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Alexei Sharov

National Institutes of Health, NIA, Faculty Member

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I started my career as ecologist, but soon realized that I have to answer more fundamental questioins: what is life, how it evolves, learns, and functions. Thus I got involved in theoretical biology at Moscow State University. Later I organized a seminar and two conferences on Biosemiotics, which is a synthesis of biology and semiotics, a theory on signs and meanings. Now I combine my theoretical interests in biosemiotics with professional work in bioinformatics and molecular biology at the National Institute on Aging (Baltimore, USA).

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The University of Queensland, Australia

mario contarini

University of Viterbo

Ruggero Petacchi

Christos T Nakas

UNIVERSITY OF THESSALY, GREECE

University of Zagreb, Forestry Faculty

Universidad de Murcia

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Papers by Alexei Sharov

Correlation of counts of gypsy moth (Lepidoptera: Lymantriidae) in pheromone traps with landscape characteristics

The user has requested enhancement of the downloaded file.

Testing for correlation in the presence of spatial autocorrelation in insect count data

Signs and values

ABSTRACT

Semiosis in self-producing systems

ABSTRACT

Quantitative analysis of gypsy moth spread in the Central Appalachians

The user has requested enhancement of the downloaded file.

Gypsy Moth (Lepidoptera: Lymantriidae) Spread in the Central Appalachians: Three Methods for Species Boundary Estimation

Environmental Entomology, 1995

Page 1. POPULATION ECOLOGY Gypsy Moth (Lepidoptera: LynIantriidae) Spread in the Central Appalach... more

Prediction of Gypsy Moth (Lepidoptera: Lymantriidae) Mating Success from Pheromone Trap Counts

Environmental Entomology, 1995

Page 1. POPULATIONECOLOGY Prediction of Gypsy Moth (Lepidoptera: Lymantriidae) Mating Success fro... more

Slow the Spread": A National program to contain the gypsy moth

Forestry

ExAtlas: An interactive online tool for meta-analysis of gene expression data

Journal of bioinformatics and computational biology, Jan 9, 2015

We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene e... more We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene expression data. In contrast to existing software tools, ExAtlas compares multi-component data sets and generates results for all combinations (e.g. all gene expression profiles versus all Gene Ontology annotations). ExAtlas handles both users' own data and data extracted semi-automatically from the public repository (GEO/NCBI database). ExAtlas provides a variety of tools for meta-analyses: (1) standard meta-analysis (fixed effects, random effects, z-score, and Fisher's methods); (2) analyses of global correlations between gene expression data sets; (3) gene set enrichment; (4) gene set overlap; (5) gene association by expression profile; (6) gene specificity; and (7) statistical analysis (ANOVA, pairwise comparison, and PCA). ExAtlas produces graphical outputs, including heatmaps, scatter-plots, bar-charts, and three-dimensional images. Some of the most widely used public data s...

Genetic Gradualism and the ExtraTerrestrial Origin of Life

Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells

DNA research : an international journal for rapid publication of reports on genes and genomes, Jan 31, 2015

Mouse embryonic stem cells (mESCs) have a remarkable capacity to maintain normal genome stability... more Mouse embryonic stem cells (mESCs) have a remarkable capacity to maintain normal genome stability and karyotype in culture. We previously showed that infrequent bursts of Zscan4 expression (Z4 events) are important for the maintenance of telomere length and genome stability in mESCs. However, the molecular details of Z4 events remain unclear. Here we show that Z4 events involve unexpected transcriptional derepression in heterochromatin regions that usually remain silent. During a Z4 event, we see rapid derepression and rerepression of heterochromatin leading to a burst of transcription that coincides with transient histone hyperacetylation and DNA demethylation, clustering of pericentromeric heterochromatin around the nucleolus, and accumulation of activating and repressive chromatin remodelling complexes. This heterochromatin-based transcriptional activity suggests that mESCs may maintain their extraordinary genome stability at least in part by transiently resetting their heterochr...

Effect of Shin-Etsu Sprayable Pheromone Formulation on Mating Success in Low-Density Gypsy Moth Populations

DESCRIPTION This paper presents the results of the study conducted in summers of 2002, 2005 and 2... more

Genome increase as a clock for the origin and evolution of life

by Alexei Sharov and Alexei Sharov

Background: The size of non-redundant functional genome can be an indicator of biological complex... more Background: The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. Several positive feedback mechanisms including gene cooperation and duplication with subsequent specialization may result in the exponential growth of biological complexity in macro-evolution.

Coenzyme autocatalytic network on the surface of oil microspheres as a model for the origin of life

International journal of molecular sciences, 2009

Coenzymes are often considered as remnants of primordial metabolism, but not as hereditary molecu... more Coenzymes are often considered as remnants of primordial metabolism, but not as hereditary molecules. I suggest that coenzyme-like molecules (CLMs) performed hereditary functions before the emergence of nucleic acids. Autocatalytic CLMs modified (encoded) surface properties of hydrocarbon microspheres, to which they were anchored, and these changes enhanced autocatalysis and propagation of CLMs. Heredity started from a single kind of self-reproducing CLM, and then evolved into more complex coenzyme autocatalytic networks containing multiple kinds of CLMs. Polymerization of CLMs on the surface of microspheres and development of template-based synthesis is a potential evolutionary path towards the emergence of nucleic acids.

Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)

BMC bioinformatics, Jan 18, 2004

Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively a... more Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively analyzes the cellular transcriptome. The analysis of SAGE libraries relies on the identification of ditags from sequencing files; however, the software used to examine SAGE libraries cannot distinguish between authentic versus false ditags ("quasi-ditags"). We provide examples of quasi-ditags that originate from cloning and sequencing artifacts (i.e. genomic contamination or random combinations of nucleotides) that are included in SAGE libraries. We have employed a mathematical model to predict the frequency of quasi-ditags in random nucleotide sequences, and our data show that clones containing less than or equal to 2 ditags (which include chromosomal cloning artifacts) should be excluded from the analysis of SAGE catalogs. Cloning and sequencing artifacts contaminating SAGE libraries could be eliminated using simple pre-screening procedure to increase the reliability of the data.

Inferring directions of evolution from patterns of variation: The legacy of Sergei Meyen

by Alexei Sharov and Alexei Sharov

A B S T R A C T In the era of the extended evolutionary synthesis, which no longer considers natu... more A B S T R A C T In the era of the extended evolutionary synthesis, which no longer considers natural selection as the only leading factor of evolution, it is meaningful to revisit the legacy of biologists who discussed the role of alternative factors. Here we analyze the evolutionary views of Sergei Meyen (1935–1987), a paleobotanist who argued that the theory of evolution should incorporate a " nomothetical " approach which infers the laws of morphogenesis (i.e., form generation) from the observed patterns of variation in living organisms and in the fossil records. Meyen developed a theory of " repeated polymorphic sets " (RPSs), which he applied consistently to describe inter-organism variation in populations, intra-organism variation of metameric organs, variation of abnormalities, heterotopy, changes during embryo development, and inter-species variation within evolutionary lineages. The notion of RPS assumes the active nature of organisms that possess hidden morphogenic and behavioral capacities. Meyen's theory is compatible with Darwin's natural selection; however, Meyen emphasized the importance of other forms of selection (e.g., selection of developmental trajectories, habitats, and behaviors) in choosing specific elements from the RPS. Finally, Meyen developed a new typological concept of time, where time represents variability (i.e., change) of real objects such as living organisms or geological formations.

Role of Utility and Inference in the Evolution of Functional Information

by Alexei Sharov and Alexei Sharov

Functional information means an encoded network of functions in living organisms from molecular s... more Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism's behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality, and they evolve towards higher adaptability on a long time scale.

Bioeconomics of Managing the Spread of Exotic Pest Species with Barrier Zones

Ecological Applications, 1998

ABSTRACT

Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray

Genome biology, 2005

The ability to quantitatively measure the expression of all genes in a given tissue or cell with ... more The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of exogenous RNA controls derived from the yeast genome (made freely available without restriction), which allow quantitative estimation of absolute endogenous transcript abundance.

Gene expression profiling of mouse embryos with microarrays

Methods in enzymology, 2010

Global expression profiling by DNA microarrays provides a snapshot of cell and tissue status and ... more Global expression profiling by DNA microarrays provides a snapshot of cell and tissue status and becomes an essential tool in biological and medical sciences. Typical questions that can be addressed by microarray analysis in developmental biology include: (1) to find a set of genes expressed in a specific cell type; (2) to identify genes expressed commonly in multiple cell types; (3) to follow the time-course changes of gene expression patterns; (4) to demonstrate cell's identity by showing similarities or differences among two or multiple cell types; (5) to find regulatory pathways and/or networks affected by gene manipulations, such as overexpression or repression of gene expression; (6) to find downstream target genes of transcription factors; (7) to find downstream target genes of cell signaling; (8) to examine the effects of environmental manipulation of cells on gene expression patterns; and (9) to find the effects of genetic manipulation in embryos and adults. Here, we de...

Correlation of counts of gypsy moth (Lepidoptera: Lymantriidae) in pheromone traps with landscape characteristics

The user has requested enhancement of the downloaded file.

Testing for correlation in the presence of spatial autocorrelation in insect count data

Signs and values

ABSTRACT

Semiosis in self-producing systems

ABSTRACT

Quantitative analysis of gypsy moth spread in the Central Appalachians

The user has requested enhancement of the downloaded file.

Gypsy Moth (Lepidoptera: Lymantriidae) Spread in the Central Appalachians: Three Methods for Species Boundary Estimation

Environmental Entomology, 1995

Page 1. POPULATION ECOLOGY Gypsy Moth (Lepidoptera: LynIantriidae) Spread in the Central Appalach... more

Prediction of Gypsy Moth (Lepidoptera: Lymantriidae) Mating Success from Pheromone Trap Counts

Environmental Entomology, 1995

Page 1. POPULATIONECOLOGY Prediction of Gypsy Moth (Lepidoptera: Lymantriidae) Mating Success fro... more

Slow the Spread": A National program to contain the gypsy moth

Forestry

ExAtlas: An interactive online tool for meta-analysis of gene expression data

Journal of bioinformatics and computational biology, Jan 9, 2015

We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene e... more We have developed ExAtlas, an on-line software tool for meta-analysis and visualization of gene expression data. In contrast to existing software tools, ExAtlas compares multi-component data sets and generates results for all combinations (e.g. all gene expression profiles versus all Gene Ontology annotations). ExAtlas handles both users' own data and data extracted semi-automatically from the public repository (GEO/NCBI database). ExAtlas provides a variety of tools for meta-analyses: (1) standard meta-analysis (fixed effects, random effects, z-score, and Fisher's methods); (2) analyses of global correlations between gene expression data sets; (3) gene set enrichment; (4) gene set overlap; (5) gene association by expression profile; (6) gene specificity; and (7) statistical analysis (ANOVA, pairwise comparison, and PCA). ExAtlas produces graphical outputs, including heatmaps, scatter-plots, bar-charts, and three-dimensional images. Some of the most widely used public data s...

Genetic Gradualism and the ExtraTerrestrial Origin of Life

Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells

DNA research : an international journal for rapid publication of reports on genes and genomes, Jan 31, 2015

Mouse embryonic stem cells (mESCs) have a remarkable capacity to maintain normal genome stability... more Mouse embryonic stem cells (mESCs) have a remarkable capacity to maintain normal genome stability and karyotype in culture. We previously showed that infrequent bursts of Zscan4 expression (Z4 events) are important for the maintenance of telomere length and genome stability in mESCs. However, the molecular details of Z4 events remain unclear. Here we show that Z4 events involve unexpected transcriptional derepression in heterochromatin regions that usually remain silent. During a Z4 event, we see rapid derepression and rerepression of heterochromatin leading to a burst of transcription that coincides with transient histone hyperacetylation and DNA demethylation, clustering of pericentromeric heterochromatin around the nucleolus, and accumulation of activating and repressive chromatin remodelling complexes. This heterochromatin-based transcriptional activity suggests that mESCs may maintain their extraordinary genome stability at least in part by transiently resetting their heterochr...

Effect of Shin-Etsu Sprayable Pheromone Formulation on Mating Success in Low-Density Gypsy Moth Populations

DESCRIPTION This paper presents the results of the study conducted in summers of 2002, 2005 and 2... more

Genome increase as a clock for the origin and evolution of life

by Alexei Sharov and Alexei Sharov

Background: The size of non-redundant functional genome can be an indicator of biological complex... more Background: The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. Several positive feedback mechanisms including gene cooperation and duplication with subsequent specialization may result in the exponential growth of biological complexity in macro-evolution.

Coenzyme autocatalytic network on the surface of oil microspheres as a model for the origin of life

International journal of molecular sciences, 2009

Coenzymes are often considered as remnants of primordial metabolism, but not as hereditary molecu... more Coenzymes are often considered as remnants of primordial metabolism, but not as hereditary molecules. I suggest that coenzyme-like molecules (CLMs) performed hereditary functions before the emergence of nucleic acids. Autocatalytic CLMs modified (encoded) surface properties of hydrocarbon microspheres, to which they were anchored, and these changes enhanced autocatalysis and propagation of CLMs. Heredity started from a single kind of self-reproducing CLM, and then evolved into more complex coenzyme autocatalytic networks containing multiple kinds of CLMs. Polymerization of CLMs on the surface of microspheres and development of template-based synthesis is a potential evolutionary path towards the emergence of nucleic acids.

Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)

BMC bioinformatics, Jan 18, 2004

Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively a... more Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively analyzes the cellular transcriptome. The analysis of SAGE libraries relies on the identification of ditags from sequencing files; however, the software used to examine SAGE libraries cannot distinguish between authentic versus false ditags ("quasi-ditags"). We provide examples of quasi-ditags that originate from cloning and sequencing artifacts (i.e. genomic contamination or random combinations of nucleotides) that are included in SAGE libraries. We have employed a mathematical model to predict the frequency of quasi-ditags in random nucleotide sequences, and our data show that clones containing less than or equal to 2 ditags (which include chromosomal cloning artifacts) should be excluded from the analysis of SAGE catalogs. Cloning and sequencing artifacts contaminating SAGE libraries could be eliminated using simple pre-screening procedure to increase the reliability of the data.

Inferring directions of evolution from patterns of variation: The legacy of Sergei Meyen

by Alexei Sharov and Alexei Sharov

A B S T R A C T In the era of the extended evolutionary synthesis, which no longer considers natu... more A B S T R A C T In the era of the extended evolutionary synthesis, which no longer considers natural selection as the only leading factor of evolution, it is meaningful to revisit the legacy of biologists who discussed the role of alternative factors. Here we analyze the evolutionary views of Sergei Meyen (1935–1987), a paleobotanist who argued that the theory of evolution should incorporate a " nomothetical " approach which infers the laws of morphogenesis (i.e., form generation) from the observed patterns of variation in living organisms and in the fossil records. Meyen developed a theory of " repeated polymorphic sets " (RPSs), which he applied consistently to describe inter-organism variation in populations, intra-organism variation of metameric organs, variation of abnormalities, heterotopy, changes during embryo development, and inter-species variation within evolutionary lineages. The notion of RPS assumes the active nature of organisms that possess hidden morphogenic and behavioral capacities. Meyen's theory is compatible with Darwin's natural selection; however, Meyen emphasized the importance of other forms of selection (e.g., selection of developmental trajectories, habitats, and behaviors) in choosing specific elements from the RPS. Finally, Meyen developed a new typological concept of time, where time represents variability (i.e., change) of real objects such as living organisms or geological formations.

Role of Utility and Inference in the Evolution of Functional Information

by Alexei Sharov and Alexei Sharov

Functional information means an encoded network of functions in living organisms from molecular s... more Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism's behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality, and they evolve towards higher adaptability on a long time scale.

Bioeconomics of Managing the Spread of Exotic Pest Species with Barrier Zones

Ecological Applications, 1998

ABSTRACT

Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray

Genome biology, 2005

The ability to quantitatively measure the expression of all genes in a given tissue or cell with ... more The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of exogenous RNA controls derived from the yeast genome (made freely available without restriction), which allow quantitative estimation of absolute endogenous transcript abundance.

Gene expression profiling of mouse embryos with microarrays

Methods in enzymology, 2010

Global expression profiling by DNA microarrays provides a snapshot of cell and tissue status and ... more Global expression profiling by DNA microarrays provides a snapshot of cell and tissue status and becomes an essential tool in biological and medical sciences. Typical questions that can be addressed by microarray analysis in developmental biology include: (1) to find a set of genes expressed in a specific cell type; (2) to identify genes expressed commonly in multiple cell types; (3) to follow the time-course changes of gene expression patterns; (4) to demonstrate cell's identity by showing similarities or differences among two or multiple cell types; (5) to find regulatory pathways and/or networks affected by gene manipulations, such as overexpression or repression of gene expression; (6) to find downstream target genes of transcription factors; (7) to find downstream target genes of cell signaling; (8) to examine the effects of environmental manipulation of cells on gene expression patterns; and (9) to find the effects of genetic manipulation in embryos and adults. Here, we de...