Difference between revisions of "UNIST Bioinformatics course syllabus"

From Biolecture.org
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><strong><span style="color:black; font-size:14pt">Syllabus</span></strong></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><strong><span style="color:black; font-size:14pt">Syllabus 2019</span></strong></div>
 
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<div style="word-break: keep-all; line-height: 160%"><strong><span style="color:black">Course Information&nbsp; Bioinformatics</span></strong></div>
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<div style="line-height: 160%; word-break: keep-all"><strong><span style="color:black">Course Information&nbsp; Bioinformatics</span></strong></div>
 
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<p><strong><span style="color:black">Instructor Information [[Dugwoo Nam]] &amp; [[Jong Bhak]]</span></strong></p>
 
<p><strong><span style="color:black">Instructor Information [[Dugwoo Nam]] &amp; [[Jong Bhak]]</span></strong></p>
 
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<p style="text-align: center"><span style="color:black; font-size:9pt">Course Code</span></p>
 
<p style="text-align: center"><span style="color:black; font-size:9pt">Course Code</span></p>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="font-size:8.5pt">BIO43101</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="font-size:8.5pt">BIO43101</span></div>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">Instructor</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt">Instructor</span></div>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">Dugwoo Nam,</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt">[[Jong Bhak]]</span></div>
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">[[Jong Bhak]]</span></div>
 
 
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<p style="text-align: center"><span style="color:black; font-size:9pt">Course Title</span></p>
 
<p style="text-align: center"><span style="color:black; font-size:9pt">Course Title</span></p>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">Bioinformatics</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt">Bioinformatics</span></div>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">Office</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt">Office</span></div>
 
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<p><span style="font-size:9pt">Room 701-8, EB1 (DN)</span></p>
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<p><span style="color:black; font-size:9pt">&nbsp;Room 301-8, Bldg 110</span></p>
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<p><span style="color:black; font-size:9pt">Room 215, Bldg 103 (JB)</span></p>
 
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">Year/Semester</span></div>
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">2015/1st</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt">2019/1st</span></div>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">Telephone</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt">Telephone</span></div>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">010 4644 6754 (JB)</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt">010 4644 6754 (JB)</span></div>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">School</span></div>
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">SLS</span></div>
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">E-mail</span></div>
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt"><a href="mailto:dougnam@unist.ac.kr">dougnam@unist.ac.kr</a> (DN)</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt"><a href="mailto:jongbhak@gmail.com">jongbhak@gmail.com</a> (JB)</span></div>
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt"><a href="mailto:jongbhak@gmail.com">jongbhak@gmail.com</a> (JB)</span></div>
 
 
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<p style="text-align: center"><span style="color:black; font-size:9pt">Course Classification</span></p>
 
<p style="text-align: center"><span style="color:black; font-size:9pt">Course Classification</span></p>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="font-size:8.5pt">TE-BIO/TE-BME/TE-BMS</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="font-size:8.5pt">TE-BIO/TE-BME/TE-BMS</span></div>
 
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<td style="height: 1.4pt; width: 81pt">
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<td style="width: 81pt; height: 1.4pt">
 
<p style="text-align: center"><span style="color:black; font-size:9pt">Office Hours</span></p>
 
<p style="text-align: center"><span style="color:black; font-size:9pt">Office Hours</span></p>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">TBA</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt">Any time</span></div>
 
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<p style="text-align: center"><span style="color:black; font-size:9pt">Classroom/Class Time</span></p>
 
<p style="text-align: center"><span style="color:black; font-size:9pt">Classroom/Class Time</span></p>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">FRI 13:00-15:30 (NSB S205)</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt">FRI 13:00-15:30 (NSB S205)</span></div>
 
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<p style="text-align: center"><span style="color:black; font-size:9pt">Grading Type</span></p>
 
<p style="text-align: center"><span style="color:black; font-size:9pt">Grading Type</span></p>
 
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black; font-size:9pt">Letter grade</span></div>
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<div style="text-align: center; line-height: 160%; word-break: keep-all"><span style="color:black; font-size:9pt">Letter grade</span></div>
 
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<div style="word-break: keep-all; line-height: 160%"><strong><span style="color:black; font-size:11pt">Course Objectives &amp; Description </span></strong></div>
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<div style="line-height: 160%; word-break: keep-all"><strong><span style="color:black; font-size:11pt">Course Objectives &amp; Description </span></strong></div>
 
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<p>Bioinformatics course contains introductory information in how to process biological data using computers.</p>
 
<p>Bioinformatics course contains introductory information in how to process biological data using computers.</p>
  
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<p>The first part of the course taught by Dougu Nam covers the basic computational methods used for biological data analysis. During the class, students will learn the concepts by short lectures and hands-on experiences. So, please bring a laptop computer to the class from the second week.</p>
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<p>During the class, students will learn the concepts by short lectures and hands-on experiences. So, please bring a laptop computer to the class from the second week.</p>
  
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<div style="word-break: keep-all; line-height: 160%">&nbsp;</div>
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<div style="line-height: 160%; word-break: keep-all">&nbsp;</div>
  
 
<p>The second part of the course taught by Jong Bhak will focus on:</p>
 
<p>The second part of the course taught by Jong Bhak will focus on:</p>
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">Grading</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:black">Grading</span></div>
 
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<td colspan="7" style="background-color: transparent; width: 505.5pt; height: 55.85pt"><font color="#ff0000">Science paper writing on bioinformatics topics.</font></td>
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<p><span style="color:red">Midterm( Two tests:&nbsp;50 %) / Final Exam(&nbsp;Team project: 50%)</span></p>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">&nbsp;</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:black">&nbsp;</span></div>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">&nbsp;</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:black">&nbsp;</span></div>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">&nbsp;</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:black">&nbsp;</span></div>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">&nbsp;</span></div>
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">&nbsp;</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:black">&nbsp;</span></div>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">&nbsp;</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:black">&nbsp;</span></div>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">Text</span></div>
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">Category</span></div>
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<p><span style="color:red">Book and PPT files, on-line links</span></p>
 
<p><span style="color:red">Book and PPT files, on-line links</span></p>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">&nbsp;</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:black">&nbsp;</span></div>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">Title</span></div>
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<div style="word-break: keep-all; line-height: 160%"><span style="color:red">Bioinformatics</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:red">Bioinformatics</span></div>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">&nbsp;</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:black">&nbsp;</span></div>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">Author</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:black">Author</span></div>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:red">Jong Bhak</span></div>
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<div style="line-height: 160%; word-break: keep-all"><span style="color:red">Jong Bhak</span></div>
 
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<p><span style="color:black">Course Reserves Designation</span></p>
 
<p><span style="color:black">Course Reserves Designation</span></p>
 
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black">References</span></div>
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<p><span style="color:black">Course Reserves Designation</span></p>
 
<p><span style="color:black">Course Reserves Designation</span></p>
 
</td>
 
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</table>
 
</table>
  
−
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<div style="line-height: 160%; word-break: keep-all">&nbsp;</div>
  
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<div style="word-break: keep-all; line-height: 160%"><span style="color:black; font-size:12pt">Weekly Schedule</span></div>
+
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+
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<div style="word-break: keep-all; text-align: center; line-height: 160%"><span style="color:black">Contents</span></div>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">01</span></div>
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<td style="height: 35.65pt; width: 462pt; background-color: transparent">
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<td style="background-color: transparent; width: 462pt; height: 35.65pt">
 
<p style="text-align: left">Introduction to Bioinformatics, Introduction to Microarray, RNA-seq</p>
 
<p style="text-align: left">Introduction to Bioinformatics, Introduction to Microarray, RNA-seq</p>
 
</td>
 
</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">02</span></div>
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</td>
 
</td>
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<td style="height: 35.65pt; width: 462pt; background-color: transparent">
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<td style="background-color: transparent; width: 462pt; height: 35.65pt">
 
<p>Microarray &amp; gene data analysis I: Normalization, Identification of DEGs (R language), Gene list analysis with DAVID and STRING(web)</p>
 
<p>Microarray &amp; gene data analysis I: Normalization, Identification of DEGs (R language), Gene list analysis with DAVID and STRING(web)</p>
 
</td>
 
</td>
 
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<div style="word-break: keep-all; text-align: center"><span style="color:black">03</span></div>
+
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<p>Microarray &amp; gene data analysis II: Clustering, (R, cluster, treeview), Dimension Reduction (PCA), survival analysis</p>
 
<p>Microarray &amp; gene data analysis II: Clustering, (R, cluster, treeview), Dimension Reduction (PCA), survival analysis</p>
 
</td>
 
</td>
 
</tr>
 
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<div style="word-break: keep-all; text-align: center"><span style="color:black">04</span></div>
+
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</td>
 
</td>
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+
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<div style="line-height: 115%">Test 1</div>
 
<div style="line-height: 115%">Test 1</div>
 
</td>
 
</td>
 
</tr>
 
</tr>
 
<tr>
 
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<div style="word-break: keep-all; text-align: center"><span style="color:black">05</span></div>
+
<div style="text-align: center; word-break: keep-all"><span style="color:black">05</span></div>
 
</td>
 
</td>
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<td style="height: 35.65pt; width: 462pt; background-color: transparent">
+
<td style="background-color: transparent; width: 462pt; height: 35.65pt">
 
<p style="text-align: left">Gene-set and pathway analysis with GSEA, Introduction to classification analysis (SVM)</p>
 
<p style="text-align: left">Gene-set and pathway analysis with GSEA, Introduction to classification analysis (SVM)</p>
 
</td>
 
</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
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<div style="word-break: keep-all; text-align: center"><span style="color:black">06</span></div>
+
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</td>
 
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+
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<div style="line-height: 115%">RNA-seq, ChIP-seq data analysis</div>
 
<div style="line-height: 115%">RNA-seq, ChIP-seq data analysis</div>
 
</td>
 
</td>
 
</tr>
 
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−
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<div style="word-break: keep-all; text-align: center"><span style="color:black">07</span></div>
+
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+
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<p style="text-align: left">Introduction to NCBI databases: data and literature search</p>
 
<p style="text-align: left">Introduction to NCBI databases: data and literature search</p>
 
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</td>
 
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<div style="word-break: keep-all; text-align: center"><span style="color:black">08</span></div>
+
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+
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<div style="word-break: keep-all; text-align: left"><span style="color:black">Test 2</span></div>
+
<div style="text-align: left; word-break: keep-all"><span style="color:black">Test 2</span></div>
 
</td>
 
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<div style="word-break: keep-all; text-align: center"><span style="color:black">09</span></div>
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<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Principles of Bioinformatics]]</span></div>
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<div style="text-align: left; word-break: keep-all"><span style="color:black">&nbsp;[[Principles of Bioinformatics]]</span></div>
 
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<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Bioprogramming]]</span></div>
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<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Genomics]]</span></div>
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<div style="word-break: keep-all; text-align: left"><span style="color:black">&nbsp;[[Transcriptomics]]</span></div>
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Latest revision as of 21:01, 22 January 2019

 

Syllabus 2019
Course Information  Bioinformatics

Instructor Information Dugwoo Nam & Jong Bhak

Course Code
BIO43101
Instructor

Course Title
Bioinformatics
Office

 Room 301-8, Bldg 110
Year/Semester
2019/1st
Telephone
010 4644 6754 (JB)
School
SLS
E-mail

Course Classification
TE-BIO/TE-BME/TE-BMS

Office Hours
Any time

Classroom/Class Time
FRI 13:00-15:30 (NSB S205)

Grading Type
Letter grade
Course Objectives & Description

Bioinformatics course contains introductory information in how to process biological data using computers.

During the class, students will learn the concepts by short lectures and hands-on experiences. So, please bring a laptop computer to the class from the second week.

 

The second part of the course taught by Jong Bhak will focus on:

1)     What Bioinformatics is

2)     How to independently read research papers

3)     How to critically analyze research papers and topics

4)     How to choose a research topic in bioinformatics and design an experiment and perform research

5)     How to write research report(paper) to make the results known to the public.

6)     The course will be done through active action-oriented learning method(AAO)

7)     Students are required to motivate themselves and bring their research topics after reading research papers.
Grading
Science paper writing on bioinformatics topics.
 
 
 
 
 
 
Text
Category

Book and PPT files, on-line links
 
Title
Bioinformatics
 
Author
Jong Bhak
 
ISBN
 
 
Remarks
 
 

Course Reserves Designation
 
 
References
Category
Book, on-line links
 
 
Title
Bioinformatics
 
 
Author
Jong Bhak
 
 
ISBN
 
 
 
Remarks
 
 
 

Course Reserves Designation
 
 
 
 
Weekly Schedule

 

Week
Contents
01

Introduction to Bioinformatics, Introduction to Microarray, RNA-seq
02

Microarray & gene data analysis I: Normalization, Identification of DEGs (R language), Gene list analysis with DAVID and STRING(web)
03

Microarray & gene data analysis II: Clustering, (R, cluster, treeview), Dimension Reduction (PCA), survival analysis
04
Test 1
05

Gene-set and pathway analysis with GSEA, Introduction to classification analysis (SVM)
06
RNA-seq, ChIP-seq data analysis
07

Introduction to NCBI databases: data and literature search
08
Test 2
09
10
11
12
13
14
15
 

UNIST Bioinformatics course  Bioinformatics.ws

 

 

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