CURRICULUM VITAE

 

Igor B. Rogozin

 

January 2015

 

ADDRESS: NCBI/NLM/NIH, 8600 Rockville Pike, Bldg. 38A/room 5N505A, Bethesda, MD 20894, USA

STATUS: Staff Scientist

E-mail: rogozin@ncbi.nlm.nih.gov, rogozin@bionet.nsc.ru, igor.rogozin@itb.cnr.it

Office tel.: 301-594-4271

Fax: 301-435-7793

URL: wwwmgs.bionet.nsc.ru/mgs/info/rogozin/

 

 

EMPLOYMENT

 

- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA (www.ncbi.nlm.nih.gov)

2004 - Present Staff Scientist

2000 - 2003 Research Fellow

 

- Foundation for Advanced Education in the Science, National Institutes of Health (FAES NIH) (www.faes.org)

2014 - Present Adjunct Lecturer

 

- Johns Hopkins University, Montgomery County Campus, 9601 Medical Center Drive, Rockville, MD 21850 (www.jhu.edu/mcc/)

2007 - Present Adjunct Lecturer

 

- Pennsylvania State University, Institute of Molecular Evolutionary Genetics, 311 Mueller Laboratory, University Park, PA 16802, USA (www.bio.psu.edu)

1998 - 2000 Visiting Scientist (supervisor M. Nei)

 

- Istituto di Technologie Biomediche Avanzate, Consiglio Nazionale Della Ricerche, via Ampere 56, 20131 Milano MI, Italy (www.itb.cnr.it)

1996-1998 Visiting Scientist

 

- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Lavrentiev Av., 10., Novosibirsk 630090 (www.bionet.nsc.ru)

1997 - 2003 Adjunct Senior Researcher, Laboratory of Molecular Mechanisms of Mutagenesis

1991 - 1997 Senior Researcher, Department of Theoretical Biology

1987 - 1991 Research Associate, Department of Theoretical Biology

1985 - 1987 Programmer, Department of Theoretical Biology

 

 

EDUCATION

 

1990 Ph.D. (Biology, Applications of computers, mathematical methods and modeling in biology), Novosibirsk State University and Novosibirsk Institute of Organic Chemistry, Siberian Branch, USSR Academy of Sciences. Thesis: Theoretical analysis of nucleotide context influence on mutagenesis (Advisors: V.V.Solovyev, N.A.Kolchanov)

 

1985 B.S./M.S. (Biology, special training in mathematical biology), Department of Cytology and Genetics, Novosibirsk State University, Novosibirsk 630090, Russia.

 

1970-1980 School N 130, Ychenikh St. 10, Novosibirsk 630090, Russia.

 

 

PRINCIPAL RESEARCH DIRECTIONS

 

Comparative analysis of completely sequenced genomes, phylogenetic analysis of sequences, theoretical analysis of mutagenesis, genome biology of carcinogenesis, computational analysis of functional regions and signals in biological sequences, comparative genomics of introns, computational analysis of mobile elements, comparative genomics of defense/offense systems in pro- and eukaryotes.

 

 

EDITORIAL BOARDS

 

2015-Present BMC Genomics, Section Editor “Comparative and evolutionary genomics”, BioMed

Central, London (www.biomedcentral.com/bmcgenomics)

2010-2014 BMC Genomics, Associate Editor and Deputy Section Editor, BioMed Central,

London (www.biomedcentral.com/bmcgenomics)

2005-Present Gene, Associate Editor, Elsevier, Amsterdam (www.journals.elsevier.com/gene/)

1999-Present Briefings in Bioinformatics, Editorial Board member, Oxford Univ. Press, Oxford

(bib.oxfordjournals.org/)

2013-Present Biology Direct, Editorial Board member, BioMed Central, London

(www.biology-direct.com/)

2013-Present PLoS ONE, Editorial Board member, PLoS, San Francisco (www.plosone.org/)

2014-Present The Journal of Human Transcriptome, Editorial Board member, Informa Healthcare,

London (www.informahealthcare.com/loi/jht)

2014-Present Plant Gene, Associate Editor, Elsevier, Amsterdam

(www.journals.elsevier.com/plant-gene/)

2012-Present Dataset Papers in Biology, Editorial Board member, the Genomics section,

Hindawi, New York (www.datasets.com/journals/biology/)

2012-Present Genomics Discovery, Editorial Board member, Herbert Open Access Journals

“HOAJ”, (www.hoajonline.com/genomics)

2012-Present Open Journal of Genomics, Editorial Board member, Ross Science Publishers

(www.rossscience.org/ojgen)

2012-Present The Open Access Journal of Science and Technology (OAJoST), Editorial Board

member, Agial Publishing House, (www.oajost.com/)

2011-Present Frontiers in Bioinformatics and Computational Biology, Review Editorial Board

member (www.frontiersin.org)

2011-Present ISRN Biomathematics, Editorial Board member, Hindawi, New York

(www.hindawi.com/isrn/biomathematics/)

2011-Present Journal of Proteome Science and Computational Biology (JPSCB), Herbert Open

Access Journals “HOAJ”, (www.hoajonline.com/Journal-of-Proteome-

Science-and-Computational.html)

2013-2014 Genetics Research International, Guest Editor, special issue "Genetics in Genomic

Era", Hindawi, New York (www.hindawi.com/journals/gri/).

2009-2010 Advances in Bioinformatics, Guest Editor, special issue "Genome Evolution",

Hindawi, New York (www.hindawi.com/journals/abi/).

 

 

HONORS AND AWARDS

 

2010 - NLM Honor Award, National Library of Medicine, National Institutes of Health.

 

2007 - BioMed Central’s Hot 100 authors, the Hot 100 authors list recognizes authors who have contributed most to the success of BioMed Central’s open access journals (December 2007, www.biomedcentral.com/profiles/hot100/)

 

2005 - The Best Paper Award, RECOMB 2005 International Workshop - Comparative Genomics (Dublin, Ireland, September 18-20).

 

1996 - D.K. Belyaev Award, Siberian Branch of the Russian Academy of Science, Novosibirsk.

 

1990-1998 - Visiting Professor, Istituto di Technologie Biomediche Avanzate, Consiglio Nazionale Della Ricerche, via Ampere 56, 20131 Milano MI, Italy, October-November 1990, November-December 1991, June-September 1992, April-May 1993, September-December 1993, May-August 1994, September-December 1995, June 1996 - May 1997, September 1997 - March 1998.

 

 

SUPERVISING EXPERIENCE

 

2001-Present Supervision of four postdocs, two programmers, two IRTA postbacs, one

undergraduate student, and five high school summer students.

National Center for Biotechnology Information, Bethesda, USA.

1993-1999           Supervision of one postdoc, two PhD students and five MS students.

Institute of Cytology and Genetics, Novosibirsk, Russia.

 

 

TEACHING EXPERIENCE

 

2015-Present Evolutionary Genomics and Computational Biology, Foundation for Advanced

Education in the Science (FAES NIH)

2014-Present Theoretical and Applied Bioinformatics, Foundation for Advanced Education in the

Science (FAES NIH)

2013-Present Algorithms for Bioinformatics, Johns Hopkins University, on-line course

2008-2011 Principles of Computational Biology, Johns Hopkins University, Montgomery County

Campus

2000-2003 Brief Introduction to Phylogenetic Analysis, National Center for Biotechnology

Information

1990 Evolutionary Genetics, Novosibirsk State University

1988-1989 Mathematical Biology, Novosibirsk State University

1987-1989 Computational Methods in Biology, Institute of Cytology and Genetics, Novosibirsk

 

 

PROJECTS

 

2012-2014 Collaborator. Characterization of lamprey B cells and antibodies. National Cancer Institute grant R01 GM100151 (Principal Investigator M.D. Cooper, Emory University, Atlanta, GA).

2008-2013 Collaborator. Control of genome stability by replicative DNA polymerases. National Cancer Institute grant 1R01 CA129925-01A2 (Principal Investigator Y.I. Pavlov, UNMC, Omaha, NE).

2002-2004 Co-Principal Investigator. Molecular mechanisms of genomic instability: computational and experimental analysis of highly mutable sites. Scientific project of the Russian Fund of Basic Research, Grant N 02-04-48342.

1999-2001 Principal Investigator. Computer and experimental analysis of hotspots of mutations and recombinations. Scientific project of the Russian Fund of Basic Research, Grant N 99-04-49535.

1996-1998 Principal Investigator. Computer analysis of molecular mechanisms of mutations and recombinations. Scientific project of the Russian Fund of Basic Research, Grant N 96-04-49957.

1996-1998 Principal Investigator. Contribution of patterns of spontaneous mutations to evolutionary variability of genomes. Scientific project of the Russian Academy of Sciences "Frontiers in Genetics", Grant N 5.1595.

 

 

GRANT REVIEW PANEL

 

2014-Present The European Research Council (erc.europa.eu)

2014-Present W. M. Keck Foundation (www.wmkeck.org)

2011-Present The Fund for Development of the Center for Elaboration and Commercialization of

New Technologies (the Skolkovo Foundation, Russia) (community.sk.ru)

2011-Present The “Dynasty” Foundation (www.dynastyfdn.com)

2006-Present The Research Grants Council (RGC) of Hong Kong (cerg1.ugc.edu.hk)

2002-2003 The Russian Fund of Basic Research (www.rfbr.ru/rffi/eng/about)

 

 

INVITED TALKS

 

2014 - Emory University, Atlanta, Georgia (January 21), “Use of mutable motifs in cancer and immunology”.

2013 - Georgia Tech, Atlanta, Georgia (June 28), “Evolutionary genomics of long non-coding RNA genes in mammals”.

2013 - Plant and Animal Genome XXI, San Diego, CA, USA (January 15), “The vast, conserved mammalian lincRNome”.

2012 - Dartmouth College, Biology Department, Hanover, NH, USA (September 28), “The vast, conserved mammalian lincRNome”.

2011 - The 6th International Conference on Genomics, ShenZhen, China (November 12), “Evolution of long non-coding RNA genes in mammals”.

2011 - National Eye Institute NIH, Bethesda, MD, USA (July 20), “Evolutionary genomics of lamprey: implications to immune system and visual cycle”.

2011 - Cleveland Clinic, Cleveland, OH, USA (April 20), “Evolutionary genomics of eukaryotes and origin of introns: the end of the debate”.

2011 - Plant and Animal Genome XVIII, San Diego, CA, USA (January 18), “Evolution of long non-coding RNAs in mammals”.

2010 - Seventh International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia (June 20), “Somatic diversification of adaptive immune receptors in jawless vertebrates”.

2009 - University of Nebraska at Omaha, Omaha, NE, USA (February 16), “Evolutionary genomics of eukaryotes: rare genomic changes”.

2008 - Loyola University, Chicago, IL, USA (October 14), “Two strikingly different modes of antigen recognition in jawless and jawed vertebrates”.

2008 - J. Craig Venter Institute, Rockville, MD, USA (July 16), ”Diversity and function of adaptive immune receptors in jawless vertebrates”.

2008 - Sixth International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia (June 22), “Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series”.

2007 - Gordon Research Conference “Bioinformatics: the interface of computation and experiment”, Proctor Academy, NH, USA (July 19), “Origin of introns: the end of the debate?”.

2007 - Institute of Cytology and Genetics, Siberian Branch RAS, Novosibirsk, Russia (March 16), “Mystery of eukaryotic introns: RNA world remnants or recently gained molecular parasites?”.

2006 - Insubria International Summer School “Breast Cancer and Melanoma: Biology, Diagnosis and Therapy”, Varese, Italy (September 15), “Computational analysis of somatic mutations in human cancers”.

2005 - Bioinformatics Interest Group (BIIG) Series, University of Nebraska at Omaha, Omaha, NE, USA (April 28), “Evolution of spliceosomal introns: insights from comparative genomics”.

2004 - Eppley Seminar Series, Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE, USA (November 18), “Positive selection of somatic mutations in human cancers”.

2004 - MDI Biological Lab Symposium "Insights from Comparative Genomic and Toxicogenomic Analyses", Salisbury Cove, ME, USA (July 16), “Insights into eukaryotic genome evolution through analysis of orthologous gene clusters”.

2003 - 5th Atlantic Symposium on Computational Biology and Genome Informatics, NC, USA (September 26), “Computational pipeline for comparative analysis of eukaryotic gene structure”.

1998 - First International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia (August 26), “Regression analysis of mutational spectra”

1997 - Moscow Seminar on Computer Genetics, Moscow, Russia (June 5), “Analysis of donor splice sites in various eukaryotic organisms”.

1997 - International Conference on Agrobiotechnology of Plants and Animals, Kiev, Ukrain (May 27), “Computational analysis of nucleotide context role in mutagenesis”.

1996 - Istituto di Genetica Biochimica ed Evoluzionistica CNR, Pavia, Italy (July 11), “Long-term evolution of repeated elements”.

1994 - Moscow Seminar on Computer Genetics, Moscow, Russia (August 16), “Gene structure prediction using information on homologous protein sequence”.

 

 

ORGANIZING COMMITTEE

 

2012 Member of the International Program Committee, The 8th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS\SB'2012), Novosibirsk, Russia, June 25-29.

2011 Member of the International Advisory Board, International Interdisciplinary Science Conference (I-ISC, 2011) on Bioinformatics: An Interface between Computer Science and Biology, Delhi, India, November 15-17.

2010 Member of the International Program Committee, The 7th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2010), Novosibirsk, Russia, June 20-26.

2008 Member of the International Program Committee, The 6th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2008), Novosibirsk, Russia, June 22-28.

2006 Member of the Program Committee, The 5th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2006), Novosibirsk, Russia, July 16-22.

2005 Member of the International Scientific Committee, 2005 BGRS International Summer School for young scientists "Evolutionary Biology and High Performance Computing Bioinformatics", Novosibirsk, September 11-16.

2003 Member of the Program Committee, Moscow Conference on Computational Molecular Biology (MCCMB’03), Moscow, July 22-25.

 

 

PRESENTATIONS AT SCIENTIFIC MEETINGS

 

2010 - Seventh International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia - session chair.

2010 - Plant and Animal Genome XVIII, San Diego, CA, USA - talk

2008 - Sixth International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia - session chair.

2006 - Annual Meeting of the Society for Molecular Biology and Evolution, Arizona State University, AZ, USA - talk.

2005 - Albany 2005: 14th Conversation, Albany, NY, USA - talk.

2004 - Annual Meeting of the Society for Molecular Biology and Evolution, State College, PA, USA - poster.

2003 - Cold Spring Harbor 68th Symposium: The Genome of Homo Sapiens, NY, USA - poster.

2002 - Gordon Research Conference “Mutagenesis”, Bates College, ME, USA - poster.

2002 - Second Annual UMass Bioinformatics Conference, Lowell, USA - talk, session chair.

2001 - In Silico Biology: Bioinformatics After the Human Genome, Atlanta, GA, USA - poster.

2001 - Annual Meeting of the Society for Molecular Biology and Evolution, Athens, GA, USA - talk.

1999 - Symposium on "Genome Diversity and Evolution", State College, PA, USA - poster.

1998 - Third Siberian Congress on Industrial and Applied Mathematics (dedicated to the memory of S.L. Sobolev, 1908-1989), Novosibirsk, Russia - talk.

1995 - International Meeting "Recombination: Mechanisms and Biological consequences", Avignon, France (October) - poster.

1995 - Third International Conference on Intelligent Systems for Molecular Biology, Cambridge, England (July) - poster.

1993 - International course "Databanks and Computer Support of the Human Genome Project", Moscow, Russia - lecture.

1992 - Workshop "Problems of recognition of functional regions in human genome sequences" (National Scientific and Technological Project "HUMAN GENOME", Section "Informatics"), Novosibirsk, Russia - talk.

1992 - International Symposium on Computational Methods in Genome Research, Heidelberg, Germany - poster.

1990 - International Symposium "Modelling and Computer Methods in Molecular Biology and Genetics", Novosibirsk, USSR - talk.

1989 - Meeting on the Computer Support of the Project "Human Genome", Pushchino, USSR - talk.

1989 - 2nd National Conference on the Problems of Evolution, Moscow, USSR - poster.

1988 - Workshop on Molecular Mechanisms of Mutagenesis, Novosibirsk, USSR - poster.

1986, 1990 - 6th, 7th National Symposia on Molecular Mechanisms of Genetic Processes, Moscow, USSR - posters.

1986 - Workshop on the Software for Molecular Biology Investigation, Moscow, USSR - talk.

1984, 1986, 1988 - 1st, 2nd, 3rd Symposia on Theoretical Investigations and Data Banks on Molecular Biology and Genetics, Novosibirsk, USSR - posters, talk.

 

 

JOURNAL REVIEW EXPERIENCE

 

Cell, Mol. Cell, Science, Nat. Rev. Genet., Nat. Genet., Nat. Communications, PLoS Biol., PLoS Comput. Biol., PLoS ONE, Mol. Biol. Evol., Trends Genet., Nucleic Acids Res., Genome Biol., Bioinformatics, Genome Res., BMC Evol. Biol., BMC Bioinformatics, BMC Genomics, BMC Mol. Biol., Biol. Direct, J. Mol. Evol., Genome Biol. Evol., Brief. Bioinform., Trends Microbiol., Genetics, J. Exp. Med., Hum. Genet., Hum. Mutat., Mol. Genet. Genomics, Proc. Natl. Acad. Sci. USA, Mol. Phylogenet. Evol., J. Theor. Biol., In Silico Biol., FEMS Microbiol. Lett., FEBS Lett., Gene, Prion, Immunogenetics, Archaea, Breast Cancer Res. Treat., Discrete Applied Mathematics, Biochim. Biophys. Acta, J. Biomol. Struct. Dyn., J. Bioinform. Comput. Biol., Revista de Biología Tropical, Int. J. Bioinf. Res. Applic., Dev. Dyn., Health, Int. J. Biochem. Cell Biol., Journal of Phylogenetics and Evolutionary Biology, Journal of Experimental Zoology, Mutat. Res., American Journal of Biomedical Sciences, J. Gastrointestinal and Liver Diseases, International Journal of Biological Sciences, Mol. Biol. (Moscow), Vestnik VOGIS (Novosibirsk), Pac. Symp. Biocomput. 2003, Pac. Symp. Biocomput. 2005

 

 

INTERNET RESOURCES

 

Datasets of alignments of orthologous genes from completely sequenced eukaryotic genomes, ftp.ncbi.nlm.nih.gov/pub/koonin/RGC_CAM/ (2006-2009, in collaboration with M. Csürös, Y.I. Wolf and E.V. Koonin)

Datasets of introns in orthologous and paralogous genes from completely sequenced eukaryotic genomes, ftp.ncbi.nlm.nih.gov/pub/koonin/intron_evolution/ and ftp.ncbi.nlm.nih.gov/pub/koonin/

carmel_introns/ (2002-2007, in collaboration with L. Camel, V.N. Babenko, Y.I. Wolf and E.V. Koonin)

WebGene: an integrated system for gene structure analysis, www.itb.cnr.it/webgene (1992-2000, in collaboration with L. Milanesi and D. D’Angelo)

WebMutation: mutation hotspot identification, www.itb.cnr.it/webmutation (1995-1998, in collaboration with G.V Glazko, L. Milanesi and D. D’Angelo)

AutoGene: a computer system for automated analysis of nucleotide sequences (1990-1995, in collaboration with A.A. Ptitsyn, V.B. Strelets, D.A. Grigorovich, A.E. Kel, L. Milanesi and N.A. Kolchanov) ftp.bionet.nsc.ru/pub/biology/aug/

DBMS: a manually curated database of mutation spectra, ftp.bionet.nsc.ru/pub/biology/dbms/ (1986-2007)

 

 

COMPUTER SKILLS

 

Hardware: PC, SUN workstations, VAX11/780, VAX8600, DEC20, SGI, PDP 11/70

Operating systems: MS Windows, Linix, Unix, VMS, MS DOS, RSX, RT

Languages: FORTRAN, C

 

 

PROFESSIONAL SOCIETIES

 

The Vavilovian Society of Geneticists and Selectionists (VOGIS, Russia)

 

 

ERDÖS NUMBER PROJECT (www.oakland.edu/enp/)

 

Erdös number 2

 

 

RESEARCH AND REVIEW PAPERS (h factor = 47)

 

Meller J., Rogozin I.B., Poliakov E., Meller N., Bedanov-Pack M., Plow E.F., Qin J., Podrez E.A., Byzova T.V. Emergence and subsequent functional specialization of Kindlins during evolution of cell adhesiveness. // Mol. Biol. Cell, (in press).

 

Poliakov E., Cooper D.N., Stepchenkova E.I., Rogozin I.B. Genetics in genomic era. // Genet. Res. Int., 364960 (in press).

 

Cheung P.P., Rogozin I.B., Choy K.T., Ng H.Y., Peiris J.S.M., Yen H.L. Comparative mutational analyses of influenza A viruses. // RNA, 2015, V. 21, N 1, 36-47.

 

Kannan S., Rogozin I.B., Koonin E.V. MitoCOGs: Clusters of Orthologous Genes from Mitochondria and implications for the evolution of eukaryotes. // BMC Evol. Biol., 2014, V. 14, 237.

Editor pick: “Going deep into the mitochondrial genome” (http://www.biomedcentral.com/bmcevolbiol/).

 

Poliakov E., Managadze D., Rogozin I.B. Generalized portrait of cancer metabolic pathways inferred from a list of genes overexpressed in cancer. // Genet. Res. Int., 2014, 646193.

 

Poliakov E., Koonin E.V., Rogozin I.B. Impairment of translation in neurons as a putative causative factor for autism. // Biol. Direct, 2014, V. 9, 16.

 

Rogozin I.B. Complexity of gene expression evolution after duplication: protein dosage rebalancing. // Genet. Res. Int., 2014, 516508.

 

Rogozin I.B., Managadze D., Shabalina S.A., Koonin E.V. Gene family level comparative analysis of gene expression in mammals validates the ortholog conjecture. // Genome Biol. Evol., 2014, V. 6, N 4, 754-762.

 

Prikhodko V.G., Sandoval-Jaime C., Abente E.J., Bok K., Parra G.I., Rogozin I.B., Ostlund E.N., Green K.Y., Sosnovtsev S.V. Genetic characterization of feline calicivirus strains associated with varying disease manifestations during an outbreak season in Missouri (1995-1996). // Virus Genes, 2014, V. 48, N 1, 96-110.

 

Lada A.G., Stepchenkova E.I., Waisertreiger I. S.-R., Noskov V.N., Dhar A., Eudy J.D., Boissy R.J., Hirano M.,, Rogozin I.B., Pavlov Y.I. Genome-wide mutation avalanches induced in diploid yeast cells by a base analog or an APOBEC deaminase. // PLoS Genet., 2013, V. 9, N 9, e1003736.

 

Loshenova P.S., Rogozin I.B., Rotskaya U.N., Malyarchuk B.A., Nevinsky G.A., Sinitsyna O.I. Somatic mutagenesis of mitochondrial cytochrome b gene from hippocampus of Wistar rats. // Ecol. Genetics, 2013, V. XI, N 2, 50-57.

 

Managadze D, Lobkovsky A.E, Wolf Y.I., Shabalina S.A., Rogozin I.B., Koonin E.V. The vast, conserved mammalian lincRNome. // PLoS Comp. Biol., 2013, V. 9, N 2, e1002917.

 

Koonin E.V., Csuros M., Rogozin I.B. Whence genes in pieces: reconstruction of the exon-intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes. // Wiley Interdiscip. Rev. RNA, 2013, V. 4, N 1, 93-105.

 

Lada A.G., Dhar A., Eudy J.D., Boissy R.J., Hirano M., Rogozin I.B., Pavlov Y.I. APOBEC cytosine deaminase induces genome-wide kataegis. // Biol. Direct, 2012, V. 7, 47.

 

Poliakov E., Gubin A., Stear O., Gentleman S., Rogozin I.B., Redmond T.M. Origin and evolution of retinoid isomerization machinery in vertebrate visual cycle: hint from jawless vertebrates. // PLoS ONE, 2012, V.7, N 11, e49975.

 

Waisertreiger I.S.-R., Liston V.G., Menezes M., Kim H.-M., Lobachev K., Stepchenkova E.I., Tahirov T.H., Rogozin I.B., Pavlov Y.I. Attenuation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools. // Environ. Mol. Mutagen., 2012, V. 53, N 9, 699-724.

 

Chernikova D., Manadagze D., Rogozin I.B., Glazko V.I. Mobile genetic elements as a basis for N.I. Vavilov’s law of homologous series. // Izvestia TSXA, 2012, N 5, 145-153.

 

Hashimoto K., Rogozin I.B., Panchenko A.R. Oncogenic potential is directly related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases. // Hum. Mutat., 2012, V. 33, N 11, 1566-1575.

Featured online on Global Medical Discovery (globalmedicaldiscovery.com).

 

Glazko G.V., Zybailov B.L., Rogozin I.B. Computational prediction of Polycomb-associated long non-coding RNAs. // PLoS ONE, 2012, V. 7, N 9, e44878.

 

Meller J., Malinin N.L., Panigrahi S., Kerr B.A., Patil A., Ma Y., Venkateswaran L., Rogozin I.B., Mohandas N., Ehlayel M.S., Podrez E.A., Chinen J., Byzova T.V. Novel aspects of Kindlin-3 function in humans based on a new case of Leukocyte Adhesion Deficiency III (LAD-III). // J. Thromb. Haemost., 2012, V. 10, N 7, 1397-1408.

 

Rogozin I.B., Carmel L., Csuros M., Koonin E.V. Origin and evolution of spliceosomal introns. // Biol. Direct, 2012, V. 7, 11.

 

Managadze D., Rogozin I.B., Chernikova D., Shabalina S.A., Koonin E.V. Negative correlation between expression level and evolutionary rates of long intergenic non-coding RNAs. // Genome Biol. Evol., 2011, V. 3, 1390-1404.

 

Lada A.G., Grabow C.E., Prakash A., Borgstahl G.E.O., Rogozin I.B., Pavlov Y.I. Replication protein A (RPA) hampers the processive action of APOBEC3G on single-stranded DNA. // PLoS ONE, 2011, V. 6, N 9, e24848.

 

Iyer L.M., Zhang D, Rogozin I.B., Aravind L. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. // Nucleic Acids Res., 2011, V. 39, N 22, 9473-9497.

 

Csürös M., Rogozin I.B., Koonin E.V. A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. // PLoS Comp. Biol., 2011, V. 7, N 9, e1002150 (video supplement: www.youtube.com/watch?v=L7SJ8NPHOSo).

 

Chernikova D., Motamedi S., Csürös M., Koonin E.V., Rogozin I.B. Late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes. // Biol. Direct, 2011, V. 6, 26.

 

Kochetov A.V., Volkova O.A., Poliakov A., Dubchak I., Rogozin I.B. Tandem termination signal in plant mRNAs. // Gene, 2011, V. 481, N 1, 1-6.

 

Colbourne J.K., Pfrender M.E., Gilbert D., ... 35 co-authors ..., Rogozin I.B., ... 27 co-authors ..., Grigoriev I.V., Lynch M., Boore J.L. The ecoresponsive genome of Daphnia pulex. // Science, 2011, V. 331, N 6017, 555-561.

Comments by D. Ebert (A genome for the environment. Science, V. 331, N 6017, 539-540), V. Gewin (Water flea genome offers revolution in toxicity testing. Nature News, www.nature.com/news/2011/110203/full/news.2011.71.html) and D. Tautz (Not just another genome. BMC Biology, 2011, V. 9, 8).

 

Lada A.G., Krick C.F., Kozmin S.G., Mayorov V.I., Karpova T.S., Rogozin I.B., Pavlov Y.I. Mutator effects and mutation signatures of editing deaminases produced in bacteria and yeast. // Biochemistry (Mosc.), 2011, V. 76, N 1, 131-146.

 

Szcześniak M.W., Ciomborowska J., Nowak W., Rogozin I.B., Makałowska I. Primate and rodent specific intron gains and the origin of retrogenes with splice variants. // Mol. Biol. Evol., 2011, V. 28, N 1, 33-37.

 

Aksenova A., Volkov K., Maceluch J., Pursell Z.F., Rogozin I.B., Kunkel T.A., Pavlov Y.I., Johansson E. Mismatch repair-independent increase in spontaneous mutagenesis in yeast lacking non-essential subunits of DNA polymerase e. // PLoS Genet., 2010, V. 6, N 11, e1001209.

 

Rotskaya U.N., Rogozin I.B., Vasyunina E.A., Malyarchuk B.A., Nevinsky G.A., Sinitsyna O.I. High frequency of somatic mutations in rat liver mitochondrial DNA. // Mutat. Res., 2010, V. 685, N 1-2, 97-102.

 

Makałowska I., Rogozin I.B., Makalowski W. Genome evolution. // Adv. Bioinformatics, 2010, 643701.

 

Carmel L., Wolf Y.I., Rogozin I.B., Koonin E.V. EREM: parameter estimation and ancestral reconstruction by expectation-maximization for a probabilistic model of genomic binary characters evolution. // Adv. Bioinformatics, 2010, 167408.

 

Stone J.E., Kissling G.E., Lujan S.A., Rogozin I.B., Carrie M., Stith C.M., Burgers P.M., Kunkel T.A. Low fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerase z. // Nucleic Acids Res., 2009, V. 37, N 11, 3774-3787.

 

Rogozin I.B., Basu M.K., Csürös M., Koonin E.V. Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes. // Genome Biol. Evol., 2009, V.1, 99-113.

 

Resch A.M., Ogurtsov A.Y., Rogozin I.B., Shabalina S.A., Koonin E.V. Evolution of alternatively spliced and constitutive regions of mammalian 5’UTRs. // BMC Genomics, 2009, V. 10, 162.

 

Basu M.K., Poliakov E., Rogozin I.B. Domain mobility in proteins: functional and evolutionary implications. // Brief. Bioinform., 2009, V. 10, N 3, 205-216.

 

Rotskaya U.N., Rogozin I.B., Vasyunina E.A., Kolosova N.G., Malyarchuk B.A., Nevinsky G.A., Sinitsyna O.I. Analysis of mitochondrial DNA somatic mutations in OXYS and Wistar strain rats. // Biochemistry (Mosc.), 2009, V. 74, N 4, 532-541.

 

Carmel L., Rogozin I.B., Wolf Y.I., Koonin E.V. A maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure. // Methods Mol. Biol., 2009, V. 541, 357-371.

 

Tahirov T.H., Makarova K.S., Rogozin I.B., Pavlov Y.I., Koonin E.V. Evolution of DNA polymerases: chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors and an inactivated polymerase-exonuclease module in Pol e. // Biol. Direct, 2009, V. 4, 11.

 

Basu M.K., Rogozin I.B., Koonin E.V. Primordial spliceosomal introns were probably U2 type. // Trends Genet., 2008, V. 24, N 11, 525-528.

 

Baranovskiy A.G., Babayeva N.D., Liston V.G., Rogozin I.B., Koonin E.V., Pavlov Y.I., Vassylyev D.G., Tahirov T.H. X-ray structure of the complex of regulatory subunits of human DNA polymerase d. // Cell Cycle, 2008, V. 7, N 19, 3026-3036.

 

Rogozin I.B., Makarova K.S., Pavlov Y.I., Koonin E.V. A highly conserved family of inactivated archaeal B family DNA polymerases. // Biol. Direct, 2008, V. 3, 32.

 

Elisafenko E.A., Kolesnikov N.N., Shevchenko A.I., Rogozin I.B., Nesterova T.B., Brockdorff N., Zakian S.M. A dual origin of the Xist gene from a protein-coding gene and a set of various transposable elements. // PLoS ONE, 2008, V. 3, N 6, e2521.

 

Rogozin I.B., Glazko V.I., Koonin E.V. The molecular-evolutionary basis for Vavilov’s law of homologous series. // Vestnik VOGIS (Novosibirsk), 2008, V.12, N 3, 362-371 ( www.bionet.nsc.ru/vogis/).

 

Churbanov A., Winters-Hilt S., Koonin E.V., Rogozin I.B. Accumulation of GC donor splice signals in mammals. // Biol. Direct, 2008, V. 3, 30.

 

Arana M.E., Seki M., Wood R.D., Rogozin I.B., Kunkel T.A. Low fidelity DNA synthesis by human DNA polymerase q. // Nucleic Acids Res., 2008, V. 36, N 11, 3847-3856.

 

Basu M.K., Makalowski W., Rogozin I.B., Koonin E.V. U12 intron positions are more strongly conserved between animals and plants than U2 intron positions. // Biol. Direct, 2008, V. 3, 19.

 

Csürös M., Rogozin I.B., Koonin E.V. Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum likelihood approach. // Mol. Biol. Evol., 2008, V. 25, N 5, 903-911.

 

Rogozin I.B., Thompson K., Csürös M., Carmel L., Koonin E.V. Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov’s law of homologous series. // Biol. Direct, 2008, V. 3, 7.

 

Basu M.K., Carmel L., Rogozin I.B., Koonin E.V. Evolution of protein domain promiscuity in eukaryotes. // Genome Res., 2008, V. 18, N 3, 449-461.

 

Bhattacharya P., Grigera F., Rogozin I.B., McCarty T., Morse H.C. III, Kenter A.L. Identification of murine B cell lines that undergo somatic hypermutation focused to A:T and G:C residues. // Eur. J. Immunol., 2008, V. 38, N 1, 227-239.

 

Basu M.K., Rogozin I.B., Deusch O., Dagan T., Martin W., Koonin E.V. Evolutionary dynamics of introns in chloroplast-derived genes in plants: saturation nearly reached but slow intron gain continues. // Mol. Biol. Evol., 2008, V. 25, N 1, 111-119.

 

Rogozin I.B., Wolf Y.I., Carmel L., Koonin E.V. Analysis of rare amino acid replacements supports the Coelomata clade. // Mol. Biol. Evol., 2007, V. 24, N 12, 2594-2597.

Reply to Irimia M., Maeso I., Penny D., Garcia-Fernandez J. and Roy S.W. // Mol. Biol. Evol., 2007, 24, N 8, 1604-7.

 

Carmel L., Rogozin I.B., Wolf Y.I., Koonin E.V. Patterns of intron gain and conservation in eukaryotic genes. // BMC Evol. Biol., 2007, V.7, 192.

 

Zheng J., Rogozin I.B., Koonin E.V., Przytycka T.M. Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. // Mol. Biol. Evol., 2007, V. 24, N 11, 2583-2592.

 

Lada A.G., Iyer L.M., Rogozin I.B., Aravind L., Pavlov Y.I. Vertebrate immunity: mutator proteins and their evolution. // Genetika (Mosc.), 2007, V. 43, N 10, 1311-1327.

 

Vitushkina M.V., Rogozin I.B., Jelkmann W., Koonin E.V., Agranovsky A.A. Completion of the mapping of transcription start sites for the five-gene block subgenomic RNAs of beet yellows closterovirus and identification of putative subgenomic promoters. // Virus Res., 2007, V. 128, N 1-2, 153-158.

 

Csürös M., Holey J.A., Rogozin I.B. In search of lost introns. // Bioinformatics, 2007, V. 23, N 13, i87-i96.

 

Resch A.M., Carmel L., Marino-Ramirez L., Ogurtsov A.Y., Shabalina S.A., Rogozin I.B., Koonin E.V. Widespread positive selection in synonymous sites of mammalian genes. // Mol. Biol. Evol., 2007, V. 24, N 8, 1821-1831.

 

Carmel L., Rogozin I.B., Wolf Y.I., Koonin E.V. Evolutionarily conserved genes preferentially accumulate introns. // Genome Res., 2007, V. 17, N 7, 1045-1050.

 

Carmel L., Wolf Y.I., Rogozin I.B., Koonin E.V. Three distinct modes of intron dynamics in the evolution of eukaryotes. // Genome Res., 2007, V. 17, N 7, 1034-1044.

 

Rogozin I.B., Iyer L.M., Liang L, Glazko G.V., Liston V.G., Pavlov Y.I., Aravind L., Pancer Z. Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. // Nat. Immunol., 2007, V. 8, N 6, 647-656.

Comments by D.G. Schatz in News & Views, Nat. Immunol., 2007, V.8, N 6, 551-3; Research Highlight, Nat. Rev. Immunol. 2007, V. 7, N 6, 415.

 

Zheng J., Rogozin I.B., Koonin E.V., Przytycka T.M. A rigorous analysis of the pattern of intron conservation supports the Coelomata clade of animals. // In: "Comparative Genomics - RECOMB 2007 International Workshop", Lect. Notes Comput. Sci., 2007, Vol. 4751, Springer, New York, 177-191.

 

Xiao Z., Ray M., Jiang C, Clark A.B., Rogozin I.B., Diaz M. Known components of the immunoglobulin A:T mutational machinery are intact in Burkitt lymphoma cell lines with G:C bias. // Mol. Immunol., 2007, V.44, N 10, 2659-2666.

 

Rogozin I.B., Wolf Y.I., Carmel L., Koonin E.V. Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements. // Mol. Biol. Evol., 2007, V. 24, N 4, 1080-1090.

 

Sverdlov A.V., Csürös M., Rogozin I.B., Koonin E.V. A glimpse of a putative pre-intron phase of eukaryotic evolution. // Trends Genet., 2007, V. 23, N 3, 105-108.

 

Dewey C.N., Rogozin I.B., Koonin E.V. Compensatory relationships between splice sites and exonic splicing signals depending on the length of vertebrate introns. // BMC Genomics, 2006, V. 7, 311.

 

Pavlov Y.I., Shcherbakova P.V., Rogozin I.B. Roles of DNA polymerases in DNA replication, repair and recombination in eukaryotes. // Int. Rev. Cytol., 2006, V. 255, 41-132.

 

Churbanov A., Rogozin I.B., Deogun J.S., Ali H. Method of predicting splice sites based on signal interactions. // Biol. Direct, 2006, V.1, 10.

 

Rogozin I.B., Pavlov Y.I. The cytidine deaminase AID exhibits similar functional properties in yeast and mammals. // Mol. Immunol., 2006, V. 43, N 9, 1481-1484.

 

Babenko V.N., Basu M.K., Kondrashov F.A., Rogozin I.B., Koonin E.V. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. // BMC Cancer, 2006, V. 6, 36.

 

Glazko G.V., Babenko V.N., Koonin E.V., Rogozin I.B. Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection. // Biol. Direct, 2006, V. 1, 4.

 

Alder M.N., Rogozin I.B., Iyer L.M., Glazko G.V., Cooper M.D., Pancer Z. Diversity and function of adaptive immune receptors in a jawless vertebrate. // Science, 2005, V. 310, N 5756, 1970-1973.

Comments by M. Beckman (Jawless fish have form of adaptive immunity. Science, 2005, V. 310, N 5756, 1892-3). Evaluated by Faculty of 1000 (BioMedCentral, F1000 Factor 3.3).

 

Rogozin I.B., Wolf Y.I., Babenko V.N., Koonin E.V. Evolution of eukaryotic genomes and maximum parsimony principle. // Vestnik VOGIS (Novosibirsk), 2005, V. 9, N 2, 141-152 ( www.bionet.nsc.ru/vogis/).

 

Carmel L., Rogozin I.B., Wolf Y.I., Koonin E.V. An expectation-maximization algorithm for analysis of evolution of exon-intron structure of eukaryotic genes. In: "Comparative Genomics - RECOMB 2005 International Workshop", Lect. Notes Comput. Sci., 2005, Vol. 3678, Springer, New York, 35-46.

 

Churbanov A., Rogozin I.B., Babenko V.N., Ali H., Koonin E.V. Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes. // Nucleic Acids Res., 2005, V. 33, N 17, 5512-5520.

 

Kravchenko J.E., Rogozin I.B., Koonin E.V., Chumakov P.M. Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. // Nature, 2005, V. 436, N 7051, 735-739.

Comments by N. LeBrasseur (A new mRNA polymerase. J. Cell Biol., 2005, V. 170, N 5, 699). Evaluated by Faculty of 1000 (BioMedCentral, F1000 Factor 6.0).

 

Rogozin I.B., Basu M.K., Jordan I.K., Pavlov Y.I., Koonin E.V. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. // Cell Cycle, 2005, V. 4, N 9, 1281-1285.

 

Malyarchuk B.A., Papuga M., Grzybowski T., Rogozin I.B., Wozniak M., Derenko M.V., Rychkov S.Y., Czarny J., Zakharov I.A., Miscicka-Sliwka D. Low variability of the POLG (CAG)n repeat in North Eurasian populations. // Hum. Biol., 2005, V. 77, N 3, 355-365.

 

Kochetov A.V., Sarai A., Rogozin I.B., Shumny V.K., Kolchanov N.A. The role of alternative translation start sites in generation of human protein polymorphism. // Mol. Genet. Genomics, 2005, V. 273, N 6, 491-496.

 

Mayorov V.I., Rogozin I.B., Adkison L.R., Frahm C.R., Kunkel T.A., Pavlov Y.I. Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes. // BMC Immunol., 2005, V. 6, 10.

 

Mayorov V.I., Rogozin I.B., Adkinson L.R., Gearhart P.J. DNA polymerase h contributes to strand bias of mutations of A versus T in immunoglobulin genes. // J. Immunol., 2005, V.174, N 12, 7781-7786.

 

Rogozin I.B., Sverdlov A.V., Babenko V.N., Koonin E.V. Analysis of evolution of exon/intron structure of eukaryotic genes. // Brief. Bioinform., 2005, V.6, N 2, 118-134.

 

Koonin E.V., Rogozin I.B., Glazko G.V. P53 gain-of-function: tumor biology and bioinformatics come together. // Cell Cycle, 2005, V.4, N 5, 686-688.

 

Sverdlov A.V., Rogozin I.B., Babenko V.N., Koonin E.V. Conservation versus parallel gains in intron evolution. // Nucleic Acids Res., 2005, V.33, N 6, 1741-1748.

 

Glazko G.V., Koonin E.V., Rogozin I.B. Molecular dating: ape bones agree with chicken entrails. // Trends Genet., 2005, V.21, N 2, 89-92.

 

Rogozin I.B., Malyarchuk B.A., Pavlov Y.I., Milanesi L. From context-dependence of mutations to molecular mechanisms of mutagenesis. In: “Pac. Symp. Biocomput. 2005”, (eds. Altman R.B., Dunker A.K., Hunter L., Jung T.A., Klein T.E.), World Scientific, Singapore, 2005, 409-420.

 

Malyarchuk B.A., Rogozin I.B. On the Etruscan mtDNA contribution to modern humans. // Am. J. Hum. Genet., 2004, V.75, N 5, 920-923.

 

Sverdlov A.V., Rogozin I.B., Babenko V.N., Koonin E.V. Reconstruction of ancestral protosplice sites. // Curr. Biol., 2004, V.14, N 16, 1505-1508.

 

Glazko G.V., Koonin E.V., Rogozin I.B. Mutation hotspots in the p53 gene in tumors of different origin: correlation with evolutionary conservation and signs of positive selection. // Biochim. Biophys. Acta, 2004, V.1679, N 2, 95-106.

 

Sverdlov A.V., Babenko V.N., Rogozin I.B., Koonin E.V. Preferential loss and gain of introns in 3’ portions of genes suggests a reverse-transcription mechanism of intron insertion. // Gene, 2004, V.338, N 1, 85-91.

 

Babenko V.N., Rogozin I.B., Mekhedov S.L., Koonin E.V. Prevalence of intron gain over intron loss in evolution of paralogous gene families. // Nucleic Acids Res., 2004, V.32, N 12, 3724-3733.

 

Rogozin I.B., Makarova K.S., Wolf Y.I., Koonin E.V. Computational approaches for analysis of gene neighborhoods in prokaryotic genomes. // Brief. Bioinform., 2004, V.5, N 2, 131-149.

 

Malyarchuk B.A., Rogozin I.B. Mutagenesis by transient misalignment in human mitochondrial DNA control region. // Ann. Hum. Genet., 2004, V.68, N 4, 324-339.

 

Shabalina S.A., Ogurtsov A.Y., Rogozin I.B., Koonin E.V., Lipman D.J. Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. // Nucleic Acids Res., 2004, V.32, N 5, 1774-1782.

 

Kouprina N., Mullokandov M., Rogozin I.B., Collins K., Solomon G., Otstot J., Risinger J.I., Koonin E.V., Barrett J.C., Larionov V. The SPANX gene family of cancer/testis specific antigens: rapid evolution and amplification in African great apes and hominids. // Proc. Natl. Acad. Sci. USA, 2004, V.101, N 9, 3077-3082.

 

Rogozin I.B., Diaz M. Cutting edge: DGYW/WRCH is a better predictor of mutability at G:C bases in immunoglobulin hypermutation than the widely accepted RGYW/WRCY motif and probably reflects a two-step activation-induced cytidine deaminase-triggered process. // J. Immunol., 2004, V.172, N 6, 3382-3384.

 

Koonin E.V., Fedorova N.D., Jackson J.D., Jacobs A.R., Krylov D.M., Makarova K.S., Mazumder R., Mekhedov S.L., Nikolskaya A.N., Rao B.S., Rogozin I.B., Smirnov S., Sorokin A.V., Sverdlov A.V., Vasudevan S., Wolf Y.I., Yin J.J., Natale D.A. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. // Genome Biol., 2004, V.5, R7.

 

Kondrashov A.S., Rogozin I.B. Context of deletions and insertions in human coding sequences. // Hum. Mutat., 2004, V.23, N 2, 177-185.

 

Wolf Y.I, Rogozin I.B., Koonin E.V. Coelomates and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. // Genome Res., 2004, V.14, N 1, 29-36.

 

Rogozin I.B., Babenko V.N., Fedorova N.D., Jackson J.D., Jacobs A.R., Krylov D.M., Makarova K.S., Mazumder R., Mekhedov S.L., Mirkin B.G., Nikolskaya A.N., Rao B.S., Smirnov S., Sorokin A.V., Sverdlov A.V., Vasudevan S., Wolf Y.I., Yin J.J., Natale D.A., Koonin E.V. Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution. // Cold Spring Harb. Symp. Quant. Biol., 2003, V. LXVIII, 293-301.

 

Sverdlov A.V., Rogozin I.B., Babenko A.V., Koonin E.V. Evidence of splice site migration from exon to intron during intron evolution. // Curr. Biol., 2003, V.13, N 24, 2170-2174.

 

Naykova T.M., Kondrakhin Y.V., Rogozin I.B., Voevoda M.I., Yudin N.S., Romaschenko A.G.. Concerted changes in DNA structure in the regions of internal promoters of eukaryotic genes for tRNAs of all specificities. // J. Mol. Evol., 2003, V.57, N 5, 520-532.

 

Rogozin I.B., Babenko V.N., Milanesi L., Pavlov Y.I. Computational analysis of mutation spectra. // Brief. Bioinform., 2003, V.4, N 3, 210-227.

 

Shcherbakova P.V., Pavlov Y.I., Chilkova O., Rogozin I.B., Johansson E., Kunkel T.A. Unique error signature of the four-subunit DNA polymerase e. // J. Biol. Chem., 2003, V.278, N 44, 43770-43780.

 

Krylov D.M., Wolf Y.I., Rogozin I.B., Koonin E.V. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. // Genome Res., 2003, V.13, N 10, 2229-2235.

Comments by I.K. Jordan (Brief. Bioinform., 2004, V.5, N 1, 75-6)

 

Omelchenko M.V., Makarova K.S., Wolf Y.I., Rogozin I.B., Koonin E.V. Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. // Genome Biol., 2003, V.4, N 9, R55.

 

Rogozin I.B., Wolf Y.I., Sorokin A.V., Mirkin B.G., Koonin E.V. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. // Curr. Biol., 2003, V.13, N 17, 1512-1517.

Comments by O.Zhaxybayeva and J.P.Gogarten (Curr. Biol., 2003, V.13, N 19, R764-6)

 

Dufresne A., Salanoubat M., Partensky F., Artiguenave F., Axmann I.M., Barbe V., Duprat S., Galperin M.Y., Koonin E.V., Le Gall F., Makarova K.S., Ostrowski M., Oztas S., Robert C., Rogozin I.B., Scanlan D.J., de Marsac N.T., Weissenbach J., Wincker P., Wolf Y.I., Hess W.R. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a minimal oxyphototrophic genome. // Proc. Natl. Acad. Sci. USA, 2003, V.100, N 17, 10020-10025.

Comments by D.A. Bryant (Proc. Natl. Acad. Sci., 2003, V.100, N 17, 9647-9)

 

Koonin E.V., Rogozin I.B. Getting positive about selection. // Genome Biol., 2003, V.4, N 8, 331.

 

McDonald J.P., Frank E.G., Plosky B.S., Rogozin I.B., Masutani C., Hanaoka F., Woodgate R., Gearhart P.J. 129-derived strains of mice are deficient in DNA polymerase i and have normal immunoglobulin hypermutation. // J. Exp. Med., 2003, V.198, N 4, 635-643.

 

Milanesi L., Rogozin I.B. ESTMAP: a system for expressed sequence tags (ESTs) mapping on genomic sequences. // IEEE Trans. NanoBioscience, 2003, V.2, N 2, 75-78.

 

Yang W., Rogozin I.B., Koonin E.V. Yeast POL5 is an evolutionarily conserved regulator of rDNA transcription unrelated to any known DNA polymerases. // Cell Cycle, 2003, V.2, N 2, 120-122.

 

Rogozin I.B., Aravind L., Koonin E.V. Differential action of natural selection on the N- and C-terminal domains of 2’-5’ oligoadenylate synthetases and the potential nuclease function of the C-terminal domain. // J. Mol. Biol., 2003, V.326, N 5, 1449-1461.

 

Liu Y., Zhou J., Omelchenko M., Beliaev A., Venkateswaran A., Stair J., Wu L., Thompson D.K., Xu D., Rogozin I.B., Gaidamakova E.K., Zhai M., Makarova K.S., Koonin E.V., Daly M.J. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. // Proc. Natl. Acad. Sci. USA, 2003, V.100, N 7, 4191-4196.

 

Glazko G.V., Koonin E.V., Rogozin I.B., Shabalina S.A. A significant fraction of conserved non-coding DNA in human and mouse consists of predicted matrix attachment regions. // Trends Genet., 2003, V.19, N 3, 119-124.

 

Koonin E.V., Makarova K.S., Rogozin I.B., Davidovic L., Letellier M.-C., Pellegrini L. The rhomboids: a near ubiquitous family of intramembrane serine proteases probably evolved via multiple ancient horizontal gene transfers. // Genome Biol., 2003, V, 4, N 3, R19.

 

Rogozin I.B., Pavlov Y.I. Theoretical analysis of mutation hotspots and their DNA sequence context specificity. // Mutat. Res., 2003, V.544, N 1, 65-85.

 

Kouprina N., Ebersole T., Koriabine M., Pak E., Rogozin I.B., Katoh M., Oshimura M., Ogi K., Peredelchuk M., Solomon G., Brown W., Barrett J.C., Larionov V. Cloning of human centromeres by transformation-associated recombination in yeast and generation of functional human artificial chromosomes. // Nucleic Acids Res., 2003, V.31, N 3, 922-934.

 

Jordan I.K., Rogozin I.B., Glazko G.V., Koonin E.V. Origin of a substantial fraction of human regulatory sequences from transposable elements. // Trends Genet., 2003, V.19, N 2, 68-72.

Evaluated by Faculty of 1000 (BioMedCentral, F1000 Factor 6.4), comments by I.K. Jordan (Brief. Bioinform., 2003, V.4, N 2,185).

 

Kochetov A.V., Sirnik O.A., Rogozin I.B., Glazko G.V., Komarova M.L., Shumny VK. Compositional properties of plant mRNA 5’ untranslated sequences. // Mol. Biol. (Mosc.), 2002, V.36, N 4, 649-656.

 

Wolf Y.I., Rogozin I.B., Grishin N.V., Koonin E.V. Genome trees and the Tree of Life. // Trends Genet., 2002, V.18, N 9, 472-479.

 

Rogozin I.B., Makarova K.S., Natale D.A., Spiridonov A.N., Tatusov R.L., Wolf Y.I., Yin J., Koonin E.V. Congruent evolution of different classes of non-coding DNA in prokaryotic genomes // Nucleic Acids Res., 2002, V.30, N 19, 4264-4271.

 

Biunno I., Castiglioni B., Rogozin I.B., DeBellis G., Malferrari G., Cattaneo M. Cross-species conservation of SEL1L, a human pancreas-specific expressing gene. // OMICS: A Journal of Integrative Biology, 2002, V.6, N 2, 187-198.

 

Pavlov Y.I, Rogozin I.B., Galkin A.P., Aksenova A.Y., Hanaoka F., Rada C., Kunkel T.A. Correlation of somatic hypermutation specificity and A-T base pair substitution errors by DNA polymerase h during copying of a mouse immunoglobulin k light chain transgene. // Proc. Natl. Acad. Sci. USA, 2002, V.99, N 15, 9954-9959.

 

Jordan I.K., Rogozin I.B., Wolf Y.I., Koonin E.V. Microevolutionary genomics of bacteria. // Theor. Popul. Biol., 2002, V.61, N 4, 435-447.

 

Malyarchuk B.A., Rogozin I.B., Berikov V.B., Derenko M.V. Analysis of phylogenetically reconstructed mutational spectra in human mitochondrial DNA control region. // Hum. Genet., 2002, V.111, N 1, 46-53.

 

Perelygin A.A., Kondrashov F.A., Rogozin I.B., Brinton M.A. Evolution of the mouse polyubiquitin C gene. // J. Mol. Evol., 2002, V.55, N 2, 202-210.

 

Jordan I.K., Rogozin I.B., Wolf Y.I., Koonin E.V. Essential genes are more evolutionarily conserved than non-essential genes in bacteria. // Genome Res., 2002, V.12, N 6, 962-968.

Comments by I.K. Jordan (Brief. Bioinform., 2002, V.3, N 3, 306-7)

 

Rogozin I.B., Makarova K.S., Murvai J., Czabarka E., Wolf Y.I., Tatusov R.L., Szekely L.A., Koonin E.V. Connected gene neighborhoods in prokaryotic genomes. // Nucleic Acids Res., 2002, V.30, N 10, 2212-2223.

Evaluated by Faculty of 1000 (BioMedCentral, F1000 Factor 6.0), comments by L. Pray (The Scientist, 2002, V.16, N 19, 43).

 

Slesarev A.I., Mezhevaya K.V., Makarova K.S., Polushin N.N., Shcherbinina O.V., Shakhova V.V., Belova G.I., Aravind L., Natale D.A., Rogozin I.B., Tatusov R.L., Wolf Y.I, Stetter K.O., Malykh A.G., Koonin E.V., Kozyavkin S.A. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. // Proc. Natl. Acad. Sci. USA, 2002, V.99, 4644-4649.

Comments by GJC (Editors' Choice: Stripped Down to the Bare Essentials, Science, 2002, V.296, N 5567, 431), Genome News Network (gnn.tigr.org/articles/04_02/methanopyrus_genome.shtml) and W. D'Haeze (A hyperthermophilic methanogen sequenced. Genome Biol. 2002, V.3, N 7, reports0038; genomebiology.com/2002/3/7/reports/0038)

 

Rogozin I.B., Spiridonov A.N., Sorokin A.V., Wolf Y.I., Jordan I.K., Tatusov R.L., Koonin E.V. Purifying and directional selection in overlapping prokaryotic genes. // Trends Genet., 2002, V.18, N 5, 228-232.

 

Kondrashov F.A., Rogozin I.B., Wolf Y.I., Koonin E.V. Selection in the evolution of gene duplications. // Genome Biol., 2002, V.3, N 2, research8.

Comments by I.K. Jordan (Brief. Bioinform., 2002, V.3, N 2, 203)

 

Makarova K.S., Aravind L., Grishin N.V., Rogozin I.B., Koonin E.V. A DNA repair system specific for thermophilic archaea and bacteria predicted by genomic context analysis. // Nucleic Acids Res., 2002, V.30, N 2, 482-496.

 

Glazko G.V., Rogozin I.B., Glazko V.I. Mutational hotspots in the p53 gene revealed by classification analysis. // Exp. Oncology (Kiev), 2002, V.24, N 1, 32-37.

 

Rogozin I.B., Kunkel T.A., Pavlov Y.I. Double strand breaks during somatic hypermutation of immunoglobulin genes: cause or consequence? // Trends Immunol., 2002, V.23, N 1, 12-13.

 

Jordan I.K., Kondrashov F.A., Rogozin I.B., Tatusov R.L., Wolf Y.I., Koonin E.V. Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins. // Genome Biol., 2001, V.2, N 12, research53.

 

Wolf Y.I., Rogozin I.B., Grishin N.V., Tatusov R.L., Koonin E.V. Genome trees constructed using five different approaches suggest new major bacterial clades. // BMC Evol. Biol., 2001, V.1, 8.

Comments by I.K. Jordan (Brief. Bioinform., 2002, V.3, N 1, 96-7)

 

Rogozin I.B., Pavlov Y.I., Kunkel T.A. Response 1 to "Smaller role for pol h?" // Nat. Immunol., 2001, V.2 , N 11, 983-984.

Reply to Dorner T. and Lipsky P.E. // Nat. Immunol., 2001, V.2, N 11, 982-3.

 

Avedisov S.N., Rogozin I.B., Koonin E.V., Thomas B.J. Rapid evolution of a cyclin A inhibitor gene, roughex, in Drosophila. // Mol. Biol. Evol., 2001, V.18, N 11, 2110-2118.

 

Rogozin I.B., Kochetov A.V., Kondrashov F.A., Koonin E.V., Milanesi L. Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a "weak" context of the start codon. // Bioinformatics, 2001, V.17, N 10, 890-900.

 

Matsuda T., Bebenek K., Masutani C., Rogozin I.B., Hanaoka F., Kunkel T.A. Error rate and specificity of human and murine DNA polymerase h. // J. Mol. Biol., 2001, V.312, N 2, 335-346.

 

Glazko G.V., Rogozin I.B., Glazkov M.V. Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix. // Biochim. Biophys. Acta, 2001, V.1517, 351-364.

 

Rogozin I.B., Pavlov Y.I., Bebenek K., Matsuda T., Kunkel T.A. Somatic mutation hotspots correlate with DNA polymerase h error spectrum. // Nat. Immunol., 2001, V.2, N 6, 530-536.

Comments by U. Storb in News & Views (Nat. Immunol., 2001, V.2, N 6, 484-5), T. Toma in Genome Biology News (genomebiology.com/spotlights/articles/SpotlightCompiler.asp?xml=20010601-1.xml), BMC News (www.biomedcentral.com/news/20010531/03), M. Hagmann in ScienceNOW (sciencenow.sciencemag.org/cgi/ content/full/2001/601/4), and Nature Cancer Update (www.nature.com/cancer/hotp/200106/1.html).

 

Nesterova T.B., Slobodyanyuk S.Y., Elisaphenko E.A., Shevchenko A.V., Johnston C., Pavlova M.E., Rogozin I.B., Kolesnikov N.N., Brockdorff N., Zakian S.M. Characterisation of the genomic Xist locus in rodents reveals conservation of overall gene structure and tandem repeats but rapid evolution of unique sequence. // Genome Res., 2001, V.11, N 5, 833-849.

Comments by C. Holding (Trends Genet., 2001, V.17, N 8, 442 and Genome Biol., 2001, V.2, N 8, reports0021; genomebiology.com/2001/2/8/reports/0021/).

 

Kulikov V.N., Derkatch I.L., Noskov V.N., Tarunina O.V., Chernoff Y.O., Rogozin I.B., Pavlov Y.I. Mutagenic specificity of the base analog 6-N-hydroxylaminopurine in the LYS2 gene of yeast Saccharomyces cerevisia. // Mutat. Res., 2001, V.473, 151-161.

 

Rogozin I.B., Berikov V.B., Vasunina E.A., Sinitsina O.I. The effect of the primary structure of DNA on induction of mutations by alkylating agents. // Genetika (Mosc.), 2001, V.37, N 6, 854-861.

 

Wolf Y.I., Rogozin I.B., Kondrashov A.S., Koonin E.V. Genome alignment, evolution of prokaryotic genome organization and prediction of gene function using genomic context. // Genome Res., 2001, V.11, N 3, 356-372.

 

Rogozin I.B., Kondrashov F.A., Glazko G.V. Use of mutation spectra analysis software. // Hum. Mutat., 2001, V.17, N 2, 83-102.

 

Konstantinov Y.M., Tarasenko V.I., Rogozin I.B. Redox modulation of activity of mitochondrial topoisomerase I from carrot (Daucus carota). // Dokl. Akad. Nauk (Mosc.), 2001, V.377, N 2, 263-265.

 

Cattaneo M., Sorio C., Malferrari G., Rogozin I.B., Bernard L., Scarpa A., Zollo M., Biunno I. Analysis of SEL1L promoter region. // DNA Cell Biol., 2001, V.29, N 1, 1-9.

 

Rogozin I.B., Lyons-Weiler J., Koonin E.V. Intron sliding in conserved gene families. // Trends Genet., 2000, V.16, N 10, 430-432.

 

Mayorov V.I., Rogozin I.B., Elisaphenko E.A., Adkinson L.R. B2 elements present in the human genome. // Mamm. Genome, 2000, V.11, 177-179.

 

Rogozin I.B., Mayorov V.I., Lavrentieva M.V., Milanesi L., Adkison L.R. Prediction and phylogenetic analysis of mammalian short interspersed elements (SINEs). // Brief. Bioinform., 2000, V.1, N 3, 260-274.

 

Glazko G.V., Rogozin I.B., Glazkov M.V. Computer prediction of DNA regions associated with the nuclear matrix. // Mol. Biol. (Mosc.), 2000, V.34, N 1, 5-10.

 

Nei M., Rogozin I.B., Piontkivska H. Purifying selection and birth-and-death evolution in the ubiquitin gene family. // Proc. Natl. Acad. Sci. USA, 2000, V.97, N 20, 10866-10871.

 

Rogozin I.B., Glazko G.V., Glazkov M.V. Computer prediction of sites associated with various elements of the nuclear matrix. // Brief. Bioinform., 2000, V.1, N 1, 33-44.

 

Khromov-Borisov N.N., Rogozin I.B., Henriques J.A.H., de Serres F.J. Similarity pattern analysis (SPAN) in mutational distributions. // Mutat. Res., 1999, V.430, N 1, 55-74.

 

Babenko V.N., Rogozin I.B. Application of the rank correlation coefficient for comparison of mutation spectra. // Biofizika (Mosc.), 1999, V.44, N 4, 632-638.

 

Berikov V.B., Rogozin I.B. Regression trees for analysis of mutational spectra in nucleotide sequences. // Bioinformatics, 1999, V.15, N 7, 553-562.

 

Milanesi L., D'Angelo D., Rogozin I.B. GeneBuilder: interactive in silico prediction of genes structure. // Bioinformatics, 1999, V.15, N 7, 612-621.

 

Mayorov V.I., Rogozin I.B., Adkinson L.R. Characterization of several LINE-1 elements in Microtus kirgizorum. // Mamm. Genome, 1999, V.10, 724-729.

 

Glazko G.V., Rogozin I.B., Sozinov A.A. Analysis of mutational spectra of p53 gene in different tumors. // Tsitol. Genet. (Kiev), 1999, V.33, N 3, 15-23.

 

Rogozin I.B., D'Angelo D., Milanesi L. Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences. // Gene, 1999, V.226, N 1, 129-137.

 

Khrapov E.A., Elisafenko E.A., Rogozin I.B., Pavlova S.V., Vorob'eva N.V., Serdiukova N.A., Sablina O.V., Graphodatsky A.S., Zakian S.M. Novel STR47 tandemly repeated DNA family of Microtus rossiaemeridionalis. // Mol. Biol. (Mosc.), 1998, V.32, 987-991.

 

Elisaphenko E.A., Nesterova T.B., Duthie S.M., Ruldugina O.V., Rogozin I.B., Brockdorff N., Zakian S.M. Common vole: cloning, characterisation and chromosome localisation of two novel complex repeats MS3 and MS4 from the genome of the East-European vole Microtus rossiaemeridionalis. // Chromosome Res., 1998, V.6, N 5, 351-360.

 

Flood W.D., Rogozin I.B., Ruvinsky A. A novel subfamily of LINE-derived elements in mice. // Mamm. Genome, 1998, V.9, 881-885.

 

Kozmin S.G., Schaaper R.M., Shcherbakova P.V., Kulikov V.N., Noskov V.N., Guetsova M.L., Alenin V.V., Rogozin I.B., Makarova K.S. Pavlov Y.I. Multiple antimutagenesis mechanisms affect mutagenic activity and specificity of the base analog 6-N-hydroxylaminopurine in bacteria and yeast. // Mutat. Res., 1998, V.402, 41-50.

 

Glazkov M.V., Rogozin I.B., Glazko G.V. Comparison of the chromosomal DNA fragments from nuclear lamina, cores of rosette-like structures (elementary chromomers), MARs/SARs and synaptonemal complexes based on simple nucleotide motifs. // Mol. Biol (Mosc.), 1998, V.32, N 5, 883-894.

 

Fedorova E.V., Rogozin I.B., Ptitsyn A.A., Cheryaukene O.V., Kaftanovskaya E.M. Revealing and analysis of highly repeated DNA from wild ram. // Tsitol. Genet. (Kiev), 1998, V.32, N 5, 67-74.

 

Glazko G.V., Milanesi L., Rogozin I.B. The subclass approach for mutational spectrum analysis: application of the SEM algorithm. // J. Theor. Biol., 1998, V.192, N 4, 475-487.

 

Biunno I., Rogozin I.B., Apierto V., Milanesi L., Mostardini M., Mumm S., Pergolizzi R., Zucchi I., DeBellis G. Sequence and gene content in 35 kb genomic clone mapping in the human Xq27.1 region. // DNA Seq., 1997, V.8, 1-15.

 

Pozdniakov M.A., Rogozin I.B., Babenko V.N., Kolchanov N.A. Analysis of neighbor base influence on spontaneous mutations in human pseudogenes. // Dokl. Akad. Nauk (Mosc.), 1997, V.356, N 4, 566-568.

 

Rogozin I.B., Milanesi L. Analysis of donor splice sites in different eukaryotic organisms. // J. Mol. Evol., 1997, V.45, 50-59.

 

Glazko G.V., Rogozin I.B., Glazko V.I., Zelenaja L.B., Sozinov A.A. Experimental and computed spectra of UBC-85 and UBC-126 amplicones (RAPD-PCR). // Tsitol. Genet. (Kiev), 1997, V.31, N 5, 79-87.

 

Mostardini M., Apierto V., Pergolizzi R., Zucchi I., Mumm S., DeBellis G., Milanesi L., Rogozin I.B., Biunno I. Identification of a U7snRNA homologue mapping to the human Xq27.1 region, between the DXS1232 and DXS119 loci. // Gene, 1997, V.187, N 2, 221-224.

 

Rogozin I.B., Milanesi L., Kolchanov N.A. Gene structure prediction using information on homologous protein sequence. // Comput. Appl. Biosci., 1996, V.12, N 3, 161-170.

 

Mayorov V.I., Adkinson L.R., Vorobyeva N.V., Khrapov Eu.A., Kholodilov N.G., Rogozin I.B., Nesterova T.B., Protopopov A.I., Sablina O.V., Grafodatsky A.S., Zakian S.M. Organization and chromosomal localization of a B1-like containing repeat of Microtus subarvalis. // Mamm. Genome, 1996, V.7, 593-597.

 

Rogozin I.B., Sredneva N.E., Kolchanov N.A. Somatic hypermutagenesis in immunoglobulin genes. III. Somatic mutations in the chicken light chain locus. // Biochim. Biophys. Acta, 1996, V.1306, 171-178.

 

Ptitsyn A.A., Rogozin I.B., Grigorovich D.A., Strelets V.B., Kel A.E., Milanesi L., Kolchanov N.A. Computer system "AutoGene" for automatic analysis of nucleotide sequences // Mol.Biol. (Mosc.), 1996, V.30, N2, 436-445.

 

Rogozin I.B., Glasko G.V., Latkin E.I. Subclass approach for mutational spectrum analysis. In "Proceedings Third International Conference on Intelligent Systems for Molecular Biology" (eds. Rawlings C., Clark D., Altman L., Hunter L., Lengauer T., Wodak S.), AAAI Press, Menlo Park, 1995, 309-313.

 

Rogozin I.B., Kolchanov N.A., Milanesi L. A computing system for protein-coding regions prediction in Diptera nucleotide sequences. // Drosophila Information Service, 1995, V.76, 185-187.

 

Kholodilov N.G., Mayorov V.I., Mullokandov M.R., Cheryaukene O.V., Nesterova T.B., Rogozin I.B., Zakian S.M. Line-1 element in the vole Microtus subarvalis. // Mamm. Genome, 1993, V.4, 624-626.

 

Filippov V.A., Fedorova E.V., Rogozin I.B., Kholodilov N.G., Ruvinsky A.O. Molecular organization and evolution of the D17Leh80-like loci in the mouse t complex. // Mamm. Genome, 1992, V.3, 11-16.

 

Rogozin I.B., Kolchanov N.A. Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis. // Biochim. Biophys. Acta, 1992, V.1171, N 1, 11-18.

Included in a list of the classic papers on somatic hypermutation (Focus on Chromatin Dynamics, Special Focus Index, Nat. Immunology 2003, V.4, N 7, www.nature.com/ni/focus/chromatin_dynamics/classics/somatic.html).

 

Filippov V.A., Fedorova E.V., Rogozin I.B., Kholodilov N.G., Ruvinsky A.O. Structure and evolution of the D17Leh80-like loci in the mouse t complex. // Genetika (Mosc.), 1992, V.XXVII, 124-135.

 

Kholodilov N.G., Mayorov V.I., Mullokandov M.R., Cheryaukene O.V., Nesterova T.B., Rogozin I.B., Zakian S.M. L1-element of the vole Microtus subarvalis. // Dokl. Akad. Nauk (Mosc.), 1992, V.323, N 5, 963-965.

 

Lavrentieva M.V., Rivkin M.I., Godovikov A.A., Rogozin I.B., Serov O.L. Unusual structure of the B2-like repeat of the American mink. // Dokl. Akad. Nauk (Mosc.), 1991, V.320, N 3, 726-728.

 

Konstantinov Y.M., Rogozin I.B., Derenko M.V. Context analysis of linear DNA from mitochondria of maize: similarity with viral sequences. // Biopolimeri i Kletka (Kiev), 1991, V.7, 30-37.

 

Rogozin I.B., Solovyov V.V., Kolchanov N.A. Somatic hypermutagenesis in immunoglobulin genes. I. Correlation between somatic mutations and repeats. Somatic mutation properties and clonal selection. // Biochim. Biophys. Acta, 1991, V.1089, 175-182.

 

Lavrentieva M.V., Rivkin M.I., Shilov A.G., Kobetz M.L., Rogozin I.B., Serov O.L. B2-like repetitive sequence from the X chromosome of the American mink (Mustela vison). // Mamm. Genome, 1991, V.1, 165-170.

 

Rogozin I.B., Kolchanov N.A., Solovyov V.V., Sredneva N.E. A computer system for the analysis of a polynucleotide context influence on point mutations. // Biopolimeri i Kletka (Kiev), 1990, V.6, N 6, 22-31.

 

Serov O.L., Zhdanova N.S., Pack S.D., Lavrentieva M.V., Shilov A.G., Rivkin M.I., Matyakhina L.D., Draber P., Kerkis A.Y., Rogozin I.B., Borodin P.M. The mink X chromosome: organization and inactivation. // Prog. Clin. Biol. Res., 1990, V.344, 589-618.

 

Naiakshin A.M., Belousov E.S., Taranin A.V., Bogachev S.S., Rogozin I.B., Baranov O.K. Cloning and sequencing of immunoglobin lambda-chain cDNA in American mink (Mustela vison). // Genetika (Mosc.), 1990, V.XXVI, N 8, 1527-1531.

 

Rogozin I.B., Solovyov V.V. Somatic hypermutagenesis in immunoglobulin genes. II. Somatic mutation properties and clonal selection. // Mol. Biol. (Mosc.), 1989, V.23, N 3, 795-802.

 

Solovyov V.V., Rogozin I.B., Kolchanov N.A. Somatic hypermutagenesis in immunoglobulin genes. I. Connection between somatic mutations and repeats. The method of statistical weights. // Mol. Biol. (Mosc.), 1989, V.23, N 3, 783-794.

 

Kolchanov N.A., Rogozin I.B., Solovyov V.V. Theoretical analysis of the mechanisms of spontaneous and induced mutations in DNA on the basis of repeated sequences. // Genetika (Mosc.), 1989, V.XXV, N 9, 1690-1698.

 

Lavrentieva M.V., Rivkin M.I., Shilov A.G., Kobetz M.L., Rogozin I.B., Serov O.L. B2-like repetitive sequence in the genome of the American mink. // Dokl. Akad. Nauk (Mosc.), 1989, V.307, N 1, 226-228.

 

Kolchanov N.A., Solovyov V.V., Rogozin I.B. Peculiarities of immunoglobulin genes structures as a basis for somatic mutation emergence. // FEBS Lett.,1987, V.214, N 1, 87-91.

 

Kolchanov N.A., Solovyov V.V., Rogozin I.B. Molecular mechanism of somatic hypermutagenesis in immunoglobulin genes. // Dokl. Akad. Nauk (Mosc.), 1985, V.281, N 4, 994-999.

 

CHAPTERS IN BOOKS

 

Rogozin I.B. Protein-coding segments: evolution of exon-intron gene structure. In: Encyclopedia of Life Sciences, John Wiley & Sons, Chichester, 2009, www.els.net (DOI: 10.1002/9780470015902.a0000887.pub2).

 

Rogozin I.B., Wolf Y.I., Babenko V.N., Koonin E.V. Dollo parsimony and reconstruction of genome evolution. In: Parsimony, Phylogeny, and Genomics (ed. Albert V.A.), Oxford Univ. Press, Oxford, 2005, 190-200.

 

Katyshev A., Rogozin I.B., Konstantinov Y. Genome-wide identification of mitochondrial DNA topoisomerase I in Arabidopsis. In: Bioinformatics of Genome Regulation and Structure II (eds. Kolchanov N., Hofestaedt R.), Springer, New York, 2005, 141-145.

 

Kondrakhin Y.V., Rogozin I.B., Naykova T.M., Yudin N.S., Voevoda M.I., Romashchenko A.G. Type-specific features of the structure of the tRNA gene promoters. In: Bioinformatics of Genome Regulation and Structure (eds. Kolchanov N., Hofestaedt R.), Kluwer Academic Publishers, Boston/Dordrecht/London, 2004, 47-60.

 

Wolf Y.I., Rogozin I.B., Grishin N.V., Koonin E.V. Evolutionary analysis based on genome-scale sequence comparisons. In: Frontiers in Computational Genomics (eds. Galperin M.Y., Koonin E.V.), Caister Academic Press, Norfolk, 2003, 241-260.

 

Milanesi L., Rogozin I.B. Gene prediction tools. In: Protein Sequence Analysis in the Post Genomic Era (eds. Casadio R., Masotti L.), CLUEB Press, Bologna, 2001.

 

Milanesi L., Rogozin I.B. Prediction of human gene structure. In: Guide to Human Genome Computing (2nd ed.) (ed. Bishop M.J.), Academic Press, Cambridge, 1998, 215-259.

 

Milanesi L., Kolchanov N., Rogozin I., Kel A., Titov I. Sequence functional inference. In: Guide to Human Genome Computing (ed. Bishop M.J.), Academic Press, Cambridge, 1994, 249-312.

 

In: Computer analysis of genetic macromolecules: structure, function and evolution (compiled by Kolchanov N.A., Lim H.A.), World Scientific, Singapore, 1994 (co-authored 6 chapters):

Rogozin I.B., Milanesi L., Kolchanov N.A. Use of the classification approach in the construction of consensuses (human splice sites as an example). 21-28

Rogozin I.B., Milanesi L., Ischenko I.V., Kel A.E., Ponomarenko M.P., Kolchanov N.A., Orlov Yu.L. Computer system GenView for recognition of exon-intron structure of genes in the human genome. 142-153.

Kolchanov N.A., Rogozin I.B., Kel A.E., Sredneva N.E. Role of polynucleotide context in mutation and recombination. 252-264.

Rogozin I.B., Sredneva N.E., Kolchanov N.A. Computer system for analysis of molecular mechanisms of mutagenesis. 265-277.

Kolchanov N.A., Rogozin I.B. Contribution of nucleotide context to spontaneous and induced mutations. 278-288.

Rogozin I.B., Solovyev V.V., Kolchanov N.A. Somatic mutations in the immunoglobulin genes. 289-299.

 

EDUCATIONAL BOOKS FOR UNIVERSTY STUDENTS

 

Rogozin I.B., Sredneva N.E., Kolchanov N.A. Fundamentals of mutation processes: single and multiple nucleotide substitutions. Novosibirsk State University, Novosibirsk (Russ.), 1992, 86 p.

 

Solovyev V.V., Kel A.E., Rogozin I.B., Kolchanov N.A. Applications of computers in molecular biology: the theory of genetic texts. Novosibirsk State University, Novosibirsk (Russ.), 1987, 90 p.

 

SELECTED PROCEEDINGS PAPERS AND ABSTRACTS

 

Rogozin I.B., Babenko V.N. Evolution of spliceosomal introns: insights from comparative genomics. // J. Biomol. Struct. Dyn., 2005, V. 22, N 6, 793.

 

Vasyunina E.A., Rogozin I.B., Sinitsina O.I., Plaksina A.S., Rotskaya U.N. Theoretical and experimental study of mutations induced by 8-oxoguanine. In: “Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure”, IC&G Press, Novosibirsk, 2004, V.1, 200-203.

 

Smolyanitsky A.G., Khromov-Borisov N.N., Popov V.I., Zaslavsky G.I., Rogozin I.B., Henriques J.A.P., Kist T.B.L., Scheil H.-G. Statistical pattern analysis of D1S80 alleles in Northwestern Russians and worldwide database using COLLAPSE software. In: “International Congress Series”, 2003, V.1239, 665-671.

 

Timchenko T.V., Vasyunina E.A., Scheglova T.V., Rogozin I.B., Sinitsyna O.I. Computational prediction and experimental analysis of the curved DNAs as the hot spots of recombination. In: "Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure", IC&G Press, Novosibirsk, 2002, V.4, 40-41.

 

Scudo F.M., Laudani U., Rogozin I.B. Close microbial symbioses and systematics, In: "From Symbiosis to Eukaryotism. ENDOCYTOBIOLOGY VII" (eds. Wagner E. et al.), University of Geneva, Geneva, 1999, 741-756.

 

Mayorov V.I., Elisaphenko E.A., Rogozin I.B., Adkinson L.R. Short interspersed repeated B2 elements in the human genome. // Georgia Journal of Science, 1999, 57, 1, 83-84.

 

Mayorov V.I., Rogozin I.B., Adkinson L.R. Cloning and characterization of 5’region sequences from LINE-1 elements in the vole (Microtus kirgizorum). // Georgia Journal of Science, 1999, 57, 1, 84.

 

Kolesnikov N.N., Rogozin I.B., Lavrentieva M.V., Elisaphenko E.A. Three subfamalies of short interdispersed elements of the dog genome: possible origin and functions. In:"Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure", IC&G Press, Novosibirsk, 1998, V.2, 330-332.

 

Taranin A.V., Rogozin I.B. Searching for the immunoglobulin superfamily in C.elegans. In: "Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure", IC&G Press, Novosibirsk, 1998, V.2, 333-335.

 

Khromov-Borisov N.N., Rogozin I.B. CTC (contingency table collapse) - methodology useful for molecular epidemiology and mutational spectra analysis. // Environ. Mol. Mutagen., 1998, V.31, Suppl. 29, 69.

 

Rogozin I.B., Kolchanov N.A. Computer system for analysis of nucleotide context role in mutagenesis (MutAn). // J. Cell. Biochem., 1995, Suppl. 21A, 345.

 

Milanesi L., Ishenko I.V., Rogozin I.B., Kapitonov V., Kolchanov N.A., Kel A.E., Ponomarenko M.P. Computer system for genes structure prediction. In: "ECB6: Proceedings of the 6th European Congress on Biotechnology" (eds. Alberghina L., Frontali L., Sensi P.), Elsevier Science Publishers B.V., Amsterdam, 1994, 657-660.

 

Milanesi L., Kolchanov N.A., Rogozin I.B., Ischenko I.V., Kel A.E., Orlov Yu.L., Ponomarenko M.P., Vezzoni P. GenViewer: a computing tool for protein-coding regions prediction in nucleotide sequences. In: "Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis" (eds. Lim H.A., Fickett J.W., Cantor C.R., Robbins R.J.), World Scientific, Singapore, 1993, 573-588.

 

Rogozin I.B., Sredneva N.E., Kolchanov N.A. Intelligent system of mutational analysis. In: "Modelling and Computer Methods in Molecular Biology and Genetics" (eds. Ratner V.A., Kolchanov N.A.), Nova Sience Publishers, NY, 1992, 63-72.

 

Solovyev V.V., Rogozin I.B., Salikhova A.K., Seledtsov I.A., Salamov A.A., Kel A.E. "Context" package of computer programs for analysis of DNA, RNA and protein sequences. Searching for sequence similarities and functional sites. In: "Modelling and Computer Methods in Molecular Biology and Genetics" (eds. Ratner V.A., Kolchanov N.A.), Nova Sience Publishers, NY, 1992, 125-130.

 

Kolchanov N.A., Rogozin I.B., Kel A.E., Ponomarenko M.P., Lihachov J.A., Milanesi L. Computer analysis and recognition of human splice sites. In:"Genome Informatics Workshop II" (ed. Kanehisa M.), Tokyo, 1991, 104-107.