Difference between revisions of "Jong Bhak's Genomics Syllabus"

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<div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="font-size:24px">'''<span style="color:black">Jong Bhak's Genomics course syllabus. 2024 (Spring)</span>'''</span></div> <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="font-size:16px;">'''<span style="color:black">(No mid-term exam)</span>'''</span></div> <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%">'''<span style="font-size:10pt"><span style="line-height:160%"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="line-height:160%"><span style="font-family:"><span style="color:black">Weekly Schedule</span></span></span></span></span></span></span></span></span>'''</div> <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%">
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<div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="font-size:24px"><strong><span style="color:black">Jong Bhak&#39;s Genomics course syllabus.</span></strong></span></div>
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{| class="Table" style="margin-left:-1px; border-collapse:collapse; border:none"
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:19px; background-color:#d6d6d6; border-top:1px solid black; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="line-height:160%"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="line-height:160%"><span style="font-family:"><span style="color:black">Week</span></span></span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:19px; background-color:#d6d6d6; border-top:1px solid black; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="line-height:160%"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="line-height:160%"><span style="font-family:"><span style="color:black">Contents: Students are required to click on all the links and listen to the Youtube channels.</span></span></span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">01</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:12pt"><span style="background:white"><span style="line-height:18.0pt"><span style="font-family:Gulim,sans-serif"><span style="font-family:"><span style="color:black">[[Introduction_to_Jong_Bhak's_genomics_course|Introduction to Jong Bhak's genomics course]]<br/> [[What_is_science?|What is science?]]<br/> [[What_is_life?|What is life?]]<br/> [[What_is_DNA?|What is DNA?]] [[What_is_RNA?|What is RNA?]]<br/> [[What_is_transcription_and_translation?|What is transcription and translation?]]<br/> [[What_is_information?|What is information?]]</span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">02</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:">[[What_is_Sequencing_in_Genomics_and_Omics?|What is Sequencing in Genomics and Omics?]]&nbsp;<br/> &nbsp; [https://www.youtube.com/watch?v=m4I7Fy0xxbk</span></span></span></span></span></span>History of Genome Sequencing by Ahmet Sacan]<br/> <br/> <br/> <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:">[[How_we_produce_genomic_big_data?|How we produce genomic big data?]]<br/> [[Sanger_sequencing|Sanger sequencing]]</span></span></span></span></span></span><br/> <span style="font-size:12pt"><span style="background:white"><span style="line-height:18.0pt"><span style="font-family:Gulim,sans-serif"><span style="font-family:"><span style="color:black">[[What_is_a_protein?|What is a protein?]]&nbsp;&nbsp;</span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">03</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:">[[Next_generation_sequencing|Next generation sequencing]].<br/> [[Illumina_sequencing|Illumina sequencing]]<br/> [[Nanoball_sequencing|Nanoball sequencing]]<br/> [[Nanopore_sequencing|Nanopore sequencing]].</span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">04</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="word-break:break-all"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:">[[Epigenomics|Epigenomics]]<br/> [[Methylation_sequencing|Methylation sequencing]] (Epigenomic sequencing).</span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">05</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="word-break:break-all"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">[[DNA_and_sequence_alignment|DNA and sequence alignment]].<br/> [[Dynamic_programming|Dynamic programming]]<br/> [[Computers_for_genomics|Computers for genomics]] ([[Bioinformatics|Bioinformatics]]).<br/> [[Turing_machine|Turing machine]]</span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">06</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="word-break:break-all"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:">[[Genome_Assembly|Genome Assembly]]. (building genomes)</span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">07</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:">[[Phylogenetic_tree|Phylogenetic tree]] (tree of life): The origin of Korean people using genome data.</span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">08</span></span></span></span></span></span></span>
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| style="border-bottom: 1px solid black; width: 700px; padding: 1px; height: 47px; border-top: none; border-right: 1px solid black; border-left: none;" | <span style="font-size:10pt"><span style="word-break:break-all"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">[[Comparative_Genomics|Comparative Genomics]] (how we can compare life using genomes)<br/> &nbsp; *&nbsp;[https://www.youtube.com/watch?v=JvUtiIfddvI Intro of Comparative Genomics by Jong Bhak]</span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">09</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="word-break:break-all"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">[[Evolution|Evolution]] (genome perspective): Is Darwinian evolution correct?</span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">10</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="word-break:break-all"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:">&nbsp;[[The_human_genome_project|The human genome project]]</span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">11</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="word-break:break-all"><span style="font-family:">&nbsp;<span style="font-size:12.0pt"><span style="font-family:">[[Korean_genome_project|Korean genome project]]: Who are Koreans?</span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">12</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:">[[Whale_genome_analyses|Whale genome analyses]]</span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">13</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:">&nbsp;[[Tiger_genome_analyses|Tiger genome analyses]]</span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">14</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">[[Cancer_genomes|Cancer genomes]] and [[Genomes_and_aging|Genomes and aging]] (telomere, Epigenomic reprogramming)</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:54px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:1px solid black" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">15</span></span></span></span></span></span></span>
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| style="border-bottom:1px solid black; width:547px; padding:1px 1px 1px 1px; height:47px; border-top:none; border-right:1px solid black; border-left:none" | <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:"><span style="font-size:12.0pt"><span style="font-family:"><span style="color:black">Research Report presentation ([[SELF|SELF]])</span></span></span></span></span></span></span>
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<div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="font-size:24px"><strong><span style="color:black">(No mid-term exam)</span></strong></span></div>
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<p style="text-align: center"><span style="font-size:22px"><span style="color:black"><span style="color:black; font-family:arial unicode ms">Contents</span></span></span></p>
 
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<p style="text-align: center"><span style="color:black; font-size:12pt"><span style="color:black; font-family:arial unicode ms">01</span></span></p>
 
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<p><span style="font-size:16px">&nbsp;</span><span style="color:black; font-size:12pt">&nbsp; [[Introduction to Jong Bhak&#39;s&nbsp;genomics&nbsp;course]]</span></p>
 
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<p><span style="font-size:16px">&nbsp; &nbsp;[[What is life?]], [[What is information?]], [[What is the universe?]] &nbsp;(as information processing objects)</span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp;&nbsp;[[What is evolution?]]</span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp;[[What is Sequencing in Genomics and Omics?]] (as an approach of understanding life)</span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt">&nbsp;[[Sequencing]]: Sanger, NGS, Methyl-seq, ATAC-seq</span><br />
 
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<p><span style="color:black; font-size:12pt">&nbsp;[[What is alignment?]], [[What is genome assembly?]], </span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp; [[What is functional annotation for Big data&nbsp;processing in biology?]]</span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt">&nbsp;Open source tools, concepts of alignment of DNA sequences.</span><br />
 
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<p><span style="color:black; font-size:12pt">&nbsp;[[How molecules and cells propagate in the universe?]] [[Evolution]].</span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp;[[Close species Comparative Genomics (CSCG) for diverse genome evolution]].</span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp;[[Phylogenetic tree]].</span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt">&nbsp;[[Selective sweep]] &nbsp;[[Convergent evolution]]</span></p>
 
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<p style="text-align: center"><span style="font-size:9px"><span style="color:black"><span style="color:black; font-family:arial unicode ms">(2016.10.07)</span></span></span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp;<strong>Human genomes</strong></span></span></p>
 
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<p><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp; &nbsp;[[KPGP]], [[KOREF]], [[The first Korean genome]]</span></span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp;Genome analyses cases</span></p>
 
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<p><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp; </span>[[Whale genomics]]</span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp;Genome analyses cases</span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp; [[<strong>Tiger genomes]]</strong></span></span></p>
 
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<p><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp;</span>Genome analyses cases</span></p>
 
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<p><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp;&nbsp; [[Vulture genomes]]</span>&nbsp;<span style="color:black; font-family:바탕,serif">&nbsp;</span></span></p>
 
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<p><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp;[[<strong>Transcriptome]]</strong>: &nbsp;</span>Genome analyses cases ([[horse transcriptome]])</span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp;Curing Cancer using genomics (Oncomics)</span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp; &nbsp;Analysing disease genomes</span></p>
 
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<p><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp;</span>Curing Cancer using genomics (Oncomics)</span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp; Diffuse type cancer analyses.</span></p>
 
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<p><span style="color:black; font-size:12pt">&nbsp;Curing Aging using genomics (Geromics)</span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp;[[Measuring aging biologically]]</span></span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp;[[Telomics]]</span></span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp;[[Geromics Lecture related links: telomeres]]</span></span></p>
 
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<p><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp;</span>Curing Aging using genomics (Geromics)</span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt">&nbsp; Aging related keywords and genes</span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp;[[Epigenomics]] (Environmental genome)</span></span></p>
 
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<p style="text-align: left"><span style="color:black; font-size:12pt"><span style="color:black; font-family:바탕,serif">&nbsp; [[Research Report presentation]]</span></span></p>
 
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Latest revision as of 10:37, 7 March 2024

Jong Bhak's Genomics course syllabus. 2024 (Spring)
(No mid-term exam)
Weekly Schedule
Week Contents: Students are required to click on all the links and listen to the Youtube channels.
01 Introduction to Jong Bhak's genomics course
What is science?
What is life?
What is DNA? What is RNA?
What is transcription and translation?
What is information?
02 What is Sequencing in Genomics and Omics? 
  History of Genome Sequencing by Ahmet Sacan


How we produce genomic big data?
Sanger sequencing
What is a protein?  
03 Next generation sequencing.
Illumina sequencing
Nanoball sequencing
Nanopore sequencing.
04 Epigenomics
Methylation sequencing (Epigenomic sequencing).
05 DNA and sequence alignment.
Dynamic programming
Computers for genomics (Bioinformatics).
Turing machine
06 Genome Assembly. (building genomes)
07 Phylogenetic tree (tree of life): The origin of Korean people using genome data.
08 Comparative Genomics (how we can compare life using genomes)
  * Intro of Comparative Genomics by Jong Bhak
09 Evolution (genome perspective): Is Darwinian evolution correct?
10  The human genome project
11  Korean genome project: Who are Koreans?
12 Whale genome analyses
13  Tiger genome analyses
14 Cancer genomes and Genomes and aging (telomere, Epigenomic reprogramming)
15 Research Report presentation (SELF)

 

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