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border=0>Research Overview</TD></TR></TBODY></TABLE>
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<!-----Research Overview text---->
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<SPAN class=SMALL1>
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<P>This web site is currently maintained by Michael Y. Galperin (<A href="ftp://ftp.ncbi.nih.gov/pub/galperin/Papers/CV.html">CV</A>, <A href="ftp://ftp.ncbi.nih.gov/pub/galperin/Papers/CV.html#Publications">publications</A>,
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<A href="ftp://ftp.ncbi.nih.gov/pub/galperin/Papers/index.html">short bio</A>) and describes some of the studies of complete microbial genomes performed by the
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<A href="https://www.ncbi.nlm.nih.gov/CBBresearch/Koonin/">Eugene Koonin's research group</A>
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at the NCBI's <A href="https://www.ncbi.nlm.nih.gov/CBBresearch/">Computational Biology Branch (CBB)</A>.
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<P>The key results include:
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<DT>- prediction of protein functions based on a variety of computer analyses</DT>
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<DT>- delineation of Clusters of Orthologous Groups of proteins</DT>
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<DT>- reconstruction of certain biochemical pathways</DT>
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<DT>- analysis of signal transduction systems in various bacteria and archaea</FONT></DT></DL>
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<UL>
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<LI><B><A HREF="https://www.ncbi.nlm.nih.gov/COG/">Clusters of Orthologous Groups (COGs)</A></FONT></B></LI>
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<LI><B><A HREF="https://www.ncbi.nlm.nih.gov/Complete_Genomes/COGupdate.html">Recently revised COG names</A></FONT></B></LI>
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<LI><B><A HREF="https://www.ncbi.nlm.nih.gov/Complete_Genomes/AnalEnzymes.html">Analogous enzymes</A></FONT></B></LI>
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<LI><B><A HREF="https://www.ncbi.nlm.nih.gov/Complete_Genomes/SignalCensus.html">Census of bacterial signal transduction proteins</A></FONT></B></LI>
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<LI><B><A HREF="https://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html">Census of bacterial response regulators</A> </FONT>(Jan. 2011 update)</B></LI>
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<LI><B><A HREF="https://www.ncbi.nlm.nih.gov/Complete_Genomes/c-di-GMP.html">Census of c-di-GMP-related proteins</A></FONT>(Sept. 2016 update)</B></LI>
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<LI><B><A HREF="https://www.ncbi.nlm.nih.gov/Complete_Genomes/LytTR.html">Listing of LytTR domain proteins</A></FONT></B></LI>
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</UL>
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</P><!-- Articles -->
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<TD class=H4 width=465 bgColor=#ccccff><IMG height=14 alt="blue bullet" src="https://www.ncbi.nlm.nih.gov/corehtml/bluebullet.gif"
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width=16 border=0>References</TD></TR></TBODY></TABLE>
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<P>1. The book <A href="https://www.ncbi.nlm.nih.gov/pubmed/21089240"><B>Sequence - Evolution - Function. Computational Approaches
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in Comparative Genomics</B></a> by E. V. Koonin and M. Y. Galperin was published
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in October 2002 by Kluwer Academic Publishers, Boston (currently <A href="http://www.springeronline.com/sgw/cda/frontpage/0,11855,4-40109-22-33269241-0,00.html">Springer</A>).
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<BR>The <A HREF="https://www.ncbi.nlm.nih.gov/books/NBK20260/"><B>full text of the book</B></a> is now freely available
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on the NCBI's <A HREF="https://www.ncbi.nlm.nih.gov/books"><B>Bookshelf</B></A></FONT>.
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<P>Some relevant papers (click <A href="https://www.ncbi.nlm.nih.gov/pubmed/?term=galperin+my%5Bau%5D"><B>here for the complete list</B></A>):<P>
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<P><B>Genome annotation</B><P>
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1. Tatusov R.L., Galperin M.Y., Natale D.A. and Koonin E.V. (2000) <FONT color=blue><B>The COG database: a tool for genome-scale analysis of protein functions and evolution</B></FONT>. <I>Nucleic Acids Res. </I><b>28</b>: 33-36.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/10592175">Abstract</A>.
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<A HREF="https://www.pubmedcentral.nih.gov/picrender.fcgi?artid=102395&action=stream&blobtype=pdf">Full text (PDF)</A></FONT>.<P>
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2. Galperin M.Y. and Koonin E.V. (2000) <B><FONT color=blue>Who's your neighbor? New computational approaches for functional genomics.</B></FONT> <I>Nature Biotech.</I> <B>18</B>: 609-613.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/10835597">Abstract</A>.
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<A HREF="mailto:galperin@ncbi.nlm.nih.gov?subject=Reprint request &body=Dear Dr. Galperin -%0a%0aPlease send a reprint of the article: Who's your neighbor? New computational approaches for functional genomics - to the following address:">Request reprint</A>.</FONT><P>
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3. Galperin M.Y., Moroz O.V., Wilson K.S. and Murzin A.G. (2006) <FONT color=blue><B>House cleaning, a part of good housekeeping. </B></FONT> <I>Mol. Microbiol.</I> <B>59</B>: 5-19.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/16359314">Abstract</A>.
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<A HREF="http://www.blackwell-synergy.com/doi/full/10.1111/j.1365-2958.2005.04950.x"> Full text (HTML)</A>.
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<A HREF="http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1365-2958.2005.04950.x">Full text (PDF)</A>.</FONT></P>
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4. Galperin M.Y. and Koonin E.V. (2010) <FONT color=blue><B>From complete genome sequence to 'complete' understanding?</B></FONT> <I>Trends Biotech.</I> <B>28</B>: 398-406.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/20647113">Abstract</A>.
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<A HREF="http://dx.doi.org/10.1016/j.tibtech.2010.05.006">Article outline</A>
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<A HREF="ftp://ftp.ncbi.nih.gov/pub/galperin/Papers/Understanding_TIBtech2010.pdf">Full text (PDF)</A>.</FONT></LI></FONT><P>
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5. Galperin M.Y., Makarova K.S., Wolf Y.I. and Koonin E.V. (2015) <FONT color=blue><B>Expanded microbial genome coverage and improved protein family annotation in the COG database.</B></FONT> <I>Nucleic Acids Res.</I> <B>43</B>: D261-D269.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/25428365">Abstract</A>.
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<A HREF="http://nar.oxfordjournals.org/content/43/D1/D261.long">Full text</A>.</FONT></LI></FONT><P>
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<P><B>Evolution</B><P>
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1. Mulkidjanian A.Y., Cherepanov D.A. and Galperin M.Y. (2003) <FONT color=blue><B>Survival of the fittest before the beginning of life: selection of the first
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oligonucleotide-like polymers by UV light.</B></FONT> <I>BMC Evol Biol. </I> <B>3</B>: 12.
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<A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12773209">Abstract</A>.
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<A HREF="http://www.biomedcentral.com/1471-2148/3/12"> Full text (HTML)</A>.
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<A HREF="http://www.biomedcentral.com/content/pdf/1471-2148-3-12.pdf">Full text (PDF)</A>.</FONT></P>
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2. Mulkidjanian A.Y., Makarova K.S., Galperin M.Y. and Koonin E.V. (2007) <FONT color=blue><B>Inventing the dynamo machine: the evolution of the F-type and V-type ATPases.</B></FONT> <I>Nature Rev. Microbiol.</I> <B>5</B>: 892-899.
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<A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17938630">Abstract</A>.
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<A HREF="mailto:galperin@ncbi.nlm.nih.gov?subject=Reprint request &body=Dear Dr. Galperin -%0a%0aPlease send a reprint of the article: Inventing the dynamo machine: the evolution of the F-type and V-type ATPases - to the following address:">Request reprint</A>.</FONT><P>
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3. Mulkidjanian A.Y. and Galperin M.Y. (2009) <FONT color=blue><B>On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
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</B></FONT> <I>Biology Direct</I> <B>4</B>: 27.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/19703275">Abstract</A>.
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<A HREF="http://www.biology-direct.com/content/4/1/27"> Full text</A>.<P>
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4. Omelchenko M.V., Galperin M.Y., Wolf Y.I., and Koonin E.V. (2010) <FONT color=blue><B>Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.
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</B></FONT> <I>Biology Direct</I> <B>5</B>: 31.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/20433725">Abstract</A>.
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<A HREF="http://www.biology-direct.com/content/5/1/31"> Full text</A>.<P>
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5. Mulkidjanian A.Y,, Bychkov A.Y., Dibrova D.V., Galperin M.Y. and Koonin E.V. (2012) <FONT color=blue><B>Origin of first cells at terrestrial, anoxic geothermal fields</B></FONT> <I>Proc Natl Acad Sci USA</I> <B>109</B>: E821-E830.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/22331915">Abstract</A>.
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<A HREF="http://www.pnas.org/content/109/14/E821.long"> Full text</A>.
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<P><B>Signal transduction</B><P>
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1. Galperin M.Y. (2004) <FONT color=blue><B>Bacterial signal transduction network in a genomic perspective.</B></FONT> <I>Environ. Microbiol.</I> <B>6</B>: 552-567.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/15142243">Abstract</A>.
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<A HREF="http://www.blackwell-synergy.com/doi/full/10.1111/j.1462-2920.2004.00633.x">Full text (HTML)</A>.
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<A HREF="http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1462-2920.2004.00633.x">Full text (PDF)</A>.<P>
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2. Galperin M.Y. (2005) <FONT color=blue><B>A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts. </B></FONT> <I>BMC Microbiol.</I> <B>5</B>: 35.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/15955239">Abstract</A>.
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<A HREF="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1183210/">Full text (HTML)</A>.
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<A HREF="https://www.biomedcentral.com/content/pdf/1471-2180-5-35.pdf">Full text (PDF)</A>.<P>
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3. Galperin M.Y. and Gomelsky M. (2005) <FONT color=blue><B>Bacterial signal transduction modules: from genomics to biology.</B></FONT> <I>ASM News</I> <B>71</B>: 326-333.
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<A HREF="ftp://ftp.ncbi.nih.gov/pub/galperin/Papers/ASMnews2005.pdf">Full text (PDF)</A>.<P>
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4. Romling U., Gomelsky M. and Galperin M.Y. (2005) <FONT color=blue><B>C-di-GMP: the dawning of a novel bacterial signalling system. </B></FONT> <I>Mol. Microbiol.</I> <B>57</B>: 629-639.
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<A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16045609&query_hl=1">Abstract</A>.
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<A HREF="http://www.blackwell-synergy.com/doi/full/10.1111/j.1365-2958.2005.04697.x"> Full text (HTML)</A>.
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<A HREF="http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1365-2958.2005.04697.x">Full text (PDF)</A>.</FONT><P>
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5. Amikam D. and Galperin M.Y. (2006) <FONT color=blue><B>PilZ domain is part of the bacterial c-di-GMP binding protein. </B></FONT> <I>Bioinformatics</I> <B>22</B>: 3-6.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/16249258">Abstract</A>.
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<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/full/22/1/3"> Full text (HTML)</A>.
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<A HREF="http://bioinformatics.oxfordjournals.org/cgi/reprint/22/1/3.pdf"> Full text (PDF)<A>.<P>
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6. Galperin M.Y. (2006) <FONT color=blue><B>Structural classification of bacterial response regulators: Diversity of output domains and domain combinations</B></FONT>.<I> J. Bacteriol.</I> <B>188</B>: 4169-4182.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/16740923">Abstract</A>.
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<A HREF="http://jb.asm.org/cgi/content/full/188/12/4169"> Full text (HTML)</A>.
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<A HREF="https://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html">Supplementary Table</A>.<P>
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7. Galperin M.Y. (2010) <FONT color=blue><B>Diversity of structure and function of response regulator output domains</B></FONT>.<I> Curr. Opin. Microbiol.</I> <B>13</B>: 150-159.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/20226724">Abstract</A>.
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<A HREF="http://dx.doi.org/10.1016/j.mib.2010.01.005"> Article outline</A>.
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<A HREF="ftp://ftp.ncbi.nih.gov/pub/galperin/Papers/RRoutputs_COMic2010.pdf"> Full text (PDF)<A>.
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<A HREF="https://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html">Supplementary Table</A>.<P>
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8. R<>mling U., Galperin M.Y. and Gomelsky M. (2013) <FONT color=blue><B>Cyclic di-GMP: the first 25 years of a universal bacterial second messenger.</B></FONT> <I>Microbiol Mol Biol Rev.</I> <B>77</B>: 1-52.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/23471616">Abstract</A>.
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<A HREF="http://mmbr.asm.org/content/77/1/1.long"> Full text (HTML)</A>.
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<A HREF="http://mmbr.asm.org/content/77/1/1.full.pdf">Full text (PDF)</A>.<P>
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9. Chou S.-H. and Galperin M.Y. (2016) <FONT color=blue><B>Diversity of cyclic di-GMP-binding proteins and mechanisms.</B></FONT> <I>J Bacteriol.</I> <B>198</B>: 32-46.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/26055114">Abstract</A>.
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<A HREF="http://jb.asm.org/content/198/1/32.long"> Full text</A>.
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<A HREF="mailto:galperin@ncbi.nlm.nih.gov?subject=Reprint request &body=Dear Dr. Galperin -%0a%0aPlease send a reprint of the article: Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms - to the following address:">Request reprint</A>.</FONT><P>
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10. Wang Y.C., Chin K.H., Tu Z.L., He J., Jones C.J., Zamorano Sanchez D., Yildiz F.H., Galperin M.Y. and Chou S.-H. (2016) <FONT color=blue><B>Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain.</B></FONT> <I>Nature Commun.</I> <B>7</B>: 12481.
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<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/27578558">Abstract</A>.
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<A HREF="http://www.nature.com/articles/ncomms12481"> Full text (HTML)</A>.
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<A HREF="http://www.nature.com/articles/ncomms12481.pdf">Full text (PDF)</A>.<P>
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<P></P><!-- address --><!-- Address title -->
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<TABLE cellSpacing=0 cellPadding=0 width=465 border=0>
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<TBODY>
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<TR>
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<TD class=H4 width=465 bgColor=#ccccff><IMG height=14 alt="blue bullet" src="https://www.ncbi.nlm.nih.gov/corehtml/bluebullet.gif" width=16 border=0>Address</TD></TR></TBODY></TABLE>
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<P>Michael Y. Galperin, PhD
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<BR>NCBI, NLM, National Institutes of Health
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<BR>8600 Rockville Pike, MSC 3830
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<BR>Bethesda, Maryland 20894, USA
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<BR>Tel.: (301) 435-5910 <BR>Fax: (301) 435-7793
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<BR>E-mail: <A HREF="mailto:galperin@ncbi.nlm.nih.gov">galperin@ncbi.nlm.nih.gov</A><BR>
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<P>Please use E-mail <A HREF="mailto:nardatabase@gmail.com?subject=NAR database issue"><B>nardatabase@gmail.com</B></A> for all correspondence regarding the <I><B>Nucleic Acids Research</B></I> Database Issue and <A HREF="mailto:mygalperin@gmail.com"><B>mygalperin@gmail.com</B></A> for correspondence regarding <I><B>Environmental Microbiology</I> Genome Updates</B>.
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<P class=SMALL1>Revised: Sept 1, 2016.
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