Difference between revisions of "2015-2016 AMS-532 Fall-Spring"

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| '''Course No.''' || AMS-532  
 
| '''Course No.''' || AMS-532  
 
|-
 
|-
−
| '''Location/Time''' || Physics P123 Wed 12:00PM - 12:53PM  
+
| '''Location/Time''' || Physics P127 Wed 12:00PM - 12:53PM  
 
|-
 
|-
 
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics
 
| '''Office Hours''' || Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics
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|-
 
|-
  
−
| 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. [http://www.pnas.org/content/103/4/915]
+
| 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. [http://www.pnas.org/content/103/4/915]
 
|-
 
|-
  
−
| 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. [http://ffamber.cnsm.csulb.edu/ffamber/pdfs/simmerling_amber99sb_2006proteins.pdf]
+
| 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. [http://ffamber.cnsm.csulb.edu/ffamber/pdfs/simmerling_amber99sb_2006proteins.pdf]
 
|-
 
|-
  
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|-
 
|-
  
−
| 2015.09.23 Wed || Cortes, Michael || -- || -- || Alberts, B. ''et al''. Rescuing US biomedical research from its systemic flaws. ''PNAS''. '''2014 March'''. ''111(16)''. 5773-5777.
+
| 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. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527279/]
 
|-
 
|-
  
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|-
 
|-
  
−
| 2015.10.07 Wed ||Jones, Peter || -- || -- || Alberts, B. ''et al''. Rescuing US biomedical research from its systemic flaws. ''PNAS''. '''2014 March'''. ''111(16)''. 5773-5777.
+
| 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 || -- || -- || Alberts, B. ''et al''. Rescuing US biomedical research from its systemic flaws. ''PNAS''. '''2014 March'''. ''111(16)''. 5773-5777.
+
| 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 || -- || -- || Alberts, B. ''et al''. Rescuing US biomedical research from its systemic flaws. ''PNAS''. '''2014 March'''. ''111(16)''. 5773-5777.
+
| 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 || -- || -- || Alberts, B. ''et al''. Rescuing US biomedical research from its systemic flaws. ''PNAS''. '''2014 March'''. ''111(16)''. 5773-5777.
+
| 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. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548308/]
 
|-
 
|-
  
−
| 2015.11.04 Wed || Banisafar, Sahar || -- || -- || Alberts, B. ''et al''. Rescuing US biomedical research from its systemic flaws. ''PNAS''. '''2014 March'''. ''111(16)''. 5773-5777.
+
| 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 || -- || -- || Alberts, B. ''et al''. Rescuing US biomedical research from its systemic flaws. ''PNAS''. '''2014 March'''. ''111(16)''. 5773-5777.
+
| 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 || -- || -- || Alberts, B. ''et al''. Rescuing US biomedical research from its systemic flaws. ''PNAS''. '''2014 March'''. ''111(16)''. 5773-5777.
+
| 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
 
| 2015.11.25 Wed || - || -- || -- || THANKSGIVING BREAK
 
|-
 
|-
−
| 2015.12.02 Wed  || Tuznik, Stanley || -- || -- || Alberts, B. ''et al''. Rescuing US biomedical research from its systemic flaws. ''PNAS''. '''2014 March'''. ''111(16)''. 5773-5777.
+
| 2015.12.02 Wed  || Tuznik, Stanley || -- || Cancer Networks || Sandhu, R. ''et al''. Graph curvature for differentiating cancer networks. Sci Rep. 2014 July. 5:12323.
 
|-
 
|-
 
|- style="background:lightgreen"
 
|- style="background:lightgreen"
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*From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?
 
*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?
 
*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?
+
*Why do people commit scientific misconduct?
 +
*What are some consequences of committing scientific misconduct?
 
|-
 
|-
  
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*What are the challenges associated with being 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 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?
 
|-
 
|-
  
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Discussion (also from the above Columbia course)
 
Discussion (also from the above Columbia course)
 
*Is it ever appropriate for authorship to change during a project or potential paper?
 
*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?
 
*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?
 
*Did Ms. Jacobs handle the proposed changes to authorship appropriately?
 +
*Why are acknowledgments so important?
 
|-
 
|-
  
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*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 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 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?   
+
*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?   
 
|-
 
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|-
 
|-
  
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| 2016.04.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
+
| 2016.04.13 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
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*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: 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?
 
*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?
−
| 2016.04.13 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
+
*Discuss the three R's?
 +
*Is our class for or against Animal testing?
 
|-
 
|-
 
| 2016.04.20 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
| 2016.04.20 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS

Latest revision as of 14:47, 10 August 2016

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 -- Cancer Networks 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


Readings (Nature articles)


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


Reading


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


Readings


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


Readings


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


Readings


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


Readings


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


Readings (3 Case Studies)


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


Readings: (Background Information, Case Studies, 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


Readings (Case Studies)


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
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