Difference between revisions of "Description of Genomics course"
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| − | < | + | <u><span style="font-size:16pt">Course Description</span></u><span style="font-size:16pt">for Genomics (General description)</span> |
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| − | + | <span style="font-size:11pt">by [[Jong_Bhak|Jong Bhak]] (jongbhak@gmail.com)</span><br/> <br/> <span style="font-size:11pt">Genomics is the new name for genetics that encompasses not only traditional<br/> genetics research and technology topics but also includes information technology, systems biology, high throughput biodata generation, processing, and analyses.</span> | |
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| − | + | <span style="font-size:11pt">It covers areas such as sequencing, DNA synthesis, and genome writing and editing.<br/> Genomics course requires the students to have been exposed to general<br/> biology, data processing, statistics, mathematics, and computer science.<br/> The genomic research can be largely divided into experimental and informatic<br/> parts. The course will not cover hands-on experiments due to space limitation.<br/> Students who took this subject will be able to understand life in terms of information processing </span><span style="font-size:11pt">with much knowledge on how to use technologies to solve problems such as curing cancer and aging.</span> | |
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| − | + | <span style="font-size:11pt">'''The topics of genomics include:'''<br/> <br/> 1. What is life, information, and the universe? (as information processing objects)<br/> 2. What is Omics? (as an approach of understanding life)<br/> 3. What is 'Big data' in biology?<br/> 4. How molecules and cells propagate in the universe?<br/> 5. Genome reading and writing</span> | |
| − | + | <span style="font-size:11pt"> Genome Sequencing</span> | |
| − | + | <span style="font-size:11pt"> Genome sequence analyses</span> | |
| − | + | <span style="font-size:11pt"> Multi-omics</span> | |
| − | + | <span style="font-size:11pt"> Transcriptomics</span> | |
| − | + | <span style="font-size:11pt"> Epigenomics</span> | |
| − | + | <span style="font-size:11pt"> Metabolomics</span> | |
| − | + | <span style="font-size:11pt"> Proteomics</span> | |
| − | + | <span style="font-size:11pt">6. Curing Cancer using genomics (Oncomics)</span> | |
| − | < | + | <span style="font-size:11pt">7. Curing Aging using genomics (Geromics)</span> |
| + | <div style="margin: 0cm 0cm 8pt"> </div> | ||
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| + | | colspan="2" style="height: 12.75pt; width: 110.95pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
| + | | style="height: 12.75pt; width: 5.6pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
| + | | style="height: 12.75pt; width: 115.55pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
| + | | style="height: 12.75pt; width: 71.9pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
| + | | colspan="2" style="height: 12.75pt; width: 73.5pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
| + | | style="height: 12.75pt; width: 73.8pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
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| + | | colspan="8" style="height: 12.75pt; width: 451.3pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black">Text</span></div> | ||
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| + | | style="height: 15.75pt; width: 106.05pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:black">Category</span></div> | ||
| + | | colspan="5" style="height: 15.75pt; width: 235.3pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:red">Book</span></div> | ||
| + | | colspan="2" style="height: 15.75pt; width: 109.95pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
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| + | | style="height: 15.75pt; width: 106.05pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:black">Title</span></div> | ||
| + | | colspan="5" style="height: 15.75pt; width: 235.3pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:red">[[Introduction_to_Genomics|Introduction to Genomics]]</span></div> | ||
| + | | colspan="2" style="height: 15.75pt; width: 109.95pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
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| + | | style="height: 15.75pt; width: 106.05pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:black">Author</span></div> | ||
| + | | colspan="5" style="height: 15.75pt; width: 235.3pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:red">Arthur M. Lesk,</span></div> | ||
| + | | colspan="2" style="height: 15.75pt; width: 109.95pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
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| + | | style="height: 15.75pt; width: 106.05pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:black">ISBN</span></div> | ||
| + | | colspan="5" style="height: 15.75pt; width: 235.3pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:black"> </span></div> | ||
| + | | colspan="2" style="height: 15.75pt; width: 109.95pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
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| + | | style="height: 15.75pt; width: 106.05pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:black">Remarks</span></div> | ||
| + | | colspan="5" style="height: 15.75pt; width: 235.3pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:black"> </span><span style="color:red">Oxford University Press</span></div> | ||
| + | | colspan="2" style="height: 15.75pt; width: 109.95pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
| + | |- | ||
| + | | style="height: 7.8pt; width: 106.05pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:black">Course Reserves Designation</span></div> | ||
| + | | colspan="5" style="height: 7.8pt; width: 235.3pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: normal"><span style="color:black"> </span></div> | ||
| + | | colspan="2" style="height: 7.8pt; width: 109.95pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black"> </span></div> | ||
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| + | | colspan="2" style="height: 15.75pt; width: 110.95pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black">References</span></div> | ||
| + | |} | ||
| − | < | + | <br/> <span style="font-size:10pt"><span style="word-break:break-all"><span style="font-family:" malgun="" gothic",sans-serif"=""><span style="font-size:12.0pt"><span style="font-family:" arial="" narrow",sans-serif"="">[[javascript:void(0)|<span style="background:white"><span style="color:#1a0dab">Korean Genome Project: 1094 Korean personal genomes with clinical information</span></span>]]. Science Advances.</span></span></span></span></span><br/> <br/> <span style="font-size:10pt"><span style="word-break:break-all"><span style="font-family:" malgun="" gothic",sans-serif"=""><span style="font-size:12.0pt"><span style="font-family:" arial="" narrow",sans-serif"="">[[javascript:void(0)|<span style="background:white"><span style="color:#1a0dab">The origin and composition of Korean ethnicity analyzed by ancient and present-day genome sequences</span></span>]].</span></span><span style="font-size:12.0pt"><span style="background:white"><span style="font-family:" arial="" narrow",sans-serif"=""><span style="color:#777777">Genome biology and evolution 12 (5), 553-565</span></span></span></span></span></span></span><br/> <br/> <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:" malgun="" gothic",sans-serif"=""><span style="font-size:12.0pt"><span style="font-family:" arial="" narrow",sans-serif"="">[[javascript:void(0)|<span style="background:white"><span style="color:#1a0dab">Depression and suicide risk prediction models using blood-derived multi-omics data</span></span>]]</span></span></span></span></span></span><br/> <span style="font-size:10pt"><span style="background:white"><span style="word-break:break-all"><span style="font-family:" malgun="" gothic",sans-serif"=""><span style="font-size:12.0pt"><span style="font-family:" arial="" narrow",sans-serif"=""><span style="color:#777777">Translational psychiatry 9 (1), 1-8</span></span></span></span></span></span></span><br/> <br/> <span style="font-size:10pt"><span style="text-autospace:ideograph-numeric ideograph-other"><span style="word-break:normal"><span style="font-family:" malgun="" gothic",sans-serif"=""><span style="font-size:12.0pt"><span style="font-family:" arial="" narrow",sans-serif"="">[[javascript:void(0)|<span style="background:white"><span style="color:#1a0dab">KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses</span></span>]]</span></span></span></span></span></span><br/> <span style="font-size:10pt"><span style="background:white"><span style="word-break:break-all"><span style="font-family:" malgun="" gothic",sans-serif"=""><span style="font-size:12.0pt"><span style="font-family:" arial="" narrow",sans-serif"=""><span style="color:#777777">Scientific reports 8 (1), 1-14</span></span></span></span></span></span></span><br/> <br/> '''<span style="font-size:11pt">The Atom of Evolution</span>'''<span style="font-size:11pt">. ''' '''Genomics & Informatics, December <span style="color:red">2004</span>, 2(4):167-173.</span> |
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| − | + | '''<span style="color:black">Genomic profile analysis of diffuse-type gastric cancers </span>''''''''<span style="color:black">Genome Biology</span>'''''<b><span style="color:black">,</span></b>'''<span style="color:red">2014</span>''' | |
| + | <div style="margin: 0cm 0cm 8pt">'''<span style="color:black"> </span>''''''<span style="color:black">Minke whale genome and aquatic adaptation in cetaceans. </span>'''''Nature Genetics'', <span style="color:red">2013</span>. (24<sup>th</sup> Nov 2013)</div> <div style="margin: 0cm 0cm 8pt">'''<span style="color:black"> </span>''''''<span style="color:black">Tiger genome and comparative analysis with lion and snow leopard genomes.</span>'''</div> <div style="margin: 0cm 0cm 12pt">''Nature Communications'', <span style="color:red">2013</span>. Sep. 17<sup>th</sup>.</div> <div style="margin: 0cm 0cm 12pt">'''<span style="color:black; font-size:11pt">Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq</span>'''</div> <div style="vertical-align: baseline; background: white; margin: 4.5pt 0cm; line-height: 13.5pt">'''''<span style="color:black; font-size:11pt">BMC Genomics</span>''<span style="color:black; font-size:11pt">. </span><span style="color:red; font-size:11pt">2012 Sep </span><span style="color:black; font-size:11pt">12;13:473. doi: 10.1186/1471-2164-13-473.</span>'''</div> <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"> </div> <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="font-size:16px">[[Jong_Bhak's_Genomics_Syllabus|Jong Bhak's Genomics Syllabus]]</span></div> <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"> </div> | ||
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| − | + | | style="height: 12.75pt; width: 120.75pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%"><span style="color:black">Grading</span></div> | |
| − | + | | style="background-color: transparent" | <div style="margin: 0cm 0cm 8pt"> </div> | |
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| − | + | | colspan="2" style="height: 55.85pt; width: 505.5pt; background-color: transparent" | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%; text-indent: 5pt"><span style="color:red">Research report writing and presentation (100%)</span></div> | |
| − | + | <span style="color:red">Each week, before, class, students are asked to submit research reports on genomics topics.</span> | |
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| − | < | + | <span style="color:red">The final grade will be given by the quality of research reports and presentations (in English)</span> |
| + | <div style="word-break: keep-all; margin: 0cm 0cm 8pt; line-height: 160%; text-indent: 5pt"><span style="color:red">The important points of grading are:</span></div> | ||
| + | <span style="color:red">1. </span><span style="color:black">Being scientific in reasoning and presenting</span> | ||
| − | < | + | <span style="color:red">2. </span><span style="color:black">Critical thinking level</span> |
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Latest revision as of 20:58, 3 February 2021
Course Descriptionfor Genomics (General description)
by Jong Bhak (jongbhak@gmail.com)
Genomics is the new name for genetics that encompasses not only traditional
genetics research and technology topics but also includes information technology, systems biology, high throughput biodata generation, processing, and analyses.
It covers areas such as sequencing, DNA synthesis, and genome writing and editing.
Genomics course requires the students to have been exposed to general
biology, data processing, statistics, mathematics, and computer science.
The genomic research can be largely divided into experimental and informatic
parts. The course will not cover hands-on experiments due to space limitation.
Students who took this subject will be able to understand life in terms of information processing with much knowledge on how to use technologies to solve problems such as curing cancer and aging.
The topics of genomics include:
1. What is life, information, and the universe? (as information processing objects)
2. What is Omics? (as an approach of understanding life)
3. What is 'Big data' in biology?
4. How molecules and cells propagate in the universe?
5. Genome reading and writing
Genome Sequencing
Genome sequence analyses
Multi-omics
Transcriptomics
Epigenomics
Metabolomics
Proteomics
6. Curing Cancer using genomics (Oncomics)
7. Curing Aging using genomics (Geromics)
Text
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Category
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Book
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Title
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Author
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Arthur M. Lesk,
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ISBN
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Remarks
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Oxford University Press
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Course Reserves Designation
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References
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Korean Genome Project: 1094 Korean personal genomes with clinical information. Science Advances.
The origin and composition of Korean ethnicity analyzed by ancient and present-day genome sequences.Genome biology and evolution 12 (5), 553-565
Depression and suicide risk prediction models using blood-derived multi-omics data
Translational psychiatry 9 (1), 1-8
KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses
Scientific reports 8 (1), 1-14
The Atom of Evolution. Genomics & Informatics, December 2004, 2(4):167-173.
Genomic profile analysis of diffuse-type gastric cancers '''Genome Biology,2014
'Minke whale genome and aquatic adaptation in cetaceans. Nature Genetics, 2013. (24th Nov 2013)
'Tiger genome and comparative analysis with lion and snow leopard genomes.
Nature Communications, 2013. Sep. 17th.
Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq
BMC Genomics. 2012 Sep 12;13:473. doi: 10.1186/1471-2164-13-473.
Grading
|
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Research report writing and presentation (100%)
Each week, before, class, students are asked to submit research reports on genomics topics. The final grade will be given by the quality of research reports and presentations (in English) The important points of grading are:
1. Being scientific in reasoning and presenting 2. Critical thinking level 3. Being independent in thinking | |
