Difference between revisions of "2017-2018 AMS-532 Fall-Spring"

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(→‎Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage)
 
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| 2017.09.06 Wed || Fallon, Zach || -- || -- || Morin, J., et al.; Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase. ''Nucleic Acids Research'' '''2015''', ''43'', 3643-3652.
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| 2017.09.06 Wed || Fallon, Zach || -- || -- || Morin et al; Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase. ''Nucleic Acids Research'' '''2015''', ''43'', 3643-3652.
 
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|-
  
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| 2017.09.20 Wed || Nassar, Roy || -- || -- || MacCallum, J., et al.; Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference. ''PNAS'' '''2015''', ''112'', 6985-6990.
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| 2017.09.20 Wed || Nassar, Roy || -- || -- || MacCallum et al; Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference. ''PNAS'' '''2015''', ''112'', 6985-6990.
 
|-
 
|-
  
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| 2017.09.27 Wed || Ignatov, Misha || -- || -- || Smith, J., et al.; ANI-1: An extensible neural network potential with DFT accuracy at force field computational cost. ''Chemical Science'' '''2017''', ''8'', 3192–3203.
+
| 2017.09.27 Wed || Ignatov, Misha || -- || -- || Smith et al; ANI-1: An extensible neural network potential with DFT accuracy at force field computational cost. ''Chemical Science'' '''2017''', ''8'', 3192–3203.
 
|-
 
|-
  
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| 2017.10.04 Wed || Cao, Xin || -- || -- || Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188.
+
| 2017.10.04 Wed || Cao, Xin || -- || -- || Coutsias et al; Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics. ''J. Chem. Theory. Comp.'' '''2016''', ''12'', 4674-4687.
 
|-
 
|-
  
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| 2017.10.11 Wed || Tang, Cathy || -- || -- || Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188.
+
| 2017.10.11 Wed || Tang, Cathy || -- || -- || Sheng et al; Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation. ''Frontiers in Immunology'' '''2017''', ''8'', Article 537.
 
|-
 
|-
  
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| 2017.10.18 Wed || Jones, George || -- || -- || Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188.
+
| 2017.10.18 Wed || Jones, George || -- || -- || Martin-Garcia et al; Serial femtosecond crystallography: A revolution in structural biology. ''Archives of Biochemistry and Biophysics'' '''2016''', ''602'', 32-47.
 
|-
 
|-
  
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| 2017.10.25 Wed || Carter, Jason || -- || -- || Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188.
+
| 2017.10.25 Wed || Carter, Jason || -- || -- || Li et al; Landscape of tumor-infiltrating T cell repertoire of human cancers. ''Nature Genetics'' '''2016''', ''48'', 725-732.
 
|-
 
|-
  
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| 2017.11.01 Wed || Telehany, Steve || -- || -- || Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188.
+
| 2017.11.01 Wed || Telehany, Steve || -- || -- || Schmidt et al; Small-Molecule Inhibitors of Dengue-Virus Entry. ''PLOS Pathogens'' '''2012''', ''8'', e1002627
 
|-
 
|-
  
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| 2017.11.08 Wed || Taouil, Adam || -- || -- || Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188.
+
| 2017.11.08 Wed || Taouil, Adam || -- || -- || Woodcock et al; MSCALE: A General Utility for Multiscale Modeling. ''J. Chem. Theory. Comp.'' '''2011''', ''7'', 1208-1219.
  
 
|-
 
|-
  
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| 2017.11.15 Wed || Manathunga, Lakshan || -- || -- || Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188.
+
| 2017.11.15 Wed || Manathunga, Lakshan || -- || -- || Philips et al; LigandRNA: computational predictor of RNA-ligand interactions. ''RNA' '''2013''', ''19'', 1605-1616.
 
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| 2016.11.29 Wed || Talis, Emma || -- || -- || Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188.
+
| 2017.11.29 Wed || Talis, Emma || -- || -- || Oprea et al; Somatic Mutations Leads to Efficient Affinity Maturation When Centrocytes Recycle Back to Centroblasts. ''J. Immunology.'' '''1997''', ''158'', 5155-5162.
 
|-
 
|-
  
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| 2016.12.06 Wed || Maria Spyrou, Ioanna || -- || -- || Cheron, N., et al.; OpenGrowth: An Automated and Rational Algorithm for Finding new Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188.
+
| 2017.12.06 Wed || Maria Spyrou, Ioanna || -- || -- || Berg et al; Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplication. ''BMC Evolutionary Biology.'' '''2004''', ''4'', 51.
 
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| 2018.03.07 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
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| 2018.03.07 Wed || -- || -- || -- || SNOW DAY
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| 2018.03.14 Wed || -- || -- || -- || SPRING BREAK
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| 2018.03.21 Wed || -- || -- || -- || SNOW DAY
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| 2018.03.28 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p68134598 Stefan Judex Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p68134598 Stefan Judex Lecture]
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*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.
 
*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"?   
 
*How many years past a publication, if asked, should a researcher be able provide "raw data"?   
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| 2018.03.14 Wed || -- || -- || -- || SPRING BREAK
 
 
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| 2018.03.21 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||
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| 2018.04.04 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p99353453 Howard Schneider Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p99353453 Howard Schneider Lecture]
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| 2018.03.28 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||
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| 2018.04.11 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p10813599 Judy Matuk Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p10813599 Judy Matuk Lecture]
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| 2018.04.04 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
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| 2018.04.18 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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*Discuss the three R's?
 
*Discuss the three R's?
 
*Is our class for or against Animal testing?
 
*Is our class for or against Animal testing?
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| 2018.04.11 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
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| 2018.04.18 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
 
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| 2018.04.25 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
| 2018.04.25 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS

Latest revision as of 10:12, 25 August 2018

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 Bldg. P117, 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)

2017 Fall Participant Rotations or Research Group Topic References

REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT

2017.08.30 Wed Rizzo, Robert -- -- Organizational Meeting
2017.09.06 Wed Fallon, Zach -- -- Morin et al; Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase. Nucleic Acids Research 2015, 43, 3643-3652.
2017.09.13 Wed -- -- -- AMS Grad Student BBQ
2017.09.20 Wed Nassar, Roy -- -- MacCallum et al; Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference. PNAS 2015, 112, 6985-6990.
2017.09.27 Wed Ignatov, Misha -- -- Smith et al; ANI-1: An extensible neural network potential with DFT accuracy at force field computational cost. Chemical Science 2017, 8, 3192–3203.
2017.10.04 Wed Cao, Xin -- -- Coutsias et al; Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics. J. Chem. Theory. Comp. 2016, 12, 4674-4687.
2017.10.11 Wed Tang, Cathy -- -- Sheng et al; Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation. Frontiers in Immunology 2017, 8, Article 537.
2017.10.18 Wed Jones, George -- -- Martin-Garcia et al; Serial femtosecond crystallography: A revolution in structural biology. Archives of Biochemistry and Biophysics 2016, 602, 32-47.
2017.10.25 Wed Carter, Jason -- -- Li et al; Landscape of tumor-infiltrating T cell repertoire of human cancers. Nature Genetics 2016, 48, 725-732.
2017.11.01 Wed Telehany, Steve -- -- Schmidt et al; Small-Molecule Inhibitors of Dengue-Virus Entry. PLOS Pathogens 2012, 8, e1002627
2017.11.08 Wed Taouil, Adam -- -- Woodcock et al; MSCALE: A General Utility for Multiscale Modeling. J. Chem. Theory. Comp. 2011, 7, 1208-1219.
2017.11.15 Wed Manathunga, Lakshan -- -- Philips et al; LigandRNA: computational predictor of RNA-ligand interactions. RNA' 2013, 19, 1605-1616.
2017.11.22 Wed -- -- -- THANKSGIVING BREAK
2017.11.29 Wed Talis, Emma -- -- Oprea et al; Somatic Mutations Leads to Efficient Affinity Maturation When Centrocytes Recycle Back to Centroblasts. J. Immunology. 1997, 158, 5155-5162.
2017.12.06 Wed Maria Spyrou, Ioanna -- -- Berg et al; Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplication. BMC Evolutionary Biology. 2004, 4, 51.
2018 Spring Participant Rotations or Research Group Topic References

SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH

2018.01.24 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
2018.01.31 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?
2018.02.07 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?
  • Who are some of your mentors?
2018.02.14 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?
2018.02.21 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?
2018.02.28 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?
2018.03.07 Wed -- -- -- SNOW DAY
2018.03.14 Wed -- -- -- SPRING BREAK
2018.03.21 Wed -- -- -- SNOW DAY
2018.03.28 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"?
2018.04.04 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?
2018.04.11 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 ?
2018.04.18 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?
2018.04.25 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
2018.05.02 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
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