<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PlaceName"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceType"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;}
p
{mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman";}
span.EmailStyle18
{mso-style-type:personal;
font-family:Arial;
color:navy;}
span.EmailStyle19
{mso-style-type:personal;
font-family:Arial;
color:navy;}
span.EmailStyle20
{mso-style-type:personal;
font-family:Arial;
color:navy;}
span.EmailStyle21
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:595.3pt 841.9pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.Section1
{page:Section1;}
-->
</style>
</head>
<body lang=EN-GB link=blue vlink=blue>
<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-IE
style='font-size:10.0pt;font-family:Arial;color:navy'>The department of
Mathematics and Statistics invites you to a seminar by </span></font><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Prof. Cathal Seoighe (<st1:place w:st="on"><st1:PlaceType w:st="on">School</st1:PlaceType>
of <st1:PlaceName w:st="on">Mathematics</st1:PlaceName></st1:place>,
Statistics and Applied Mathematics, NUIG): <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-IE
style='font-size:10.0pt;font-family:Arial;color:navy'>---------------------------------------------------------------------------------------</span></font><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-IE
style='font-size:10.0pt;font-family:Arial;color:navy'>Title: </span></font><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>A Phylogenetic Hidden Markov Model for Immune Epitope Discovery<o:p></o:p></span></font></p>
<p><font size=2 color=navy face=Arial><span lang=EN-IE style='font-size:10.0pt;
font-family:Arial;color:navy'>Abstract: </span></font><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>We describe a phylogenetic model of protein-coding sequence
evolution that includes environmental variables. We apply it to a set of viral
sequences from individuals with known human leukocyte antigen (HLA) genotype
and include parameters to model selective pressures affecting mutations within
immunogenic (epitope) regions that facilitate viral evasion of immune
responses. We combine this evolutionary model with a hidden Markov model to
identify regions of the HIV-1 genome that evolve under immune pressure in the
presence of specific HLA class I alleles and may therefore represent potential
T cell epitopes. This phylogenetic hidden Markov model provides a probabilistic
framework that can be combined with sequence or structural information to
enhance epitope prediction. <o:p></o:p></span></font></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'>--------------------------------------------------------------------------------------</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>The seminar will take place on <b><span
style='font-weight:bold'>Wednesday 21st April, at 4pm</span></b>, in A2-002.</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>If you have any questions regarding this
seminar, please direct them to Sarah Mitchell (061 202259, <span
class=MsoHyperlink><font color=navy title="blocked::mailto:sarah.mitchell@ul.ie"><span
title="blocked::mailto:sarah.mitchell@ul.ie"><span style='color:navy;
text-decoration:none'>sarah.mitchell@ul.ie</span></span></font></span>).
A full list of Seminars for this semester can be found at: </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-IE
style='font-size:10.0pt;font-family:Arial;color:navy'><a
href="http://www.staff.ul.ie/mitchells/MACSI_seminars.html"
title="http://www.staff.ul.ie/mitchells/MACSI_seminars.html blocked::http://www.staff.ul.ie/mitchells/MACSI_seminars.html"><font
color=navy
title="http://www.staff.ul.ie/mitchells/MACSI_seminars.html blocked::http://www.staff.ul.ie/mitchells/MACSI_seminars.html"><span
title="http://www.staff.ul.ie/mitchells/MACSI_seminars.html blocked::http://www.staff.ul.ie/mitchells/MACSI_seminars.html"><span
title="http://www.staff.ul.ie/mitchells/MACSI_seminars.html blocked::http://www.staff.ul.ie/mitchells/MACSI_seminars.html"><span
style='color:navy;text-decoration:none'><span
title="http://www.staff.ul.ie/mitchells/MACSI_seminars.html">http://www.staff.ul.ie/mitchells/MACSI_seminars.html</span></span></span></font></span></a></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-IE
style='font-size:10.0pt;font-family:Arial;color:navy'>----------------------------------------------------------------------------</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-IE
style='font-size:10.0pt;font-family:Arial;color:navy'>Supported by Science
Foundation Ireland Mathematics Initiative funding, MACSI - the Mathematics
Applications Consortium for Science and Industry (<span class=MsoHyperlink><span
title="blocked::www.macsi.ie"><font color=navy title="blocked::www.macsi.ie"><span
title="blocked::www.macsi.ie"><span style='color:navy;text-decoration:none'>www.macsi.ul.ie</span></span></font></span></span>),
centred at the University of Limerick, is dedicated to the mathematical
modelling and solution of problems which arise in science, engineering and
industry in Ireland</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-IE
style='font-size:10.0pt;font-family:Arial;color:navy'>----------------------------------------------</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><img border=0 width=142 height=142
id="_x0000_i1029" src="cid:image002.jpg@01CAE12C.37D4BD20"></span></font><o:p></o:p></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
</div>
</body>
</html>