2015-2016 AMS-532 Fall-Spring

Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage

Instructor	Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
Course No.	AMS-532
Location/Time	Physics P127 Wed 12:00PM - 12:53PM
Office Hours	Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics

Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring)

2015 Fall	Participant	Rotations or Research Group	Topic	References REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT
2015.08.26 Wed	Last name, First name	--	--	Organizational Meeting
2015.09.02 Wed	Belfon, Kellon	Dr. Simmerling's Group	Protein Dynamics	Hornak, V. et al. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. PNAS. 2006 January. 103(4). 915-920. [1]
2015.09.09 Wed	Tian, Chuan	Dr. Simmerling's Group	Force Field Development	Hornak, V. et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics. 2006 June. 65(3). 712-725. [2]
2015.09.16 Wed	--	--	--	AMS Grad Student BBQ
2015.09.23 Wed	Cortes, Michael	Dr. Balazsi's Group	Gene regulation	Weitz, J. S. et al. Collective decision making in bacterial viruses. Biophys J. 2008 September. 95(6). 2673-2680. [3]
2015.09.30 Wed	Singleton, Courtney	Dr. Rizzo's Group	Genetic Algorithms for De Novo Design	Kawai, K. et al. De Novo Design of Drug-Like Molecules by a Fragment-Based Molecular Evolutionary Approach. J. Chem. Inf. Model. 2014. 54(1). 49-56.
2015.10.07 Wed	Jones, Peter	--	Gene Circuit's	Nevozha, D. et al. Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit. PLOS Comp Bio. 2012. 8, e1002480
2015.10.14 Wed	Awwa, Monaf	--	Modelling ECGC in Cancer Implicated Proteins	Van Aller, Glenn S., et al. "Epigallocatechin gallate (EGCG), a major component of green tea, is a dual phosphoinositide-3-kinase/mTOR inhibitor." Biochemical and biophysical research communications 406.2 (2011): 194-199.
2015.10.21 Wed	Xue, Jing	--	PIPER:An FFT-Based Protein Docking Program with Pairwise Potentials	Kozakov, D., Brenke, R., Comeau, S. R. and Vajda, S. (2006), PIPER: An FFT-based protein docking program with pairwise potentials. Proteins, 65: 392–406. doi: 10.1002/prot.21117
2015.10.28 Wed	Shapiro, Maxwell	Dr. Rest Lab	Gene Expression, Fitness Functions	Rest JS, Morales CM, Waldron JB, et al. Nonlinear Fitness Consequences of Variation in Expression Level of a Eukaryotic Gene. Molecular Biology and Evolution. 2013;30(2):448-456. doi:10.1093/molbev/mss248. [4]
2015.11.04 Wed	Banisafar, Sahar	--	Image Processing	ANGENENT, S. et al. MATHEMATICAL METHODS IN MEDICAL IMAGE PROCESSING. BULLETIN (New Series) OF THE AMERICAN MATHEMATICAL SOCIETY. 2006. 43. 365.
2015.11.11 Wed	Guo, Haoyue	--	Gene Expression Noise	Charlebois, D. A. et al. Gene Expression Noise Facilitates Adaptation and Drug Resistance Independently of Mutation. PHYSICAL REVIEW LETTERS. 2011. 107. 218101.
2015.11.18 Wed	Jiang, Beilei	--	Structure-based Design	Lai, C-T. et al. Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA. Biochemistry, 2015, 54, 4683−4691
2015.11.25 Wed	-	--	--	THANKSGIVING BREAK
2015.12.02 Wed	Tuznik, Stanley	--	--	Sandhu, R. et al. Graph curvature for differentiating cancer networks. Sci Rep. 2014 July. 5:12323.
2016 Spring	Participant	Rotations or Research Group	Topic	References SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH
2016.01.27 Wed	Class discussion	Responsible Conduct of Research (RCR)	(1) Course Overview: Fulfilling Responsible Conduct in Research Training	Discussion of Overall Course Requirements which include: View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) 2010.06.08_hadjiargyrou.pdf 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 and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics
2016.02.03 Wed	Class discussion	Responsible Conduct of Research (RCR)	(2) Integrity in Scholarship (Introduction to Ethics and Science)	Stony Brook Lecture Peter 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?
2016.02.10 Wed	Class discussion	Responsible Conduct of Research (RCR)	(3) Scientific Misconduct	Stony Brook Lecture Michael Hadjiargyrou Lecture Reading Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct 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? Why do people commit scientific misconduct? What are some consequences of committing scientific misconduct?
2016.02.17 Wed	Class discussion	Responsible Conduct of Research (RCR)	(4) Mentoring	Stony Brook Lecture Clinton Rubin Lecture Readings Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring 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? What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?
2016.02.24 Wed	Class discussion	Responsible Conduct of Research (RCR)	(5) Ownership and Authorship	Stony Brook Lecture Peter Gergen Lecture Readings Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review Discussion (also from the above Columbia course) Is it ever appropriate for authorship to change during a project or potential paper? How should authorship roles be defined? What are some abuses of authorship? Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper? Did Ms. Jacobs handle the proposed changes to authorship appropriately? Why are acknowledgments so important?
2016.03.02 Wed	Class discussion	Responsible Conduct of Research (RCR)	(6) Plagiarism	Stony Brook Lecture Richard 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?
2016.03.09 Wed	Class discussion	Responsible Conduct of Research (RCR)	(7) Data Management	Stony Brook Lecture Stefan Judex Lecture Readings Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management 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. How many years past a publication, if asked, should a researcher be able provide "raw data"?
2016.03.16 Wed	--	--	--	SPRING BREAK
2016.03.23 Wed	Class discussion	Responsible Conduct of Research (RCR)	(8) Journalism and Science	Stony Brook Lecture Howard 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 a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? 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 run hospital which might violate patients privacy?
2016.03.30 Wed	Class discussion	Responsible Conduct of Research (RCR)	(9) Responsible Conduct of Research Involving Human Subjects	Stony Brook Lecture Judy Matuk Lecture Readings: (Background Information, Case Studies, Helsinki Manuscript) Human Subjects handout Helsinki manuscript Discussion From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not? From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's? From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?
2016.04.13 Wed	Class discussion	Responsible Conduct of Research (RCR)	(10) Responsible Conduct of Research Involving Laboratory Animals	Stony Brook Lecture Tom Zimmerman Lecture Readings (Case Studies) Animal Subjects handout Discussion From Case Study 1: What are some of the troublesome issues associated with this set of experiments? From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans? From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled? From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects? What are some advantages of using Animals in experiments? Discuss the three R's? Is our class for or against Animal testing?
2016.04.20 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS
2016.04.27 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS
2016.05.04 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS