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Items: 1 to 50 of 73

1.

Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism.

Bäckström D, Yutin N, Jørgensen SL, Dharamshi J, Homa F, Zaremba-Niedwiedzka K, Spang A, Wolf YI, Koonin EV, Ettema TJG.

mBio. 2019 Mar 5;10(2). pii: e02497-18. doi: 10.1128/mBio.02497-18.

2.

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.

Alneberg J, Karlsson CMG, Divne AM, Bergin C, Homa F, Lindh MV, Hugerth LW, Ettema TJG, Bertilsson S, Andersson AF, Pinhassi J.

Microbiome. 2018 Sep 28;6(1):173. doi: 10.1186/s40168-018-0550-0.

3.

Evolutionary forces affecting synonymous variations in plant genomes.

Clément Y, Sarah G, Holtz Y, Homa F, Pointet S, Contreras S, Nabholz B, Sabot F, Sauné L, Ardisson M, Bacilieri R, Besnard G, Berger A, Cardi C, De Bellis F, Fouet O, Jourda C, Khadari B, Lanaud C, Leroy T, Pot D, Sauvage C, Scarcelli N, Tregear J, Vigouroux Y, Yahiaoui N, Ruiz M, Santoni S, Labouisse JP, Pham JL, David J, Glémin S.

PLoS Genet. 2017 May 22;13(5):e1006799. doi: 10.1371/journal.pgen.1006799. eCollection 2017 May.

4.

Herpesvirus Capsid Assembly and DNA Packaging.

Heming JD, Conway JF, Homa FL.

Adv Anat Embryol Cell Biol. 2017;223:119-142. doi: 10.1007/978-3-319-53168-7_6. Review.

5.

The C Terminus of the Herpes Simplex Virus UL25 Protein Is Required for Release of Viral Genomes from Capsids Bound to Nuclear Pores.

Huffman JB, Daniel GR, Falck-Pedersen E, Huet A, Smith GA, Conway JF, Homa FL.

J Virol. 2017 Jul 12;91(15). pii: e00641-17. doi: 10.1128/JVI.00641-17. Print 2017 Aug 1.

6.

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.

Hammond M, Homa F, Andersson-Svahn H, Ettema TJ, Joensson HN.

Microbiome. 2016 Oct 6;4(1):52.

7.

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives.

Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, Chair H, Scarcelli N, Billot C, Yahiaoui N, Bacilieri R, Khadari B, Boccara M, Barnaud A, Péros JP, Labouisse JP, Pham JL, David J, Glémin S, Ruiz M.

Mol Ecol Resour. 2017 May;17(3):565-580. doi: 10.1111/1755-0998.12587. Epub 2016 Aug 29.

PMID:
27487989
8.

Extensive subunit contacts underpin herpesvirus capsid stability and interior-to-exterior allostery.

Huet A, Makhov AM, Huffman JB, Vos M, Homa FL, Conway JF.

Nat Struct Mol Biol. 2016 Jun;23(6):531-9. doi: 10.1038/nsmb.3212. Epub 2016 Apr 25.

9.

Exploring the Balance between DNA Pressure and Capsid Stability in Herpesviruses and Phages.

Bauer DW, Li D, Huffman J, Homa FL, Wilson K, Leavitt JC, Casjens SR, Baines J, Evilevitch A.

J Virol. 2015 Sep;89(18):9288-98. doi: 10.1128/JVI.01172-15. Epub 2015 Jul 1.

10.

SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.

Dereeper A, Homa F, Andres G, Sempere G, Sarah G, Hueber Y, Dufayard JF, Ruiz M.

Nucleic Acids Res. 2015 Jul 1;43(W1):W295-300. doi: 10.1093/nar/gkv351. Epub 2015 Jun 3.

11.

Genome-wide prediction methods in highly diverse and heterozygous species: proof-of-concept through simulation in grapevine.

Fodor A, Segura V, Denis M, Neuenschwander S, Fournier-Level A, Chatelet P, Homa FA, Lacombe T, This P, Le Cunff L.

PLoS One. 2014 Nov 3;9(11):e110436. doi: 10.1371/journal.pone.0110436. eCollection 2014.

12.

Solid-to-fluid DNA transition inside HSV-1 capsid close to the temperature of infection.

Sae-Ueng U, Li D, Zuo X, Huffman JB, Homa FL, Rau D, Evilevitch A.

Nat Chem Biol. 2014 Oct;10(10):861-7. doi: 10.1038/nchembio.1628. Epub 2014 Sep 7. Erratum in: Nat Chem Biol. 2015 Feb;11(2):172.

13.

Major capsid reinforcement by a minor protein in herpesviruses and phage.

Sae-Ueng U, Liu T, Catalano CE, Huffman JB, Homa FL, Evilevitch A.

Nucleic Acids Res. 2014 Aug;42(14):9096-107. doi: 10.1093/nar/gku634. Epub 2014 Jul 22.

14.

Isolation and characterization of the herpes simplex virus 1 terminase complex.

Heming JD, Huffman JB, Jones LM, Homa FL.

J Virol. 2014 Jan;88(1):225-36. doi: 10.1128/JVI.02632-13. Epub 2013 Oct 23.

15.

Herpes virus genome, the pressure is on.

Bauer DW, Huffman JB, Homa FL, Evilevitch A.

J Am Chem Soc. 2013 Jul 31;135(30):11216-21. doi: 10.1021/ja404008r. Epub 2013 Jul 23.

16.

Structure of the pseudorabies virus capsid: comparison with herpes simplex virus type 1 and differential binding of essential minor proteins.

Homa FL, Huffman JB, Toropova K, Lopez HR, Makhov AM, Conway JF.

J Mol Biol. 2013 Sep 23;425(18):3415-28. doi: 10.1016/j.jmb.2013.06.034. Epub 2013 Jul 1.

17.

The herpes simplex virus 1 UL17 protein is the second constituent of the capsid vertex-specific component required for DNA packaging and retention.

Toropova K, Huffman JB, Homa FL, Conway JF.

J Virol. 2011 Aug;85(15):7513-22. doi: 10.1128/JVI.00837-11. Epub 2011 Jun 1.

18.

Residues of the UL25 protein of herpes simplex virus that are required for its stable interaction with capsids.

Cockrell SK, Huffman JB, Toropova K, Conway JF, Homa FL.

J Virol. 2011 May;85(10):4875-87. doi: 10.1128/JVI.00242-11. Epub 2011 Mar 16.

19.

Labeling and localization of the herpes simplex virus capsid protein UL25 and its interaction with the two triplexes closest to the penton.

Conway JF, Cockrell SK, Copeland AM, Newcomb WW, Brown JC, Homa FL.

J Mol Biol. 2010 Mar 26;397(2):575-86. doi: 10.1016/j.jmb.2010.01.043. Epub 2010 Jan 25.

20.

Polarized DNA ejection from the herpesvirus capsid.

Newcomb WW, Cockrell SK, Homa FL, Brown JC.

J Mol Biol. 2009 Oct 2;392(4):885-94. doi: 10.1016/j.jmb.2009.07.052. Epub 2009 Jul 23.

21.

Role of the UL25 protein in herpes simplex virus DNA encapsidation.

Cockrell SK, Sanchez ME, Erazo A, Homa FL.

J Virol. 2009 Jan;83(1):47-57. doi: 10.1128/JVI.01889-08. Epub 2008 Oct 22.

22.

Amino acids 143 to 150 of the herpes simplex virus type 1 scaffold protein are required for the formation of portal-containing capsids.

Huffman JB, Newcomb WW, Brown JC, Homa FL.

J Virol. 2008 Jul;82(13):6778-81. doi: 10.1128/JVI.00473-08. Epub 2008 Apr 16.

23.

Allosteric signaling and a nuclear exit strategy: binding of UL25/UL17 heterodimers to DNA-Filled HSV-1 capsids.

Trus BL, Newcomb WW, Cheng N, Cardone G, Marekov L, Homa FL, Brown JC, Steven AC.

Mol Cell. 2007 May 25;26(4):479-89.

24.
27.

Crystal structure of the herpes simplex virus 1 DNA polymerase.

Liu S, Knafels JD, Chang JS, Waszak GA, Baldwin ET, Deibel MR Jr, Thomsen DR, Homa FL, Wells PA, Tory MC, Poorman RA, Gao H, Qiu X, Seddon AP.

J Biol Chem. 2006 Jun 30;281(26):18193-200. Epub 2006 Apr 24.

28.

4-Oxo-4,7-dihydrothieno[2,3-b]pyridines as non-nucleoside inhibitors of human cytomegalovirus and related herpesvirus polymerases.

Schnute ME, Cudahy MM, Brideau RJ, Homa FL, Hopkins TA, Knechtel ML, Oien NL, Pitts TW, Poorman RA, Wathen MW, Wieber JL.

J Med Chem. 2005 Sep 8;48(18):5794-804.

PMID:
16134946
29.

Involvement of the portal at an early step in herpes simplex virus capsid assembly.

Newcomb WW, Homa FL, Brown JC.

J Virol. 2005 Aug;79(16):10540-6.

30.

Identification of a region in the herpes simplex virus scaffolding protein required for interaction with the portal.

Singer GP, Newcomb WW, Thomsen DR, Homa FL, Brown JC.

J Virol. 2005 Jan;79(1):132-9.

31.

Structure and polymorphism of the UL6 portal protein of herpes simplex virus type 1.

Trus BL, Cheng N, Newcomb WW, Homa FL, Brown JC, Steven AC.

J Virol. 2004 Nov;78(22):12668-71.

32.

Herpes simplex virus type 1 capsid protein VP26 interacts with dynein light chains RP3 and Tctex1 and plays a role in retrograde cellular transport.

Douglas MW, Diefenbach RJ, Homa FL, Miranda-Saksena M, Rixon FJ, Vittone V, Byth K, Cunningham AL.

J Biol Chem. 2004 Jul 2;279(27):28522-30. Epub 2004 Apr 26.

35.

The UL6 gene product forms the portal for entry of DNA into the herpes simplex virus capsid.

Newcomb WW, Juhas RM, Thomsen DR, Homa FL, Burch AD, Weller SK, Brown JC.

J Virol. 2001 Nov;75(22):10923-32.

36.
37.

New antiherpetic 1,3-phenylene derivatives, inhibitors of the interaction of the HSV-1 origin binding protein (OBP) with DNA.

Font M, Sanmartín C, Alonso ML, Gracia L, Losa MJ, Marquiegui B, Merino I, Nadal E, Ruiz I, Monge A, Bengoechea MT, Cabodevilla F, Elena S, Martinez-Irujo JJ, Odriozola L, Peñuelas I, Santiago E, Homa F, Wathen MW.

Drug Des Discov. 2000;16(4):295-315.

PMID:
10807035
38.
39.

Assembly of the herpes simplex virus capsid: preformed triplexes bind to the nascent capsid.

Spencer JV, Newcomb WW, Thomsen DR, Homa FL, Brown JC.

J Virol. 1998 May;72(5):3944-51.

40.

The product of the herpes simplex virus type 1 UL25 gene is required for encapsidation but not for cleavage of replicated viral DNA.

McNab AR, Desai P, Person S, Roof LL, Thomsen DR, Newcomb WW, Brown JC, Homa FL.

J Virol. 1998 Feb;72(2):1060-70.

41.

Hexon-only binding of VP26 reflects differences between the hexon and penton conformations of VP5, the major capsid protein of herpes simplex virus.

Wingfield PT, Stahl SJ, Thomsen DR, Homa FL, Booy FP, Trus BL, Steven AC.

J Virol. 1997 Dec;71(12):8955-61.

42.

Capsid assembly and DNA packaging in herpes simplex virus.

Homa FL, Brown JC.

Rev Med Virol. 1997 Jul;7(2):107-122.

PMID:
10398476
43.

Assembly of herpes simplex virus capsids using the human cytomegalovirus scaffold protein: critical role of the C terminus.

Oien NL, Thomsen DR, Wathen MW, Newcomb WW, Brown JC, Homa FL.

J Virol. 1997 Feb;71(2):1281-91.

44.

The herpes simplex virus procapsid: structure, conformational changes upon maturation, and roles of the triplex proteins VP19c and VP23 in assembly.

Trus BL, Booy FP, Newcomb WW, Brown JC, Homa FL, Thomsen DR, Steven AC.

J Mol Biol. 1996 Nov 1;263(3):447-62.

PMID:
8918600
45.

Assembly of the herpes simplex virus capsid: characterization of intermediates observed during cell-free capsid formation.

Newcomb WW, Homa FL, Thomsen DR, Booy FP, Trus BL, Steven AC, Spencer JV, Brown JC.

J Mol Biol. 1996 Nov 1;263(3):432-46.

PMID:
8918599
46.

Organization of a human UDP-GalNAc:polypeptide, N-acetylgalactosaminyltransferase gene and a related processed pseudogene.

Meurer JA, Drong RF, Homa FL, Slightom JL, Elhammer AP.

Glycobiology. 1996 Mar;6(2):231-41.

PMID:
8727794
48.

Herpes simplex virus capsids assembled in insect cells infected with recombinant baculoviruses: structural authenticity and localization of VP26.

Trus BL, Homa FL, Booy FP, Newcomb WW, Thomsen DR, Cheng N, Brown JC, Steven AC.

J Virol. 1995 Nov;69(11):7362-6.

49.

cDNA cloning, expression, and chromosomal localization of a human UDP-GalNAc:polypeptide, N-acetylgalactosaminyltransferase.

Meurer JA, Naylor JM, Baker CA, Thomsen DR, Homa FL, Elhammer AP.

J Biochem. 1995 Sep;118(3):568-74.

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