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Mikhail Gelfand

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Physiology

Genes & Molecular Sequences

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Michael J Cipriano; Adam P Arkin; Mikhail S Gelfand; Alexey E Kazakov; Pavel N Novichkov; Dmitry A Rodionov; Inna Dubchak
RegTransBase - a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.
Marat D Kazanov; Xiaoqing Li; Andrei Osterman; Mikhail S Gelfand; Dmitry A Rodionov
Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.
I A Suvorova; Dmitry A Ravcheev; Mikhail S Gelfand
Regulation and evolution of malonate and propionate catabolism in proteobacteria.

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2013: Michael J Cipriano; Adam P Arkin; Mikhail S Gelfand; Alexey E Kazakov; Pavel N Novichkov; Dmitry A Rodionov; Inna Dubchak
RegTransBase - a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.
BMC genomics 2013;14():213.
2013: Marat D Kazanov; Xiaoqing Li; Andrei Osterman; Mikhail S Gelfand; Dmitry A Rodionov
Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.
Nucleic acids research 2013;41(2):790-803.
2012: I A Suvorova; Dmitry A Ravcheev; Mikhail S Gelfand
Regulation and evolution of malonate and propionate catabolism in proteobacteria.
Journal of bacteriology 2012;194(12):3234-40.
2012: Olga Pavlova; Dmitry A Ravcheev; Konstantin Severinov; Marko Djordjevic; Mikhail S Gelfand; Evgeny Klimuk; Daria Lavysh; Natalja Akulenko
Temporal regulation of gene expression of the Escherichia coli bacteriophage phiEco32.
Journal of molecular biology 2012;416(3):389-99.
2012: Olga V Tsoy; Marat D Kazanov; Mikhail A Pyatnitskiy; Mikhail S Gelfand
Evolution of transcriptional regulation in closely related bacteria.
BMC evolutionary biology 2012;12():200.
2012: Natalia V Sernova; Mikhail S Gelfand
Comparative genomics of CytR, an unusual member of the LacI family of transcription factors.
PloS one 2012;7(9):e44194.
2012: Jessica De Ingeniis; Mikhail S Gelfand; Marat D Kazanov; Andrei L Osterman; Konstantin Shatalin; Leonardo Sorci
Glutamine versus ammonia utilization in the NAD synthetase family.
PloS one 2012;7(6):e39115.
2012: Ekaterina E Khrameeva; Mikhail S Gelfand
Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments.
BMC bioinformatics 2012;13 Suppl 6():S4.
2012: Ekaterina E Khrameeva; Andrey A Mironov; Gennady G Fedonin; Philipp Khaitovich; Mikhail S Gelfand
Spatial proximity and similarity of the epigenetic state of genome domains.
PloS one 2012;7(4):e33947.
2011: Vassili N Lazarev; S A Levitskii; D B Malko; Sergey I Rogov; Marina V Serebryakova; N V Sernova; V V Vereshchagin; Alexey G Vitreschak; N N Vtyurin; Tatiana A Akopian; Dmitry Alexeev; Y I Basovskii; M M Chukin; I A Demina; M A Galyamina; Mikhail S Gelfand; M D Kazanov; ES Kostrjukova; G Y Kovaleva; VG Ladygina; Vadim M Govorun
Complete genome and proteome of Acholeplasma laidlawii.
Journal of bacteriology 2011;193(18):4943-53.
2011: Anna Gerasimova; Alexey E Kazakov; Adam P Arkin; Inna Dubchak; Mikhail S Gelfand
Comparative genomics of the dormancy regulons in mycobacteria.
Journal of bacteriology 2011;193(14):3446-52.
2011: Dmitry A Rodionov; Irina A Rodionova; Margaret F Romine; Elena D Stavrovskaya; Adam P Arkin; Inna Dubchak; James K Fredrickson; Anna V Gerasimova; Alexey E Kazakov; Marat D Kazanov; Galina Yu Kovaleva; Olga N Laikova; Xiaoqing Li; Pavel Novichkov; Andrei Osterman; Ross Overbeek; Elizaveta A Permina; Dmitry A Ravcheev; Mikhail S Gelfand
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.
BMC genomics 2011;12 Suppl 1():S3.
2011: Yerbol Z Kurmangaliyev; Alexander Goland; Mikhail S Gelfand
Evolutionary patterns of phosphorylated serines.
Biology direct 2011;6():8.
2011: Maria D Logacheva; Artem S Kasianov; Dmitriy V Vinogradov; Tagir H Samigullin; Mikhail S Gelfand; Vsevolod Makeev; Aleksey Penin
De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum).
BMC genomics 2011;12():30.
2010: Farida N Enikeeva; Konstantin V Severinov; Mikhail S Gelfand
Restriction-modification systems and bacteriophage invasion: who wins?
Journal of theoretical biology 2010;266(4):550-9.
2010: Pavel Novichkov; Dmitry A Rodionov; Elena D Stavrovskaya; Elena S Novichkova; Alexey E Kazakov; Mikhail S Gelfand; Adam P Arkin; Andrey A Mironov; Inna Dubchak
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.
Nucleic acids research 2010;38(Web Server issue):W299-307.
2010: Valery A Sorokin; Mikhail S Gelfand; Irena I Artamonova
Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome.
Applied and environmental microbiology 2010;76(7):2136-44.
2010: Konstantin Y Gorbunov; Olga N Laikova; Mikhail S Gelfand; Dmitry A Rodionov; Vassily A Lyubetsky
Evolution of regulatory motifs of bacterial transcription factors.
In silico biology 2010;10(3):163-83.
2010: Valery Sorokin; Konstantin Severinov; Mikhail S Gelfand
Large-scale identification and analysis of C-proteins.
Methods in molecular biology (Clifton, N.J.) 2010;674():269-82.
2010: Alexander Y Panchin; Mikhail S Gelfand; Vasily E Ramensky; Irena I Artamonova
Asymmetric and non-uniform evolution of recently duplicated human genes.
Biology direct 2010;5():54.
2010: Pavel V Mazin; Mikhail S Gelfand; Andrey A Mironov; Aleksandra B Rakhmaninova; Anatoly R Rubinov; Robert B Russell; Olga V Kalinina
An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.
Algorithms for molecular biology : AMB 2010;5():29.
2010: Pavel Novichkov; Olga N Laikova; Elena S Novichkova; Mikhail S Gelfand; Adam P Arkin; Inna Dubchak; Dmitry A Rodionov
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Nucleic acids research 2010;38(Database issue):D111-8.
2009: Valeriy Sorokin; Konstantin Severinov; Mikhail S Gelfand
Systematic prediction of control proteins and their DNA binding sites.
Nucleic acids research 2009;37(2):441-51.
2009: Ramil N Nurtdinov; Andrey A Mironov; Mikhail S Gelfand
Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs.
BMC evolutionary biology 2009;9():142.
2008: Natalia V Sernova; Mikhail S Gelfand
Identification of replication origins in prokaryotic genomes.
Briefings in bioinformatics 2008;9(5):376-91.
2008: Mikhail S Gelfand
Some alphabets easily beat Russian letter count.
Nature 2008;454(7205):691.
2008: VE Ramensky; Ramil N Nurtdinov; Alexei D Neverov; Andrei A Mironov; Mikhail S Gelfand
Positive selection in alternatively spliced exons of human genes.
American journal of human genetics 2008;83(1):94-8.
2008: Alexey G Vitreschak; Andrey A Mironov; Vassily A Lyubetsky; Mikhail S Gelfand
Comparative genomic analysis of T-box regulatory systems in bacteria.
RNA (New York, N.Y.) 2008;14(4):717-35.
2008: Dmitry A Rodionov; Xiaoqing Li; Irina A Rodionova; Chen Yang; Leonardo Sorci; Etienne Dervyn; Dariusz Martynowski; Hong Zhang; Mikhail S Gelfand; Andrei Osterman
Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon.
Nucleic acids research 2008;36(6):2032-46.
2008: Yerbol Z Kurmangaliyev; Mikhail S Gelfand
Computational analysis of splicing errors and mutations in human transcripts.
BMC genomics 2008;9():13.
2007: Galina Yu Kovaleva; Mikhail S Gelfand
Transcriptional regulation of the methionine and cysteine transport and metabolism in streptococci.
FEMS microbiology letters 2007;276(2):207-15.
2007: Ekaterina O Ermakova; Ramil N Nurtdinov; Mikhail S Gelfand
Overlapping alternative donor splice sites in the human genome.
Journal of bioinformatics and computational biology 2007;5(5):991-1004.
2007: Konstantin Severinov; Ekaterina Semenova; Alexey Kazakov; Teymur Kazakov; Mikhail S Gelfand
Low-molecular-weight post-translationally modified microcins.
Molecular microbiology 2007;65(6):1380-94.
2007: Grigory Kolesov; Zeba Wunderlich; Olga N Laikova; Mikhail S Gelfand; Leonid A Mirny
How gene order is influenced by the biophysics of transcription regulation.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(35):13948-53.
2007: Irena I Artamonova; Mikhail S Gelfand
Comparative genomics and evolution of alternative splicing: the pessimists' science.
Chemical reviews 2007;107(8):3407-30.
2007: Andrew W B Johnston; Jonathan todd Todd; Andrew R J Curson; Sun Lei; Nefeli Nikolaidou-Katsaridou; Mikhail S Gelfand; Dmitry A Rodionov
Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria.
Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 2007;20(3-4):501-11.
2007: Barbara O Gvakharia; Elizabeth A Permina; Mikhail S Gelfand; Peter J Bottomley; Luis A Sayavedra-Soto; Daniel J Arp
Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane.
Applied and environmental microbiology 2007;73(10):3440-5.
2007: Anastasiya Sevostyanova; Marko Djordjevic; Konstantin Kuznedelov; Tatyana Naryshkina; Mikhail S Gelfand; Konstantin Severinov; Leonid Minakhin
Temporal regulation of viral transcription during development of Thermus thermophilus bacteriophage phiYS40.
Journal of molecular biology 2007;366(2):420-35.
2007: Ramil N Nurtdinov; Alexei D Neverov; Alexander Favorov; Andrey A Mironov; Mikhail S Gelfand
Conserved and species-specific alternative splicing in mammalian genomes.
BMC evolutionary biology 2007;7():249.
2007: Marat D Kazanov; Alexey G Vitreschak; Mikhail S Gelfand
Abundance and functional diversity of riboswitches in microbial communities.
BMC genomics 2007;8():347.
2007: Kira S Makarova; Marina V Omelchenko; Elena K Gaidamakova; Vera Y Matrosova; Alexander Vasilenko; Min Zhai; Alla Lapidus; Alex Copeland; Edwin Kim; Miriam Land; Konstantinos Mavrommatis; Samuel Pitluck; Paul M Richardson; Chris Detter; Thomas S Brettin; Elizabeth Saunders; Barry Lai; Bruce Ravel; Kenneth M Kemner; Yuri I Wolf; Alexei Sorokin; Anna V Gerasimova; Mikhail S Gelfand; James K Fredrickson; Eugene V Koonin; Michael J Daly
Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.
PloS one 2007;2(9):e955.
2007: Farida N Enikeeva; Ekaterina A Kotelnikova; Mikhail S Gelfand; Vsevolod Makeev
A model of evolution with constant selective pressure for regulatory DNA sites.
BMC evolutionary biology 2007;7():125.
2007: Dmitry A Ravcheev; Anna V Gerasimova; Andrey A Mironov; Mikhail S Gelfand
Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae).
BMC genomics 2007;8():54.
2007: Leila Mamirova; Konstantin Popadin; Mikhail S Gelfand
Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria.
BMC evolutionary biology 2007;7():17.
2007: Alexei E Kazakov; Michael J Cipriano; Pavel Novichkov; Simon Minovitsky; Dmitry V Vinogradov; Adam P Arkin; Andrey A Mironov; Mikhail S Gelfand; Inna Dubchak
RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
Nucleic acids research 2007;35(Database issue):D407-12.
2006: Dmitry A Rodionov; Mikhail S Gelfand; Jonathan todd Todd; Andrew R J Curson; Andrew W B Johnston
Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria.
PLoS computational biology 2006;2(12):e163.
2006: Chen Yang; Dmitry A Rodionov; Xiaoqing Li; Olga N Laikova; Mikhail S Gelfand; Olga Zagnitko; Margaret F Romine; Anna Y Obraztsova; Kenneth H Nealson; Andrei Osterman
Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis.
The Journal of biological chemistry 2006;281(40):29872-85.
2006: Nataliya S Sadovskaya; Roman A Sutormin; Mikhail S Gelfand
Recognition of transmembrane segments in proteins: review and consistency-based benchmarking of internet servers.
Journal of bioinformatics and computational biology 2006;4(5):1033-56.
2006: Galina Yu Kovaleva; Georgii A Bazykin; Michael Brudno; Mikhail S Gelfand
Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter.
Journal of bioinformatics and computational biology 2006;4(5):981-98.
2006: Olga V Kalinina; Mikhail S Gelfand
Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenases.
Proteins 2006;64(4):1001-9.
2006: Victor Spirin; Mikhail S Gelfand; Andrey A Mironov; Leonid A Mirny
A metabolic network in the evolutionary context: multiscale structure and modularity.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(23):8774-9.
2006: Mikhail S Gelfand
Evolution of transcriptional regulatory networks in microbial genomes.
Current opinion in structural biology 2006;16(3):420-9.
2006: Dmitry B Malko; Vsevolod Makeev; Andrey A Mironov; Mikhail S Gelfand
Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes.
Genome research 2006;16(4):505-9.
2006: Dmitry A Rodionov; Mikhail S Gelfand
Computational identification of BioR, a transcriptional regulator of biotin metabolism in Alphaproteobacteria, and of its binding signal.
FEMS microbiology letters 2006;255(1):102-7.
2006: Elizaveta A Permina; A E Kazakov; O V Kalinina; Mikhail S Gelfand
Comparative genomics of regulation of heavy metal resistance in Eubacteria.
BMC microbiology 2006;6():49.
2006: Ekaterina O Ermakova; Ramil N Nurtdinov; Mikhail S Gelfand
Fast rate of evolution in alternatively spliced coding regions of mammalian genes.
BMC genomics 2006;7():84.
2006: Dmitry A Rodionov; Peter Hebbeln; Mikhail S Gelfand; Thomas Eitinger
Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters.
Journal of bacteriology 2006;188(1):317-27.
2005: Irena I Artamonova; Goar Frishman; Mikhail S Gelfand; Dmitrij Frishman
Mining sequence annotation databanks for association patterns.
Bioinformatics (Oxford, England) 2005;21 Suppl 3():iii49-57.
2005: Dmitry A Rodionov; Inna Dubchak; Adam P Arkin; Eric J Alm; Mikhail S Gelfand
Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.
PLoS computational biology 2005;1(5):e55.
2005: Juan Pablo Fededa; Ezequiel Petrillo; Mikhail S Gelfand; Alexei D Neverov; Sebastián Kadener; Guadalupe Nogués; Federico Pelisch; Francisco E Baralle; Andrés F Muro; Alberto R Kornblihtt
A polar mechanism coordinates different regions of alternative splicing within a single gene.
Molecular cell 2005;19(3):393-404.
2005: Anna V Gerasimova; Mikhail S Gelfand
Evolution of the NadR regulon in Enterobacteriaceae.
Journal of bioinformatics and computational biology 2005;3(4):1007-19.
2005: Dmitry A Rodionov; Mikhail S Gelfand
Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling.
Trends in genetics : TIG 2005;21(7):385-9.
2005: Alexander Favorov; Mikhail S Gelfand; Anna V Gerasimova; Dmitry A Ravcheev; Andrey A Mironov; Vsevolod Makeev
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
Bioinformatics (Oxford, England) 2005;21(10):2240-5.
2005: Ekaterina A Kotelnikova; Vsevolod Makeev; Mikhail S Gelfand
Evolution of transcription factor DNA binding sites.
Gene 2005;347(2):255-63.
2005: Alexei D Neverov; Irena I Artamonova; Ramil N Nurtdinov; Dmitrij Frishman; Mikhail S Gelfand; Andrey A Mironov
Alternative splicing and protein function.
BMC bioinformatics 2005;6():266.
2005: Alexander V Seliverstov; Harald Putzer; Mikhail S Gelfand; Vassily A Lyubetsky
Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria.
BMC microbiology 2005;5():54.
2005: Nina J Oparina; Olga V Kalinina; Mikhail S Gelfand; Lev L Kisselev
Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications.
Nucleic acids research 2005;33(16):5226-34.
2004: Irena I Artamonova; Mikhail S Gelfand
Evolution of the exon-intron structure and alternative splicing of the MAGE-A family of cancer/testis antigens.
Journal of molecular evolution 2004;59(5):620-31.
2004: Dmitry A Rodionov; Mikhail S Gelfand; Nicole Hugouvieux-Cotte-Pattat
Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria.
Microbiology (Reading, England) 2004;150(Pt 11):3571-90.
2004: Pavel Novichkov; Marina V Omelchenko; Mikhail S Gelfand; Andrey A Mironov; Yuri I Wolf; Eugene V Koonin
Genome-wide molecular clock and horizontal gene transfer in bacterial evolution.
Journal of bacteriology 2004;186(19):6575-85.
2004: Nickolay V Zinin; Anna V Serkina; Mikhail S Gelfand; Alexei B Shevelev; Sergei P Sineoky
Gene cloning, expression and characterization of novel phytase from Obesumbacterium proteus.
FEMS microbiology letters 2004;236(2):283-90.
2004: Olga V Kalinina; Pavel Novichkov; Andrey A Mironov; Mikhail S Gelfand; Aleksandra B Rakhmaninova
SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins.
Nucleic acids research 2004;32(Web Server issue):W424-8.
2004: Alexey G Vitreschak; Elena V Lyubetskaya; Maxim A Shirshin; Mikhail S Gelfand; Vassily A Lyubetsky
Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis.
FEMS microbiology letters 2004;234(2):357-70.
2004: Marc N Offman; Ramil N Nurtdinov; Mikhail S Gelfand; Dmitrij Frishman
No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions.
BMC bioinformatics 2004;5():41.
2004: Olga V Kalinina; Andrey A Mironov; Mikhail S Gelfand; Aleksandra B Rakhmaninova
Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families.
Protein science : a publication of the Protein Society 2004;13(2):443-56.
2004: Dmitry A Rodionov; Inna Dubchak; Adam P Arkin; Eric J Alm; Mikhail S Gelfand
Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.
Genome biology 2004;5(11):R90.
2004: Dmitry A Rodionov; Alexey G Vitreschak; Andrey A Mironov; Mikhail S Gelfand
Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems.
Nucleic acids research 2004;32(11):3340-53.
2004: Alexey G Vitreschak; Dmitry A Rodionov; Andrey A Mironov; Mikhail S Gelfand
Riboswitches: the oldest mechanism for the regulation of gene expression?
Trends in genetics : TIG 2004;20(1):44-50.
2003: Dmitry A Rodionov; Alexey G Vitreschak; Andrey A Mironov; Mikhail S Gelfand
Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?
Nucleic acids research 2003;31(23):6748-57.
2003: Dmitry A Rodionov; Alexey G Vitreschak; Andrey A Mironov; Mikhail S Gelfand
Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes.
The Journal of biological chemistry 2003;278(42):41148-59.
2003: Alexey G Vitreschak; Dmitry A Rodionov; Andrey A Mironov; Mikhail S Gelfand
Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element.
RNA (New York, N.Y.) 2003;9(9):1084-97.
2003: Ekaterina M Panina; Andrey A Mironov; Mikhail S Gelfand
Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(17):9912-7.
2003: Zhongge Zhang; Jerome N Feige; Abraham B Chang; Iain J Anderson; Vadim M Brodianski; Alexei G Vitreschak; Mikhail S Gelfand; Milton H Saier
A transporter of Escherichia coli specific for L- and D-methionine is the prototype for a new family within the ABC superfamily.
Archives of microbiology 2003;180(2):88-100.
2003: Ramil N Nurtdinov; Irena I Artamonova; Andrey A Mironov; Mikhail S Gelfand
Low conservation of alternative splicing patterns in the human and mouse genomes.
Human molecular genetics 2003;12(11):1313-20.
2003: Ekaterina M Panina; Alexey G Vitreschak; Andrey A Mironov; Mikhail S Gelfand
Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria.
FEMS microbiology letters 2003;222(2):211-20.
2003: Roman A Sutormin; Aleksandra B Rakhmaninova; Mikhail S Gelfand
BATMAS30: amino acid substitution matrix for alignment of bacterial transporters.
Proteins 2003;51(1):85-95.
2003: Evgenia Kriventseva; Ina Koch; Rolf Apweiler; Martin Vingron; Peer Bork; Mikhail S Gelfand; Shamil Sunyaev
Increase of functional diversity by alternative splicing.
Trends in genetics : TIG 2003;19(3):124-8.
2003: Elizaveta A Permina; Mikhail S Gelfand
Heat shock (sigma32 and HrcA/CIRCE) regulons in beta-, gamma- and epsilon-proteobacteria.
Journal of molecular microbiology and biotechnology 2003;6(3-4):174-81.
2003: Olga V Kalinina; Vsevolod Makeev; Roman A Sutormin; Mikhail S Gelfand; Aleksandra B Rakhmaninova
The channel in transporters is formed by residues that are rare in transmembrane helices.
In silico biology 2003;3(1-2):197-204.
2003: Ludmila V Danilova; Vassily A Lyubetsky; Mikhail S Gelfand
An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation.
In silico biology 2003;3(1-2):33-47.
2003: Alexei E Kazakov; Olga Vassieva; Mikhail S Gelfand; Andrei Osterman; Ross Overbeek
Bioinformatics classification and functional analysis of PhoH homologs.
In silico biology 2003;3(1-2):3-15.
2003: Eleazar Eskin; Uri Keich; Mikhail S Gelfand; Pavel A Pevzner
Genome-wide analysis of bacterial promoter regions.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003;():29-40.
2002: Dmitry A Rodionov; Alexey G Vitreschak; Andrey A Mironov; Mikhail S Gelfand
Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms.
The Journal of biological chemistry 2002;277(50):48949-59.
2002: Dmitry A Rodionov; Andrey A Mironov; Mikhail S Gelfand
Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea.
Genome research 2002;12(10):1507-16.
2002: Leonid A Mirny; Mikhail S Gelfand
Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.
Journal of molecular biology 2002;321(1):7-20.
2002: Alexey G Vitreschak; Dmitry A Rodionov; Andrey A Mironov; Mikhail S Gelfand
Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.
Nucleic acids research 2002;30(14):3141-51.
2002: Elizaveta A Permina; Andrey A Mironov; Mikhail S Gelfand
Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements.
Gene 2002;293(1-2):133-40.
2002: Mikhail V Baytaluk; Mikhail S Gelfand; Andrey A Mironov
Exact mapping of prokaryotic gene starts.
Briefings in bioinformatics 2002;3(2):181-94.
2002: Leonid A Mirny; Mikhail S Gelfand
Structural analysis of conserved base pairs in protein-DNA complexes.
Nucleic acids research 2002;30(7):1704-11.
2002: Leonid A Mirny; Mikhail S Gelfand
Using orthologous and paralogous proteins to identify specificity determining residues.
Genome biology 2002;3(3):PREPRINT0002.
2002: Julia V Ponomarenko; Galina V Orlova; Anatoly S Frolov; Mikhail S Gelfand; Mikhail P Ponomarenko
SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data.
Nucleic acids research 2002;30(1):195-9.
2001: Olga N Laikova; Andrey A Mironov; Mikhail S Gelfand
Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria.
FEMS microbiology letters 2001;205(2):315-22.
2001: Dmitry A Rodionov; Andrey A Mironov; Mikhail S Gelfand
Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria.
FEMS microbiology letters 2001;205(2):305-14.
2001: Ekaterina M Panina; Andrey A Mironov; Mikhail S Gelfand
Comparative analysis of FUR regulons in gamma-proteobacteria.
Nucleic acids research 2001;29(24):5195-206.
2001: Pavel Novichkov; Mikhail S Gelfand; Andrey A Mironov
Gene recognition in eukaryotic DNA by comparison of genomic sequences.
Bioinformatics (Oxford, England) 2001;17(11):1011-8.
2001: Ekaterina M Panina; Alexey G Vitreschak; Andrey A Mironov; Mikhail S Gelfand
Regulation of aromatic amino acid biosynthesis in gamma-proteobacteria.
Journal of molecular microbiology and biotechnology 2001;3(4):529-43.
2001: Michael Brudno; Mikhail S Gelfand; SJ Spengler; M Zorn; Inna Dubchak; John G Conboy
Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing.
Nucleic acids research 2001;29(11):2338-48.
2001: Dmitry A Rodionov; Mikhail S Gelfand; Andrey A Mironov; Aleksandra B Rakhmaninova
Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria.
Journal of molecular microbiology and biotechnology 2001;3(2):319-24.
2001: Andrey A Mironov; Pavel Novichkov; Mikhail S Gelfand
Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors.
Bioinformatics (Oxford, England) 2001;17(1):13-5.
2000: Mikhail S Gelfand; Pavel Novichkov; E S Novichkova; Andrey A Mironov
Comparative analysis of regulatory patterns in bacterial genomes.
Briefings in bioinformatics 2000;1(4):357-71.
2000: Dmitry A Rodionov; Andrey A Mironov; Aleksandra B Rakhmaninova; Mikhail S Gelfand
Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria.
Molecular microbiology 2000;38(4):673-83.
2000: Mikhail S Gelfand; E V Koonin; Andrey A Mironov
Prediction of transcription regulatory sites in Archaea by a comparative genomic approach.
Nucleic acids research 2000;28(3):695-705.
2000: I Dralyuk; Michael Brudno; Mikhail S Gelfand; M Zorn; Inna Dubchak
ASDB: database of alternatively spliced genes.
Nucleic acids research 2000;28(1):296-7.
1999: A A Mironov; E V Koonin; Mikhail A Roytberg; Mikhail S Gelfand
Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes.
Nucleic acids research 1999;27(14):2981-9.
1999: Mikhail S Gelfand; Inna Dubchak; I Dralyuk; M Zorn
ASDB: database of alternatively spliced genes.
Nucleic acids research 1999;27(1):301-2.
1997: Mikhail S Gelfand; E V Koonin
Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes.
Nucleic acids research 1997;25(12):2430-9.
1996: Mikhail S Gelfand; A A Mironov; Pavel A Pevzner
Gene recognition via spliced sequence alignment.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(17):9061-6.
1996: Mikhail S Gelfand; L I Podolsky; T V Astakhova; Mikhail A Roytberg
Recognition of genes in human DNA sequences.
Journal of computational biology : a journal of computational molecular cell biology 1996;3(2):223-34.
1995: Mikhail S Gelfand
FANS-REF: a bibliography on statistics and functional analysis of nucleotide sequences.
Computer applications in the biosciences : CABIOS 1995;11(5):541.
1995: A R Rubinov; Mikhail S Gelfand
Reconstruction of a string from substring precedence data.
Journal of computational biology : a journal of computational molecular cell biology 1995;2(2):371-81.
1995: Mikhail S Gelfand
Prediction of function in DNA sequence analysis.
Journal of computational biology : a journal of computational molecular cell biology 1995;2(1):87-115.
1993: Mikhail S Gelfand
Genetic language: metaphore or analogy?
Bio Systems 1993;30(1-3):277-88.
1993: Mikhail S Gelfand; Mikhail A Roytberg
Prediction of the exon-intron structure by a dynamic programming approach.
Bio Systems 1993;30(1-3):173-82.
1992: Mikhail S Gelfand
Statistical analysis and prediction of the exonic structure of human genes.
Journal of molecular evolution 1992;35(3):239-52.
1992: Mikhail S Gelfand; C G Kozhukhin; Pavel A Pevzner
Extendable words in nucleotide sequences.
Computer applications in the biosciences : CABIOS 1992;8(2):129-35.