Course Descriptions

Course Descriptions

Core Course

During the first year, this course meets three hours daily for 16 weeks during the fall and spring semesters. Topics are presented through a mix of didactic lecture and discussion focused on research papers. Students are expected to present papers and lead conversations in which the group analyzes publications.

The course is divided into six sections:

  • Genome Biology and Proteins, including genes and gene organization, chromosome biology, the maintenance of genomic integrity, and methods of manipulating genes
  • Gene Expression, including proteins and their synthesis, enzymes and their mechanisms, protein structure and function, and regulation of gene expression
  • Cell Biology and Cell Cycle Control, including cellular organization, cell cycle control, and cellular response to external and internal stimuli
  • Signaling and Development, including cell signaling pathways and mechanisms, cell differentiation, tissue formation, and organ development
  • Cancer Immunology, including antigen processing and presentation, innate and cognate immunity, immune surveillance, leukemia, and lymphoma
  • Cancer Biology, including the nature of evidence-based medicine, imaging, cancer metabolism, cancer genomics, cancer epigenetics, cancer susceptibility, kinase inhibitors, and model systems
Observing in the Clinic

An important aspect of integrating basic and clinical sciences is developing an appreciation of the human side of disease, observing real-life challenges faced by clinical practitioners, and understanding the gap between a good research idea and its execution in the clinic. During the first year of the program, students visit various clinics as observers.

Laboratory Rotations

Students complete three five-week laboratory rotations during the first year. Students choose their first rotation in consultation with the dean prior to their arrival on campus. Students who wish to join their thesis laboratory after completing two rotations may opt out of the third rotation upon permission by the dean. Rotations provide students with an opportunity to get to know the faculty, students, and postdocs in the laboratory. There is no coursework during the rotations, allowing students to focus on developing an appreciation for the ongoing research, the style and approach of the principal investigator, and the personality and dynamics of the laboratory, as well as ideas for potential thesis projects.
Students prepare a two-page written summary at the end of each rotation. Each student’s performance in the rotation is assessed via a written evaluation by the rotation mentor in discussion with the student. In the spring semester, students present a 15 minute chalk talk, based on research from one of their rotations, for their fellow students, first year mentors, and rotation mentor.

Logic and Critical Analysis

All first-year students complete this course during the first rotation period. Scientific papers are used to help set the foundation for students to develop their ability to think logically, critically analyze information and data, and present scientific results to a group.

Students are encouraged to develop an approach to understanding the scientific literature, which includes asking the following questions about each experiment: What is the question the authors asked? How was the experiment performed? What techniques were used and why? What is the nature of the data produced? What represents a significant result? What were the conclusions made by the authors? Does the authors’ data justify the conclusions made? What conclusions would the student make?

Responsible Conduct of Research

All students are required to complete this course in the fall semester of the first year. It provides formal training related to issues of research integrity.

The goals of this course are to:

  • heighten the awareness of trainees to ethical considerations relevant to conducting research
  • inform trainees of federal, state, and institutional policies, regulations, and procedures applicable to conducting ethical research
  • provide trainees with the opportunity to engage with senior faculty and peers, in a relatively informal setting, about the implications of policies and procedures on their behavior in a research environment
President’s Research Seminar Series Journal Club

All students complete two semesters of this course during the first year. The President’s Research Seminar Series brings some of the most-distinguished scientists in the world to Memorial Sloan Kettering. The topics presented include some of the most exciting recent developments in modern biology.

Students participate in a journal club the day before the President’s Research Seminar Series meets, in order to review some of the speaker’s published work, and they meet with the speaker on the day of the seminar.

Biostatistics and Computational Biology

This practicum is divided into two sections.

Fall: The first section is an eight hour mini-course that focuses on the practical statistical knowledge required to work with large data sets. This mini-course currently runs in the fall and is taken by the first year students. There are four one and a half hour lectures.

Specific topics focus on methodological issues that biologists face, illustrated with concrete examples using published journal articles, focusing on large scale genomics data like TCGA and ExAC. The practicum covers 1) basic statistical terminologies and definitions; 2) statistical model development; 3) inferential statistics, hypothesis testing, regression and ANOVA, t-test and nonparametric tests and when to use what test, introduction to general linear models; and 4) multidimensional data analysis.

Spring: The second section which runs in the spring includes twenty hours of instruction and meets once a week for 10 weeks. Students in this course will learn to apply quantitative exploratory data analysis techniques to different forms of experimental data. The course will begin with an introduction for students to computing via the UNIX shell, and to computing in the R programming language. The remaining lessons will be a blend of practical skills and theoretical concepts. Students will become comfortable performing exploratory data analysis, and will understand how concepts from statistics underlie the tools they use. Overall the goal of this course is to serve as a practical primer for various bioinformatic analyses, and should provide students with the foundation for future selfguided learning and skill acquisition in this discipline. These skills will enable them both to collaborate effectively with computational biologists, as well as begin to carry out their own computational experiments.

Specific topics include: practical aspects of data formatting and management; visualization of data; an introduction to probability, elementary statistics and hypothesis testing; experimental design and tools for differential expression analysis in RNA-seq and ChIPseq; common data structures for working with biological sequences; enrichment testing for ranked gene sets; common bioinformatics tools and data quality assessment tools; introduction to structural biology and tools for visualization. GSK Student & Faculty Handbook 15 Towards the end of the course, students will be assigned a guided problem set to utilize the concepts and skills described in the course.

Course Topics

  • Quantifying a sample distribution
  • Probability density functions and the normal distribution
  • Practical R (part I), introduction and common data structures
  • Confidence intervals and contingency tables
  • p-Values and formal statistical testing
  • Practical R (part II), libraries and ggplot, data driven graphics
  • Statistical power and experimental design
  • Practical R (part III), control structures and programming
  • Multiple hypothesis testing and non-parametric tests
  • Bayesian methods
  • Correlation vs. linear regression
  • Fitting model parameters to data
  • Practical R (part IV), data wrangling with melt, cast, and plyr
  • Quantitative comparison of models
Graduate Student Seminar

Developing the ability to present and discuss the results of your research in a coherent, logical and compelling fashion is an important feature of becoming a successful scientist. From the first through the fourth years in the program, all students are required to attend and participate in presentations that will help to develop these skills, from chalk talks in the first and second years, to formal graduate student seminars presented in years three and four. Each student presents his or her project, and fellow students provide critical feedback.

Current Topics Journal Club

Students participate in this student-run course beginning in the second year and continuing throughout their fifth year in the graduate program. There are eight sections of roughly five participants each. Students select papers of interest (based on the section’s topic) and present them to the group for discussion.

A journal club of this type is important in that it helps prevent the tunnel vision that can sometimes develop as students focus on their thesis research. Because the entire student body participates, the forum includes diverse topics and a continued exchange of ideas within the graduate community.

Clinical Apprenticeship

The goal of the Clinical Apprenticeship is to inspire and encourage students to think about solutions to clinical challenges using their basic science knowledge. The apprenticeship also helps students learn the clinical landscape, so they can have meaningful scientific exchanges with clinicians.

These goals are met via student engagement with a clinical mentor (CM), a unique component of our educational program. The CM is a member of the Memorial Hospital attending staff who is involved in patient-oriented research. Selection of a CM is guided in large part by the student’s research project.

For example, a student studying meiosis might have a CM who studies and treats patients with germ cell tumors. Similarly, a student studying the Wnt signaling pathway might have a CM who studies and treats patients with colon cancer.

This clinical perspective is best achieved through a series of informal meetings over a period of two years (years three and four in the graduate program), in which CMs share experiences, bring students to clinical visits, and identify pressing challenges in their areas of expertise.

CMs guide students in attending various hospital-based academic activities such as grand rounds, residents’ reports, Specialized Programs of Research Excellence (SPORE) and program project meetings, and disease management team conferences that can help the student appreciate current clinical issues, and provide opportunities to learn more about the specific clinical discipline.