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</o:shapedefaults></xml><![endif]--><!--[if gte mso 9]><xml> <o:shapelayout v:ext="edit"> <o:idmap v:ext="edit" data="1"/> </o:shapelayout></xml><![endif]--> </head> <body lang=EN-US link=blue vlink="#CC0000" style='tab-interval:.5in' alink="#ffffff"> <div class=WordSection1> <h1 align=center style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt; margin-left:0in;text-align:center'><span style='font-family:"Helvetica","sans-serif"'>Analysis of Biological Networks, <span class=GramE>Spring</span> 2011</span><br> <span style='font-size:12.0pt;font-family:"Helvetica","sans-serif"'>0368-4212-01</span></h1> <p class=MsoNormal align=center style='text-align:center'><o:p>&nbsp;</o:p></p> <p class=MsoNormal style='line-height:150%'><b style='mso-bidi-font-weight: normal'>Instructor: <a href="http://www.cs.tau.ac.il/~roded/Default.html">Roded <span class=SpellE>Sharan</span></a><br> Time: Tuesday 13-16<o:p></o:p></b></p> <div class=MsoNormal align=center style='text-align:center'> <hr size=2 width="100%" align=center> </div> <h3 style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt;margin-left: 0in'><span style='font-size:16.0pt'>Syllabus and Handouts<o:p></o:p></span></h3> <p style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt;margin-left:0in'>The syllabus for the course is <a href="http://www.cs.tau.ac.il/~roded/courses/bnet-a06/bnet.pdf">here</a></p> <p style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt;margin-left:0in'>A recommended book on biological networks is: &quot;<a href="http://www.worldscibooks.com/lifesci/6459.html">Biological networks</a>&quot; by <span class=SpellE>Kepes</span>. A recommended book on introduction to biology is 'Molecular Biology of the Cell' by <span class=SpellE>Alberts</span> et al.</p> <p style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt;margin-left:0in'><b style='mso-bidi-font-weight:normal'>Scribe instructions</b> can be found <a href="bnet-09/scribe.pdf">here</a></p> <p style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt;margin-left:0in'>Following is a tentative outline of the course, which will be updated according to what is actually studied in class:</p> <p style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt;margin-left:0in'>&nbsp;</p> <div align=center> <table class=MsoNormalTable border=1 cellspacing=0 cellpadding=0 style='mso-cellspacing:0in;mso-yfti-tbllook:1184;mso-padding-alt:0in 0in 0in 0in; mso-border-insideh:.75pt outset windowtext;mso-border-insidev:.75pt outset windowtext'> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes;height:26.25pt'> <td width=78 style='width:58.8pt;background:#E0E0E0;padding:0in 0in 0in 0in; height:26.25pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>Week</span></b><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p> </td> <td width=84 style='width:63.0pt;background:#E0E0E0;padding:0in 0in 0in 0in; height:26.25pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>Date<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=353 style='width:264.75pt;background:#E0E0E0;padding:0in 0in 0in 0in; height:26.25pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>Lecture scribes</span></b><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p> </td> <td width=195 style='width:146.6pt;background:#E0E0E0;padding:0in 0in 0in 0in; height:26.25pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>Read more <o:p></o:p></span></b></p> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>(refs. are below)<o:p></o:p></span></b></p> </td> </tr> <tr style='mso-yfti-irow:1;height:33.25pt'> <td width=78 style='width:58.8pt;background:#FFCC99;padding:0in 0in 0in 0in; height:33.25pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>1</span></b><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p> </td> <td width=84 style='width:63.0pt;background:#FFCC99;padding:0in 0in 0in 0in; height:33.25pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>22 Feb<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FFCC99;padding:0in 0in 0in 0in; height:33.25pt'> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt;color:black'><a href="http://www.cs.tau.ac.il/~roded/courses/bnet-a06/lec01.pdf">Introduction to cell biology and networks</a><o:p></o:p></span></p> </td> <td width=195 style='width:146.6pt;background:#FFCC99;padding:0in 0in 0in 0in; height:33.25pt'> <p class=MsoNormal align=center style='text-align:center'>Molecular biology of the cell, <span class=SpellE>Alberts</span> et al.</p> </td> </tr> <tr style='mso-yfti-irow:2;height:33.6pt'> <td width=78 style='width:58.8pt;background:#FFCC99;padding:0in 0in 0in 0in; height:33.6pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>2</span></b><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p> </td> <td width=84 style='width:63.0pt;background:#FFCC99;padding:0in 0in 0in 0in; height:33.6pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>1 Mar<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FFCC99;padding:0in 0in 0in 0in; height:33.6pt'> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt;color:black'><a href="http://www.cs.tau.ac.il/~roded/courses/bnet-a06/lec02.pdf">Network measures and random network models</a> <o:p></o:p></span></p> </td> <td width=195 style='width:146.6pt;background:#FFCC99;padding:0in 0in 0in 0in; height:33.6pt'> <p class=MsoNormal align=center style='text-align:center'>Tutorials; <br> Network motif papers</p> </td> </tr> <tr style='mso-yfti-irow:3;height:28.5pt'> <td width=78 style='width:58.8pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>3</span></b><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p> </td> <td width=84 style='width:63.0pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt;color:black'>8 Mar<o:p></o:p></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt;color:black'><a href="http://www.cs.tau.ac.il/~roded/courses/bnet-a06/lec03.pdf">Protein-protein interaction networks : data processing &amp; functional annotation</a><o:p></o:p></span></p> </td> <td width=195 style='width:146.6pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'>PPI preprocessing papers; Functional annotation papers</p> </td> </tr> <tr style='mso-yfti-irow:4;height:28.5pt'> <td width=78 style='width:58.8pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>4</span></b><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p> </td> <td width=84 style='width:63.0pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>15 Mar<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt'>Integer Linear Programming<span style='color:black'><o:p></o:p></span></span></p> </td> <td width=195 style='width:146.6pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'></td> </tr> <tr style='mso-yfti-irow:5;height:28.5pt'> <td width=78 style='width:58.8pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt;color:black'>5<o:p></o:p></span></p> </td> <td width=84 style='width:63.0pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p align=center style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt; margin-left:0in;text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>22 Mar<o:p></o:p></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p align=center style='text-align:center'><span style='font-size:14.0pt; color:black'>(<span class=SpellE>Shiur</span> <span class=SpellE>Halshlama</span> on 26.4)<o:p></o:p></span></p> <p align=center style='text-align:center'><span style='font-size:14.0pt; color:black'>Network querying</span><span style='font-size:14.0pt'><o:p></o:p></span></p> </td> <td width=195 style='width:146.6pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><a href="../qpath.pdf">Shlomi'06</a>; <a href="../qnet.pdf">Dost'07</a>; <a href="../torque.pdf">Bruckner'09</a><span style='font-size:10.0pt'><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:6;height:28.5pt'> <td width=78 style='width:58.8pt;background:#FF99CC;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>6<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=84 style='width:63.0pt;background:#FF99CC;padding:0in 0in 0in 0in; height:28.5pt'> <p align=center style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt; margin-left:0in;text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>29 Mar <o:p></o:p></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FF99CC;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt;color:black'><a href="bnet-09/lec08.pdf">Global network alignment</a><o:p></o:p></span></p> </td> <td width=195 style='width:146.6pt;background:#FF99CC;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><a href="http://www.cs.tau.ac.il/~roded/orthology.pdf">Bandyopadhyay'05</a>; <a href="../hrp.pdf">Yosef'08</a>; <a href="http://www.pnas.org/content/105/35/12763.long">Singh '08</a></p> </td> </tr> <tr style='mso-yfti-irow:7;height:28.5pt'> <td width=78 style='width:58.8pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>7</span></b><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p> </td> <td width=84 style='width:63.0pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>5 Apr <span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p align=center style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt; margin-left:0in;text-align:center'><span style='font-size:14.0pt'><a href="http://www.cs.tau.ac.il/~roded/courses/bnet-09/lec04.pdf">Network modules</a><o:p></o:p></span></p> </td> <td width=195 style='width:146.6pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><a href="http://www.math.tau.ac.il/~nogaa/PDFS/col5.pdf">Alon'95</a>; <a href="http://www.cs.tau.ac.il/~roded/jcolorcoding.pdf">Scott'05</a><span style='font-size:10.0pt'><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:8;height:28.5pt'> <td width=78 style='width:58.8pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>8</span></b><span style='font-size:14.0pt;color:black'><o:p></o:p></span></p> </td> <td width=84 style='width:63.0pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p align=center style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt; margin-left:0in;text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>12 Apr <o:p></o:p></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt;color:black'><a href="bnet-09/lec07.pdf">Local network alignment</a> <o:p></o:p></span></p> </td> <td width=195 style='width:146.6pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><a href="http://www.cs.tau.ac.il/~roded/pathblast.pdf">Kelley'03</a>; <a href="http://www.cs.tau.ac.il/~roded/jcpi.pdf">Sharan'05a</a>; <a href="http://www.cs.tau.ac.il/~roded/gb.pdf">Sharan'05b</a>; <a href="http://www.cs.purdue.edu/people/koyuturk/papers/ppi_alignment_jcb.pdf">Koyuturk'05</a><span style='mso-bidi-font-size:10.0pt'><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:9;height:28.5pt'> <td width=78 style='width:58.8pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>9<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=84 style='width:63.0pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>3 May<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt'><a href="bnet-09/lec11.pdf">Networks in disease</a> <span style='color:black'><o:p></o:p></span></span></p> </td> <td width=195 style='width:146.6pt;background:#FFCC99;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030096"><span lang=NO-BOK style='mso-ansi-language:NO-BOK'>Liu '07</span></a><span lang=NO-BOK style='mso-ansi-language:NO-BOK'>; </span><a href="http://www.nature.com/nbt/journal/v26/n5/abs/nbt1397.html"><span lang=NO-BOK style='mso-ansi-language:NO-BOK'>Kutalik '08</span></a><span lang=NO-BOK style='mso-ansi-language:NO-BOK'>; </span><span lang=SV style='mso-ansi-language:SV'><a href="http://www.pnas.org/content/104/21/8685.abstract"><span lang=NO-BOK style='mso-ansi-language:NO-BOK'>Goh '07</span></a>;</span><span lang=NO-BOK style='mso-ansi-language:NO-BOK'><span style='mso-spacerun:yes'>  </span></span><a href="http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html"><span lang=NO-BOK style='mso-ansi-language:NO-BOK'>Yilderim '07</span></a></p> </td> </tr> <tr style='mso-yfti-irow:10;height:28.5pt'> <td width=78 style='width:58.8pt;background:#FF99CC;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>10<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=84 style='width:63.0pt;background:#FF99CC;padding:0in 0in 0in 0in; height:28.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>17 May<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FF99CC;padding:0in 0in 0in 0in; height:28.5pt'> <p align=center style='margin-top:.1pt;margin-right:0in;margin-bottom:.1pt; margin-left:0in;text-align:center'><span style='font-size:14.0pt;color:black'>Networks in drug development</span><span style='font-size:14.0pt'><o:p></o:p></span></p> </td> <td width=195 style='width:146.6pt;background:#FF99CC;padding:0in 0in 0in 0in; height:28.5pt'></td> </tr> <tr style='mso-yfti-irow:11;height:22.5pt'> <td width=78 style='width:58.8pt;background:#FFCC99;padding:0in 0in 0in 0in; height:22.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>11<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=84 style='width:63.0pt;background:#FFCC99;padding:0in 0in 0in 0in; height:22.5pt'> <p class=MsoNormal align=center style='text-align:center'><b style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>24 May<span style='color:black'><o:p></o:p></span></span></b></p> </td> <td width=353 style='width:264.75pt;background:#FFCC99;padding:0in 0in 0in 0in; height:22.5pt'> <p class=MsoNormal align=center style='text-align:center'><span style='font-size:14.0pt'><a href="bnet-09/lec10.pdf">Network integration</a><span style='color:black'> <o:p></o:p></span></span></p> </td> <td width=195 style='width:146.6pt;background:#FFCC99;padding:0in 0in 0in 0in; height:22.5pt'> <p class=MsoNormal align=center style='text-align:center'><a href="http://jbiol.com/content/4/2/6/abstract">Zhang'05</a>; <a href="../ppd.pdf">Tan'07</a>; <a href="http://www.nature.com/nature/journal/v436/n7052/abs/nature03876.html">Gunsalus'05</a>; <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=15285891&amp;dopt=Abstract">Yeang'04</a>; <a href="http://www.nature.com/nature/journal/v431/n7006/abs/nature02782.html">Luscombe'04</a><span style='font-size:10.0pt'><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:12;mso-yfti-lastrow:yes;height:22.5pt'> <td width=78 style='width:58.8pt;background:#FFCC99;padding:0in 0in 0in 0in; 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