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<div class=Section1>
<p class=MsoNormal align=center style='margin-left:.5in;text-align:center;
text-indent:-.5in'><b style='mso-bidi-font-weight:normal'><span
style='font-size:16.0pt'>Supplementary material from different publications<o:p></o:p></span></b></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><o:p>&nbsp;</o:p></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'>Please click on
the links to access the supplementary information.</p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><o:p>&nbsp;</o:p></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><b
style='mso-bidi-font-weight:normal'>2010<o:p></o:p></b></p>
<p class=MsoBodyText style='margin-left:.5in;text-indent:-.25in;mso-list:l1 level1 lfo11;
tab-stops:list .5in'><![if !supportLists]><span style='mso-bidi-font-weight:
bold'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><![endif]>Iyer LM, Abhiman S, de Souza RF, Aravind L.<span
style='mso-bidi-font-weight:bold'> (2010). <a
href="http://nar.oxfordjournals.org/cgi/content/full/gkq265">Origin and
evolution of peptide-modifying dioxygenases and identification of the
wybutosine hydroxylase/hydroperoxidase.</a> </span><span class=jrnl><i
style='mso-bidi-font-style:normal'>Nucleic Acids Res</i></span></span><span
class=src>. Manuscript accepted for publication. <a
href="ftp://ftp.ncbi.nih.gov/pub/aravind/WYBUTOSINE/wybutosine.html">Supplementary
material</a>.</span><span style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><b
style='mso-bidi-font-weight:normal'>2009<o:p></o:p></b></p>
<p class=MsoBodyText style='margin-left:.5in;text-indent:-.25in;mso-list:l4 level1 lfo13;
tab-stops:list .5in'><![if !supportLists]><span style='mso-bidi-font-weight:
bold'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><![endif]><span style='mso-bidi-font-weight:bold'>Iyer,
L.M., Abhiman, S., Burroughs A.M., Aravind, L. (2009). <a
href="http://www.rsc.org/delivery/_ArticleLinking/DisplayHTMLArticleforfree.cfm?JournalCode=MB&amp;Year=2009&amp;ManuscriptID=b917682a&amp;Iss=12">Amidoligases
with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains:
synthesis of novel metabolites and peptide modifications of proteins.</a> <i
style='mso-bidi-font-style:normal'>Mol Biosyst</i>.</span> <span
style='mso-bidi-font-weight:bold'>5(12):1636-60. <a
href="ftp://ftp.ncbi.nih.gov/pub/aravind/peptide_ligases/supplementary_material_novel_peptide_synthesis.html">Supplementary
material</a>.<o:p></o:p></span></p>
<p class=MsoBodyText style='margin-left:.5in;text-indent:-.25in;mso-list:l4 level1 lfo13;
tab-stops:list .5in'><![if !supportLists]><span style='mso-bidi-font-weight:
bold'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><![endif]><span style='mso-bidi-font-weight:bold'>Iyer,
L.M., Tahiliani, M., Rao, A., Aravind, L.<span style='mso-spacerun:yes'><EFBFBD>
</span>(2009). <a
href="http://www.landesbioscience.com/journals/cc/article/8580/">Prediction of
novel families of enzymes involved in oxidative and other complex modifications
of bases in nucleic acids.</a> <i style='mso-bidi-font-style:normal'>Cell Cycle</i>.
27;8(11). <a
href="ftp://ftp.ncbi.nih.gov/pub/aravind/DONS/supplementary_material_DONS.html">Supplementary
Material</a>.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><b
style='mso-bidi-font-weight:normal'><o:p>&nbsp;</o:p></b></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><b
style='mso-bidi-font-weight:normal'>2008<o:p></o:p></b></p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span style='mso-list:
Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]>Burroughs AM, Iyer LM, Aravind L (2008/2009).Natural history
of the E1-like superfamily: Implication for adenylation, sulfur transfer, and
ubiquitin conjugation. Proteins. Oct 15. [Epub ahead of print]. <a
href="http://www.ncbi.nlm.nih.gov/CBBresearch/Lakshmin/E1/">Supplementary
material in html format</a>.</p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span style='mso-list:
Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]>Iyer LM, Burroughs AM, Aravind L. (2008). Unraveling
the biochemistry and provenance of pupylation: a prokaryotic analog of
ubiquitination. Biol Direct. 2008 3;3:45. <a
href="http://www.biology-direct.com/content/3/1/45">Open access article.</a> <a
href="ftp://ftp.ncbi.nih.gov/pub/aravind/PUP/PafA.html">Supplementary material</a>.</p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span style='mso-list:
Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]>Iyer LM, Abhiman S, Aravind L. (2008). A new family of
polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent
RNA polymerases. <span class=journalname>Biol Direct</span>. 2008 4;3:39. <a
href="http://www.biology-direct.com/content/3/1/39">Open access article</a>. <a
href="ftp://ftp.ncbi.nih.gov/pub/aravind/TV_pol/TV_Pol.html">Supplementary
material</a>.</p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span style='mso-list:
Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]>Iyer LM, Abhiman S, Aravind L. (2008). MutL homologs in
restriction-modification systems and the origin of eukaryotic MORC ATPases.
Biol Direct. 2008 17;3:8. <a href="http://www.biology-direct.com/content/3/1/8">Open
Access article</a>. <a
href="ftp://ftp.ncbi.nih.gov/pub/aravind/temp/MORC/MORC_supplementary.html">Supplementary
material</a></p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span style='mso-list:
Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]>Burroughs AM, Jaffee M, Iyer LM, Aravind L. (2008).
Anatomy of the E2 ligase fold: Implications for enzymology and evolution of
ubiquitin/Ub-like protein conjugation. J Struct Biol. <i style='mso-bidi-font-style:
normal'>In Press. </i><span style='mso-spacerun:yes'><EFBFBD></span><a
href="E2/index.html">Supplementary material</a>.</p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span style='mso-list:
Ignore'>6.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]>Abhiman S, Iyer LM, Aravind L. (2008) BEN: a novel
domain in chromatin factors and DNA viral proteins.
Bioinformatics;24(4):458-61.<span style='mso-spacerun:yes'><EFBFBD> </span><a
href="http://bioinformatics.oxfordjournals.org/cgi/content/full/24/4/458">Open
Access article</a>, <a href="BEN/index.html">Supplementary material</a></p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span style='mso-list:
Ignore'>7.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><a href="chromatin/index.html">Iyer L.M., Anantharaman
V., Wolf M.Y., Aravind L. (2008). Comparative genomics of transcription factors
and chromatin proteins in parasitic protists and other eukaryotes.<span
style='mso-spacerun:yes'><EFBFBD> </span>Int J Parasitol. </a><span class=volume>38</span>(<span
class=issue>1</span>):<span class=pages>1-31</span>.</p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><b
style='mso-bidi-font-weight:normal'>2007<o:p></o:p></b></p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-list:
Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]>Burroughs, A.M., Iyer, L.M., Aravind, L. (2007)
Comparative Genomics and Evolutionary Trajectories of Viral ATP Dependent
DNA-Packaging Systems. <i style='mso-bidi-font-style:normal'>In</i> Gene and
Protein Evolution, Genome dynamics. Basel, Karger, Editor: Volff, J.N.; 3:
48-65. <a
href="http://content.karger.com/ProdukteDB/produkte.asp?Aktion=ShowPDF&amp;ArtikelNr=000107603&amp;Ausgabe=0&amp;ProduktNr=233258&amp;filename=000107603.pdf">Open
Access Article</a>. <a
href="http://www.ncbi.nlm.nih.gov/CBBresearch/Lakshmin/viral_packaging/viral_packaging_supplementary_material.pdf">Supplementary
Material</a>. </p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l2 level1 lfo4'><![if !supportLists]><span style='mso-list:
Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]>Iyer L.M., Anantharaman V., Aravind L. (2007)<a
href="domon/domon_supplementary_material.html">The DOMON domains are involved
in heme and sugar recognition</a>. Bioinformatics</abbr>;<span class=volume>23</span>(<span
class=issue>20</span>):<span class=pages>2660-4</span>. </p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l2 level1 lfo4'><![if !supportLists]><b><span style='mso-list:
Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></b><![endif]>Anantharaman V, Iyer L.M., Balaji S., Aravind
L.(2007) <a
href="apicomplexan_adhesion/apicomplexa_adhesion_2007_supp_material.html">Adhesion
molecules and other secreted host-interaction determinants in apicomplexa: insights
from comparative genomics.</a> Int Rev Cytol;262:1-74. <b><o:p></o:p></b></p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.5in'><b>2006<o:p></o:p></b></p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l0 level1 lfo6'><![if !supportLists]><b><span style='mso-list:
Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></b><![endif]><span style='mso-bidi-font-weight:bold'>Iyer, L.M.<b>,</b>
Burroughs, A.M., Aravind, L. (2006) The prokaryotic antecedents of the
ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp
domains. Genome Biol.: 7(7):R60. <a href="UB/prok_ub_supplement_file_1.html">Supp
file 1</a>, <a href="UB/prok_ub_supplement_file_2.html">Supp file 2</a> <a
href="UB/prok_ub_supplement_file_3.html">Supp file3</a>.<b><o:p></o:p></b></span></p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-bidi-font-weight:
bold'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><![endif]><b><a href="orc2/orc2_alignment.pdf"><span
style='font-weight:normal;mso-bidi-font-weight:bold'>Iyer, L.M.</span>, <span
style='font-weight:normal;mso-bidi-font-weight:bold'>Aravind, L. (2006). </span><span
style='font-weight:normal'>Phyletic Distribution And Evolutionary Relatedness
Of Proteins Involved In Prereplication Complex Assembly. </span><span
style='font-weight:normal;mso-bidi-font-weight:bold'><span
style='mso-spacerun:yes'><EFBFBD></span><i style='mso-bidi-font-style:normal'>In</i> </span><span
style='font-weight:normal'>DNA Replication and Human Disease Cold Spring Harbor
Laboratory Press, Cold Spring Harbor , NY.</span></a></b><span
style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l0 level1 lfo6'><![if !supportLists]><b><span style='mso-list:
Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></b><![endif]><b><a
href="hiran_supp/hiran_supplementary_material.pdf"><span style='font-weight:
normal;mso-bidi-font-weight:bold'>Iyer, L.M</span>., <span style='font-weight:
normal;mso-bidi-font-weight:bold'>Babu, M.M., Aravind, L.</span> <span
style='font-weight:normal;mso-bidi-font-weight:bold'>(2006)</span>. <span
style='font-weight:normal;mso-bidi-font-weight:bold'>The HIRAN domain and
recruitment of chromatin remodeling and repair activities to damaged DNA.</span>
<i style='mso-bidi-font-style:normal'><span style='font-weight:normal;
mso-bidi-font-weight:bold'>Cell Cycle</span></i><span style='font-weight:normal;
mso-bidi-font-weight:bold'>: 5(7):775-82.</span></a><o:p></o:p></b></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo6'><![if !supportLists]><span
style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><a href="aschsupplementary.html">Iyer LM, Burroughs AM,
Aravind L. (2006). The ASCH superfamily: novel domains with a fold related to
the PUA domain and a potential role in RNA metabolism. Bioinformatics. 2006 Feb
1;22(3):257-63.</a></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><b
style='mso-bidi-font-weight:normal'>2005<o:p></o:p></b></p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l5 level1 lfo8'><![if !supportLists]><span style='mso-bidi-font-weight:
bold'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><![endif]><b><a href="primase_supplementary_material.html"><span
style='font-weight:normal;mso-bidi-font-weight:bold'>Iyer L.M., Koonin E.V.,
Leipe D.D., Aravind L. (2005). Origin and evolution of the archaeo-eukaryotic
primase superfamily and related palm-domain proteins: structural insights and
new members.. <i style='mso-bidi-font-style:normal'>Nucleic Acids Res.</i>
33(12):3875-3896</span></a></b><span style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>
<p class=MsoBodyText style='margin-left:.5in;text-align:justify;text-indent:
-.25in;mso-list:l5 level1 lfo8'><![if !supportLists]><span style='mso-bidi-font-weight:
bold'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><![endif]><span style='mso-bidi-font-weight:bold'>L. Aravind,
Anantharaman, V., Balaji, S., Babu, M.M., Iyer, L.M. (2005). The many faces of
the helix-turn-helix domain: Transcription regulation and beyond. <i
style='mso-bidi-font-style:normal'>FEMS Micr. Rev. 2005 </i>Apr;29(2):231-262<i
style='mso-bidi-font-style:normal'>. </i><span
style='mso-spacerun:yes'><EFBFBD></span><a href="hth_gis_supplementalmaterial.html">Supp(gis)</a>,
<a href="hthalignments.txt">Supp (alignments)</a>.<o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><b
style='mso-bidi-font-weight:normal'>2004<o:p></o:p></b></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><b style='mso-bidi-font-weight:normal'><a
href="aaaplus_supp/AAA+supplementary.html"><span style='font-weight:normal'>Iyer,
L.M., Leipe, D.D., Koonin, E.V. Aravind, L. (2004).<span
style='mso-spacerun:yes'><EFBFBD> </span>Evolutionary history and higher order
classification of AAA+ ATPases. <i style='mso-bidi-font-style:normal'>J Str.
Biol.</i> 146(1-2):11-31</span></a></b></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><b
style='mso-bidi-font-weight:normal'><o:p>&nbsp;</o:p></b></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><b
style='mso-bidi-font-weight:normal'>2002<o:p></o:p></b></p>
<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
class=MsoHyperlink><span style='text-decoration:none;text-underline:none'><span
style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span></span><![endif]><span lang=NO-BOK style='mso-ansi-language:
NO-BOK'><a href="kilA_supplementary.html">Iyer LM, Koonin EV, Aravind L.
(2002). <span lang=EN-US style='mso-ansi-language:EN-US'>Extensive domain
shuffling in transcription regulators of DNA viruses and implications for the
origin of fungal APSES transcription factors.</span></a></span><span
class=MsoHyperlink><o:p></o:p></span></p>
<p class=MsoListParagraphCxSpLast><span class=MsoHyperlink><a
href="kilA_supplementary.html">Genome Biol. 3(3):RESEARCH0012.</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><b
style='mso-bidi-font-weight:normal'>2001<o:p></o:p></b></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
style='mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>3.<span
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
style='mso-bidi-font-weight:normal'><a href="START_domain_supplementary.html"><span
style='font-weight:normal'>Iyer, L.M.<span style='mso-bidi-font-weight:bold'>,
Koonin, E.V., and Aravind, L (2001). Adaptations of the helix-grip fold for
ligand binding and catalysis in the START domain superfamily. <i>Proteins</i>.
43(2):134-44.</span></span></a></b><span style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>
<p class=MsoNormal><o:p>&nbsp;</o:p></p>
<p class=MsoNormal><o:p>&nbsp;</o:p></p>
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