LSCI5004: Advanced Topics in Genomics, Proteomics and Metabolomics
Molecular analysis of genomes:
genomics, functional genomics and beyond 2011-2012
Prof. HS Kwan
Date : 24/2, 2/3, 9/3, and Date to be decided
Time :
9:30 pm - 12:15
pm
Venue : SC297
Instruction: The students responsible for each paper
should read the paper thoroughly, present it as a “WHITEBOARD PRESENTATION”. Powerpoint should be used only to show Tables, Figures and Diagrams. The
students
responsible for discussing a
topic will ask questions
and lead discussions
of the paper. All students should read
every paper and engage fully
to discuss the paper.
The following
scenario is close to what we are trying to do in this section of LSCI5004:
You have glanced
through a few issues of Science and found a few articles in these issues
interesting--they are articles concerning molecular analysis of genomes. Although you have little background in this
area, you have decided to read them. How
can you get the best of them? Some suggestions:
refer to textbooks for the basic terms and experiments, talk to fellow students
who may have better background, try to understand the logic and approach of the
research reports rather than just read through them, etc. Understand
the figures and tables first. Also find out what the paper is trying to tell
you. Read actively, not passively. Don’t be afraid of difficult articles!
The arrangement for
discussion: Two to three students are responsible to read one to two papers. One
student will be picked randomly to present one part of the paper each time.
When a student fails to explain the part of paper, a second student will take
over to explain the part. Another two to three students will be assigned to ask
questions about the paper. Students fail to explain his/her part of paper or
fail to ask question will have marks deducted.
A. General Reading for Everyone
- Lander, E.S. 2011. Initial impact of the sequencing of the human genome. Nature. 470:187-97.
- Green, E.D. and M.S. Guyer. 2011. Charting a course for genomic medicine from base pairs to bedside. Nature 470: 204-213.
- Li, R., Y. Li, H. Zheng, R. Luo, H. Zhu, Q. Li, W. Qian, Y. Ren, G. Tian, J. Li et
- al. 2010. Building the sequence map of the human pan-genome. Nat Biotechnol 28: 57-63.
- Altshuler, D., M.J. Daly, and E.S. Lander. 2008. Genetic Mapping in Human Disease. Science 322: 881-888.
- Hood, L., Heath, J. R., Phelps, M. E., Lin, B. 2004. Systems Biology and New Technologies Enable Predictive and Preventative Medicine. Science 306: 640-643
- Collins et al., 2003. The U.S. Human Genome Project: Lessons from Large-Scale Biology. Science 300:286-290.
- Collins F.S., Green E.D., Guttmacher A.E., and Guyer M.S. 2003. A vision for the future of genomics research. Nature 422:835-847.
- Collins et al., 1998. New Goals for the U.S. Human Genome Project: 1998–2003. Science 282:682-689.
Human
genome project timeline: go to
24 Fabruary,
2012—Introduction by Professor H.S. Kwan
B. Specific reading list for paper discussion:
2 March, 2012—the
first discussion session
|
|
Paper 1:
|
Cherf
GM, Lieberman KR, Rashid H, Lam CE, Karplus K, Akeson M.
2012.
Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å
precision. Nat Biotechnol. doi: 10.1038/nbt.2147. [Epub ahead of print] See
also:
|
Students:
|
AU, Ka Yee 歐嘉儀,
LIU, Ming 劉明
______________________________________________________
|
Paper 2
+ 2a:
|
Ozsolak,
F., A.R. Platt, D.R. Jones, J.G. Reifenberger, L.E. Sass, P. McInerney, J.F.
Thompson, J. Bowers, M. Jarosz, and P.M. Milos. 2009. Direct RNA sequencing. Nature
461: 814-U873.
Drmanac,
R., A.B. Sparks, M.J. Callow, A.L. Halpern, N.L. Burns, B.G. Kermani, P.
Carnevali, I. Nazarenko, G.B. Nilsen, G. Yeung et al. 2009. Human genome sequencing using unchained base reads
on self-assembling DNA nanoarrays. Science 327: 78-81.
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Students:
|
CHANG, Jinhui 常金輝,
LOO, Fong Chuen 盧芳泉
_______________________________________________________
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Paper 3:
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Jones, S., X.S. Zhang, D.W. Parsons,
J.C.H. Lin, R.J. Leary, P. Angenendt, P. Mankoo, H. Carter, H. Kamiyama, A.
Jimeno et al. 2008. Core signaling pathways in human pancreatic cancers
revealed by global genomic analyses. Science
321: 1801-1806.
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Students:
|
CHENG, Hong Yiu 鄭康堯,
SOU, Weng Hong 蘇詠虹______________________________________________________
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Paper 4:
|
Ley,
T.J., E.R. Mardis, L. Ding, B. Fulton, M.D. McLellan, K. Chen, D. Dooling,
B.H. Dunford-Shore, S. McGrath, M. Hickenbotham et al. 2008. DNA sequencing
of a cytogenetically normal acute myeloid leukaemia genome. Nature 456:
66-72.
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Students:
|
CHENG, Xuanjin 程旋晋,
TAM, Yeuk Fei 譚若菲
|
_________________________________________________________________
9 March, 2012—the
second discussion session
|
|
Paper 5:
|
Emilsson,
V., G. Thorleifsson, B. Zhang, A.S. Leonardson, F. Zink, J. Zhu, S. Carlson,
A. Helgason, G.B. Walters, S. Gunnarsdottir et al. 2008. Genetics of gene expression
and its effect on disease. Nature 452: 423-U422.
|
Students:
|
CHIU, Wai Yin Vivien
趙熭然, WANG, Wei 王偉
_____________________________________________________
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Paper 6:
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Bignell, G.R., C.D. Greenman,
H. Davies, A.P. Butler, S. Edkins, J.M. Andrews, G. Buck, L. Chen, D. Beare,
C. Latimer et al. 2010. Signatures
of mutation and selection in the cancer genome. Nature 463:
893-898.
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Students:
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FAN, Long 樊隆,
WEN, Chaoqing 温潮清
______________________________________________________
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Paper 7:
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Maher,
C.A., C. Kumar-Sinha, X.H. Cao, S. Kalyana-Sundaram, B. Han, X.J. Jing, L.
Sam, T. Barrette, N. Palanisamy, and A.M. Chinnaiyan. 2009. Transcriptome
sequencing to detect gene fusions in cancer. Nature 458:
97-U99.
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Students:
|
LAU, Sze Nga 劉詩雅,
WONG, Ho Chun 黃浩俊
_______________________________________________________
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Paper 8:
|
Turnbaugh,
P.J., R.E. Ley, M.A. Mahowald, V. Magrini, E.R. Mardis, and J.I. Gordon.
2006. An obesity-associated gut microbiome with increased capacity for energy
harvest. Nature 444: 1027-1031.
Read
also--Ley, R.E., P.J. Turnbaugh, S. Klein, and J.I. Gordon. 2006. Microbial
ecology: human gut microbes associated with obesity. Nature 444: 1022-1023.
|
Student:
|
LAW, Hiu Tung 羅曉彤,
WU, Tsz Huen 胡芷萱_______________________________________________________
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Date to be
decided—the third discussion session
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Paper 9:
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Costello,
E.K., C.L. Lauber, M. Hamady, N. Fierer, J.I. Gordon, and R. Knight. 2009.
Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697.
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Students:
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LEUNG, Chun Ning 梁振寧,
YAU, Ka Long 丘嘉朗
______________________________________________________
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Paper 10:
|
Turnbaugh, P.J., M. Hamady, T.
Yatsunenko, B.L. Cantarel, A. Duncan, R.E. Ley, M.L. Sogin, W.J. Jones, B.A.
Roe, J.P. Affourtit et al. 2009. A core gut microbiome in obese and lean
twins. Nature 457: 480-484.
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Students:
|
LI, Jiexin 黎婕昕,
YEUNG, Hing Yuen 楊興源
________________________________________________________
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Paper
11:
|
Qin, J., R. Li, J. Raes, M.
Arumugam, K.S. Burgdorf, C. Manichanh, T. Nielsen, N. Pons, F. Levenez, T.
Yamada et al. 2010. A human gut microbial gene
catalogue established by metagenomic sequencing. Nature 464:
59-65.
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Students:
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LI, Man Wah 李敏華,ZHANG, Zhiwei 張志偉 ZHENG, Shanyuan 鄭善元_______________________________________________________
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