Search filters

List of works by Yuri Wolf

2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

scientific article published on 04 September 2020

2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

A comprehensive census of horizontal gene transfers from prokaryotes to unikonts

scientific article published on 19 September 2011

A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

scientific article

A korarchaeal genome reveals insights into the evolution of the Archaea

scientific article

A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches

scientific article (publication date: 15 June 2010)

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

scientific article

A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action

scientific article

A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes

scientific article published on January 2012

A unique insert in the genomes of high-risk human papillomaviruses with a predicted dual role in conferring oncogenic risk

scientific article published on 02 July 2019

A universal trend of amino acid gain and loss in protein evolution

scientific article published on 19 January 2005

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation

scientific article

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

scientific article published on 09 October 2008

Allosteric Activation of SARS-CoV-2 RNA-Dependent RNA Polymerase by Remdesivir Triphosphate and Other Phosphorylated Nucleotides

scientific article

An insertion in the catalytic trigger loop gates the secondary channel of RNA polymerase

scientific article

An updated evolutionary classification of CRISPR-Cas systems

scientific article

Analysis of rare amino acid replacements supports the Coelomata clade

scientific article published on 5 October 2007

Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell

scientific article

Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes

scientific article published on 13 July 2021

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

scientific article published in 2023

Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts

scientific article published on 07 May 2019

Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales

scientific article

Arginyltransferase is an ATP-independent self-regulating enzyme that forms distinct functional complexes in vivo

scientific article

Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae

scientific article

Birth and death of protein domains: a simple model of evolution explains power law behavior

scientific article

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

scientific article published on 09 November 2020

CRISPR Arrays Away from <i>cas</i> Genes

scientific article published on 01 December 2020

Cellular differentiation into hyphae and spores in halophilic archaea

scientific article published in 2023

Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?

scientific article published on 01 October 2018

Classify viruses - the gain is worth the pain

scientific article published on 01 February 2019

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

scientific article

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

scientific article published in January 2004

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution.

scientific article

Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems

scientific article published on 14 August 2018

Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance

scientific article published on 20 October 2005

Comparative genomics of defense systems in archaea and bacteria ⬇️

scientific article published on March 6, 2013

Comparison of phylogenetic trees and search for a central trend in the "forest of life".

scientific article

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

scientific article

Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

scientific article

Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes

scientific article published in June 2004

Computational methods for Gene Orthology inference

scientific article

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

scientific article

Connected gene neighborhoods in prokaryotic genomes

scientific article

Conservation and coevolution in the scale-free human gene coexpression network

scientific article published on 28 July 2004

Constraints and plasticity in genome and molecular-phenome evolution

scientific article

Coping with the quantitative genomics 'elephant': the correlation between the gene dispensability and evolution rate

scientific article published on 11 May 2006

Cressdnaviricota: a virus phylum unifying 7 families of Rep-encoding viruses with single-stranded, circular DNA genomes

scientific article published on 08 April 2020

Criticality in tumor evolution and clinical outcome

article published in the Proceedings of the National Academy of Sciences of the United States of America

Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes.

scientific article

Deep phylogeny of cancer drivers and compensatory mutations

scientific article published on 02 October 2020

Defense islands in bacterial and archaeal genomes and prediction of novel defense systems

scientific article

Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks

scientific article

Differential translation tunes uneven production of operon-encoded proteins

scientific article published on 5 September 2013

Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis

scientific article

Diverse enzymatic activities mediate antiviral immunity in prokaryotes

scientific article published on 01 August 2020

Diverse functions of homologous actin isoforms are defined by their nucleotide, rather than their amino acid sequence

scientific article

Diversity and evolution of class 2 CRISPR-Cas systems

scientific article

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

scientific article published on 20 July 2020

Drastic neofunctionalization associated with evolution of the timezyme AANAT 500 Mya

scientific article

Duplicated gelsolin family genes in zebrafish: a novel scinderin-like gene (scinla) encodes the major corneal crystallin

scientific article

Duplicated genes evolve slower than singletons despite the initial rate increase

scientific article

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

scientific article

Early vertebrate origin and diversification of small transmembrane regulators of cellular ion transport

scientific article

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

scientific article

Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

scientific article (publication date: 2008)

Erratum to: No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly

scientific article

Escherichia coli ItaT is a type II toxin that inhibits translation by acetylating isoleucyl-tRNAIle

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

scientific article

Estimation of prokaryotic supergenome size and composition from gene frequency distributions

scientific article

Estimation of universal and taxon-specific parameters of prokaryotic genome evolution

scientific article published on 13 April 2018

Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution

scientific article

Evolution and classification of the CRISPR-Cas systems

scientific article (publication date: June 2011)

Evolution of DNA packaging in gene transfer agents

scientific article

Evolution of Human Respiratory Virus Epidemics

scientific article published on 24 November 2020

Evolution of gene fusions: horizontal transfer versus independent events

scientific article

Evolution of human respiratory virus epidemics

scientific article published on 29 July 2021

Evolution of human respiratory virus epidemics

scientific article published on 04 June 2021

Evolution of microbes and viruses: a paradigm shift in evolutionary biology? ⬇️

scientific article published on September 13, 2012

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

scientific article

Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A

scientific article published in 2024

Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus-host coevolution

scientific article

Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape

scientific article

Evolutionarily conserved genes preferentially accumulate introns

scientific article

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

scientific article published on 28 June 2017

Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense

scientific article published on 31 July 2020

Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants

scientific article published on 19 December 2019

Evolutionary dynamics of N-glycosylation sites of influenza virus hemagglutinin.

scientific article

Evolutionary dynamics of the prokaryotic adaptive immunity system CRISPR-Cas in an explicit ecological context

scientific article published on 21 June 2013

Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire

scientific article published on 14 October 2019

Evolutionary plasticity of protein families: coupling between sequence and structure variation

scientific article published in November 2005

Evolutionary primacy of sodium bioenergetics

scientific article published on April 2008

Evolutionary systems biology: links between gene evolution and function

scientific article published on 8 September 2006

Evolvability of an Optimal Recombination Rate

scientific article published on 10 December 2015

Expanded microbial genome coverage and improved protein family annotation in the COG database

scientific article

Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families

scientific article published on 13 September 2017

Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

scientific article published on 12 June 2015

Game-Theoretical Modeling of Interviral Conflicts Mediated by Mini-CRISPR Arrays

scientific article published on 20 March 2020

Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models

scientific article

Gene frequency distributions reject a neutral model of genome evolution

scientific article

Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence

scientific article published on 26 November 2019

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

scientific article

Genome reduction as the dominant mode of evolution

scientific article published on 25 June 2013

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

scientific article

Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy

scientific article

Genome trees and the tree of life

scientific article

Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life

scientific article published on 01 January 2019

Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family

scientific article published on 21 September 2006

Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life

scientific article

Genome-wide molecular clock and horizontal gene transfer in bacterial evolution

scientific article

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes

scientific article

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses

scientific article published on 08 April 2020

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses

scientific article published on 10 June 2020

Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes

scientific article

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

scientific article

Global Organization and Proposed Megataxonomy of the Virus World

scientific article published on 04 March 2020

Global analysis of posttranslational protein arginylation

scientific article

Grammar of protein domain architectures

scientific article published on 07 February 2019

High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.

scientific article published on 28 July 2017

Histidine-Triad Hydrolases Provide Resistance to Peptide-Nucleotide Antibiotics

scientific article published on 07 April 2020

Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches

scientific article published in 2022

Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs

scientific article

Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems

scientific article

In silico learning of tumor evolution through mutational time series

scientific article published on 23 April 2019

Inevitability of genetic parasites

scientific article

Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states

scientific article published on 4 December 2017

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park

scientific article

Integrated mobile genetic elements in Thaumarchaeota.

scientific article

Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability

scientific article published on 06 March 2020

Is evolution Darwinian or/and Lamarckian?

scientific article

Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms

scientific article published on 24 February 2016

Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus

scientific article

Machine-learning approach expands the repertoire of anti-CRISPR protein families

scientific article published on 29 July 2020

Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes

scientific article published on 22 June 2020

Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing

scientific article published on 18 August 2015

Microbial genome analysis: the COG approach

scientific article

Microevolutionary genomics of bacteria

scientific article

Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes

scientific article published on 04 November 2020

Molecular adaptations during viral epidemics

scientific article published on 18 July 2022

Multiplicative fitness, rapid haplotype discovery, and fitness decay explain evolution of human MHC

scientific article published on 21 June 2019

Mutation-selection balance and compensatory mechanisms in tumour evolution

scientific article published on 30 November 2020

Nature and intensity of selection pressure on CRISPR-associated genes

scientific article

Net Evolutionary Loss of Residue Polarity in Drosophilid Protein Cores Indicates Ongoing Optimization of Amino Acid Composition

scientific article

No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales

scientific article published on 24 February 2015

No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly

scientific article

No waves of intelligent design

scientific article published on 01 August 2020

Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution

scientific article published on 30 April 2010

On the feasibility of saltational evolution

scientific article published on 30 September 2019

On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization

scientific article

Ongoing Adaptive Evolution and Globalization of Sars-Cov-2

scientific article published on 13 October 2020

Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life

scientific article

Origins and Evolution of the Global RNA Virome

scientific article published on 27 November 2018

Patterns of intron gain and conservation in eukaryotic genes

scientific article

Photosystem I gene cassettes are present in marine virus genomes

scientific article

Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems

scientific article published on 20 December 2017

Phylogenomic analysis of the diversity of graspetides and proteins involved in their biosynthesis

scientific article published on 21 March 2022

Phylogenomics of Cas4 family nucleases

scientific article published on 28 November 2017

Phylogenomics of prokaryotic ribosomal proteins

scientific article

Phylogenomics of prokaryotic ribosomal proteins

Physical foundations of biological complexity

article published in the Proceedings of the National Academy of Sciences of the United States of America

Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins

scientific article

Potential genomic determinants of hyperthermophily

scientific article published in April 2003

Predictability of evolutionary trajectories in fitness landscapes

scientific article

Prediction of the incubation period for COVID-19 and future virus disease outbreaks

scientific article published on 30 November 2020

Projection of seasonal influenza severity from sequence and serological data

scientific article

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

scientific article

Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia".

scientific article published on 23 January 2018

Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues

scientific article published on 06 August 2019

Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis

scientific article

Publisher Correction: Mutation-selection balance and compensatory mechanisms in tumour evolution

scientific article published on 14 December 2020

Purifying and directional selection in overlapping prokaryotic genes

scientific article

Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes

scientific article

Reconstruction of the evolution of microbial defense systems

scientific article

Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes

scientific article

Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution

scientific article

Reply to "codon usage frequency of RNA virus genomes from high-temperature acidic-environment metagenomes".

scientific article published on February 2013

Reply to 'Evolutionary placement of Methanonatronarchaeia'

scientific article published on 01 April 2019

Reply to Hedrick and Klitz: High haplotype discovery rate in the HLA locus

scientific article published on 29 October 2019

Reply to Holmes and Duchêne, "Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?": Deep Phylogenetic Analysis of RNA Viruses Is Highly Challenging but Not Meaningless

scientific article published on 16 April 2019

Role of hypermutability in the evolution of the genus Oenococcus

scientific article

Scale-free networks in biology: new insights into the fundamentals of evolution?

scientific article

Search for a 'Tree of Life' in the thicket of the phylogenetic forest

scientific article

Seeing the Tree of Life behind the phylogenetic forest

scientific article

Seeker: alignment-free identification of bacteriophage genomes by deep learning

scientific article published on 12 October 2020

Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents

scientific article published on 14 July 2020

Selection in the evolution of gene duplications

scientific article

Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?

scientific article published in October 2003

Small proteins can no longer be ignored

scientific article

Stability along with extreme variability in core genome evolution

scientific article

Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve

scientific article published on 14 December 2018

Substantial Impact of Post Vaccination Contacts on Cumulative Infections during Viral Epidemics

scientific article published on 24 December 2020

Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics

scientific article published on 23 April 2021

Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics

scientific article published on 26 August 2021

Systematic prediction of functionally linked genes in bacterial and archaeal genomes

scientific article published on 13 September 2019

Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis

article

Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018.

scientific article published on 21 April 2018

Taxonomy of the order Mononegavirales: update 2018.

scientific article published on 11 April 2018

The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups

scientific article

The COG database: an updated version includes eukaryotes

scientific article

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

scientific article published on 19 September 2017

The basic building blocks and evolution of CRISPR-CAS systems

scientific article published on December 2013

The common ancestry of life

scientific article (publication date: 18 November 2010)

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

scientific article

The cyanobacterial genome core and the origin of photosynthesis

scholarly article

The deep archaeal roots of eukaryotes

scientific article

The ecoresponsive genome of Daphnia pulex

scientific article

The fundamental units, processes and patterns of evolution, and the tree of life conundrum

scientific article

The origins of phagocytosis and eukaryogenesis

scientific article

The role of lineage-specific gene family expansion in the evolution of eukaryotes

scientific article

The structure of the protein universe and genome evolution

scientific article

The tree and net components of prokaryote evolution

scientific article

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

scientific article (publication date: 5 May 2009)

The vast, conserved mammalian lincRNome

scientific article

Theory of prokaryotic genome evolution

scientific article

Three distinct modes of intron dynamics in the evolution of eukaryotes

scientific article

Towards functional characterization of archaeal genomic dark matter

scientific article published on 01 February 2019

Translational coupling via termination-reinitiation in archaea and bacteria

scientific article published on 05 September 2019

Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes

scientific article

Two fundamentally different classes of microbial genes

scientific article

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

scientific article

Unifying measures of gene function and evolution

scientific article published on 01 June 2006

Universal distribution of protein evolution rates as a consequence of protein folding physics

scientific article

Universal pacemaker of genome evolution

scientific article (publication date: 2012)

Universal pacemaker of genome evolution in animals and fungi and variation of evolutionary rates in diverse organisms

scientific article

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

scientific article published on 14 December 2012

Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales

Viral diversity threshold for adaptive immunity in prokaryotes

scientific article

Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

scientific article published on 05 March 2019

Virus-host arms race at the joint origin of multicellularity and programmed cell death

scientific article published on January 2014

Paulina is supported by:

About Paulina

Help