Discussion arrangement 2012

		Paper	Discussion Leader
Presenting Students			24/2	2/3	9/3	To be decided
AU, Ka Yee 歐嘉儀 LIU, Ming 劉明		1		CHIU, Wai Yin Vivien 趙熭然 WANG, Wei 王偉
CHANG, Jinhui 常金輝 LOO, Fong Chuen 盧芳泉		2		FAN, Long 樊隆 WEN, Chaoqing  温潮清
CHENG, Hong Yiu 鄭康堯 SOU, Weng Hong 蘇詠虹		3		LAU, Sze Nga 劉詩雅 WONG, Ho Chun 黃浩俊
CHENG, Xuanjin 程旋晋 TAM, Yeuk Fei 譚若菲		4		LAW, Hiu Tung 羅曉彤 WU, Tsz Huen 胡芷萱
CHIU, Wai Yin Vivien   趙熭然 WANG, Wei 王偉		5			LEUNG, Chun Ning 梁振寧 YAU, Ka Long 丘嘉朗
FAN, Long 樊隆 WEN, Chaoqing 温潮清		6			LI, Jiexin 黎婕昕 YEUNG, Hing Yuen 楊興源
LAU, Sze Nga 劉詩雅 WONG, Ho Chun 黃浩俊		7			LI, Man Wah 李敏華 ZHANG, Zhiwei   張志偉      ZHENG, Shanyuan   鄭善元
LAW, Hiu Tung 羅曉彤 WU, Tsz Huen 胡芷萱		8			AU, Ka Yee 歐嘉儀 LIU, Ming 劉明
LEUNG, Chun Ning 梁振寧 YAU, Ka Long 丘嘉朗		9				CHANG, Jinhui 常金輝 LOO, Fong Chuen 盧芳泉
LI, Jiexin 黎婕昕 YEUNG, Hing Yuen 楊興源		10				CHENG, Hong Yiu 鄭康堯 SOU, Weng Hong 蘇詠虹
LI, Man Wah 李敏華 ZHANG, Zhiwei 張志偉      ZHENG, Shanyuan 鄭善元		11				CHENG, Xuanjin   程旋晋 TAM, Yeuk Fei 譚若菲

Schedule 2012

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.

·         http://www.sciencemag.org/feature/plus/sfg/research/index.shtml

Human genome project timeline: go to

http://www.sciencemag.org/feature/plus/sfg/human/timeline.shtml

http://www.nhgri.nih.gov/educationkit/guide.html

http://www.sciencemag.org/feature/plus/sfg/special/index.shtml

http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v422/n6934/full/nature01626_fs.html

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.
Students:	CHANG, Jinhui 常金輝, LOO, Fong Chuen 盧芳泉 _______________________________________________________
Paper 3:	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.
Students:	CHENG, Hong Yiu 鄭康堯, SOU, Weng Hong 蘇詠虹______________________________________________________
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.
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 _____________________________________________________
Paper 6:	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.
Students:	FAN, Long 樊隆, WEN, Chaoqing 温潮清 ______________________________________________________
Paper 7:	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.
Students:	LAU, Sze Nga 劉詩雅, WONG, Ho Chun 黃浩俊 _______________________________________________________
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_______________________________________________________
Date to be decided—the third discussion  session
Paper 9:	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.
Students:	LEUNG, Chun Ning 梁振寧, YAU, Ka Long 丘嘉朗 ______________________________________________________
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.
Students:	LI, Jiexin 黎婕昕, YEUNG, Hing Yuen 楊興源 ________________________________________________________
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.
Students:	LI, Man Wah 李敏華,ZHANG, Zhiwei 張志偉   ZHENG, Shanyuan 鄭善元_______________________________________________________