Eugene Koonin
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Biology
Eugene Koonin's Degrees
- PhD Molecular Biology Moscow State University
Why Is Eugene Koonin Influential?
(Suggest an Edit or Addition)According to Wikipedia, Eugene Viktorovich Koonin is a Russian-American biologist and Senior Investigator at the National Center for Biotechnology Information . He is a recognised expert in the field of evolutionary and computational biology.
Eugene Koonin's Published Works
Published Works
- Initial sequencing and analysis of the human genome. (2001) (15222)
- The COG database: an updated version includes eukaryotes (2003) (4142)
- The COG database: a tool for genome-scale analysis of protein functions and evolution (2000) (3563)
- A genomic perspective on protein families. (1997) (3519)
- Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System (2015) (2978)
- Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes (2008) (2144)
- In vivo genome editing using Staphylococcus aureus Cas9 (2015) (2132)
- Evolution and classification of the CRISPR–Cas systems (2011) (2084)
- The COG database: new developments in phylogenetic classification of proteins from complete genomes (2001) (1869)
- An updated evolutionary classification of CRISPR–Cas systems (2015) (1822)
- AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. (1999) (1807)
- De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signalling (2004) (1736)
- Nucleic acid detection with CRISPR-Cas13a/C2c2 (2017) (1699)
- Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. (1998) (1603)
- Molecular Cloning and Disease Association of Hepatitis G Virus: A Transfusion-Transmissible Agent (1996) (1396)
- Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. (2000) (1382)
- C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector (2016) (1335)
- Comparative genomics of the lactic acid bacteria (2006) (1274)
- The Ecoresponsive Genome of Daphnia pulex (2011) (1152)
- Horizontal gene transfer in prokaryotes: quantification and classification. (2001) (1152)
- Helicases: amino acid sequence comparisons and structure-function relationships (1993) (1140)
- Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. (1993) (1112)
- Classification and evolution of P-loop GTPases and related ATPases. (2002) (1087)
- Identification of paracaspases and metacaspases: two ancient families of caspase-like proteins, one of which plays a key role in MALT lymphoma. (2000) (1077)
- 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 (2006) (1065)
- Expanded microbial genome coverage and improved protein family annotation in the COG database (2014) (1062)
- Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26S Proteasome (2002) (1037)
- Microbial culturomics: paradigm shift in the human gut microbiome study. (2012) (909)
- Orthologs, Paralogs, and Evolutionary Genomics 1 (2005) (900)
- Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants (2019) (899)
- Diversity, classification and evolution of CRISPR-Cas systems. (2017) (891)
- The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. (1991) (882)
- Cleavage of Cohesin by the CD Clan Protease Separin Triggers Anaphase in Yeast (2000) (865)
- Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. (2015) (853)
- Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum (2001) (814)
- A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes (2004) (810)
- A superfamily of conserved domains in DNA damage‐ responsive cell cycle checkpoint proteins (1997) (789)
- Orthologs, paralogs, and evolutionary genomics. (2005) (773)
- A minimal gene set for cellular life derived by comparison of complete bacterial genomes. (1996) (772)
- Evolutionary history and higher order classification of AAA+ ATPases. (2004) (770)
- Role of Predicted Metalloprotease Motif of Jab1/Csn5 in Cleavage of Nedd8 from Cul1 (2002) (711)
- Selection in the evolution of gene duplications (2002) (710)
- Regeneration of Peroxiredoxins by p53-Regulated Sestrins, Homologs of Bacterial AhpD (2004) (709)
- Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics (2001) (680)
- Diversity and evolution of class 2 CRISPR–Cas systems (2017) (674)
- Novel domains of the prokaryotic two-component signal transduction systems. (2001) (673)
- Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world (2008) (645)
- The ancient Virus World and evolution of cells (2006) (638)
- Comparative genomics, minimal gene-sets and the last universal common ancestor (2003) (591)
- The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode (2005) (588)
- Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria (1992) (566)
- The structure of the protein universe and genome evolution (2002) (566)
- Origin of a substantial fraction of human regulatory sequences from transposable elements. (2003) (561)
- Conserved domains in DNA repair proteins and evolution of repair systems. (1999) (554)
- Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. (2002) (543)
- Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. (2006) (539)
- Hedgehog Patterning Activity: Role of a Lipophilic Modification Mediated by the Carboxy-Terminal Autoprocessing Domain (1996) (535)
- SAP - a putative DNA-binding motif involved in chromosomal organization. (2000) (516)
- Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses (2001) (508)
- Comparative genomics and evolution of proteins involved in RNA metabolism. (2002) (499)
- The virophage as a unique parasite of the giant mimivirus (2008) (498)
- Selection for short introns in highly expressed genes (2002) (496)
- One-component systems dominate signal transduction in prokaryotes. (2005) (493)
- Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems (2016) (486)
- Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. (1998) (482)
- Consensus statement: Virus taxonomy in the age of metagenomics (2017) (481)
- 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. (1992) (478)
- Complete sequence of the citrus tristeza virus RNA genome. (1995) (470)
- Introns and the origin of nucleus–cytosol compartmentalization (2006) (468)
- The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases (2001) (467)
- Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome (2003) (465)
- Origins and evolution of eukaryotic RNA interference. (2008) (460)
- The HD domain defines a new superfamily of metal-dependent phosphohydrolases. (1998) (457)
- Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. (1999) (446)
- Comparison of the complete protein sets of worm and yeast: orthology and divergence. (1998) (442)
- The role of lineage-specific gene family expansion in the evolution of eukaryotes. (2002) (439)
- Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA (2016) (438)
- Functional and evolutionary implications of gene orthology (2013) (435)
- Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems (2011) (423)
- 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. (2004) (420)
- Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. (1999) (413)
- 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. (1993) (412)
- Remarkable Interkingdom Conservation of Intron Positions and Massive, Lineage-Specific Intron Loss and Gain in Eukaryotic Evolution (2003) (412)
- The domains of death: evolution of the apoptosis machinery. (1999) (408)
- Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes (2009) (404)
- The U box is a modified RING finger — a common domain in ubiquitination (2000) (402)
- Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. (2003) (401)
- Orthology, paralogy and proposed classification for paralog subtypes. (2002) (397)
- Origins and evolution of viruses of eukaryotes: The ultimate modularity (2015) (394)
- Origin and evolution of eukaryotic apoptosis: the bacterial connection (2002) (392)
- 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 (2003) (387)
- Classification and evolution of type II CRISPR-Cas systems (2014) (383)
- The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase☆ (1991) (373)
- Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. (2000) (373)
- 'Conserved hypothetical' proteins: prioritization of targets for experimental study. (2004) (370)
- Genome trees and the tree of life. (2002) (369)
- Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation (2003) (369)
- Cas13b is a Type VI-B CRISPR-associated RNA-Guided RNase differentially regulated by accessory proteins Csx27 and Csx28 (2016) (368)
- A new superfamily of putative NTP‐binding domains encoded by genomes of small DNA and RNA viruses (1990) (358)
- A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. (2002) (356)
- Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. (1998) (356)
- Cysteine proteases of positive strand RNA viruses and chymotrypsin‐like serine proteases (1989) (342)
- Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons. (2001) (340)
- Comparative genomics of defense systems in archaea and bacteria (2013) (339)
- Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms (2009) (337)
- A superfamily of ATPases with diverse functions containing either classical or deviant ATP-binding motif. (1993) (336)
- On the origin of genomes and cells within inorganic compartments (2005) (336)
- Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. (2001) (335)
- Genome Sequence of a Human Tumorigenic Poxvirus: Prediction of Specific Host Response-Evasion Genes (1996) (334)
- Did DNA replication evolve twice independently? (1999) (333)
- 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‐, α‐ and coronaviruses (1991) (333)
- Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. (1999) (332)
- Origin of first cells at terrestrial, anoxic geothermal fields (2012) (330)
- Predicting functions from protein sequences—where are the bottlenecks? (1998) (329)
- Eukaryotic DNA Polymerases: Proposal for a Revised Nomenclature* (2001) (329)
- The evolutionary journey of Argonaute proteins (2014) (327)
- Novel families of putative protein kinases in bacteria and archaea: evolution of the "eukaryotic" protein kinase superfamily. (1998) (326)
- RNA-guided DNA insertion with CRISPR-associated transposases (2019) (326)
- Who's your neighbor? New computational approaches for functional genomics (2000) (325)
- The Logic of Chance: The Nature and Origin of Biological Evolution (2011) (324)
- Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. (1998) (323)
- DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. (1999) (322)
- Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems (2013) (321)
- Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea (1997) (316)
- Pineal Serotonin N-Acetyltransferase: Expression Cloning and Molecular Analysis (1995) (316)
- IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices (1999) (313)
- How many genes can make a cell: the minimal-gene-set concept. (2000) (313)
- Origin and evolution of the genetic code: The universal enigma (2008) (312)
- The origin and early evolution of eukaryotes in the light of phylogenomics (2010) (312)
- Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. (2004) (309)
- The NACHT family - a new group of predicted NTPases implicated in apoptosis and MHC transcription activation. (2000) (308)
- Genome trees constructed using five different approaches suggest new major bacterial clades (2001) (308)
- Lineage-specific loss and divergence of functionally linked genes in eukaryotes. (2000) (306)
- Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli (1996) (304)
- The cyanobacterial genome core and the origin of photosynthesis (2006) (304)
- 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. (2001) (295)
- SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. (2000) (294)
- Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search. (1994) (293)
- Origins and Evolution of the Global RNA Virome (2018) (291)
- The Impact of Comparative Genomics on Our Understanding of Evolution (2000) (290)
- The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens (2002) (289)
- Global Organization and Proposed Megataxonomy of the Virus World (2020) (289)
- Non-orthologous gene displacement. (1996) (288)
- Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution (2009) (288)
- A novel superfamily of nucleoside triphosphate‐binding motif containing proteins which are probably involved in duplex unwinding in DNA and RNA replication and recombination (1988) (287)
- Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. (1999) (286)
- Minimum Information about an Uncultivated Virus Genome (MIUViG) (2018) (286)
- Origin and evolution of spliceosomal introns (2012) (286)
- Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL domain-containing accessory protein (2018) (286)
- Evolution and classification of P-loop kinases and related proteins. (2003) (285)
- A korarchaeal genome reveals insights into the evolution of the Archaea (2008) (282)
- Systems biology of bacteriophage proteins and new dimensions of the virus world discovered through metagenomics (2011) (282)
- RNA sequence of astrovirus: distinctive genomic organization and a putative retrovirus-like ribosomal frameshifting signal that directs the viral replicase synthesis. (1993) (276)
- Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. (2001) (268)
- The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold. (1998) (268)
- Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems (2011) (266)
- The STAS domain — a link between anion transporters and antisigma-factor antagonists (2000) (265)
- DNA-binding proteins and evolution of transcription regulation in the archaea. (1999) (265)
- Abundance of type I toxin–antitoxin systems in bacteria: searches for new candidates and discovery of novel families (2010) (264)
- Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation (2016) (264)
- A universal trend of amino acid gain and loss in protein evolution (2005) (263)
- Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. (2001) (263)
- Search for a 'Tree of Life' in the thicket of the phylogenetic forest (2009) (263)
- Crystal Structure of a Hedgehog Autoprocessing Domain: Homology between Hedgehog and Self-Splicing Proteins (1997) (263)
- Is evolution Darwinian or/and Lamarckian? (2009) (263)
- Evolutionary Genomics of Lactic Acid Bacteria (2006) (261)
- A diverse superfamily of enzymes with ATP‐dependent carboxylate—amine/thiol ligase activity (1997) (260)
- Genome-wide Analysis of Substrate Specificities of the Escherichia coli Haloacid Dehalogenase-like Phosphatase Family* (2006) (260)
- The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? (2006) (260)
- A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae. (2000) (259)
- Genome reduction as the dominant mode of evolution (2013) (258)
- A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair (2011) (253)
- No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly (2003) (250)
- The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups (2008) (249)
- Phosphoesterase domains associated with DNA polymerases of diverse origins. (1998) (247)
- Darwinian evolution in the light of genomics (2008) (246)
- Annotation and Classification of CRISPR-Cas Systems. (2015) (244)
- Comparative Genomics, Evolution and Origins of the Nuclear Envelope and Nuclear Pore Complex (2004) (244)
- Functionally diverse type V CRISPR-Cas systems (2019) (243)
- Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members (2005) (243)
- Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases (2003) (242)
- The genome of molluscum contagiosum virus: analysis and comparison with other poxviruses. (1997) (241)
- COG database update: focus on microbial diversity, model organisms, and widespread pathogens (2020) (241)
- Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. (1997) (235)
- Computer-assisted identification of a putative methyltransferase domain in NS5 protein of flaviviruses and lambda 2 protein of reovirus. (1993) (231)
- The 35-kDa protein from the N-terminus of the potyviral polyprotein functions as a third virus-encoded proteinase. (1991) (231)
- The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers (2003) (229)
- “Megavirales”, a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses (2013) (226)
- Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks (2007) (226)
- Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. (1996) (225)
- The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages (2009) (221)
- Evolution of diverse cell division and vesicle formation systems in Archaea (2010) (221)
- Myosin XI-K Is Required for Rapid Trafficking of Golgi Stacks, Peroxisomes, and Mitochondria in Leaf Cells of Nicotiana benthamiana1[W][OA] (2008) (218)
- Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation. (1991) (218)
- Sequence ― Evolution ― Function: Computational Approaches in Comparative Genomics (2010) (218)
- Adaptations of the helix‐grip fold for ligand binding and catalysis in the START domain superfamily (2001) (216)
- Computational methods for Gene Orthology inference (2011) (215)
- Analysis of evolution of exon-intron structure of eukaryotic genes (2005) (214)
- Estimating the number of protein folds and families from complete genome data. (2000) (212)
- Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia (2008) (211)
- Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. (2006) (209)
- Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. (2003) (209)
- Evolution of cell-cell signaling in animals: did late horizontal gene transfer from bacteria have a role? (2004) (209)
- Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. (2000) (208)
- CRISPR EVOLUTION C 2 c 2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector (2016) (207)
- Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements (2009) (207)
- A conserved NTP-motif in putative helicases (1988) (206)
- Evolutionary Genomics of Defense Systems in Archaea and Bacteria. (2017) (205)
- The HORMA domain: a common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair. (1998) (203)
- A Novel Family of Sequence-specific Endoribonucleases Associated with the Clustered Regularly Interspaced Short Palindromic Repeats* (2008) (203)
- Connected gene neighborhoods in prokaryotic genomes. (2002) (201)
- Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing (2013) (201)
- A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. (2004) (201)
- Engineering of CRISPR-Cas12b for human genome editing (2019) (201)
- Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut (2017) (200)
- The origins of phagocytosis and eukaryogenesis (2009) (200)
- Role of CED-4 in the activation of CED-3 (1997) (199)
- Conservation and coevolution in the scale-free human gene coexpression network. (2004) (198)
- A virocentric perspective on the evolution of life (2013) (197)
- Analogous enzymes: independent inventions in enzyme evolution. (1998) (197)
- The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin. (1995) (196)
- Provirophages and transpovirons as the diverse mobilome of giant viruses (2012) (195)
- Gene order is not conserved in bacterial evolution. (1996) (195)
- Kinase Activity of Overexpressed HipA Is Required for Growth Arrest and Multidrug Tolerance in Escherichia coli (2006) (194)
- Photosystem I gene cassettes are present in marine virus genomes (2009) (194)
- A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches (2010) (192)
- The bacterial replicative helicase DnaB evolved from a RecA duplication. (2000) (191)
- Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily. (1999) (190)
- Inventing the dynamo machine: the evolution of the F-type and V-type ATPases (2007) (189)
- Fold prediction and evolutionary analysis of the POZ domain: structural and evolutionary relationship with the potassium channel tetramerization domain. (1999) (189)
- Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus (2006) (189)
- Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement, and operon disruption (1998) (189)
- Evolution of protein domain promiscuity in eukaryotes. (2008) (188)
- Origin and Evolution of Eukaryotic Large Nucleo-Cytoplasmic DNA Viruses (2010) (187)
- Birth and death of protein domains: A simple model of evolution explains power law behavior (2002) (187)
- Molecular Biology and Evolution of Closteroviruses: Sophisticated Build-up of Large RNA Genomes (1994) (186)
- Classification and evolutionary history of the single-strand annealing proteins, RecT, Redβ, ERF and RAD52 (2002) (185)
- Duplicated genes evolve slower than singletons despite the initial rate increase (2004) (185)
- Giant viruses with an expanded complement of translation system components (2017) (184)
- Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea (2007) (184)
- On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization (2007) (184)
- Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements (2014) (184)
- Distribution of protein folds in the three superkingdoms of life. (1999) (183)
- Novel Predicted RNA-Binding Domains Associated with the Translation Machinery (1999) (182)
- Evidence for common ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand RNA plant viruses. (1991) (181)
- Origins and evolution of CRISPR-Cas systems (2019) (180)
- Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces (2002) (180)
- Multiple origins of viral capsid proteins from cellular ancestors (2017) (179)
- Lineage-specific gene expansions in bacterial and archaeal genomes. (2001) (178)
- Complete pathway for protein disulfide bond formation encoded by poxviruses (2002) (175)
- Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance (2005) (175)
- Diverse enzymatic activities mediate antiviral immunity in prokaryotes (2020) (174)
- The Deep Archaeal Roots of Eukaryotes (2008) (174)
- A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases (1999) (174)
- Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales (2015) (173)
- Computer-assisted dissection of rolling circle DNA replication. (1993) (172)
- Three distinct modes of intron dynamics in the evolution of eukaryotes. (2007) (171)
- Evolution of genome architecture. (2009) (171)
- From complete genome sequence to 'complete' understanding? (2010) (169)
- Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell (2005) (169)
- Diverse groups of plant RNA and DNA viruses share related movement proteins that may possess chaperone-like activity. (1991) (166)
- Searching for drug targets in microbial genomes. (1999) (166)
- Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes (2014) (166)
- Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA replication initiator proteins. (1992) (165)
- G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins. (1999) (165)
- Classification of the caspase–hemoglobinase fold: Detection of new families and implications for the origin of the eukaryotic separins (2002) (165)
- Beet yellows closterovirus: complete genome structure and identification of a leader papain-like thiol protease. (1994) (164)
- The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes (2017) (163)
- 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 (2001) (160)
- Phylogenomics of prokaryotic ribosomal proteins (2011) (160)
- SEALS: A System for Easy Analysis of Lots of Sequences (1997) (160)
- Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity (2014) (159)
- Constraints and plasticity in genome and molecular-phenome evolution (2010) (158)
- The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A (2011) (156)
- A superfamily of metalloenzymes unifies phosphopentomutase and cofactor‐independent phosphoglycerate mutase with alkaline phosphatases and sulfatases (1998) (156)
- A novel family of predicted phosphoesterases includes Drosophila prune protein and bacterial RecJ exonuclease. (1998) (155)
- Taxonomy of the order Mononegavirales: update 2018 (2018) (155)
- Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis (2017) (155)
- Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon (2001) (155)
- Recruitment of CRISPR-Cas systems by Tn7-like transposons (2017) (155)
- Biological applications of the theory of birth-and-death processes (2005) (154)
- Eukaryotic translation elongation factor 1γ contains a glutathione transferase domain—Study of a diverse, ancient protein super family using motif search and structural modeling (1994) (153)
- The relationship of protein conservation and sequence length (2002) (153)
- Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution (2014) (153)
- Protein sequence motifs. (1996) (152)
- A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases. (1997) (152)
- Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ (2003) (152)
- Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs) (2000) (151)
- Evolution of adaptive immunity from transposable elements combined with innate immune systems (2014) (151)
- Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. (1999) (151)
- A viral member of the ERV1/ALR protein family participates in a cytoplasmic pathway of disulfide bond formation. (2000) (150)
- A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes (2011) (150)
- Beyond complete genomes: from sequence to structure and function. (1998) (150)
- Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer (2012) (150)
- Detection of new genes in a bacterial genome using Markov models for three gene classes. (1995) (150)
- Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction (1996) (150)
- Evolutionary primacy of sodium bioenergetics (2008) (148)
- GINS, a central nexus in the archaeal DNA replication fork (2006) (148)
- Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon. (2006) (148)
- Origin of alternative splicing by tandem exon duplication. (2001) (148)
- Divergence and Convergence in Enzyme Evolution* (2011) (147)
- Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. (1997) (147)
- Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation (2006) (147)
- Complete Genomic Sequence and Phylogenetic Analysis of the Lactate Dehydrogenase-Elevating Virus (LDV) (1993) (147)
- Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins. (2003) (147)
- SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. (2002) (146)
- CRISPR–Cas in mobile genetic elements: counter-defence and beyond (2019) (146)
- The Tree and Net Components of Prokaryote Evolution (2010) (146)
- A distinct abundant group of microbial rhodopsins discovered using functional metagenomics (2018) (146)
- Evolutionary significance of gene expression divergence. (2005) (146)
- Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange. (1999) (145)
- Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018 (2018) (145)
- The basic building blocks and evolution of CRISPR-CAS systems. (2013) (144)
- Genome structure and phylogenetic analysis of lettuce infectious yellows virus, a whitefly-transmitted, bipartite closterovirus. (1995) (144)
- CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems (2014) (144)
- APOBEC4, a New Member of the AID/APOBEC Family of Polynucleotide (Deoxy)Cytidine Deaminases Predicted by Computational Analysis (2005) (144)
- Co-evolution of primordial membranes and membrane proteins. (2009) (142)
- Trends in protein evolution inferred from sequence and structure analysis. (2002) (142)
- The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing (2016) (142)
- Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer (2017) (141)
- A duplicated catalytic motif in a new superfamily of phosphohydrolases and phospholipid synthases that includes poxvirus envelope proteins. (1996) (139)
- Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP‐ATPase nucleotide‐binding domains: implications for protein evolution in the RNA world (2002) (139)
- Nucleic acid detection with CRISPR-Cas 13 a / C 2 c 2 Citation (2017) (138)
- Genome sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy (2004) (138)
- Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes (2012) (138)
- Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites (2013) (137)
- The fukutin protein family – predicted enzymes modifying cell-surface molecules (1999) (137)
- Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life. (2014) (135)
- Viruses of archaea: Structural, functional, environmental and evolutionary genomics. (2018) (135)
- Prokaryotic genomes: the emerging paradigm of genome-based microbiology. (1997) (135)
- SnapShot: Class 2 CRISPR-Cas Systems (2017) (134)
- Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution (2010) (132)
- Prevalence of intron gain over intron loss in the evolution of paralogous gene families. (2004) (132)
- CRISPR-Cas (2013) (131)
- Genome sequence comparison and scenarios for gene rearrangements: a test case. (1995) (131)
- The enigmatic archaeal virosphere (2017) (130)
- The Biological Big Bang model for the major transitions in evolution (2007) (130)
- A specialized version of the HD hydrolase domain implicated in signal transduction. (1999) (130)
- Evolution of microbes and viruses: a paradigm shift in evolutionary biology? (2012) (129)
- Saccharomyces cerevisiae SMT4 encodes an evolutionarily conserved protease with a role in chromosome condensation regulation. (2001) (129)
- Comparative genome analysis. (2001) (127)
- A family of lysozyme-like virulence factors in bacterial pathogens of plants and animals. (1996) (126)
- Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes (2012) (125)
- An expanding family of helicases within the 'DEAD/H' superfamily. (1993) (124)
- 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales (2020) (122)
- The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates (2000) (122)
- Congruent evolution of different classes of non-coding DNA in prokaryotic genomes. (2002) (120)
- Origin of viruses: primordial replicators recruiting capsids from hosts (2019) (120)
- Microbial genome analysis: the COG approach (2019) (120)
- On the Origin of Cells and Viruses (2009) (120)
- Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes (2008) (120)
- A P‐loop‐like motif in a widespread ATP pyrophosphatase domain: Implications for the evolution of sequence motifs and enzyme activity (1994) (119)
- Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses (2020) (119)
- Organization and evolution of bacterial and bacteriophage primase-helicase systems (1992) (118)
- Purifying and directional selection in overlapping prokaryotic genes. (2002) (116)
- Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions (2016) (115)
- 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 (2012) (115)
- A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans (2008) (115)
- Horizontal Gene Transfer Can Rescue Prokaryotes from Muller’s Ratchet: Benefit of DNA from Dead Cells and Population Subdivision (2013) (114)
- A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme? (1994) (114)
- Origin and Evolution of the Universal Genetic Code. (2017) (114)
- Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? (2015) (113)
- Evolution of gene fusions: horizontal transfer versus independent events (2002) (113)
- Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity (2018) (113)
- Sequence — Evolution — Function (2003) (113)
- Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire (2019) (113)
- Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ε and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors (2009) (112)
- Identification of the catalytic sites of a papain-like cysteine proteinase of murine coronavirus (1993) (112)
- Intrinsic and extrinsic approaches for detecting genes in a bacterial genome. (1994) (111)
- Viruses and mobile elements as drivers of evolutionary transitions (2016) (111)
- Endonuclease (R) subunits of type‐I and type‐III restriction‐modification enzymes contain a helicase‐like domain (1991) (111)
- A new family of carbon‐nitrogen hydrolases (1994) (111)
- Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications. (1995) (111)
- TSG101 may be the prototype of a class of dominant negative ubiquitin regulators (1997) (111)
- The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria (2006) (110)
- Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism. (2019) (110)
- Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis (2018) (110)
- Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery (2021) (110)
- Theory of prokaryotic genome evolution (2016) (110)
- Conserved sequence pattern in a wide variety of phosphoesterases (1994) (110)
- Scale-free networks in biology: new insights into the fundamentals of evolution? (2002) (109)
- Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. (2004) (109)
- Viral AlkB proteins repair RNA damage by oxidative demethylation (2008) (107)
- A community experiment with fully open and published peer review (2006) (106)
- Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences. (2003) (106)
- Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) (2001) (106)
- Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back (2017) (106)
- Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape (2007) (106)
- A highly conserved sequence motif defining the family of MutT-related proteins from eubacteria, eukaryotes and viruses. (1993) (105)
- Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question. (2016) (105)
- Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs (2012) (105)
- Evolutionary conservation suggests a regulatory function of AUG triplets in 5′-UTRs of eukaryotic genes (2005) (105)
- A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea. (2004) (105)
- Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors (2002) (105)
- Identification of Paracaspases and Metacaspases (2000) (105)
- Eukaryote-specific domains in translation initiation factors: implications for translation regulation and evolution of the translation system. (2000) (104)
- Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome (2020) (103)
- Mathematical modeling of tumor therapy with oncolytic viruses: Regimes with complete tumor elimination within the framework of deterministic models (2006) (103)
- The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. (2014) (103)
- Viral Diversity Threshold for Adaptive Immunity in Prokaryotes (2012) (103)
- Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes (2010) (102)
- Power Laws, Scale-Free Networks and Genome Biology (2006) (102)
- Similarities in RNA helicases (1991) (102)
- SnapShot: Class 1 CRISPR-Cas Systems (2017) (102)
- A new group of putative RNA helicases. (1992) (102)
- Sequencing and analysis of bacterial genomes (1996) (102)
- Comparative genomics of archaea: how much have we learned in six years, and what's next? (2003) (102)
- Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin. (2009) (102)
- Are There Laws of Genome Evolution? (2011) (101)
- A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. (2003) (101)
- Evolutionary systems biology: links between gene evolution and function. (2006) (101)
- Functional Long Non-coding RNAs Evolve from Junk Transcripts (2020) (101)
- Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes (2012) (101)
- Classify viruses — the gain is worth the pain (2019) (100)
- A family of ubiquitin‐like proteins binds the ATPase domain of Hsp70‐like Stch (2000) (100)
- Conservation versus parallel gains in intron evolution (2005) (99)
- Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses (2020) (99)
- Intron sliding in conserved gene families. (2000) (99)
- Microevolutionary genomics of bacteria. (2002) (99)
- Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes (2009) (98)
- Yeast chromosome III: new gene functions. (1994) (98)
- A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes (2012) (98)
- Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park (2013) (97)
- Replaying the Tape of Life: Quantification of the Predictability of Evolution (2012) (97)
- Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies (2013) (97)
- Novel Predicted Peptidases with a Potential Role in the Ubiquitin Signaling Pathway (2004) (97)
- Widespread positive selection in synonymous sites of mammalian genes. (2007) (96)
- Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution (2004) (95)
- Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family (2013) (95)
- Protein fold recognition using sequence profiles and its application in structural genomics. (2000) (95)
- Scores of RINGS but No PHDs in Ubiquitin Signaling (2003) (95)
- No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales (2015) (94)
- Bacterial-type DNA holliday junction resolvases in eukaryotic viruses. (2000) (94)
- A new family of peptidyl-prolyl isomerases. (1995) (94)
- Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. (2004) (94)
- Expanded diversity of Asgard archaea and their relationships with eukaryotes (2021) (93)
- Comparative genomics and structural biology of the molecular innovations of eukaryotes. (2006) (93)
- Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon (2015) (92)
- Archaeal origin of tubulin (2012) (90)
- The cytidylyltransferase superfamily: Identification of the nucleotide‐binding site and fold prediction (1995) (90)
- Ongoing global and regional adaptive evolution of SARS-CoV-2 (2021) (90)
- CRISPR-Cas: an adaptive immunity system in prokaryotes (2009) (90)
- Identification of a DinB/UmuC homolog in the archeon Sulfolobus solfataricus. (1996) (90)
- Viruses with More Than 1,000 Genes: Mamavirus, a New Acanthamoeba polyphaga mimivirus Strain, and Reannotation of Mimivirus Genes (2011) (89)
- The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes (2012) (89)
- Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids (2019) (88)
- Identification of the Primase Active Site of the Herpes Simplex Virus Type 1 Helicase-Primase (*) (1995) (88)
- Proteorhodopsin genes in giant viruses (2012) (86)
- Role of mRNA structure in the control of protein folding (2016) (86)
- Planctomycetes and eukaryotes: A case of analogy not homology (2011) (86)
- Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses (2014) (86)
- Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context (2013) (85)
- Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2 (2020) (85)
- YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics. (2002) (85)
- Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs (2011) (85)
- Potential genomic determinants of hyperthermophily. (2003) (84)
- Nature and Intensity of Selection Pressure on CRISPR-Associated Genes (2011) (84)
- The SPANX gene family of cancer/testis-specific antigens: rapid evolution and amplification in African great apes and hominids. (2004) (83)
- Programmable RNA targeting with the single-protein CRISPR effector Cas7-11 (2021) (83)
- Substantial DNA methylation differences between two major neuronal subtypes in human brain (2015) (83)
- Using the COG Database to Improve Gene Recognition in Complete Genomes (2004) (83)
- THUMP--a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases. (2001) (83)
- Evolutionarily conserved genes preferentially accumulate introns. (2007) (82)
- Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1 (2008) (82)
- Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses (2015) (82)
- Dynein light chains of the Roadblock/LC7 group belong to an ancient protein superfamily implicated in NTPase regulation (2000) (82)
- Unifying measures of gene function and evolution (2006) (82)
- Expression, Splicing, and Evolution of the Myosin Gene Family in Plants1[W][OA] (2011) (81)
- Coupling immunity and programmed cell suicide in prokaryotes: Life‐or‐death choices (2016) (81)
- Phylogenomics of Prokaryotic Ribosomal Proteins (2012) (81)
- Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions. (2005) (81)
- Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns (2006) (80)
- Mathematical modeling of evolution of horizontally transferred genes. (2005) (80)
- Global similarity and local divergence in human and mouse gene co-expression networks (2006) (80)
- From complete genomes to measures of substitution rate variability within and between proteins. (2000) (80)
- Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements (2016) (79)
- Patterns of intron gain and conservation in eukaryotic genes (2007) (79)
- Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence (2017) (79)
- Genomic and biological analysis of Grapevine leafroll-associated virus 7 reveals a possible new genus within the family Closteroviridae. (2012) (79)
- X-ray structure of the complex of regulatory subunits of human DNA polymerase delta (2008) (79)
- Comparative Genome Analysis of the Pathogenic Spirochetes Borrelia burgdorferi and Treponema pallidum (2000) (79)
- Cancer-mutation network and the number and specificity of driver mutations (2018) (78)
- Diversity and Evolution of Type IV pili Systems in Archaea (2016) (77)
- A poxvirus protein with a RING zinc finger motif is of crucial importance for virulence. (1994) (77)
- The 64-Kilodalton Capsid Protein Homolog of Beet Yellows Virus Is Required for Assembly of Virion Tails (2003) (77)
- How stands the Tree of Life a century and a half after The Origin? (2011) (76)
- Intron-dominated genomes of early ancestors of eukaryotes. (2009) (76)
- Cressdnaviricota: a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes (2020) (76)
- Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin (2005) (76)
- Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion. (2004) (75)
- The Incredible Expanding Ancestor of Eukaryotes (2010) (75)
- Identification of Myosin XI Receptors in Arabidopsis Defines a Distinct Class of Transport Vesicles[W][OPEN] (2013) (75)
- The Escherichia coli hflA locus encodes a putative GTP-binding protein and two membrane proteins, one of which contains a protease-like domain. (1993) (74)
- An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication (1989) (74)
- SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes. (2002) (73)
- TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus. (2012) (73)
- The Origin at 150: is a new evolutionary synthesis in sight? (2009) (73)
- Cas 13 b Is a Type VIB CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx 27 and Csx 28 (2017) (72)
- Splendor and misery of adaptation, or the importance of neutral null for understanding evolution (2016) (72)
- Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery. (2017) (72)
- New genes in old sequence: a strategy for finding genes in the bacterial genome. (1994) (71)
- Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. (2007) (71)
- PAMP and PARL, two novel putative metalloproteases interacting with the COOH-terminus of Presenilin-1 and -2. (2001) (71)
- Predictability of Evolutionary Trajectories in Fitness Landscapes (2011) (70)
- Classification and quantification of bacteriophage taxa in human gut metagenomes (2014) (70)
- Virus taxonomy in the age of metagenomics (2017) (70)
- Putative 65 kDa protein of beet yellows closterovirus is a homologue of HSP70 heat shock proteins. (1991) (70)
- Poxvirus DNA primase (2007) (69)
- [18] Protein sequence comparison at genome scale (1996) (69)
- Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes (2004) (69)
- TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes. (2001) (68)
- A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons (2018) (68)
- The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases (2021) (68)
- Phylogeny of capsid proteins of small icosahedral RNA plant viruses. (1991) (68)
- Differential translation tunes uneven production of operon-encoded proteins. (2013) (67)
- Mathematical modeling of tumor therapy with oncolytic viruses: effects of parametric heterogeneity on cell dynamics (2006) (67)
- Evolution of alternative and constitutive regions of mammalian 5'UTRs (2009) (67)
- Sobemovirus genome appears to encode a serine protease related to cysteine proteases of picornaviruses (1988) (67)
- Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics. (1996) (67)
- Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses (2018) (67)
- An apology for orthologs - or brave new memes (2001) (67)
- Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses (2014) (67)
- Small cysteine-rich proteins of different groups of plant RNA viruses are related to different families of nucleic acid-binding proteins. (1991) (66)
- Self-regulated Cleavage of the Mitochondrial Intramembrane-cleaving Protease PARL Yields Pβ, a Nuclear-targeted Peptide*[boxs] (2004) (66)
- Physical foundations of biological complexity (2018) (66)
- Inevitability of Genetic Parasites (2016) (65)
- Nucleotide sequence of the 3'-terminal half of beet yellows closterovirus RNA genome: unique arrangement of eight virus genes. (1991) (65)
- Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain. (2005) (64)
- A natural classification of ribonucleases. (2001) (64)
- Classification and Nomenclature of CRISPR-Cas Systems: Where from Here? (2018) (64)
- Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae (2015) (64)
- Multidomain organization of eukaryotic guanine nucleotide exchange translation initiation factor eIF‐2B subunits revealed by analysis of conserved sequence motifs (1995) (64)
- Gene Frequency Distributions Reject a Neutral Model of Genome Evolution (2013) (63)
- A colipase fold in the carboxy-terminal domain of the Wnt antagonists – the Dickkopfs (1998) (63)
- Coat protein gene duplication in a filamentous RNA virus of plants. (1992) (63)
- Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota (2017) (63)
- Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism (2018) (62)
- Universal distribution of protein evolution rates as a consequence of protein folding physics (2010) (62)
- Molecular Characterization and Developmental Expression of a Retinoid- and Fatty Acid-binding Glycoprotein from Drosophila (1996) (62)
- Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery (2014) (62)
- Taming of the shrewd: novel eukaryotic genes from RNA viruses (2010) (62)
- A novel group of diverse Polinton-like viruses discovered by metagenome analysis (2015) (61)
- Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models (2004) (61)
- Horizontal gene transfer: the path to maturity (2003) (61)
- Archaeal ancestors of eukaryotes: not so elusive any more (2015) (61)
- On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems (2011) (61)
- Does the central dogma still stand? (2012) (61)
- Salmon Gill Poxvirus, the Deepest Representative of the Chordopoxvirinae (2015) (60)
- Common origins and host-dependent diversity of plant and animal viromes. (2011) (60)
- Classification and quantification of bacteriophage taxa in human gut metagenomes (2014) (60)
- Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems. (2016) (60)
- Cell-to-cell movement of plant viruses (1993) (60)
- The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum (2009) (59)
- Seeker: Alignment-free identification of bacteriophage genomes by deep learning (2020) (59)
- Thousands of previously unknown phages discovered in whole-community human gut metagenomes (2020) (59)
- A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes (2011) (58)
- A family of DNA virus genes that consists of fused portions of unrelated cellular genes. (1992) (58)
- DnaC protein contains a modified ATP-binding motif and belongs to a novel family of ATPases including also DnaA. (1992) (58)
- The Vast, Conserved Mammalian lincRNome (2013) (58)
- Pandoraviruses are highly derived phycodnaviruses (2013) (58)
- Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). (2006) (58)
- Origins and impact of constraints in evolution of gene families. (2006) (58)
- Evolution of Eukaryotic Cell Cycle Regulation Stepwise Addition of Regulatory Kinases and Late Advent of the CDKs (2003) (58)
- Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens. (2013) (58)
- The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases. (2016) (57)
- Multiple evolutionary origins of giant viruses (2018) (57)
- Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences (2001) (57)
- The ATP-cone: an evolutionarily mobile, ATP-binding regulatory domain. (2000) (57)
- Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis (2018) (56)
- Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states (2017) (56)
- Structure and Regulation of the Mouse ing1 Gene (1999) (56)
- A conserved domain in putative bacterial and bacteriophage transglycosylases. (1994) (56)
- Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases (2006) (55)
- Autogenous translation regulation by Escherichia coli ATPase SecA may be mediated by an intrinsic RNA helicase activity of this protein (1992) (55)
- Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach. (2008) (55)
- Evolution of complexity in the viral world: the dawn of a new vision. (2006) (55)
- Gene Family Level Comparative Analysis of Gene Expression in Mammals Validates the Ortholog Conjecture (2014) (55)
- The LUCA and its complex virome (2020) (55)
- Polintons, virophages and transpovirons: a tangled web linking viruses, transposons and immunity. (2017) (55)
- Assembly , Operation , and Disassembly of Protein Complexes : A Class of Chaperone-Like ATPases Associated with the + AAA (1999) (55)
- CRISPR-Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity. (2019) (54)
- Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features (2021) (54)
- Simple stochastic birth andz death models of genome evolution: was there enough time for us to evolve? (2003) (54)
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- Evolution of Human Respiratory Virus Epidemics (2020) (13)
- Capsid‐Less RNA Viruses (2012) (13)
- Universal distribution of mutational effects on protein stability, uncoupling of protein robustness from sequence evolution and distinct evolutionary modes of prokaryotic and eukaryotic proteins (2015) (13)
- Unprecedented Diversity of Unique CRISPR-Cas-Related Systems and Cas1 Homologs in Asgard Archaea. (2020) (13)
- 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. (2019) (13)
- Cargo genes of Tn7-like transposons comprise an enormous diversity of defense systems, mobile genetic elements and antibiotic resistance genes (2021) (13)
- Virology: A parasite's parasite saves host's neighbours (2016) (13)
- 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 (2019) (13)
- Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection (2006) (13)
- The logic of virus evolution. (2022) (13)
- A unique insert in the genomes of high-risk human papillomaviruses with a predicted dual role in conferring oncogenic risk (2019) (13)
- New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures. (2019) (13)
- Structure and function of virion RNA polymerase of a crAss-like phage (2020) (13)
- CRISPR Arrays Away from cas Genes. (2020) (12)
- Rapid evolution of a cyclin A inhibitor gene, roughex, in Drosophila. (2001) (12)
- Allosteric Activation of SARS-CoV-2 RNA-Dependent RNA Polymerase by Remdesivir Triphosphate and Other Phosphorylated Nucleotides (2021) (12)
- A putative RNA-interference-based immune system in prokaryotes: The epitome of prokaryotic genomic diversity (2006) (12)
- Thousands of previously unknown phages discovered in whole-community human gut metagenomes (2021) (12)
- Birth and Death Models of Genome Evolution (2006) (12)
- Identification of Dephospho-Coenzyme A (Dephospho-CoA) Kinase in Thermococcus kodakarensis and Elucidation of the Entire CoA Biosynthesis Pathway in Archaea (2019) (11)
- Evolution of thymidine and thymidylate kinases: The possibility of independent capture of TK genes by different groups of viruses (1992) (11)
- Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis (2014) (11)
- Horizontal Gene Transfer and its Role in the Evolution of Prokaryotes (2002) (11)
- 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. (2007) (11)
- Cellular homologs of the double jelly-roll major capsid proteins clarify the origins of an ancient virus kingdom (2022) (11)
- Evolvability of an Optimal Recombination Rate (2015) (11)
- Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems (2015) (11)
- Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea (2017) (11)
- Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo's paradox (2022) (11)
- Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents (2020) (11)
- 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 (2016) (11)
- Origin of programmed cell death from antiviral defense? (2019) (11)
- Winnowing sequences from a database search (1999) (11)
- The Evolutionary Origins of Life and Death (2020) (11)
- Defining Life: An Exercise in Semantics or A Route to Biological Insights? (2012) (11)
- Evolution of Central Metabolic Pathways: The Playground of Non-Orthologous Gene Displacement (2003) (11)
- Encephalomyocarditis virus replication complexes that prefer nucleoside diphosphates as substrates for viral RNA synthesis. (1983) (11)
- Frontiers in computational genomics. (2003) (10)
- Deep phylogeny of cancer drivers and compensatory mutations (2020) (10)
- Ongoing Adaptive Evolution and Globalization of Sars-Cov-2. (2020) (10)
- The sounds of science—a symphony for many instruments and voices (2019) (10)
- Estimation of prokaryotic supergenome size and composition from gene frequency distributions (2014) (10)
- Nonessential Ribosomal Proteins in Bacteria and Archaea Identified Using Clusters of Orthologous Genes (2021) (10)
- Tale of two serines (1989) (10)
- Reviving a culture of scientific debate (2006) (10)
- Independent Evolution of Heavy Metal-Associated Domains in Copper Chaperones and Copper-Transporting ATPases (2001) (10)
- Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families (2017) (10)
- Substantial Impact of Post Vaccination Contacts on Cumulative Infections during Viral Epidemics (2020) (10)
- A putative nucleic acid-binding domain in Werner's and Bloom's syndrome helicases (1997) (10)
- Paralogs and mutational robustness linked through transcriptional reprogramming. (2005) (10)
- Impairment of translation in neurons as a putative causative factor for autism (2014) (10)
- Evolution of Type IV CRISPR-Cas Systems: Insights from CRISPR Loci in Integrative Conjugative Elements of Acidithiobacillia. (2021) (9)
- Cellular origin of the viral capsid-like bacterial microcompartments (2017) (9)
- Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve (2018) (9)
- An alternating active-dormitive strategy enables disadvantaged prey to outcompete the perennially active prey through Parrondo’s paradox (2021) (9)
- Open questions: CRISPR biology (2018) (9)
- Structure-based insights into evolution of rhodopsins (2021) (9)
- Chance and necessity in cellular response to challenge (2007) (9)
- Three families of Asgard archaeal viruses identified in metagenome-assembled genomes (2022) (9)
- Gene prediction accuracy in large DNA sequences. (2003) (9)
- RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease (2022) (9)
- Dependencies among Editing Sites in Serotonin 2C Receptor mRNA (2012) (9)
- Evolution and Classification of CRISPR-Cas Systems and Cas Protein Families (2013) (9)
- A three-organelle complex made by wrappER contacts with peroxisome and mitochondria responds to liver lipid flux changes. (2021) (9)
- Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array. (2019) (9)
- Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution. (2003) (8)
- 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales (2022) (8)
- The CRISPR spacer space is dominated by sequences from the species-specific mobilome (2017) (8)
- Encephalomyocarditis virus replication complexes preferentially utilizing nucleoside diphosphates as substrates for viral RNA synthesis. Nucleotide kinases specifically associated with the complex channel RNA precursor. (1984) (8)
- Adomaviruses: an emerging virus family provides insights into DNA virus evolution (2018) (8)
- A unique insert in the genomes of high-risk human papillomaviruses with a predicted dual role in conferring oncogenic risk. (2019) (8)
- Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues (2019) (8)
- Evolution of regulatory signatures in primate cortical neurons at cell-type resolution (2020) (8)
- Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting (2018) (7)
- Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process? (2022) (7)
- Chordopoxvirus protein F12 implicated in enveloped virion morphogenesis is an inactivated DNA polymerase (2014) (7)
- Extending the Lifespan of Multicellular Organisms via Periodic and Stochastic Intercellular Competition. (2022) (7)
- Can Environmental Manipulation Help Suppress Cancer? Non‐Linear Competition Among Tumor Cells in Periodically Changing Conditions (2020) (7)
- The Structure and Evolutionary Role of the PenelopeMobile Element in the Drosophila virilisSpecies Group (2001) (7)
- EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution (2010) (7)
- Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants that merit monitoring (2021) (7)
- The origin and evolution of eukaryotes : a subject collection from Cold Spring Harbor perspectives in biology (2014) (7)
- Parabolic replicator dynamics and the principle of minimum Tsallis information gain (2013) (7)
- Cell cycle and apoptosis: possible roles of Gadd45 and MyD118 proteins inferred from their homology to ribosomal proteins. (1997) (7)
- Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes. (2013) (7)
- Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach (2020) (6)
- Correlations between Quantitative Measures of Genome Evolution, Expression and Function (2006) (6)
- Swift publication would reward good reviewers (2003) (6)
- Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota Identified by Genome-Centric Metagenomics (2017) (6)
- How genetic parasites persist despite the purge of natural selection (2018) (6)
- Estimation of universal and taxon-specific parameters of prokaryotic genome evolution (2017) (6)
- Human choroideremia protein contains a FAD-binding domain (1996) (6)
- A maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure. (2009) (6)
- Phages build anti-defence barriers (2019) (6)
- Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators? (2022) (6)
- Biology direct: celebrating 7 years of open, published peer review (2013) (6)
- The global virome: how much diversity and how many independent origins? (2022) (6)
- Environmental microbiology and metagenomics: the Brave New World is here, what's next? (2018) (6)
- CRISPRclassify: Repeat-Based Classification of CRISPR Loci. (2021) (6)
- Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles: by L. Aravind, Roman L. Tatusov, Yuri I. Wolf, D. Roland Walker and Eugene Koonin Trends Genet. 14, 442–444 (1999) (6)
- Molecular adaptations during viral epidemics (2022) (6)
- 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. (2014) (6)
- Chapter 17 FUNCTIONAL GENOMICS AND ENZYME EVOLUTION Homologous and Analogous Enzymes Encoded in Microbial (1999) (6)
- Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, “Methanonatronarchaeia” (2018) (5)
- Science in times of war: oppose Russian aggression but support Russian scientists (2022) (5)
- Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales (2021) (5)
- Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes (2020) (5)
- Monitoring the partitioning of hepatic fatty acids in vivo: keeping track of control (1994) (5)
- 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 (1994) (5)
- SURVEY AND SUMMARY Did DNA replication evolve twice independently ? (1999) (5)
- Plasmodium falciparum protein associated with the invasion junction contains a conserved oxidoreductase domain. (1995) (5)
- Four principles to establish a universal virus taxonomy (2023) (5)
- Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes (2022) (5)
- Crossing fitness valleys via double substitutions within codons (2019) (5)
- Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. (2004) (5)
- Cargo Genes of Tn7-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes (2021) (5)
- Conservation and Evolution of the Sporulation Gene Set in Diverse Members of the Firmicutes (2022) (5)
- Hunting for Treasure Chests in Microbial Defense Islands. (2018) (5)
- Genome analysis using clusters of orthologous groups (COGs) (1998) (5)
- Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants of potential concern (2021) (5)
- Evolution in the weak-mutation limit: Stasis periods punctuated by fast transitions between saddle points on the fitness landscape (2021) (5)
- Reply to “Codon Usage Frequency of RNA Virus Genomes from High-Temperature Acidic-Environment Metagenomes” (2013) (4)
- Fishing for phages in metagenomes: what do we catch, what do we miss? (2021) (4)
- Reply to ‘Evolutionary placement of Methanonatronarchaeia’ (2019) (4)
- The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism (2022) (4)
- Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo’s Paradox (2021) (4)
- Genome as a stochastic evolutionary machine: comment on "How life changes itself: the Read-Write (RW) genome" by James Shapiro. (2013) (4)
- Genomic microbiology: Right on target? (1998) (4)
- Escherichia coli Protein Sequences : Functional and Evolutionary Implications (1999) (4)
- New variants of known folds: do they bring new biology? (2010) (4)
- Assessment of assumptions underlying models of prokaryotic pangenome evolution (2021) (4)
- Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape (2021) (4)
- FMN- or DNA-binding? (1994) (4)
- Comparative Genomics Approaches to Identifying Functionally Related Genes (2014) (4)
- 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. (1980) (4)
- The miniature CRISPR-Cas12m effector binds DNA to block transcription. (2022) (4)
- Game-Theoretical Modeling of Interviral Conflicts Mediated by Mini-CRISPR Arrays (2020) (4)
- Allosteric activation of SARS-CoV-2 RdRp by remdesivir triphosphate and other phosphorylated nucleotides (2021) (4)
- Erratum for Gjessing et al., Salmon Gill Poxvirus, the Deepest Representative of the Chordopoxvirinae (2015) (3)
- Protein evolution: Causes of trends in amino-acid gain and loss (Reply) (2006) (3)
- Comparative Genomics and New Evolutionary Biology (2003) (3)
- RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-protease complex (2022) (3)
- Proteomic and Genomic Signatures of Repeat-instability in Cancer and Adjacent Normal Tissues (2018) (3)
- Unique genomic features of crAss-like phages, the dominant component of the human gut virome (2020) (3)
- Researchisofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution (2010) (3)
- Viruses of Asgard archaea (2021) (3)
- A family of novel immune systems targets early infection of nucleus-forming jumbo phages (2022) (3)
- Constraints, Plasticity, and Universal Patterns in Genome and Phenome Evolution (2010) (3)
- Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity (2014) (3)
- Obituary: Walter Fitch and the orthology paradigm (2011) (3)
- A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea (2015) (3)
- Corrigendum: A universal trend of amino acid gain and loss in protein evolution (2005) (3)
- Viral channelrhodopsins: calcium-dependent Na+/K+ selective light-gated channels (2020) (3)
- ViroidDB: a database of viroids and viroid-like circular RNAs (2021) (3)
- Horizontal Gene Transfer and Prokaryotic Genome Evolution (2004) (3)
- Escherichia Coli — Functional and Evolutionary Implications of Genome Scale Computer-Aided Protein Sequence Analysis (1996) (3)
- Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life. (2019) (3)
- Horizontal transfer beyond genes (2014) (3)
- A Novel Flavi-like Virus in Alfalfa (Medicago sativa L.) Crops along the Snake River Valley (2022) (3)
- Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes (2020) (3)
- 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 (1993) (3)
- tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector (2021) (2)
- Towards comprehensive characterization of CRISPR-linked genes (2018) (2)
- Corrigendum to “Novel domains of the prokaryotic two-component signal transduction systems”: [FEMS Microbiol. Lett. 203 (2001) 11–21] (2001) (2)
- An interview with Drs. Eugene V. Koonin and L. Aravind on their highly cited paper published in Cell Cycle (2009) (2)
- SURVEY AND SUMMARY Darwinian evolution in the light of genomics (2009) (2)
- Phylogenomic analysis of the diversity of graspetides and proteins involved in their biosynthesis (2022) (2)
- Multiple evolutionary origins of giant viruses [version 1; peer review: 4 approved] (2021) (2)
- Genome-wide Analysis of Substrate Specificities of the Escherichia coli Haloacid Dehalogenase-like (2006) (2)
- Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches (2021) (2)
- A novel group of negative-sense RNA viruses associated with epizootics in managed and free-ranging freshwater turtles in Florida, USA (2022) (2)
- Bacterial genes in eukaryotes: Relatively rare but real and important (Comment on DOI 10.1002/bies.201300095) (2014) (2)
- A comprehensive census of horizontal gene transfers from prokaryotes to unikonts (2011) (2)
- Computer Analysis of Amino Acid Sequences (1998) (2)
- Origin and evolution of spliceosomal introns (2012) (2)
- Information Sources for Genomics (2003) (2)
- Useful Web Sites (2003) (2)
- Inevitability of the emergence and persistence of genetic parasites caused by thermodynamic instability of parasite-free states (2017) (2)
- A method for search of structure motifs in amlnoacid sequences program site of the GenBee package (1990) (2)
- Homologous recombination substantially delays sequence but not gene content divergence of prokaryotic populations (2019) (2)
- Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity (2018) (2)
- Viruses with more than 1000 genes: Mamavirus, a new Acanthamoeba castellanii mimivirus 3 strain, and reannotation of mimivirus genes 4 5 Short title: Mamavirus, a new Mimivirus strain 6 7 (2011) (2)
- Non-essential ribosomal proteins in bacteria and archaea identified using COGs (2021) (2)
- A half‐century after the molecular clock: new dimensions of molecular evolution (2012) (2)
- Faculty Opinions recommendation of Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere. (2018) (2)
- How Does Large-Scale Genomic Analysis Shape Our Understanding of COVID Variants in Real Time? (2021) (2)
- Supplementary Data for Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2 (2021) (2)
- Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs (2023) (2)
- Genome plasticity, a key factor of evolution in prokaryotes (2018) (2)
- Comparative analysis of lipid biosynthesis in archaea, bacteria and eukaryotes: What was the structure of the first membrane lipids? (2012) (2)
- Prediction of the virus incubation period for COVID-19 and future outbreaks (2020) (2)
- Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain. (2002) (2)
- MicrobiologyThe Evolution and Emergence of RNA Viruses.Oxford Series in Ecology and Evolution. ByEdwardC.Holmes. Oxford and New York: Oxford University Press. $130.00 (hardcover); $60.00 (paper). xii 254 p.; ill.; index. ISBN: 9780199211128 (hc); 9780199211135 (pb). 2009. (2010) (1)
- Chordopoxvirus protein F12 implicated in enveloped virion morphogenesis is an inactivated DNA polymerase (2014) (1)
- The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes (2012) (1)
- Exaptation of inactivated host enzymes for structural roles in orthopoxviruses and novel protein folds revealed by protein structure modeling (2022) (1)
- Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes (2014) (1)
- Phylogenetic evidence of headful packaging strategy in gene transfer agents (2020) (1)
- Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family (2013) (1)
- No waves of intelligent design (2020) (1)
- The cancer-mutation network and the number and specificity of driver mutations (2017) (1)
- Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis (2014) (1)
- Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions (2022) (1)
- Identification of combinations of somatic mutations that predict cancer survival and immunotherapy benefit (2021) (1)
- A novel group of diverse Polinton-like viruses discovered by metagenome analysis (2015) (1)
- Origin and Evolution of Photosynthesis: Clues from Genome Comparison (2008) (1)
- Evolution of the Genomic Universe (2016) (1)
- Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA (2022) (1)
- Does the central dogma still stand? (2012) (1)
- A Minimal Gene Complement for Cellular Life and Reconstruction of Primitive Life Forms by Analysis of Complete Bacterial Genomes (1998) (1)
- Compensatory relationship between low-complexity regions and gene paralogy in the evolution of prokaryotes (2022) (1)
- Connected gene neighborhoods in prokaryotic (2002) (1)
- Allele fixation probability in a Moran model with fluctuating fitness landscapes. (2019) (1)
- : A new viral order unifying five families of reverse-transcribing viruses. (2018) (1)
- Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes (2012) (1)
- Pervasive conditional selection of driver mutations and modular epistasis networks in cancer (2022) (1)
- Structural insights into light-driven anion pumping in cyanobacteria (2022) (1)
- Estimation of prokaryotic supergenome size and composition from gene frequency distributions (2014) (1)
- Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park (2013) (1)
- Co-evolution of Eukaryotic-like Vps4 and ESCRT-III Subunits in the Asgard Archaea (2020) (1)
- Punctuated equilibrium as the default mode of evolution of large populations on fitness landscapes dominated by saddle points in the weak-mutation limit (2020) (1)
- Uncertainty-aware and interpretable evaluation of Cas9–gRNA and Cas12a–gRNA specificity for fully matched and partially mismatched targets with Deep Kernel Learning (2021) (1)
- A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains (2021) (1)
- Impairment of translation in neurons as a putative causative factor for autism (2014) (1)
- A superfamily of proteins that contain the cold-shock domain (1998) (1)
- KaiC-like ATPases as Signal Transduction Hubs in Archaea (2017) (1)
- SURVEY AND SUMMARY Classification and evolution of type II CRISPR-Cas systems (2014) (1)
- Elaborate security TRAINing to fight against expression of genomic junk (2013) (1)
- Genome sequencing: a glimpse of the area at the brink of the virus era. (1993) (1)
- Reply to Hedrick and Klitz: High haplotype discovery rate in the HLA locus (2019) (1)
- Parabolic replicator dynamics and the principle of minimum Tsallis information gain (2013) (1)
- Crystal structure of the SIRV3 AcrID1 (gp02) anti-CRISPR protein (2018) (1)
- INITIATION OF THE ENCEPHALOMYOCARDITIS VIRAL-RNA SYNTHESIS IN CELL-FREE SYSTEM AND THE PROBABLE PARTICIPATION OF VPG PROTEIN IN THIS PROCESS (1982) (1)
- Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales (2022) (1)
- Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes (2012) (1)
- Why genome analysis? (1999) (1)
- Lamarckian or not, CRISPR-Cas is an elaborate engine of directed evolution (2019) (1)
- Genomes and the Protein Universe (2003) (1)
- An alternating active-dormitive strategy enables disadvantaged prey to outcompete the perennially active prey through Parrondo’s paradox (2021) (1)
- A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals (2007) (1)
- Genomes and evolution. Glimpses of an emerging synthesis (1999) (1)
- Computer analysis of amino acid sequences. The case of plant virus capsid proteins. (1998) (1)
- Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses (2014) (1)
- Publisher Correction: Mutation–selection balance and compensatory mechanisms in tumour evolution (2020) (1)
- CRISPR‐Cas Systems and Cas Protein Families (2013) (1)
- MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes (2014) (1)
- Seeing the Tree of Life behind the phylogenetic forest (2013) (1)
- A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes (2022) (1)
- The evolution of microbial defense systems (2021) (1)
- A natural taxonomy of gene families from complete genomes (1997) (1)
- Mathematical modeling of anti-tumor virus therapy: Regimes with complete recovery within the framework of deterministic models (2005) (1)
- Defense Against Viruses and Other Genetic Parasites in Prokaryotes (2019) (1)
- Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer (2023) (1)
- The Role of Energy in the Emergence of Biology from Chemistry (2012) (1)
- The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic (2005) (1)
- Key role of recombination in evolutionary processes with migration between two habitats. (2019) (1)
- COGs: an evolutionary classification of genes and proteins from sequenced genomes (2005) (1)
- A Ratio-Dependent Model of Replicator-Genetic Parasite Coevolution Demonstrates Instability of the Parasite-Free State (2021) (1)
- A life LINE for large viruses (2022) (0)
- Genome Maps: 11 The Human Genome (2001) (0)
- Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes (2020) (0)
- DNA Repair: Evolution (2006) (0)
- Crossing fitness valleys via double substitutions within codons (2019) (0)
- Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity (2018) (0)
- Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity (2018) (0)
- Biology Direct:celebrating 7 years of open, published peer review (2013) (0)
- Comparative Analysis of Biopolymer Sequences: Reflections on the Validity of the Methodology and the Underlying General Principles (1992) (0)
- Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection (2015) (0)
- Creation of new order, Ortervirales, for 5 families of reverse-transcribing viruses (2017) (0)
- Stability of host-parasite systems: you must differ to coevolve (2018) (0)
- How genes evolve 7281 Predicting reward and punishment (2009) (0)
- , and in Two Different Oceanic Provinces Genotypic Variants in a Single Population Comparative Genomic Analysis of Archaeal (2001) (0)
- Recognition of Specific Uridines in tRNA Substrates by Dihydrouridine Synthases (2016) (0)
- Microbiology (2010) (0)
- Taxonomy of the order Mononegavirales: update 2018 (2018) (0)
- Lamarckian or not, CRISPR-Cas is an elaborate engine of directed evolution (2019) (0)
- Table 5, Conserved portions of hypothetical minimal gene sets for different lifestyles (2002) (0)
- Pandoraviruses are highly derived phycodnaviruses (2013) (0)
- Modified base-binding EVE and DCD Domains Implicated in the Origins of Programmed Cell Death and the piRNA Pathway (2020) (0)
- Viriforms—A New Category of Classifiable Virus-Derived Genetic Elements (2023) (0)
- THE EMERGING GENERALIZATIONS OF PROKARYOTIC GENOMICS (2008) (0)
- Host Age Structure Defines Interactions with Pathogens: Grandparent Effect under Collaboration and Virulent Mutualism under Competition (2022) (0)
- SURVEY AND SUMMARY Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense (2020) (0)
- Phages build anti-defence barriers (2019) (0)
- Table 2, Examples of horizontally transferred operons (2002) (0)
- Differential Expression of Gelsolin-Like Genes in Zebrafish: Initial Promoter Analysis of the Corneal Crystallin, Scinla. (2007) (0)
- Systems biology of bacteriophage proteins and new dimensions of the virus world discovered through metagenomics (2011) (0)
- Fixation Probability of a Mutant in the Wright–Fisher Model under Strong Selection and Fluctuating Fitness Landscape (2020) (0)
- The complex domain architecture of SAMD9 family proteins, predicted STAND-like NTPases, suggests new links to inflammation and apoptosis (2017) (0)
- Comparative Human Genomics (2008) (0)
- Open questions: CRISPR biology (2018) (0)
- Theory of microbial genome evolution (2017) (0)
- Figure 2.10, Phyletic patterns of the three forms of phosphoglycerate mutase (2003) (0)
- Engineering of CRISPR-Cas12b for human genome editing (2019) (0)
- Table 1, Examples of probable horizontal gene transfers identified using phyletic patterns in COGs a (2002) (0)
- Final Report for Grant No. DE-FG02-01ER63220 "The Dynamics of Cellular Stress Responses in Deinococcus radiodurans" (2006) (0)
- Reconstitution of the L . shahii C 2 c 2 locus in Escherichia coli confers RNA-guided immunity (2016) (0)
- A flea has smaller fleas that on him prey: giant viruses, their parasites and evolutionary networks (2013) (0)
- Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing (2013) (0)
- Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018 (2018) (0)
- Host age structure reshapes parasite symbiosis: collaboration begets pathogens, competition begets virulent mutualists (2022) (0)
- A comprehensive census of horizontal gene transfers from prokaryotes to unikonts (2011) (0)
- Comparative Methods in Biology and Genomics (2005) (0)
- Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire (2019) (0)
- Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability (2020) (0)
- to heavy membranes: implications for Omi/HtrA2 and PARL activity in the regulation of mitochondrial stress and apoptosis (2009) (0)
- Faculty Opinions recommendation of Giant viruses of amoebae: A journey through innovative research and paradigm changes. (2018) (0)
- Table 9, Examples of eukaryotic-prokaryotic transfer of functionally diverse genes (2002) (0)
- Faculty Opinions recommendation of The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea. (2018) (0)
- 541. Use of Endogenous Viral Elements to Deduce the Sequence of an Ancient Adeno-Associated Virus That Circulated Amongst Australian Marsupials ~30 Million Years Ago (2016) (0)
- Faculty of 1000 evaluation for The dualistic nature of integrative and conjugative elements. (2016) (0)
- Figure 4.12, Results of the CD search for the TSG101 protein (2003) (0)
- Table 6, Apparent phylogenetic affinities of eukaryotic best hits in bacteria and archaea (2002) (0)
- Universal genome cutters: from selfish genetic elements to antivirus defence and genome editing tools (2016) (0)
- Human and mouse homologs of Escherichia coli DinB ( DNA polymerase IV ) , members of the UmuC y DinB superfamily (0)
- Erratum for Kogay et al., “Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents” (2020) (0)
- Faculty Opinions recommendation of Diversity and evolution of the emerging Pandoraviridae family. (2018) (0)
- The Greater Virus World and Its Evolution (2019) (0)
- The replication machinery of LUCA: common origin of DNA replication and transcription (2020) (0)
- Figure 2, [Phylogenetic trees illustrating xenologous gene...]. (2002) (0)
- A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea (2015) (0)
- Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon (2015) (0)
- Horizontal gene transfer barrier shapes the evolution of prokaryotic pangenomes (2020) (0)
- Taxonomic affinities of ArCOGs with bacteria and eukaryotes (2011) (0)
- CRISPR–Cas in mobile genetic elements: counter-defence and beyond (2019) (0)
- Genomics: From Phage to Human (2003) (0)
- Table 5, Classification of candidate horizontal gene transfer events in selected genomes a (2002) (0)
- Molecular Evolution in the Genomic Era (2000) (0)
- Widespread PRC barrel proteins play critical roles in archaeal cell division (2023) (0)
- Abstracts of Papers Presented at The International Workshop onBemisia Spp. (1994) (0)
- Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer (2012) (0)
- Faculty Opinions recommendation of Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. (2004) (0)
- The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life (2015) (0)
- Comparative Genomics: Is It Changing the Paradigm of Evolutionary Biology? (1998) (0)
- Faculty Opinions recommendation of Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area. (2019) (0)
- Bridging the gap between sequence & function : abstracts of papers presented at the 1999 workshop, September 7-September 9, 1999 (1999) (0)
- Bioinformatics: in silico biology, biological networks, from genomics to epidemiology (2003) (0)
- Phylogenomics of Cas4 family nucleases (2017) (0)
- Parallelized screening of virus accessory genes reveals diverse defense and counter-defense mechanisms (2023) (0)
- Genome of the Extremely Radiation-Resistant Bacterium <italic toggle='yes'>Deinococcus radiodurans</italic> Viewed from the Perspective of Comparative Genomics (2001) (0)
- Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states (2017) (0)
- Evolution of human respiratory virus epidemics [version 1; peer review: 1 approved with reservations] (2021) (0)
- Faculty of 1000 evaluation for Integrative and conjugative elements (ices): what they do and how they work. (2016) (0)
- Open Questions on the Origin of Life at Anoxic Geothermal Fields (2012) (0)
- Table 1, Coverage of completely-sequenced genomes by conserved families of orthologs (2002) (0)
- CRYSTAL STRUCTURE OF BACILLUS SUBTILIS MAF PROTEIN (2000) (0)
- Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes (2014) (0)
- Faculty of 1000 evaluation for Bacterial gene import and mesophilic adaptation in archaea. (2016) (0)
- The Abundant Gelsolin–Like Corneal Protein of Zebrafish Is Adseverin (2006) (0)
- Correspondence between eukaryotic and prokaryotic orthologous gene sets (2011) (0)
- All You Ever Wanted to Know about Microevolution (2000) (0)
- Archaeal ancestors of eukaryotes: not so elusive any more (2015) (0)
- Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease (2015) (0)
- Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions (2022) (0)
- Reviewer Acknowledgement (2015) (0)
- Faculty Opinions recommendation of Proteasomes can degrade a significant proportion of cellular proteins independent of ubiquitination. (2009) (0)
- Table 8, Horizontal transfer of eukaryotic aaRS genes into different bacterial lineages a (2002) (0)
- Table 7, Examples of eukaryotic-bacterial transfer of genes coding for proteins and domains involved in signal transduction a (2002) (0)
- Origin of viruses: primordial replicators recruiting capsids from hosts (2019) (0)
- Structure of the archaeal beta-CASP protein with N-terminal KH domains from Methanothermobacter thermautotrophicus (2011) (0)
- Corrigendum: Genome and Environmental Activity of a Chrysochromulina parva Virus and Its Virophages (2019) (0)
- ANNIVERSAR Y UPD AT E Open Access (2013) (0)
- Table 4, Candidate horizontal gene transfers between major bacterial lineages: a quantitative assessment a (2002) (0)
- 94 Origin and evolution of adaptive immunity systems (2015) (0)
- Table 2, Phylogenetic patterns in the full COG a collection and in the minimal gene set classified by functional classes of proteins (2002) (0)
- Faculty Opinions recommendation of Giant viruses come of age. (2018) (0)
- Faculty Opinions recommendation of A giant virus infecting green algae encodes key fermentation genes. (2018) (0)
- Evolution of human respiratory virus epidemics [version 1; peer review: awaiting peer review] (2021) (0)
- Faculty Opinions recommendation of Loop fold structure of proteins: resolution of Levinthas paradox. (2002) (0)
- Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes (2023) (0)
- A Reverse Transcriptase-C as 1 Fusion Protein Contains a Cas 6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition Graphical (2018) (0)
- Faculty Opinions recommendation of The large marseillevirus explores different entry pathways by forming giant infectious vesicles. (2018) (0)
- Crystal Structure of the Cas6 Domain of Marinomonas mediterranea MMB-1 Cas6-RT-Cas1 Fusion Protein (2018) (0)
- Table 3, Candidate horizontal transfers between bacteria, archaea, and eukaryotes: a quantitative assessment a (2002) (0)
- Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies (2013) (0)
- A distinct abundant group of microbial rhodopsins discovered using functional metagenomics (2018) (0)
- Conflict-driven evolution (2021) (0)
- Gene-influx-driven evolution. (2022) (0)
- Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes (2015) (0)
- Faculty Opinions recommendation of Giants among larges: how gigantism impacts giant virus entry into amoebae. (2018) (0)
- On planctomycetes, eukaryotes, and analogy (2011) (0)
- Protocol for comparing gene-level selection on coding mutations between two groups of samples with Coselens (2023) (0)
- Faculty Opinions recommendation of Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses. (2018) (0)
- Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling (2023) (0)
- Faculty Opinions recommendation of Genomes in flux: the evolution of archaeal and proteobacterial gene content. (2002) (0)
- Why the Central Dogma: on the nature of the great biological exclusion principle (2015) (0)
- Figure 1, [A generalized procedure for constructing...]. (2002) (0)
- Faculty Opinions recommendation of Orpheovirus IHUMI-LCC2: A New Virus among the Giant Viruses. (2018) (0)
- NT~-binding domains encoded by genomes of small DNA and RNA viruses (2001) (0)
- Table 3, Members of the original minimal gene set that show scattered phylogenetic patterns and are predicted to be dispensable (examples) (2002) (0)
- Author Correction: Programmable RNA targeting with the single-protein CRISPR effector Cas7-11 (2022) (0)
- Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae (2015) (0)
- Widespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems (2023) (0)
- Faculty Opinions recommendation of Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina - Blastocystis Stramenopile Lineage. (2019) (0)
- Expanding networks of RNA virus evolution (2012) (0)
- The rhomboids: a near ubiquitous family of intramembrane serine proteases evolved via multiple horizontal gene transfers (2002) (0)
- Cellular differentiation into hyphae and spores in halophilic archaea (2023) (0)
- The first Microbe (2017) (0)
- Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail (2022) (0)
- List of contributors (2021) (0)
- Figure 4.5, The BLOSUM 62 substitution matrix (2003) (0)
- Faculty Opinions recommendation of Evolutionary dynamics of giant viruses and their virophages. (2014) (0)
- E. coli dihydrouridine synthase C (DusC) in complex with tRNAPhe (2015) (0)
- The LUCA and its complex virome (2020) (0)
- “Megavirales”, a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses (2013) (0)
- The origins of cellular life (2014) (0)
- The virome of the last eukaryotic common ancestor and eukaryogenesis. (2023) (0)
- Contents Vol. 5, 2003 (2003) (0)
- Selection on codon usage and amino acid sequences in prokaryotes (2013) (0)
- Faculty Opinions recommendation of Complex molecular architecture of beet yellows virus particles. (2004) (0)
- Ancient systems of sodium/potassium homeostasis as predecessors of membrane bioenergetics (2015) (0)
- The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA) (2001) (0)
- The Proposed Plant Connexin Is a Protein Kinase-Like Protein [with Reply] (1993) (0)
- Systems biology of phage proteins: using orthologous groups to study bacteriophage evolution; and new dimensions of the virus world discovered through metagenomics (2011) (0)
- Phylogenomic analysis of the diversity of graspetides and proteins involved in their biosynthesis (2022) (0)
- C1/2 Energetics of the first bacteria as inferred from genome analysis (2008) (0)
- Table 2.3, Examples of non-orthologous gene displacement between M. genitalium and H. influenzae (2003) (0)
- Archaeal origin of tubulin (2012) (0)
- The Internal Language of Proteins (2020) (0)
- Purifying and positive selection in the evolution of stop codons (2018) (0)
- Functional breakdown of genes in each of the sequenced archaeal genomes (2011) (0)
- Structural atlas of a human gut crassvirus. (2023) (0)
- Figure 7.6, Distribution of tryptophan biosynthesis enzymes in organisms with completely sequenced genomes (2003) (0)
- Erratum: Human choroideremia protein contains a FAD-binding domain (1996) (0)
- Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms (2016) (0)
- Author Correction: Programmable RNA targeting with the single-protein CRISPR effector Cas7-11 (2022) (0)
- Cellular origin of the viral capsid-like bacterial microcompartments (2017) (0)
- Decision letter: Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus (2020) (0)
- Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence (2017) (0)
- Nucleic Acids Research (2011) (0)
- Editor's evaluation: A computational screen for alternative genetic codes in over 250,000 genomes (2021) (0)
- A hypothetical scenario for the origin and dissemination of the rhomboid family proteases (2011) (0)
- Faculty Opinions recommendation of Updating strategies for isolating and discovering giant viruses. (2018) (0)
- NMR SOLUTION STRUCTURE OF THE PRODUCT OF THE E. COLI YCIH GENE. (1999) (0)
- Faculty Opinions recommendation of Genome of Xanthomonas oryzae bacteriophage Xp10: an odd T-odd phage. (2003) (0)
- Figure 1, [Distribution of the clusters of...]. (2002) (0)
- Reply to ‘Evolutionary placement of Methanonatronarchaeia’ (2019) (0)
- Epilogue: Peering through the crystal ball (2003) (0)
- Table 4, Nonorthologous gene displacement (NOD) within the minimal gene set (examples) (2002) (0)
- Faculty Opinions recommendation of Mimivirus: leading the way in the discovery of giant viruses of amoebae. (2018) (0)
- Alternating active-dormitive strategy enables overtaking by disadvantaged prey through Parrondo's paradox (2021) (0)
- Prediction of the incubation period for COVID-19 and future virus disease outbreaks (2020) (0)
- Table of Contents (1994) (0)
- Splendor and misery of adaptation, or the importance of neutral null for understanding evolution (2016) (0)
- Assessment of assumptions underlying models of prokaryotic pangenome evolution (2021) (0)
- Proteorhodopsin genes in giant viruses (2012) (0)
- Clostridium acetobutylicum Bacterium Analysis of the Solvent-Producing Genome Sequence and Comparative (2001) (0)
- Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve (2018) (0)
- Classify viruses — the gain is worth the pain (2019) (0)
- Faculty Opinions recommendation of Global transcriptome analysis of the aphelid Paraphelidium tribonemae supports the phagotrophic origin of fungi. (2019) (0)
- Searching for FLASH domains. Authors' reply (1999) (0)
- A new family of hybrid virophages from an animal gut metagenome (2015) (0)
- Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems (2015) (0)
- Subject Index Vol. 5, 2003 (2003) (0)
- Reconstruction of the evolution of microbial defense systems (2017) (0)
- Reviewer acknowledgement (2015) (0)
- Figure 3.8, Results of the CD-search of the pppGpp synthetase RelA from Bacillus subtilis (O54408, RELA_BACSU) (2003) (0)
- Introduction: Personal Interludes (2003) (0)
- Hypervariable Proteins in Microbes (2019) (0)
- 17-kDA fragment of hedgehog C-terminal autoprocessing domain (1997) (0)
- Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis (2018) (0)
- Deep phylogeny of cancer drivers and compensatory mutations (2020) (0)
- Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions (2017) (0)
- Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes (2020) (0)
- Conservation versus parallel gains in intron evolution (2005) (0)
- Insights into protein evolution landscapes from folding models (2011) (0)
- Faculty Opinions recommendation of Chalcone isomerase family and fold: no longer unique to plants. (2004) (0)
- CRYSTAL STRUCTURE OF B. SUBTILIS MAF PROTEIN COMPLEXED WITH D-(UTP) (2000) (0)
- Mutator Model with Migration (2023) (0)
- Structure-based insights into evolution of rhodopsins (2021) (0)
- Erratum for Benler et al., “Cargo Genes of Tn7-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes” (2022) (0)
- Thermodynamic selection: mechanisms and scenarios (2022) (0)
- CRISPR: a new principle of genome engineering linked to conceptual shifts in evolutionary biology (2019) (0)
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Other Resources About Eugene Koonin
What Schools Are Affiliated With Eugene Koonin?
Eugene Koonin is affiliated with the following schools:
- Moscow State University
- University of Sheffield
- University of Oxford
- University of Regensburg
- Loyola University Chicago
- Uniformed Services University of the Health Sciences
- University of St Andrews
- Oregon State University
- Umeå University
- Michigan State University
- University of Washington
- Texas A&M University
- University of Texas Southwestern Medical Center