Curriculum
During the first year, BCMB Allied students must complete the program’s core curriculum courses and three (3) lab rotations. Lab rotations are an important component of the students’ first year in that they help him/her to decide on a research focus and select a thesis mentor, which is required by the end of the first year.
Year 1
Course Director: Baran Ersoy
This course covers core principles of biochemistry and biophysics, such as enzyme kinetics and reaction mechanisms, ligand binding, protein, nucleic and membrane structure and introduces techniques and approaches for macromolecular analysis.
Course Directors: Mara Sherman and Yicheng Long
This course is organized around the principles of genetic analysis, with examples chosen from organisms that best illustrate those principles. The course is based on lectures, problem sets and discussion sections. Topics covered include: the nature of the gene, linkage and physical maps, recombination mechanisms, nature of mutations, mutations as tools to dissect gene function, transposition, epigenetics, cancer genetics, genetic analysis of development and cell-cell signaling.
Course Directors: Jessica Sheu-Gruttadauria and Naama Aviram
This discussion-based course introduces students to the foundational critical thinking skills that underpin rigorous scientific discovery, from identifying compelling questions to evaluating evidence and building sound scientific arguments.
Students will examine the scientific method through multiple lenses: formal logic and causal inference, the structure of scientific arguments, and the role of creativity and intuition alongside scientific rigor, drawing on case studies drawn from primary literature.
Students will also explore how publication culture and career structures can shape scientific practice and how AI is transforming epistemic judgment in modern research. Grading is based on participation and small-group presentations.
Course Directors: John Maciejowski and Benjamin Kleaveland
This course is Module I of a two-part course that explores the regulatory mechanisms that govern information flow all the way from DNA to cells, involving topics including DNA replication and repair, transcription and RNA splicing, mRNA processing and translation, quality control, cytoskeleton, membranes, metabolism, and aspects of cellular homeostasis. The course is taught in 2-day segments involving a focused lecture on one day, followed by a discussion of relevant primary research literature on the next day.
Directors: Lydia Finley and David Simon
This course is Module II of a two-part course that explores how groups of cells function and are arranged within organisms, and mechanisms of cell dysfunction that lead to disease. Specific topics include cell division and cell death, cell adhesion, cell signaling, mechanisms of organismal development, stem cells, aging-related disorders, infection, and cancer. The course is taught in a format involving primary literature-based learning, where research papers are matched to a lecture and examined by classroom-based discussion.
The RCR course is open to all members of the Tri-Institutional (Tri-I) and WCMC Clinical and Translational Science Center (CTSC) communities. Successful completion of the course is required for all trainees, fellows, participants, and scholars receiving support through NIH or NSF Institutional Research Training Grants, Individual Fellowship Awards, Career Development Awards (Institutional and Individual), Research Education Grants, Dissertation Research Grants, or other grant programs with a training component that requires instruction in responsible conduct of research as noted in the Funding Opportunity Announcement. The responsible conduct of research is the practice of scientific investigation with integrity. Training in this area is an essential component of research training; awareness and application of established professional norms and ethical principles is required in the performance of all activities related to scientific research. Weill Cornell Medical College is committed to fostering an environment that promotes the practice of scientific investigation with integrity. This course is intended to help fulfill that commitment.
Throughout the first year, 1st year students meet every two weeks with the program directors and select faculty in an informal setting to discuss discuss their progress in the curriculum. As a means to practice presentation skills, 2-3 students also present chalk talks on their current rotation projects at each meeting. In addition, select faculty are invited to present chalk talks at these meetings to introduce their research programs and potential rotation projects.
Course Directors: Dirk Remus and Lukas Dow
Learning how to effectively communicate one's science is an important skill to acquire during the PhD training. BCMB student seminars involve two 30-minute research-in-progress presentations from BCMB graduate students. These occur on Friday afternoons from 4:00 – 5:00 pm. BCMB students are required to attend in years 1-5 and are required to present seminars in years 3-5. All other BCMB students are encouraged to attend, and opportunities to present are available to 2nd year students on a volunteer basis.
Year 2
All students enrolled in PhD programs within the Weill Graduate School of Biomedical Sciences are required to complete a one quarter course in Biostatistics. For BCMB students, this course will be taken during Quarter I of their second year in the program.
The qBio course will prepare students to apply quantitative techniques to the analysis of experimental data and the modeling of biological systems. To emphasize both practical and theoretical skills, the material will be presented whenever possible in a hands-on workshop style, and the completion of several projects by the students will be required. Topics include: practical aspects of data formatting and management; communication of quantitative concepts (verbal, graphical and mathematical); a review of statistics, with emphasis on the selection of appropriate statistical tests; the use of modern software packages; the interpretation of results; the formulation, evaluation and analysis of mathematical models of biological function, with an emphasis on linear and non-linear regression, determination of model parameters; and the critical comparison of alternative models with regard to over-parameterization. The formal components will introduce (and demystify) ordinary and partial differential equations and basic principles of non-linear dynamics, in order to enable quantitative modeling in biological arenas such as neural function, enzyme kinetics, cardiac dynamics and signaling pathways. Additional special topics will also be presented (e.g., control theory, machine learning, information theory, and image analysis) and their application will be illustrated with ongoing research in the laboratories of participating faculty.
Learning how to effectively communicate one's science is an important skill to acquire during the PhD training. BCMB student seminars involve two 30-minute research-in-progress presentations from BCMB graduate students. These occur on Friday afternoons from 4:00 – 5:00 pm. BCMB students are required to attend in years 1-5 and are required to present seminars in years 3-5. All other BCMB students are encouraged to attend, and opportunities to present are available to 2nd year students on a volunteer basis.
Years 3-5
Before graduation, students must complete two (2) elective courses prior to submission of their thesis. The electives vary and serve to fit the specific interests of each student.
Below are the elective courses offered by the BCMB Allied Program for students in Year 3 and above. Students may also take courses offered at other local institutions, including Rockefeller University.
Core Principles in Molecular Biophysics
An overview of the diversity of modern biophysical experimental techniques used in the study of biological systems at the cellular and molecular level. Topics covered will include methods that examine both structure and function of biological systems. Topics include light microscopy, fluorescence microscopy, image processing, confocal and multiphoton microscopy, phase contrast, electron microscopy, x-ray diffraction and protein structure determination, multidimensional NMR, spectroscopy, chromophores, calcium measurements, resonance energy transfer, membrane biophysics, electrophysiology, ion channels, action potentials, ligand-gated channels, fluctuation analysis, patch-clamp, molecular biology of ion channels, capacitance measurements, amperometry, optical traps, and molecular force measurements. The course is intended for students who seek an introduction to modern biophysical experimental methods. Due to the interdisciplinary nature of the course, students will have diverse backgrounds. A basic knowledge of and interest in physics and mathematics is expected but strong attempts are made to give an intuitive understanding of the mathematics and physics involved. Some knowledge of physical chemistry, molecular and cell biology, or neurobiology will be helpful. Depending on individual background most students will find certain aspects easy and other aspects demanding.
Principles of Developmental Biology
The course presents key concepts in Developmental Biology that will draw on research in several invertebrate and vertebrate model systems, including fly, nematodes, zebrafish, frog, chick and mouse. In the first part, general principles that have emerged in Developmental Biology are discussed. The second part focuses on how these principles operate during lineage development and organogenesis. The last part examines how errors in developmental pathways result in congenital disorders and human disease.
This is an elective course that is aimed primarily towards 2nd and 3rd year graduate students; however, it is open to students from all years and from all WCGS Programs of Study. Students should have finished the BCMB Core Course requirements, or equivalent courses covering molecular and cell biology and genetics. The course consists of 16 lectures taught by WCMC and SKI faculty and two additional guest lectures by Dr. Shai Shaham (Rockefeller U) and Natasza Kurpios (Cornell U, Ithaca). In addition, students will lead six interactive group discussions of selected research papers.
Cryoelectron Microscopy of Macromolecular Assemblies
This course, which is held on the premises of the New York Structural Biology Center, will cover the theory and practice of solving molecular structures by electron microscopy. It blends a series of lectures from local experts followed by student-led discussion sessions with practical sessions that parallel the topics introduced during the lectures. The course first covers optics, sample preparation and a basic mathematical description of diffraction before moving into a detailed exploration of the three main methods of structure determination: tomography, single particle analysis and 2D crystallography. The course ends with a discussion of map interpretation and molecular fitting.
Elective for Year 3 and above, offered at the New York Structural Biology Center.
Learning how to effectively communicate one's science is an important skill to acquire during the PhD training. BCMB student seminars involve two 30-minute research-in-progress presentations from BCMB graduate students. These occur on Friday afternoons from 4:00 – 5:00 pm. BCMB students are required to attend in years 1-5 and are required to present seminars in years 3-5. All other BCMB students are encouraged to attend, and opportunities to present are available to 2nd year students on a volunteer basis.