Difference between revisions of "Description of Genomics course"
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<p><font size="+0"><u><span style="font-size: 16pt; line-height: 107%">Course Description</span></u><span style="font-size: 16pt; line-height: 107%"> for BME324, Genomics</span></font></p> | <p><font size="+0"><u><span style="font-size: 16pt; line-height: 107%">Course Description</span></u><span style="font-size: 16pt; line-height: 107%"> for BME324, Genomics</span></font></p> | ||
| − | <p style="margin: 0cm 0cm 8pt"><span style="font-size: 11pt; line-height: 107%"><font size="+0">by [[Jong Bhak]] (jongbhak@gmail.com)</font></span><span><br /> | + | <p style="margin: 0cm 0cm 8pt"><span style="font-size: 11pt; line-height: 107%"><font size="+0">by [[Jong Bhak]] (jongbhak@gmail.com)</font></span><span><br /> |
| − | <font size="+0"><font size="2"><br /> | + | <font size="+0"><font size="2"><br /> |
| − | </font></font></span><span style="font-size: 11pt; line-height: 107%"><font size="+0">Genomics is the new name for genetics that encompasses not only traditional<br /> | + | </font></font></span><span style="font-size: 11pt; line-height: 107%"><font size="+0">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. </font></span></p> | genetics research and technology topics but also includes information technology, systems biology, high throughput biodata generation, processing, and analyses. </font></span></p> | ||
| − | <p style="margin: 0cm 0cm 8pt"><span style="font-size: 11pt; line-height: 107%"><font size="+0">It covers areas such as sequencing, DNA synthesis, and genome writing and editing.<br /> | + | <p style="margin: 0cm 0cm 8pt"><span style="font-size: 11pt; line-height: 107%"><font size="+0">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 /> | + | Genomics course requires the students to have been exposed to general<br /> |
| − | biology, data processing, statistics, mathematics, and computer science.<br /> | + | biology, data processing, statistics, mathematics, and computer science.<br /> |
| − | The genomic research can be largely divided into experimental and informatic<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 /> | + | 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 </font></span><span style="font-size: 11pt; line-height: 107%"><font size="+0">with much knowledge on how to use technologies to solve problems such as curing cancer and aging.<br /> | + | Students who took this subject will be able to understand life in terms of information processing </font></span><span style="font-size: 11pt; line-height: 107%"><font size="+0">with much knowledge on how to use technologies to solve problems such as curing cancer and aging.<br /> |
</font></span></p> | </font></span></p> | ||
| − | <p style="margin: 0cm 0cm 8pt"><span style="font-size: 11pt; line-height: 107%"><font size="+0">The topics of genomics include:<br /> | + | <p style="margin: 0cm 0cm 8pt"><span style="font-size: 11pt; line-height: 107%"><font size="+0">The topics of genomics include:<br /> |
| − | <br /> | + | <br /> |
| − | 1. What is life, information, and the universe? (as information processing objects)<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 /> | + | 2. What is Omics? (as an approach of understanding life)<br /> |
| − | 3. What is 'Big data' in biology?<br /> | + | 3. What is 'Big data' in biology?<br /> |
| − | 4. How molecules and cells propagate in the universe?<br /> | + | 4. How molecules and cells propagate in the universe?<br /> |
5. Genome reading and writing</font></span></p> | 5. Genome reading and writing</font></span></p> | ||
<p style="margin: 0cm 0cm 8pt"><span style="font-size: 11pt; line-height: 107%"><font size="+0">6. Curing Cancer using genomics (Oncomics)</font></span></p> | <p style="margin: 0cm 0cm 8pt"><span style="font-size: 11pt; line-height: 107%"><font size="+0">6. Curing Cancer using genomics (Oncomics)</font></span></p> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: 160%; -ms-word-break: keep-all"><span style="color: black; line-height: 160%"><font size="2">Text</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: 160%; -ms-word-break: keep-all"><span style="color: black; line-height: 160%"><font size="2">Text</font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">Category</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">Category</font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: red"><font size="2">Book</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: red"><font size="2">Book</font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">Title</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">Title</font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: red"><font size="2">[[Introduction to Genomics]]</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: red"><font size="2">[[Introduction to Genomics]]</font></span></div> | ||
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| − | <td style="border-top: rgb(0,0,0) 0px; height: 15.75pt; border-right: black 1pt solid; width: 109.95pt; border-bottom: rgb(0,0,0) 0px; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent; border-image: none" | + | <td style="border-top: rgb(0,0,0) 0px; height: 15.75pt; border-right: black 1pt solid; width: 109.95pt; border-bottom: rgb(0,0,0) 0px; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent; border-image: none" colspan="2" width="183"> |
<div style="margin: 0cm 0cm 8pt; line-height: 160%; -ms-word-break: keep-all"><span style="color: black; line-height: 160%"><font size="2"> </font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: 160%; -ms-word-break: keep-all"><span style="color: black; line-height: 160%"><font size="2"> </font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">Author</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">Author</font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: red"><font size="2">Arthur M. Lesk,</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: red"><font size="2">Arthur M. Lesk,</font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">ISBN</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">ISBN</font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">Remarks</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">Remarks</font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2"> </font></span><span style="color: red"><font size="2">Oxford University Press</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2"> </font></span><span style="color: red"><font size="2">Oxford University Press</font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">Course Reserves Designation</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: normal; -ms-word-break: keep-all"><span style="color: black"><font size="2">Course Reserves Designation</font></span></div> | ||
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| − | <td style="border-top: rgb(0,0,0) 0px; height: 7.8pt; border-right: black 1pt solid; width: 109.95pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" | + | <td style="border-top: rgb(0,0,0) 0px; height: 7.8pt; border-right: black 1pt solid; width: 109.95pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" colspan="2" width="183"> |
<div style="margin: 0cm 0cm 8pt; line-height: 160%; -ms-word-break: keep-all"><span style="color: black; line-height: 160%"><font size="2"> </font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: 160%; -ms-word-break: keep-all"><span style="color: black; line-height: 160%"><font size="2"> </font></span></div> | ||
</td> | </td> | ||
</tr> | </tr> | ||
<tr style="height: 15.75pt"> | <tr style="height: 15.75pt"> | ||
| − | <td style="border-top: rgb(0,0,0) 0px; height: 15.75pt; border-right: rgb(0,0,0) 0px; width: 110.95pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent; border-image: none" | + | <td style="border-top: rgb(0,0,0) 0px; height: 15.75pt; border-right: rgb(0,0,0) 0px; width: 110.95pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent; border-image: none" colspan="2" width="185"> |
<div style="margin: 0cm 0cm 8pt; line-height: 160%; -ms-word-break: keep-all"><span style="color: black; line-height: 160%"><font size="2">References</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: 160%; -ms-word-break: keep-all"><span style="color: black; line-height: 160%"><font size="2">References</font></span></div> | ||
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<div style="margin: 0cm 0cm 8pt; line-height: 160%; -ms-word-break: keep-all"><span style="font-size: 12pt; color: black; line-height: 160%">Weekly Schedule</span></div> | <div style="margin: 0cm 0cm 8pt; line-height: 160%; -ms-word-break: keep-all"><span style="font-size: 12pt; color: black; line-height: 160%">Weekly Schedule</span></div> | ||
<p> | <p> | ||
| − | <table style="border-collapse: collapse" cellspacing="0" cellpadding | + | <table border="0" style="border-collapse: collapse" cellspacing="0" cellpadding="0"> |
<tbody> | <tbody> | ||
<tr style="height: 14.7pt"> | <tr style="height: 14.7pt"> | ||
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<td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 410.2pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" width="684"> | <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 410.2pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" width="684"> | ||
<div style="text-align: left; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="left"> </div> | <div style="text-align: left; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="left"> </div> | ||
| − | <div style="text-align: left; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> (Course orientation | + | <div style="text-align: left; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> (Course orientation, Self-Cricial Evaluation: SCE), Homework, Presentation, and Research</font></span></div> |
| − | + | <div style="text-align: left; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> </font></span></div> | |
| − | <div style="text-align: left; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> | ||
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<div style="text-align: center; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="center"><span style="color: black; line-height: 107%"><font size="2">02</font></span></div> | <div style="text-align: center; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="center"><span style="color: black; line-height: 107%"><font size="2">02</font></span></div> | ||
</td> | </td> | ||
| − | <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 410.2pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" width="684"> | + | <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 410.2pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" width="684"> |
| − | + | <div style="text-align: left; margin: 0cm 0cm 8pt; text-indent: 5pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> Chemistry and Biochemistry of Genomics</font></span></div> | |
| − | <div style="text-align: left; margin: 0cm 0cm 8pt; text-indent: 5pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> Biochemistry | + | <div style="text-align: left; margin: 0cm 0cm 8pt; text-indent: 5pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> [[Sequencing]], [[PCR]], </font></span></div> |
| − | <div style="text-align: left; margin: 0cm 0cm 8pt; text-indent: 5pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> [[Sequencing]]</font></span></div> | ||
<div style="text-align: left; margin: 0cm 0cm 8pt; text-indent: 5pt; -ms-word-break: keep-all" align="left"> </div> | <div style="text-align: left; margin: 0cm 0cm 8pt; text-indent: 5pt; -ms-word-break: keep-all" align="left"> </div> | ||
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<td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 410.2pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" width="684"> | <td style="border-top: rgb(0,0,0) 0px; height: 35.65pt; border-right: black 1pt solid; width: 410.2pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: rgb(0,0,0) 0px; padding-right: 1.4pt; background-color: transparent" width="684"> | ||
| − | <div style="text-align: left; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> </font></span></div> | + | <div style="text-align: left; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> What is reference?</font></span></div> |
| + | <div style="text-align: left; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="left"><span style="color: black; line-height: 107%; serif: "><font size="2"> [[Alignment]]</font></span></div> | ||
| + | <div style="text-align: left; margin: 0cm 0cm 8pt; -ms-word-break: keep-all" align="left"> </div> | ||
</td> | </td> | ||
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| − | <table style="border-collapse: collapse" cellspacing="0" cellpadding | + | <table border="0" style="border-collapse: collapse" cellspacing="0" cellpadding="0"> |
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| − | <td style="border-top: rgb(0,0,0) 0px; height: 55.85pt; border-right: black 1pt solid; width: 505.5pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: black 1pt solid; padding-right: 1.4pt; background-color: transparent; border-image: none" | + | <td style="border-top: rgb(0,0,0) 0px; height: 55.85pt; border-right: black 1pt solid; width: 505.5pt; border-bottom: black 1pt solid; padding-bottom: 1.4pt; padding-top: 1.4pt; padding-left: 1.4pt; border-left: black 1pt solid; padding-right: 1.4pt; background-color: transparent; border-image: none" colspan="2" width="843"> |
<div style="margin: 0cm 0cm 8pt; line-height: 160%; text-indent: 5pt; -ms-word-break: keep-all"><span style="color: red; line-height: 160%"><font size="2">Research report writing and presentation (100%)</font></span></div> | <div style="margin: 0cm 0cm 8pt; line-height: 160%; text-indent: 5pt; -ms-word-break: keep-all"><span style="color: red; line-height: 160%"><font size="2">Research report writing and presentation (100%)</font></span></div> | ||
<p style="margin: 0cm 0cm 8pt; line-height: 160%; text-indent: 5pt; -ms-word-break: keep-all"><span style="color: red; line-height: 160%"><font size="2">Each week, before, class, students are asked to submit research reports on genomics topics.</font></span></p> | <p style="margin: 0cm 0cm 8pt; line-height: 160%; text-indent: 5pt; -ms-word-break: keep-all"><span style="color: red; line-height: 160%"><font size="2">Each week, before, class, students are asked to submit research reports on genomics topics.</font></span></p> | ||
Revision as of 12:18, 7 September 2015
Course Description for BME324, Genomics
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
6. Curing Cancer using genomics (Oncomics)
7. Curing Aging using genomics (Geromics)
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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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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.
Weekly Schedule
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Week
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Contents
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01
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(Course orientation, Self-Cricial Evaluation: SCE), Homework, Presentation, and Research
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02
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Chemistry and Biochemistry of Genomics
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03
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What is reference?
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04
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05
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What is Information?
Informatics
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06
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What is Programming?
Perl, Bioperl, Algorithm
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07
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What is Bioinformatics?
Principles of Bioinformatics
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08
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What is Omics?
Various omics
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09
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What is Genomics?
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10
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What is Evolution?
Darwinian evolution
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11
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What is Sequence?
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12
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What is Cancer?
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13
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What is Aging?
Measuring aging
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14
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Research Report presentation
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15
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Research Report presentation
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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 |
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