Curriculum

Course Directors: Jason R. Banfelder, MChE; Dr. Luce Skrabanek, PhD; and Dr. Derek Shore

This course prepares students to analyze experimental data using quantitative techniques. To emphasize practical skills as well as theoretical knowledge, the course will involve several hands-on workshops and require the completion of several projects. Students will be well positioned to meet the emerging requirements of funding agencies for formally planned experiments and fully reproducible and documented data analysis methods. 

Specific topics in Quantitative Understanding in Biology (QBio) I include: practical aspects of data formatting and management; graphical, mathematical and verbal communication of quantitative concepts; a review of statistics, with emphasis on the selection of appropriate statistical tests, the use of modern software packages, the interpretation of results, and the design of experiments; 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. 

Qbio II further prepares students to apply quantitative techniques to the analysis of experimental data and the modeling of dynamic biological systems. In the two modules of this class, we explore dynamic biological systems. Both continuous- and discrete-time systems are treated, as are both linear and non-linear systems. Examples are taken from a spectrum of biologically relevant domains including population biology, genetic evolution, auditory processing, enzyme kinetics, and the dynamics of ion channels. To emphasize both practical and theoretical skills, the course will involve hands-on work-shops, and the completion of two projects by the students will be required.

Syllabi are available here.

Course Director: Dr. Luce Skrabanek

This core course is a year-long modular course which will integrate statistics, experimental data, quantitative methods, and interpretation of results, each within the context of a single topic or idea. Emphasis will be placed on depth of quantitative understanding. Each module, anchored on one or a few papers from the primary literature, will explore a topic in-depth, providing students with the theoretical and biological background necessary to understand the topic, the experimental techniques of data acquisition, as well as the practical aspects of approaching and analyzing the data.

Module 1: Introduction to Next-Gen Sequencing includes an introduction to the theory, the biological background, the different short- and long-read sequencing technologies, and library preps, as well as the diverse applications of NGS. Emphasizing the importance of quality control at each step, details the lifecycle of analyzing a typical RNA-seq dataset. Introduces students broadly to the topics that will be covered in more detail in each module.

Module 2: DNA Sequencing looks at point mutation and indel detection, identification of structural variants, copy number detection, functional interpretation, meta-genomics analysis, and the application of variant calling in population genom and GWAS.

Module 3: Transcriptional Regulation and Epigenetics will cover the use of techniques such as ATAC-seq, ChIP-seq, RNA-seq, PRO-seq, methylation assays, and perturbation analysis to study DNA structure and chromatin accessibility, 3D nuclear architecture, transcriptional and post-transcriptional regulation, and genetic and epigenetic perturbations.

Module 4: Metabolomics and Proteomics explores how assaying the metabolome and proteome differ from NGS, and how this information differs from, and complements, the quantification of nucleic acid-based technologies. Includes the use of Gaussian Graphical Models to infer metabolomic and proteomic networks and pathways.

Module 5: Image Analysis is an introduction to image acquisition modalities and noise sources, classic computer vision strategies for cell tracking, particle tracking and correlation spectroscopy, active contouring, source separation and image registration, thinking in k-space, deep learning approaches for pathology images, and spatial transcriptomics image analysis with machine learning.

Module 6: Single Cell Technologies looks at the extra information that measurements from single cells afford over bulk measurements, sample and library preps, what are the advantages and disadvantages of single cell sequencing, analysis techniques including normalization, dataset integration, clustering, trajectory inference, lineage tracing, how we can identify even rare cell types, and how that has transformed the way we look at the cells and how we explore diseases and develop therapies. Advanced techniques such as CITE-seq, scATAC-seq, Perturb-Seq, single cell multi-omics approaches.

The syllabus is available here.

Course Directors: Dr. Alessio Accardi and Dr. Jeremy Dittman 

This core course aims to build a deep quantitative understanding of the biophysical basis of cellular processes. The course is articulated in 6 modules, 3 in each semester. Each module is centered around a specific biological question and will provide students with the conceptual (i.e., theoretical basis, mathematical approaches) and practical (i.e., experimental techniques, computational approaches, analysis strategies) tools to approach them. Modules will consist of lectures, journal clubs, and Problem Based Learning classes where students present their homework solutions to the class. The course includes a grant-writing component that both cements students’ understanding of course content and teaches skills in scientific writing. 

Module 1 – Thinking on the nanoscale level: Proteins, Membranes, and Electricity introduces foundational concepts in molecular biophysics, from the basic principles of membrane and protein structure to the experimental and mathematical approaches used to quantitatively describe their function.

Module 2 – Thermodynamic principles of molecular interactions describes the thermodynamic basis of protein-protein and protein-ligand interactions with a focus on the approaches used to quantify the molecular forces that underlie them.

Module 3 –Basis of kinetics and signaling in cellular processes focuses on the principles of cellular signaling, focusing on the quantitative approaches used to describe them, from diffusion of molecules to the description of basic cellular pathways that control signaling mechanisms and membrane fusion processes.

Module 4 – Introduction to Signal Transmission analyzes the basis of signal transmission, from the generation and propagation of the action potential in the brain and heart, to the molecular basis of sensory transduction.

Module 5 – Metabolism and Signaling Associated with Decisions on Cell State presents fundamental cellular signaling pathways, from transmembrane signaling, to DNA damage response and ubiquitin signaling.

Module 6 – Integration of Signaling for Information Transmission analyzes fast signaling mechanisms such as sensory transduction and synaptic transmission.

The syllabus is available here.

Course Director: Alessio Accardi, PhD 

This year-long course exposes students to recent research developments in PBSB faculty focus areas including:  

• Biophysical and Physiological Mechanisms of Membrane and Membrane Protein Function
• Quantitative and Integrative Biology
• Organogenesis and Physiological Genomics
• Biological and Biomedical Imaging  

The syllabus is available here.

Course Director: Emre Aksay, PhD 

Required for all 1st year PBSB graduate students, this course is also open to all WCGS students. Program faculty will introduce the research in their laboratories and discuss potential rotation and thesis projects. 

Syllabi are available here.

Per Weill Cornell Medicine policy, the RCR course is mandatory for all graduate students at Weill Cornell Graduate School of Medical Sciences and for all post-doctoral scholars at Weill Cornell Medicine, independent of their funding source.  This is a strong commitment of Weill Cornell Medicine as a research institution dedicated to promoting the value of the responsible conduct of research within its community of graduate students, post-docs, and faculty. As a result, WCM requires a formal RCR course that is designed to meet all NIH and NSF requirements.

Goals of the RCR Course

1. Heighten the awareness of trainees to ethical considerations relevant to the conduct of research;
2. Inform trainees of federal, state, and institutional policies, regulations, and procedures applicable to the ethical conduct of research; and
3. Provide trainees with the opportunity to discuss, in a relatively informal setting, with senior faculty and among their peers, the implications of these policies and procedures for their own behavior in a research environment.

The RCR course is a tri-institutional program involving Weill Cornell Medicine, Sloan Kettering Institute, and The Rockefeller University. For more details, visit here.

Course Directors: Dr. Alessio Accardi and Dr. Jeremy Dittman (continuation of BPCP from Fall) 

This core course aims to build a deep quantitative understanding of the biophysical basis of cellular processes. The course is articulated in 6 modules, 3 in each semester. Each module is centered around a specific biological question and will provide students with the conceptual (i.e., theoretical basis, mathematical approaches) and practical (i.e., experimental techniques, computational approaches, analysis strategies) tools to approach them. Modules will consist of lectures, journal clubs, and Problem Based Learning classes where students present their homework solutions to the class. The course includes a grant-writing component that both cements students’ understanding of course content and teaches skills in scientific writing. 

Module 1 – Thinking on the nanoscale level: Proteins, Membranes, and Electricity introduces foundational concepts in molecular biophysics, from the basic principles of membrane and protein structure to the experimental and mathematical approaches used to quantitatively describe their function.

Module 2 – Thermodynamic principles of molecular interactions describes the thermodynamic basis of protein-protein and protein-ligand interactions with a focus on the approaches used to quantify the molecular forces that underlie them.

Module 3 –Basis of kinetics and signaling in cellular processes focuses on the principles of cellular signaling, focusing on the quantitative approaches used to describe them, from diffusion of molecules to the description of basic cellular pathways that control signaling mechanisms and membrane fusion processes.

Module 4 – Introduction to Signal Transmission analyzes the basis of signal transmission, from the generation and propagation of the action potential in the brain and heart, to the molecular basis of sensory transduction.

Module 5 – Metabolism and Signaling Associated with Decisions on Cell State presents fundamental cellular signaling pathways, from transmembrane signaling, to DNA damage response and ubiquitin signaling.

Module 6 – Integration of Signaling for Information Transmission analyzes fast signaling mechanisms such as sensory transduction and synaptic transmission.

The syllabus is available here.

Course Director: Alessio Accardi, PhD 

This year-long course exposes students to recent research developments in PBSB faculty focus areas including:  

• Biophysical and Physiological Mechanisms of Membrane and Membrane Protein Function
• Quantitative and Integrative Biology
• Organogenesis and Physiological Genomics
• Biological and Biomedical Imaging  

The syllabus is available here.

Course Directors: Dr. Christopher Mason, Dr. Robert Schwartz, and Dr. Eduard Reznik

This course is required for all 1st and 2nd year PBSB graduate students, but is open to all WGSMS students. It is designed to train students in scientific presentation and critique. The structure is a formalized, in depth "journal club." Each 1st year student will choose a paper from a list provided by the Course Directors. Each 2nd year student will select a paper in their thesis field, subject to approval of the Course Directors. Each session will consist of a student formally presenting their selected paper to the class, which is expected to serve as a critical audience. The presentation should consist of an introduction of the relevant background literature, an objective presentation of the study, a subjective analysis/critique of the work, and suggestions for future work. Presentations by 2nd year students will be scheduled first, giving the 1st year students the opportunity to learn from their more senior colleagues. Grading will be based on presentation quality and contribution to constructive feedback. 

Course Director: Alessio Accardi, PhD 

This year-long course exposes students to recent research developments in PBSB faculty focus areas including:  

• Biophysical and Physiological Mechanisms of Membrane and Membrane Protein Function
• Quantitative and Integrative Biology
• Organogenesis and Physiological Genomics
• Biological and Biomedical Imaging  

The syllabus is available here.

Course Directors: Dr. Christopher Mason, Dr. Robert Schwartz, and Dr. Eduard Reznik

This course is required for all 1st and 2nd year PBSB graduate students, but is open to all WGSMS students. It is designed to train students in scientific presentation and critique. The structure is a formalized, in depth "journal club." Each 1st year student will choose a paper from a list provided by the Course Directors. Each 2nd year student will select a paper in their thesis field, subject to approval of the Course Directors. Each session will consist of a student formally presenting their selected paper to the class, which is expected to serve as a critical audience. The presentation should consist of an introduction of the relevant background literature, an objective presentation of the study, a subjective analysis/critique of the work, and suggestions for future work. Presentations by 2nd year students will be scheduled first, giving the 1st year students the opportunity to learn from their more senior colleagues. Grading will be based on presentation quality and contribution to constructive feedback. 

See list of electives for further details.

The ACE consists of two parts: a written exam in the form of an NIH R01 proposal, and an oral exam, which includes discussion of the written research proposal. Students are expected to take this exam by July of their second year. The exam provides an opportunity for students to demonstrate that they have attained the requisite breadth of knowledge to continue in the PhD program and are prepared to undertake full-time thesis research. After completing the ACE, the student's annual (or more frequent) meetings with the Special Committee provide the forum for the student to report on his/her progress and agree upon future research directions. 

Course Director: Dr. Doug Ballon

This survey course will cover the basic physical, biochemical, computational, and engineering principles underlying current medical imaging techniques, including magnetic resonance imaging, positron emission tomography, radionuclide production and radiochemistry, optical imaging, x-ray computed tomography, and ultrasound. The goal of the course will be to provide students with a broad knowledge of the concepts and implementation strategies of various imaging methods relevant in current research and clinical practice. Practical applications will be used to illustrate the main themes of the course. Tours of the Biomedical Imaging Core Facility and other imaging laboratories will augment the formal course material. At the end of the course students will be able to identify appropriate imaging strategies for clinical research and have a working knowledge of the major techniques available to the investigator.

Course Director: Dr. Yi Wang

Prerequisite: Calculus based physics is required.

This survey course will cover the basic physical, biochemical, computational, and engineering principles underlying current medical imaging techniques including: magnetic resonance imaging, positron emission tomography, radionuclide production and radiochemistry, optical imaging, X-ray computed tomography, and ultrasound. The goal of the course will be to provide students with a broad knowledge of the concepts and implementation strategies of various imaging methods relevant in current research and clinical practice. Practical applications will be used to illustrate the main themes of the course. Tours of the Biomedical Imaging Core Facility and other imaging laboratories will augment the formal course material. At the end of the course students will be able to identify appropriate imaging strategies for clinical research and have a working knowledge of the major techniques available to the investigator. 

Syllabi are available here.

NOTE: This course is video conferenced from Ithaca most of the time.

NOTE: Taught on both the Ithaca and Weill campus by video-conference

A rigorous treatment of analysis techniques used to understand complex genetic systems. This course will cover both the fundamentals and advances in statistical methodology used to identify genetic loci responsible for disease, agriculturally relevant, and evolutionarily important phenotypes. Data focus will be genome-wide data collected for association, inbred, and pedigree experimental designs. Analysis techniques will focus on the central importance of generalized linear models in quantitative genomics with an emphasis on both frequentist and Bayesian computational approaches to inference.

Course Director: Dr. Jonathan Victor

Prerequisite: Familiarity with matrices and basic linear algebra, complex numbers, and calculus, preferably multivariate.

The course will present a range of mathematical approaches that play a central role in systems neuroscience, both for model-driven and data-driven investigations. We will take an approach beginning with the mathematical fundamentals, and emphasize concepts rather than theorems.

Typical topics include time series analysis, linear and nonlinear systems theory, point processes, dimension reduction techniques, and information theory; these can be tuned to the needs of the group. For topics, notes, and homework problems from previous years, please see: 

• http://www-users.med.cornell.edu/~jdvicto/mathcourse1011.html
• http://www-users.med.cornell.edu/~jdvicto/mathcourse0809.html 

NOTE: Offered alternating years. 

Course Director: Dr. Wesley Tansey

This course will cover the foundations of modern data science from a probabilistic modeling perspective. We will cover the basics of statistical modeling: likelihoods, priors, and posteriors. We will compare and contrast different ways to fit these models, focusing on the trade-offs made between computation and objectives like uncertainty quantification or accuracy. 

Syllabi are available here.

Course Director: Dr. Christopher Mason 

Sequencing-based research has become the dominant investigative practice within the biological sciences. Single-molecule sequencing: training, methods, and applications, responds to this development by providing a hands-on and in-depth introduction to sequencing for first year PhD and MD-PhD students, from Sanger to third-generation technologies. Utilizing an alternating lecture-lab schedule, students are introduced to fundamental basic principles of DNA & RNA science, progressing to cutting-edge library preparation and sequencing analysis techniques with Illumina and Nanopore technologies. Students will have the opportunity to perform direct-RNA sequencing samples on research samples, and experience first-hand the ethical implications of this data. Relevant concepts in biology and computer science will be addressed.

Syllabi are available here.

• Analysis of Next-Generation Sequencing Data 
• Applied Machine Learning
• Data Structures and Algorithms for Computational Biology 
• Dynamical Models in Biology 
• Functional Interpretation of High-Throughput Data