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GS21 1017: Foundations of Biomedical Research

GS21 1018: Foundations of Biomedical Research for Quantitative Students

Course Directors: 
Swathi Arur, PhD
[email protected]
Office Hours: Email Dr. Arur to set up an appointment

Catherine Denicourt, PhD
[email protected] 
Office Hours: Email Dr. Denicourt to set up an appointment

Wassim Chehab, PhD
[email protected]
BSRB S3.8435
Office Hours: Email Dr. Chehab to set up an appointment

Biostatistics Module Instructor:

John Magnotti, PhD
[email protected]
Office Hours: Email Dr. Magnotti to set up an appointment

Next Generation Sequencing Module Instructor:
Ambro van Hoof, PhD
[email protected]  
Office Hours: Email Dr. van Hoof to set up an appointment

Regular Module TA (Weeks 1-7)

Jian Yang
[email protected]
Office Hours: Email Jian to set up an appointment

Regular Module TA (Weeks 8-14)
Kiara Bornes 
[email protected]
Office Hours: Email Kiara to set up an appointment

Biostats Module TA (Weeks 1-14)
Mariana Najjar
[email protected] 
Office Hours: Email Mariana to set up an appointment

Next Generation Sequencing Module TA (Weeks 1-14)
Sayef Ahammed
[email protected]

Office Hours: Email Sayef to set up an appointment

Dates: August 26 - December 6, 2024 

           ( No class on Labor Day and Thanksgiving Week)

When: Mondays (8:30 am - 10:15 am)  
            Tuesdays, Wednesdays and Fridays (8:30 am - 11:00 am) 
            Thursdays (8:30 am - 9:45 am) 

Where: The Regular and Applied Next Generation Sequencing Modules will be held in the Large Classroom at BSRB

              The  Biostats Module will be held Via Zoom. (Zoom link information is provided on the Canvas Core Course Website).   

Grades: A-F (GS21 1017) or P/F (GS21 1018)

DATE 2024 WEEK TOPIC TOPIC LEADER
Aug 26 - Aug 30 Week 1 How Did We Get Here: A Brief History of Biomedical Science Lorenz
Sept 3 - 6 Week 2 Genetics Arur
Sept 9 - 13 Week 3 DNA Structure, Chromatin, epigenetics, transcription  Bartholomew 
Sept 16- 20 Week 4 Cell Cycle, DNA Replication, DNA Damage and Repair Machinery Cole 
Sept 23 - 27 Week 5 RNA and the Transcriptome van Hoof
Sept 30 - Oct 4 Week 6 Birth and Destruction of Proteins  Denicourt
Oct 7 - 11 Week 7 Cell Biology Kim
Oct 14 - 18 Week 8 Cytoskeletal Dynamics and Cell Motility  Eisenhoffer
Oct 21 - 25 Week 9 Extracellular and Intracellular Signaling Cunha
Oct 28 - Nov 1 Week 10 Developmental Biology Behringer/Miller
Nov 4 - 8 Week 11 Infectious Diseases and Antimicrobial Drug Resistance Lorenz / Arur
Nov 11 - 15 Week 12 Introduction to Quantitative Sciences  Hart
Nov 18 - Nov 22 Week 13 Immune cells, functions and therapies Reuben
Nov 25 - Nov 29 Thanksgiving No core course classes this week N/A
Dec 2 - 6 Week 14 Neuroscience Venkatachalam

Core Course FAQs

  • My primary interests are in biostatistics (or another quantitative area of biology) can I take the core course Pass/Fail?

    If you are committed to a quantitative or computational degree track and will complete extensive coursework in these areas, you may register for GS21 1018 - Foundations of Biomedical Research for Quantitative Students. You must obtain permission from the Office of Academic Affairs. These students will attend all class sessions as those students enrolled in GS21 1017 but are NOT expected to participate in breakout sessions, neither in the biostats or applied next generation sequencing modules. Students registering for the GS21 1018 will be graded Pass/Fail based only on class attendance.

  • Is Ethics included in the Core Course?
    • The GSBS Course Ethical Dimensions of Biomedical Science will directly follow the core course on Thursdays.
    • This is a stand-alone course and it is not integrated into the core course. You must register for it separately from the core course.
    • All first year students are expected to enroll in the Ethics course.
    • Other interested students/trainees may also enroll in the Ethics course.
  • How will students be evaluated?
    • The Core Course will not have traditional in-class exams.
    • Each week, students will be given a take home assignment (developed by the Topic leader and lecturers) focused on critical thinking and concepts.
    • Examples:
      • Design an experiment to test a specified hypothesis (including controls and expected outcomes/pitfalls).
      • Develop and test a hypothesis, what experiments support a particular scientific “fact” and experiments refute this “fact”.
    • The students will have a biostats and another applied next generation sequencing graded assignments each week.
    • All students are expected to ask at least one question or make a substantive comment each week. This will be recorded by the TA.
    • Breakout session participation and assignments will also contribute to each student’s overall grade.
    • Since participation is an important part of the course, please contact the course director if you will be absent due to illness or other circumstance. In some cases, an alternative assignment will be given to make up for missed class work.
    • Final Grades will be based on:
      • Attendance/Participation 30%
      • Weekly Biostats homework 20%
      • Weekly Applied Next Generation Sequencing homework 20%
      • Weekly Topic Week homework 30%
  • Course Learning Aids

    All students will be required to have a laptop for class.

  • Will students have an opportunity to evaluate the course?
    • Yes, students will have the opportunity to evaluate the course each week through a free-text link. They can share their views about specific week's content, instructors, and the overall course. 
    • Feedback will be reviewed by Course Directors, Core Course Faculty, and the GSBS Curriculum Committee to improve the course.
    • Student input is crucial for the course's success and refinement.
  • Who are the Course Directors?

    Course Directors:

    Dr. Swathi Arur ([email protected]), Dr. Catherine Denicourt ([email protected]), and Dr. Wassim Chehab ([email protected])

    • Will attend class sessions.
    • Will provide feedback to lecturers/instructors.
    • Will hold office hours to assist students.
    • Will identify and counsel students who are having difficulty in the class.
    • Will review weekly evaluations.
    • Will answer any questions students have about the Core Course.

  • Who is required to take the core course?

    Most first year PhD students are required to take the course. See Dr. Chehab in the Office of Academic Affairs if you have questions.

  • I am not a first year PhD student, can I take the core course?

    The course is also open to first year MS students. See Dr. Chehab in the Office of Academic Affairs if you have questions.

  • How is the course organized?

    The course is divided into 14 one-week units each covering a separate broad topic area (e.g., Cell Biology, Genetics).

    • Each week will be led by a Topic Leader (a GSBS faculty member) who has organized a team of expert faculty to participate in teaching.
    • Each week will consist of daily lectures and breakout sessions.
    • The lectures will be concept-driven, focused on the big questions in the field, cutting edge findings/approaches, case studies, and clinical applications.
    • The course will also include a weekly biostats module and an applied next generation sequencing module.
  • What are Breakout sessions?
    • Breakout sessions will consist of a variety of individual and team exercises and hands-on workshops that will complement the lectures and the week’s overall topic.
    • The breakout sessions are designed to develop skills that you will need to succeed as a scientist (critical thinking, hypothesis development and testing, presentation skills, and teamwork). These sessions will also expose students to powerful scientific methods and software tools.
    • In most breakout sessions, the class will be divided into small groups.
    • The sessions will take different forms, for example:
      • Journal Club (papers assigned in advance)
      • Hypothesis building - based on ideas from lecture or literature
      • Critical analysis of experimental design
      • Student presentations
      • Problem solving
      • Software workshops
    • The groups will be led by the students themselves with oversight from faculty, TAs, and course volunteers. The Course Directors, Course Coordinator, and TAs will also be available to “float” between groups to facilitate discussions.
    • Students will be graded on individual participation and as teams where appropriate (presentations, projects, etc.).
  • Where can I find course materials?
    • All course material and assignments will be on Canvas. All enrolled students will be provided access to the Canvas Core Course. Please contact Dr. Chehab if you have problems accessing Canvas.
    • The Canvas site will provide the overall course syllabus, weekly schedules, and content.
  • Are Biostatistics and Bioinformatics included in the course?
    • The core course will include a biostats module and an applied next generation sequencing module.
    • The biostats module will be taught every Thursday by Dr. John Magnotti.
    • The applied next generation sequencing module will be taught every Monday by Dr. Ambro van Hoof.
    • There will be a graded weekly take home assignment for these modules.