Difference between revisions of "2012-2013 AMS-532 Fall-Spring"

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| '''2011 Fall
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| '''2012 Fall
 
| '''Participant'''  
 
| '''Participant'''  
 
| '''Rotations or Research Group'''
 
| '''Rotations or Research Group'''
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|-
 
|-
  
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| 2011.00.00 || Last name, First name || -- || topic || paper
+
| 2012.08.29 || -- || -- || -- || --
 
|-
 
|-
  
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| 2011.09.07 || Cao，Yiwei || Green || Protein Design || Georgiev, I., et al., Algorithm for backrub motions in protein design. ''Bioinformatics'' '''2008''', ''24(13)'', i196-i204.
+
| 2012.09.05 || Zhou, Yuchen || Rizzo || Topic || Armstrong, MS., et al., ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics. ''J Comput Aided Mol Des.'' '''2010 Sep''', ''24(9)'', 789-801.
 
|-
 
|-
  
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| 2011.09.14 || Yao， Yuan || Wang || topic || Siegel, J., et al., Computational Design of an Enzyme Catalyst for a Stereoselective Biomolecular Diels-Alder Reaction. ''Science'' '''2010''', ''329'', 309-313
+
| 2012.09.12 || Chen, Jeffrey || MacCarthy || Topic || Hershberg, U., et al., Differences in potential for amino acid change after mutation reveals distinct strategies for κ and λ light-chain variation. ''PNAS'' '''2006 Oct''', ''vol. 103 no. 43'', 15963-15968.
 
|-
 
|-
  
−
| 2011.09.21 || Gardin，Justin || futcher || topic || Exact Discovery of Time Series Motifs. '''2008'''
+
| 2012.09.19 || Sin, Jeewoen || MacCarthy || Topic || Leclerc, RD., Survival of the sparsest: robust gene networks are parsimonious. ''Mol Syst Biol.'' '''2008''' ''4:213''.
 
|-
 
|-
  
−
| 2011.09.28 || - || -- || topic || followed a Friday schedule
+
| 2012.09.26 || Krantsevich, Nikolay || Rizzo || Topic|| Barrciro, G., et al., From Docking False-Positive to Active Anti-HIV Agent. ''J. Med. Chem.'' '''2007''', ''50'', 5324-5329.
 
|-
 
|-
  
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| 2011.10.05 || Fochtman, Brian || Rizzo || topic || Efficient Inclusion of Receptor Flexibility in Grid-Based Protein-Ligand Docking. ''J. of Comp. Chem.'' '''2011'''
+
| 2012.10.03 || -- || -- || Postponed || AMS Graduate Party
 
|-
 
|-
  
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| 2011.10.12 || Chen, Jeff || -- || topic || Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. ''Genome Biology'' '''2009''', ''10(3)'', R25.1-10
+
| 2012.10.10 || Li, Xindi || Rizzo || Topic || Chang, C., et al., Pharmacophore-based discovery of ligands for drug transporters. ''Adv Drug Deliv Rev.'' '''2006 Nov''', ''58(12-13)'', 1431-1450.
 
|-
 
|-
  
−
| 2011.10.19 || Sinayev, Roman || -- || topic || Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin. ''Science'' '''2011''', ''332'', 816-821
+
| 2012.10.17 || Krantsevich, Artyom || MacCarthy || Topic || MacCarthy, T., et al., Differential regulation drives plasticity in sex determination gene networks. ''BMC Evolutionary Biology.'' '''2010''' ''10:388''.
 
|-
 
|-
  
−
| 2011.10.26 || Xia, Yunting || -- || topic || paper
+
| 2012.10.25 || Yuan, Chaohui || MacCarthy || Topic || Cohen, RM., Somatic hypermutation targeting is influenced by location within the immunoglobulin V region. ''Molecular Immunology'' '''2011''', ''48'', 1477-1483.
 
|-
 
|-
  
−
| 2011.11.02 || Zhou, Yuchen || -- || topic || paper
+
| 2012.10.31 || -- || -- || -- || No Class: Hurricane Sandy
 
|-
 
|-
  
−
| 2011.11.09 || Yuan, Joanna || -- || topic || paper
+
| 2012.11.07 || -- || -- || Group Study || Test Preparation for AMS 535
 
|-
 
|-
  
−
| 2011.11.16 || Sin, Jeewoen || -- || topic || paper
+
| 2012.11.14 || Li, Xindi and Yuan, Chaohui || -- || Topic || FIRST ROTATION/RESEARCH PRESENTATIONS
 
|-
 
|-
  
−
| 2011.11.23 || - || -- || -- || THANKSGIVING BREAK
+
| 2012.11.21 || - || -- || -- || THANKSGIVING BREAK
 
|-
 
|-
  
−
| 2011.11.30 || Sin, Jeewoen and Xia, Yunting and Chen, Jeff || -- || topic || FIRST ROTATION/RESEARCH PRESENTATIONS
+
| 2012.11.28 || -- || -- || Group Study || Test Preparation for AMS 535
 
|-
 
|-
−
| 2011.12.07 (last class) || Sinayev, Roman and Zhou, Yuchen || -- || topic || FIRST ROTATION/RESEARCH PRESENTATIONS
+
| 2012.12.05 (last class) || -- || -- || Group Study || Test Preparation for AMS 535
 
|-
 
|-
 
|- style="background:lightgreen"
 
|- style="background:lightgreen"
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| '''2012 Spring'''
+
| '''2013 Spring'''
 
| '''Participant'''  
 
| '''Participant'''  
 
| '''Rotations or Research Group'''
 
| '''Rotations or Research Group'''
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SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
 
SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
 
|-
 
|-
−
| -- || Work to be Done Outside of class|| Responsible Conduct of Research (RCR) || (0) Additional requirements to fulfill RCR training ||
 
  
−
Requirements
+
 
−
*View the Responsible Conduct of Research and Scholarship - Presentation given to department chairs by professor Michael Hadjiargyrou [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]
+
| 2013.01.30 || Guo, Jiaye || Boon || Topic || Henares, BM., et al., Discovery of a Nitric Oxide Responsive Quorum Sensing Circuit in ''Vibrio harveyi''. ''ACS Chem. Biol.'', '''2012''', ''7(8)'', 1331-1336.
−
*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
 
 
|-
 
|-
−
| 2012.01.25 || Class discussion|| Responsible Conduct of Research (RCR) || (1) Integrity in Scholarship (Introduction to Ethics and Science) ||
 
−
Stony Brook Lecture
 
−
*[https://meeting.sinc.stonybrook.edu/p42411560 Peter Williams Lecture]
 
  
  
−
Readings (Nature articles)
+
| 2013.02.06 || Krantsevich, Nikolay, Krantsevich, Artyom, and Shan, Jiahui|| -- || Topic || FIRST ROTATION/RESEARCH PRESENTATIONS
−
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]
+
|-
−
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]
 
−
*[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]
 
  
  
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Discussion
+
| 2013.02.13 || Yuan, Chaohui, Li, Xindi, and Guo, Jiaye || -- || Topic || SECOND ROTATION/RESEARCH PRESENTATIONS
−
*Why is the class important?
 
−
*How should we behave as scientists?
 
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*How is science a social enterprise?
 
 
|-
 
|-
  
−
| 2012.02.01 || Class discussion  || Responsible Conduct of Research (RCR) || (2) Scientific Misconduct ||
 
−
Stony Brook Lecture
 
−
*[https://meeting.sinc.stonybrook.edu/p30629381 Michael Hadjiargyrou Lecture]
 
  
−
 
+
| 2013.02.20 || Krantsevich, Nikolay, Krantsevich, Artyom, and Amgalan, Anar || -- || Topic || SECOND ROTATION/RESEARCH PRESENTATIONS
−
Reading
+
|-
−
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]
 
  
  
−
Discussion
+
| 2013.02.27 || Chen, Ye || MacCarthy || Topic || Liu, M., et al., Two levels of protection for the B cell genome during somatic hypermutation. ''Nature'', '''451''', 841-845.
−
*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?
 
 
|-
 
|-
  
−
| 2012.02.08 || Class discussion || Responsible Conduct of Research (RCR) || (3) Mentoring ||
 
−
Stony Brook Lecture
 
−
*[https://meeting.sinc.stonybrook.edu/p20134531 Clinton Rubin Lecture]
 
  
 +
| 2013.03.06 || Yuan, Chaohui || Green || Topic || Green, DF., A Statistical Framework for Hierarchical Methods in Molecular Simulation and Design. ''J. Chem. Theory Comput.'', '''2010''', ''6(5)'', 1682–1697.
 +
|-
  
−
Readings
 
−
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]
 
  
 +
| 2013.03.13 || Krantsevich, Nikolay || Shatz || Topic || Koren, S., et al., Hybrid error correction and de novo assembly of single-molecule sequencing reads. ''Nature Biology'', '''30''', 693–700
 +
|-
  
−
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?
 
  
 +
| 2013.03.20 || Spring Break || Spring Break || Spring Break || Spring Break
 
|-
 
|-
−
| 2012.02.15 || Class discussion || Responsible Conduct of Research (RCR) || (4) Ownership and Authorship ||
 
−
Stony Brook Lecture
 
−
*[https://meeting.sinc.stonybrook.edu/p32819600 Peter Gergen Lecture]
 
  
  
−
Readings
+
| 2013.03.27 || Krantsevich, Artyom || -- || -- || --
−
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship 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)
+
| 2013.04.03 || Li, Xindi || -- || -- || --
−
*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?
 
 
|-
 
|-
−
 
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| 2012.02.22|| Class discussion || Responsible Conduct of Research (RCR) || (5) Plagiarism ||
 
−
Stony Brook Lecture
 
−
*[https://meeting.sinc.stonybrook.edu/p41971516 Richard Clark Lecture]
 
−
 
−
 
−
Readings
 
−
*[http://www.stonybrook.edu/uaa/academicjudiciary/policies.shtml Stony Brook's Policy on Academic Dishonesty]
 
  
  
−
Discussion
+
| 2013.04.10 || Guo, Jiaye || -- || -- || --
−
*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?
 
 
|-
 
|-
  
  
−
| 2012.02.29|| Class discussion || Responsible Conduct of Research (RCR) || (6) Data Management ||
+
| 2013.04.17 || Chen, Ye || -- || -- || --
−
Stony Brook Lecture
 
−
*[https://meeting.sinc.stonybrook.edu/p68134598 Stefan Judex Lecture]
 
−
 
 
−
 
 
−
Readings
 
−
*[http://ccnmtl.columbia.edu/projects/rcr/rcr_data 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. 
 
 
|-
 
|-
−
 
−
| 2012.03.07 || Class discussion || Responsible Conduct of Research (RCR) || (7) Journalism and Science ||
 
−
Stony Brook Lecture
 
−
*[https://meeting.sinc.stonybrook.edu/p99353453 Howard Schneider Lecture]
 
  
  
−
Readings (3 Case Studies)
+
| 2013.04.24 || -- || -- || -- || --  
−
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2011-2010_AMS532_Fall_and_Spring/scientists_and_reporters.pdf 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 hospital which might violate patients privacy? 
 
−
 
 
 
|-
 
|-
−
| 2012.03.14 || Class discussion || Responsible Conduct of Research (RCR) || (8) Responsible Conduct of Research Involving Human Subjects ||
 
−
Stony Brook Lecture
 
−
*[https://meeting.sinc.stonybrook.edu/p10813599 Judy Matuk Lecture]
 
−
 
−
 
−
Readings: (Background Information, Case Studies, Helsinki manuscript)
 
−
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]
 
−
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]
 
−
 
−
Discussion
 
−
*From Human Subjects handout, Background History: Why does the Helsinki Declaration limit the use of Placebo's?
 
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*From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?
 
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*From Helsinki manuscript: Do you agree with the authors that placebo-controlled trails are in many cases necessary ?  Why ?
 
−
 
  
  
 +
| 2013.05.01 || -- || -- || -- || --
 
|-
 
|-
−
| 2012.03.21 || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Laboratory Animals ||
 
−
Stony Brook Lecture
 
−
*[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
 
−
 
−
 
−
Readings (Case Studies)
 
−
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]
 
−
 
  
  
−
Discussion
+
| 2013.05.08 (last class) || -- || -- || -- || --
−
*From Case Study 1: What are some of the troublesome issues associated with this set of experiments?
 
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*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?
 
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*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?
 
−
 
 
−
 
 
−
|-
 
−
| 2012.03.28 || Sin, Jeewoen and Xia, Yunting and Chen, Jeff || -- || Second rotation presentations || --
 
−
|-
 
−
| 2012.04.04 || Spring Break || Spring Break  || Spring Break || Spring Break
 
−
|-
 
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| 2012.04.11 || URECA Celebration || URECA Celebration || SAC Ballrooms A&B || 10am-4 pm ALL DAY
 
−
|-
 
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| 2012.04.18 || Sinayev, Roman and Zhou, Yuchen || -- || Second rotation presentations || --
 
−
|-
 
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| 2012.04.25 || Sin, Jeewoen and Xia, Yunting and Chen, Jeff || -- || Third rotation presentations || --
 
−
|-
 
−
| 2012.05.02 (last class) || Sinayev, Roman and Zhou, Yuchen || -- || Third rotation presentations || --
 
 
|-
 
|-
 
|}
 
|}

Latest revision as of 16:11, 23 January 2014

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

2012 Fall Participant Rotations or Research Group Topic References

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

2012.08.29 -- -- -- --
2012.09.05 Zhou, Yuchen Rizzo Topic Armstrong, MS., et al., ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics. J Comput Aided Mol Des. 2010 Sep, 24(9), 789-801.
2012.09.12 Chen, Jeffrey MacCarthy Topic Hershberg, U., et al., Differences in potential for amino acid change after mutation reveals distinct strategies for κ and λ light-chain variation. PNAS 2006 Oct, vol. 103 no. 43, 15963-15968.
2012.09.19 Sin, Jeewoen MacCarthy Topic Leclerc, RD., Survival of the sparsest: robust gene networks are parsimonious. Mol Syst Biol. 2008 4:213.
2012.09.26 Krantsevich, Nikolay Rizzo Topic Barrciro, G., et al., From Docking False-Positive to Active Anti-HIV Agent. J. Med. Chem. 2007, 50, 5324-5329.
2012.10.03 -- -- Postponed AMS Graduate Party
2012.10.10 Li, Xindi Rizzo Topic Chang, C., et al., Pharmacophore-based discovery of ligands for drug transporters. Adv Drug Deliv Rev. 2006 Nov, 58(12-13), 1431-1450.
2012.10.17 Krantsevich, Artyom MacCarthy Topic MacCarthy, T., et al., Differential regulation drives plasticity in sex determination gene networks. BMC Evolutionary Biology. 2010 10:388.
2012.10.25 Yuan, Chaohui MacCarthy Topic Cohen, RM., Somatic hypermutation targeting is influenced by location within the immunoglobulin V region. Molecular Immunology 2011, 48, 1477-1483.
2012.10.31 -- -- -- No Class: Hurricane Sandy
2012.11.07 -- -- Group Study Test Preparation for AMS 535
2012.11.14 Li, Xindi and Yuan, Chaohui -- Topic FIRST ROTATION/RESEARCH PRESENTATIONS
2012.11.21 - -- -- THANKSGIVING BREAK
2012.11.28 -- -- Group Study Test Preparation for AMS 535
2012.12.05 (last class) -- -- Group Study Test Preparation for AMS 535
2013 Spring Participant Rotations or Research Group Topic References

SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH

2013.01.30 Guo, Jiaye Boon Topic Henares, BM., et al., Discovery of a Nitric Oxide Responsive Quorum Sensing Circuit in Vibrio harveyi. ACS Chem. Biol., 2012, 7(8), 1331-1336.
2013.02.06 Krantsevich, Nikolay, Krantsevich, Artyom, and Shan, Jiahui -- Topic FIRST ROTATION/RESEARCH PRESENTATIONS
2013.02.13 Yuan, Chaohui, Li, Xindi, and Guo, Jiaye -- Topic SECOND ROTATION/RESEARCH PRESENTATIONS
2013.02.20 Krantsevich, Nikolay, Krantsevich, Artyom, and Amgalan, Anar -- Topic SECOND ROTATION/RESEARCH PRESENTATIONS
2013.02.27 Chen, Ye MacCarthy Topic Liu, M., et al., Two levels of protection for the B cell genome during somatic hypermutation. Nature, 451, 841-845.
2013.03.06 Yuan, Chaohui Green Topic Green, DF., A Statistical Framework for Hierarchical Methods in Molecular Simulation and Design. J. Chem. Theory Comput., 2010, 6(5), 1682–1697.
2013.03.13 Krantsevich, Nikolay Shatz Topic Koren, S., et al., Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biology, 30, 693–700
2013.03.20 Spring Break Spring Break Spring Break Spring Break
2013.03.27 Krantsevich, Artyom -- -- --
2013.04.03 Li, Xindi -- -- --
2013.04.10 Guo, Jiaye -- -- --
2013.04.17 Chen, Ye -- -- --
2013.04.24 -- -- -- --
2013.05.01 -- -- -- --
2013.05.08 (last class) -- -- -- --
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