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

Trimmomatic: a flexible trimmer for Illumina sequence data

Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works

UCSF Chimera—A visualization system for exploratory research and analysis

Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,260 · see citing works

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works

Features and development of Coot

Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. D. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 27,510 · see citing works

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 25,691 · see citing works

<i>PHENIX</i> : a comprehensive Python-based system for macromolecular structure solution

Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716 · see citing works

<i>MolProbity</i> : all-atom structure validation for macromolecular crystallography

Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115 · see citing works

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288 · see citing works

WebLogo: A Sequence Logo Generator: Figure 1Preprint

Crooks, G. E., Hon, G. C., Chandonia, J., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,433 · see citing works

Prodigal: prokaryotic gene recognition and translation initiation site identification

Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,426 · see citing works

Overview of the <i>CCP</i> 4 suite and current developments

Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910045749 · Cited by 12,353 · see citing works

FIMO: scanning for occurrences of a given motif

Grant, C. E., Bailey, T. L., & Noble, W. S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr064 · Cited by 4,247 · see citing works

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

Krissinel, E., & Henrick, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904026460 · Cited by 3,785 · see citing works

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

Liao, Y., Smyth, G. K., & Shi, W. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz114 · Cited by 2,965 · see citing works

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

Laslett, D. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh152 · Cited by 2,714 · see citing works

Integration, scaling, space-group assignment and post-refinement

Kabsch, W. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909047374 · Cited by 2,494 · see citing works

The Buccaneer software for automated model building. 1. Tracing protein chains

Cowtan, K. D. (2006) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444906022116 · Cited by 1,834 · see citing works

Structural Mechanism for Rifampicin Inhibition of Bacterial RNA Polymerase

Campbell, E. A., Korzheva, N., Mustaev, A., Murakami, K., Nair, S., Goldfarb, A., & Darst, S. A. (2001) · Cell · doi:10.1016/s0092-8674(01)00286-0 · Cited by 1,556 · see citing works

Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution

Cramer, P., Bushnell, D. A., & Kornberg, R. D. (2001) · Science · doi:10.1126/science.1059493 · Cited by 1,247 · see citing works

Experimental phasing with SHELXC/D/E: combining chain tracing with density modification

Sheldrick, G. M. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909038360 · Cited by 1,093 · see citing works

Crystal Structure of Thermus aquaticus Core RNA Polymerase at 3.3 Å Resolution

Zhang, G., Campbell, E. A., Minakhin, L., Richter, C., Severinov, K., & Darst, S. A. (1999) · Cell · doi:10.1016/s0092-8674(00)81515-9 · Cited by 813 · see citing works

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

Dutilh, B. E., Cassman, N. A., McNair, K., Sanchez, S. E., Silva, A. E. T., Boling, L., Barr, J. J., Speth, D. R., Seguritan, V., Aziz, R. K., et al. (2014) · Nature Communications · doi:10.1038/ncomms5498 · Cited by 799 · see citing works

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution

Vassylyev, D. G., Sekine, S., Laptenko, O., Lee, J., Vassylyeva, M. N., Borukhov, S. I., & Yokoyama, S. (2002) · Nature · doi:10.1038/nature752 · Cited by 744 · see citing works

HKL2MAP: a graphical user interface for macromolecular phasing withSHELXprograms

Pape, T., & Schneider, T. R. (2004) · Journal of Applied Crystallography · doi:10.1107/s0021889804018047 · Cited by 743 · see citing works

Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase

Cogoni, C., & Macino, G. (1999) · Nature · doi:10.1038/20215 · Cited by 664 · see citing works

Origins and evolution of eukaryotic RNA interference

Shabalina, S. A., & Koonin, E. V. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.06.005 · Cited by 559 · see citing works

Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.

Wang, D., Bushnell, D., Westover, K., Kaplan, C., & Kornberg, R. (2006) · Cell · doi:10.1016/j.cell.2006.11.023 · Cited by 452 · see citing works

Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS

Kettenberger, H., Armache, K., & Cramer, P. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.11.040 · Cited by 437 · see citing works

Evolution of multisubunit RNA polymerases in the three domains of life

Werner, F., & Grohmann, D. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2507 · Cited by 431 · see citing works

Recent developments in classical density modification

Cowtan, K. D. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744490903947x · Cited by 422 · see citing works

Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution

Paget, M. S. B. (2015) · Biomolecules · doi:10.3390/biom5031245 · Cited by 387 · see citing works

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

Shkoporov, A. N., Khokhlova, E. V., Fitzgerald, C. B., Stockdale, S. R., Draper, L. A., Ross, R. P., & Hill, C. (2018) · Nature Communications · doi:10.1038/s41467-018-07225-7 · Cited by 314 · see citing works

Structural basis for substrate loading in bacterial RNA polymerase

Vassylyev, D., Vassylyeva, M. N., Zhang, J.-W., Palangat, M., Artsimovitch, I., & Landick, R. (2007) · Nature · doi:10.1038/nature05931 · Cited by 306 · see citing works

Benchmarking fold detection by DaliLite v.5

Holm, L. (2019) · Bioinform. · doi:10.1093/bioinformatics/btz536 · Cited by 305 · see citing works

Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

Guerin, E., Shkoporov, A. N., Stockdale, S. R., Clooney, A. G., Ryan, F. J., Sutton, T., Draper, L. A., González-Tortuero, E., Ross, R. P., & Hill, C. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.10.002 · Cited by 297 · see citing works

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

Yutin, N., Makarova, K., Gussow, A. B., Krupovic, M., Segall, A., Edwards, R., & Koonin, E. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0053-y · Cited by 270 · see citing works

"Dark" Purkinje cells of the cerebellar cortex.

Leranth, C., & Hámori, J. (1970) · PubMed · Cited by 264 · see citing works

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

Iyer, L. M., Koonin, E. V., & Aravind, L. (2003) · BMC Structural Biology · doi:10.1186/1472-6807-3-1 · Cited by 261 · see citing works

Ligand binding and protein dynamics: a fluorescence depolarization study of aspartate transcarbamylase from Escherichia coli

Royer, C. A., Tauc, P., Hervé, G., & Brochon, J. (1987) · Biochemistry · doi:10.1021/bi00394a027 · Cited by 238 · see citing works

RNA polymerase I structure and transcription regulation

Engel, C., Sainsbury, S., Cheung, A. C. M., Kostrewa, D., & Cramer, P. (2013) · Nature · doi:10.1038/nature12712 · Cited by 218 · see citing works

Bacteriophage origins of mitochondrial replication and transcription proteins

Shutt, T. E., & Gray, M. W. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.11.007 · Cited by 212 · see citing works

Crystal structure of the 14-subunit RNA polymerase I

Fernández‐Tornero, C., Moreno‐Morcillo, M., Rashid, U. J., Taylor, N. M. I., Ruiz, F. M., Gruene, T., Legrand, P., Steuerwald, U., & Müller, C. W. (2013) · Nature · doi:10.1038/nature12636 · Cited by 194 · see citing works

Large Variabilities in Host Strain Susceptibility and Phage Host Range Govern Interactions between Lytic Marine Phages and Their Flavobacterium Hosts

Holmfeldt, K., Middelboe, M., Nybroe, O., & Riemann, L. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01399-07 · Cited by 194 · see citing works

Twelve previously unknown phage genera are ubiquitous in global oceans

Holmfeldt, K., Solonenko, N., Shah, M. B., Corrier, K., Riemann, L., VerBerkmoes, N. C., & Sullivan, M. B. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305956110 · Cited by 191 · see citing works

Crucial Role of the RNA:DNA Hybrid in the Processivity of Transcription

Sidorenkov, I. V., Komissarova, N. V., & Kashlev, M. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80113-6 · Cited by 190 · see citing works

Proteolytic and Conformational Control of Virus Capsid Maturation: The Bacteriophage HK97 System

Conway, J. F., Duda, R. L., Cheng, N., Hendrix, R. W., & Steven, A. C. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0538 · Cited by 182 · see citing works

The Proteolytic Regulation of Virus Cell Entry by Furin and Other Proprotein Convertases

Izaguirre, G. (2019) · Viruses · doi:10.3390/v11090837 · Cited by 169 · see citing works

Retroviral proteases and their roles in virion maturation

Konvalinka, J., Kräusslich, H.-G., & Müller, B. (2015) · Virology · doi:10.1016/j.virol.2015.03.021 · Cited by 148 · see citing works

Molecular Evolution of Multisubunit RNA Polymerases: Structural Analysis

Lane, W. J., & Darst, S. A. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.10.063 · Cited by 134 · see citing works

Using SAD data inPhaser

Read, R. J., & McCoy, A. J. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910051371 · Cited by 112 · see citing works

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

Koonin, E. V., & Yutin, N. (2020) · Trends in Microbiology · doi:10.1016/j.tim.2020.01.010 · Cited by 101 · see citing works

The Structure of an RNAi Polymerase Links RNA Silencing and Transcription

Salgado, P. S., Koivunen, M. R. L., Makeyev, E. V., Bamford, D. H., Stuart, D. I., & Grimes, J. M. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040434 · Cited by 92 · see citing works

The DNA/RNA-Dependent RNA Polymerase QDE-1 Generates Aberrant RNA and dsRNA for RNAi in a Process Requiring Replication Protein A and a DNA Helicase

Lee, H.-C., Aalto, A. P., Yang, Q., Chang, S.-S., Huang, G., Fisher, D. W., Cha, J., Poranen, M. M., Bamford, D. H., & Liu, Y. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000496 · Cited by 84 · see citing works

Structural evolution of multisubunit RNA polymerases

Werner, F. (2008) · Trends in Microbiology · doi:10.1016/j.tim.2008.03.008 · Cited by 71 · see citing works

Structural Basis for DNA-Hairpin Promoter Recognition by the Bacteriophage N4 Virion RNA Polymerase

Gleghorn, M. L., Davydova, E. K., Rothman‐Denes, L. B., & Murakami, K. S. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.11.010 · Cited by 47 · see citing works

Structure and Function of RNA Polymerases and the Transcription Machineries

Griesenbeck, J., Tschochner, H., & Grohmann, D. (2017) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-319-46503-6_9 · Cited by 37 · see citing works

The Extended “Two-Barrel” Polymerases Superfamily: Structure, Function and Evolution

Sauguet, L. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.05.017 · Cited by 30 · see citing works

X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase

Murakami, K. S., Davydova, E. K., & Rothman‐Denes, L. B. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712325105 · Cited by 26 · see citing works

The Bridge Helix of RNA Polymerase Acts as a Central Nanomechanical Switchboard for Coordinating Catalysis and Substrate Movement

Weinzierl, R. O. J. (2011) · Archaea · doi:10.1155/2011/608385 · Cited by 26 · see citing works

A non-canonical multisubunit RNA polymerase encoded by the AR9 phage recognizes the template strand of its uracil-containing promoters

Sokolova, M. L., Borukhov, S. I., Lavysh, D., Артамонова, Т. О., Khodorkovskii, M. A., & Severinov, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx264 · Cited by 22 · see citing works

In Vitro Activities of the Multifunctional RNA Silencing Polymerase QDE-1 of Neurospora crassa*

Aalto, A. P., Poranen, M. M., Grimes, J. M., Stuart, D. I., & Bamford, D. H. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.139121 · Cited by 17 · see citing works

Highly accurate protein structure prediction with AlphaFold

Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works

Mechanisms and clinical importance of bacteriophage resistance

Egido, J. E., Costa, A. R., Aparicio-Maldonado, C., Haas, P., & Brouns, S. J. J. (2021) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuab048 · Cited by 326 · see citing works

Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features

Yutin, N., Benler, S., Shmakov, S., Wolf, Y. I., Tolstoy, I., Rayko, M., Antipov, D., Pevzner, P. A., & Koonin, E. V. (2021) · Nature Communications · doi:10.1038/s41467-021-21350-w · Cited by 166 · see citing works

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

Koonin, E. V., Krupovìč, M., Ishino, S., & Ishino, Y. (2020) · BMC Biology · doi:10.1186/s12915-020-00800-9 · Cited by 110 · see citing works

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

Shkoporov, A. N., Khokhlova, E. V., Stephens, N., Hueston, C. M., Seymour, S., Hryckowian, A. J., Scholz, D., Ross, R. P., & Hill, C. (2021) · BMC Biology · doi:10.1186/s12915-021-01084-3 · Cited by 115 · see citing works

Implications of <i>AlphaFold</i> 2 for crystallographic phasing by molecular replacement

McCoy, A. J., Sammito, M. D., & Read, R. J. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798321012122 · Cited by 104 · see citing works

The healthy human virome: from virus–host symbiosis to disease

Koonin, E. V., Dolja, V. V., & Krupovìč, M. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.02.002 · Cited by 86 · see citing works

Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts

Gulyaeva, A. A., Garmaeva, S., Ruigrok, R. A. A. A., Wang, D., Riksen, N. P., Netea, M. G., Wijmenga, C., Weersma, R. K., Fu, J., Vila, A. V., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2021.110204 · Cited by 56 · see citing works

The Current Landscape of Phage–Antibiotic Synergistic (PAS) Interactions

Supina, B. S. I., & Dennis, J. J. (2025) · Antibiotics · doi:10.3390/antibiotics14060545 · Cited by 62 · see citing works

Structural atlas of a human gut crassvirus

Bayfield, O. W., Shkoporov, A. N., Yutin, N., Khokhlova, E. V., Smith, J. L. R., Hawkins, D. E. D. P., Koonin, E. V., Hill, C., & Antson, A. A. (2023) · Nature · doi:10.1038/s41586-023-06019-2 · Cited by 48 · see citing works

Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome?

Smith, L. A., Goldobina, E., Govi, B., & Shkoporov, A. N. (2023) · Biomolecules · doi:10.3390/biom13040584 · Cited by 49 · see citing works

Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2

Fukudome, A., Singh, J., Mishra, V., Reddem, E. R., Martínez-Márquez, F., Wenzel, S., Yan, R., Shiozaki, M., Yu, Z., Wang, J. C., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2115899118 · Cited by 40 · see citing works

Target Classification in the 14th Round of the Critical Assessment of Protein Structure Prediction (CASP14).

Kinch, L. N., Schaeffer, D. R., Kryshtafovych, A., & Grishin, N. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26202 · Cited by 38 · see citing works

Physics‐based protein structure refinement in the era of artificial intelligence

Heo, L., Janson, G., & Feig, M. (2021) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26161 · Cited by 31 · see citing works

Atomistic basis of force generation, translocation, and coordination in a viral genome packaging motor

Pajak, J., Dill, E. A., Reyes-Aldrete, E., White, M. A., Kelch, B. A., Jardine, P. J., Arya, G., & Morais, M. C. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab372 · Cited by 29 · see citing works

Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes

Benler, S., & Koonin, E. V. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.821197 · Cited by 28 · see citing works

Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14

Li, Y., Zhang, C., Zheng, W. H., Zhou, X., Bell, E. W., Yu, D., & Zhang, Y. (2021) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26211 · Cited by 23 · see citing works

Structure of the recombinant RNA polymerase from African Swine Fever Virus

Pilotto, S., Sýkora, M., Cackett, G., Dulson, C., & Werner, F. (2024) · Nature Communications · doi:10.1038/s41467-024-45842-7 · Cited by 21 · see citing works

Exploring the transcriptional landscape of phage–host interactions using novel high-throughput approaches

Putzeys, L., Wicke, L., Brandão, A., Boon, M., Pires, D. P., Azeredo, J., Vogel, J., Lavigne, R., & Gerovac, M. (2024) · Current Opinion in Microbiology · doi:10.1016/j.mib.2023.102419 · Cited by 20 · see citing works

Fishing for phages in metagenomes: what do we catch, what do we miss?

Benler, S., & Koonin, E. V. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.05.008 · Cited by 19 · see citing works

The cellular RNA ‐dependent RNA polymerases in plants

Du, X. (2024) · New Phytologist · doi:10.1111/nph.20046 · Cited by 14 · see citing works

Pectobacterium versatile Bacteriophage Possum: A Complex Polysaccharide-Deacetylating Tail Fiber as a Tool for Host Recognition in Pectobacterial Schitoviridae

Lukianova, A. A., Evseev, P. V., Shneider, M. M., Dvoryakova, E. A., Tokmakova, A. D., Shpirt, A. M., Kabilov, M. R., Obraztsova, E. A., Shashkov, A. S., Ignatov, A. N., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231911043 · Cited by 10 · see citing works

Asymmetric structure of podophage N4 from the Schitoviridae family reveals a type of tube-sheath short-tail architecture

Zheng, J., Pang, H., Xiao, H. J., Zhou, J., Liu, Z., Chen, W., & Liu, H. (2025) · Structure · doi:10.1016/j.str.2025.04.008 · Cited by 9 · see citing works

Tail-Tape-Fused Virion and Non-Virion RNA Polymerases of a Thermophilic Virus

Chaban, A., Станиславович, М. Л., Goldobina, E., Bae, B., Hao, Y., Borukhov, S. I., Putzeys, L., Boon, M., Kabinger, F., Lavigne, R., et al. (2022) · Nature Communications · doi:10.1038/s41467-023-44630-z · Cited by 9 · see citing works

Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1

Cui, R., Li, H., Zhao, J., Li, X., Gan, J., & Ma, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac727 · Cited by 7 · see citing works

Genome Analysis of Epsilon CrAss-like Phages

Babkin, I. V., Tikunov, A. Y., Константинович, Б. И., Витальевна, М. В., & Викторовна, Т. Н. (2024) · Viruses · doi:10.3390/v16040513 · Cited by 5 · see citing works

Genomics and Geographic Diversity of Bacteriophages Associated With Endosymbionts in the Guts of Workers and Alates of Coptotermes Species (Blattodea: Rhinotermitidae)

Chen, J., Gissendanner, C. R., Tikhe, C. V., Li, H., Sun, Q., & Husseneder, C. (2022) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2022.881538 · Cited by 5 · see citing works

Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion

Li, Z., Fan, H.-F., & Ding, W. (2023) · IUCrJ · doi:10.1107/s2052252523010291 · Cited by 4 · see citing works

Function of the bacteriophage P2 baseplate central spike Apex domain in the infection processPreprint

Miller, J. M., Knyazhanskaya, E. S., Buth, S. A., Prokhorov, N. S., & Leiman, P. G. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.25.529910 · Cited by 4 · see citing works

Unique genomic features of crAss-like phages, the dominant component of the human gut viromePreprint

Yutin, N., Benler, S., Shmakov, S., Wolf, Y. I., Tolstoy, I., Rayko, M., Antipov, D., Pevzner, P. A., & Koonin, E. V. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.20.212944 · Cited by 3 · see citing works

Zeta CrAss-like Phages, a Separate Phage Family Using a Variety of Adaptive Mechanisms to Persist in Their Hosts

Babkin, I. V., Fedorets, V. A., Tikunov, A. Y., Константинович, Б. И., Panina, E. A., & Викторовна, Т. Н. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26167694 · Cited by 1 · see citing works

Ancient Protein Folds in RNA Polymerase and Ribosomes

Yagi, S., & Tagami, S. (2025) · Nucleic acids and molecular biology · doi:10.1007/978-3-032-03300-0_2 · Cited by 1 · see citing works

Whole-Genome Sequencing of Sinorhizobium Phage AP-202, a Novel Siphovirus from Agricultural Soil

Roumiantseva, M. L., Kozlova, A. P., Muntyan, V. S., Vladimirova, M. E., Saksaganskaia, A. S., Gorshkov, A. N., Kabilov, M. R., & Симаров, Б. В. (2026) · Data · doi:10.3390/data11010015 · Cited by 1 · see citing works

Effect of Aeromonas hydrophila infected on metabolomic response and gut microbial 16S rRna of Charybdis japonicaPreprint

Han, M., Zhu, C., Zakaria, Z., Gao, T., Yang, Y., Zhang, T., Ji, F., & Jiang, Q. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.25.465830 · Cited by 1 · see citing works

Genome Analysis of Epsilon Crass-like Phages Revealed That Some of Them Can Be Temperate Phages Encoding Atypical Diversity-Generating RetroelementsPreprint

Babkin, I. V., Tikunov, A. Y., Константинович, Б. И., Витальевна, М. В., & Викторовна, Т. Н. (2023) · Preprints.org · doi:10.20944/preprints202312.0623.v1 · Cited by 1 · see citing works

The spike tip protein of bacteriophage T4Preprint

Mattenberger, Y., Knyazhanskaya, E. S., Shneider, M. M., Buth, S. A., Nazarov, S., Robins, W. P., Leiman, P. G., & Belin, D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.28.672839 · Cited by 1 · see citing works

Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold.

Arulanandam, A. J. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.740477161.793587548

Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold.

Chakraborty, S. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.740477161.793587538

The spike tip protein of bacteriophage T4Preprint

Mattenberger, Y., Knyazhanskaya, E. S., Shneider, M. M., Buth, S. A., Nazarov, S., Robins, W. P., Leiman, P. G., & Belin, D. (2026) · eLife · doi:10.7554/elife.109535

The spike tip protein of bacteriophage T4Preprint

Mattenberger, Y., Knyazhanskaya, E. S., Shneider, M. M., Buth, S. A., Nazarov, S., Robins, W. P., Leiman, P. G., & Belin, D. (2026) · eLife · doi:10.7554/elife.109535.1

Boreal and subarctic freshwaters harbour a diversity of jumbophages

Niemi, M., Karneyeva, K., Sundberg, L., Oksanen, H. M., & Laanto, E. (2026) · ISME Communications · doi:10.1093/ismeco/ycag239

A Comprehensive Review of the Effect of Diet on Intestinal Phages

Zhang, Z., Zhao, X., Yu, B., & Cui, B. (2026) · Food Reviews International · doi:10.1080/87559129.2026.2669386

Origin and Evolution of Transcription Elongation Complexes

Osina, E. V., Korovina, A. N., Gerasimova, N. S., Sokolova, O. S., & Stanishneva-Konovalova, T. B. (2026) · BIOPHYSICS · doi:10.1134/s0006350926700041

Primer: Functions and evolution of viral proteins

Koonin, E. V., & Krupovìč, M. (2026) · Journal of Virology · doi:10.1128/jvi.01202-26

FAIRsharing record for: AlphaFold Protein Structure Database

FAIRsharing Team, & Liang, Y. (2025) · FAIRsharing.org · doi:10.25504/fairsharing.246086

Tail-Tape-Fused Virion and Non-Virion RNA Polymerases of a Thermophilic VirusPreprint

Chaban, A., Станиславович, М. Л., Goldobina, E., Bae, B., Hao, Y., Borukhov, S. I., Putzeys, L., Boon, M., Lavigne, R., Makarova, K. S., et al. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4309039

The phage RNA polymerases are related to DNA polymerases and reverse transcriptases

McAllister, W. T., & Raskin, C. A. (1993) · Molecular Microbiology · doi:10.1111/j.1365-2958.1993.tb00897.x · Cited by 92 · see citing works

Tail-Tape-Fused Virion and Non-Virion RNA Polymerases of a Thermophilic Virus

Chaban, A., Станиславович, М. Л., Goldobina, E., Bae, B., Hao, Y., Borukhov, S. I., Putzeys, L., Boon, M., Kabinger, F., Lavigne, R., et al. (2022) · Nature Communications · doi:10.1038/s41467-023-44630-z · Cited by 9 · see citing works

The phage N4 virion RNA polymerase catalytic domain is related to single‐subunit RNA polymerases

Kazmierczak, K. M., Davydova, E. K., MUSTAEV, A. A., & Rothman‐Denes, L. B. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf584 · Cited by 54 · see citing works

X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase

Murakami, K. S., Davydova, E. K., & Rothman‐Denes, L. B. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712325105 · Cited by 26 · see citing works