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style='text-align:center'><span style='font-size:14.0pt'>Genome Evolution</span></p> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt'>&nbsp;</span></p> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt'>Spring 2012</span></p> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt'>Amos <span class=SpellE>Tanay</span>, Tuesdays, 9am-11pm, <span class=SpellE>Ziskind</span> 1</span></p> <p class=MsoNormal align=left style='text-align:left'><span style='font-size: 14.0pt'>&nbsp;</span></p> <p class=MsoNormal align=left style='text-align:left'>The course provides an overview of the basic forces of evolution using two complementary approaches: in the first half, population genetics is introduced as a theory for quantitative modeling of drift, mutation, selection and recombination in evolving populations. In the second half, computational techniques for the inference of evolutionary models given modern massive genomic sequences are described. Together, this combination aims to provide students with insights and technique that are important in practically any field of current biology. </p> <p class=MsoNormal align=left style='text-align:left'><o:p>&nbsp;</o:p></p> <table class=MsoNormalTable border=1 cellspacing=0 cellpadding=0 style='margin-left:-5.8pt;border-collapse:collapse;border:none;mso-border-alt: solid windowtext .5pt;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-border-insideh:.5pt solid windowtext;mso-border-insidev:.5pt solid windowtext'> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes;mso-yfti-lastrow:yes; height:212.45pt'> <td width=348 valign=top style='width:260.95pt;border:solid windowtext 1.0pt; mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt;height:212.45pt'> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Schedule (Tentative)</b></p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 1: </b>Historical introduction</p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 2: </b>Pop Genetics I: Models and drift<b style='mso-bidi-font-weight: normal'><o:p></o:p></b></p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 3:</b> Pop Genetics II: Recombination and Mutation</p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 4:</b> Pop Genetics III: selection</p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 5:</b> Cancer evolution: Basic models (Amir Bar)</p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 6:</b> Selection/Mutation. Species and speciation</p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 7: </b>Intro to sequence-based molecular evolution </p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 8: </b>The simple tree model (Inference, Learning)</p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 9 (Short): </b>Mutations and context  dependent substitution models<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 10: </b><span class=SpellE>Variational</span> inference, Sampling and trees</p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 11: </b>Selection on protein coding genes<b style='mso-bidi-font-weight: normal'><o:p></o:p></b></p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 12: </b>Evolution of regulatory sequences<b style='mso-bidi-font-weight: normal'><o:p></o:p></b></p> <p class=MsoNormal align=left style='text-align:left'><b style='mso-bidi-font-weight: normal'>Lecture 13: </b>More on evolution of regulation<b style='mso-bidi-font-weight: normal'>, </b>networks<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p> </td> <td width=120 valign=top style='width:1.25in;border:solid windowtext 1.0pt; border-left:none;mso-border-left-alt:solid windowtext .5pt;mso-border-alt: solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt;height:212.45pt'> <p class=MsoNormal align=left style='text-align:left'><o:p>&nbsp;</o:p></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'>ppt1<span style='mso-spacerun:yes'>      </span>(</span><a href="ex1.doc"><span lang=DE style='mso-ansi-language:DE'>ex1</span></a>)<span style='mso-ansi-language:DE'> <span lang=DE><o:p></o:p></span></span></p> <p class=MsoNormal align=left style='text-align:left'><a href="GenomeEvo12_Lec2.pptx"><span lang=DE style='mso-ansi-language:DE'>ppt2</span></a><u><span lang=DE style='color:blue;mso-ansi-language:DE'><o:p></o:p></span></u></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><a href="GenomeEvo12_Lec3.ppt">ppt3</a><u><span style='color:blue'><o:p></o:p></span></u></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><a href="GenomeEvo12_Lec4.ppt">ppt4</a><u><span style='color:blue'><o:p></o:p></span></u></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'>Notes5<span style='mso-spacerun:yes'>   </span>(<a href="ex2.docx">ex2</a>)<o:p></o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><a href="GenomeEvo12_Lec6.ppt">ppt6</a><u><span style='color:blue'><o:p></o:p></span></u></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><a href="GenomeEvo12_Lec6.ppt">ppt9</a><o:p></o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><a href="GenomeEvo12_Lec9.ppt">ppt10</a><o:p></o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><a href="GenomeEvo12_Lec11.ppt">ppt11</a><o:p></o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><a href="GenomeEvo12_Lec12.ppt">ppt12</a><o:p></o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><a href="GenomeEvo12_Lec13.ppt">ppt13</a><o:p></o:p></span></p> </td> </tr> </table> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'><o:p>&nbsp;</o:p></span></p> <p class=MsoNormal align=left style='text-align:left'><span lang=DE style='mso-ansi-language:DE'>ppt4<o:p></o:p></span></p> <p class=MsoNormal align=left style='text-align:left'>Notes:</p> <p class=MsoNormal align=left style='text-align:left'><o:p>&nbsp;</o:p></p> <p class=MsoNormal align=left style='text-align:left'>14/3/12: Welcome. 2010 course is <a href="http://www.wisdom.weizmann.ac.il/~atanay/GenomeEvo10/">here</a></p> <p class=MsoNormal align=left style='text-align:left'>29/3/12: Exercise 1 updated  you can go ahead solving it</p> <p class=MsoNormal align=left style='text-align:left'><o:p>&nbsp;</o:p></p> </div> </body> </html>