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List of works by Eugene Koonin

"Megavirales", a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses

scientific article

'Conserved hypothetical' proteins: prioritization of targets for experimental study

scientific article

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

94 Origin and evolution of adaptive immunity systems

scientific article published on May 2015

A Comparative Study on the u.v. Resistance of Double-stranded and Single-stranded Encephalomyocarditis Virus RNAs: Evaluation of the Possible Contribution of Host-mediated Repair ⬇️

scientific article published on August 1, 1980

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

scientific article published on January 15, 2002

A Genomic Perspective on Protein Families ⬇️

scientific article (publication date: 24 October 1997)

A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes

scientific article published on 14 January 2020

A Novel Flavi-like Virus in Alfalfa (Medicago sativa L.) Crops along the Snake River Valley

A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity.

scientific article

A Reverse Transcriptase-Cas1 Fusion Protein Contains a Cas6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition

scientific article published on 18 October 2018

A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea

scientific article published on 27 February 2004

A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea

scientific article published on 10 November 2015

A colipase fold in the carboxy-terminal domain of the Wnt antagonists – the Dickkopfs ⬇️

scientific article published on July 2, 1998

A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications

scientific article published in July 2004

A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication

scientific article

A community experiment with fully open and published peer review

scientific article

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 conserved NTP-motif in putative helicases

scientific article published in Nature

A conserved ancient domain joins the growing superfamily of 3′–5′ exonucleases ⬇️

scientific article published on October 1, 1997

A conserved domain in putative bacterial and bacteriophage transglycosylases

scientific article published on March 1994

A conserved poxvirus NlpC/P60 superfamily protein contributes to vaccinia virus virulence in mice but not to replication in cell culture

scientific article published on 20 February 2008

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

scientific article

A distinct abundant group of microbial rhodopsins discovered using functional metagenomics

scientific article published in Nature

A diverse superfamily of enzymes with ATP‐dependent carboxylate—amine/thiol ligase activity ⬇️

scientific article published on December 1, 1997

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair

scientific article

A duplicated catalytic motif in a new superfamily of phosphohydrolases and phospholipid synthases that includes poxvirus envelope proteins

scientific article

A family of DNA virus genes that consists of fused portions of unrelated cellular genes

scientific article published on June 1, 1992

A family of lysozyme-like virulence factors in bacterial pathogens of plants and animals

scientific article published on July 1996

A family of ubiquitin-like proteins binds the ATPase domain of Hsp70-like Stch

scientific article

A flea has smaller fleas that on him prey: giant viruses, their parasites and evolutionary networks

scientific article published in 2013

A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans

scientific article

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

scientific article

A half‐century after the molecular clock: new dimensions of molecular evolution ⬇️

scientific article published on July 13, 2012

A highly conserved family of inactivated archaeal B family DNA polymerases

scientific article published on 6 August 2008

A highly conserved sequence motif defining the family of MutT-related proteins from eubacteria, eukaryotes and viruses

scientific article published in October 1993

A korarchaeal genome reveals insights into the evolution of the Archaea

scientific article

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

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 minimal gene set for cellular life derived by comparison of complete bacterial genomes

scientific article (publication date: 17 September 1996)

A natural classification of ribonucleases

scientific article

A network perspective on the virus world

scientific article

A new family of carbon-nitrogen hydrolases

scientific article

A new family of hybrid virophages from an animal gut metagenome

scientific article

A new family of peptidyl-prolyl isomerases

scientific article published on January 1995

A new group of putative RNA helicases

scientific article published on December 1, 1992

A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses

scientific article published on 01 March 1990

A non-adaptationist perspective on evolution of genomic complexity or the continued dethroning of man.

scientific article published in March 2004

A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?

scientific article

A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain

scientific article

A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease

scientific article

A novel family of predicted retroviral-like aspartyl proteases with a possible key role in eukaryotic cell cycle control

scientific article

A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats

scientific article

A novel group of diverse Polinton-like viruses discovered by metagenome analysis

scientific article

A novel group of negative-sense RNA viruses associated with epizootics in managed and free-ranging freshwater turtles in Florida, USA

scientific article published in 2022

A novel superfamily of nucleoside triphosphate-binding motif containing proteins which are probably involved in duplex unwinding in DNA and RNA replication and recombination

scientific article

A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae

scientific article

A phylogenetic approach to target selection for structural genomics: solution structure of YciH

scientific article

A positive definition of prokaryotes

scientific article published in Nature

A poxvirus protein with a RING zinc finger motif is of crucial importance for virulence

scientific article published in January 1994

A primase subunit essential for efficient primer synthesis by an archaeal eukaryotic-type primase

scientific article

A protein splice-junction motif in hedgehog family proteins

scientific article published on April 1995

A putative FAD-binding domain in a distinct group of oxidases including a protein involved in plant development

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 putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases

scientific article published on November 1997

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

scientific article

A simple tool to search for sequence motifs that are conserved in BLAST outputs

scientific article published on July 1994

A specialized version of the HD hydrolase domain implicated in signal transduction

scientific article

A superfamily of ATPases with diverse functions containing either classical or deviant ATP-binding motif

scientific article

A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases

scientific article

A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins

scientific article (publication date: 1997)

A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases

scientific article (publication date: August 1998)

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

scientific article published on January 2012

A unique gene expression signature associated with serotonin 2C receptor RNA editing in the prefrontal cortex and altered in suicide

scientific article

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 unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons

scientific article published on 26 September 2018

A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes

scientific article

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

scientific article published on 19 January 2005

A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants

scientific article published on 01 October 2021

A viral member of the ERV1/ALR protein family participates in a cytoplasmic pathway of disulfide bond formation

scientific article

A virocentric perspective on the evolution of life ⬇️

scientific article published on July 12, 2013

AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes

scientific article (publication date: 1999)

APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis

scientific article

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

Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families

scientific article

Accumulation of GC donor splice signals in mammals

scientific article published on 9 July 2008

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

scientific article

Adaptation of mRNA structure to control protein folding

scientific article published on 19 July 2017

Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily.

scientific article

Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea

scientific article

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

scientific article

Allele fixation probability in a Moran model with fluctuating fitness landscapes

scientific article published on 01 February 2019

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

scientific article

An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication

scientific article published on March 1989

An RNA-making reactor for the origin of life

scientific article (publication date: 29 May 2007)

An alternating active-dormitive strategy enables disadvantaged prey to outcompete the perennially active prey through Parrondo’s paradox

scientific article published on 23 August 2021

An apology for orthologs - or brave new memes

scientific article

An expanding family of helicases within the 'DEAD/H' superfamily

scientific article

An insect picornavirus may have genome organization similar to that of caliciviruses

scientific article published in February 1992

An updated evolutionary classification of CRISPR-Cas systems

scientific article

Analogous Enzymes: Independent Inventions in Enzyme Evolution ⬇️

scientific article published on August 1, 1998

Analysis of evolution of exon-intron structure of eukaryotic genes

scientific article

Analysis of rare amino acid replacements supports the Coelomata clade

scientific article published on 5 October 2007

Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes

scientific article

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

Ancient Systems of Sodium/Potassium Homeostasis as Predecessors of Membrane Bioenergetics

scientific article

Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes

scientific article published on April 1996

Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes

article

Annotation and Classification of CRISPR-Cas Systems.

scientific article

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

Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity

scientific article published on 5 March 2018

Anti-CRISPRs on the march

scientific article published in Science

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

scientific article published on 07 May 2019

Apoptosis. Searching for FLASH domains

scientific article

Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons

scientific article

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

scientific article

Archaeal Ubiquitin-Like Proteins: Functional Versatility and Putative Ancestral Involvement in tRNA Modification Revealed by Comparative Genomic Analysis ⬇️

scientific article published on September 26, 2010

Archaeal ancestors of eukaryotes: not so elusive any more

scientific article

Archaeal origin of tubulin

scientific article

Archaebacterial virus SSV1 encodes a putative DnaA-like protein ⬇️

scientific article published on March 11, 1992

Archaeology of Eukaryotic DNA Replication ⬇️

scientific article published on November 1, 2013

Are There Laws of Genome Evolution? ⬇️

scientific article published on August 25, 2011

Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question

scientific article

Assessment of assumptions underlying models of prokaryotic pangenome evolution

scientific article published in 2021

Ataxin-2, global regulators and bacterial gene expression, and spliceosomal snRNP proteins share a conserved domain ⬇️

scientific article published on 01 January 1998

Author Correction: Programmable RNA targeting with the single-protein CRISPR effector Cas7-11

correction of a scholarly article

Autogenous translation regulation by Escherichia coli ATPase SecA may be mediated by an intrinsic RNA helicase activity of this protein

scientific article published in February 1992

Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes

scientific article published on June 1997

BRCA1 protein products ... Functional motifs...

scientific article published in July 1996

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

scientific article

Bacterial and bacteriophage protein phosphatases

scientific article published in May 1993

Bacterial genes in eukaryotes: relatively rare but real and important (Comment on DOI 10.1002/bies.201300095).

scientific article

Bacterial homologs of the small subunit of eukaryotic DNA primase

scientific article

Bacterial rhodopsin: evidence for a new type of phototrophy in the sea

scientific article (publication date: 15 September 2000)

Bacterial-type DNA holliday junction resolvases in eukaryotic viruses

scientific article published on August 2000

Bacteriophage P2: genes involved in baseplate assembly

scientific article published in October 1995

Beet yellows closterovirus: complete genome structure and identification of a leader papain-like thiol protease

scientific article published on January 1994

Beyond complete genomes: from sequence to structure and function

scientific article

Big time for small genomes.

scientific article

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

scientific article

Biological applications of the theory of birth-and-death processes

scientific article published in March 2006

Biology Direct: celebrating 7 years of open, published peer review

scientific article published on 30 April 2013

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

scientific article

Birnavirus RNA polymerase is related to polymerases of positive strand RNA viruses

scientific article published on August 1988

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

scientific article

Bridging the gap between sequence and function

scientific article published on 01 January 2000

C1/2 Energetics of the first bacteria as inferred from genome analysis

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

scientific article

CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems

scientific article published on 30 April 2014

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

CRISPR-Cas in mobile genetic elements: counter-defence and beyond

scientific article published on 01 August 2019

CRISPR-Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity

scientific article published on 05 September 2018

CRISPR-Cas: an adaptive immunity system in prokaryotes

scientific article

CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes

scientific article published on 25 February 2013

CRISPR: a new principle of genome engineering linked to conceptual shifts in evolutionary biology

scientific article published on 19 January 2019

CRISPRidentify: identification of CRISPR arrays using machine learning approach

scientific article published on 08 December 2020

Calorie restriction à Lamarck

scientific article

Can Environmental Manipulation Help Suppress Cancer? Non-Linear Competition Among Tumor Cells in Periodically Changing Conditions

scientific article published on 01 July 2020

Cancer-mutation network and the number and specificity of driver mutations

scientific article published on 12 June 2018

Capsid-Less RNA Viruses

scholarly article published 16 July 2012

Cargo Genes of Tn<i>7</i>-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes

scientific article published on 07 December 2021

Carl Woese's vision of cellular evolution and the domains of life

scientific article

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28.

scientific article

Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein

scientific article published on 9 March 2018

Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems

scientific article

Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity

scientific article

Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery

scientific article

Causes of trends in amino-acid gain and loss (Reply)

scientific article published in Nature

Cell cycle and apoptosis: possible roles of Gadd45 and MyD118 proteins inferred from their homology to ribosomal proteins

scientific article (publication date: April 1997)

Cell-to-cell movement of plant viruses. Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems

scientific article

Cellular differentiation into hyphae and spores in halophilic archaea

scientific article published in 2023

Cellular origin of the viral capsid-like bacterial microcompartments

scientific article published on 13 November 2017

Chance and necessity in cellular response to challenge

scientific article

Chilo iridescent virus encodes a putative helicase belonging to a distinct family within the "DEAD/H" superfamily: implications for the evolution of large DNA viruses

scientific article published on March 1994

Chordopoxvirus protein F12 implicated in enveloped virion morphogenesis is an inactivated DNA polymerase

scientific article

Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum

scientific article (publication date: 6 November 1998)

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

scientific article published on 01 October 2018

Classification and Nomenclature of Metacaspases and Paracaspases: No More Confusion with Caspases

scientific article published on 01 March 2020

Classification and evolution of P-loop GTPases and related ATPases

scientific article (publication date: 15 March 2002)

Classification and evolution of type II CRISPR-Cas systems

scientific article

Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52

scientific article

Classification and quantification of bacteriophage taxa in human gut metagenomes

scientific article

Classification of prokaryotic genetic replicators: between selfishness and altruism

scientific article

Classification of the caspase-hemoglobinase fold: detection of new families and implications for the origin of the eukaryotic separins

scientific article

Classify viruses - the gain is worth the pain

scientific article published on 01 February 2019

Cleavage of cohesin by the CD clan protease separin triggers anaphase in yeast

scientific article

Cloning the human and mouse MMS19 genes and functional complementation of a yeast mms19 deletion mutant

scientific article

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

scientific article

Co-evolution of primordial membranes and membrane proteins

scientific article published on 18 March 2009

Coat protein gene duplication in a filamentous RNA virus of plants ⬇️

scientific article published on October 1, 1992

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

scientific article published in January 2004

Coevolution of Eukaryote-like Vps4 and ESCRT-III Subunits in the Asgard Archaea

scientific article published on 19 May 2020

Common origin of four diverse families of large eukaryotic DNA viruses

scientific article

Common origins and host-dependent diversity of plant and animal viromes ⬇️

scientific article published on November 1, 2011

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

scientific article

Comparative Genomics Approaches to Identifying Functionally Related Genes

article

Comparative analysis of in vivo interactions between Rev1 protein and other Y-family DNA polymerases in animals and yeasts

scientific article

Comparative analysis of lipid biosynthesis in archaea, bacteria and eukaryotes: What was the structure of the first membrane lipids?

Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals

scientific article published on 18 March 2004

Comparative genome analysis

Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum

scientific article

Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces

scientific article

Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems

scientific article published on 9 January 2015

Comparative genomics and evolution of proteins involved in RNA metabolism

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 and structural biology of the molecular innovations of eukaryotes

scientific article published on 5 May 2006

Comparative genomics of Archaea: how much have we learned in six years, and what's next?

scientific article

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

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

scientific article

Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging

scientific article published on 5 October 2004

Comparative genomics of the lactic acid bacteria

scientific article

Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex

scientific article

Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex

scientific article published in July 2009

Comparative genomics, minimal gene-sets and the last universal common ancestor

scientific article published in November 2003

Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea ⬇️

scientific article published on August 1, 1997

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

scientific article

Comparison of the complete protein sets of worm and yeast: orthology and divergence

scientific article

Compelling reasons why viruses are relevant for the origin of cells

scientific article published in August 2009

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

scientific article published on 8 December 2006

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

scientific article

Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics

scientific article published on December 1996

Complete genomic sequence and phylogenetic analysis of the lactate dehydrogenase-elevating virus (LDV).

scientific article published on June 1993

Complete pathway for protein disulfide bond formation encoded by poxviruses

scientific article

Complete sequence of the citrus tristeza virus RNA genome

scientific article published on April 1995

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

scientific article published on 22 May 2007

Complex selection on 5' splice sites in intron-rich organisms

scientific article published on 10 September 2009

Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

scientific article

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

scientific article

Computational analysis of human disease-associated genes and their protein products

scientific article

Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes

scientific article published in June 2004

Computational genomics

scientific article (publication date: 6 March 2001)

Computational methods for Gene Orthology inference

scientific article

Computer analysis of amino acid sequences. The case of plant virus capsid proteins

scientific article

Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search

scientific article

Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes

scientific article

Computer-assisted assignment of functional domains in the nonstructural polyprotein of hepatitis E virus: delineation of an additional group of positive-strand RNA plant and animal viruses ⬇️

scientific article published on September 1, 1992

Computer-assisted dissection of rolling circle DNA replication

Computer-assisted identification of a putative methyltransferase domain in NS5 protein of flaviviruses and lambda 2 protein of reovirus

scientific article published on April 1993

Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein

scientific article

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

scientific article

Connected gene neighborhoods in prokaryotic genomes

scientific article

Connections between alternative transcription and alternative splicing in mammals

scientific article

Consensus statement: Virus taxonomy in the age of metagenomics

scientific article

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

scientific article published on 28 July 2004

Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses

scientific article

Conservation of the putative methyltransferase domain: a hallmark of the 'Sindbis-like' supergroup of positive-strand RNA viruses

scientific article

Conservation versus parallel gains in intron evolution

scientific article

Conservation versus parallel gains in intron evolution

scientific article (published 2005-09-25)

Conserved domains in DNA repair proteins and evolution of repair systems

scientific article

Conserved sequence motifs in bacterial and bacteriophage chaperonins

scientific article published on January 1995

Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria ⬇️

scientific article published on July 11, 1992

Conserved sequence pattern in a wide variety of phosphoesterases

scientific article

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

scientific article published on November 20, 2001

Constraints and plasticity in genome and molecular-phenome evolution

scientific article

Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage

scientific article

Contribution of phage‐derived genomic islands to the virulence of facultative bacterial pathogens ⬇️

scientific article published on October 4, 2012

Coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis.

scientific article published on June 1989

Corrigendum: Genome and Environmental Activity of a Chrysochromulina parva Virus and Its Virophages

scholarly article published in Frontiers in Microbiology

Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea

scientific article

Coupling immunity and programmed cell suicide in prokaryotes: Life-or-death choices

scientific article

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system

scientific article

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

Crossing fitness valleys via double substitutions within codons

scientific article published on 16 December 2019

Crossing fitness valleys via double substitutions within codons: Supplementary information

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA

scientific article

Crystal Structure of a Hedgehog Autoprocessing Domain: Homology between Hedgehog and Self-Splicing Proteins ⬇️

scientific article published on October 3, 1997

Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain

scientific article

Crystal structure of Mil (Mth680): internal duplication and similarity between the Imp4/Brix domain and the anticodon-binding domain of class IIa aminoacyl-tRNA synthetases

scientific article

Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion

scientific article published on 16 March 2006

Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold

scientific article

DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history

scientific article

DNA-binding proteins and evolution of transcription regulation in the archaea

scientific article

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

scientific article

Darwinian evolution in the light of genomics

scientific article

De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling

scientific article

Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response

scientific article published on 30 July 2015

Deep Roots and Splendid Boughs of the Global Plant Virome

scientific article published on 27 May 2020

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

Defining Life: An Exercise in Semantics or A Route to Biological Insights? ⬇️

scientific article published on January 1, 2012

Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks

scientific article

Dependencies among Editing Sites in Serotonin 2C Receptor mRNA ⬇️

scientific article published on September 6, 2012

Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks

scientific article

Detection of new genes in a bacterial genome using Markov models for three gene classes

scientific article

Did DNA replication evolve twice independently?

scientific article

Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites

scientific article

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

scientific article

Differential translation tunes uneven production of operon-encoded proteins

scientific article published on 5 September 2013

Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions

scientific article

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

scientific article

Discovery of Oligonucleotide Signaling Mediated by CRISPR-Associated Polymerases Solves Two Puzzles but Leaves an Enigma

scientific article

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.

scientific article published on 13 November 2017

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

scientific article

Disentangling the effects of selection and loss bias on gene dynamics

scientific article

Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales

scientific article

Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes

scientific article published on April 2010

Distribution of protein folds in the three superkingdoms of life.

scientific article

Divergence and convergence in enzyme evolution

scientific article

Diverse Groups of Plant RNA and DNA Viruses Share Related Movement Proteins that may Possess Chaperone-like Activity

scientific article published on December 1, 1991

Diverse enzymatic activities mediate antiviral immunity in prokaryotes

scientific article published on 01 August 2020

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

scientific article

Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon

scientific article published on 21 November 2005

Diversity and Evolution of Type IV pili Systems in Archaea

scientific article

Diversity and evolution of class 2 CRISPR-Cas systems

scientific article

Diversity, classification and evolution of CRISPR-Cas systems

scientific article

DnaC protein contains a modified ATP-binding motif and belongs to a novel family of ATPases including also DnaA.

scientific article

Does the central dogma still stand?

scientific article

Dollo parsimony and the reconstruction of genome evolution

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

Dynein light chains of the Roadblock/LC7 group belong to an ancient protein superfamily implicated in NTPase regulation

scientific article

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

scientific article

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

scientific article

Elaborate security TRAINing to fight against expression of genomic junk ⬇️

scientific article published on January 31, 2013

Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins

scientific article

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

scientific article (publication date: 2008)

Encephalomyocarditis virus RNA synthesis in vitro is protein-primed ⬇️

scientific article published on November 1, 1984

Encephalomyocarditis virus replication complexes preferentially utilizing nucleoside diphosphates as substrates for viral RNA synthesis. Nucleotide kinases specifically associated with the complex channel RNA precursor ⬇️

scientific article published on October 15, 1984

Encephalomyocarditis virus replication complexes that Prefer nucleoside diphosphates as substrates for viral RNA synthesis ⬇️

scientific article published on September 1, 1983

Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain

scientific article published on October 1991

Energetics and population genetics at the root of eukaryotic cellular and genomic complexity

scientific article published on 23 December 2015

Engineering of CRISPR–Cas12b for human genome editing

scientific article published in Nature Communications

Environmental microbiology and metagenomics: the Brave New World is here, what's next?

scientific article published on 15 October 2018

Erratum for Gjessing et al., Salmon Gill Poxvirus, the Deepest Representative of the Chordopoxvirinae

scientific article published in November 2015

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

Erratum: Classification and quantification of bacteriophage taxa in human gut metagenomes

scholarly article by Alison S Waller et al published 24 June 2014 in The ISME Journal

Escherichia coli dinG gene encodes a putative DNA helicase related to a group of eukaryotic helicases including Rad3 protein

scientific article

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

scientific article

Estimating the number of protein folds and families from complete genome data

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

Eugene V. Koonin

scientific article published in February 2004

Eukaryote-specific domains in translation initiation factors: implications for translation regulation and evolution of the translation system

scientific article

Eukaryotic DNA polymerases: proposal for a revised nomenclature.

scientific article

Eukaryotic RNAse H shares a conserved domain with caulimovirus proteins that facilitate translation of polycistronic RNA.

scientific article published in October 1994

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

scientific article

Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer

scientific article

Eukaryotic transcription regulators derive from ancient enzymatic domains ⬇️

scientific article published on February 12, 1998

Eukaryotic translation elongation factor 1 gamma contains a glutathione transferase domain--study of a diverse, ancient protein superfamily using motif search and structural modeling

scientific article

Evidence for a family of archaeal ATPases

scientific article published on 01 March 1997

Evidence for common ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand RNA plant viruses

scientific article published on December 1991

Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles

article

Evidence of splice signal migration from exon to intron during intron evolution

scientific article

Evolution and classification of P-loop kinases and related proteins

scientific article published in October 2003

Evolution and classification of the CRISPR-Cas systems

scientific article (publication date: June 2011)

Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences

scientific article

Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals

scientific article

Evolution of AANAT: expansion of the gene family in the cephalochordate amphioxus

scientific article

Evolution of DNA ligases of nucleo-cytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity

scientific article

Evolution of DNA packaging in gene transfer agents

scientific article

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

scientific article

Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii

scientific article published on 16 April 2018

Evolution of Human Respiratory Virus Epidemics

scientific article published on 24 November 2020

Evolution of RNA genomes: does the high mutation rate necessitate high rate of evolution of viral proteins?

scientific article published on June 1989

Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence

scientific article

Evolution of adaptive immunity from transposable elements combined with innate immune systems

scientific article published on 9 December 2014

Evolution of alternative and constitutive regions of mammalian 5'UTRs.

scientific article

Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences

scientific article

Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.

scientific article

Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease

scientific article

Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer

scientific article

Evolution of cell division: from shear mechanics to complex molecular machineries

scientific article

Evolution of cell–cell signaling in animals: did late horizontal gene transfer from bacteria have a role?

scientific article

Evolution of complexity in the viral world: the dawn of a new vision

scientific article published on 23 February 2006

Evolution of diverse cell division and vesicle formation systems in Archaea

scientific article

Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses

scientific article

Evolution of eukaryotic cell cycle regulation: stepwise addition of regulatory kinases and late advent of the CDKs

scientific article

Evolution of eukaryotic cysteine sulfinic acid reductase, sulfiredoxin (Srx), from bacterial chromosome partitioning protein ParB.

scientific article published on 25 July 2005

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

scientific article

Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses

scientific article

Evolution of gene fusions: horizontal transfer versus independent events

scientific article

Evolution of genome architecture

scientific article

Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation

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 protein domain promiscuity in eukaryotes

scientific article

Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery

scientific article (publication date: 2014)

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

scientific article

Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism

Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon

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

Evolution of thymidine and thymidylate kinases: The possibility of independent capture of TK genes by different groups of viruses ⬇️

scientific article published on April 1, 1992

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 and functional genomics of the Archaea

scientific article published in October 2005

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

scientific article published on 19 December 2019

Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases

scientific article

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

scientific article

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

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 genomics of archaeal viruses: unique viral genomes in the third domain of life

scientific article

Evolutionary genomics of lactic acid bacteria

scientific article published on 3 November 2006

Evolutionary genomics of nucleo-cytoplasmic large DNA viruses

scientific article

Evolutionary history and higher order classification of AAA+ ATPases

scientific article (publication date: 2004)

Evolutionary primacy of sodium bioenergetics

scientific article published on April 2008

Evolutionary significance of gene expression divergence

scientific article published on 29 December 2004

Evolutionary switches between two serine codon sets are driven by selection

scientific article

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

Exceptional error minimization in putative primordial genetic codes

scientific article

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

scientific article

Expanding networks of RNA virus evolution ⬇️

scientific article published on June 20, 2012

Expression of the vaccinia virus A2.5L redox protein is required for virion morphogenesis

scientific article published on September 2002

Expression, splicing, and evolution of the myosin gene family in plants

scientific article published on 13 January 2011

Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors

scientific article

Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families

scientific article published on 13 September 2017

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

scientific article

FMN- or DNA-binding?

scientific article

Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis ⬇️

scientific article published on October 10, 2003

Fold prediction and evolutionary analysis of the POZ domain: structural and evolutionary relationship with the potassium channel tetramerization domain

scientific article

Footprints of primordial introns on the eukaryotic genome: still no clear traces ⬇️

scientific article published on 01 September 2001

Fowlpox virus encodes a protein related to human deoxycytidine kinase: further evidence for independent acquisition of genes for enzymes of nucleotide metabolism by different viruses

scientific article published on September 1993

Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction

article

From complete genome sequence to 'complete' understanding?

scientific article

From complete genomes to measures of substitution rate variability within and between proteins

scientific article

Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code

scientific article

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

scientific article published on 12 June 2015

Functional Long Non-coding RNAs Evolve from Junk Transcripts

scientific article published on 13 October 2020

Functional and evolutionary implications of gene orthology.

scientific article

Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes

scientific article

Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP

scientific article

Functionally diverse type V CRISPR-Cas systems

scientific article published on 06 December 2018

Fusion of a superfamily 1 helicase and an inactivated DNA polymerase is a signature of common evolutionary history of Polintons, polinton-like viruses, Tlr1 transposons and transpovirons

scientific article

G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins

scientific article published on 01 September 1999

GINS, a central nexus in the archaeal DNA replication fork

scientific article

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

scientific article published on 20 March 2020

Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA replication initiator proteins

scientific article published on October 1, 1992

Gene A32 product of vaccinia virus may be an ATPase involved in viral DNA packaging as indicated by sequence comparisons with other putative viral ATPases

scientific article published in February 1993

Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae

scientific article published on January 2001

Gene duplication with displacement and rearrangement: origin of the bacterial replication protein PriB from the single-stranded DNA-binding protein Ssb.

scientific article

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

scientific article

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

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

Gene order is not conserved in bacterial evolution

scientific article published on 01 August 1996

Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection

scientific article published on 16 April 2015

Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis

scientific article

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

scientific article

Genome and Environmental Activity of a Virus and Its Virophages

scientific article published in 2019

Genome as a stochastic evolutionary machine: comment on "How life changes itself: the Read-Write (RW) genome" by James Shapiro

scientific article

Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics

scientific article

Genome reduction as the dominant mode of evolution

scientific article published on 25 June 2013

Genome replication/expression strategies of positive-strand RNA viruses: A simple version of a combinatorial classification and prediction of new strategies ⬇️

scientific article published on 01 July 1991

Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum

scientific article

Genome sequence comparison and scenarios for gene rearrangements: a test case

scientific article published in November 1995

Genome sequence of a human tumorigenic poxvirus: prediction of specific host response-evasion genes

scientific article published on August 1996

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 sequences: Genome sequence of a model prokaryote ⬇️

scientific article published on October 1, 1997

Genome sequencing: a glimpse of the area at the brink of the virus era.

scientific article published on January 1993

Genome structure and phylogenetic analysis of lettuce infectious yellows virus, a whitefly-transmitted, bipartite closterovirus

scientific article published on April 1995

Genome trees and the tree of life

scientific article

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

scientific article published on October 20, 2001

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 and biological analysis of Grapevine leafroll-associated virus 7 reveals a possible new genus within the family Closteroviridae ⬇️

scientific article published on October 25, 2011

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 microbiology: Right on target? ⬇️

scientific article published on 01 September 1998

Genomics and biology of Rudiviruses, a model for the study of virus-host interactions in Archaea

scientific article published on February 2013

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

scientific article

Genomics: Re-evaluation of translation machinery evolution ⬇️

scientific article published on April 9, 1998

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

scientific article

Getting positive about selection

scientific article

Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms

scientific article

Giant viruses with an expanded complement of translation system components

scientific article (publication date: 6 April 2017)

Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches

scientific article (publication date: 16 April 1999)

Global Organization and Proposed Megataxonomy of the Virus World

scientific article published on 04 March 2020

Global similarity and local divergence in human and mouse gene co-expression networks

scientific article published on 12 September 2006

Grammar of protein domain architectures

scientific article published on 07 February 2019

Hax1 lacks BH modules and is peripherally associated to heavy membranes: implications for Omi/HtrA2 and PARL activity in the regulation of mitochondrial stress and apoptosis

scientific article

Hedgehog patterning activity: role of a lipophilic modification mediated by the carboxy-terminal autoprocessing domain

scientific journal article

Helicases: amino acid sequence comparisons and structure-function relationships

Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes ⬇️

scientific article published on August 14, 2012

Homologous Capsid Proteins Testify to the Common Ancestry of Retroviruses, Caulimoviruses, Pseudoviruses, and Metaviruses

scientific article published on 29 March 2017

Homologous recombination substantially delays sequence but not gene content divergence of prokaryotic populations

article

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

scientific article

Horizontal gene transfer can rescue prokaryotes from Muller's ratchet: benefit of DNA from dead cells and population subdivision

scientific article

Horizontal gene transfer in prokaryotes: quantification and classification

scientific article (publication date: 2001)

Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions

scientific article

Horizontal gene transfer: the path to maturity ⬇️

scientific article published on November 1, 2003

Horizontal transfer beyond genes

scientific article

How Many Genes Can Make a Cell: The Minimal-Gene-Set Concept ⬇️

scientific article published on January 1, 2000

How stands the Tree of Life a century and a half after The Origin?

scientific article (publication date: 30 June 2011)

Human DNA polymerase kappa: a novel DNA polymerase of unknown biological function encoded by the DINB1 gene

scientific article

Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily

scientific article

Human choroideremia protein contains a FAD-binding domain

scientific article published on 01 March 1996

Human choroideremia protein contains a FAD-binding domain

scientific article published on 01 April 1996

Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches

scientific article published in 2022

Hunting for Treasure Chests in Microbial Defense Islands

scientific article published on 07 June 2018

IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices

scientific article

ISC, a Novel Group of Bacterial and Archaeal DNA Transposons That Encode Cas9 Homologs

scientific article published on 28 December 2015

Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism

scientific article

Identification and properties of the largest subunit of the DNA-dependent RNA polymerase of fish lymphocystis disease virus: dramatic difference in the domain organization in the family Iridoviridae

scientific article published on May 1995

Identification of Dephospho-Coenzyme A (Dephospho-CoA) Kinase in Thermococcus kodakarensis and Elucidation of the Entire CoA Biosynthesis Pathway in Archaea

scientific article published on 23 July 2019

Identification of a DinB/UmuC homolog in the archeon Sulfolobus solfataricus

scientific article published on October 1996

Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea

scientific article published on 14 October 2009

Identification of genes encoding zinc finger proteins, non-histone chromosomal HMG protein homologue, and a putative GTP phosphohydrolase in the genome of Chilo iridescent virus

scientific article

Identification of myosin XI receptors in Arabidopsis defines a distinct class of transport vesicles

scientific article

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

scientific article

Identification of paracaspases and metacaspases: two ancient families of caspase-like proteins, one of which plays a key role in MALT lymphoma

scientific article

Identification of the catalytic sites of a papain-like cysteine proteinase of murine coronavirus.

scientific article published on October 1993

Identification of the primase active site of the herpes simplex virus type 1 helicase-primase

scientific article

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

scientific article

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

scientific article (publication date: 10 July 2014)

Implications for proteasome nuclear localization revealed by the structure of the nuclear proteasome tether protein Cut8 ⬇️

scientific article published on October 5, 2011

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

scientific article (publication date: 15 July 2001)

In silico learning of tumor evolution through mutational time series

scientific article published on 23 April 2019

In vivo genome editing using Staphylococcus aureus Cas9

scientific article

Incorporating Machine Learning into Established Bioinformatics Frameworks

scientific article

Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting atpases

scientific article

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

Insect iridescent virus type 6 encodes a polypeptide related to the largest subunit of eukaryotic RNA polymerase II.

scientific article published on July 1994

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

Interkingdom gene fusions ⬇️

scientific article

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

scientific article published on 06 March 2020

Intrinsic and extrinsic approaches for detecting genes in a bacterial genome ⬇️

scientific article

Intron sliding in conserved gene families.

scientific article

Intron-dominated genomes of early ancestors of eukaryotes

scientific article

Introns and the origin of nucleus-cytosol compartmentalization

scientific article (publication date: 2 March 2006)

Inventing the dynamo machine: the evolution of the F-type and V-type ATPases

scientific article published in November 2007

Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process?

Is evolution Darwinian or/and Lamarckian?

scientific article

Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases

scientific article (publication date: November 1998)

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

scientific article published on 24 February 2016

Key role of recombination in evolutionary processes with migration between two habitats

scientific article published on 01 September 2019

Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli

scientific article

Lineage-specific gene expansions in bacterial and archaeal genomes

scientific article

Lineage-specific loss and divergence of functionally linked genes in eukaryotes

scientific article

Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes

scientific article

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

scientific article

MOLECULAR BIOLOGY AND EVOLUTION OF CLOSTEROVIRUSES: Sophisticated Build-up of Large RNA Genomes

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

scientific article published on 29 July 2020

Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases

scientific article published on 22 April 2015

Male-specific lethal 2, a dosage compensation gene of Drosophila, undergoes sex-specific regulation and encodes a protein with a RING finger and a metallothionein-like cysteine cluster.

scientific article published on June 1995

Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery

scientific article published in 2021

Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes

scientific article published on 22 June 2020

Mathematical modeling of evolution of horizontally transferred genes

scientific article published on 18 May 2005

Mathematical modeling of tumor therapy with oncolytic viruses: effects of parametric heterogeneity on cell dynamics

scientific article published on 3 October 2006

Mathematical modeling of tumor therapy with oncolytic viruses: regimes with complete tumor elimination within the framework of deterministic models

scientific article

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli

scientific article published on March 1996

Metagenomic sorcery and the expanding protein universe

scientific article published on 01 May 2007

Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer

scientific article published on 2 November 2017

Metaviromics: a tectonic shift in understanding virus evolution

scientific article published in February 2018

Methanonatronarchaeum thermophilum gen. nov., sp. nov. and 'Candidatus Methanohalarchaeum thermophilum', extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia cla...

article

Microbial culturomics: paradigm shift in the human gut microbiome study

scientific article (publication date: December 2012)

Microbial genome analysis: the COG approach

scientific article

Microbial genomics challenge Darwin

scientific article published on 12 October 2012

MicrobiologyThe Evolution and Emergence of RNA Viruses. Oxford Series in Ecology and Evolution. By EdwardC.Holmes. Oxford and New York: Oxford University Press. $130.00 (hardcover); $60.00 (paper). xii 254 p.; ill.; index. ISBN: 9780199211128 (hc); 9

article

Microevolutionary genomics of bacteria

scientific article

Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family

scientific article published on 4 April 2013

Minimum Information about an Uncultivated Virus Genome (MIUViG)

scientific article published on 17 December 2018

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

scientific article

Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back

scientific article

Modeling genome evolution with a diffusion approximation of a birth-and-death process

scientific article published in November 2005

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

Molecular characterization and developmental expression of a retinoid- and fatty acid-binding glycoprotein from Drosophila. A putative lipophorin

scientific article

Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin

scientific article

Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent

scientific article (publication date: 26 January 1996)

Molecular dating: ape bones agree with chicken entrails

scientific article published in February 2005

Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA.

scientific article

Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia coli.

scientific article published in April 1994

Multidomain organization of eukaryotic guanine nucleotide exchange translation initiation factor eIF-2B subunits revealed by analysis of conserved sequence motifs

scientific article

Multiple evolutionary origins of giant viruses

Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing

scientific article published on 2 April 2015

Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids

scientific article published on 31 July 2019

Multiple origins of viral capsid proteins from cellular ancestors

scientific article

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

scientific article published on 21 June 2019

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

scientific article published on 01 August 2004

Mutation-selection balance and compensatory mechanisms in tumour evolution

scientific article published on 30 November 2020

Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection

scientific article

Myosin XI-K Is required for rapid trafficking of Golgi stacks, peroxisomes, and mitochondria in leaf cells of Nicotiana benthamiana

scientific article published on 4 January 2008

Myosin-driven transport network in plants

scientific article

N-terminal domains of putative helicases of flavi- and pestiviruses may be serine proteases

scientific article (publication date: 25 May 1989)

Nature and intensity of selection pressure on CRISPR-associated genes

scientific article

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

scientific article

Nested genes and increasing organizational complexity of metazoan genomes

scientific article

New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures

article

New dimensions of the virus world discovered through metagenomics

scientific article

New genes in old sequence: a strategy for finding genes in the bacterial genome

scientific article published on 01 August 1994

New variants of known folds: do they bring new biology? ⬇️

scientific article published on July 6, 2010

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

scientific article published on 24 February 2015

No footprints of primordial introns in a eukaryotic genome

scientific article

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

Non-orthologous gene displacement

scientific article published on 01 September 1996

Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota

scientific article

Novel Families of Putative Protein Kinases in Bacteria and Archaea: Evolution of the “Eukaryotic” Protein Kinase Superfamily ⬇️

scientific article published on October 1, 1998

Novel bacteriophages containing a genome of another bacteriophage within their genomes

scientific article

Novel domains of the prokaryotic two-component signal transduction systems

scientific article (publication date: 11 September 2001)

Novel predicted RNA-binding domains associated with the translation machinery

scientific article

Novel predicted peptidases with a potential role in the ubiquitin signaling pathway

scientific article

Nucleic acid detection with CRISPR-Cas13a/C2c2

scientific article

Nucleotide sequence of XhoI O fragment of ectromelia virus DNA reveals significant differences from vaccinia virus

scientific article published on October 1993

Nucleotide sequence of the 3'-terminal half of beet yellows closterovirus RNA genome: unique arrangement of eight virus genes

scientific article published on January 1991

Obituary: Walter Fitch and the orthology paradigm ⬇️

scientific article published on September 1, 2011

On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems ⬇️

scientific article published on March 24, 2011

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

scientific article

On the feasibility of saltational evolution

scientific article published on 30 September 2019

On the origin of cells and viruses: primordial virus world scenario

scientific article

On the origin of genomes and cells within inorganic compartments

scientific article published on 11 October 2005

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

One more conserved sequence motif in helicases ⬇️

scientific article published on August 11, 1988

One-component systems dominate signal transduction in prokaryotes

scientific article published on February 2005

Ongoing Adaptive Evolution and Globalization of Sars-Cov-2

scientific article published on 13 October 2020

Open questions on the origin of life at anoxic geothermal fields

scientific article published on October 2012

Open questions: CRISPR biology

article published in 2018

Organization and evolution of bacterial and bacteriophage primase-helicase systems

scientific article published on April 1, 1992

Origin and Evolution of the Universal Genetic Code

scientific article published on 30 August 2017

Origin and evolution of eukaryotic apoptosis: the bacterial connection

scientific article

Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses

scientific article

Origin and evolution of spliceosomal introns

scientific article

Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members

scientific article

Origin and evolution of the genetic code: the universal enigma

scientific article

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

scientific article (publication date: February 2003)

Origin of alternative splicing by tandem exon duplication ⬇️

scientific article published on November 1, 2001

Origin of an animal mitochondrial DNA polymerase subunit via lineage-specific acquisition of a glycyl-tRNA synthetase from bacteria of the Thermus-Deinococcus group

scientific article

Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?

scientific article (publication date: 26 September 2015)

Origin of first cells at terrestrial, anoxic geothermal fields

scientific article

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

scientific article

Origin of programmed cell death from antiviral defense?

scientific article published on 09 July 2019

Origin of viruses: primordial replicators recruiting capsids from hosts

scientific article published on 01 July 2019

Origins and Evolution of the Global RNA Virome

scientific article published on 27 November 2018

Origins and Evolution of the Global RNA Virome

scientific article published on 24 October 2018

Origins and evolution of CRISPR-Cas systems

Origins and evolution of eukaryotic RNA interference

scientific article

Origins and evolution of viruses of eukaryotes: The ultimate modularity

scientific article

Origins and impact of constraints in evolution of gene families

scientific article

Ortervirales: A new viral order unifying five families of reverse-transcribing viruses

scientific article published on 4 April 2018

Orthologous gene clusters and taxon signature genes for viruses of prokaryotes

scientific article

Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota".

scientific article

Orthologs, paralogs, and evolutionary genomics

scientific article (publication date: 2005)

Orthology, paralogy and proposed classification for paralog subtypes

scientific article published on 01 December 2002

PAMP and PARL, two novel putative metalloproteases interacting with the COOH-terminus of Presenilin-1 and -2

scientific article (publication date: April 2001)

Pandoraviruses are highly derived phycodnaviruses

scientific article

Parabolic replicator dynamics and the principle of minimum Tsallis information gain ⬇️

scientific article (publication date: 11 August 2013)

Paralogs and mutational robustness linked through transcriptional reprogramming

scientific article published in September 2005

Patterns of intron gain and conservation in eukaryotic genes

scientific article

Peptide-N-glycanases and DNA repair proteins, Xp-C/Rad4, are, respectively, active and inactivated enzymes sharing a common transglutaminase fold

scientific article

Phage lysis-lysogeny switches and programmed cell death: Danse macabre

scientific article published on 12 November 2020

Phages build anti-defence barriers

scientific article published on 01 January 2020

Phosphoesterase domains associated with DNA polymerases of diverse origins ⬇️

scientific article published on August 15, 1998

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 Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes

scientific article

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

Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems

scientific article

Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation

scientific article published in September 1991

Phylogeny of capsid proteins of small icosahedral RNA plant viruses

scientific article published on 01 July 1991

Physical foundations of biological complexity

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

Pineal serotonin N-acetyltransferase: expression cloning and molecular analysis

scientific article published on December 1995

Planctomycetes and eukaryotes: a case of analogy not homology

scientific article (publication date: November 2011)

Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes

scientific article published in 2015

Plasmodium falciparum protein associated with the invasion junction contains a conserved oxidoreductase domain

scientific article

Polintons, virophages and transpovirons: a tangled web linking viruses, transposons and immunity.

scientific article published on 30 June 2017

Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution

scientific article published on 22 December 2014

Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs

scientific article

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

Poxvirus DNA primase

scholarly article

Predator Dormancy is a Stable Adaptive Strategy due to Parrondo's Paradox

scientific article published on 12 December 2019

Predictability of evolutionary trajectories in fitness landscapes

scientific article

Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array

scientific article published on 01 April 2019

Predicted poxvirus FEN1-like nuclease required for homologous recombination, double-strand break repair and full-size genome formation

scientific article published on October 2009

Predicting functions from protein sequences--where are the bottlenecks?

scientific article published on April 1998

Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120.

scientific article

Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach

scientific article

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

scientific article published on 30 November 2020

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

scientific article published on 21 May 2020

Prediction of transcription regulatory sites in Archaea by a comparative genomic approach

scientific article

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

scientific article published in August 2004

Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ‘weak’ context of the start codon ⬇️

scientific article published on October 1, 2001

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

scientific article

Preview. The incredible expanding ancestor of eukaryotes

scientific article published on March 2010

Primordial spliceosomal introns were probably U2-type

scientific article

Projection of seasonal influenza severity from sequence and serological data

scientific article

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

scientific article

Prokaryotic genomes: the emerging paradigm of genome-based microbiology

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

Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system

scientific article

Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea

scientific article published on 5 December 2017

Protein fold recognition using sequence profiles and its application in structural genomics

scientific article

Protein sequence comparison at genome scale

scientific article published on January 1996

Protein sequence motifs

scientific article published on June 1996

Protein sequence similarity searches using patterns as seeds ⬇️

scientific article published on September 1, 1998

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

Proteorhodopsin genes in giant viruses ⬇️

scientific article published on October 4, 2012

Provirophages and transpovirons as the diverse mobilome of giant viruses

scientific article

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

scientific article

Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases

scientific article

Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity

scholarly article by Fei He et al published 21 June 2018 in Nature Microbiology

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

Purifying and positive selection in the evolution of stop codons.

scientific article published on 18 June 2018

Putative 65 kDa protein of beet yellows closterovirus is a homologue of HSP70 heat shock proteins

scientific article published on February 1991

Putative papain-related thiol proteases of positive-strand RNA viruses. Identification of rubi- and aphthovirus proteases and delineation of a novel conserved domain associated with proteases of rubi-, alpha- and coronaviruses

scientific article published in August 1991

Q & A

article published in 2004

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

scientific article

Quod erat demonstrandum?The mystery of experimental validation of apparently erroneous computational analyses of protein sequences ⬇️

scientific article published on November 13, 2001

RNA sequence of astrovirus: distinctive genomic organization and a putative retrovirus-like ribosomal frameshifting signal that directs the viral replicase synthesis

scientific article published on November 1993

RNA-guided DNA insertion with CRISPR-associated transposases

scientific article published on 06 June 2019

RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease

scientific article published on 25 November 2022

RNase T shares conserved sequence motifs with DNA proofreading exonucleases

scientific article

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

scientific article published in November 2001

Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity

scientific article published on 13 January 2016

Reconstruction of ancestral protosplice sites

scientific article

Reconstruction of the evolution of microbial defense systems

scientific article

Recruitment of CRISPR-Cas systems by Tn7-like transposons

scientific article published on 15 August 2017

Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain

scientific article

Regeneration of peroxiredoxins by p53-regulated sestrins, homologs of bacterial AhpD

scientific journal article

Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains.

scientific article

Related domains in yeast tRNA ligase, bacteriophage T4 polynucleotide kinase and RNA ligase, and mammalian myelin 2',3'-cyclic nucleotide phosphohydrolase revealed by amino acid sequence comparison

scientific article published in July 1990

Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the megavirus lineage

scientific article published on January 2012

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

Replaying the tape of life: quantification of the predictability of evolution ⬇️

scientific article published on November 26, 2012

Reply

article published in 1999

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

Response to Comment on "RNA-guided DNA insertion with CRISPR-associated transposases"

scientific article published on 01 June 2020

Reviewer acknowledgement

Reviving a culture of scientific debate

scientific article published in Nature

Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange

scientific article

Role of CED-4 in the activation of CED-3 ⬇️

scientific article published on August 21, 1997

Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome

scientific article

Role of mRNA structure in the control of protein folding

scientific article

Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1.

scientific article

SAP - a putative DNA-binding motif involved in chromosomal organization

scientific article (publication date: March 2000)

SEALS: a system for easy analysis of lots of sequences

scientific article published on January 1, 1997

SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases

scientific article published on January 1, 2002

STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer

scientific article

SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories

scientific article

SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes

scientific article

Saccharomyces cerevisiae SMT4 encodes an evolutionarily conserved protease with a role in chromosome condensation regulation

scientific article

Salmon Gill Poxvirus, the Deepest Representative of the Chordopoxvirinae

scientific article

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

scientific article

Scores of RINGS but No PHDs in Ubiquitin Signaling ⬇️

scientific article published on March 1, 2003

Screening of the closterovirus genome by degenerate primer-mediated polymerase chain reaction

scientific article published on June 1994

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

scientific article

Searching for drug targets in microbial genomes

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 for minimization of translational frameshifting errors as a factor in the evolution of codon usage

scientific article

Selection for short introns in highly expressed genes

scientific article

Selection in the evolution of gene duplications

scientific article

Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions

scientific article published on 29 September 2017

Self-regulated cleavage of the mitochondrial intramembrane-cleaving protease PARL yields Pbeta, a nuclear-targeted peptide

scientific article

Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems

scientific article

Sequence - Evolution - Function: Computational Approaches in Comparative Genomics

scientific article published on 7 December 2010

Sequence analysis of an exceptionally conserved operon suggests enzymes for a new link between histidine and purine biosynthesis

scientific article published in April 1997

Sequence analysis of eukaryotic developmental proteins: ancient and novel domains

scientific article

Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications

scientific article

Sequencing and analysis of bacterial genomes

scientific article published on April 1996

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

scientific article published on 9 February 2006

Similarities in RNA helicases ⬇️

scientific article published on July 25, 1991

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

scientific article published in October 2003

Site-selected mutagenesis of a conserved nucleotide binding HXGH motif located in the ATP sulfurylase domain of human bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase

scientific article

Small CRISPR RNAs guide antiviral defense in prokaryotes

scientific article

Small cysteine-rich proteins of different groups of plant RNA viruses are related to different families of nucleic acid-binding proteins

scientific article published on March 1991

Small cytoplasmic RNA from mouse cells covalently linked to a protein

scientific article published on 01 May 1988

SnapShot: Class 1 CRISPR-Cas Systems

scientific article

SnapShot: Class 2 CRISPR-Cas Systems

scientific article published on 12 January 2017

Sobemovirus genome appears to encode a serine protease related to cysteine proteases of picornaviruses

scientific article published on 01 August 1988

Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption.

scientific article

Specific Expansion of Protein Families in the Radioresistant Bacterium Deinococcus Radiodurans

article

Splendor and misery of adaptation, or the importance of neutral null for understanding evolution

scientific article

SpoU protein of Escherichia coli belongs to a new family of putative rRNA methylases

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

Structure and Activity of a Novel Archaeal β-CASP Protein with N-Terminal KH Domains

scientific article

Structure and function of virion RNA polymerase of a crAss-like phage

scientific article published on 18 November 2020

Structure and regulation of the mouse ing1 gene. Three alternative transcripts encode two phd finger proteins that have opposite effects on p53 function

scientific article

Structure of the L (polymerase) protein gene of sonchus yellow net virus ⬇️

scientific article published on July 1, 1992

Structure-based insights into evolution of rhodopsins

scientific article published on 30 June 2021

Substantial DNA methylation differences between two major neuronal subtypes in human brain

scientific article published on 26 November 2015

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

Superfamily of UvrA-related NTP-binding proteins. Implications for rational classification of recombination/repair systems

scientific article

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

scientific article

Swift publication would reward good reviewers

scientific article published in March 2003

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

Systemic determinants of gene evolution and function

scientific article published on 13 September 2005

Systems biology of bacteriophage proteins and new dimensions of the virus world discovered through metagenomics.

scientific article published on 19 September 2011

THUMP--a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases

scientific article

TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus ⬇️

scientific article published on December 12, 2011

TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes

scientific article

TSG101 may be the prototype of a class of dominant negative ubiquitin regulators ⬇️

scientific article (publication date: August 1997)

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

scientific article

Tale of two serines

scientific article published in April 1989

Taming of the shrewd: novel eukaryotic genes from RNA viruses

scientific article published in 2010

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

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

scientific article published on 30 November 2021

Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases

scientific article (publication date: 18 December 2006)

Temporal regulation of gene expression of the Thermus thermophilus bacteriophage P23-45.

scientific article

Tentative identification of RNA-dependent RNA polymerases of dsRNA viruses and their relationship to positive strand RNA viral polymerases

scientific article

The 35-kDa protein from the N-terminus of the potyviral polyprotein functions as a third virus-encoded proteinase

scientific article published in December 1991

The 64-kilodalton capsid protein homolog of Beet yellows virus is required for assembly of virion tails

scientific article

The ATP-cone: an evolutionarily mobile, ATP-binding regulatory domain.

scientific article published in April 2000

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

scientific article

The Biological Big Bang model for the major transitions in evolution

scientific article published in 2007

The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes ⬇️

scientific article published on February 13, 2012

The COG database: a tool for genome-scale analysis of protein functions and evolution

scientific article

The COG database: an updated version includes eukaryotes

scientific article

The COG database: new developments in phylogenetic classification of proteins from complete genomes

scientific article

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

scientific article published on 19 September 2017

The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases

scientific article

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing

scientific article

The Escherichia coli hflA locus encodes a putative GTP-binding protein and two membrane proteins, one of which contains a protease-like domain

scientific article published on November 1993

The HD domain defines a new superfamily of metal-dependent phosphohydrolases

scientific article

The HORMA domain: a common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair ⬇️

scientific article published on August 1, 1998

The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria

scientific article published on 8 August 2006

The LUCA and its complex virome

scientific article published on 14 July 2020

The Miniature CRISPR-Cas12m Effector Binds DNA To Block Transcription

scientific article published in 2021

The NACHT family - a new group of predicted NTPases implicated in apoptosis and MHC transcription activation

scientific article (publication date: May 2000)

The Origin at 150: is a new evolutionary synthesis in sight?

scientific article

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

scholarly article

The STAS domain - a link between anion transporters and antisigma-factor antagonists

scientific article published on 01 January 2000

The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life

scientific article published on 18 April 2015

The U box is a modified RING finger — a common domain in ubiquitination

scientific article published on 01 February 2000

The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode

scientific article

The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates

scientific article

The ancient Virus World and evolution of cells

scientific article published in 2006

The bacterial replicative helicase DnaB evolved from a RecA duplication

scientific article (publication date: 2000)

The basic building blocks and evolution of CRISPR-CAS systems

scientific article published on December 2013

The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold

scientific article

The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin

scientific article

The closterovirus-derived gene expression and RNA interference vectors as tools for research and plant biotechnology ⬇️

scientific article published on April 11, 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 complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase ⬇️

scientific article published on February 1, 1991

The complex domain architecture of SAMD9 family proteins, predicted STAND-like NTPases, suggests new links to inflammation and apoptosis

scientific article

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life

scientific article

The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome

scientific article published on 28 February 2020

The cyanobacterial genome core and the origin of photosynthesis

scholarly article

The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction

scientific article published on July 1995

The deep archaeal roots of eukaryotes

scientific article

The depths of virus exaptation

The depths of virus exaptation

The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes

scientific article

The domains of death: evolution of the apoptosis machinery

scientific article

The double-edged sword of Lamarck: comment on "Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems" by Edwin L. Cooper and Nicola Overstreet

scientific article

The ecoresponsive genome of Daphnia pulex

scientific article

The emerging paradigm and open problems in comparative genomics

scientific article

The enigmatic archaeal virosphere

scientific article published in November 2017

The evolution of eukaryotes

scientific article

The evolutionary journey of Argonaute proteins

scientific article

The fukutin protein family--predicted enzymes modifying cell-surface molecules

scientific article published on 01 November 1999

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

scientific article

The gene for the longest known Escherichia coli protein is a member of helicase superfamily II.

scientific article published on October 1995

The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases

scientific article

The genome of molluscum contagiosum virus: analysis and comparison with other poxviruses

scientific article published on June 1997

The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A ⬇️

scientific article published on December 24, 2010

The impact of comparative genomics on our understanding of evolution

scientific article

The meaning of biological information

scientific article published in March 2016

The miniature CRISPR-Cas12m effector binds DNA to block transcription

scientific article published in 2022

The origin and early evolution of eukaryotes in the light of phylogenomics

scientific article

The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?

scientific article

The origins of cellular life

article published in 2014

The origins of phagocytosis and eukaryogenesis

scientific article

The phylogenetic forest and the quest for the elusive tree of life

scientific article

The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses

scientific article (publication date: September 1991)

The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system

scientific article

The proposed plant connexin is a protein kinase-like protein

scientific article

The relationship of protein conservation and sequence length

scientific article

The replication machinery of LUCA: common origin of DNA replication and transcription

scientific article published on 09 June 2020

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

scientific article

The role of energy in the emergence of biology from chemistry

scientific article published on October 2012

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

scientific article

The second cholera toxin, Zot, and its plasmid-encoded and phage-encoded homologues constitute a group of putative ATPases with an altered purine NTP-binding motif

scientific article published on November 2, 1992

The structure and evolution of Penelope in the virilis species group of Drosophila: an ancient lineage of retroelements

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The structure of the protein universe and genome evolution

scientific article

The superfamily of UvrA-related ATPases includes three more subunits of putative ATP-dependent nucleases

scientific article published on January 1, 1992

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

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The virophage as a unique parasite of the giant mimivirus

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The wonder world of microbial viruses ⬇️

scientific article published on October 1, 2010

Theory of prokaryotic genome evolution

scientific article

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

scientific article published on 29 March 2021

Three distinct modes of intron dynamics in the evolution of eukaryotes

scientific article

Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

scientific article published in 2022

Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins ⬇️

scientific article published on September 15, 1998

Towards a postmodern synthesis of evolutionary biology

scientific article

Towards functional characterization of archaeal genomic dark matter

scientific article published on 01 February 2019

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)

scientific article

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

scientific article

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

scholarly article

Translational coupling via termination-reinitiation in archaea and bacteria

scientific article published on 05 September 2019

Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes

scientific article

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

scientific article

Trends in protein evolution inferred from sequence and structure analysis.

scientific article

Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins

scientific article

Two domains of superfamily I helicases may exist as separate proteins

scientific article

Two early genes of bacteriophage T5 encode proteins containing an NTP-binding sequence motif and probably involved in DNA replication, recombination and repair

scientific article published in July 1989

Two fundamentally different classes of microbial genes

scientific article

Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea

scientific article

Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes

scientific article

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

scientific article

Ultrastructural localization and epitope mapping of the methyltransferase-like and helicase-like proteins of Beet yellows virus

scientific article published in August 2001

Uncertainty-aware and interpretable evaluation of Cas9–gRNA and Cas12a–gRNA specificity for fully matched and partially mismatched targets with Deep Kernel Learning

scientific article published on 12 November 2021

Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering

scientific article published on 23 November 2023

Unexpected connections between type VI-B CRISPR-Cas systems, bacterial natural competence, ubiquitin signaling network and DNA modification through a distinct family of membrane proteins

scientific article published on 01 April 2019

Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity

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

Unique structure and function of viral rhodopsins

scientific article published on 30 October 2019

Universal distribution of mutational effects on protein stability, uncoupling of protein robustness from sequence evolution and distinct evolutionary modes of prokaryotic and eukaryotic proteins

scientific article published on 30 April 2015

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

Unusual insertion element polymorphisms in the promoter and terminator regions of the mucAB-like genes of R471a and R446b ⬇️

scientific article published on February 2, 1998

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

Using the COG database to improve gene recognition in complete genomes

scientific article

Vaccinia virus F16 protein, a predicted catalytically inactive member of the prokaryotic serine recombinase superfamily, is targeted to nucleoli

scientific article

Vaccinia virus encodes four putative DNA and/or RNA helicases distantly related to each other

scientific article published on April 1, 1992

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

Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis

scientific article published on 10 April 2018

Viral AlkB proteins repair RNA damage by oxidative demethylation

scientific article published on 21 August 2008

Viral diversity threshold for adaptive immunity in prokaryotes

scientific article

Viral proteins containing the purine NTP-binding sequence pattern

scientific article

Viral rhodopsins 1 are an unique family of light-gated cation channels

scientific article published on 11 November 2020

Viriforms-A New Category of Classifiable Virus-Derived Genetic Elements

scientific article published in 2023

ViroidDB: a database of viroids and viroid-like circular RNAs

scientific article published on 01 January 2022

Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators?

Virology: A parasite's parasite saves host's neighbours

scientific article

Virology: Gulliver among the Lilliputians

scientific article published in March 2005

Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies

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 world as an evolutionary network of viruses and capsidless selfish elements

scientific article

Virus-borne mini-CRISPR arrays are involved in interviral conflicts

scientific article published on 15 November 2019

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

scientific article published on January 2014

Viruses Defined by the Position of the Virosphere within the Replicator Space

scientific article published on 01 September 2021

Viruses and mobile elements as drivers of evolutionary transitions

scientific article

Viruses know more than one way to don a cap

scientific article

Viruses of archaea: Structural, functional, environmental and evolutionary genomics.

scientific article published on 22 November 2017

Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes

scientific article

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

scientific article

Who's your neighbor? New computational approaches for functional genomics

scientific article

Why the Central Dogma: on the nature of the great biological exclusion principle

scientific article published on 16 September 2015

Widespread positive selection in synonymous sites of mammalian genes

scientific article

Winnowing sequences from a database search

scientific article published in February 2000

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

scientific article

Yeast POL5 is an evolutionarily conserved regulator of rDNA transcription unrelated to any known DNA polymerases

scientific article

Yeast chromosome III: new gene functions.

scientific article published on February 1994

Yeast protein controlling inter-organelle communication is related to bacterial phosphatases containing the Hsp 70-type ATP-binding domain

scientific article published on April 1994

YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics

scientific article

dlg-R proteins: modified guanylate kinases

scientific article published in December 1992

p53 gain-of-function: tumor biology and bioinformatics come together

scientific article published on 28 May 2005

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