State Research Institute of Genetics And Selection of Industrial Microorganism



RECENT PUBLICATIONS


Полищук М.С., Хайнцель, А., Фаворов А.В., Макеев В.Ю.
Сравнительный анализ участков связывания белков-регуляторов транскрипции в раннем развитии Drosophila Melanogaster, определенных методом ChIP-chip, и вычислительно предсказанных кластеров сайтов связывания этих белков
Биофизика. 2008, 53(5):754-7. Russian.

Bogush VG, Sokolova OS, Davydova LI, Klinov DV, Sidoruk KV, Esipova NG, Neretina TV, Orchanskyi IA, Makeev VY, Tumanyan VG, Shaitan KV, Debabov VG, Kirpichnikov MP
A Novel Model System for Design of Biomaterials Based on Recombinant Analogs of Spider Silk Proteins.
J Neuroimmune Pharmacol. 2008 Oct 7.

Лифанов А.П., Власов П.К., Макеев В.Ю., Есипова Н.Г.
Нуклеосомный повтор и расположение экзонов и интронов в генах коллагенов типов I и VII
Биофизика. 2008, 53(3):524-8. Russian.

Рахманов С.В., Макеев В.Ю.
Использование невзаимодействующих проб в пространстве белковой структуры для построения статистических потенциалов межатомного взаимодействия
Биофизика, 2008; 53(3):389-96. Russian.

Britanova LV, Makeev VJ, Kuprash DV
In vitro selection of optimal RelB/p52 DNA-binding motifs.
Biochem Biophys Res Commun. 2008 Jan 18;365(3):583-8. Epub 2007 Nov 9.

2007


Boeva V, Clement J, Regnier M, Roytberg MA, Makeev VJ
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.
Algorithms Mol Biol. 2007 Oct 10;2:13.

Enikeeva FN, Kotelnikova EA, Gelfand MS, Makeev VJ
A model of evolution with constant selective pressure for regulatory DNA sites.
BMC Evol Biol. 2007 Jul 27;7:125.

Д.Г.Наумов
Структура и эволюция генов мальтазы-глюкоамилазы и сахаразы-изомальтазы млекопитающих.
Молекулярная биология, 2007; Том 41, №6: 1056-1068. Russian

Ravcheev DA, Gerasimova AV, Mironov AA, Gelfand MS
Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae).
BMC Genomics. 2007 Feb 21;8:54.

S.V. Rahmanov, V.J. Makeev
Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling.
BMC Structural Biology 2007, 7:19 (30 March 2007).

2006-...


A.E.Kazakov, E.A.Permina, O.V.Kalinina, M.S.Gelfand
Comparative genomics of regulation of heavy metal resistance in Eubacteria.
BMC Microbiology. 2006, 6: 49.

D.B.Malko, V.J.Makeev, A.A.Mironov, M.S.Gelfand
Evolution of the exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes.
Genome Research. 2006, 16: 505-509.

A.D.Neverov, A.A.Mironov, M.S.Gelfand
Similarity-based gene recognition.
Handbook of Computational Molecular Biology (Chapman & Hall/CRC), 2006, Chapter 2.

V.A. Boeva, M. Regnier, D. Papatsenko, V. Ju. Makeev
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression.
Bioinformatics. 2006, 22:676-84.

O.O. Favorova, A.V. Favorov, A.N. Boiko, T.V. Andreewski, M.A. Sudomoina, A.D. Alekseenkov, O.G. Kulakova, E.I. Gusev, G. Parmigiani, M.F. Ochs
Three allele combinations associated with multiple sclerosis.
BMC Med. Genet. 2006, 7:63.

L.V. Danilova, D.D. Pervouchine, A.V. Favorov, A.A. Mironov
RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA.
J Bioinform Comput Biol. 2006, 4(2):589-596.

S. V. Rahmanov and V. Y. Makeev
Atomic hydration potentials using Monte Carlo reference state advance protein solvation modeling.
FEBS Journal 2006, Vol. 273 (s1), 62.

A. Yuryev, Z. Mulyukov, E. Kotelnikova, S. Maslov, S. Egorov, A. Nikitin, N. Daraselia and I.Mazo
Automatic Pathway Building in Biological Association Networks.
BMC Bioinformatics. 2006, Mar 24;7:171.

Neverov A, Mironov A, Gelfand M
Splice alignment and similarity-based gene recognition.
Handbook of computational molecular biology, Aluru S, Chapman & Hall 2006, 2:1-18.

Е.О.Ермакова, Д.Б.Малько, М.С.Гельфанд
Эволюционные отличия альтернативных и постоянных белок-кодирующих участков альтернативно сплайсируемых генов Drosophila.
Биофизика. 2006, 51: 581-588.

Р.Н.Нуртдинов, А.Д.Неверов, Д.Б.Малько, И.А.Космодемьянский, Е.О.Ермакова, В.Е.Раменский, А.А.Миронов, М.С.Гельфанд
EDAS - база данных альтернативно сплайсированных генов человека.
Биофизика. 2006, 51: 589-592.

Е.Д.Ставровская, В.Ю.Макеев, А.А.Миронов
CLUSTERTREE-RS: алгоритм кластеризации регуляторных сигналов с помощью бинарного дерева.
Молекулярная биология. 2006, 40: 524-532.

Р.А.Сутормин, А.М.Миронов
Вероятностный метод предсказания трансмембранных участков по множественным выравниваниям аминокислотных последовательностей.
Молекулярная биология. 2006, 40: 541-545.

В.А. Боева, М.В. Фридман, В.Ю. Макеев
Эволюция микро- и мнинисателлитов в геноме человека.
Биофизика. 2006, 51:650-655.

Д.Г.Наумов
Филогенетический анализ семейства белков-гомологов.
Zbio (http://zbio.net/bio/001/003.html). 2006, V.1. Art.3.

Kotelnikova E., Makeev V., Gelfand M.
Evolution of transcription factor DNA binding sites.
BGene. 2005, 347 (2): 255-263.

Gelfand MS, Gerasimova AV, Kotelnikova EA, Laikova ON, Makeev VY, Mironov AA, Panina EM, Ravcheev DA, Rodionov DA, Vitreschak AG
Comparative genomics and evolution of bacterial regulatory systems.
Bioinformatics of Genome Regulation and Structure II (Springer Science+Business Media, Inc.) P. 111-119 (2005)
Eds. Kolchanov N. and Hofestaedt R.

Favorov AV,, Andreewski TV, Sudomoina MA, Favorova OO, Parmigiani G, Ochs MF.
A markov chain monte carlo technique for identification of combinations of allelic variants underlying complex diseases in humans.
Genetics. 2005 Dec;171(4):2113-21. Epub 2005 Aug 22.

Fededa JP, Petrillo E, Gelfand MS, Neverov AD, Kadener S, Nogues G, Pelisch F, Baralle FE, Muro A, Kornblihtt AR.
A polar mechanism coordinates different regions of alternative splicing within a single gene.
Molecular Cell. 2005, 19 (3): 393-404.

Rodionov DA, Gelfand MS.
Identification of a Bacterial Regulatory System for Ribonucleotide Reductases by Phylogenetic Profiling.
Trends. Genet. 2005, 21 (7): 385-389.

Favorov AV, Gelfand MS, Gerasimova AV, Ravcheev DA, Mironov AA, Makeev VYu.
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
Bioinformatics. 2005, 21(10):2240-5.

Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z.
Assessing computational tools for the discovery of transcription factor binding sites.
Nat Biotechnol. 2005, 23(1):137-44.

D.G. Naumoff
GH97 is a new family of glycoside hydrolases, which is related to the α-galactosidase superfamily.
BMC Genomics. 2005, V.6, Art.112.
Abstract PDF

D.G. Naumoff, Y. Xu, V. Stalon, N. Glansdorff, and B. Labedan.
The difficulty of annotating genes: the case of putrescine carbamoyltransferase.
Microbiology. 2004, V.150, N.12, P.3908-3911.

D.A.Rodionov, A.G.Vitreschak, A.A.Mironov, M.S.Gelfand.
Comparative genomics of the regulation of methionine metabolism in Gram-positive bacteria.
Nucleic Acids Res. 2004, V.32, N.11, P.3340-3353.

O.V.Kalinina, P.S.Novichkov, A.A.Mironov, M.S.Gelfand, A.B.Rakhmaninova.
SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins.
Nucleic Acids Res. 2004, V.32, Web server issue, P.W424-W428.

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. 2004, V.150, N.11, P.3571-3590.

O.V.Kalinina, A.A.Mironov, M.S.Gelfand, A.B.Rakhmaninova.
Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families.
Protein Science. 2004, V.13, N.2, P.443-456.

P.S.Novichkov, M.V.Omelchenko, M.S.Gelfand, A.A.Mironov, Y.I.Wolf, E.V.Koonin.
Genome-wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution.
J.Bacteriology. 2004, V.186, N.19, P.6575-6585.

Dmitry A Rodionov, Inna Dubchak, Adam P Arkin, Eric Alm and Mikhail S Gelfand.
Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.
Genome Biol. 2004, V.5, N.11, P.R90.

A.G.Vitreschak, E.V.Lyubetskaya, M.A.Shirshin, M.S.Gelfand, V.A.Lyubetsky.
Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis.
FEMS Microbiol. Lett. 2004, V.234, N.2, P.357-70.

N.V.Zinin, A.V.Serkina, M.S.Gelfand, A.B.Shevelev, S.P.Sineokii.
Gene cloning, expression and characterization of novel phytase from Obesumbacterium proteus.
FEMS Microbiol. Lett. 2004, V.236, N.2, P.283-290.

M.Offman, R.N.Nurtdinov, M.S.Gelfand, D.Frishman.
No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions.
BMC Bioinformatics. 2004, V.5, P.41.

D.G. Naumoff, Y. Xu, N. Glansdorff, and B. Labedan.
Retrieving sequences of enzymes experimentally characterized but erroneously annotated: the case of the putrescine carbamoyltransferase.
BMC Genomics. 2004, V.5, Art.52.

Kattenhorn LM, Mills R, Wagner M, Lomsadze A, Makeev V, Borodovsky M, Ploegh HL, Kessler BM.
Identification of proteins associated with murine cytomegalovirus virions.
J Virol. 2004, Oct;78(20):11187-97.

Наумов Д.Г.
Филогенетический анализ α-галактозидаз семейства GH27.
Молекулярная биология. 2004, т. 38, №3, стр. 463-476.

Pons T., Naumoff D.G., Martinez-Fleites C., and Hernandez L.
Three acidic residues at the active site in the β- propeller architecture for the glycoside hydrolase families 32, 43, 62, and 68.
Proteins: Structure, Function, and Bioinformatics, 2004, V. 54, P. 424-432.
Supplemented materials

Labedan B., Xu Y., Naumoff D.G., and Glansdorff N.
Using quaternary structures to assess the evolutionary history of proteins: the case of the aspartate carbamoyltransferase.
Molecular Biology and Evolution, 2004, V. 21, P. 364-373.

Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS.
Riboswitches: the oldest mechanism for the regulation of gene expression?
Trends Genet. 2004;20(1):44-50.

А.А.Миронов, М.С.Гельфанд.
Предсказание и компьютернай анализ экзон-интронной структуры генов человека.
Молекулярная биология. 2004;38(1):82-91.