Mikhail S Gelfand

Mikhail S Gelfand

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

Biochim Biophys Acta Proteins Proteom 2019 11 19;1867(11):140253. Epub 2019 Jul 19.

A.A.Kharkevich Institute of Information Transmission Problems, Moscow 127051, Russia; Skolkovo Institute of Science and Technology, Moscow 121205, Russia; Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117997, Russia. Electronic address:

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http://dx.doi.org/10.1016/j.bbapap.2019.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6745255PMC
November 2019

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

BMC Evol Biol 2019 03 27;19(1):83. Epub 2019 Mar 27.

Kharkevich Institute for Information Transmission Problems, 19, Bolshoy Karetny per., Moscow, 127051, Russia.

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http://dx.doi.org/10.1186/s12862-019-1403-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437910PMC
March 2019

Comparative Genomic Analysis of the Regulation of Aromatic Metabolism in Betaproteobacteria.

Front Microbiol 2019 29;10:642. Epub 2019 Mar 29.

Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia.

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http://dx.doi.org/10.3389/fmicb.2019.00642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449761PMC
March 2019

Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.

BMC Genomics 2018 Dec 27;19(1):965. Epub 2018 Dec 27.

Kharkevich Institute for Information Transmission Problems, Moscow, Russia.

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http://dx.doi.org/10.1186/s12864-018-5245-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307245PMC
December 2018

Comparative genomic analysis of fungal TPP-riboswitches.

Fungal Genet Biol 2018 05 13;114:34-41. Epub 2018 Mar 13.

A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoy Karetny per. 19, Moscow 127051, Russia; Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Vorobievy Gory 1-73, Moscow 119991, Russia,; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia; Faculty of Computer Science, Higher School of Economics, Kochnovsky pr. 3, Moscow 125319, Russia.

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http://dx.doi.org/10.1016/j.fgb.2018.03.004DOI Listing
May 2018

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

RNA 2018 04 23;24(4):585-596. Epub 2018 Jan 23.

Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.

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http://dx.doi.org/10.1261/rna.064931.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855957PMC
April 2018

Neanderthal and Denisovan ancestry in Papuans: A functional study.

J Bioinform Comput Biol 2018 04;16(2):1840011

† Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute for Science and Technology, Moscow, Russia.

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http://dx.doi.org/10.1142/S0219720018400115DOI Listing
April 2018

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

Front Microbiol 2018 12;9:428. Epub 2018 Mar 12.

A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (RAS), Moscow, Russia.

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http://dx.doi.org/10.3389/fmicb.2018.00428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5857598PMC
March 2018

Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci.

Biol Direct 2017 Nov 25;12(1):28. Epub 2017 Nov 25.

A.A.Kharkevich Institute for Information Transmission Problems, RAS, Bolshoy Karetny per. 19, Moscow, 127051, Russia.

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http://dx.doi.org/10.1186/s13062-017-0200-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702140PMC
November 2017

Evolution of the Exon-Intron Structure in Ciliate Genomes.

PLoS One 2016 7;11(9):e0161476. Epub 2016 Sep 7.

A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoy Karetny per. 19, Moscow, 127994, Russia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161476PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014332PMC
August 2017

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

Front Microbiol 2016 26;7:1343. Epub 2016 Aug 26.

Research and Training Center on Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia; Faculty of Bioengineering and Bioinformatics, Moscow State UniversityMoscow, Russia; Skolkovo Institute of Science and TechnologySkolkovo, Russia; Faculty of Computer Science, Higher School of EconomicsMoscow, Russia.

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http://dx.doi.org/10.3389/fmicb.2016.01343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999443PMC
September 2016

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

PLoS One 2016;11(9):e0162681. Epub 2016 Sep 30.

A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162681PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045206PMC
September 2016

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

PLoS One 2015 7;10(7):e0132618. Epub 2015 Jul 7.

Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132618PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494728PMC
April 2016

Detection of homologous recombination in closely related strains.

J Bioinform Comput Biol 2016 04 14;14(2):1641001. Epub 2016 Jan 14.

* A. A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia.

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http://dx.doi.org/10.1142/S0219720016410018DOI Listing
April 2016

History of chromosome rearrangements reflects the spatial organization of yeast chromosomes.

J Bioinform Comput Biol 2016 04 28;14(2):1641002. Epub 2016 Jan 28.

3 Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1142/S021972001641002XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882907PMC
April 2016

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

Genome Biol Evol 2016 Mar 23;8(3):840-50. Epub 2016 Mar 23.

CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, China Skolkovo Institute for Science and Technology, Skolkovo, Russia Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany School of Life Science and Technology, ShanghaiTech University, Shanghai, China

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http://dx.doi.org/10.1093/gbe/evw038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824147PMC
March 2016

Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria.

PLoS One 2014 20;9(11):e113714. Epub 2014 Nov 20.

A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113714PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239095PMC
December 2015

Horizontal gene transfer and genome evolution in Methanosarcina.

BMC Evol Biol 2015 Jun 5;15:102. Epub 2015 Jun 5.

A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia.

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http://dx.doi.org/10.1186/s12862-015-0393-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455057PMC
June 2015

Dynasty Foundation: Russian science loses to politics.

Nature 2015 Jun;522(7557):419

Russian Academy of Sciences, Moscow, Russia.

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http://dx.doi.org/10.1038/522419aDOI Listing
June 2015

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

Front Microbiol 2014 11;5:294. Epub 2014 Jun 11.

Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia ; Department of Bioinformatics, Sanford-Burnham Medical Research Institute La Jolla, CA, USA.

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http://journal.frontiersin.org/article/10.3389/fmicb.2014.00
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http://dx.doi.org/10.3389/fmicb.2014.00294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4052901PMC
June 2014

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

Genome Biol Evol 2014 May 14;6(6):1437-47. Epub 2014 May 14.

Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, RussiaLife Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan.

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http://dx.doi.org/10.1093/gbe/evu100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079205PMC
May 2014

Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans.

Nat Commun 2014 Apr 1;5:3584. Epub 2014 Apr 1.

1] CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China [2] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.

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http://www.nature.com/articles/ncomms4584
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http://dx.doi.org/10.1038/ncomms4584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988804PMC
April 2014

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

PLoS Genet 2013 3;9(10):e1003756. Epub 2013 Oct 3.

Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France ; Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France.

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http://dx.plos.org/10.1371/journal.pgen.1003756
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http://dx.doi.org/10.1371/journal.pgen.1003756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789822PMC
March 2014

Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs.

BMC Genomics 2014 Mar 17;15:202. Epub 2014 Mar 17.

N, I, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str, 3, Moscow 119991, Russia.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-15-202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004331PMC
March 2014

Sequence-derived structural features driving proteolytic processing.

Proteomics 2014 Jan 11;14(1):42-50. Epub 2013 Dec 11.

Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia.

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http://dx.doi.org/10.1002/pmic.201300416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926948PMC
January 2014

Evolution of regulatory motifs of bacterial transcription factors.

In Silico Biol 2010 ;10(3):163-83

Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia.

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http://dx.doi.org/10.3233/ISB-2010-0425DOI Listing
September 2013

Functional implications of splicing polymorphisms in the human genome.

Hum Mol Genet 2013 Sep 2;22(17):3449-59. Epub 2013 May 2.

Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow 127994, Russia.

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http://dx.doi.org/10.1093/hmg/ddt200DOI Listing
September 2013

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

J Bacteriol 2013 Jun 12;195(12):2786-92. Epub 2013 Apr 12.

NI Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.

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http://dx.doi.org/10.1128/JB.02285-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697250PMC
June 2013

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

PLoS One 2012 24;7(9):e44194. Epub 2012 Sep 24.

AA Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044194PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3454398PMC
March 2013

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

Nucleic Acids Res 2013 Jan 2;41(2):790-803. Epub 2012 Dec 2.

Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gks1184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553997PMC
January 2013

Glutamine versus ammonia utilization in the NAD synthetase family.

PLoS One 2012 15;7(6):e39115. Epub 2012 Jun 15.

Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039115PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376133PMC
December 2012

Evolution of transcriptional regulation in closely related bacteria.

BMC Evol Biol 2012 Oct 6;12:200. Epub 2012 Oct 6.

Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, Moscow 127994, Russia.

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http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2148-12-200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3735044PMC
October 2012

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

PLoS One 2012 4;7(4):e33947. Epub 2012 Apr 4.

Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033947PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319547PMC
August 2012

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

BMC Bioinformatics 2012 Apr 19;13 Suppl 6:S4. Epub 2012 Apr 19.

Institute for Information Transmission Problems, Russian Academy of Sciences, 19 Bolshoy Karetny per., Moscow, 127994, Russia.

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http://dx.doi.org/10.1186/1471-2105-13-S6-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358657PMC
April 2012

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

RNA 2012 Jan 29;18(1):1-15. Epub 2011 Nov 29.

Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119992, GSP-2 Russia.

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http://dx.doi.org/10.1261/rna.029249.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261731PMC
January 2012

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

J Bacteriol 2011 Aug 27;193(15):3956-63. Epub 2011 May 27.

State Research Institute of Genetics and Selection of Industrial Microorganisms (GosNIIGenetika), Moscow, Russia.

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http://dx.doi.org/10.1128/JB.00277-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147527PMC
August 2011

Comparative genomics of the dormancy regulons in mycobacteria.

J Bacteriol 2011 Jul 20;193(14):3446-52. Epub 2011 May 20.

Energy Bioscience Institute, University of California, Berkeley, California 94720, USA.

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http://jb.asm.org/cgi/doi/10.1128/JB.00179-11
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http://dx.doi.org/10.1128/JB.00179-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133309PMC
July 2011

Evolutionary patterns of phosphorylated serines.

Biol Direct 2011 Feb 9;6. Epub 2011 Feb 9.

Institute for Information Transmission Problems (Kharkevich Institute) RAS, Bolshoi Karetny pereulok 19, Moscow, 127994, Russia.

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http://biologydirect.biomedcentral.com/articles/10.1186/1745
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http://dx.doi.org/10.1186/1745-6150-6-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044110PMC
February 2011

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

BMC Genomics 2011 Jan 13;12:30. Epub 2011 Jan 13.

Department of Evolutionary Biochemistry, AN Belozersky Institute of Physico-Chemical Biology, MV Lomonosov Moscow State University, Moscow, Russia.

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http://dx.doi.org/10.1186/1471-2164-12-30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3027159PMC
January 2011

Large-scale identification and analysis of C-proteins.

Methods Mol Biol 2010 ;674:269-82

Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia.

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http://dx.doi.org/10.1007/978-1-60761-854-6_17DOI Listing
December 2010

Restriction-modification systems and bacteriophage invasion: who wins?

J Theor Biol 2010 Oct 13;266(4):550-9. Epub 2010 Jul 13.

Institute for Information Transmission Problems, the Kharkevich Institute of RAS, Bolshoi Karetny pereulok 19, GSP-4, Moscow 127994, Russia.

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http://linkinghub.elsevier.com/retrieve/pii/S002251931000349
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http://dx.doi.org/10.1016/j.jtbi.2010.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953645PMC
October 2010

Asymmetric and non-uniform evolution of recently duplicated human genes.

Biol Direct 2010 Sep 8;5:54. Epub 2010 Sep 8.

M. V. Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Vorobyevy Gory 1-73, Moscow, 119992, Russia.

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http://dx.doi.org/10.1186/1745-6150-5-54DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2942815PMC
September 2010

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

Appl Environ Microbiol 2010 Apr 29;76(7):2136-44. Epub 2010 Jan 29.

N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, ul. Gubkina 3, Moscow 119991, Russia.

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http://dx.doi.org/10.1128/AEM.01985-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849227PMC
April 2010

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

Nucleic Acids Res 2010 Jan 1;38(Database issue):D111-8. Epub 2009 Nov 1.

Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, State Scientific Center GosNIIGenetika, Moscow 117545, Russia.

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http://dx.doi.org/10.1093/nar/gkp894DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808921PMC
January 2010

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

Nucleic Acids Res 2009 Aug 22;37(14):4533-44. Epub 2009 May 22.

Center for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003 Barcelona, Spain.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkp407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2724269PMC
August 2009

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

BMC Evol Biol 2009 Jun 26;9:142. Epub 2009 Jun 26.

Departament of Bioengineering and Bioinformatics, M V Lomonosov Moscow State University, Moscow, Russia.

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http://dx.doi.org/10.1186/1471-2148-9-142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711938PMC
June 2009

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

Nucleic Acids Res 2009 May 5;37(8):2493-503. Epub 2009 Mar 5.

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1093/nar/gkp079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677863PMC
May 2009

Systematic prediction of control proteins and their DNA binding sites.

Nucleic Acids Res 2009 Feb 4;37(2):441-51. Epub 2008 Dec 4.

Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia.

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http://dx.doi.org/10.1093/nar/gkn931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632904PMC
February 2009

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization.

BMC Genomics 2009 Feb 10;10:78. Epub 2009 Feb 10.

Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, NE 68588-0664, USA.

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http://dx.doi.org/10.1186/1471-2164-10-78DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667541PMC
February 2009

Identification of replication origins in prokaryotic genomes.

Brief Bioinform 2008 Sep 26;9(5):376-91. Epub 2008 Jul 26.

Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetny pereulok, 19, Moscow, 127994, Russia.

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https://academic.oup.com/bib/article/267693/Identification
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http://dx.doi.org/10.1093/bib/bbn031DOI Listing
September 2008

Some alphabets easily beat Russian letter count.

Nature 2008 Aug;454(7205):691

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http://www.nature.com/articles/454691a
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http://dx.doi.org/10.1038/454691aDOI Listing
August 2008

Positive selection in alternatively spliced exons of human genes.

Am J Hum Genet 2008 Jul 19;83(1):94-8. Epub 2008 Jun 19.

Bioinformatics and Systems Biology Lab, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.

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http://dx.doi.org/10.1016/j.ajhg.2008.05.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2443848PMC
July 2008

Comparative genomic analysis of T-box regulatory systems in bacteria.

RNA 2008 Apr;14(4):717-35

Institute for Information Transmission Problems (The Kharkevich Institute), Russian Academy of Sciences, Moscow 127994, Russia.

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http://www.rnajournal.org/cgi/doi/10.1261/rna.819308
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http://dx.doi.org/10.1261/rna.819308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2271356PMC
April 2008

Computational analysis of splicing errors and mutations in human transcripts.

BMC Genomics 2008 Jan 14;9:13. Epub 2008 Jan 14.

Institute for Information Transmission Problems (the Kharkevich Institute) RAS, Bolshoi Karetny pereulok 19, Moscow, 127994, Russia.

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http://dx.doi.org/10.1186/1471-2164-9-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2234086PMC
January 2008

Conserved and species-specific alternative splicing in mammalian genomes.

BMC Evol Biol 2007 Dec 22;7:249. Epub 2007 Dec 22.

Faculty of Bioengineering and Bioinformatics, M,V, Lomonosov Moscow State University, Vorbyevy Gory 1-73, Moscow, 119992, Russia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2231371PMC
December 2007

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

FEMS Microbiol Lett 2007 Nov;276(2):207-15

Institute for Information Transmission Problems, RAS, Moscow, Russia.

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http://dx.doi.org/10.1111/j.1574-6968.2007.00934.xDOI Listing
November 2007

Abundance and functional diversity of riboswitches in microbial communities.

BMC Genomics 2007 Oct 1;8:347. Epub 2007 Oct 1.

Institute for Information Transmission Problems (the Kharkevich Institute) RAS, Bolshoi Karetnyi per, 19, Moscow, 127994, Russia.

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http://dx.doi.org/10.1186/1471-2164-8-347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211319PMC
October 2007

Overlapping alternative donor splice sites in the human genome.

J Bioinform Comput Biol 2007 Oct;5(5):991-1004

Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetny per. 19, 127994 Moscow, Russia.

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http://dx.doi.org/10.1142/s0219720007003089DOI Listing
October 2007

Low-molecular-weight post-translationally modified microcins.

Mol Microbiol 2007 Sep 17;65(6):1380-94. Epub 2007 Aug 17.

Waksman Institute for Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1111/j.1365-2958.2007.05874.xDOI Listing
September 2007

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

Chem Rev 2007 Aug 24;107(8):3407-30. Epub 2007 Jul 24.

Group of Bioinformatics, Vavilov Institute of General Genetics, RAS, Gubkina 3, Moscow 119991, Russia.

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http://dx.doi.org/10.1021/cr068304cDOI Listing
August 2007

How gene order is influenced by the biophysics of transcription regulation.

Proc Natl Acad Sci U S A 2007 Aug 20;104(35):13948-53. Epub 2007 Aug 20.

Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0700672104
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1955771PMC
August 2007

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

BMC Evol Biol 2007 Jul 27;7:125. Epub 2007 Jul 27.

Institute for Information Transmission Problems (the Kharkevich Institute) of RAS, Bolshoi Karetny pereulok, 19, GSP-4, Moscow, 127994, Russia.

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http://dx.doi.org/10.1186/1471-2148-7-125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1978210PMC
July 2007

Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane.

Appl Environ Microbiol 2007 May 16;73(10):3440-5. Epub 2007 Mar 16.

Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.

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http://dx.doi.org/10.1128/AEM.02831-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1907119PMC
May 2007

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

BMC Evol Biol 2007 Feb 12;7:17. Epub 2007 Feb 12.

Institute for Information Transmission Problems RAS, Bolshoi Karetny pereulok 19, Moscow 127994, Russia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1803777PMC
February 2007