Difference between revisions of "2023-2024 AMS-532 Fall-Spring"
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| − | | 2023.09.20 Wed || Glukhov, Ernest || -- || | + | | 2023.09.20 Wed || Glukhov, Ernest || -- || In class discussion || Greener et al; A guide to machine learning for biologists. ''Nature Reviews: Molecular Cell Biology'' '''2022''', ''23'', 40 |
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| − | | 2023.09.27 Wed || Cheung, Andrew || -- || | + | | 2023.09.27 Wed || Cheung, Andrew || -- || In class discussion || Luecken et al; Current best practices in single-cell RNA-seq analysis: a tutorial. ''Molecular Systems Biology'' '''2019''', ''15'', e8746 |
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| − | | 2023.10.04 Wed || Zhu, Zeru || -- || | + | | 2023.10.04 Wed || Zhu, Zeru || -- || In class discussion|| Fimmel et al; Mathematical fundamentals for the noise immunity of the genetic code. ''BioSystems'' '''2018''', ''164'', 186-198 |
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| − | | 2023.10.11 Wed || Moy, Olivia || -- || | + | | 2023.10.11 Wed || Moy, Olivia || -- || In class discussion || Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. ''BMC Bioinformatics'' '''2018''', ''19'', 163 |
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| − | | 2023.10.18 Wed || Li, Stan || -- || | + | | 2023.10.18 Wed || Li, Stan || -- || In class discussion || Wang et al et al; Predicting Biomolecular Binding Kinetics: A Review. ''Journal of Chemical Theory and Computation'' '''2023''', ''19'', 2135-2148 |
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| − | | 2023.10.25 Wed || Cheung, Andrew || -- || | + | | 2023.10.25 Wed || Cheung, Andrew || -- || In class discussion || Li et al; Fast and accurate short read aliggnmetn with Burrows-Wheeler transform. ''Bioinformatics'' '''2009''', ''25'', 1754-1760 |
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| − | | 2023.11.01 Wed || Glukhov, Ernest || -- || | + | | 2023.11.01 Wed || Glukhov, Ernest || -- || In class discussion || Wiedermann et al; Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. ''Frontiers in Chemistry'' '''2020''', ''8'', Article 280 |
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| − | | 2023.11.08 Wed || Zhu, Zeru || -- || | + | | 2023.11.08 Wed || Zhu, Zeru || -- || In class discussion || Eraslan et al; Deep learning: new computational modeling techniques for genomics. ''Nature Reviews'' '''2019''', ''20'', 389 |
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| − | | 2023.11.15 Wed || | + | | 2023.11.15 Wed || -- || -- || -- || CLASS POSTPONED |
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| − | | 2023.11.29 Wed || | + | | 2023.11.29 Wed || Moy, Olivia || -- || In class discussion || Ruffolo et al; Antibody structure prediction using interpretable deep learning. ''Patterns'' '''2022''', ''3'', 100406 |
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Latest revision as of 13:51, 15 November 2023
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 12:00PM - 12:53PM, 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)
| 2023 Fall | Participant | Rotations or Research Group | Topic | References
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT |
| 2023.08.30 Wed | -- | -- | -- | First year students will attend AMS-539 meeting (Faculty research presentations). |
| 2023.09.06 Wed | -- | -- | -- | First year students will attend AMS-539 meeting (Faculty research presentations). |
| 2023.09.13 Wed | Li, Stan | FIRST DAY of CLASS | -- | Ignatov et al; High Accuracy Prediction of PROTAC Complex Structure. JACS 2023, 145, 7123-7135 |
| 2023.09.20 Wed | Glukhov, Ernest | -- | In class discussion | Greener et al; A guide to machine learning for biologists. Nature Reviews: Molecular Cell Biology 2022, 23, 40 |
| 2023.09.27 Wed | Cheung, Andrew | -- | In class discussion | Luecken et al; Current best practices in single-cell RNA-seq analysis: a tutorial. Molecular Systems Biology 2019, 15, e8746 |
| 2023.10.04 Wed | Zhu, Zeru | -- | In class discussion | Fimmel et al; Mathematical fundamentals for the noise immunity of the genetic code. BioSystems 2018, 164, 186-198 |
| 2023.10.11 Wed | Moy, Olivia | -- | In class discussion | Shapiro et al; The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. BMC Bioinformatics 2018, 19, 163 |
| 2023.10.18 Wed | Li, Stan | -- | In class discussion | Wang et al et al; Predicting Biomolecular Binding Kinetics: A Review. Journal of Chemical Theory and Computation 2023, 19, 2135-2148 |
| 2023.10.25 Wed | Cheung, Andrew | -- | In class discussion | Li et al; Fast and accurate short read aliggnmetn with Burrows-Wheeler transform. Bioinformatics 2009, 25, 1754-1760 |
| 2023.11.01 Wed | Glukhov, Ernest | -- | In class discussion | Wiedermann et al; Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Frontiers in Chemistry 2020, 8, Article 280 |
| 2023.11.08 Wed | Zhu, Zeru | -- | In class discussion | Eraslan et al; Deep learning: new computational modeling techniques for genomics. Nature Reviews 2019, 20, 389 |
| 2023.11.15 Wed | -- | -- | -- | CLASS POSTPONED |
| 2023.11.22 Wed | -- | -- | -- | THANKSGIVING BREAK |
| 2023.11.29 Wed | Moy, Olivia | -- | In class discussion | Ruffolo et al; Antibody structure prediction using interpretable deep learning. Patterns 2022, 3, 100406 |
| 2023.12.06 Wed | TBD | LAST DAY OF CLASS | -- | TBD |
| 2024 Spring | Participant | Rotations or Research Group | Topic | NOTE: This semester (Spring 2024) 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 |
| 2024.01.26 Wed | Class discussion | Responsible Conduct of Research (RCR) | (1) Course Overview: Fulfilling Responsible Conduct in Research Training |
Discussion of Overall Course Requirements which include:
|
| 2024.02.02 Wed | Class discussion | Responsible Conduct of Research (RCR) | (2) Integrity in Scholarship (Introduction to Ethics and Science) |
Stony Brook Lecture
|
| 2024.02.09 Wed | Class discussion | Responsible Conduct of Research (RCR) | (3) Scientific Misconduct |
Stony Brook Lecture
|
| 2024.02.16 Wed | Class discussion | Responsible Conduct of Research (RCR) | (4) Mentoring |
Stony Brook Lecture
|
| 2024.02.23 Wed | Class discussion | Responsible Conduct of Research (RCR) | (5) Ownership and Authorship |
Stony Brook Lecture
|
| 2024.03.02 Wed | Class discussion | Responsible Conduct of Research (RCR) | (6) Plagiarism |
Stony Brook Lecture
|
| 2024.03.09 Wed | Class discussion | Responsible Conduct of Research (RCR) | (7) Data Management |
Stony Brook Lecture
|
| 2024.03.16 Wed | -- | -- | -- | SPRING BREAK |
| 2024.03.23 Wed | Class discussion | Responsible Conduct of Research (RCR) | (8) Journalism and Science |
Stony Brook Lecture
|
| 2024.03.30 Wed | Class discussion | Responsible Conduct of Research (RCR) | (9) Responsible Conduct of Research Involving Human Subjects |
Stony Brook Lecture
Discussion
|
| 2024.04.06 Wed | Class discussion | Responsible Conduct of Research (RCR) | (10) Responsible Conduct of Research Involving Laboratory Animals |
Stony Brook Lecture
Discussion
|
| 2024.04.13 Wed | -- | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
| 2024.04.20 Wed | -- | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
| 2024.04.27 Wed | -- | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
| 2024.05.04 Wed | -- | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
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
