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DNA polymerase swapping in Caudoviricetes bacteriophages.
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- Virology Journal, 2024, v. 21, n. 1, p. 1, doi. 10.1186/s12985-024-02482-z
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- Article
Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.
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- BMC Biology, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12915-024-01937-7
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- Article
Defence systems and horizontal gene transfer in bacteria.
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- Environmental Microbiology, 2024, v. 26, n. 4, p. 1, doi. 10.1111/1462-2920.16630
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- Article
Addendum: Cellular differentiation into hyphae and spores in halophilic archaea.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-44821-2
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- Article
Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-44806-1
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- Article
Unidirectional gene pairs in archaea and bacteria require overlaps or very short intergenic distances for translational coupling via termination-reinitiation and often encode subunits of heteromeric complexes.
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- Frontiers in Microbiology, 2023, p. 1, doi. 10.3389/fmicb.2023.1291523
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- Article
Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems.
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- Nucleic Acids Research, 2023, v. 51, n. 15, p. 8150, doi. 10.1093/nar/gkad495
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- Article
Cellular differentiation into hyphae and spores in halophilic archaea.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37389-w
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- Article
Host age structure reshapes parasite symbiosis: collaboration begets pathogens, competition begets virulent mutualists.
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- Biology Direct, 2022, v. 17, n. 1, p. 1, doi. 10.1186/s13062-022-00343-9
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- Article
Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales.
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- Viruses (1999-4915), 2022, v. 14, n. 9, p. 1842, doi. 10.3390/v14091842
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Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions.
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- Biology Direct, 2022, v. 17, n. 1, p. 1, doi. 10.1186/s13062-022-00337-7
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- Article
Molecular adaptations during viral epidemics.
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- EMBO Reports, 2022, v. 23, n. 8, p. 1, doi. 10.15252/embr.202255393
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- Article
A Novel Flavi-like Virus in Alfalfa (Medicago sativa L.) Crops along the Snake River Valley.
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- Viruses (1999-4915), 2022, v. 14, n. 6, p. N.PAG, doi. 10.3390/v14061320
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- Article
tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism.
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- Nucleic Acids Research, 2022, v. 50, n. 8, p. 4601, doi. 10.1093/nar/gkac271
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- Article
Phylogenomic analysis of the diversity of graspetides and proteins involved in their biosynthesis.
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- Biology Direct, 2022, v. 17, n. 1, p. 1, doi. 10.1186/s13062-022-00320-2
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- Article
A novel group of negative-sense RNA viruses associated with epizootics in managed and free-ranging freshwater turtles in Florida, USA.
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- PLoS Pathogens, 2022, v. 18, n. 3, p. 1, doi. 10.1371/journal.ppat.1010258
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- Article
A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains.
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- Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.721392
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- Article
Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21350-w
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- Article
Assessment of assumptions underlying models of prokaryotic pangenome evolution.
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- BMC Biology, 2021, v. 19, n. 1, p. 1, doi. 10.1186/s12915-021-00960-2
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- Article
COG database update: focus on microbial diversity, model organisms, and widespread pathogens.
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- Nucleic Acids Research, 2021, v. 49, n. D1, p. D274, doi. 10.1093/nar/gkaa1018
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- Article
Evolution of DNA packaging in gene transfer agents.
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- Virus Evolution, 2021, v. 7, n. 1, p. 1, doi. 10.1093/ve/veab015
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Seeker: alignment-free identification of bacteriophage genomes by deep learning.
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- Nucleic Acids Research, 2020, v. 48, n. 21, p. e121, doi. 10.1093/nar/gkaa856
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Prediction of the incubation period for COVID-19 and future virus disease outbreaks.
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- BMC Biology, 2020, v. 18, n. 1, p. 1, doi. 10.1186/s12915-020-00919-9
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- Article
Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes.
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- BMC Biology, 2020, v. 18, n. 1, p. N.PAG, doi. 10.1186/s12915-020-00885-2
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Deep phylogeny of cancer drivers and compensatory mutations.
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- Communications Biology, 2020, v. 3, n. 1, p. N.PAG, doi. 10.1038/s42003-020-01276-7
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Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense.
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- Nucleic Acids Research, 2020, v. 48, n. 16, p. 8828, doi. 10.1093/nar/gkaa635
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- Article
Machine-learning approach expands the repertoire of anti-CRISPR protein families.
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- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17652-0
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- Article
Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes.
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- Communications Biology, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42003-020-1014-1
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- Article
Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability.
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- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15094-2
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- Article
Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence.
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- Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-13429-2
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- Article
Systematic prediction of functionally linked genes in bacterial and archaeal genomes.
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- Nature Protocols, 2019, v. 14, n. 10, p. 3013, doi. 10.1038/s41596-019-0211-1
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- Article
Translational coupling via termination-reinitiation in archaea and bacteria.
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- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-11999-9
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- Article
Microbial genome analysis: the COG approach.
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- Briefings in Bioinformatics, 2019, p. 1063, doi. 10.1093/bib/bbx117
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- Article
Integrated mobile genetic elements in Thaumarchaeota.
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- Environmental Microbiology, 2019, v. 21, n. 6, p. 2056, doi. 10.1111/1462-2920.14564
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- Article
Towards functional characterization of archaeal genomic dark matter.
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- Biochemical Society Transactions, 2019, v. 47, n. 1, p. 389, doi. 10.1042/BST20180560
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- Article
Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve.
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- Biology Direct, 2018, v. 13, n. 1, p. N.PAG, doi. 10.1186/s13062-018-0230-9
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- Article
Escherichia coli ItaT is a type II toxin that inhibits translation by acetylating isoleucyl-tRNAIle.
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- Nucleic Acids Research, 2018, v. 46, n. 15, p. 7873, doi. 10.1093/nar/gky560
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- Article
Estimation of universal and taxon-specific parameters of prokaryotic genome evolution.
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- PLoS ONE, 2018, v. 13, n. 4, p. 1, doi. 10.1371/journal.pone.0195571
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- Article
Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia".
- Published in:
- Genes, 2018, v. 9, n. 2, p. 28, doi. 10.3390/genes9020028
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Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states.
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- Biology Direct, 2017, v. 12, p. 1, doi. 10.1186/s13062-017-0202-5
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- Article
Diverse functions of homologous actin isoforms are defined by their nucleotide, rather than their amino acid sequence.
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- eLife, 2017, p. 1, doi. 10.7554/eLife.31661
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- Article
Phylogenomics of Cas4 family nucleases.
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- BMC Evolutionary Biology, 2017, v. 17, p. 1, doi. 10.1186/s12862-017-1081-1
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- Article
Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families.
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- Genome Biology & Evolution, 2017, v. 9, n. 10, p. 2791, doi. 10.1093/gbe/evx189
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- Article
Net Evolutionary Loss of Residue Polarity in Drosophilid Protein Cores Indicates Ongoing Optimization of Amino Acid Composition.
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- Genome Biology & Evolution, 2017, v. 9, n. 10, p. 2879, doi. 10.1093/gbe/evx191
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- Article
‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ.
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- Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-00104-7
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- Article
Early vertebrate origin and diversification of small transmembrane regulators of cellular ion transport.
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- Journal of Physiology, 2017, v. 595, n. 14, p. 4611, doi. 10.1113/JP274254
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Reconstruction of the evolution of microbial defense systems.
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- BMC Evolutionary Biology, 2017, v. 17, p. 1, doi. 10.1186/s12862-017-0942-y
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- Article
ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. D1, p. D210, doi. 10.1093/nar/gkw934
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- Article
Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins.
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- Nature Communications, 2016, v. 7, n. 11, p. 13570, doi. 10.1038/ncomms13570
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- Article
Inevitability of Genetic Parasites.
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- Genome Biology & Evolution, 2016, v. 8, n. 9, p. 2867, doi. 10.1093/gbe/evw193
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- Article