved and species-specific alternative splicing in mammalian genomes
Nurtdinov, Ramil N, Neverov, Alexey D, Favorov, Alexander V, Mironov, Andrey A, Gelfand, Mikhail S
How gene order is influenced by the biophysics of transcription regulation
Kolesov, Grigory, Wunderlich, Zeba, Laikova, Olga N., Gelfand, Mikhail S., Mirny, Leonid A.
What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to...
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 determine the functional specificity of...
Rodionov, Dmitry A., Li, Xiaoqing, Rodionova, Irina A., Yang, Chen, Sorci, Leonardo, Dervyn, Etienne, ...
A comparative genomic approach was used to reconstruct transcriptional regulation of NAD biosynthesis in bacteria containing orthologs of Bacillus subtilis gene yrxA, a previously identified...
Comparative genomic analysis of T-box regulatory systems in bacteria
Vitreschak, Alexey G., Mironov, Andrei A., Lyubetsky, Vassily A., Gelfand, Mikhail S.
T-box antitermination is one of the main mechanisms of regulation of genes involved in amino acid metabolism in Gram-positive bacteria. T-box regulatory sites consist of conserved sequence and RNA...
Systematic prediction of control proteins and their DNA binding sites
Sorokin, Valeriy, Severinov, Konstantin, Gelfand, Mikhail S.
We present here the results of a systematic bioinformatics analysis of control (C) proteins, a class of DNA-binding regulators that control time-delayed transcription of their own genes as well as...
Positive Selection in Alternatively Spliced Exons of Human Genes
Ramensky, Vasily E., Nurtdinov, Ramil N., Neverov, Alexei D., Mironov, Andrei A., Gelfand, Mikhail S.
Alternative splicing is a well-recognized mechanism of accelerated genome evolution. We have studied single-nucleotide polymorphisms and human-chimpanzee divergence in the exons of 6672 alternatively...
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization
Zhang, Yan, Rodionov, Dmitry A, Gelfand, Mikhail S, Gladyshev, Vadim N
Engineering transcription factors with novel DNA-binding specificity using comparative genomics
Desai, Tasha A., Rodionov, Dmitry A., Gelfand, Mikhail S., Alm, Eric J., Rao, Christopher V.
The transcriptional program for a gene consists of the promoter necessary for recruiting RNA polymerase along with neighboring operator sites that bind different activators and repressors. From a...
A Novel Class of Modular Transporters for Vitamins in Prokaryotes ▿ †
Rodionov, Dmitry A., Hebbeln, Peter, Eudes, Aymerick, Ter Beek, Josy, Rodionova, Irina A., Erkens, Guus B., ...
The specific and tightly controlled transport of numerous nutrients and metabolites across cellular membranes is crucial to all forms of life. However, many of the transporter proteins involved have...
Kazakov, Alexey E., Rodionov, Dmitry A., Alm, Eric, Arkin, Adam Paul, Dubchak, Inna, Gelfand, Mikhail S.
Bacteria can use branched-chain amino acids (ILV, i.e., isoleucine, leucine, valine) and fatty acids (FAs) as sole carbon and energy sources converting ILV into acetyl-coenzyme A (CoA),...
Modulation of alternative splicing by long-range RNA structures in Drosophila
Raker, Veronica A., Mironov, Andrei A., Gelfand, Mikhail S., Pervouchine, Dmitri D.
Accurate and efficient recognition of splice sites during pre-mRNA splicing is essential for proper transcriptome expression. Splice site usage can be modulated by secondary structures, but it is...