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Items: 26

1.

Structural comparison strengthens the higher-order classification of proteases related to chymotrypsin.

Mönttinen HAM, Ravantti JJ, Poranen MM.

PLoS One. 2019 May 17;14(5):e0216659. doi: 10.1371/journal.pone.0216659. eCollection 2019.

2.

Virus found in a boreal lake links ssDNA and dsDNA viruses.

Laanto E, Mäntynen S, De Colibus L, Marjakangas J, Gillum A, Stuart DI, Ravantti JJ, Huiskonen JT, Sundberg LR.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8378-8383. doi: 10.1073/pnas.1703834114. Epub 2017 Jul 17.

3.

Complete Genome Sequence of an Aquaculture-Associated Phage, FL-1, Infecting Flavobacterium spp.

Laanto E, Ravantti JJ, Sundberg LR.

Genome Announc. 2017 Jun 8;5(23). pii: e00014-17. doi: 10.1128/genomeA.00014-17.

4.

HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae.

Demina TA, Pietilä MK, Svirskaitė J, Ravantti JJ, Atanasova NS, Bamford DH, Oksanen HM.

Viruses. 2017 Feb 18;9(2). pii: E32. doi: 10.3390/v9020032. Review.

5.

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification.

Sinclair RM, Ravantti JJ, Bamford DH.

J Virol. 2017 Mar 29;91(8). pii: e02275-16. doi: 10.1128/JVI.02275-16. Print 2017 Apr 15.

6.

Archaeal Haloarcula californiae Icosahedral Virus 1 Highlights Conserved Elements in Icosahedral Membrane-Containing DNA Viruses from Extreme Environments.

Demina TA, Pietilä MK, Svirskaitė J, Ravantti JJ, Atanasova NS, Bamford DH, Oksanen HM.

MBio. 2016 Jul 19;7(4). pii: e00699-16. doi: 10.1128/mBio.00699-16.

7.

Common Structural Core of Three-Dozen Residues Reveals Intersuperfamily Relationships.

Mönttinen HA, Ravantti JJ, Poranen MM.

Mol Biol Evol. 2016 Jul;33(7):1697-710. doi: 10.1093/molbev/msw047. Epub 2016 Mar 1.

PMID:
26931141
8.

Buried Alive: Microbes from Ancient Halite.

Jaakkola ST, Ravantti JJ, Oksanen HM, Bamford DH.

Trends Microbiol. 2016 Feb;24(2):148-160. doi: 10.1016/j.tim.2015.12.002. Epub 2016 Jan 13. Review.

PMID:
26796472
9.

The complete genome of a viable archaeum isolated from 123-million-year-old rock salt.

Jaakkola ST, Pfeiffer F, Ravantti JJ, Guo Q, Liu Y, Chen X, Ma H, Yang C, Oksanen HM, Bamford DH.

Environ Microbiol. 2016 Feb;18(2):565-79. doi: 10.1111/1462-2920.13130. Epub 2016 Jan 18.

PMID:
26628271
10.

The use of phage FCL-2 as an alternative to chemotherapy against columnaris disease in aquaculture.

Laanto E, Bamford JK, Ravantti JJ, Sundberg LR.

Front Microbiol. 2015 Aug 19;6:829. doi: 10.3389/fmicb.2015.00829. eCollection 2015.

11.

New enveloped dsRNA phage from freshwater habitat.

Mäntynen S, Laanto E, Kohvakka A, Poranen MM, Bamford JK, Ravantti JJ.

J Gen Virol. 2015 May;96(Pt 5):1180-9. doi: 10.1099/vir.0.000063. Epub 2015 Jan 22.

PMID:
25614591
12.

Automated structural comparisons clarify the phylogeny of the right-hand-shaped polymerases.

Mönttinen HA, Ravantti JJ, Stuart DI, Poranen MM.

Mol Biol Evol. 2014 Oct;31(10):2741-52. doi: 10.1093/molbev/msu219. Epub 2014 Jul 24.

PMID:
25063440
13.

Plate tectonics of virus shell assembly and reorganization in phage φ8, a distant relative of mammalian reoviruses.

El Omari K, Sutton G, Ravantti JJ, Zhang H, Walter TS, Grimes JM, Bamford DH, Stuart DI, Mancini EJ.

Structure. 2013 Aug 6;21(8):1384-95. doi: 10.1016/j.str.2013.06.017. Epub 2013 Jul 25.

14.

Evidence for a non-catalytic ion-binding site in multiple RNA-dependent RNA polymerases.

Mönttinen HA, Ravantti JJ, Poranen MM.

PLoS One. 2012;7(7):e40581. doi: 10.1371/journal.pone.0040581. Epub 2012 Jul 11.

15.

Snapshot of virus evolution in hypersaline environments from the characterization of a membrane-containing Salisaeta icosahedral phage 1.

Aalto AP, Bitto D, Ravantti JJ, Bamford DH, Huiskonen JT, Oksanen HM.

Proc Natl Acad Sci U S A. 2012 May 1;109(18):7079-84. doi: 10.1073/pnas.1120174109. Epub 2012 Apr 16.

16.

An ancient mechanism for splicing control: U11 snRNP as an activator of alternative splicing.

Verbeeren J, Niemelä EH, Turunen JJ, Will CL, Ravantti JJ, Lührmann R, Frilander MJ.

Mol Cell. 2010 Mar 26;37(6):821-33. doi: 10.1016/j.molcel.2010.02.014.

17.

The single substitution I259T, conserved in the plasminogen activator Pla of pandemic Yersinia pestis branches, enhances fibrinolytic activity.

Haiko J, Kukkonen M, Ravantti JJ, Westerlund-Wikström B, Korhonen TK.

J Bacteriol. 2009 Aug;191(15):4758-66. doi: 10.1128/JB.00489-09. Epub 2009 May 22.

18.

Geminiviruses: a tale of a plasmid becoming a virus.

Krupovic M, Ravantti JJ, Bamford DH.

BMC Evol Biol. 2009 May 21;9:112. doi: 10.1186/1471-2148-9-112.

19.

Insights into the pre-initiation events of bacteriophage phi 6 RNA-dependent RNA polymerase: towards the assembly of a productive binary complex.

Sarin LP, Poranen MM, Lehti NM, Ravantti JJ, Koivunen MR, Aalto AP, van Dijk AA, Stuart DI, Grimes JM, Bamford DH.

Nucleic Acids Res. 2009 Mar;37(4):1182-92. doi: 10.1093/nar/gkn1035. Epub 2009 Jan 7.

20.

Global transcriptional responses of Pseudomonas aeruginosa to phage PRR1 infection.

Ravantti JJ, Ruokoranta TM, Alapuranen AM, Bamford DH.

J Virol. 2008 Mar;82(5):2324-9. Epub 2007 Dec 12.

21.
22.

Global changes in cellular gene expression during bacteriophage PRD1 infection.

Poranen MM, Ravantti JJ, Grahn AM, Gupta R, Auvinen P, Bamford DH.

J Virol. 2006 Aug;80(16):8081-8.

23.

Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica.

Bamford DH, Ravantti JJ, Rönnholm G, Laurinavicius S, Kukkaro P, Dyall-Smith M, Somerharju P, Kalkkinen N, Bamford JK.

J Virol. 2005 Jul;79(14):9097-107.

24.

A snapshot of viral evolution from genome analysis of the tectiviridae family.

Saren AM, Ravantti JJ, Benson SD, Burnett RM, Paulin L, Bamford DH, Bamford JK.

J Mol Biol. 2005 Jul 15;350(3):427-40.

PMID:
15946683
25.
26.

A data mining approach for analyzing density maps representing macromolecular structures.

Ravantti JJ, Bamford DH.

J Struct Biol. 1999 Apr-May;125(2-3):216-22.

PMID:
10222277

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