Finnish Centre of Excellence in Virus Research

Publications

• Primary articles
• Review articles

Primary articles

Abrescia NG, Grimes JM, Oksanen HM, Bamford JK, Bamford DH, Stuart DI. (2011). The use of low-resolution phasing followed by phase extension from 7.6 to 2.5 A resolution with noncrystallographic symmetry to solve the structure of a bacteriophage capsid protein. Acta Crystallogr D Biol Crystallogr 67(Pt 3), 228-232. [PubMed]

Alhoranta AM, Lehtinen JK, Urtti AO, Butcher SJ, Aseyev VO, Tenhu HJ. (2011). Cationic amphiphilic star and linear block copolymers: synthesis, self-assembly, and in vitro gene transfection. Biomacromolecules 12(9), 3213-3222. [PubMed]

Fornelos N, Bamford JK, Mahillon J. (2011). Phage-Borne Factors and Host LexA Regulate the Lytic Switch in Phage GIL01. J Bacteriol 193(21), 6008-6019. [PubMed]

Friman VP, Hiltunen T, Jalasvuori M, Lindstedt C, Laanto E, Ormala AM, Laakso J, Mappes J, Bamford JK. (2011). High temperature and bacteriophages can indirectly select for bacterial pathogenicity in environmental reservoirs. PLoS One 6(3), e17651. [PubMed]

Graham SC, Sarin LP, Bahar MW, Myers RA, Stuart DI, Bamford DH, Grimes JM. (2011). The N-terminus of the RNA polymerase from infectious pancreatic necrosis virus is the determinant of genome attachment. PLoS Pathog 7(6), e1002085. [PubMed]

Jalasvuori M, Friman VP, Nieminen A, Bamford JK, Buckling A. (2011). Bacteriophage selection against a plasmid-encoded sex apparatus leads to the loss of antibiotic-resistance plasmids. Biol Lett 7(6), 902-905. [PubMed]

Jiang M, Osterlund P, Sarin LP, Poranen MM, Bamford DH, Guo D, Julkunen I. (2011). Innate immune responses in human monocyte-derived dendritic cells are highly dependent on the size and the 5' phosphorylation of RNA molecules. J Immunol 187(4), 1713-1721. [PubMed]

Kumar V, Butcher SJ, Oorni K, Engelhardt P, Heikkonen J, Kaski K, Ala-Korpela M, Kovanen PT. (2011). Three-Dimensional cryoEM Reconstruction of Native LDL Particles to 16A Resolution at Physiological Body Temperature. PLoS One 6(5), e18841. [PubMed]

Laanto E, Sundberg LR, Bamford JK. (2011). Phage Specificity of the Freshwater Fish Pathogen Flavobacterium columnare. Appl Environ Microbiol 77(21), 7868-7872. [PubMed]

Leo JC, Lyskowski A, Hattula K, Hartmann MD, Schwarz H, Butcher SJ, Linke D, Lupas AN, Goldman A. (2011). The structure of E. coli IgG-binding protein D suggests a general model for bending and binding in trimeric autotransporter adhesins. Structure 19(7), 1021-1030. [PubMed]

Liljeroos L, Huiskonen JT, Ora A, Susi P, Butcher SJ. (2011). Electron cryotomography of measles virus reveals how matrix protein coats the ribonucleocapsid within intact virions. Proc Natl Acad Sci U S A 108(44), 18085-18090. [PubMed]

Aalto AP, Poranen MM, Grimes JM, Stuart DI, Bamford DH. (2010). In vitro activities of the multifunctional RNA silencing polymerase QDE-1 of Neurospora crassa. J Biol Chem 285(38), 29367-29374. [PubMed]

Cvirkaite-Krupovic V, Krupovic M, Daugelavicius R, Bamford DH. (2010). Calcium ion-dependent entry of the membrane-containing bacteriophage PM2 into its Pseudoalteromonas host. Virology 405(1), 120-128. [PubMed]

Cvirkaite-Krupovic V, Poranen MM, Bamford DH. (2010). Phospholipids act as secondary receptor during the entry of the enveloped, double-stranded RNA bacteriophage phi6. J Gen Virol 91(Pt 8), 2116-2120. [PubMed]

Daugelavicius R, Buivydas A, Sencilo A, Bamford DH. (2010). Assessment of the activity of RND-type multidrug efflux pumps in Pseudomonas aeruginosa using tetraphenylphosphonium ions. Int J Antimicrob Agents 36(3), 234-238. [PubMed]

Happonen LJ, Redder P, Peng X, Reigstad LJ, Prangishvili D, Butcher SJ. (2010). Familial relationships in hyperthermo- and acidophilic archaeal viruses. J Virol 84(9), 4747-4754. [PubMed]

Huiskonen JT, Hepojoki J, Laurinmaki P, Vaheri A, Lankinen H, Butcher SJ, Grunewald K. (2010). Electron Cryo-Tomography of Tula Hantavirus Suggests a Unique Assembly Paradigm for Enveloped Viruses. J Virol 84(10), 4889-4897. [PubMed]

Jalasvuori M, Bamford JKH. (2010). Viruses and life: Can there be one without the other? J Cosmol 103446-3454.

Jalasvuori M, Jalasvuori MP, Bamford JK. (2010). Dynamics of a laterally evolving community of ribozyme-like agents as studied with a rule-based computing system. Orig Life Evol Biosph 40(3), 319-334. [PubMed]

Jalasvuori M, Pawlowski A, Bamford JK. (2010). A unique group of virus-related, genome-integrating elements found solely in the bacterial family Thermaceae and the archaeal family Halobacteriaceae. J Bacteriol 192(12), 3231-3234. [PubMed]

Krupovic M, Cvirkaite-Krupovic V, Bamford DH. (2010). Protein A33 responsible for antibody-resistant spread of Vaccinia virus is homologous to C-type lectin-like proteins. Virus Res 151(1), 97-101. [PubMed]

Krupovic M, Forterre P, Bamford DH. (2010). Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria. J Mol Biol 397(1), 144-160. [PubMed]

Krupovic M, Gribaldo S, Bamford DH, Forterre P. (2010). The Evolutionary History of Archaeal MCM Helicases: A Case Study of Vertical Evolution Combined with Hitchhiking of Mobile Genetic Elements. Mol Biol Evol 27(12), 2716-2732. [PubMed]

Lee HC, Aalto AP, Yang Q, Chang SS, Huang G, Fisher D, Cha J, Poranen MM, Bamford DH, Liu Y. (2010). 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. PLoS Biol 8(10), e1000496. [PubMed]

Ora A, Oksanen E, Kajander T, Goldman A, Butcher SJ. (2010). Crystallization and preliminary crystallographic analysis of mouse peroxiredoxin II with significant pseudosymmetry. Acta Crystallogr Sect F Struct Biol Cryst Commun 66(Pt 3), 357-360. [PubMed]

Paasonen L, Sipila T, Subrizi A, Laurinmaki P, Butcher SJ, Rappolt M, Yaghmur A, Urtti A, Yliperttula M. (2010). Gold-embedded photosensitive liposomes for drug delivery: triggering mechanism and intracellular release. J Control Release 147(1), 136-143. [PubMed]

Pietila MK, Laurinavicius S, Sund J, Roine E, Bamford DH. (2010). The single-stranded DNA genome of novel archaeal virus halorubrum pleomorphic virus 1 is enclosed in the envelope decorated with glycoprotein spikes. J Virol 84(2), 788-798. [PubMed]

Roine E, Kukkaro P, Paulin L, Laurinavicius S, Domanska A, Somerharju P, Bamford DH. (2010). New, closely related haloarchaeal viral elements with different nucleic Acid types. J Virol 84(7), 3682-3689. [PubMed]

Seitsonen J, Susi P, Heikkila O, Sinkovits RS, Laurinmaki P, Hyypia T, Butcher SJ. (2010). Interaction of alphaVbeta3 and alphaVbeta6 integrins with human parechovirus 1. J Virol 84(17), 8509-8519. [PubMed]

Jalasvuori M, Bamford JK. (2009). Did the ancient crenarchaeal viruses from the dawn of life survive exceptionally well the eons of meteorite bombardment? Astrobiology 9(1), 131-137. [PubMed]

Jalasvuori M, Jaatinen ST, Laurinavicius S, Ahola-Iivarinen E, Kalkkinen N, Bamford DH, Bamford JK. (2009). The closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea. J Virol 83(18), 9388-9397. [PubMed]

Jalasvuori M, Ormala AM, Bamford JKH. (2009). On the astrobiological relevance of viruses in extraterrestrial ecosystems. Int J Astrobiol 8(2), 95-100.

Krupovic M, Bamford DH. (2009). Does the evolution of viral polymerases reflect the origin and evolution of viruses? Nat Rev Microbiol 7(3), 250. [PubMed]

Krupovic M, Ravantti JJ, Bamford DH. (2009). Geminiviruses: a tale of a plasmid becoming a virus. BMC Evol Biol 9112. [PubMed]

Kukkaro P, Bamford DH. (2009). Virus-host interactions in environments with a wide range of ionic strengths. Environ Microbiol Reports 1(1), 71-77.

Lee HC, Chang SS, Choudhary S, Aalto AP, Maiti M, Bamford DH, Liu Y. (2009). qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459(7244), 274-277. [PubMed]

Nygardas M, Vuorinen T, Aalto AP, Bamford DH, Hukkanen V. (2009). Inhibition of coxsackievirus B3 and related enteroviruses by antiviral short interfering RNA pools produced using phi6 RNA-dependent RNA polymerase. J Gen Virol 90(Pt 10), 2468-2473. [PubMed]

Pietila MK, Roine E, Paulin L, Kalkkinen N, Bamford DH. (2009). An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope. Mol Microbiol 72(2), 307-319. [PubMed]

Polianskyte Z, Peitsaro N, Dapkunas A, Liobikas J, Soliymani R, Lalowski M, Speer O, Seitsonen J, Butcher S, Cereghetti GM, Linder MD, Merckel M, Thompson J, Eriksson O. (2009). LACTB is a filament-forming protein localized in mitochondria. Proc Natl Acad Sci U S A 106(45), 18960-18965. [PubMed]

Psencik J, Collins AM, Liljeroos L, Torkkeli M, Laurinmaki P, Ansink HM, Ikonen TP, Serimaa RE, Blankenship RE, Tuma R, Butcher SJ. (2009). Structure of chlorosomes from the green filamentous bacterium Chloroflexus aurantiacus. J Bacteriol 191(21), 6701-6708. [PubMed]

Saarikangas J, Zhao H, Pykalainen A, Laurinmaki P, Mattila PK, Kinnunen PK, Butcher SJ, Lappalainen P. (2009). Molecular mechanisms of membrane deformation by I-BAR domain proteins. Curr Biol 19(2), 95-107. [PubMed]

Sarin LP, Poranen MM, Lehti NM, Ravantti JJ, Koivunen MR, Aalto AP, van Dijk AA, Stuart DI, Grimes JM, Bamford DH. (2009). Insights into the pre-initiation events of bacteriophage phi 6 RNA-dependent RNA polymerase: towards the assembly of a productive binary complex. Nucleic Acids Res 37(4), 1182-1192. [PubMed]

Wallin AE, Ojala H, Ziedaite G, Degerth L, Bamford D, Haeggstrom E. (2009). High-resolution optical tweezers for investigating DNA-binding/translocating molecular motors. Proc SPIE 7400

Ziedaite G, Kivela HM, Bamford JK, Bamford DH. (2009). Purified membrane-containing procapsids of bacteriophage PRD1 package the viral genome. J Mol Biol 386(3), 637-647. [PubMed]

Abrescia NG, Grimes JM, Kivela HM, Assenberg R, Sutton GC, Butcher SJ, Bamford JK, Bamford DH, Stuart DI. (2008). Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2. Mol Cell 31(5), 749-761. [PubMed]

Jaalinoja HT, Roine E, Laurinmaki P, Kivela HM, Bamford DH, Butcher SJ. (2008). Structure and host-cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus. Proc Natl Acad Sci U S A 105(23), 8008-8013. [PubMed]

Jaatinen ST, Happonen LJ, Laurinmaki P, Butcher SJ, Bamford DH. (2008). Biochemical and structural characterisation of membrane-containing icosahedral dsDNA bacteriophages infecting thermophilic Thermus thermophilus. Virology 379(1), 10-19. [PubMed]

Jalasvuori M, Bamford JK. (2008). Structural co-evolution of viruses and cells in the primordial world. Orig Life Evol Biosph 38(2), 165-181. [PubMed]

Kainov DE, Mancini EJ, Telenius J, Lisal J, Grimes JM, Bamford DH, Stuart DI, Tuma R. (2008). Structural Basis of Mechanochemical Coupling in a Hexameric Molecular Motor. J Biol Chem 283(6), 3607-3617. [PubMed]

Kivela HM, Abrescia NG, Bamford JK, Grimes JM, Stuart DI, Bamford DH. (2008). Selenomethionine labeling of large biological macromolecular complexes: Probing the structure of marine bacterial virus PM2. J Struct Biol 161(2), 204-210. [PubMed]

Kivela HM, Madonna S, Krupovic M, Tutino ML, Bamford JK. (2008). Genetics for Pseudoalteromonas provides tools to manipulate marine bacterial virus PM2. J Bacteriol 190(4), 1298-1307. [PubMed]

Krupovic M, Bamford DH. (2008). Archaeal proviruses TKV4 and MVV extend the PRD1-adenovirus lineage to the phylum Euryarchaeota. Virology 375(1), 292-300. [PubMed]

Krupovic M, Bamford DH. (2008). Virus evolution: how far does the double beta-barrel viral lineage extend? Nat Rev Microbiol 6(12), 941-948. [PubMed]

Krupovic M, Cvirkaite-Krupovic V, Bamford DH. (2008). Identification and functional analysis of the Rz/Rz1-like accessory lysis genes in the membrane-containing bacteriophage PRD1. Mol Microbiol 68(2), 492-503. [PubMed]

Poranen MM, Butcher SJ, Simonov VM, Laurinmaki P, Bamford DH. (2008). Roles of the minor capsid protein P7 in the assembly and replication of double-stranded RNA bacteriophage phi6. J Mol Biol 383(3), 529-538. [PubMed]

Poranen MM, Koivunen MR, Bamford DH. (2008). Nontemplated terminal nucleotidyltransferase activity of double-stranded RNA bacteriophage phi6 RNA-dependent RNA polymerase. J Virol 82(18), 9254-9264. [PubMed]

Poranen MM, Salgado PS, Koivunen MR, Wright S, Bamford DH, Stuart DI, Grimes JM. (2008). Structural explanation for the role of Mn2+ in the activity of phi6 RNA-dependent RNA polymerase. Nucleic Acids Res 36(20), 6633-6644. [PubMed]

Ravantti JJ, Ruokoranta TM, Alapuranen AM, Bamford DH. (2008). Global transcriptional responses of Pseudomonas aeruginosa to phage PRR1 infection. J Virol 82(5), 2324-2329. [PubMed]

Seitsonen JJ, Susi P, Lemmetty A, Butcher SJ. (2008). Structure of the mite-transmitted Blackcurrant reversion nepovirus using electron cryo-microscopy. Virology 378(1), 162-168. [PubMed]

Sozhamannan S, McKinstry M, Lentz SM, Jalasvuori M, McAfee F, Smith A, Dabbs J, Ackermann HW, Bamford JK, Mateczun A, Read TD. (2008). Molecular characterization of a variant of Bacillus anthracis-specific phage AP50 with improved bacteriolytic activity. Appl Environ Microbiol 74(21), 6792-6796. [PubMed]

Suchanova B, Tuma R. (2008). Folding and assembly of large macromolecular complexes monitored by hydrogen-deuterium exchange and mass spectrometry. Microb Cell Fact 712. [PubMed]

Vilfan ID, Candelli A, Hage S, Aalto AP, Poranen MM, Bamford DH, Dekker NH. (2008). Reinitiated viral RNA-dependent RNA polymerase resumes replication at a reduced rate. Nucleic Acids Res 36(22), 7059-7067. [PubMed]

Wallin E, A., Ojala H, Haeggstrom E, Tuma R. (2008). Stiffer optical tweezer through real-time feedback control. Appl Phys Lett 92, 224104,DOI:10.1063/1.2940339.

Aalto AP, Sarin LP, van Dijk AA, Saarma M, Poranen MM, Arumae U, Bamford DH. (2007). Large-scale production of dsRNA and siRNA pools for RNA interference utilizing bacteriophage phi6 RNA-dependent RNA polymerase. RNA 13(3), 422-429. [PubMed]

Daugelavicius R, Gaidelyte A, Cvirkaite-Krupovic V, Bamford DH. (2007). On-line monitoring of changes in host cell physiology during the one-step growth cycle of Bacillus phage Bam35. J Microbiol Methods 69(1), 174-179. [PubMed]

Gaidelyte A, Vaara M, Bamford DH. (2007). Bacteria, phages and septicemia. PLoS ONE 2(11), e1145. [PubMed]

Huiskonen JT, Jaalinoja HT, Briggs JA, Fuller SD, Butcher SJ. (2007). Structure of a hexameric RNA packaging motor in a viral polymerase complex. J Struct Biol 158(2), 156-164. [PubMed]

Huiskonen JT, Manole V, Butcher SJ. (2007). Tale of two spikes in bacteriophage PRD1. Proc Natl Acad Sci U S A 104(16), 6666-6671. [PubMed]

Jaalinoja HT, Huiskonen JT, Butcher SJ. (2007). Electron cryomicroscopy comparison of the architectures of the enveloped bacteriophages phi6 and phi8. Structure 15(2), 157-167. [PubMed]

Karhu NJ, Ziedaite G, Bamford DH, Bamford JK. (2007). Efficient DNA packaging of bacteriophage PRD1 requires the unique vertex protein P6. J Virol 81(6), 2970-2979. [PubMed]

Krupovic M, Bamford DH. (2007). Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria. BMC Genomics 8236. [PubMed]

Krupovic M, Daugelavicius R, Bamford DH. (2007). A novel lysis system in PM2, a lipid-containing marine double-stranded DNA bacteriophage. Mol Microbiol 64(6), 1635-1648. [PubMed]

Krupovic M, Daugelavicius R, Bamford DH. (2007). Polymyxin B induces lysis of marine pseudoalteromonads. Antimicrob Agents Chemother 51(11), 3908-3914. [PubMed]

Laurinavicius S, Bamford DH, Somerharju P. (2007). Transbilayer distribution of phospholipids in bacteriophage membranes. Biochim Biophys Acta 1768(10), 2568-2577. [PubMed]

Mancini EJ, Assenberg R, Verma A, Walter TS, Tuma R, Grimes JM, Owens RJ, Stuart DI. (2007). Structure of the Murray Valley encephalitis virus RNA helicase at 1.9 Angstrom resolution. Protein Sci 16(10), 2294-2300. [PubMed]

Wallin AE, Ojala H, Korsback A, Haeggstrom E, Tuma R. (2007). Real-time control of optical tweezers. Proc SPIE 6644(1Y),

Wallin AE, Salmi A, Tuma R. (2007). Step length measurement--theory and simulation for tethered bead constant-force single molecule assay. Biophys J 93(3), 795-805. [PubMed]

Zabranska H, Tuma R, Kluh I, Svatos A, Ruml T, Hrabal R, Pichova I. (2007). The role of the S-S bridge in retroviral protease function and virion maturation. J Mol Biol 365(5), 1493-1504. [PubMed]

Gaidelyte A, Cvirkaite-Krupovic V, Daugelavicius R, Bamford JK, Bamford DH. (2006). The entry mechanism of membrane-containing phage Bam35 infecting Bacillus thuringiensis. J Bacteriol 188(16), 5925-5934. [PubMed]

Huiskonen JT, de Haas F, Bubeck D, Bamford DH, Fuller SD, Butcher SJ. (2006). Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging. Structure 14(6), 1039-1048. [PubMed]

Kivela HM, Roine E, Kukkaro P, Laurinavicius S, Somerharju P, Bamford DH. (2006). Quantitative dissociation of archaeal virus SH1 reveals distinct capsid proteins and a lipid core. Virology 356(1-2), 4-11. [PubMed]

Krupovic M, Vilen H, Bamford JK, Kivela HM, Aalto JM, Savilahti H, Bamford DH. (2006). Genome Characterization of Lipid-Containing Marine Bacteriophage PM2 by Transposon Insertion Mutagenesis. J Virol 80(18), 9270-9278. [PubMed]

Lisal J, Kainov DE, Lam TT, Emmett MR, Wei H, Gottlieb P, Marshall AG, Tuma R. (2006). Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage. Virology 351(1), 73-79. [PubMed]

Poranen MM, Ravantti JJ, Grahn AM, Gupta R, Auvinen P, Bamford DH. (2006). Global changes in cellular gene expression during bacteriophage PRD1 infection. J Virol 80(16), 8081-8088. [PubMed]

Ruokoranta TM, Grahn AM, Ravantti JJ, Poranen MM, Bamford DH. (2006). Complete Genome Sequence of the Broad Host Range Single-Stranded RNA Phage PRR1 Places It in the Levivirus Genus with Characteristics Shared with Alloleviviruses. J Virol 80(18), 9326-9330. [PubMed]

Salgado PS, Koivunen MR, Makeyev EV, Bamford DH, Stuart DI, Grimes JM. (2006). The Structure of an RNAi Polymerase Links RNA Silencing and Transcription. PLoS Biol 4(12), e434. [PubMed]

Abrescia NG, Kivela HM, Grimes JM, Bamford JK, Bamford DH, Stuart DI. (2005). Preliminary crystallographic analysis of the major capsid protein P2 of the lipid-containing bacteriophage PM2. Acta Crystallograph Sect F Struct Biol Cryst Commun 61(Pt 8), 762-765. [PubMed]

Bamford DH, Grimes JM, Stuart DI. (2005). What does structure tell us about virus evolution? Curr Opin Struct Biol 15(6), 655-663. [PubMed]

Bamford DH, Ravantti JJ, Ronnholm G, Laurinavicius S, Kukkaro P, Dyall-Smith M, Somerharju P, Kalkkinen N, Bamford JK. (2005). Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica. J Virol 79(14), 9097-9107. [PubMed]

Briggs JA, Huiskonen JT, Fernando KV, Gilbert RJ, Scotti P, Butcher SJ, Fuller SD. (2005). Classification and three-dimensional reconstruction of unevenly distributed or symmetry mismatched features of icosahedral particles. J Struct Biol 150(3), 332-339. [PubMed]

Daugelavicius R, Cvirkaite V, Gaidelyte A, Bakiene E, Gabrenaite-Verkhovskaya R, Bamford DH. (2005). Penetration of Enveloped Double-Stranded RNA Bacteriophages phi13 and phi6 into Pseudomonas syringae Cells. J Virol 79(8), 5017-5026. [PubMed]

Gaidelyte A, Jaatinen ST, Daugelavicius R, Bamford JK, Bamford DH. (2005). The linear double-stranded DNA of phage Bam35 enters lysogenic host cells, but the late phage functions are suppressed. J Bacteriol 187(10), 3521-3527. [PubMed]

Laurila MR, Salgado PS, Makeyev EV, Nettelship J, Stuart DI, Grimes JM, Bamford DH. (2005). Gene silencing pathway RNA-dependent RNA polymerase of Neurospora crassa: yeast expression and crystallization of selenomethionated QDE-1 protein. J Struct Biol 149(1), 111-115. [PubMed]

Laurila MR, Salgado PS, Stuart DI, Grimes JM, Bamford DH. (2005). Back-priming mode of phi6 RNA-dependent RNA polymerase. J Gen Virol 86(Pt 2), 521-526. [PubMed]

Laurinmaki PA, Huiskonen JT, Bamford DH, Butcher SJ. (2005). Membrane proteins modulate the bilayer curvature in the bacterial virus bam35. Structure (Camb) 13(12), 1819-1828. [PubMed]

Lisal J, Lam TT, Kainov DE, Emmett MR, Marshall AG, Tuma R. (2005). Functional visualization of viral molecular motor by hydrogen-deuterium exchange reveals transient states. Nat Struct Mol Biol 12(5), 460-466. [PubMed]

Lisal J, Tuma R. (2005). Cooperative mechanism of RNA packaging motor. J Biol Chem 280(24), 23157-23164. [PubMed]

Meier C, Mancini EJ, Bamford DH, Walsh MA, Stuart DI, Grimes JM. (2005). Overcoming the false-minima problem in direct methods: structure determination of the packaging enzyme P4 from bacteriophage phi13. Acta Crystallogr D Biol Crystallogr 61(Pt 9), 1238-1244. [PubMed]

Merckel MC, Huiskonen JT, Bamford DH, Goldman A, Tuma R. (2005). The Structure of the Bacteriophage PRD1 Spike Sheds Light on the Evolution of Viral Capsid Architecture. Mol Cell 18(2), 161-170. [PubMed]

Porter K, Kukkaro P, Bamford JK, Bath C, Kivela HM, Dyall-Smith ML, Bamford DH. (2005). SH1: A novel, spherical halovirus isolated from an Australian hypersaline lake. Virology 335(1), 22-33. [PubMed]

Salgado PS, Walsh MA, Laurila MR, Stuart DI, Grimes JM. (2005). Going soft and SAD with manganese. Acta Crystallogr D Biol Crystallogr 61(Pt 1), 108-111. [PubMed]

Saren AM, Ravantti JJ, Benson SD, Burnett RM, Paulin L, Bamford DH, Bamford JK. (2005). A snapshot of viral evolution from genome analysis of the tectiviridae family. J Mol Biol 350(3), 427-440. [PubMed]

Stromsten NJ, Bamford DH, Bamford JK. (2005). In vitro DNA Packaging of PRD1: A Common Mechanism for Internal-membrane Viruses. J Mol Biol 348(3), 617-629. [PubMed]

Ziedaite G, Daugelavicius R, Bamford JK, Bamford DH. (2005). The Holin protein of bacteriophage PRD1 forms a pore for small-molecule and endolysin translocation. J Bacteriol 187(15), 5397-5405. [PubMed]

Abrescia NG, Cockburn JJ, Grimes JM, Sutton GC, Diprose JM, Butcher SJ, Fuller SD, San Martin C, Burnett RM, Stuart DI, Bamford DH, Bamford JK. (2004). Insights into assembly from structural analysis of bacteriophage PRD1. Nature 432(7013), 68-74. [PubMed]

Benson SD, Bamford JK, Bamford DH, Burnett RM. (2004). Does common architecture reveal a viral lineage spanning all three domains of life? Mol Cell 16(5), 673-685. [PubMed]

Cockburn JJ, Abrescia NG, Grimes JM, Sutton GC, Diprose JM, Benevides JM, Thomas GJ,Jr, Bamford JK, Bamford DH, Stuart DI. (2004). Membrane structure and interactions with protein and DNA in bacteriophage PRD1. Nature 432(7013), 122-125. [PubMed]

Huiskonen JT, Kivela HM, Bamford DH, Butcher SJ. (2004). The PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes. Nat Struct Mol Biol 11(9), 850-856. [PubMed]

Jaatinen ST, Viitanen SJ, Bamford DH, Bamford JK. (2004). Integral membrane protein P16 of bacteriophage PRD1 stabilizes the adsorption vertex structure. J Virol 78(18), 9790-9797. [PubMed]

Kainov DE, Lisal J, Bamford DH, Tuma R. (2004). Packaging motor from double-stranded RNA bacteriophage phi12 acts as an obligatory passive conduit during transcription. Nucleic Acids Res 32(12), 3515-3521. [PubMed]

Kainov DE, Simonov V, Bamford DH, Tuma R, Gottlieb P, Wei H, Walsh MA, Belrhali H, Merckel MC. (2004). Crystallization and preliminary X-ray diffraction analysis of bacteriophage phi12 packaging factor P7. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 2), 2368-2370. [PubMed]

Kivela HM, Daugelavicius R, Hankkio RH, Bamford JK, Bamford DH. (2004). Penetration of membrane-containing double-stranded-DNA bacteriophage PM2 into Pseudoalteromonas hosts. J Bacteriol 186(16), 5342-5354. [PubMed]

Laurinavicius S, Kakela R, Bamford DH, Somerharju P. (2004). The origin of phospholipids of the enveloped bacteriophage phi6. Virology 326(1), 182-190. [PubMed]

Laurinavicius S, Kakela R, Somerharju P, Bamford DH. (2004). Phospholipid molecular species profiles of tectiviruses infecting Gram-negative and Gram-positive hosts. Virology 322(2), 328-336. [PubMed]

Lisal J, Kainov DE, Bamford DH, Thomas GJ,Jr, Tuma R. (2004). Enzymatic mechanism of RNA translocation in double-stranded RNA bacteriophages. J Biol Chem 279(2), 1343-1350. [PubMed]

Makeyev EV, Bamford DH. (2004). Evolutionary potential of an RNA virus. J Virol 78(4), 2114-2120. [PubMed]

Mancini EJ, Kainov DE, Grimes JM, Tuma R, Bamford DH, Stuart DI. (2004). Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation. Cell 118(6), 743-755. [PubMed]

Mancini EJ, Kainov DE, Wei H, Gottlieb P, Tuma R, Bamford DH, Stuart DI, Grimes JM. (2004). Production, crystallization and preliminary X-ray crystallographic studies of the bacteriophage phi 12 packaging motor. Acta Crystallogr D Biol Crystallogr 60(Pt 3), 588-590. [PubMed]

Psencik J, Ikonen TP, Laurinmaki P, Merckel MC, Butcher SJ, Serimaa RE, Tuma R. (2004). Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria. Biophys J 87(2), 1165-1172. [PubMed]

Salgado PS, Makeyev EV, Butcher SJ, Bamford DH, Stuart DI, Grimes JM. (2004). The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase. Structure (Camb) 12(2), 307-316. [PubMed]

Yang H, Makeyev EV, Kang Z, Ji S, Bamford DH, van Dijk AA. (2004). Cloning and sequence analysis of dsRNA segments 5, 6 and 7 of a novel non-group A, B, C adult rotavirus that caused an outbreak of gastroenteritis in China. Virus Res 106(1), 15-26. [PubMed]

Bamford DH. (2003). Do viruses form lineages across different domains of life? Res Microbiol 154(4), 231-236. [PubMed]

Cockburn JJ, Bamford JK, Grimes JM, Bamford DH, Stuart DI. (2003). Crystallization of the membrane-containing bacteriophage PRD1 in quartz capillaries by vapour diffusion. Acta Crystallogr D Biol Crystallogr 59(Pt 3), 538-540. [PubMed]

Doan DN, Lee KC, Laurinmaki P, Butcher S, Wong SM, Dokland T. (2003). Three-dimensional reconstruction of hibiscus chlorotic ringspot virus. J Struct Biol 144(3), 253-261. [PubMed]

Gowen B, Bamford JK, Bamford DH, Fuller SD. (2003). The tailless icosahedral membrane virus PRD1 localizes the proteins involved in genome packaging and injection at a unique vertex. J Virol 77(14), 7863-7871. [PubMed]

Huiskonen JT, Laakkonen L, Toropainen M, Sarvas M, Bamford DH, Bamford JK. (2003). Probing the ability of the coat and vertex protein of the membrane-containing bacteriophage PRD1 to display a meningococcal epitope. Virology 310(2), 267-279. [PubMed]

Ikonen T, Kainov DE, Timmins P, Serimaa R, Tuma R. (2003). Locating the minor components of double-stranded RNA bacteriophage phi6 by neutron scattering. J Appl Cryst 36525-529.

Kainov DE, Butcher SJ, Bamford DH, Tuma R. (2003). Conserved intermediates on the assembly pathway of double-stranded RNA bacteriophages. J Mol Biol 328(4), 791-804. [PubMed]

Kainov DE, Pirttimaa M, Tuma R, Butcher SJ, Thomas GJ,Jr, Bamford DH, Makeyev EV. (2003). RNA packaging device of double-stranded RNA bacteriophages, possibly as simple as hexamer of P4 protein. J Biol Chem 278(48), 48084-48091. [PubMed]

Mancini EJ, Grimes JM, Malby R, Sutton GC, Kainov DE, Juuti JT, Makeyev EV, Tuma R, Bamford DH, Stuart DI. (2003). Order and disorder in crystals of hexameric NTPases from dsRNA bacteriophages. Acta Crystallogr D Biol Crystallogr 59(Pt 12), 2337-2341. [PubMed]

Mannisto RH, Grahn AM, Bamford DH, Bamford JK. (2003). Transcription of bacteriophage PM2 involves phage-encoded regulators of heterologous origin. J Bacteriol 185(11), 3278-3287. [PubMed]

Rabel C, Grahn AM, Lurz R, Lanka E. (2003). The VirB4 family of proposed traffic nucleoside triphosphatases: common motifs in plasmid RP4 TrbE are essential for conjugation and phage adsorption. J Bacteriol 185(3), 1045-1058. [PubMed]

Ravantti JJ, Gaidelyte A, Bamford DH, Bamford JK. (2003). Comparative analysis of bacterial viruses Bam35, infecting a gram-positive host, and PRD1, infecting gram-negative hosts, demonstrates a viral lineage. Virology 313(2), 401-414. [PubMed]

Rydman PS, Bamford DH. (2003). Identification and mutational analysis of bacteriophage PRD1 holin protein P35. J Bacteriol 185(13), 3795-3803. [PubMed]

Stromsten NJ, Bamford DH, Bamford JK. (2003). The unique vertex of bacterial virus PRD1 is connected to the viral internal membrane. J Virol 77(11), 6314-6321. [PubMed]

Stromsten NJ, Benson SD, Burnett RM, Bamford DH, Bamford JK. (2003). The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state. J Bacteriol 185(23), 6985-6989. [PubMed]

Wang S, Chandramouli P, Butcher S, Dokland T. (2003). Cleavage leads to expansion of bacteriophage P4 procapsids in vitro. Virology 314(1), 1-8. [PubMed]

Xu L, Benson SD, Butcher SJ, Bamford DH, Burnett RM. (2003). The receptor binding protein P2 of PRD1, a virus targeting antibiotic-resistant bacteria, has a novel fold suggesting multiple functions. Structure (Camb) 11(3), 309-322. [PubMed]

Yang H, Gottlieb P, Wei H, Bamford DH, Makeyev EV. (2003). Temperature requirements for initiation of RNA-dependent RNA polymerization. Virology 314(2), 706-715. [PubMed]

Yang H, Makeyev EV, Butcher SJ, Gaidelyte A, Bamford DH. (2003). Two distinct mechanisms ensure transcriptional polarity in double-stranded RNA bacteriophages. J Virol 77(2), 1195-1203. [PubMed]

Bamford DH, Burnett RM, Stuart DI. (2002). Evolution of viral structure. Theor Popul Biol 61(4), 461-470. [PubMed]

Bamford JK, Cockburn JJ, Diprose J, Grimes JM, Sutton G, Stuart DI, Bamford DH. (2002). Diffraction quality crystals of PRD1, a 66-MDa dsDNA virus with an internal membrane. J Struct Biol 139(2), 103-112. [PubMed]

Benevides JM, Juuti JT, Tuma R, Bamford DH, Thomas GJ,Jr. (2002). Characterization of subunit-specific interactions in a double-stranded RNA virus: Raman difference spectroscopy of the phi6 procapsid. Biochemistry 41(40), 11946-11953. [PubMed]

Benson SD, Bamford JK, Bamford DH, Burnett RM. (2002). The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 A resolution. Acta Crystallogr D Biol Crystallogr 58(Pt 1), 39-59. [PubMed]

Grahn AM, Daugelavicius R, Bamford DH. (2002). Sequential model of phage PRD1 DNA delivery: active involvement of the viral membrane. Mol Microbiol 46(5), 1199-1209. [PubMed]

Grahn AM, Daugelavicius R, Bamford DH. (2002). The small viral membrane-associated protein P32 is involved in bacteriophage PRD1 DNA entry. J Virol 76(10), 4866-4872. [PubMed]

Kivela HM, Kalkkinen N, Bamford DH. (2002). Bacteriophage PM2 has a protein capsid surrounding a spherical proteinaceous lipid core. J Virol 76(16), 8169-8178. [PubMed]

Laurila MR, Makeyev EV, Bamford DH. (2002). Bacteriophage phi 6 RNA-dependent RNA polymerase: molecular details of initiating nucleic acid synthesis without primer. J Biol Chem 277(19), 17117-17124. [PubMed]

Makeyev EV, Bamford DH. (2002). Cellular RNA-dependent RNA polymerase involved in posttranscriptional gene silencing has two distinct activity modes. Mol Cell 10(6), 1417-1427. [PubMed]

Ojala PJ, Paavilainen VO, Vartiainen MK, Tuma R, Weeds AG, Lappalainen P. (2002). The two ADF-H domains of twinfilin play functionally distinct roles in interactions with actin monomers. Mol Biol Cell 13(11), 3811-3821. [PubMed]

Pirttimaa MJ, Paatero AO, Frilander MJ, Bamford DH. (2002). Nonspecific nucleoside triphosphatase P4 of double-stranded RNA bacteriophage phi6 is required for single-stranded RNA packaging and transcription. J Virol 76(20), 10122-10127. [PubMed]

Rydman PS, Bamford DH. (2002). The lytic enzyme of bacteriophage PRD1 is associated with the viral membrane. J Bacteriol 184(1), 104-110. [PubMed]

San Martin C, Huiskonen JT, Bamford JK, Butcher SJ, Fuller SD, Bamford DH, Burnett RM. (2002). Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid. Nat Struct Biol 9(10), 756-763. [PubMed]

Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart DI. (2001). A mechanism for initiating RNA-dependent RNA polymerization. Nature 410(6825), 235-240. [PubMed]

Makeyev EV, Bamford DH. (2001). Primer-independent RNA sequencing with bacteriophage phi6 RNA polymerase and chain terminators. RNA 7(5), 774-781. [PubMed]

Martin CS, Burnett RM, de Haas F, Heinkel R, Rutten T, Fuller SD, Butcher SJ, Bamford DH. (2001). Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Structure (Camb) 9(10), 917-930. [PubMed]

Poranen MM, Paatero AO, Tuma R, Bamford DH. (2001). Self-assembly of a viral molecular machine from purified protein and RNA constituents. Mol Cell 7(4), 845-854. [PubMed]

Rydman PS, Bamford JK, Bamford DH. (2001). A minor capsid protein P30 is essential for bacteriophage PRD1 capsid assembly. J Mol Biol 313(4), 785-795. [PubMed]

Sokolova A, Malfois M, Caldentey J, Svergun DI, Koch MH, Bamford DH, Tuma R. (2001). Solution structure of bacteriophage PRD1 vertex complex. J Biol Chem 276(49), 46187-46195. [PubMed]

Tuma R, Coward LU, Kirk MC, Barnes S, Prevelige PE,Jr. (2001). Hydrogen-deuterium exchange as a probe of folding and assembly in viral capsids. J Mol Biol 306(3), 389-396. [PubMed]

Tuma R, Tsuruta H, Benevides JM, Prevelige PE,Jr, Thomas GJ,Jr. (2001). Characterization of subunit structural changes accompanying assembly of the bacteriophage P22 procapsid. Biochemistry 40(3), 665-674. [PubMed]

Yang H, Makeyev EV, Bamford DH. (2001). Comparison of polymerase subunits from double-stranded RNA bacteriophages. J Virol 75(22), 11088-11095. [PubMed]

Bamford JK, Bamford DH. (2000). A new mutant class, made by targeted mutagenesis, of phage PRD1 reveals that protein P5 connects the receptor binding protein to the vertex. J Virol 74(17), 7781-7786. [PubMed]

Butcher SJ, Makeyev EV, Grimes JM, Stuart DI, Bamford DH. (2000). Crystallization and preliminary X-ray crystallographic studies on the bacteriophage phi6 RNA-dependent RNA polymerase. Acta Crystallogr D Biol Crystallogr 56 ( Pt 11)(Pt 11), 1473-1475. [PubMed]

Caldentey J, Tuma R, Bamford DH. (2000). Assembly of bacteriophage PRD1 spike complex: role of the multidomain protein P5. Biochemistry 39(34), 10566-10573. [PubMed]

Daugelavicius R, Bakiene E, Bamford DH. (2000). Stages of polymyxin B interaction with the Escherichia coli cell envelope. Antimicrob Agents Chemother 44(11), 2969-2978. [PubMed]

Daugelavicius R, Bakiene E, Berzinskiene J, Bamford DH. (2000). Use of lipophilic anions for estimation of biomass and cell viability. Biotechnol Bioeng 71(3), 208-216. [PubMed]

Grahn AM, Haase J, Bamford DH, Lanka E. (2000). Components of the RP4 conjugative transfer apparatus form an envelope structure bridging inner and outer membranes of donor cells: implications for related macromolecule transport systems. J Bacteriol 182(6), 1564-1574. [PubMed]

Holopainen JM, Saily M, Caldentey J, Kinnunen PK. (2000). The assembly factor P17 from bacteriophage PRD1 interacts with positively charged lipid membranes. Eur J Biochem 267(20), 6231-6238. [PubMed]

Kivioja T, Ravantti J, Verkhovsky A, Ukkonen E, Bamford D. (2000). Local average intensity-based method for identifying spherical particles in electron micrographs. J Struct Biol 131(2), 126-134. [PubMed]

Makeyev EV, Bamford DH. (2000). The polymerase subunit of a dsRNA virus plays a central role in the regulation of viral RNA metabolism. EMBO J 19(22), 6275-6284. [PubMed]

Makeyev EV, Bamford DH. (2000). Replicase activity of purified recombinant protein P2 of double-stranded RNA bacteriophage phi6. EMBO J 19(1), 124-133. [PubMed]

Pirttimaa MJ, Bamford DH. (2000). RNA secondary structures of the bacteriophage phi6 packaging regions. RNA 6(6), 880-889. [PubMed]

Rydman PS, Bamford DH. (2000). Bacteriophage PRD1 DNA entry uses a viral membrane-associated transglycosylase activity. Mol Microbiol 37(2), 356-363. [PubMed]

Xu L, Butcher SJ, Benson SD, Bamford DH, Burnett RM. (2000). Crystallization and preliminary X-ray analysis of receptor-binding protein P2 of bacteriophage PRD1. J Struct Biol 131(2), 159-163. [PubMed]

Benson SD, Bamford JK, Bamford DH, Burnett RM. (1999). Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures. Cell 98(6), 825-833. [PubMed]

Caldentey J, Hanninen AL, Holopainen JM, Bamford JK, Kinnunen PK, Bamford DH. (1999). Purification and characterization of the assembly factor P17 of the lipid-containing bacteriophage PRD1. Eur J Biochem 260(2), 549-558. [PubMed]

de Haas F, Paatero AO, Mindich L, Bamford DH, Fuller SD. (1999). A symmetry mismatch at the site of RNA packaging in the polymerase complex of dsRNA bacteriophage phi6. J Mol Biol 294(2), 357-372. [PubMed]

de Sousa PC,Jr, Tuma R, Prevelige PE,Jr, Silva JL, Foguel D. (1999). Cavity defects in the procapsid of bacteriophage P22 and the mechanism of capsid maturation. J Mol Biol 287(3), 527-538. [PubMed]

Grahn AM, Caldentey J, Bamford JK, Bamford DH. (1999). Stable packaging of phage PRD1 DNA requires adsorption protein P2, which binds to the IncP plasmid-encoded conjugative transfer complex. J Bacteriol 181(21), 6689-6696. [PubMed]

Helin J, Caldentey J, Kalkkinen N, Bamford DH. (1999). Analysis of the multimeric state of proteins by matrix assisted laser desorption/ionization mass spectrometry after cross-linking with glutaraldehyde. Rapid Commun Mass Spectrom 13(3), 185-190. [PubMed]

Jenkins RH, Tuma R, Juuti JT, Bamford DH, Thomas GJ,Jr. (1999). A novel Raman spectrophotometric method for quantitative measurement of nucleoside triphosphate hydrolysis. Biospectroscopy 5(1), 3-8. [PubMed]

Kivela HM, Mannisto RH, Kalkkinen N, Bamford DH. (1999). Purification and protein composition of PM2, the first lipid-containing bacterial virus to be isolated. Virology 262(2), 364-374. [PubMed]

Lanman J, Tuma R, Prevelige PE,Jr. (1999). Identification and characterization of the domain structure of bacteriophage P22 coat protein. Biochemistry 38(44), 14614-14623. [PubMed]

Mannisto RH, Kivela HM, Paulin L, Bamford DH, Bamford JK. (1999). The complete genome sequence of PM2, the first lipid-containing bacterial virus To Be isolated. Virology 262(2), 355-363. [PubMed]

Poranen MM, Bamford DH. (1999). Packaging and replication regulation revealed by chimeric genome segments of double-stranded RNA bacteriophage phi6. RNA 5(3), 446-454. [PubMed]

Poranen MM, Daugelavicius R, Ojala PM, Hess MW, Bamford DH. (1999). A novel virus-host cell membrane interaction. Membrane voltage-dependent endocytic-like entry of bacteriophage straight phi6 nucleocapsid. J Cell Biol 147(3), 671-682. [PubMed]

Ravantti JJ, Bamford DH. (1999). A data mining approach for analyzing density maps representing macromolecular structures. J Struct Biol 125(2-3), 216-222. [PubMed]

Rydman PS, Caldentey J, Butcher SJ, Fuller SD, Rutten T, Bamford DH. (1999). Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex. J Mol Biol 291(3), 575-587. [PubMed]

Tuma R, Bamford JK, Bamford DH, Thomas GJ,Jr. (1999). Assembly dynamics of the nucleocapsid shell subunit (P8) of bacteriophage phi6. Biochemistry 38(45), 15025-15033. [PubMed]

Butcher SJ, Aitken J, Mitchell J, Gowen B, Dargan DJ. (1998). Structure of the human cytomegalovirus B capsid by electron cryomicroscopy and image reconstruction. J Struct Biol 124(1), 70-76. [PubMed]

Juuti JT, Bamford DH, Tuma R, Thomas GJ,Jr. (1998). Structure and NTPase activity of the RNA-translocating protein (P4) of bacteriophage phi 6. J Mol Biol 279(2), 347-359. [PubMed]

Paatero AO, Mindich L, Bamford DH. (1998). Mutational analysis of the role of nucleoside triphosphatase P4 in the assembly of the RNA polymerase complex of bacteriophage phi6. J Virol 72(12), 10058-10065. [PubMed]

Tuma R, Parker MH, Weigele P, Sampson L, Sun Y, Krishna NR, Casjens S, Thomas GJ,Jr, Prevelige PE,Jr. (1998). A helical coat protein recognition domain of the bacteriophage P22 scaffolding protein. J Mol Biol 281(1), 81-94. [PubMed]

Tuma R, Prevelige PE,Jr, Thomas GJ,Jr. (1998). Mechanism of capsid maturation in a double-stranded DNA virus. Proc Natl Acad Sci U S A 95(17), 9885-9890. [PubMed]

Vohnik S, Hanson C, Tuma R, Fuchs JA, Woodward C, Thomas GJ,Jr. (1998). Conformation, stability, and active-site cysteine titrations of Escherichia coli D26A thioredoxin probed by Raman spectroscopy. Protein Sci 7(1), 193-200. [PubMed]

Benevides JM, Tsuboi M, Bamford JK, Thomas GJ,Jr. (1997). Polarized Raman spectroscopy of double-stranded RNA from bacteriophage phi6: local Raman tensors of base and backbone vibrations. Biophys J 72(6), 2748-2762. [PubMed]

Butcher SJ, Dokland T, Ojala PM, Bamford DH, Fuller SD. (1997). Intermediates in the assembly pathway of the double-stranded RNA virus phi6. EMBO J 16(14), 4477-4487. [PubMed]

Daugelavicius R, Bakiene E, Berzinskiene J, Bamford DH. (1997). Binding of lipophilic anions to microbial cells. Bioelectrochem Bioenerg 42263-274.

Daugelavicius R, Bamford JK, Bamford DH. (1997). Changes in host cell energetics in response to bacteriophage PRD1 DNA entry. J Bacteriol 179(16), 5203-5210. [PubMed]

Daugelavicius R, Bamford JK, Grahn AM, Lanka E, Bamford DH. (1997). The IncP plasmid-encoded cell envelope-associated DNA transfer complex increases cell permeability. J Bacteriol 179(16), 5195-5202. [PubMed]

Grahn AM, Haase J, Lanka E, Bamford DH. (1997). Assembly of a functional phage PRD1 receptor depends on 11 genes of the IncP plasmid mating pair formation complex. J Bacteriol 179(15), 4733-4740. [PubMed]

Hanninen AL, Bamford DH, Bamford JK. (1997). Assembly of membrane-containing bacteriophage PRD1 is dependent on GroEL and GroES. Virology 227(1), 207-210. [PubMed]

Hanninen AL, Bamford DH, Bamford JK. (1997). Probing phage PRD1-specific proteins with monoclonal and polyclonal antibodies. Virology 227(1), 198-206. [PubMed]

Juuti JT, Bamford DH. (1997). Protein P7 of phage phi6 RNA polymerase complex, acquiring of RNA packaging activity by in vitro assembly of the purified protein onto deficient particles. J Mol Biol 266(5), 891-900. [PubMed]

Palmer KJ, Tichelaar W, Myers N, Burns NR, Butcher SJ, Kingsman AJ, Fuller SD, Saibil HR. (1997). Cryo-electron microscopy structure of yeast Ty retrotransposon virus-like particles. J Virol 71(9), 6863-6868. [PubMed]

Tuma R, Thomas GJ,Jr. (1997). Mechanisms of virus assembly probed by Raman spectroscopy: the icosahedral bacteriophage P22. Biophys Chem 68(1-3), 17-31. [PubMed]

Vainio EJ, Moilanen A, Koivula TT, Bamford DH, Hantula J. (1997). Comparison of partial 16S rRNA gene sequences obtained from activated sludge bacteria. Appl Microbiol Biotechnol 48(1), 73-79. [PubMed]

Fuller SD, Butcher SJ, Cheng RH, Baker TS. (1996). Three-dimensional reconstruction of icosahedral particles--the uncommon line. J Struct Biol 116(1), 48-55. [PubMed]

Hantula J, Koivula TT, Luo C, Bamford DH. (1996). Bacterial diversity at surface water in three locations within the Baltic sea as revealed by culture-dependent molecular techniques. J Basic Microbiol 36(3), 163-176. [PubMed]

Tuma R, Bamford JH, Bamford DH, Russell MP, Thomas GJ,Jr. (1996). Structure, interactions and dynamics of PRD1 virus I. Coupling of subunit folding and capsid assembly. J Mol Biol 257(1), 87-101. [PubMed]

Tuma R, Bamford JH, Bamford DH, Thomas GJ,Jr. (1996). Structure, interactions and dynamics of PRD1 virus II. Organization of the viral membrane and DNA. J Mol Biol 257(1), 102-115. [PubMed]

Tuma R, Prevelige PE,Jr, Thomas GJ,Jr. (1996). Structural transitions in the scaffolding and coat proteins of P22 virus during assembly and disassembly. Biochemistry 35(14), 4619-4627. [PubMed]

Tuma R, Thomas GJ,Jr. (1996). Theory, design, and characterization of a microdialysis flow cell for Raman spectroscopy. Biophys J 71(6), 3454-3466. [PubMed]

Butcher SJ, Bamford DH, Fuller SD. (1995). DNA packaging orders the membrane of bacteriophage PRD1. EMBO J 14(24), 6078-6086. [PubMed]

Frilander M, Bamford DH. (1995). In vitro packaging of the single-stranded RNA genomic precursors of the segmented double-stranded RNA bacteriophage phi 6: the three segments modulate each other's packaging efficiency. J Mol Biol 246(3), 418-428. [PubMed]

Frilander M, Poranen M, Bamford DH. (1995). The large genome segment of dsRNA bacteriophage phi6 is the key regulator in the in vitro minus and plus strand synthesis. RNA 1(5), 510-518. [PubMed]

Fuller SD, Berriman JA, Butcher SJ, Gowen BE. (1995). Low pH induces swiveling of the glycoprotein heterodimers in the Semliki Forest virus spike complex. Cell 81(5), 715-725. [PubMed]

Haase J, Lurz R, Grahn AM, Bamford DH, Lanka E. (1995). Bacterial conjugation mediated by plasmid RP4: RSF1010 mobilization, donor-specific phage propagation, and pilus production require the same Tra2 core components of a proposed DNA transport complex. J Bacteriol 177(16), 4779-4791. [PubMed]

Hantula J, Bamford DH. (1995). Dependence of flocculation on aggregate formation and buoyant density in Flavobacterium sp. Appl Microbiol Biotechnol 43137-142.

Juuti JT, Bamford DH. (1995). RNA binding, packaging and polymerase activities of the different incomplete polymerase complex particles of dsRNA bacteriophage phi 6. J Mol Biol 249(3), 545-554. [PubMed]

Muttilainen S, Butcher SJ, Runeberg K, Nurminen M, Idanpaan-Heikkila I, Wahlstrom E, Sarvas M. (1995). Heterologous production of the P1 porin of Neisseria meningitidis in bacillus subtilis: the effect of an N-terminal extension on the presentation of native-like epitopes. Microb Pathog 18(5), 365-371. [PubMed]

Ojala PM, Bamford DH. (1995). In vitro transcription of the double-stranded RNA bacteriophage phi 6 is influenced by purine NTPs and calcium. Virology 207(2), 400-408. [PubMed]

Paatero AO, Syvaoja JE, Bamford DH. (1995). Double-stranded RNA bacteriophage phi 6 protein P4 is an unspecific nucleoside triphosphatase activated by calcium ions. J Virol 69(11), 6729-6734. [PubMed]

Tuma R, Russell M, Rosendahl M, Thomas GJ,Jr. (1995). Solution conformation of the extracellular domain of the human tumor necrosis factor receptor probed by Raman and UV-resonance Raman spectroscopy: structural effects of an engineered PEG linker. Biochemistry 34(46), 15150-15156. [PubMed]

van Dijk AA, Frilander M, Bamford DH. (1995). Differentiation between minus- and plus-strand synthesis: polymerase activity of dsRNA bacteriophage phi 6 in an in vitro packaging and replication system. Virology 211(1), 320-323. [PubMed]

Vasala A, Valkkila M, Caldentey J, Alatossava T. (1995). Genetic and biochemical characterization of the Lactobacillus delbrueckii subsp. lactis bacteriophage LL-H lysin. Appl Environ Microbiol 61(11), 4004-4011. [PubMed]

Caldentey J, Hanninen AL, Bamford DH. (1994). Gene XV of bacteriophage PRD1 encodes a lytic enzyme with muramidase activity. Eur J Biochem 225(1), 341-346. [PubMed]

Gottlieb P, Qiao X, Strassman J, Frilander M, Mindich L. (1994). Identification of the packaging regions within the genomic RNA segments of bacteriophage phi 6. Virology 200(1), 42-47. [PubMed]

Grahn AM, Bamford JK, O'Neill MC, Bamford DH. (1994). Functional organization of the bacteriophage PRD1 genome. J Bacteriol 176(10), 3062-3068. [PubMed]

Hanninen AL, Bamford DH, Grisshammer R. (1994). Expression in Escherichia coli of rat neurotensin receptor fused to membrane proteins from the membrane-containing bacteriophage PRD1. Biol Chem Hoppe Seyler 375(12), 833-836. [PubMed]

Mindich L, Qiao X, Onodera S, Gottlieb P, Frilander M. (1994). RNA structural requirements for stability and minus-strand synthesis in the dsRNA bacteriophage phi 6. Virology 202(1), 258-263. [PubMed]

Ojala PM, Paatero AO, Bamford DH. (1994). NTP binding induces conformational changes in the double-stranded RNA bacteriophage o6 subviral particles. Virology 205(1), 170-178. [PubMed]

Walin L, Tuma R, Thomas GJ,Jr, Bamford DH. (1994). Purification of viruses and macromolecular assemblies for structural investigations using a novel ion exchange method. Virology 201(1), 1-7. [PubMed]

Bamford JK, Bamford DH, Li T, Thomas GJ,Jr. (1993). Structural studies of the enveloped dsRNA bacteriophage phi 6 of Pseudomonas syringae by Raman spectroscopy. II. Nucleocapsid structure and thermostability of the virion, nucleocapsid and polymerase complex. J Mol Biol 230(2), 473-482. [PubMed]

Bamford JK, Luo C, Juuti JT, Olkkonen VM, Bamford DH. (1993). Topology of the major capsid protein P3 of bacteriophage PRD1: analysis using monoclonal antibodies and C-terminally truncated proteins. Virology 197(2), 652-658. [PubMed]

Caldentey J, Blanco L, Bamford DH, Salas M. (1993). In vitro replication of bacteriophage PRD1 DNA. Characterization of the protein-primed initiation site. Nucleic Acids Res 21(16), 3725-3730. [PubMed]

Caldentey J, Luo C, Bamford DH. (1993). Dissociation of the lipid-containing bacteriophage PRD1: effects of heat, pH, and sodium dodecyl sulfate. Virology 194(2), 557-563. [PubMed]

Kotilainen MM, Grahn AM, Bamford JK, Bamford DH. (1993). Binding of an Escherichia coli double-stranded DNA virus PRD1 to a receptor coded by an IncP-type plasmid. J Bacteriol 175(10), 3089-3095. [PubMed]

Li T, Bamford DH, Bamford JK, Thomas GJ,Jr. (1993). Structural studies of the enveloped dsRNA bacteriophage phi 6 of Pseudomonas syringae by Raman spectroscopy. I. The virion and its membrane envelope. J Mol Biol 230(2), 461-472. [PubMed]

Luo C, Butcher S, Bamford DH. (1993). Isolation of a phospholipid-free protein shell of bacteriophage PRD1, an Escherichia coli virus with an internal membrane. Virology 194(2), 564-569. [PubMed]

Luo C, Hantula J, Tichelaar W, Bamford DH. (1993). Bacteriophage PRD1 proteins: cross-linking and scanning transmission electron microscopy analysis. Virology 194(2), 570-575. [PubMed]

Niemi RM, Niemela SI, Bamford DH, Hantula J, Hyvarinen T, Forsten T, Raateland A. (1993). Presumptive fecal streptococci in environmental samples characterized by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Appl Environ Microbiol 59(7), 2190-2196. [PubMed]

Ojala PM, Juuti JT, Bamford DH. (1993). Protein P4 of double-stranded RNA bacteriophage phi 6 is accessible on the nucleocapsid surface: epitope mapping and orientation of the protein. J Virol 67(5), 2879-2886. [PubMed]

Onodera S, Qiao X, Gottlieb P, Strassman J, Frilander M, Mindich L. (1993). RNA structure and heterologous recombination in the double-stranded RNA bacteriophage phi 6. J Virol 67(8), 4914-4922. [PubMed]

Pakula TM, Caldentey J, Gutierrez C, Olkkonen VM, Salas M, Bamford DH. (1993). Overproduction, purification, and characterization of DNA-binding protein P19 of bacteriophage PRD1. Gene 126(1), 99-104. [PubMed]

Savilahti H, Bamford DH. (1993). Protein-primed DNA replication: role of inverted terminal repeats in the Escherichia coli bacteriophage PRD1 life cycle. J Virol 67(8), 4696-4703. [PubMed]

Stewart PL, Ghosh S, Bamford DH, Burnett RM. (1993). Crystallization of the major coat protein of PRD1, a bacteriophage with an internal membrane. J Mol Biol 230(1), 349-352. [PubMed]

Tuma R, Vohnik S, Li H, Thomas GJ,Jr. (1993). Cysteine conformation and sulfhydryl interactions in proteins and viruses. 3. Quantitative measurement of the Raman S-H band intensity and frequency. Biophys J 65(3), 1066-1072. [PubMed]

Caldentey J, Bamford DH. (1992). The lytic enzyme of the Pseudomonas phage phi 6. Purification and biochemical characterization. Biochim Biophys Acta 1159(1), 44-50. [PubMed]

Caldentey J, Blanco L, Savilahti H, Bamford DH, Salas M. (1992). In vitro replication of bacteriophage PRD1 DNA. Metal activation of protein-primed initiation and DNA elongation. Nucleic Acids Res 20(15), 3971-3976. [PubMed]

Frilander M, Gottlieb P, Strassman J, Bamford DH, Mindich L. (1992). Dependence of minus-strand synthesis on complete genomic packaging in the double-stranded RNA bacteriophage phi 6. J Virol 66(8), 5013-5017. [PubMed]

Gottlieb P, Strassman J, Qiao X, Frilander M, Frucht A, Mindich L. (1992). In vitro packaging and replication of individual genomic segments of bacteriophage phi 6 RNA. J Virol 66(5), 2611-2616. [PubMed]

Kenney JM, Hantula J, Fuller SD, Mindich L, Ojala PM, Bamford DH. (1992). Bacteriophage phi 6 envelope elucidated by chemical cross-linking, immunodetection, and cryoelectron microscopy. Virology 190(2), 635-644. [PubMed]

Onodera S, Olkkonen VM, Gottlieb P, Strassman J, Qiao XY, Bamford DH, Mindich L. (1992). Construction of a transducing virus from double-stranded RNA bacteriophage phi6: establishment of carrier states in host cells. J Virol 66(1), 190-196. [PubMed]

Aho S, Olkkonen V, Jalava T, Paloheimo M, Buhler R, Niku-Paavola ML, Bamford DH, Korhola M. (1991). Monoclonal antibodies against core and cellulose-binding domains of Trichoderma reesei cellobiohydrolases I and II and endoglucanase I. Eur J Biochem 200(3), 643-649. [PubMed]

Bamford JK, Bamford DH. (1991). Large-scale purification of membrane-containing bacteriophage PRD1 and its subviral particles. Virology 181(1), 348-352. [PubMed]

Bamford JK, Hanninen AL, Pakula TM, Ojala PM, Kalkkinen N, Frilander M, Bamford DH. (1991). Genome organization of membrane-containing bacteriophage PRD1. Virology 183(2), 658-676. [PubMed]

Hantula J, Bamford DH. (1991). Bacteriophage resistance and flocculation deficiency of Flavobacterium sp. are phenotypically interrelated. Appl Microbiol Biotechnol 36105-108.

Hantula J, Bamford DH. (1991). The efficiency of the protein dependent flocculation of Flavobacterium sp. is sensitive to the composition of growth medium. Appl Microbiol Biotechnol 36100-104.

Hantula J, Kurki A, Vuoriranta P, Bamford DH. (1991). Ecology of bacteriophages infecting activated sludge bacteria. Appl Environ Microbiol 57(8), 2147-2151. [PubMed]

Hantula J, Kurki A, Vuoriranta P, Bamford DH. (1991). Rapid classification of bacterial strains by SDS-polyacrylamide gel electrophoresis: Population dynamics of the dominant dispersed phase bacteria of activated sludge. Appl Microbiol Biotechnol 34551-555.

Lyra C, Savilahti H, Bamford DH. (1991). High-frequency transfer of linear DNA containing 5'-covalently linked terminal proteins: electroporation of bacteriophage PRD1 genome into Escherichia coli. Mol Gen Genet 228(1-2), 65-69. [PubMed]

Olkkonen VM, Ojala PM, Bamford DH. (1991). Generation of infectious nucleocapsids by in vitro assembly of the shell protein on to the polymerase complex of the dsRNA bacteriophage phi 6. J Mol Biol 218(3), 569-581. [PubMed]

Savilahti H, Caldentey J, Lundstrom K, Syvaoja JE, Bamford DH. (1991). Overexpression, purification, and characterization of Escherichia coli bacteriophage PRD1 DNA polymerase. In vitro synthesis of full-length PRD1 DNA with purified proteins. J Biol Chem 266(28), 18737-18744. [PubMed]

Bamford DH, Bamford JK. (1990). Collagenous proteins multiply. Nature 344(6266), 497. [PubMed]

Bamford DH, Bamford JK, Towse SA, Thomas GJ,Jr. (1990). Structural study of the lipid-containing bacteriophage PRD1 and its capsid and DNA components by laser Raman spectroscopy. Biochemistry 29(25), 5982-5987. [PubMed]

Bamford JK, Bamford DH. (1990). Capsomer proteins of bacteriophage PRD1, a bacterial virus with a membrane. Virology 177(2), 445-451. [PubMed]

Hantula J, Korhonen TK, Bamford DH. (1990). Determination of taxonomic resolution capacity of conventional one-dimensional SDS-polyacrylamide gel electrophoresis of whole-cell proteins using Enterobacteriaceae. FEMS Microbiol Lett 58(3), 325-330. [PubMed]

Ojala PM, Romantschuk M, Bamford DH. (1990). Purified phi 6 nucleocapsids are capable of productive infection of host cells with partially disrupted outer membranes. Virology 178(2), 364-372. [PubMed]

Olkkonen VM, Gottlieb P, Strassman J, Qiao XY, Bamford DH, Mindich L. (1990). In vitro assembly of infectious nucleocapsids of bacteriophage phi 6: formation of a recombinant double-stranded RNA virus. Proc Natl Acad Sci U S A 87(23), 9173-9177. [PubMed]

Pakula TM, Caldentey J, Serrano M, Gutierrez C, Hermoso JM, Salas M, Bamford DH. (1990). Characterization of a DNA binding protein of bacteriophage PRD1 involved in DNA replication. Nucleic Acids Res 18(22), 6553-6557. [PubMed]

Kurki A, Hantula J, Bamford DH, Vuoriranta P. (1989). Floc formation of activated sludge bacteria. Wat Sci Tech 211637-1638.

Olkkonen VM, Bamford DH. (1989). Quantitation of the adsorption and penetration stages of bacteriophage phi 6 infection. Virology 171(1), 229-238. [PubMed]

Pakula TM, Savilahti H, Bamford DH. (1989). The organization of the right-end early region of bacteriophage PRD1 genome. Gene 85(1), 53-58. [PubMed]

Pakula TM, Savilahti H, Bamford DH. (1989). Comparison of the amino acid sequence of the lytic enzyme from broad-host-range bacteriophage PRD1 with sequences of other cell-wall-peptidoglycan lytic enzymes. Eur J Biochem 180(1), 149-152. [PubMed]

Savilahti H, Caldentey J, Bamford DH. (1989). Bacteriophage PRD1 terminal protein: expression of gene VIII in Escherichia coli and purification of the functional P8 product. Gene 85(1), 45-51. [PubMed]

Gottlieb P, Metzger S, Romantschuk M, Carton J, Strassman J, Bamford DH, Kalkkinen N, Mindich L. (1988). Nucleotide sequence of the middle dsRNA segment of bacteriophage phi 6: placement of the genes of membrane-associated proteins. Virology 163(1), 183-190. [PubMed]

Gottlieb P, Strassman J, Bamford DH, Mindich L. (1988). Production of a polyhedral particle in Escherichia coli from a cDNA copy of the large genomic segment of bacteriophage phi 6. J Virol 62(1), 181-187. [PubMed]

Hantula J, Bamford DH. (1988). Chemical crosslinking of bacteriophage phi 6 nucleocapsid proteins. Virology 165(2), 482-488. [PubMed]

Mindich L, Nemhauser I, Gottlieb P, Romantschuk M, Carton J, Frucht S, Strassman J, Bamford DH, Kalkkinen N. (1988). Nucleotide sequence of the large double-stranded RNA segment of bacteriophage phi 6: genes specifying the viral replicase and transcriptase. J Virol 62(4), 1180-1185. [PubMed]

Olkkonen VM, Pekkala PM, Bamford DH. (1988). Monoclonal antibodies to the major structural proteins of bacteriophage phi 6. Virology 165(1), 317-320. [PubMed]

Romantschuk M, Olkkonen VM, Bamford DH. (1988). The nucleocapsid of bacteriophage phi 6 penetrates the host cytoplasmic membrane. EMBO J 7(6), 1821-1829. [PubMed]

Bamford DH, Romantschuk M, Somerharju PJ. (1987). Membrane fusion in prokaryotes: bacteriophage phi 6 membrane fuses with the Pseudomonas syringae outer membrane. EMBO J 6(5), 1467-1473. [PubMed]

Olkkonen VM, Bamford DH. (1987). The nucleocapsid of the lipid-containing double-stranded RNA bacteriophage phi 6 contains a protein skeleton consisting of a single polypeptide species. J Virol 61(8), 2362-2367. [PubMed]

Romantschuk M, Bamford DH. (1987). Chromosomally coded pili of Pseudomonas syringae pv phaseolicocola function as adhesions in early step of halo blight of bean. In “Plant pathogenic bacteria” (E. L. Civerolo, A. Collimer, R. E. Davis, A. G. Gillapsie, Eds.)572-577.

Savilahti H, Bamford DH. (1987). The complete nucleotide sequence of the left very early region of Escherichia coli bacteriophage PRD1 coding for the terminal protein and the DNA polymerase. Gene 57(1), 121-130. [PubMed]

Romantschuk M, Bamford DH. (1986). The causal agent of halo blight in bean, Pseudomonas syringae pv. phaseolicola, attaches to stomata via its pili. Microb Pathog 1(2), 139-148. [PubMed]

Savilahti H, Bamford DH. (1986). Linear DNA replication: inverted terminal repeats of five closely related Escherichia coli bacteriophages. Gene 49(2), 199-205. [PubMed]

Mindich L, MacKenzie G, Strassman J, McGraw T, Metzger S, Romantschuk M, Bamford D. (1985). cDNA cloning of portions of the bacteriophage phi 6 genome. J Bacteriol 162(3), 992-999. [PubMed]

Romantschuk M, Bamford DH. (1985). Function of pili in bacteriophage phi 6 penetration. J Gen Virol 66 ( Pt 11)(Pt 11), 2461-2469. [PubMed]

Bamford DH, Mindich L. (1984). Characterization of the DNA-protein complex at the termini of the bacteriophage PRD1 genome. J Virol 50(2), 309-315. [PubMed]

Bamford D, McGraw T, MacKenzie G, Mindich L. (1983). Identification of a protein bound to the termini of bacteriophage PRD1 DNA. J Virol 47(2), 311-316. [PubMed]

Bamford D, Mindich L. (1982). Structure of the lipid-containing bacteriophage PRD1: disruption of wild-type and nonsense mutant phage particles with guanidine hydrochloride. J Virol 44(3), 1031-1038. [PubMed]

Bamford DH, Lounatmaa K. (1982). Further electron microscopic studies on the infection process of the lipid-containing bacteriophage phi6. J Gen Virol 61149-152.

Karvinen VP, Bamford D, Granroth G. (1982). Changes in muscle subcellular fractions of Baltic herring (Culpea Herangus membras) during cold and frozen storage. J Sci Food Agricult 33763-770.

Mindich L, Bamford D, Goldthwaite C, Laverty M, Mackenzie G. (1982). Isolation of nonsense mutants of lipid-containing bacteriophage PRD1. J Virol 44(3), 1013-1020. [PubMed]

Mindich L, Bamford D, McGraw T, Mackenzie G. (1982). Assembly of bacteriophage PRD1: particle formation with wild-type and mutant viruses. J Virol 44(3), 1021-1030. [PubMed]

Bamford DH. (1981). lipid-containing bacterial viruses: disruption studies on phi 6. Prog Clin Biol Res 64477-489. [PubMed]

Bamford DH, Rouhiainen L, Takkinen K, Soderlund H. (1981). Comparison of the lipid-containing bacteriophages PRD1, PR3, PR4, PR5 and L17. J Gen Virol 57(Pt 2), 365-373. [PubMed]

Romantschuk M, Bamford DH. (1981). phi 6-resistant phage-producing mutants of Pseudomonas phaseolicola. J Gen Virol 56(Pt 2), 287-295. [PubMed]

Bamford DH, Mindich L. (1980). Electron microscopy of cells infected with nonsense mutants of bacteriophage phi 6. Virology 107(1), 222-228. [PubMed]

Bamford DH, Palva ET. (1980). Structure of the lipid-containing bacteriophage phi 6. Disruption by Triton X-100 treatment. Biochim Biophys Acta 601(2), 245-259. [PubMed]

Lundstrom KH, Bamford DH, Palva ET, Lounatmaa K. (1979). Lipid-containing bacteriophage PR4: structure and life cycle. J Gen Virol 43(3), 583-592. [PubMed]

Bamford DH, Lounatmaa K. (1978). Freeze-fracturing of Pseudomonas phaseoli-cola infected by the lipid-containing bacteriophage phi6. J Gen Virol 39161-170.

Liljestrom PT, Bamford DH. (1978). Genetics of plaque-size mutants of double-stranded RNA bacteriophage phi6. Hereditas 88(1), 135-137. [PubMed]

Bamford D, Sorsa M, Gripenberg U, Laamanen I, Meretoja T. (1976). Mutagenicity and toxicity of amitrole. III. Microbial tests. Mutat Res 40(3), 197-202. [PubMed]

Bamford DH, Palva ET, Lounatmaa K. (1976). Ultrastructure and life cycle of the lipid-containing bacteriophage phi 6. J Gen Virol 32(2), 249-259. [PubMed]

Laamanen I, Sorsa M, Bamford D, Gripenberg U, Meretoja T. (1976). Mutagenicity and toxicity of amitrole. I. Drosophila tests. Mutat Res 40(3), 185-190. [PubMed]

Meretoja T, Gripenberg U, Bamford D, Laamanen I, Sorsa M. (1976). Mutagenicity and toxicity of amitrole. II. Human lymphocyte culture tests. Mutat Res 40(3), 191-196. [PubMed]

Review articles

Krupovic M, Bamford DH. (2011). Virology. Revealing virus-host interplay. Science 333(6038), 45-46. [PubMed]

Krupovic M, Bamford DH. (2011). Protein Conservation in Virus Evolution. Encyclopedia of Life Sciences (ELS)

Krupovic M, Bamford DH. (2011). Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly. Curr Opin Virol 1118-124.

Krupovic M, Prangishvili D, Hendrix RW, Bamford DH. (2011). Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere. Microbiol Mol Biol Rev 75(4), 610-635. [PubMed]

Roine E, Oksanen HM. (2011). Viruses from the hypersaline environment. Halophiles and Hypersaline Environments: Current Research and Future Trends (eds A. Ventosa, A. Oren and Y. Ma)153-172.

Abrescia NGA, Grimes JM, Fry EE, Ravantti JJ, Bamford DH, Stuart DI. (2010). What Does it Take to Make a Virus: The Concept of the Viral "Self". Emerging Topics in Physical Virology (ed P.G.Stockley and R.Twarock)35-58.

Krupovic M, Bamford DH. (2010). Order to the Viral Universe. J Virol 84(24), 12476-12479. [PubMed]

Oksanen HM, Poranen MM, Bamford DH. (2010). Bacteriophages: Lipid-containing. Encyclopedia of Life Sciences (ELS)1-11.

Bamford JKH, Butcher SJ. (2008). Icosahedral dsDNA Bacterial Viruses with an Internal Membrane. Encyclopedia of Virology, Third Edition (ed B.W.J. Mahy and M.H.V. Van Regenmortel), Vol 5, 1-6.

Koivunen MRL, Sarin LP, Bamford DH. (2008). Structure-Function insights into the RNA-dependent RNA polymerase of the dsRNA bacteriophage phi6. Segmented Double Stranded RNA Viruses:Structure and molecular biology (ed J.T. Patton),239-257.

Krupovic M, Bamford DH. (2008). Holin of bacteriophage lambda: structural insights into a membrane lesion. Mol Microbiol 69(4), 781-783. [PubMed]

Poranen MM, Bamford DH. (2008). Entry of a segmented dsRNA virus into the bacterial cell. Segmented Double Stranded RNA Viruses:Structure and molecular biology (ed J.T. Patton),215-226.

Poranen MM, Domanska. A. (2008). Virus Entry to Bacterial Cells. Encyclopedia of Virology, Third Edition (ed B.W.J. Mahy and M.H.V. Van Regenmortel), Vol 5, 365-370.

Poranen MM, Tuma R, Bamford DH. (2008). Dissecting the assembly pathway of bacterial dsRNA viruses: Infectious nucleocapsids produced by self-assembly. Segmented Double Stranded RNA Viruses:Structure and molecular biology (ed J.T. Patton),115-132.

Arraiano CM, Bamford J, Brussow H, Carpousis AJ, Pelicic V, Pfluger K, Polard P, Vogel J. (2007). Recent advances in the expression, evolution, and dynamics of prokaryotic genomes. J Bacteriol 189(17), 6093-6100. [PubMed]

Huiskonen JT, Butcher SJ. (2007). Membrane-containing viruses with icosahedrally symmetric capsids. Curr Opin Struct Biol 17(2), 229-236. [PubMed]

Bamford DH, Bamford JKH. (2006). Lipid-containing bacteriophage PM2, the type-organism of Corticoviridae. The Bacteriophages (ed R Calendar)171-174.

Grahn AM, Butcher SJ, Bamford JKH, Bamford DH. (2006). PRD1 - dissecting the genome, structure and entry. The Bacteriophages (ed R Calendar)161-170.

Kainov DE, Tuma R, Mancini EJ. (2006). Hexameric molecular motors: P4 packaging ATPase unravels the mechanism. Cell Mol Life Sci 63(10), 1095-1105. [PubMed]

Pirttimaa MJ, Bamford DH. (2005). Nucleic acid packaging of RNA viruses. Encyclopedia of Molecular Cell Biology and Molecular Medicine (ed R A Mayers)9, 2nd Edition363-375.

Poranen MM, Pirttimaa MJ, Bamford DH. (2005). Encapsidation of the segmented double-stranded RNA genome of bacteriophage phi6. Viral Genome Packaging Machines:Genetics, Structure, and Mechanisms,117-130.

Poranen MM, Tuma R, Bamford DH. (2005). Assembly of double-stranded RNA bacteriophages. Adv Virus Res 6415-43. [PubMed]

Tuma R. (2005). Raman spectroscopy of proteins: from peptides to large assemblies. J. Raman Spectrosc. 36307-319.

Bamford DH, Mindich L. (2004). Viral molecular machines: replication systems within the inner cores of dsRNA viruses. Virus Res 101(1), 1-100.

Makeyev EV, Grimes JM. (2004). RNA-dependent RNA polymerases of dsRNA bacteriophages. Virus Res 101(1), 45-55. [PubMed]

Poranen MM, Tuma R. (2004). Self-assembly of double-stranded RNA bacteriophages. Virus Res 101(1), 93-100. [PubMed]

van Dijk AA, Makeyev EV, Bamford DH. (2004). Initiation of viral RNA-dependent RNA polymerization. J Gen Virol 85(Pt 5), 1077-1093. [PubMed]

Bamford DH. (2003). Self-organization: making complex infectious viral particles from purified precursors. Philos Transact Ser A Math Phys Eng Sci 361(1807), 1187-1203. [PubMed]

Bamford DH. (2002). Those magnificent molecular machines: logistics in dsRNA virus transcription. EMBO Rep 3(4), 317-318. [PubMed]

Poranen MM, Daugelavicius R, Bamford DH. (2002). Common principles in viral entry. Annu Rev Microbiol 56521-538. [PubMed]

Rydman PS, Bamford DH. (2002). Phage enzymes digest peptidoglycan to deliver DNA ASM News 68330-335.

Bamford DH. (2001). Genus Tectivirus (Tectiviridae). The Springer Index of Viruses (C.A. Tidona and C.D. Darai, Eds.) Springer, www.springer.de/viruses/

Bamford DH. (2001). Genus Cystovirus (Cystoviridae). The Springer Index of Viruses (C.A. Tidona and C.D. Darai, Eds.) Springer,www.springer.de/viruses/

Bamford DH, Gilbert RJ, Grimes JM, Stuart DI. (2001). Macromolecular assemblies: greater than their parts. Curr Opin Struct Biol 11(1), 107-113. [PubMed]

Bamford DH. (2000). Virus structures: Those magnificent molecular machines. Curr Biol 10(15), R558-61. [PubMed]

Bamford DH. (2000). Family Cystoviridae. Virus Taxonomy, Classification and Nomenclature of Viruses (M. Regenmortel et al., eds.)389-393.

Bamford DH, Ackermann H. (2000). Family Tectiviridae. Virus Taxonomy, Classification and Nomenclature of Viruses (M. Regenmortel et al., eds)111-116.

Zechner EL, de la Cruz F, Eisenbrandt R, Grahn AM, Koraimann G, Lanka E, Muth G, Pansegrau W, Thomas CM, Wilkins BM, Zatyka M. (2000). "Conjugative DNA transfer processes" in The horizontal gene pool Bacterial plasmids and gene spread (C.M. Thomas ed.)87-174.

Bamford DH. (1999). Bacteriophages: lipid-containing Encyclopedia of Life-Sciences

Bamford DH. (1999). Bacteriophage PRD1 (Tectiviridae). Encyclopedia of Virology, 2nd Edition (R. Webster and A. Granoff, Eds)1210-1212.

Bamford DH. (1999). Bacteriophage phi6 (Cystoviridae). Encyclopedia of Virology, 2nd Edition (R. Webster and A. Granoff, Eds.)1205-1208.

Caldentey J. (1998). Murein endopeptidase P5 (from phage phi6). Handbook of proteolytic enzymes (A.J. Barret, N.D Rawlings and J.F. Woessner, Jr. )1578-1579.

Bamford DH. (1997). Viruses, RNA packaging of The Encyclopedia of Molecular Biology and Molecular Medicine (R.A. Mayers, ed.)217-223.

Ackermann H, Bamford DH. (1995). Tectiviridae. Virus Taxonomy, Classification and Nomenclature of Viruses (F.A. Murphy, C.M. Fauquet, D.H.L. Bishop, S.A. Ghabrial, A.W. Jarvis, G.P. Martelli, M.A. Mayo, M.D. Summers, eds.)64-66.

Bamford DH. (1995). Cystoviridae. Virus Taxonomy, Classification and Nomenclature of Viruses (F.A. Murphy, C.M. Fauquet, D.H.L. Bishop, S.A. Ghabrial, A.W. Jarvis, G.P. Martelli, M.A. Mayo, M.D. Summers, eds.)205-207.

Bamford DH. (1995). Viruses RNA packaging of Molecular Biology and Biotechnology (R.A. Mayers, ed.)957-960.

Bamford DH, Caldentey J, Bamford JK. (1995). Bacteriophage PRD1: a broad host range DSDNA tectivirus with an internal membrane. Adv Virus Res 45281-319. [PubMed]

Bamford DH, Ojala PM, Frilander M, Walin L, Bamford JKH. (1995). Isolation, purification and function of the assembly intermediates and subviral particles of bacteriophages PRD1 and phi6. Methods in Molecular Genetics, (K.W. Adolph, ed.) 6455-474.

Bamford DH. (1994). PRD1 Bacteriophage. Encyclopedia of Virology (R. Webster and A. Granoff, Eds.)1165-1168.

Bamford DH. (1994). Bacteriophage phi6 Encyclopedia of Virology (R. Webster and A. Granoff, Eds.)978-980.

Bamford DH, Wickner RB. (1994). Assembly of double-stranded RNA Viruses: bacteriophage phi6 and yeast virus. L-A. Seminars in Virology (ed. P. Guo) 561-69.

Caldentey J, Bamford JK, Bamford DH. (1990). Structure and assembly of bacteriophage PRD1, and Escherichia coli virus with a membrane. J Struct Biol 104(1-3), 44-51. [PubMed]

Mindich L, Bamford DH. (1988). Lipid-containing bacteriophages In "The bacteriophages" (R. Calendar, Ed.)475-520.

Korhonen T, Haahtela K, Romantschuk M, Bamford DH. (1986). Role of fimbriae and pili in the attachment of Klebsiella, Enterobacter and Pseudomonas to plant surfaces. In "Recognition in microbe-plant symbiotic and pathogenic interactions" (B. Lugtenberg, Ed.)229-241.

Palva T, Bamford DH. (1980). Attachment and penetration of lipid-containing bacteriophages. In "Receptors and Recognition", Series B (L. Philipson and L. Randall, Eds.)95-114.