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Items: 1 to 50 of 208

1.

Genome-Wide Changes in Protein Translation Efficiency Are Associated with Autism.

Rogozin IB, Gertz EM, Baranov PV, Poliakov E, Schaffer AA.

Genome Biol Evol. 2018 Aug 1;10(8):1902-1919. doi: 10.1093/gbe/evy146.

2.

Purifying and positive selection in the evolution of stop codons.

Belinky F, Babenko VN, Rogozin IB, Koonin EV.

Sci Rep. 2018 Jun 18;8(1):9260. doi: 10.1038/s41598-018-27570-3.

3.

The Presence of Genotoxic and/or Pro-inflammatory Bacterial Genes in Gut Metagenomic Databases and Their Possible Link With Inflammatory Bowel Diseases.

Roche-Lima A, Carrasquillo-Carrión K, Gómez-Moreno R, Cruz JM, Velázquez-Morales DM, Rogozin IB, Baerga-Ortiz A.

Front Genet. 2018 Apr 10;9:116. doi: 10.3389/fgene.2018.00116. eCollection 2018.

4.

Diverse roles of RAD18 and Y-family DNA polymerases in tumorigenesis.

Yang Y, Gao Y, Zlatanou A, Tateishi S, Yurchenko V, Rogozin IB, Vaziri C.

Cell Cycle. 2018;17(7):833-843. doi: 10.1080/15384101.2018.1456296. Epub 2018 May 8.

5.

Recombination Is Responsible for the Increased Recovery of Drug-Resistant Mutants with Hypermutated Genomes in Resting Yeast Diploids Expressing APOBEC Deaminases.

Lada AG, Stepchenkova EI, Zhuk AS, Kliver SF, Rogozin IB, Polev DE, Dhar A, Pavlov YI.

Front Genet. 2017 Dec 12;8:202. doi: 10.3389/fgene.2017.00202. eCollection 2017.

6.

Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite Leishmania.

Grybchuk D, Akopyants NS, Kostygov AY, Konovalovas A, Lye LF, Dobson DE, Zangger H, Fasel N, Butenko A, Frolov AO, Votýpka J, d'Avila-Levy CM, Kulich P, Moravcová J, Plevka P, Rogozin IB, Serva S, Lukeš J, Beverley SM, Yurchenko V.

Proc Natl Acad Sci U S A. 2018 Jan 16;115(3):E506-E515. doi: 10.1073/pnas.1717806115. Epub 2017 Dec 28.

7.

DNA polymerase η mutational signatures are found in a variety of different types of cancer.

Rogozin IB, Goncearenco A, Lada AG, De S, Yurchenko V, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI.

Cell Cycle. 2018;17(3):348-355. doi: 10.1080/15384101.2017.1404208. Epub 2018 Feb 15.

PMID:
29139326
8.

Involvement of DNA mismatch repair in the maintenance of heterochromatic DNA stability in Saccharomyces cerevisiae.

Dahal BK, Kadyrova LY, Delfino KR, Rogozin IB, Gujar V, Lobachev KS, Kadyrov FA.

PLoS Genet. 2017 Oct 25;13(10):e1007074. doi: 10.1371/journal.pgen.1007074. eCollection 2017 Oct.

9.

Phylogenetic analysis of the metazoan carotenoid oxygenase superfamily: a new ancestral gene assemblage of BCO-like (BCOL) proteins.

Poliakov E, Soucy J, Gentleman S, Rogozin IB, Redmond TM.

Sci Rep. 2017 Oct 16;7(1):13192. doi: 10.1038/s41598-017-13521-x.

10.

Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions.

Belinky F, Rogozin IB, Koonin EV.

Sci Rep. 2017 Sep 29;7(1):12422. doi: 10.1038/s41598-017-12619-6.

11.

Mutational signatures and mutable motifs in cancer genomes.

Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN.

Brief Bioinform. 2017 May 11. doi: 10.1093/bib/bbx049. [Epub ahead of print]

PMID:
28498882
12.

Exploring background mutational processes to decipher cancer genetic heterogeneity.

Goncearenco A, Rager SL, Li M, Sang QX, Rogozin IB, Panchenko AR.

Nucleic Acids Res. 2017 Jul 3;45(W1):W514-W522. doi: 10.1093/nar/gkx367.

13.

Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers.

Rogozin IB, Lada AG, Goncearenco A, Green MR, De S, Nudelman G, Panchenko AR, Koonin EV, Pavlov YI.

Sci Rep. 2016 Dec 7;6:38133. doi: 10.1038/srep38133.

14.

Evolutionary switches between two serine codon sets are driven by selection.

Rogozin IB, Belinky F, Pavlenko V, Shabalina SA, Kristensen DM, Koonin EV.

Proc Natl Acad Sci U S A. 2016 Nov 15;113(46):13109-13113. Epub 2016 Oct 31.

15.

Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals.

Chernikova D, Managadze D, Glazko GV, Makalowski W, Rogozin IB.

Life (Basel). 2016 Jul 15;6(3). pii: E27. doi: 10.3390/life6030027.

16.

Germline viral "fossils" guide in silico reconstruction of a mid-Cenozoic era marsupial adeno-associated virus.

Smith RH, Hallwirth CV, Westerman M, Hetherington NA, Tseng YS, Cecchini S, Virag T, Ziegler ML, Rogozin IB, Koonin EV, Agbandje-McKenna M, Kotin RM, Alexander IE.

Sci Rep. 2016 Jul 5;6:28965. doi: 10.1038/srep28965.

17.

Retention of duplicated ITAM-containing transmembrane signaling subunits in the tetraploid amphibian species Xenopus laevis.

Guselnikov SV, Grayfer L, De Jesús Andino F, Rogozin IB, Robert J, Taranin AV.

Dev Comp Immunol. 2015 Nov;53(1):158-68. doi: 10.1016/j.dci.2015.07.002. Epub 2015 Jul 11.

18.

Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes.

Kannan S, Chernikova D, Rogozin IB, Poliakov E, Managadze D, Koonin EV, Milanesi L.

Front Bioeng Biotechnol. 2015 Jun 9;3:71. doi: 10.3389/fbioe.2015.00071. eCollection 2015.

19.

Disruption of Transcriptional Coactivator Sub1 Leads to Genome-Wide Re-distribution of Clustered Mutations Induced by APOBEC in Active Yeast Genes.

Lada AG, Kliver SF, Dhar A, Polev DE, Masharsky AE, Rogozin IB, Pavlov YI.

PLoS Genet. 2015 May 5;11(5):e1005217. doi: 10.1371/journal.pgen.1005217. eCollection 2015 May.

20.

Genetics in genomic era.

Poliakov E, Cooper DN, Stepchenkova EI, Rogozin IB.

Genet Res Int. 2015;2015:364960. doi: 10.1155/2015/364960. Epub 2015 Mar 25. No abstract available.

21.

Emergence and subsequent functional specialization of kindlins during evolution of cell adhesiveness.

Meller J, Rogozin IB, Poliakov E, Meller N, Bedanov-Pack M, Plow EF, Qin J, Podrez EA, Byzova TV.

Mol Biol Cell. 2015 Feb 15;26(4):786-96. doi: 10.1091/mbc.E14-08-1294. Epub 2014 Dec 24.

22.

MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes.

Kannan S, Rogozin IB, Koonin EV.

BMC Evol Biol. 2014 Nov 25;14:237. doi: 10.1186/s12862-014-0237-5.

23.

Comparative mutational analyses of influenza A viruses.

Cheung PP, Rogozin IB, Choy KT, Ng HY, Peiris JS, Yen HL.

RNA. 2015 Jan;21(1):36-47. doi: 10.1261/rna.045369.114. Epub 2014 Nov 17.

24.

Generalized portrait of cancer metabolic pathways inferred from a list of genes overexpressed in cancer.

Poliakov E, Managadze D, Rogozin IB.

Genet Res Int. 2014;2014:646193. doi: 10.1155/2014/646193. Epub 2014 Aug 27.

25.

Complexity of gene expression evolution after duplication: protein dosage rebalancing.

Rogozin IB.

Genet Res Int. 2014;2014:516508. doi: 10.1155/2014/516508. Epub 2014 Aug 17. Review.

26.

Impairment of translation in neurons as a putative causative factor for autism.

Poliakov E, Koonin EV, Rogozin IB.

Biol Direct. 2014 Jul 10;9:16. doi: 10.1186/1745-6150-9-16.

27.

Gene family level comparative analysis of gene expression in mammals validates the ortholog conjecture.

Rogozin IB, Managadze D, Shabalina SA, Koonin EV.

Genome Biol Evol. 2014 Apr;6(4):754-62. doi: 10.1093/gbe/evu051.

28.

Genetic characterization of feline calicivirus strains associated with varying disease manifestations during an outbreak season in Missouri (1995-1996).

Prikhodko VG, Sandoval-Jaime C, Abente EJ, Bok K, Parra GI, Rogozin IB, Ostlund EN, Green KY, Sosnovtsev SV.

Virus Genes. 2014 Feb;48(1):96-110. doi: 10.1007/s11262-013-1005-0. Epub 2013 Nov 12.

PMID:
24217871
29.

Genome-wide mutation avalanches induced in diploid yeast cells by a base analog or an APOBEC deaminase.

Lada AG, Stepchenkova EI, Waisertreiger IS, Noskov VN, Dhar A, Eudy JD, Boissy RJ, Hirano M, Rogozin IB, Pavlov YI.

PLoS Genet. 2013;9(9):e1003736. doi: 10.1371/journal.pgen.1003736. Epub 2013 Sep 5.

30.

The vast, conserved mammalian lincRNome.

Managadze D, Lobkovsky AE, Wolf YI, Shabalina SA, Rogozin IB, Koonin EV.

PLoS Comput Biol. 2013;9(2):e1002917. doi: 10.1371/journal.pcbi.1002917. Epub 2013 Feb 28.

31.

AID/APOBEC cytosine deaminase induces genome-wide kataegis.

Lada AG, Dhar A, Boissy RJ, Hirano M, Rubel AA, Rogozin IB, Pavlov YI.

Biol Direct. 2012 Dec 18;7:47; discussion 47. doi: 10.1186/1745-6150-7-47.

32.

Origin and evolution of retinoid isomerization machinery in vertebrate visual cycle: hint from jawless vertebrates.

Poliakov E, Gubin AN, Stearn O, Li Y, Campos MM, Gentleman S, Rogozin IB, Redmond TM.

PLoS One. 2012;7(11):e49975. doi: 10.1371/journal.pone.0049975. Epub 2012 Nov 27.

33.

Whence genes in pieces: reconstruction of the exon-intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes.

Koonin EV, Csuros M, Rogozin IB.

Wiley Interdiscip Rev RNA. 2013 Jan-Feb;4(1):93-105. doi: 10.1002/wrna.1143. Epub 2012 Nov 8. Review.

PMID:
23139082
34.

Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools.

Waisertreiger IS, Liston VG, Menezes MR, Kim HM, Lobachev KS, Stepchenkova EI, Tahirov TH, Rogozin IB, Pavlov YI.

Environ Mol Mutagen. 2012 Dec;53(9):699-724. doi: 10.1002/em.21735. Epub 2012 Oct 10. Review.

35.

Computational prediction of polycomb-associated long non-coding RNAs.

Glazko GV, Zybailov BL, Rogozin IB.

PLoS One. 2012;7(9):e44878. doi: 10.1371/journal.pone.0044878. Epub 2012 Sep 13.

36.

Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases.

Hashimoto K, Rogozin IB, Panchenko AR.

Hum Mutat. 2012 Nov;33(11):1566-75. doi: 10.1002/humu.22145. Epub 2012 Jul 16.

37.

Novel aspects of Kindlin-3 function in humans based on a new case of leukocyte adhesion deficiency III.

Meller J, Malinin NL, Panigrahi S, Kerr BA, Patil A, Ma Y, Venkateswaran L, Rogozin IB, Mohandas N, Ehlayel MS, Podrez EA, Chinen J, Byzova TV.

J Thromb Haemost. 2012 Jul;10(7):1397-408. doi: 10.1111/j.1538-7836.2012.04768.x.

38.

Origin and evolution of spliceosomal introns.

Rogozin IB, Carmel L, Csuros M, Koonin EV.

Biol Direct. 2012 Apr 16;7:11. doi: 10.1186/1745-6150-7-11. Review.

39.

Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs.

Managadze D, Rogozin IB, Chernikova D, Shabalina SA, Koonin EV.

Genome Biol Evol. 2011;3:1390-404. doi: 10.1093/gbe/evr116. Epub 2011 Nov 9.

40.

Replication protein A (RPA) hampers the processive action of APOBEC3G cytosine deaminase on single-stranded DNA.

Lada AG, Waisertreiger IS, Grabow CE, Prakash A, Borgstahl GE, Rogozin IB, Pavlov YI.

PLoS One. 2011;6(9):e24848. doi: 10.1371/journal.pone.0024848. Epub 2011 Sep 15.

41.

A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes.

Csuros M, Rogozin IB, Koonin EV.

PLoS Comput Biol. 2011 Sep;7(9):e1002150. doi: 10.1371/journal.pcbi.1002150. Epub 2011 Sep 15.

42.

Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems.

Iyer LM, Zhang D, Rogozin IB, Aravind L.

Nucleic Acids Res. 2011 Dec;39(22):9473-97. doi: 10.1093/nar/gkr691. Epub 2011 Sep 3.

43.

A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes.

Chernikova D, Motamedi S, Csürös M, Koonin EV, Rogozin IB.

Biol Direct. 2011 May 19;6:26. doi: 10.1186/1745-6150-6-26.

44.

Mutator effects and mutation signatures of editing deaminases produced in bacteria and yeast.

Lada AG, Krick CF, Kozmin SG, Mayorov VI, Karpova TS, Rogozin IB, Pavlov YI.

Biochemistry (Mosc). 2011 Jan;76(1):131-46.

45.

Tandem termination signal in plant mRNAs.

Kochetov AV, Volkova OA, Poliakov A, Dubchak I, Rogozin IB.

Gene. 2011 Jul 15;481(1):1-6. doi: 10.1016/j.gene.2011.04.002. Epub 2011 Apr 22.

46.

The ecoresponsive genome of Daphnia pulex.

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL.

Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761.

47.

Mismatch repair-independent increase in spontaneous mutagenesis in yeast lacking non-essential subunits of DNA polymerase ε.

Aksenova A, Volkov K, Maceluch J, Pursell ZF, Rogozin IB, Kunkel TA, Pavlov YI, Johansson E.

PLoS Genet. 2010 Nov 18;6(11):e1001209. doi: 10.1371/journal.pgen.1001209.

48.

Primate and rodent specific intron gains and the origin of retrogenes with splice variants.

Szcześniak MW, Ciomborowska J, Nowak W, Rogozin IB, Makałowska I.

Mol Biol Evol. 2011 Jan;28(1):33-7. doi: 10.1093/molbev/msq260. Epub 2010 Oct 1.

49.

EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution.

Carmel L, Wolf YI, Rogozin IB, Koonin EV.

Adv Bioinformatics. 2010:167408. doi: 10.1155/2010/167408. Epub 2010 May 6.

50.

Genome evolution.

Makałowska I, Rogozin IB, Makałowski W.

Adv Bioinformatics. 2010;2010:643701. doi: 10.1155/2010/643701. Epub 2011 Jul 21. No abstract available.

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