Difference between revisions of "2024-2025 AMS-532 Fall-Spring"
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REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT''' | REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT''' | ||
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− | | | + | | 2024.09.11 Wed || Glukhov, Ernest || -- || In class discussion || Angermueller et al; Deep learning for computational biology. ''Molecular Systems Biology'' '''2016''', ''12'', 878 |
|- | |- | ||
− | | | + | | 2024.09.18 Wed || Zhu, Zeru || -- || In class discussion || Ronquist et al; Algorithm for cellular reprogramming. ''PNAS'' '''2017''', ''114'', 11832-11837 |
|- | |- | ||
− | | | + | | 2024.09.25 Wed || Lu, Hongbo || -- || In class discussion || Hopf et al; Mutation effects predicted from sequence co-variation. ''Nature Biotechnology'' '''2017''', ''35'', 128-139 |
|- | |- | ||
− | | | + | | 2024.10.02 Wed || Hailegeorgis, Derara || -- || In class discussion|| Qin et al; Fast Method for Computing Chemical Potentials and Liquid-Liquid Phase Equilibria of Macromolecular Solutions. ''J Phys Chem B'' '''2016''', ''120'', 8164-8174 |
|- | |- | ||
− | | | + | | 2024.10.09 Wed || Okisamen, Benjamin || -- || In class discussion || Cengiz et al; Sinonasal Tract Malignancies: Prognostic Factors and Surgery Outcomes. ''Iran Red Cres Med J'' '''2013''', ''15'', 4118 |
|- | |- | ||
− | | | + | | 2024.10.16 Wed || Averkava, Veranika || -- || In class discussion || Glukhov et al; Phospho-Tune: Enhanced Structural Modeling of Phosphorylated Protein Interactions. ''bioRxiv preprint'' '''2024''', doi.org/10.1101/2024.02.29.582580 |
|- | |- | ||
− | | | + | | 2024.10.23 Wed || Jordan, Claire || -- || In class discussion || Behn et al; Abnormal Sleep/Wake Dynamics in Orexin Knockout Mice. ''SLEEP'' '''2010''', ''33'', No. 3 |
|- | |- | ||
− | | | + | | 2024.10.30 Wed || Augustynowicz, Gabriel || -- || In class discussion || Cheng et al; Network-based prediction of drug combinations. ''Nature Communications'' '''2019''', ''10'', 1197 |
|- | |- | ||
− | | | + | | 2024.11.06 Wed || Kennedy, Chris || -- || In class discussion || Xu et al; Quantifying Personalized Shift-Work Molecular Portraits Underlying Alzheimer’s Disease through Computational Biology. ''J Prev Alz Dis'' '''2024''', dx.doi.org/10.14283/jpad.2024.161 |
|- | |- | ||
− | | | + | | 2024.11.13 Wed ||O'Reilly, Owen || -- || In class discussion ||Sanjuan et al; In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutations ''Mol Bio Evolv'' '''2006''', ''23'', 1427-1436 |
|- | |- | ||
− | | | + | | 2024.11.20 Wed || Spector, Evan || -- || In class discussion || Gurevich et al; Directed Enzyme Evolution and Encapsulation in Peptide Nanospheres of Quorum Quenching Lactonase as an Antibacterial Treatment against Plant Pathogen. ''ACS Appl. Mater. Interfaces'' '''2021''', ''13'', 2179-2188 |
+ | <br> '''Last day of Journal Club for this semester''' | ||
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− | | | + | | 2024.11.27 Wed || -- || -- || -- || '''No Class, Thanksgiving Break''' |
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|- style="background:lightgreen" | |- style="background:lightgreen" | ||
− | | ''' | + | | '''2025 Spring''' |
| '''Participant''' | | '''Participant''' | ||
| '''Rotations or Research Group''' | | '''Rotations or Research Group''' | ||
| '''Topic''' | | '''Topic''' | ||
− | | '''NOTE: This semester (Spring | + | | '''NOTE: This semester (Spring 2025) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:''' |
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500 | https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500 | ||
|- | |- | ||
− | | | + | | TBD || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training || |
Discussion of Overall Course Requirements which include: | Discussion of Overall Course Requirements which include: | ||
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− | | | + | | TBD || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) || |
Stony Brook Lecture | Stony Brook Lecture | ||
*[https://youtu.be/av3P2n8t2qc Peter Williams Lecture] | *[https://youtu.be/av3P2n8t2qc Peter Williams Lecture] | ||
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|- | |- | ||
− | | | + | | TBD || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct || |
Stony Brook Lecture | Stony Brook Lecture | ||
*[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture] | *[https://youtu.be/RayszjsMDH8 Michael Hadjiargyrou Lecture] | ||
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|- | |- | ||
− | | | + | | TBD || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring || |
Stony Brook Lecture | Stony Brook Lecture | ||
*[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture] | *[https://youtu.be/ko-PWjRyLEU Clinton Rubin Lecture] | ||
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|- | |- | ||
− | | | + | | TBD || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship || |
Stony Brook Lecture | Stony Brook Lecture | ||
*[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture] | *[https://youtu.be/7TPqqGWKjsg Peter Gergen Lecture] | ||
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|- | |- | ||
− | | | + | | TBD || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism || |
Stony Brook Lecture | Stony Brook Lecture | ||
*[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture] | *[https://youtu.be/wrokaKkeCw4 Richard Clark Lecture] | ||
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|- | |- | ||
− | | | + | | TBD || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management || |
Stony Brook Lecture | Stony Brook Lecture | ||
*[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture] | *[https://youtu.be/sIUkSVJEMus Stefan Judex Lecture] | ||
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*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"? | ||
|- | |- | ||
− | | | + | | TBD || -- || -- || -- || SPRING BREAK |
|- | |- | ||
− | | | + | | TBD || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science || |
Stony Brook Lecture | Stony Brook Lecture | ||
*[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture] | *[https://youtu.be/q5j_vqa-OI8 Howard Schneider Lecture] | ||
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|- | |- | ||
− | | | + | | TBD || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects || |
Stony Brook Lecture | Stony Brook Lecture | ||
*[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture] | *[https://youtu.be/Fa_Z9EMZzHc Judy Matuk Lecture] | ||
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|- | |- | ||
− | | | + | | TBD || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals || |
Stony Brook Lecture | Stony Brook Lecture | ||
*[https://youtu.be/Fa_Z9EMZzHc Tom Zimmerman Lecture] | *[https://youtu.be/Fa_Z9EMZzHc 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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Latest revision as of 10:51, 20 November 2024
Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage
Instructor | Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com] |
---|---|
Course No. | AMS-532 |
Location/Time | Wed 11:00PM - 11:55PM, Math Tower AMS seminar room (122A, First Floor) |
Office Hours | Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics |
GENERAL INFORMATION: GENERAL INFORMATION: In this course, students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students. Students register for AMS 532 in both the Fall and Spring semesters of the first year and Fall of the second year.
Learning Objectives:
- (1) Actively participate in Journal Club discussions on Computationally Biology literature.
- (2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531).
- (3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).
- (4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections:
- (i) Course Overview: Fulfilling Responsible Conduct in Research Training
- (ii) Integrity in Scholarship
- (iii) Scientific Misconduct
- (iv) Mentoring
- (v) Ownership and Authorship
- (vi) Plagiarism
- (vii) Data Management
- (viii) Journalism and Science
- (ix) Responsible Conduct of Research Involving Human Subjects
- (x) Responsible Conduct of Research Involving Laboratory Animals
(1) Journal Club: The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader. If a class participant is unable to come to a specific class due to unforseen circumstances they can submit a 1-page max paper summary that includes: (i) What was the primary purpose of the study ? (ii) What aspects of the study do you feel was particularly well described or was compelling ? (iii) What aspects of the study do you feel needs improvement ?
(2) Responsible Conduct of Research (RCR): The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings.
LITERATURE DISCLAIMER: Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.
PRESENTATION DISCLAIMER: Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.
Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring)
2024 Fall | Participant | Rotations or Research Group | Topic | References
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT |
2024.09.11 Wed | Glukhov, Ernest | -- | In class discussion | Angermueller et al; Deep learning for computational biology. Molecular Systems Biology 2016, 12, 878 |
2024.09.18 Wed | Zhu, Zeru | -- | In class discussion | Ronquist et al; Algorithm for cellular reprogramming. PNAS 2017, 114, 11832-11837 |
2024.09.25 Wed | Lu, Hongbo | -- | In class discussion | Hopf et al; Mutation effects predicted from sequence co-variation. Nature Biotechnology 2017, 35, 128-139 |
2024.10.02 Wed | Hailegeorgis, Derara | -- | In class discussion | Qin et al; Fast Method for Computing Chemical Potentials and Liquid-Liquid Phase Equilibria of Macromolecular Solutions. J Phys Chem B 2016, 120, 8164-8174 |
2024.10.09 Wed | Okisamen, Benjamin | -- | In class discussion | Cengiz et al; Sinonasal Tract Malignancies: Prognostic Factors and Surgery Outcomes. Iran Red Cres Med J 2013, 15, 4118 |
2024.10.16 Wed | Averkava, Veranika | -- | In class discussion | Glukhov et al; Phospho-Tune: Enhanced Structural Modeling of Phosphorylated Protein Interactions. bioRxiv preprint 2024, doi.org/10.1101/2024.02.29.582580 |
2024.10.23 Wed | Jordan, Claire | -- | In class discussion | Behn et al; Abnormal Sleep/Wake Dynamics in Orexin Knockout Mice. SLEEP 2010, 33, No. 3 |
2024.10.30 Wed | Augustynowicz, Gabriel | -- | In class discussion | Cheng et al; Network-based prediction of drug combinations. Nature Communications 2019, 10, 1197 |
2024.11.06 Wed | Kennedy, Chris | -- | In class discussion | Xu et al; Quantifying Personalized Shift-Work Molecular Portraits Underlying Alzheimer’s Disease through Computational Biology. J Prev Alz Dis 2024, dx.doi.org/10.14283/jpad.2024.161 |
2024.11.13 Wed | O'Reilly, Owen | -- | In class discussion | Sanjuan et al; In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutations Mol Bio Evolv 2006, 23, 1427-1436 |
2024.11.20 Wed | Spector, Evan | -- | In class discussion | Gurevich et al; Directed Enzyme Evolution and Encapsulation in Peptide Nanospheres of Quorum Quenching Lactonase as an Antibacterial Treatment against Plant Pathogen. ACS Appl. Mater. Interfaces 2021, 13, 2179-2188
|
2024.11.27 Wed | -- | -- | -- | No Class, Thanksgiving Break |
2025 Spring | Participant | Rotations or Research Group | Topic | NOTE: This semester (Spring 2025) students will fulfill RCR training by registering for AMS-500 instead of AMS-532. Please resgister for AMS-500 and follow that schedule:
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500 |
TBD | Class discussion | Responsible Conduct of Research (RCR) | (1) Course Overview: Fulfilling Responsible Conduct in Research Training |
Discussion of Overall Course Requirements which include:
|
TBD | Class discussion | Responsible Conduct of Research (RCR) | (2) Integrity in Scholarship (Introduction to Ethics and Science) |
Stony Brook Lecture
|
TBD | Class discussion | Responsible Conduct of Research (RCR) | (3) Scientific Misconduct |
Stony Brook Lecture
|
TBD | Class discussion | Responsible Conduct of Research (RCR) | (4) Mentoring |
Stony Brook Lecture
|
TBD | Class discussion | Responsible Conduct of Research (RCR) | (5) Ownership and Authorship |
Stony Brook Lecture
|
TBD | Class discussion | Responsible Conduct of Research (RCR) | (6) Plagiarism |
Stony Brook Lecture
|
TBD | Class discussion | Responsible Conduct of Research (RCR) | (7) Data Management |
Stony Brook Lecture
|
TBD | -- | -- | -- | SPRING BREAK |
TBD | Class discussion | Responsible Conduct of Research (RCR) | (8) Journalism and Science |
Stony Brook Lecture
|
TBD | Class discussion | Responsible Conduct of Research (RCR) | (9) Responsible Conduct of Research Involving Human Subjects |
Stony Brook Lecture
Discussion
|
TBD | Class discussion | Responsible Conduct of Research (RCR) | (10) Responsible Conduct of Research Involving Laboratory Animals |
Stony Brook Lecture
Discussion
|
Required Syllabi Statements:
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php
Student Accessibility Support Center Statement: If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.
Academic Integrity Statement: Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html
Critical Incident Management: Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php