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Items: 1 to 50 of 54

1.

Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018).

Siddell SG, Walker PJ, Lefkowitz EJ, Mushegian AR, Adams MJ, Dutilh BE, Gorbalenya AE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert M, Rubino L, Sabanadzovic S, Sanfaçon H, Simmonds P, Varsani A, Zerbini FM, Davison AJ.

Arch Virol. 2019 Jan 20. doi: 10.1007/s00705-018-04136-2. [Epub ahead of print]

PMID:
30663020
2.

Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018).

King AMQ, Lefkowitz EJ, Mushegian AR, Adams MJ, Dutilh BE, Gorbalenya AE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert ML, Rubino L, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Davison AJ.

Arch Virol. 2018 May 12. doi: 10.1007/s00705-018-3847-1. [Epub ahead of print]

PMID:
29754305
3.

Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017).

Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ.

Arch Virol. 2017 Aug;162(8):2505-2538. doi: 10.1007/s00705-017-3358-5. Epub 2017 Apr 22.

PMID:
28434098
4.

50 years of the International Committee on Taxonomy of Viruses: progress and prospects.

Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert ML, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Orton RJ, Smith DB, Gorbalenya AE, Davison AJ.

Arch Virol. 2017 May;162(5):1441-1446. doi: 10.1007/s00705-016-3215-y. Epub 2017 Jan 11.

PMID:
28078475
5.

Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials.

Postler TS, Clawson AN, Amarasinghe GK, Basler CF, Bavari S, Benko M, Blasdell KR, Briese T, Buchmeier MJ, Bukreyev A, Calisher CH, Chandran K, Charrel R, Clegg CS, Collins PL, Juan Carlos T, Derisi JL, Dietzgen RG, Dolnik O, Dürrwald R, Dye JM, Easton AJ, Emonet S, Formenty P, Fouchier RAM, Ghedin E, Gonzalez JP, Harrach B, Hewson R, Horie M, Jiang D, Kobinger G, Kondo H, Kropinski AM, Krupovic M, Kurath G, Lamb RA, Leroy EM, Lukashevich IS, Maisner A, Mushegian AR, Netesov SV, Nowotny N, Patterson JL, Payne SL, PaWeska JT, Peters CJ, Radoshitzky SR, Rima BK, Romanowski V, Rubbenstroth D, Sabanadzovic S, Sanfaçon H, Salvato MS, Schwemmle M, Smither SJ, Stenglein MD, Stone DM, Takada A, Tesh RB, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Volchkov VE, Wahl-Jensen V, Walker PJ, Wang LF, Varsani A, Whitfield AE, Zerbini FM, Kuhn JH.

Syst Biol. 2017 May 1;66(3):463-473. doi: 10.1093/sysbio/syw096.

6.

Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016).

Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ.

Arch Virol. 2016 Oct;161(10):2921-49. doi: 10.1007/s00705-016-2977-6. Epub 2016 Jul 16.

PMID:
27424026
7.

Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe.

Artamonova II, Lappi T, Zudina L, Mushegian AR.

Environ Microbiol. 2015 Jul;17(7):2203-8. doi: 10.1111/1462-2920.12854. Epub 2015 Apr 28.

PMID:
25919787
8.

Distinct circular single-stranded DNA viruses exist in different soil types.

Reavy B, Swanson MM, Cock PJ, Dawson L, Freitag TE, Singh BK, Torrance L, Mushegian AR, Taliansky M.

Appl Environ Microbiol. 2015 Jun 15;81(12):3934-45. doi: 10.1128/AEM.03878-14. Epub 2015 Apr 3.

9.

Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes.

Mushegian AR, Elena SF.

Virology. 2015 Feb;476:304-315. doi: 10.1016/j.virol.2014.12.012. Epub 2015 Jan 7.

10.

Chordopoxvirus protein F12 implicated in enveloped virion morphogenesis is an inactivated DNA polymerase.

Yutin N, Faure G, Koonin EV, Mushegian AR.

Biol Direct. 2014 Nov 6;9(1):22. doi: 10.1186/1745-6150-9-22.

11.

Genome sequence analysis indicates that the model eukaryote Nematostella vectensis harbors bacterial consorts.

Artamonova II, Mushegian AR.

Appl Environ Microbiol. 2013 Nov;79(22):6868-73. doi: 10.1128/AEM.01635-13. Epub 2013 Aug 30.

12.

Orthologous gene clusters and taxon signature genes for viruses of prokaryotes.

Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV.

J Bacteriol. 2013 Mar;195(5):941-50. doi: 10.1128/JB.01801-12. Epub 2012 Dec 7.

13.

Computational methods for Gene Orthology inference.

Kristensen DM, Wolf YI, Mushegian AR, Koonin EV.

Brief Bioinform. 2011 Sep;12(5):379-91. doi: 10.1093/bib/bbr030. Epub 2011 Jun 19.

14.

New dimensions of the virus world discovered through metagenomics.

Kristensen DM, Mushegian AR, Dolja VV, Koonin EV.

Trends Microbiol. 2010 Jan;18(1):11-9. doi: 10.1016/j.tim.2009.11.003. Epub 2009 Nov 26.

15.

Comparison of pattern detection methods in microarray time series of the segmentation clock.

Dequéant ML, Ahnert S, Edelsbrunner H, Fink TM, Glynn EF, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian AR, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquié O.

PLoS One. 2008 Aug 6;3(8):e2856. doi: 10.1371/journal.pone.0002856.

16.

Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms.

Glynn EF, Chen J, Mushegian AR.

Bioinformatics. 2006 Feb 1;22(3):310-6. Epub 2005 Nov 22.

PMID:
16303799
17.

Natural history of S-adenosylmethionine-binding proteins.

Kozbial PZ, Mushegian AR.

BMC Struct Biol. 2005 Oct 14;5:19.

18.
19.

Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomes.

Melko OM, Mushegian AR.

Bioinformatics. 2004 Jan 1;20(1):67-74.

PMID:
14693810
20.

The evolution of Runx genes I. A comparative study of sequences from phylogenetically diverse model organisms.

Rennert J, Coffman JA, Mushegian AR, Robertson AJ.

BMC Evol Biol. 2003 Mar 24;3:4. Epub 2003 Mar 24.

21.

SHORT INTEGUMENTS1/SUSPENSOR1/CARPEL FACTORY, a Dicer homolog, is a maternal effect gene required for embryo development in Arabidopsis.

Golden TA, Schauer SE, Lang JD, Pien S, Mushegian AR, Grossniklaus U, Meinke DW, Ray A.

Plant Physiol. 2002 Oct;130(2):808-22.

22.

Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.

Iyer LM, Aravind L, Bork P, Hofmann K, Mushegian AR, Zhulin IB, Koonin EV.

Genome Biol. 2001;2(12):RESEARCH0051. Epub 2001 Nov 13.

23.

Functional specialization and evolution of leader proteinases in the family Closteroviridae.

Peng CW, Peremyslov VV, Mushegian AR, Dawson WO, Dolja VV.

J Virol. 2001 Dec;75(24):12153-60.

24.

Conserved phosphoprotein interaction motif is functionally interchangeable between ataxin-7 and arrestins.

Mushegian AR, Vishnivetskiy SA, Gurevich VV.

Biochemistry. 2000 Jun 13;39(23):6809-13.

PMID:
10841760
25.

Annotations of biochemically uncharacterized open reading frames (ORFs)

Mushegian AR.

Mol Microbiol. 2000 Feb;35(3):697-8. No abstract available.

26.

Computer analysis of amino acid sequences. The case of plant virus capsid proteins.

Koonin EV, Mushegian AR, Dolja VV.

Methods Mol Biol. 1998;81:319-37. No abstract available.

PMID:
9760522
28.

A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases.

Morozov V, Mushegian AR, Koonin EV, Bork P.

Trends Biochem Sci. 1997 Nov;22(11):417-8. Review. No abstract available.

PMID:
9397680
30.

The Drosophila Beat protein is related to adhesion proteins that contain immunoglobulin domains.

Mushegian AR.

Curr Biol. 1997 Jun 1;7(6):R336-8. No abstract available.

31.

Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs.

Mushegian AR, Bassett DE Jr, Boguski MS, Bork P, Koonin EV.

Proc Natl Acad Sci U S A. 1997 May 27;94(11):5831-6.

32.

Discrete regions of the sensor protein virA determine the strain-specific ability of Agrobacterium to agroinfect maize.

Heath JD, Boulton MI, Raineri DM, Doty SL, Mushegian AR, Charles TC, Davies JW, Nester EW.

Mol Plant Microbe Interact. 1997 Mar;10(2):221-7.

33.

Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics.

Koonin EV, Mushegian AR.

Curr Opin Genet Dev. 1996 Dec;6(6):757-62. Review.

PMID:
8994848
34.

The SPO1 gene product required for meiosis in yeast has a high similarity to phospholipase B enzymes.

Tevzadze GG, Mushegian AR, Esposito RE.

Gene. 1996 Oct 24;177(1-2):253-5.

PMID:
8921875
35.
36.

A minimal gene set for cellular life derived by comparison of complete bacterial genomes.

Mushegian AR, Koonin EV.

Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10268-73.

37.

Non-orthologous gene displacement.

Koonin EV, Mushegian AR, Bork P.

Trends Genet. 1996 Sep;12(9):334-6. No abstract available.

PMID:
8855656
38.

Evidence for selection in evolution of alpha satellite DNA: the central role of CENP-B/pJ alpha binding region.

Romanova LY, Deriagin GV, Mashkova TD, Tumeneva IG, Mushegian AR, Kisselev LL, Alexandrov IA.

J Mol Biol. 1996 Aug 23;261(3):334-40.

PMID:
8780776
39.

Gene order is not conserved in bacterial evolution.

Mushegian AR, Koonin EV.

Trends Genet. 1996 Aug;12(8):289-90. No abstract available.

PMID:
8783936
40.

A family of lysozyme-like virulence factors in bacterial pathogens of plants and animals.

Mushegian AR, Fullner KJ, Koonin EV, Nester EW.

Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7321-6.

41.

Organization of the 3'-terminal half of beet yellow stunt virus genome and implications for the evolution of closteroviruses.

Karasev AV, Nikolaeva OV, Mushegian AR, Lee RF, Dawson WO.

Virology. 1996 Jul 1;221(1):199-207.

42.

Sequencing and analysis of bacterial genomes.

Koonin EV, Mushegian AR, Rudd KE.

Curr Biol. 1996 Apr 1;6(4):404-16. Review.

43.

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli.

Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV.

Curr Biol. 1996 Mar 1;6(3):279-91.

44.

Genetic elements of plant viruses as tools for genetic engineering.

Mushegian AR, Shepherd RJ.

Microbiol Rev. 1995 Dec;59(4):548-78. Review.

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