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1. Full Text Tolerance to Selenoprotein Loss Differs between Human and Mouse
by Santesmasses, Didac and Mariotti, Marco and Gladyshev, Vadim N
Molecular Biology and Evolution, ISSN 0737-4038, 09/2019
Abstract Mouse has emerged as the most common model organism in biomedicine. Here, we analyzed the tolerance to the loss-of-function (LoF) of selenoprotein... 
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2. Full Text Svist4get: A simple visualization tool for genomic tracks from sequencing experiments
by Egorov, Artyom A and Sakharova, Ekaterina A and Anisimova, Aleksandra S and Dmitriev, Sergey E and Gladyshev, Vadim N and Kulakovskiy, Ivan V
BMC Bioinformatics, ISSN 1471-2105, 03/2019, Volume 20, Issue 1, pp. 113 - 6
BackgroundHigh-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer... 
Visualization | Genome browser | Next-generation sequencing | High-throughput sequencing | RNA-Seq | Genomic tracks | Ribo-Seq | Python | BROWSER | BIOCHEMICAL RESEARCH METHODS | DATASETS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | RNA sequencing | Technology application | RNA | Genomics | Software | Genomes | Web browsers | Tracking | Mapping | Software development tools | Experiments | Annotations | User interface | Computer graphics | Life sciences | Bioinformatics | Image resolution | Data analysis | Data processing | Line interfaces | Source code | Gene expression | Ribonucleic acid--RNA | Computer programs | Acids | Graphical user interface | Molecular biology | Gene mapping
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3. Full Text Ribonuclease selection for ribosome profiling
by Gerashchenko, Maxim V and Gladyshev, Vadim N
Nucleic acids research, 01/2017, Volume 45, Issue 2, p. e6
Ribosome profiling has emerged as a powerful method to assess global gene translation, but methodological and analytical challenges often lead to... 
Protein Biosynthesis | Helminths - genetics | Saccharomyces cerevisiae - genetics | Ribosomes - metabolism | RNA Stability | Ribonucleases - metabolism | Saccharomyces cerevisiae - metabolism | Animals | Mice | Drosophila - metabolism | Protein Stability | Helminths - metabolism | Drosophila - genetics
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4. Full Text Evidence that mutation accumulation does not cause aging in Saccharomyces cerevisiae
by Kaya, Alaattin and Lobanov, Alexei V and Gladyshev, Vadim N
Aging Cell, ISSN 1474-9718, 06/2015, Volume 14, Issue 3, pp. 366 - 371
Summary The concept that mutations cause aging phenotypes could not be directly tested previously due to inability to identify age‐related mutations in somatic... 
thiol peroxidase | mutations | DNA damage | lifespan | mitochondria | aging | yeast | Mutations | Mitochondria | Yeast | Thiol peroxidase | Aging | Lifespan | LIFE-SPAN | INSTABILITY | DAMAGE | CELL BIOLOGY | GERIATRICS & GERONTOLOGY | LONGEVITY | GENE | ALIGNMENT | TANDEM REPEATS | DNA-REPAIR | AGE | Mutation Accumulation | DNA, Mitochondrial - genetics | Mitochondria - genetics | Saccharomyces cerevisiae - genetics | Mutation Rate | Saccharomyces cerevisiae Proteins - genetics | Mutation - genetics | Genetic aspects | Mitochondrial DNA | Thiols | Gene mutations | Analysis | Genomics | Original
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5. Full Text Selenium and Methionine Sulfoxide Reduction
by Gladyshev, Vadim N
Free radical biology & medicine, ISSN 0891-5849, 10/2014, Volume 75 Suppl 1, pp. S8 - S9
Selenium is an essential trace element because it is present in proteins in the form of selenocysteine residue. Functionally characterized selenoproteins are... 
Oxidases | Amino acids | Selenium | Muscle proteins
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6. Full Text Integrating cellular senescence with the concept of damage accumulation in aging: Relevance for clearance of senescent cells
by Ogrodnik, Mikolaj and Salmonowicz, Hanna and Gladyshev, Vadim N
Aging Cell, ISSN 1474-9718, 02/2019, Volume 18, Issue 1, pp. e12841 - n/a
Understanding the aging process and ways to manipulate it is of major importance for biology and medicine. Among the many aging theories advanced over the... 
molecular damage | theories of aging | cellular senescence | evolutionary biology | lifespan | aging | deleteriome | LIFE-SPAN | LIPOFUSCIN ACCUMULATION | OXIDATIVE STRESS | PROTEASOME INHIBITION | DNA-DAMAGE | ALTERED DEGRADATION | ONCOGENE-INDUCED SENESCENCE | CELL BIOLOGY | GERIATRICS & GERONTOLOGY | PREMATURE SENESCENCE | SHOCK-PROTEIN HSP72 | HEMATOPOIETIC STEM-CELLS | Aging | Senescence | Macromolecules | Reviews | Review
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7. Full Text Aging: progressive decline in fitness due to the rising deleteriome adjusted by genetic, environmental, and stochastic processes
by Gladyshev, Vadim N
Aging cell, 08/2016, Volume 15, Issue 4, p. 594
Different theories posit that aging is caused by molecular damage, genetic programs, continued development, hyperfunction, antagonistic pleiotropy alleles,... 
Animals | Aging - genetics | Aging - physiology | Stochastic Processes | Models, Biological | Humans | Environment | Physical Fitness | Metabolome - genetics
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8. Full Text Symposium 6: Trace Elements S6-1 - Selenium and Methionine Sulfoxide Reduction
by Gladyshev, Vadim N
Free Radical Biology and Medicine, ISSN 0891-5849, 10/2014, Volume 75, pp. S8 - S9
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9. Full Text Selenium Deficiency Is Associated with Pro-longevity Mechanisms
by Yim, Sun Hee and Clish, Clary B and Gladyshev, Vadim N
Cell Reports, ISSN 2211-1247, 05/2019, Volume 27, Issue 9, pp. 2785 - 2797.e3
Selenium (Se) is an essential trace element because of its presence in selenoproteins in the form of selenocysteine residue. Both Se deficiency, which... 
metabolic pathway | nutrition | selenium | lifespan | transcriptome | miRNA | aging | selenoproteins | metabolite profiling | gene expression
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10. Full Text Aging: progressive decline in fitness due to the rising deleteriome adjusted by genetic, environmental, and stochastic processes
by Gladyshev, Vadim N
Aging Cell, ISSN 1474-9718, 08/2016, Volume 15, Issue 4, pp. 594 - 602
Summary Different theories posit that aging is caused by molecular damage, genetic programs, continued development, hyperfunction, antagonistic pleiotropy... 
Aging | Evolution | Lifespan | Theories of aging | Deleteriome | PROFILES | MECHANISMS | CELL BIOLOGY | GERIATRICS & GERONTOLOGY | LONGEVITY | ORIGIN | MUTATION | SENESCENCE | DEFINES | SELECTION | AGE | Environmental aspects | Stochastic processes | Analysis | Stochastic models | Reviews | Review
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11. Full Text The Free Radical Theory of Aging Is Dead. Long Live the Damage Theory
by Gladyshev, Vadim N
Antioxidants & Redox Signaling, ISSN 1523-0864, 02/2014, Volume 20, Issue 4, pp. 727 - 731
The free radical theory of aging posits that aging is caused by accumulation of damage inflicted by reactive oxygen species (ROS). Although this concept has... 
Letter to the Editor | LIFE-SPAN | OVEREXPRESSION | OXIDATIVE STRESS | GENETICS | ELEGANS | BIOCHEMISTRY & MOLECULAR BIOLOGY | CALORIC RESTRICTION | ROS | EXTEND | ENDOCRINOLOGY & METABOLISM | SUPEROXIDE-DISMUTASE | REVEALS | Animals | Reactive Oxygen Species - metabolism | Oxidation-Reduction | Oxidative Stress | Life Expectancy | Humans | Aging
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12. Full Text Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum
by Heaphy, Stephen M and Mariotti, Marco and Gladyshev, Vadim N and Atkins, John F and Baranov, Pavel V
Molecular Biology and Evolution, ISSN 0737-4038, 11/2016, Volume 33, Issue 11, pp. 2885 - 2889
mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of... 
alternative genetic decoding | translation termination | the genetic code | stop codon reassignment | ciliates | TRANSLATIONAL TERMINATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | EUPLOTES-OCTOCARINATUS | GENOME | EVOLUTIONARY BIOLOGY | DATABASE | GENETICS & HEREDITY | EFFICIENCY | Amino Acid Sequence | Sequence Alignment - methods | Protein Biosynthesis | Codon | Genetic Code | Peptide Termination Factors - genetics | Open Reading Frames | Ciliophora - genetics | Genetic Variation - genetics | Codon, Terminator | Alveolata - genetics | Discoveries
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13. Full Text On the cause of aging and control of lifespan: Heterogeneity leads to inevitable damage accumulation, causing aging; Control of damage composition and rate of accumulation define lifespan
by Gladyshev, Vadim N
BioEssays, ISSN 0265-9247, 11/2012, Volume 34, Issue 11, pp. 925 - 929
What the causes of aging are and which factors define lifespan are key questions in the understanding of aging. Here, it is argued that cellular life involves... 
Animals | DNA Damage | Time Factors | Cellular Senescence | DNA Repair | Humans | Life spans (Biology) | Cell death | Cancer cells | Aging | Physiological aspects | Cell physiology | Research
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14. Full Text Cytochrome cperoxidase facilitates the beneficial useof [H.sub.2][O.sub.2] in prokaryotes
by Kaya, Alaattin and Mariotti, Marco and Gladyshev, Vadim N
Proceedings of the National Academy of Sciences of the United States, ISSN 0027-8424, 08/2017, Volume 114, Issue 33, p. 8678
Properties | Microbiological research | Cytochrome P-450
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15. A Disease or Not a Disease? Aging As a Pathology
by Timothy V Gladyshev and Vadim N Gladyshev
Trends in Molecular Medicine, ISSN 1471-4914, 12/2016, Volume 22, Issue 12, p. 995
The debate on the relationship between aging and disease is centered on whether aging is a normal/natural/physiological process or it represents a pathology.... 
Pathology | Disease | Aging | Aging (natural) | Molecular biology
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16. Full Text High-throughput identification of catalytic redox-active cystein residues
by Fomenko, Dmitri E and Xing, Weibing and Adair, Blakely M and Thomas, David J and Gladyshev, Vadim N
Science, ISSN 0036-8075, 01/2007, Volume 315, Issue 5810, pp. 387 - 389
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17. Full Text A whole lifespan mouse multi-tissue DNA methylation clock
by Meer, Margarita V and Meer, Margarita V and Podolskiy, Dmitriy I and Podolskiy, Dmitriy I and Tyshkovskiy, Alexander and Tyshkovskiy, Alexander and Gladyshev, Vadim N and Gladyshev, Vadim N
eLife, ISSN 2050-084X, 11/2018, Volume 7
Age predictors based on DNA methylation levels at a small set of CpG sites, DNAm clocks, have been developed for humans and extended to several other species.... 
mouse | biological age | lifespan | chromosomes | DNA methylation | aging | clock | gene expression | BIOLOGY | AGE | Age Factors | Myocardium - chemistry | Hippocampus - chemistry | Epigenesis, Genetic | Lung - chemistry | Male | Rejuvenation - physiology | DNA Methylation | Myocardium - metabolism | Female | Lung - metabolism | Induced Pluripotent Stem Cells - cytology | Fibroblasts - metabolism | Induced Pluripotent Stem Cells - metabolism | Datasets as Topic | Liver - metabolism | Mice, Transgenic | DNA - metabolism | Longevity - genetics | Mice, Inbred Strains | Organ Specificity | Liver - chemistry | DNA - genetics | Hippocampus - metabolism | Animals | CpG Islands | Fibroblasts - cytology | Mice | Liver | Genomes | Gene expression | Datasets | Life span | Aging | Biomarkers | Fibroblasts | Methylation | Age | Deoxyribonucleic acid--DNA | CpG islands | Inhibitory postsynaptic potentials
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