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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.


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.


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;476:304-15. doi: 10.1016/j.virol.2014.12.012. Epub 2015 Jan 7.


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.


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.


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.


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.


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.


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.


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.


Natural history of S-adenosylmethionine-binding proteins.

Kozbial PZ, Mushegian AR.

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


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.


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.


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.


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.


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.


Annotations of biochemically uncharacterized open reading frames (ORFs)

Mushegian AR.

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


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.

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