2010-2011 AMS-532 Fall-Spring

Announcement

• Posted on 09/01 by Trent:

1. Each participant please update the Wiki as required

• Posted on 09/10 by Lingling:

1. Lab rotation is a very important part of this course. It is recommended （required for PhD track) that every new student in Computational Biology track to do three rotations in research groups of his/her special interests. Student must contacted four professors and get their permissions to do a rotation in their group. If you have any questions in regard to choosing a lab, please feel free to talk to professor Rizzo and his students （Trent Balius and Lingling Jiang）. Rizzo lab is located in Room 3-129, Math Tower.

• Posted on 09/15 by Lingling:

1. Since some students find that the presentation is scheduled close to their AMS535 presentation, I modified the schedule so that people can prepare one at a time.

• Posted on 11/17 by Lingling:

1. I set up the rotation presentation schedule. Please prepare for a 15 minutes talk about your first rotation.
2. We won't have journal club next Wednesday as it will follow a Friday schedule then.

Journal Club Participants, Topics, References, and Schedule

2010 Fall	Participant	Rotations or Research Group	Topic	References NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT
2010.09.08	Adler, Jeremy	--	Network identification	Chu LH, Chen BS. Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targetsBMC Syst Biol. 2008 Jun 30;2:56.
2010.09.15	Vo, Emily	--	GWAS	Liu, J. Z.; et al., A versatile gene-based test for genome-wide association studies. Am. J. Hum. Genet. 2010, 87, 139-145.
2010.09.22	Jiang, Lingling	--	HIV-gp41	Shi, W. X.; et al., Structural Characterization of HIV gp41 with the Membrane-proximal External Region. J. Bio. Che. 2010, 285, 24290-24298.
2010.09.29	Grinshpun, Boris	Maslov	Prokaryotic Metabolic Networks - Quadratic Scaling	Maslov, S.; et al., Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc. Natl. Acad. Sci. 2009, 106, 9743-9748.
2010.10.06	Liu, Jiangyang	--	--	--
2010.10.13	Li, Miao	Wei Zhu	Normalization and DE Evaluation	Bullard et al.: Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010 11:94.
2010.10.20	Yao, Yuan	Wang	Enzyme Conformation	Wei Min; et al., Two-Dimensional Reaction Free Energy Surfaces of Catalytic Reaction: Effects of Protein Conformational Dynamics on Enzyme Catalysis. J. Phys. Chem. B 2008, 112, 454-466
2010.10.27	Gardin, Justin Michael	--	--	--
2010.11.03	Chen, Jia Ruo	--	--	--
2010.11.10	Cao, Yiwei	Green	Protein Design	Shannon A. M.; et al., One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations. Protein Sci. 2005, 14, 1293-1304.
2010.11.17	Balius, Trent	Rizzo	Drug design	Jorgensen W. L., Efficient Drug Lead Discovery and Optimization. Acc. Chem. Res. 2009, 42, (6), 724-733
2010.12.01	Grinshpun, B; Liu, J; Li, M	--	rotation presentation	--
2010.12.08	Gardin, J; Chen, J; Cao, Y; Yao, Y	--	rotation presentation	--
2011 Spring	Participant	Rotations or Research Group	Topic	References NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT
2010.01.27	Outside of class	Scientific Integrity Course	(0) Additional requirements to fulfill RCR training	Requirements View the Responsible Conduct of Research and Scholarship - Presentation under the POLICY heading located at http://www.stonybrook.edu/research/orc/rcr/index.shtml Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org Following the schedule below, view the seven online lectures, read the additional accompanying materials, and think about the discussion topics, prior to coming to each class
2010.01.27	Class discussion	Scientific Integrity Course	(1) Introduction to the Course & to Ethics and Science	Stony Brook Lecture Williams Lecture Readings (Nature articles) Article 1 Article 2 Article 3 Discussion Why is the class important? How should we behave as scientists? How is science a social enterprise?
2010.02.03	Class discussion	Scientific Integrity Course	(2) Scientific Misconduct	Stony Brook Lecture Hadjiargyrou Lecture Reading Introduction and Case Study 1 Sections from Columbia University online RCR course Discussion From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays? From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now? How can the pressure to publish influence the conduct of research?
2010.02.10	Class discussion	Scientific Integrity Course	(3) Mentorship	Stony Brook Lecture Rubin Lecture Readings Read Introduction and Case Study 1 Sections from Columbia University online RCR course Discussion What qualities do you want in a mentor? What are the challenges associated with being a mentor? What does Professor Rubin mean when he says it is very important not to burn bridges?
2010.02.17	Class discussion	Scientific Integrity Course	(4) Authorship	Stony Brook Lecture Gergen Lecture Readings Read Introduction and Case Study 1 Sections from Columbia University online RCR course Discussion (also from the above Columbia course) Is it ever appropriate for authorship to change during a project or potential paper? Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?
2010.02.24	Class discussion	Scientific Integrity Course	(5) Plagiarism	Stony Brook Lecture Clark Lecture Readings Stony Brook's Policy on Academic Dishonesty Discussion Is plagiarism really that bad? If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?
2010.03.03	Class discussion	Scientific Integrity Course	(6) Managing Data	Stony Brook Lecture Huddy Lecture Readings Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR course Discussion From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples? From Case Study 2: Under what condition is copying allowed? Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.
2010.03.10	Class discussion	Scientific Integrity Course	(7) Journalism	Stony Brok Lecture Schneider Lecture Readings (3 Case Studies) Scientist and Reporters handout Discussion From Case Study 1: A reporter from a major newspaper is scheduled to do a story on the drug. Do you call him, disclose your concerns and slip him copies of the records that show abnormally high death rates among the second generation of mice? Why? From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why? From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly, to uncover the truth in an apparently poorly hospital, which might violate patients privacy?
2010.03.31	--	--	--	Spring Break.