This page is not always up to date, but you can check Google Scholar for more up to date publications and citations: 

https://scholar.google.com/citations?user=UxV_kBMAAAAJ

Preprints:

• LoVis4u: Locus Visualisation tool for comparative genomics Artyom A. Egorov, Gemma C. Atkinson https://www.biorxiv.org/content/10.1101/2024.09.11.612399v1

• Systematic annotation of hyper-variability hotspots in phage genomes and plasmids
  Artyom A. Egorov, Vasili Hauryliuk, Gemma C. Atkinson https://www.biorxiv.org/content/10.1101/2024.10.15.618418v1

Publications and links:

• Mechanisms of neutralization of toxSAS from toxin-antitoxin modules. Dominguez-Molina L, Kurata T, Cepauskas A, Echemendia-Blanco D, Zedek S, Talavera-Perez A, Atkinson GC, Hauryliuk V, Garcia-Pino A. Nat Chem Biol. 2024 Jun 4. doi: 10.1038/s41589-024-01630-4
  
  
• Mechanism of phage sensing and restriction by toxin-antitoxin-chaperone systems. Mets T, Kurata T, Ernits K, Johansson MJO, Craig SZ, Evora GM, Buttress JA, Odai R, Wallant KC, Nakamoto JA, Shyrokova L, Egorov AA, Doering CR, Brodiazhenko T, Laub MT, Tenson T, Strahl H, Martens C, Harms A, Garcia-Pino A, Atkinson GC, Hauryliuk V. Cell Host Microbe. 2024 Jul 10;32(7):1059-1073.e8. doi: 10.1016/j.chom.2024.05.003
  
  
• Activity, structure, and diversity of Type II proline-rich antimicrobial peptides from insects. Huang W, Baliga C, Aleksandrova EV, Atkinson G, Polikanov YS, Vázquez-Laslop N, Mankin AS.EMBO Rep. 2024 Nov;25(11):5194-5211. doi: 10.1038/s44319-024-00277-5
  
  
• A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases Tesson F, Planel R, Egorov A, Georjon H, Vaysset H, Brancotte B, Néron B, Mordret E, Bernheim A, Atkinson GC, Cury J.
  10.24072/pcjournal.470 – Peer Community Journal, Volume 4 (2024), article no. e91.
  
  
• Peptidyl-tRNA hydrolase is the nascent chain release factor in bacterial ribosome-associated quality control. Svetlov MS, Dunand CF, Nakamoto JA, Atkinson GC, Safdari HA, Wilson DN, Vázquez-Laslop N, Mankin AS. Mol Cell. 2024 Feb 15;84(4):715-726.e5. doi: 10.1016/j.molcel.2023.12.002. Epub 2024 Jan 5.PMID: 38183984
  
  
• Toxic Small Alarmone Synthetase FaRel2 inhibits translation by pyrophosphorylating tRNA^Gly and tRNA^Thr. Kurata T, Takegawa M, Ohira T, Syroegin EA, Atkinson GC, Johansson MJO, Polikanov YS, Garcia-Pino A, Suzuki T, Hauryliuk V. Sci Adv. 2024 Nov 15;10(46):eadr9624. doi: 10.1126/sciadv.adr9624
  
  
• A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis. Takada H, Paternoga H, Fujiwara K, Nakamoto JA, Park EN, Dimitrova-Paternoga L, Beckert B, Saarma M, Tenson T, Buskirk AR, Atkinson GC, Chiba S, Wilson DN, Hauryliuk V. Nucleic Acids Res. 2024 Aug 12;52(14):8483-8499. doi: 10.1093/nar/gkae399.
  
  
• Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it. Aleksandrova EV, Wu KJY, Tresco BIC, Syroegin EA, Killeavy EE, Balasanyants SM, Svetlov MS, Gregory ST, Atkinson GC, Myers AG, Polikanov YS. Nat Chem Biol. 2024 Jul;20(7):867-876. doi: 10.1038/s41589-023-01525-w.
  
  
• Resolution of ribosomal stalling by EF-P and ABCF ATPases YfmR and YkpA/YbiT. Takada H, Fujiwara K, Atkinson GC, Chiba S, Hauryliuk V.Nucleic Acids Res. 2024 Sep 9;52(16):9854-9866. doi: 10.1093/nar/gkae556.
  
  
• The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems. Ernits K, Saha CK, Brodiazhenko T, Chouhan B, Shenoy A, Buttress JA, Duque-Pedraza JJ, Bojar V, Nakamoto JA, Kurata T, Egorov AA, Shyrokova L, Johansson MJO, Mets T, Rustamova A, Džigurski J, Tenson T, Garcia-Pino A, Strahl H, Elofsson A, Hauryliuk V, Atkinson GC. Proc Natl Acad Sci U S A. 2023 Aug 15;120(33):e2305393120. doi: 10.1073/pnas.2305393120
  
  
• Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR. Obana N, Takada H, Crowe-McAuliffe C, Iwamoto M, Egorov AA, Wu KJY, Chiba S, Murina V, Paternoga H, Tresco BIC, Nomura N, Myers AG, Atkinson GC, Wilson DN, Hauryliuk V.Nucleic Acids Res. 2023 May 22;51(9):4536-4554.
  
  
• uORF4u: a tool for annotation of conserved upstream open reading frames Egorov AA and Atkinson GC Bioinformatics btad323 2023
  
  
• Direct activation of a bacterial innate immune system by a viral capsid protein. Zhang T, Tamman H, ’t Wallant KC, Kurata T, LeRoux M, Srikant S, Brodiazhenko T, Cepauskas A, Talavera A, Martens C, Atkinson GC, Hauryliuk V, Garcia-Pino A & Laub MT Nature 2022
  
  
• Structural basis for HflXr-mediated antibiotic resistance in Listeria monocytogenes. Koller TO, Turnbull KJ, Vaitkevicius K, Crowe-McAuliffe C, Roghanian M, Bulvas O, Nakamoto JA, Kurata T, Julius C, Atkinson GC, Johansson J, Hauryliuk V, Wilson DN.Nucleic Acids Res. 2022 Oct 28;50(19):11285-11300. doi: 10.1093/nar/gkac934
  
  
• Context-based sensing of orthosomycin antibiotics by the translating ribosome. Mangano K, Marks J, Klepacki D, Saha CK, Atkinson GC, Vázquez-Laslop N, Mankin AS.Nat Chem Biol. 2022 Nov;18(11):1277-1286. doi: 10.1038/s41589-022-01138-9.
  
  
• Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp. Takada H, Mandell ZF, Yakhnin H, Glazyrina A, Chiba S, Kurata T, Wu KJY, Tresco BIC, Myers AG, Atkinson GC, Babitzke P, Hauryliuk V. Nucleic Acids Res. 2022 Jun 24;50(11):6174-6189. doi: 10.1093/nar/gkac497.
  
  
• Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics. Crowe-McAuliffe C, Murina V, Turnbull KJ, Huch S, Kasari M, Takada H, Nersisyan L, Sundsfjord A, Hegstad K, Atkinson GC, Pelechano V, Wilson DN, Hauryliuk V.Nat Commun. 2022 Apr 6;13(1):1860. doi: 10.1038/s41467-022-29274-9.
  
  
• Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci. Mohamad M, Nicholson D, Saha CK, Hauryliuk V, Edwards TA, Atkinson GC, Ranson NA, O’Neill AJ. Nucleic Acids Res. 2022 50(4):2128-2142. doi: 10.1093/nar/gkac058.
  
  
  
• Panacea: a hyperpromiscuous antitoxin protein domain for the neutralisation of diverse toxin domains. Kurata T, Saha CK, Buttress JA, Mets T, Brodiazhenko T, Turnbull KJ, Awoyomi OF, Oliveira SRA, Jimmy S, Ernits K, Delannoy M, Persson K, Tenson T, Strahl H, Hauryliuk V, Atkinson GC PNAS 2022
  
  
• (p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains. Roghanian M, Van Nerom K, Takada H, Caballero-Montes J, Tamman H, Kudrin P, Talavera A, Dzhygyr I, Ekström S, Atkinson GC, Garcia-Pino A, Hauryliuk V. (2021) Molecular Cell, in press
  
  
• RelA-SpoT Homologue toxins modify the CCA end of tRNA to inhibit protein synthesis.Kurata T, Brodiazhenko T, Oliveira SRO, Roghanian M, Turnbull KJ, Ondřej Bulvas, Takada H, Pohl R, Garcia-Pino A, Rejman D, Tenson T, Atkinson GC, Hauryliuk V. (2021) Molecular Cell, in press
  
  
• Structural basis of resistance to lincosamide, streptogramin A, and pleuromutilin antibiotics by ABCF ATPases in Gram-positive pathogens. Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O’Neill A, Hauryliuk V, Wilson DN. Nature Communications, 2021 doi.org/10.1038/s41467-021-23753-1
  
  
• Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP.
  Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V. Mol Cell. 2020 Nov 19:S1097-2765(20)30780-2. doi: 10.1016/j.molcel.2020.11.002. 
  
  
• FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation. Saha CK, Pires RS, Brolin H, Delannoy M, Atkinson GC, Bioinformatics doi: 10.1093/bioinformatics/btaa788
  
  
• A holin/peptidoglycan hydrolase-dependent protein secretion system. 1. Palmer T, Finney A , Saha CK , Atkinson, GC, Sargent, F, Molecular Microbiology 2020 https://doi.org/10.1111/mmi.14599
  
  
• Elevated levels of VCA0117 in response to external signals activates type VI secretion in Vibrio cholerae A1552. Seibt H, Aung KM, Ishikawa T, Sjöström A, Atkinson GC, Wai SN, Shingler V, Accepted in Environmental Microbiology, 2020
  
  
• Target protection as a key antibiotic resistance mechanism. Wilson DN, Hauryliuk V, Atkinson GC , O’Neill AJ. Nat Rev Microbiol. 2020 Jun 25. doi: 10.1038/s41579-020-0386-z.
  
  
• A widespread toxin-antitoxin system exploiting growth control via alarmone signaling. Jimmy S, Saha CK, Kurata T, Stavropoulos C, Oliveira SRA, Koh A, Cepauskas A, Takada H, Rejman D, Tenson T, Strahl H, Garcia-Pino A, Hauryliuk V, Atkinson GC . Proc Natl Acad Sci U S A. 2020 May 12;117(19):10500-10510.
  
  
• The C-terminal RRM/ACT domain is crucial for fine-tuning the activation of ‘long’RelA-SpoT Homolog enzymes by ribosomal complexes Hiraku Takada, Mohammad Roghanian,Victoriia Murina, Ievgen Dzhygyr, Rikinori Murayama, Genki Akanuma, Atkinson GC , Abel Garcia-Pino, Vasili Hauryliuk Frontiers in Microbiology 2020 11
  
  
• A role for the Saccharomyces cerevisiae ABCF protein New1 during translation termination Villu Kasari, Agnieszka A. Pochopien, Tõnu Margus, Victoriia Murina, Yang Zhou, Tracy Nissan, Michael Graf, Jiří Nováček, Atkinson GC , Marcus J.O. Johansson, Daniel N. Wilson, Vasili Hauryliuk Nucleic Acids Res, 47 (16), 8807-8820 2019
  
  
• ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic Resistance: Structural and Functional Diversification across the Tree of Life. Murina V, Kasari M, Takada H, Hinnu M, Saha CK, Grimshaw JW, Seki T, Reith M, Putrinš M, Tenson T, Strahl H, Hauryliuk V,  Atkinson GC . J Mol Biol . 2018  doi: 10.1016/j.jmb.2018.12.013
  
  
• Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae. Kasari V, Margus T,  Atkinson GC , Johansson MJO, Hauryliuk V. Sci Rep . 2019 Feb 28;9(1):3037. doi: 10.1038/s41598-019-39403-y.
  
  
• Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR Crowe-McAuliffe C, Graf M, Huter P, Takada H, Abdelshahid M, Nováček J, Murina V, Atkinson GC , Hauryliuk V, Wilson DN. Proc Natl Acad Sci U S A . https://doi.org/10.1073/pnas.1808535115
  
  
• Antibiotic resistance ABCF proteins reset the peptidyl transferase centre of the ribosome to counter translational arrest Murina, V, Kasari, M, Hauryliuk V,  Atkinson GC . Nucleic Acids Research . gky050, https://doi.org/10.1093/nar/gky050
  
  
• Small Alarmone Synthetases as novel bacterial RNA-binding proteins. Hauryliuk V,  Atkinson GC . RNA Biol . 2017 Aug 18:1-5. doi: 10.1080/15476286.2017.1367889
  
  
• Negative allosteric regulation of Enterococcus faecalis small alarmone synthetase RelQ by single-stranded RNA. Beljantseva J, Kudrin P, Andresen L, Shingler V, Atkinson GC , Tenson T, Hauryliuk V. Proc Natl Acad Sci U S A . 2017 Mar 20. pii: 201617868. doi: 10.1073/pnas.1617868114.
  
  
• Aim-less translation: loss of Saccharomyces cerevisiae mitochondrial translation initiation factor mIF3/Aim23 leads to unbalanced protein synthesis. Kuzmenko A, Derbikova K, Salvatori R, Tankov S, Atkinson GC , Tenson T, Ott M, Kamenski P, Hauryliuk V. Sci Rep . 2016 Jan 5;6:18749. doi: 10.1038/srep18749.
  
  
• Recent functional insights into the role of (p)ppGpp in bacterial physiology. Hauryliuk V, Atkinson GC , Murakami KS, Tenson T, Gerdes K. Nat Rev Microbiol . 2015 May;13(5):298-309. doi: 10.1038/nrmicro3448. Review.
  
  
• The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life. Atkinson GC . BMC Genomics . 2015 Feb 14;16:78. doi: 10.1186/s12864-015-1289-7.
  
  
• A conserved proline triplet in Val-tRNA synthetase and the origin of elongation factor P. Starosta AL, Lassak J, Peil L, Atkinson GC , Woolstenhulme CJ, Virumäe K, Buskirk A, Tenson T, Remme J, Jung K, Wilson DN. Cell Rep . 2014 Oct 23;9(2):476-83. doi: 10.1016/j.celrep.2014.09.008.
  
  
• Translational stalling at polyproline stretches is modulated by the sequence context upstream of the stall site. Starosta AL, Lassak J, Peil L, Atkinson GC , Virumäe K, Tenson T, Remme J, Jung K, Wilson DN. Nucleic Acids Res . 2014;42(16):10711-9. doi: 10.1093/nar/gku768.
  
  
• Macrolide antibiotics allosterically predispose the ribosome for translation arrest. Sothiselvam S, Liu B, Han W, Ramu H, Klepacki D, Atkinson GC , Brauer A, Remm M, Tenson T, Schulten K, Vázquez-Laslop N, Mankin AS. Proc Natl Acad Sci U S A . 2014 Jul 8;111(27):9804-9. doi: 10.1073/pnas.1403586111.
  
  
• An evolutionary ratchet leading to loss of elongation factors in eukaryotes. Atkinson GC , Kuzmenko A, Chicherin I, Soosaar A, Tenson T, Carr M, Kamenski P, Hauryliuk V. BMC Evol Biol . 2014 Feb 24;14(1):35. doi: 10.1186/1471-2148-14-35.
  
  
• Protein biosynthesis in mitochondria. Kuzmenko AV, Levitskii SA, Vinogradova EN, Atkinson GC , Hauryliuk V, Zenkin N, Kamenski PA. Biochemistry (Mosc) . 2013 Aug;78(8):855-66. doi: 10.1134/S0006297913080014. Review.
  
  
• Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P. Peil L, Starosta AL, Lassak J, Atkinson GC , Virumäe K, Spitzer M, Tenson T, Jung K, Remme J, Wilson DN. Proc Natl Acad Sci U S A . 2013 Sep 17;110(38):15265-70. doi: 10.1073/pnas.1310642110.
  
  
• Mitochondrial translation initiation machinery: conservation and diversification. Kuzmenko A, Atkinson GC , Levitskii S, Zenkin N, Tenson T, Hauryliuk V, Kamenski P. Biochimie . 2014 May;100:132-40. doi: 10.1016/j.biochi.2013.07.024. Review.
  
  
• Distinction between the Cfr methyltransferase conferring antibiotic resistance and the housekeeping RlmN methyltransferase. Atkinson GC , Hansen LH, Tenson T, Rasmussen A, Kirpekar F, Vester B. Antimicrob Agents Chemother . 2013 Aug;57(8):4019-26. doi: 10.1128/AAC.00448-13.
  
  
• Mechanism of tetracycline resistance by ribosomal protection protein Tet(O). Li W, Atkinson GC , Thakor NS, Allas U, Lu CC, Chan KY, Tenson T, Schulten K, Wilson KS, Hauryliuk V, Frank J. Nat Commun . 2013;4:1477. doi: 10.1038/ncomms2470.
  
  
• GTPases IF2 and EF-G bind GDP and the SRL RNA in a mutually exclusive manner. Mitkevich VA, Shyp V, Petrushanko IY, Soosaar A, Atkinson GC , Tenson T, Makarov AA, Hauryliuk V. Sci Rep . 2012;2:843. doi: 10.1038/srep00843.
  
  
• Lys34 of translation elongation factor EF-P is hydroxylated by YfcM. Peil L, Starosta AL, Virumäe K, Atkinson GC , Tenson T, Remme J, Wilson DN. Nat Chem Biol . 2012 Aug;8(8):695-7. doi: 10.1038/nchembio.1001.
  
  
• SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments. Ajawatanawong P, Atkinson GC , Watson-Haigh NS, Mackenzie B, Baldauf SL. Nucleic Acids Res . 2012 Jul;40(Web Server issue):W340-7. doi: 10.1093/nar/gks561.
  
  
• Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae. Atkinson GC , Kuzmenko A, Kamenski P, Vysokikh MY, Lakunina V, Tankov S, Smirnova E, Soosaar A, Tenson T, Hauryliuk V. Nucleic Acids Res . 2012 Jul;40(13):6122-34. doi: 10.1093/nar/gks272.
  
  
• The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. Atkinson GC , Tenson T, Hauryliuk V. PLoS One . 2011;6(8):e23479. doi: 10.1371/journal.pone.0023479.
  
  
• An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea. Atkinson GC , Hauryliuk V, Tenson T. BMC Evol Biol . 2011 Jan 21;11:22. doi: 10.1186/1471-2148-11-22.
• Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms. Atkinson GC , Baldauf SL. Mol Biol Evol . 2011 Mar;28(3):1281-92. doi: 10.1093/molbev/msq316.
  
  
• GTP-dependent structural rearrangement of the eRF1:eRF3 complex and eRF3 sequence motifs essential for PABP binding. Kononenko AV, Mitkevich VA, Atkinson GC , Tenson T, Dubovaya VI, Frolova LY, Makarov AA, Hauryliuk V. Nucleic Acids Res . 2010 Jan;38(2):548-58. doi: 10.1093/nar/gkp908.
  
  
• Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components. Atkinson GC , Baldauf SL, Hauryliuk V. BMC Evol Biol . 2008 Oct 23;8:290. doi: 10.1186/1471-2148-8-290.