I. Rogozin

发表

Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution.

D. M. Krylov, E. Koonin, Y. Wolf, 2003, Genome research.

Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.

E. Koonin, Y. Wolf, A. Kondrashov, 2001, Genome research.

Analysis of phylogenetically reconstructed mutational spectra in human mitochondrial DNA control region

I. Rogozin, B. Malyarchuk, V. Berikov, 2002, Human Genetics.

Mutation hotspots in the p53 gene in tumors of different origin: correlation with evolutionary conservation and signs of positive selection.

G. Glazko, E. Koonin, I. Rogozin, 2004, Biochimica et biophysica acta.

Use of mutation spectra analysis software

G. Glazko, F. Kondrashov, I. Rogozin, 2001, Human mutation.

Selection in the evolution of gene duplications

E. Koonin, Y. Wolf, F. Kondrashov, 2002, Genome Biology.

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens

Darren A. Natale, L. Aravind, Igor B. Rogozin, 2002, Proceedings of the National Academy of Sciences of the United States of America.

A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.

Nick V Grishin, Eugene V Koonin, Kira S Makarova, 2002, Nucleic acids research.

Purifying and directional selection in overlapping prokaryotic genes.

Eugene V Koonin, I King Jordan, Yuri I Wolf, 2002, Trends in genetics : TIG.

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

L. Aravind, Igor B. Rogozin, Lakshminarayan M. Iyer, 2011, Nucleic acids research.

Dollo parsimony and the reconstruction of genome evolution

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, 2006 .

Tandem termination signal in plant mRNAs.

O. A. Volkova, I. Dubchak, Alexander Poliakov, 2011, Gene.

Origin and evolution of spliceosomal introns

Liran Carmel, Eugene V Koonin, Miklos Csuros, 2012, Biology Direct.

Connected gene neighborhoods in prokaryotic genomes.

Eugene V Koonin, Yuri I Wolf, Roman L Tatusov, 2002, Nucleic acids research.

Conservation versus parallel gains in intron evolution

E. Koonin, I. Rogozin, V. Babenko, 2005, Nucleic acids research.

Three distinct modes of intron dynamics in the evolution of eukaryotes.

E. Koonin, Y. Wolf, L. Carmel, 2007, Genome research.

Patterns of intron gain and conservation in eukaryotic genes

E. Koonin, Y. Wolf, L. Carmel, 2007, BMC Evolutionary Biology.

Evolution of protein domain promiscuity in eukaryotes.

E. Koonin, L. Carmel, I. Rogozin, 2008, Genome research.

Essential genes are more evolutionarily conserved than are nonessential genes in bacteria.

E. Koonin, Y. Wolf, I. Rogozin, 2002, Genome research.

Remarkable Interkingdom Conservation of Intron Positions and Massive, Lineage-Specific Intron Loss and Gain in Eukaryotic Evolution

E. Koonin, Y. Wolf, B. Mirkin, 2003, Current Biology.

Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.

A. N. Spiridonov, E. Koonin, Y. Wolf, 2002, Nucleic acids research.

Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants

I. Rogozin, M. Szcześniak, I. Makałowska, 2010, Molecular biology and evolution.

Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis.

E. Koonin, Y. Wolf, I. Rogozin, 2003, Genome research.

Evolution of protein domain promiscuity in eukaryotes data

L. Carmel, I. Rogozin, Kumar Basu, 2008 .

Genome trees constructed using five different approaches suggest new major bacterial clades

N. Grishin, E. Koonin, Y. Wolf, 2001, BMC Evolutionary Biology.

The Ecoresponsive Genome of Daphnia pulex

Todd H. Oakley, Abraham E. Tucker, Rupali Patwardhan, 2011, Science.

Method of predicting Splice Sites based on signal interactions

J. Deogun, I. Rogozin, Hesham H. Ali, 2006, Biology Direct.

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

A. Panchenko, K. Hashimoto, I. Rogozin, 2012, Human mutation.

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

Jodie J. Yin, D. M. Krylov, E. Koonin, 2004, Genome Biology.

Origin of a substantial fraction of human regulatory sequences from transposable elements.

G. Glazko, E. Koonin, I. Rogozin, 2003, Trends in genetics : TIG.

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ

E. Koonin, Y. Wolf, K. Makarova, 2003, Genome Biology.

Genome trees and the tree of life.

N. Grishin, E. Koonin, Y. Wolf, 2002, Trends in genetics : TIG.

Intron sliding in conserved gene families.

E. Koonin, James Lyons-Weiler, I. Rogozin, 2000, Trends in genetics : TIG.

Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns

Colin N. Dewey, E. Koonin, I. Rogozin, 2006, BMC Genomics.

Evolutionarily conserved genes preferentially accumulate introns.

E. Koonin, Y. Wolf, L. Carmel, 2007, Genome research.

Evolutionary conservation suggests a regulatory function of AUG triplets in 5′-UTRs of eukaryotic genes

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, 2005, Nucleic acids research.

Evolution of alternative and constitutive regions of mammalian 5'UTRs

Eugene V Koonin, Aleksey Y Ogurtsov, Alissa M. Resch, 2009, BMC Genomics.

Genetics in Genomic Era

D. Cooper, I. Rogozin, E. Poliakov, 2015, Genetics research international.

GenViewer: A computing tool for protein-coding regions prediction in nucleotide sequences

Alexander E. Kel, Luciano Milanesi, Nikolay A. Kolchanov, 1993 .

Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins

Eugene V Koonin, I King Jordan, Yuri I Wolf, 2001, Genome Biology.

Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome

Michael Y. Galperin, Igor B. Rogozin, Patrick Wincker, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

Liran Carmel, Miklós Csürös, Eugene V Koonin, 2008, Biology Direct.

Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements.

Liran Carmel, Eugene V Koonin, Yuri I Wolf, 2007, Molecular biology and evolution.

Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation.

Jie Zheng, Eugene V Koonin, Teresa M Przytycka, 2007, Molecular biology and evolution.

Analysis of rare amino acid replacements supports the Coelomata clade.

E. Koonin, Y. Wolf, L. Carmel, 2007, Molecular biology and evolution.

Analysis of donor splice sites in different eukaryotic organisms

Luciano Milanesi, Igor B. Rogozin, L. Milanesi, 1997, Journal of Molecular Evolution.

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

E. Koonin, I. Rogozin, M. Csűros, 2013, Wiley interdisciplinary reviews. RNA.

Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues.

E. Koonin, I. Rogozin, W. Martin, 2007, Molecular biology and evolution.

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

V. I. Mayorov, I. Rogozin, T. Karpova, 2011, Biochemistry (Moscow).

Microevolutionary genomics of bacteria.

Eugene V Koonin, I King Jordan, Yuri I Wolf, 2002, Theoretical population biology.

Volatile Evolution of Long Non-Coding RNA Repertoire in Retinal Pigment Epithelium: Insights from Comparison of Bovine and Human RNA Expression Profiles

I. Rogozin, V. Babenko, G. Nudelman, 2019, Genes.

Evidence of Splice Signal Migration from Exon to Intron during Intron Evolution

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, 2003, Current Biology.

Evolution of Exons and the Exon–Intron Structure of Long Intergenic Noncoding RNA Genes in Placental Mammals

I. Rogozin, V. Babenko, I. A. Sidorenko, 2019, Biology Bulletin Reviews.

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

G. Glazko, W. Makałowski, I. Rogozin, 2016, Life.

Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes

E. Koonin, L. Milanesi, I. Rogozin, 2015, Front. Bioeng. Biotechnol..

Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs

Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin, 2011, Genome biology and evolution.

Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes

G. Glazko, D. Cooper, I. Rogozin, 2019, Cancers.

From Context-Dependence of Mutations to Molecular Mechanisms of Mutagenesis

Luciano Milanesi, Igor B. Rogozin, Youri I. Pavlov, 2004, Pacific Symposium on Biocomputing.

Context of deletions and insertions in human coding sequences

Alexey S Kondrashov, A. Kondrashov, I. Rogozin, 2004, Human mutation.

Stable Intronic Sequences and Exon Skipping Events in the Human RPE65 Gene: Analysis of Expression in Retinal Pigment Epithelium Cells and Cell Culture Models

I. Rogozin, N. Golestaneh, T. Redmond, 2019, Front. Genet..

Low Variability of the POLG (CAG) n Repeat in North Eurasian Populations

I. Rogozin, S. Rychkov, B. Malyarchuk, 2005, Human biology.

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

E. Koonin, I. Rogozin, E. Poliakov, 2014, Biology Direct.

Complexity of Gene Expression Evolution after Duplication: Protein Dosage Rebalancing

I. Rogozin, 2014, Genetics research international.

Crossing fitness valleys via double substitutions within codons

E. Koonin, I. Rogozin, Frida Belinky, 2019, BMC Biology.

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

E. Gertz, P. Baranov, I. Rogozin, 2018, Genome biology and evolution.

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

A. Panchenko, D. Cooper, S. De, 2018, Cell cycle.

AUTOGENE: A COMPUTER SYSTEM FOR NUCLEOTIDE SEQUENCE ANALYSIS

L. Milanesi, A. Kel, N. Kolchanov, 1996 .

A maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure.

E. Koonin, Y. Wolf, L. Carmel, 2009, Methods in molecular biology.

F. D. de Serres, I. Rogozin, N. Khromov-Borisov, 1999, Mutation research.

ESTMAP: a system for expressed sequence tags mapping on genomic sequences

L. Milanesi, I. Rogozin, 2003, IEEE Transactions on NanoBioscience.

[Context organization of mRNA 5'-untranslated regions of higher plants].

G. Glazko, I. Rogozin, A. Kochetov, 2002, Molekuliarnaia biologiia.

Crossing fitness valleys via double substitutions within codons

E. Koonin, I. Rogozin, Frida Belinky, 2019, BMC Biology.

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.

E. Koonin, L. Aravind, I. Rogozin, 2003, Journal of molecular biology.

Evolutionary switches between two serine codon sets are driven by selection

E. Koonin, D. Kristensen, S. Shabalina, 2016, Proceedings of the National Academy of Sciences.

Template switching and duplications in SARS-CoV-2 genomes give rise to insertion variants that merit monitoring

E. Koonin, I. Rogozin, S. Garushyants, 2021, Communications Biology.

Molecular organization and evolution of the D17Leh80-like loci in the mouse t complex

I. Rogozin, E. V. Fedorova, N. Kholodilov, 2004, Mammalian Genome.

U12 intron positions are more strongly conserved between animals and plants than U2 intron positions

E. Koonin, W. Makałowski, I. Rogozin, 2008, Biology Direct.

Protein-Coding Segments: Evolution of Exon–Intron Gene Structure

I. Rogozin, 2009 .

Analysis of Stop Codons within Prokaryotic Protein-Coding Genes Suggests Frequent Readthrough Events

I. Rogozin, Frida Belinky, V. Yurchenko, 2021, International journal of molecular sciences.

Low-fidelity DNA synthesis by the L 979 F mutator derivative of Saccharomyces cerevisiae DNA polymerase zeta

T. Kunkel, I. Rogozin, G. Kissling, 2018 .

Purifying and positive selection in the evolution of stop codons

E. Koonin, I. Rogozin, V. Babenko, 2018, Scientific Reports.

Comparative mutational analyses of influenza A viruses

J. Peiris, I. Rogozin, H. Yen, 2015, RNA.

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

I. Rogozin, C. Vaziri, V. Yurchenko, 2018, Cell cycle.

No evidence for widespread positive selection on double substitutions within codons in primates and yeasts

I. Rogozin, Frida Belinky, V. Yurchenko, 2022, Frontiers in Genetics.

Compensation for the absence of the catalytically active half of DNA polymerase ε in yeast by positively selected mutations in CDC28 gene

I. Rogozin, R. Fedorov, E. Tarakhovskaya, 2020, bioRxiv.

Accumulation of GC donor splice signals in mammals

E. Koonin, I. Rogozin, S. Winters-Hilt, 2008, Biology Direct.

Sequence and gene content in 35 kb genomic clone mapping in the human Xq27.1 region.

L. Milanesi, R. Pergolizzi, I. Rogozin, 1997, DNA sequence : the journal of DNA sequencing and mapping.

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

E. Podrez, I. Rogozin, T. Byzova, 2012, Journal of thrombosis and haemostasis : JTH.

Palmitoylation of Metazoan Carotenoid Oxygenases

I. Rogozin, S. Uppal, T Michael Redmond, 2020, Molecules.

Elimination of LRVs Elicits Different Responses in Leishmania spp.

E. Servienė, I. Rogozin, V. Yurchenko, 2022, mSphere.

Characterization of several LINE-1 elements in Microtus kirgisorum

I. Rogozin, V. Mayorov, L. Adkison, 1999, Mammalian Genome.

Redox Modulation of the Activity of DNA Topoisomerase I from Carrot (Daucus carota) Mitochondria

I. Rogozin, V. Tarasenko, Y. Konstantinov, 2001, Doklady Biochemistry and Biophysics.

Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix.

M. V. Glazkov, G. Glazko, I. Rogozin, 2001, Biochimica et biophysica acta.

Frequent Recombination Events in Leishmania donovani: Mining Population Data

I. Rogozin, V. Babenko, V. Yurchenko, 2020, Pathogens.

Mismatch Repair–Independent Increase in Spontaneous Mutagenesis in Yeast Lacking Non-Essential Subunits of DNA Polymerase ε

T. Kunkel, I. Rogozin, Z. Pursell, 2010, PLoS genetics.

Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis.

N A Kolchanov, N. Kolchanov, I. Rogozin, 1992, Biochimica et biophysica acta.

The effect of the Primary Structure of DNA on Induction of Mutations by Alkylating Agents

I. Rogozin, V. Berikov, O. Sinitsina, 2001, Russian Journal of Genetics.

Response 1 to 'Smaller role for pol η?'

I. Rogozin, Y. Pavlov, T. Kunkel, 2001, Nature Immunology.

[The mutational spectra of gene p53 in different types of tumors].

G. Glazko, I. Rogozin, A. Sozinov, 1999, TSitologiia i genetika.

Cloning of human centromeres by transformation-associated recombination in yeast and generation of functional human artificial chromosomes.

M. Koriabine, M. Oshimura, J. Barrett, 2003, Nucleic acids research.

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta

E. Koonin, I. Rogozin, T. Tahirov, 2008, Cell cycle.

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.

E. Koonin, I. Rogozin, W. Jelkmann, 2007, Virus Research.

Correlation of somatic hypermutation specificity and A-T base pair substitution errors by DNA polymerase η during copying of a mouse immunoglobulin κ light chain transgene

T. Kunkel, C. Rada, I. Rogozin, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Analysis of mitochondrial DNA somatic mutations in OXYS and Wistar strain rats

I. Rogozin, B. Malyarchuk, O. Sinitsyna, 2009, Biochemistry (Moscow).

Comment on “A commensal strain of Staphylococcus epidermidis protects against skin neoplasia” by Nakatsuji et al.

R. Schaaper, I. Rogozin, S. Kozmin, 2019, Science Advances.

Multiple antimutagenesis mechanisms affect mutagenic activity and specificity of the base analog 6-N-hydroxylaminopurine in bacteria and yeast.

V. Noskov, K. Makarova, R. Schaaper, 1998, Mutation research.

The SPANX gene family of cancer/testis-specific antigens: rapid evolution and amplification in African great apes and hominids.

E. Koonin, J. Barrett, N. Kouprina, 2004, Proceedings of the National Academy of Sciences of the United States of America.

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes

Igor B. Rogozin, Miklós Csürös, Eugene V. Koonin, 2011, PLoS Comput. Biol..

Computational Prediction of Polycomb-Associated Long Non-Coding RNAs

Galina V. Glazko, Igor B. Rogozin, G. Glazko, 2012, PloS one.

On the Etruscan mitochondrial DNA contribution to modern humans.

I. Rogozin, B. Malyarchuk, 2004, American journal of human genetics.

B2-like repetitive sequence from the X Chromosome of the American mink (Mustela vison)

M. V. Lavrentieva, A. G. Shilov, I. Rogozin, 2004, Mammalian Genome.

The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers

E. Koonin, K. Makarova, I. Rogozin, 2003, Genome Biology.

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

E. Koonin, I. Rogozin, E. Poliakov, 2014, Biology Direct.

Dopamine response gene pathways in dorsal striatum MSNs from a gene expression viewpoint: cAMP-mediated gene networks

I. Rogozin, V. Babenko, D. Smagin, 2019, BMC Neuroscience.

Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes

I. Rogozin, V. Brover, V. Yurchenko, 2023, Microorganisms.

Genome-Wide Mutation Avalanches Induced in Diploid Yeast Cells by a Base Analog or an APOBEC Deaminase

Igor B. Rogozin, Youri I. Pavlov, Artem G. Lada, 2013, PLoS genetics.

Widespread positive selection in synonymous sites of mammalian genes.

Liran Carmel, Eugene V Koonin, Aleksey Y Ogurtsov, 2007, Molecular biology and evolution.

Theoretical analysis of mutation hotspots and their DNA sequence context specificity.

I. Rogozin, Igor B Rogozin, Y. Pavlov, 2003, Mutation research.

Cross-species conservation of SEL1L, a human pancreas-specific expressing gene.

I. Rogozin, I. Biunno, B. Castiglioni, 2002, Omics : a journal of integrative biology.

Cloning and functional analysis of SEL1L promoter region, a pancreas-specific gene.

I. Rogozin, I. Biunno, M. Zollo, 2001, DNA and cell biology.

Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.

Eugene V Koonin, Aleksey Y Ogurtsov, David J Lipman, 2004, Nucleic acids research.

A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions.

Eugene V Koonin, G. Glazko, E. Koonin, 2003, Trends in genetics : TIG.

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

I. Rogozin, F. Kadyrov, K. Delfino, 2017, PLoS genetics.

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

I. Rogozin, T. Tahirov, M. Menezes, 2012, Environmental and molecular mutagenesis.

The Vast, Conserved Mammalian lincRNome

Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin, 2013, PLoS Comput. Biol..

Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis

Eugene V Koonin, Fyodor A Kondrashov, E. Koonin, 2006, BMC Cancer.

Molecular dating: ape bones agree with chicken entrails.

G. Glazko, E. Koonin, I. Rogozin, 2005, Trends in genetics : TIG.

129-derived Strains of Mice Are Deficient in DNA Polymerase ι and Have Normal Immunoglobulin Hypermutation

E. G. Frank, R. Woodgate, I. Rogozin, 2003, The Journal of experimental medicine.

Replication Protein A (RPA) Hampers the Processive Action of APOBEC3G Cytosine Deaminase on Single-Stranded DNA

G. Borgstahl, I. Rogozin, I. Waisertreiger, 2011, PloS one.

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

Igor B. Rogozin, Youri I. Pavlov, Artem G. Lada, 2015, PLoS genetics.

Somatic mutation hotspots correlate with DNA polymerase η error spectrum

Toshiro Matsuda, T. Kunkel, I. Rogozin, 2001, Nature Immunology.

Prediction and Phylogenetic Analysis of Mammalian Short Interspersed Elements (SINEs)

Luciano Milanesi, Igor B. Rogozin, V. I. Mayorov, 2000, Briefings Bioinform..

Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences.

L Milanesi, L. Milanesi, I. Rogozin, 1999, Gene.

10 – Prediction of Human Gene Structure

Luciano Milanesi, Igor B. Rogozin, L. Milanesi, 1998 .

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

Subhajyoti De, Anna R. Panchenko, Igor B. Rogozin, 2016, Scientific Reports.

Unravelling roles of error-prone DNA polymerases in shaping cancer genomes

I. Rogozin, C. Vaziri, Tovah A. Day, 2021, Oncogene.

Immunoglobulin Genes Bias of Mutations of A versus T in Contributes to Strand η DNA Polymerase

I. Rogozin, P. Gearhart, V. Mayorov, 2013 .

Low-fidelity DNA synthesis by human DNA polymerase theta

T. Kunkel, I. Rogozin, R. Wood, 2008, Nucleic acids research.

Identification of murine B cell lines that undergo somatic hypermutation focused to A:T and G:C residues

A. Kenter, I. Rogozin, H. Morse, 2008, European journal of immunology.

Incarnation of classical pro- and eukaryotic mechanisms of mutagenesis in hypermutagenesis and immunity of vertebrates

L. Aravind, I. Rogozin, Y. Pavlov, 2007, Russian Journal of Genetics.

Known components of the immunoglobulin A:T mutational machinery are intact in Burkitt lymphoma cell lines with G:C bias.

I. Rogozin, A. B. Clark, Chuancang Jiang, 2007, Molecular immunology.

Roles of DNA polymerases in replication, repair, and recombination in eukaryotes.

I. Rogozin, P. V. Shcherbakova, Y. Pavlov, 2006, International review of cytology.

DNA Polymerase η Contributes to Strand Bias of Mutations of A versus T in Immunoglobulin Genes1

I. Rogozin, P. Gearhart, V. Mayorov, 2005, The Journal of Immunology.

Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes

T. Kunkel, I. Rogozin, C. Frahm, 2005, BMC Immunology.

Cutting Edge: DGYW/WRCH Is a Better Predictor of Mutability at G:C Bases in Ig Hypermutation Than the Widely Accepted RGYW/WRCY Motif and Probably Reflects a Two-Step Activation-Induced Cytidine Deaminase-Triggered Process

I. Rogozin, Igor B Rogozin, Marilyn Diaz, 2004, The Journal of Immunology.

Deaminase-Triggered Process a Two-Step Activation-Induced Cytidine RGYW/WRCY Motif and Probably Reflects Hypermutation Than the Widely Accepted Predictor of Mutability at G:C Bases in Ig Cutting Edge: DGYW/WRCH Is a Better

I. Rogozin, M. Diaz, 2004 .

Computational analysis of mutation spectra

Luciano Milanesi, Igor B. Rogozin, Vladimir N. Babenko, 2003, Briefings Bioinform..

Double-strand breaks in DNA during somatic hypermutation of Ig genes: cause or consequence?

T. Kunkel, I. Rogozin, Y. Pavlov, 2002, Trends in immunology.

DNA Methylation, Deamination, and Translesion Synthesis Combine to Generate Footprint Mutations in Cancer Driver Genes in B-Cell Derived Lymphomas and Other Cancers

A. Panchenko, D. Cooper, I. Rogozin, 2021, Frontiers in Genetics.

Mutational signatures and mutable motifs in cancer genomes

Subhajyoti De, Anna R. Panchenko, Eugenia Poliakov, 2017, Briefings Bioinform..

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

I. Rogozin, Y. Pavlov, A. G. Lada, 2017, Front. Genet..

Exploring background mutational processes to decipher cancer genetic heterogeneity

Anna R. Panchenko, Minghui Li, Igor B. Rogozin, 2017, Nucleic Acids Res..

Characterization of the genomic Xist locus in rodents reveals conservation of overall gene structure and tandem repeats but rapid evolution of unique sequence.

T B Nesterova, N. Brockdorff, I. Rogozin, 2001, Genome research.

Origin and Evolution of Retinoid Isomerization Machinery in Vertebrate Visual Cycle: Hint from Jawless Vertebrates

I. Rogozin, A. Gubin, Yan Li, 2012, PloS one.

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

E. Koonin, Miklós Csürös, I. Rogozin, 2011, Biology Direct.

AID and APOBECs as Multifaceted Intrinsic Virus-Restricting Factors: Emerging Concepts in the Light of COVID-19

P. Zimmermann, I. Rogozin, P. Pietschmann, 2021, Frontiers in Immunology.

Yeast POL5 Is an Evolutionarily Conserved Regulator of rDNA Transcription Unrelated to Any Known DNA Polymerases

E. Koonin, I. Rogozin, Wei Yang, 2003, Cell cycle.

GeneBuilder: interactive in silico prediction of gene structure

Luciano Milanesi, Igor B. Rogozin, D. D'Angelo, 1999, Bioinform..

Gene structure prediction using information on homologous protein sequence

Luciano Milanesi, Nikolay A. Kolchanov, Igor B. Rogozin, 1996, Comput. Appl. Biosci..

In search of lost introns

Igor B. Rogozin, Miklós Csürös, J. Andrew Holey, 2007, ISMB/ECCB.

LINE-1 element in the vole Microtus subarvalis

I. Rogozin, M. Mullokandov, T. Nesterova, 2004, Mammalian Genome.

APOBEC4, a New Member of the AID/APOBEC Family of Polynucleotide (Deoxy)Cytidine Deaminases Predicted by Computational Analysis

E. Koonin, I. Rogozin, I. K. Jordan, 2005, Cell cycle.

A Dual Origin of the Xist Gene from a Protein-Coding Gene and a Set of Transposable Elements

N. Brockdorff, I. Rogozin, T. Nesterova, 2008, PloS one.

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

I. Rogozin, P. Plevka, J. Lukeš, 2017, Proceedings of the National Academy of Sciences.

Prevalence of intron gain over intron loss in the evolution of paralogous gene families.

Eugene V Koonin, E. Koonin, I. Rogozin, 2004, Nucleic acids research.

Evolution of the Mouse Polyubiquitin-C Gene

F. Kondrashov, I. Rogozin, M. Brinton, 2002, Journal of Molecular Evolution.

Purifying selection and birth-and-death evolution in the ubiquitin gene family.

M. Nei, I. Rogozin, H. Piontkivska, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin

Igor B. Rogozin, Eugene V. Koonin, E. Koonin, 2005, Nature.

Concerted Changes in the Nucleotide Sequences of the Intragenic Promoter Regions of Eukaryotic Genes for tRNAs of All Specificities

A. G. Romaschenko, I. Rogozin, M. Voevoda, 2003, Journal of Molecular Evolution.

High frequency of somatic mutations in rat liver mitochondrial DNA.

I. Rogozin, B. Malyarchuk, G. Nevinsky, 2010, Mutation research.

Mutagenesis by Transient Misalignment in the Human Mitochondrial DNA Control Region

I. Rogozin, B. Malyarchuk, I. B. Rogozin, 2004, Annals of human genetics.

Domain mobility in proteins: functional and evolutionary implications

Malay Kumar Basu, Eugenia Poliakov, Igor B. Rogozin, 2008, Briefings Bioinform..

Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes

E. Koonin, Miklós Csürös, I. Rogozin, 2009, Genome biology and evolution.

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Eugene V Koonin, Dorothea K. Thompson, Kira S Makarova, 2003, Proceedings of the National Academy of Sciences of the United States of America.

The Functional Consequences of the Novel Ribosomal Pausing Site in SARS-CoV-2 Spike Glycoprotein RNA

I. Rogozin, S. Uppal, M. Kane, 2021, International journal of molecular sciences.

Generalized Portrait of Cancer Metabolic Pathways Inferred from a List of Genes Overexpressed in Cancer

David Managadze, I. Rogozin, Igor B Rogozin, 2014, Genetics research international.

Primordial spliceosomal introns were probably U2-type.

E. Koonin, I. Rogozin, M. K. Basu, 2008, Trends in genetics : TIG.

Title: Viral discovery and diversity in trypanosomatids with a focus on relatives of the human parasite Leishmania

I. Rogozin, P. Plevka, J. Lukeš, 2018 .

P53 Gain-of-Function: Tumor Biology and Bioinformatics Come Together

G. Glazko, E. Koonin, I. Rogozin, 2005, Cell cycle.

A novel subfamily of LINE-derived elements in mice

I. Rogozin, A. Ruvinsky, W. Flood, 1998, Mammalian Genome.

Somatic hypermutagenesis in immunoglobulin genes. I. Correlation between somatic mutations and repeats. Somatic mutation properties and clonal selection.

N. Kolchanov, I. Rogozin, V. V. Solovyov, 1991, Biochimica et biophysica acta.

The role of alternative translation start sites in the generation of human protein diversity

Nikolay A. Kolchanov, Igor B. Rogozin, Alex V. Kochetov, 2005, Molecular Genetics and Genomics.

Somatic hypermutagenesis in immunoglobulin genes. III. Somatic mutations in the chicken light chain locus.

N A Kolchanov, N. Kolchanov, I. Rogozin, 1996, Biochimica et biophysica acta.

Pecularities of immunoglobulin gene structures as a basis for somatic mutation emergence

V. V. Solovyov, N. A. Kolchanov, I. Rogozin, 1987, FEBS letters.

Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase

G. Glazko, L. Aravind, L. Iyer, 2007, Nature Immunology.

AID/APOBEC cytosine deaminase induces genome-wide kataegis

I. Rogozin, M. Hirano, R. Boissy, 2012, Biology Direct.

Review Article Complexity of Gene Expression Evolution after Duplication: Protein Dosage Rebalancing 1. Models of Gene Duplications

I. Rogozin, 2022 .

Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon

Luciano Milanesi, Igor B. Rogozin, Alexey V. Kochetov, 2001, Bioinform..

Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants of potential concern

E. Koonin, I. Rogozin, S. Garushyants, 2021 .

Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants that merit monitoring

E. Koonin, I. Rogozin, S. Garushyants, 2021, bioRxiv.

Aberrant RNA splicing is the major pathogenic effect in a knock‐in mouse model of the dominantly inherited c.1430A>G human RPE65 mutation

I. Rogozin, L. Gieser, Lijin Dong, 2019, Human mutation.

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

Claus V. Hallwirth, E. Koonin, R. Kotin, 2016, Scientific Reports.

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

K. Bok, I. Rogozin, E. Ostlund, 2014, Virus Genes.

Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions

Eugene V Koonin, E. Koonin, I. Rogozin, 2017, Scientific Reports.

Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes

Igor B. Rogozin, Kira S. Makarova, Eugene V. Koonin, 2004, Briefings Bioinform..

Reconstruction of Ancestral Protosplice Sites

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, 2004, Current Biology.

A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals

Teresa M. Przytycka, Jie Zheng, Igor B. Rogozin, 2007, RECOMB-CG.

Organization and chromosomal localization of a B1-like containing repeat of Microtus subarvalis

I. Rogozin, A. Graphodatsky, T. Nesterova, 1996, Mammalian Genome.

Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach.

Eugene V Koonin, E. Koonin, I. Rogozin, 2008, Molecular biology and evolution.

Analysis of evolution of exon-intron structure of eukaryotic genes

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, 2005, Briefings Bioinform..

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

E. Koonin, I. Rogozin, S. Kannan, 2014, BMC Evolutionary Biology.

A glimpse of a putative pre-intron phase of eukaryotic evolution.

Eugene V Koonin, Miklos Csuros, E. Koonin, 2007, Trends in genetics : TIG.

An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes

Liran Carmel, Igor B. Rogozin, Eugene V. Koonin, 2005, Comparative Genomics.

Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion.

Eugene V Koonin, E. Koonin, I. Rogozin, 2004, Gene.

Computer Prediction of Sites Associated with Various Elements of the Nuclear Matrix

Galina V. Glazko, Igor B. Rogozin, M. V. Glazkov, 2000, Briefings Bioinform..

Diversity and Function of Adaptive Immune Receptors in a Jawless Vertebrate

Galina V. Glazko, Igor B. Rogozin, Lakshminarayan M. Iyer, 2005, Science.

Gene Family Level Comparative Analysis of Gene Expression in Mammals Validates the Ortholog Conjecture

Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin, 2014, Genome biology and evolution.

Impact of CpG Islands on lncRNA Conservation

I. Rogozin, I. A. Sidorenko, V. Babenko, 2021, Biology Bulletin Reviews.

Error rate and specificity of human and murine DNA polymerase eta.

K Bebenek, T. Kunkel, I. Rogozin, 2001, Journal of molecular biology.

Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions

E. Koonin, I. Rogozin, Frida Belinky, 2017, Scientific Reports.

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

J. Qin, E. Podrez, I. Rogozin, 2015, Molecular biology of the cell.

[Computer prediction of DNa binding sites involved in interaction with different nuclear matrix elements].

M. V. Glazkov, G. Glazko, I. Rogozin, 2000, Молекулярная биология.

[Comparative study of fragments of chromosomal DNA, isolated from the nuclear lamina, core of rosette-like structures (elementary chromomeres), MARs/SARs and synaptonemal complex using a series of simple nucleotide motifs].

M. V. Glazkov, G. Glazko, I. Rogozin, 1998, Molekuliarnaia biologiia.

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

I. Rogozin, T Michael Redmond, E. Poliakov, 2017, Scientific Reports.

Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ε and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors

Eugene V Koonin, Kira S Makarova, E. Koonin, 2009, Biology Direct.

Identification of a U7snRNA homologue mapping to the human Xq27.1 region, between the DXS1232 and DXS119 loci.

L. Milanesi, R. Pergolizzi, I. Rogozin, 1997, Gene.

Low-fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerase ζ

T. Kunkel, I. Rogozin, G. Kissling, 2009, Nucleic acids research.

A highly conserved family of inactivated archaeal B family DNA polymerases

E. Koonin, K. Makarova, I. Rogozin, 2008, Biology Direct.

Rapid evolution of a cyclin A inhibitor gene, roughex, in Drosophila.

E V Koonin, E. Koonin, I. Rogozin, 2001, Molecular biology and evolution.

Genome Evolution

Igor B. Rogozin, Izabela Makalowska, Wojciech Makalowski, 2011, Adv. Bioinformatics.

Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution.

D. M. Krylov, E. Koonin, K. Makarova, 2003, Cold Spring Harbor symposia on quantitative biology.

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

Liran Carmel, Igor B. Rogozin, Eugene V. Koonin, 2010, Adv. Bioinformatics.

A Genome-Wide Identification of Mitochondrial DNA Topoisomerase I in Arabidopsis

I. Rogozin, Y. Konstantinov, A. Katyshev, 2006 .

[Computer system "AutoGene" for automatic analysis of nucleotide sequences].

N A Kolchanov, D A Grigorovich, A A Ptitsyn, 1996, Molekuliarnaia biologiia.

[Neighboring base effect on emergence of spontaneous mutations in human pseudogenes].

I. Rogozin, V. Babenko, M. Pozdniakov, 1997, Doklady Akademii nauk.

Regression trees for analysis of mutational spectra in nucleotide sequences

Igor B. Rogozin, V. B. Berikov, I. Rogozin, 1999, Bioinform..

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

I. Rogozin, J. Robert, L. Grayfer, 2015, Developmental and comparative immunology.

Unique Error Signature of the Four-subunit Yeast DNA Polymerase ϵ*

T. Kunkel, I. Rogozin, E. Johansson, 2003, Journal of Biological Chemistry.

Mutagenic specificity of the base analog 6-N-hydroxylaminopurine in the LYS2 gene of yeast Saccharomyces cerevisiae.

V. Noskov, I. Rogozin, Y. Chernoff, 2001, Mutation research.

Getting positive about selection

Eugene V Koonin, E. Koonin, I. Rogozin, 2003, Genome Biology.

Evolutionary aspects and enzymology of metazoan carotenoid cleavage oxygenases.

I. Rogozin, S. Uppal, T Michael Redmond, 2020, Biochimica et biophysica acta. Molecular and cell biology of lipids.

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

I. Rogozin, A. Baerga-Ortiz, Abiel Roche-Lima, 2018, Front. Genet..

The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

G. Glazko, I. Rogozin, V. Yurchenko, 2023, BMC Genomics.

The cytidine deaminase AID exhibits similar functional properties in yeast and mammals.

I. Rogozin, Y. Pavlov, 2006, Molecular immunology.

Low-Density Lipoprotein Receptor (LDLR) Is Involved in Internalization of Lentiviral Particles Pseudotyped with SARS-CoV-2 Spike Protein in Ocular Cells

I. Rogozin, T. Eggerman, S. Uppal, 2023, International journal of molecular sciences.

The subclass approach for mutational spectrum analysis: application of the SEM algorithm.

Luciano Milanesi, Igor B. Rogozin, L. Milanesi, 1998, Journal of theoretical biology.

Repetitive DNA Sequences in the Common Vole: Cloning, Characterization and Chromosome Localization of Two Novel Complex Repeats MS3 and MS4 from the Genome of the East European Vole Microtus Rossiaemeridionalis

N. Brockdorff, I. Rogozin, S. Duthie, 1998, Chromosome Research.

Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins

E. Koonin, Y. Wolf, R. Tatusov, 2001, Genome Biology.

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ

E. Koonin, Y. Wolf, K. Makarova, 2003, Genome Biology.

Diversity and Function of Adaptive Immune Receptors in a Jawless Vertebrate

G. Glazko, L. Iyer, I. Rogozin, 2005, Science.

Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase

G. Glazko, L. Aravind, L. Iyer, 2007, Nature Immunology.

Biology Direct Homoplasy in Genome-wide Analysis of Rare Amino Acid Replacements: the Molecular-evolutionary Basis for Vavilov's Law of Homologous Series

E. Koonin, Miklós Csürös, L. Carmel, 2022 .

Mutational signatures and mutable motifs in cancer genomes

A. Panchenko, D. Cooper, S. De, 2017, Briefings Bioinform..

Genome trees constructed using five different approaches suggest new major bacterial clades

N. Grishin, E. Koonin, Y. Wolf, 2001, BMC Evolutionary Biology.

Domain mobility in proteins: functional and evolutionary implications

I. Rogozin, M. K. Basu, E. Poliakov, 2008, Briefings Bioinform..

Contextual analysis of linear plasmid-like DNA of maize mitochondria: homology with virus sequences

I. Rogozin, M. Derenko, Y. M. Konstantinov, 1991 .