The goal of this course is to develop a deeper understanding of techniques and concepts used in Computational Biology. Both theoretical and practical aspects of a range of methods will be covered. Theoretical aspects will include statistical analysis, modeling, and algorithm design. This course cannot provide a comprehensive survey of the field but focuses on a select core set of topics and data types. We will discuss the genome browser, alignment algorithms, classical and non-parametric statistics, pathway analysis, dimensionality reduction, GWAS, multiple testing and machine learning, with primary focus on biomedical data. UNIX, R and Python will be utilized to learn to execute big data analysis pipelines, including RNA-Seq and DNA-Seq. UNIX and R will be taught from first principles but programming experience in Python is expected. Students without prior experience with Python should consider taking PHYS 1100 before taking this class. You will be provided with a computational (cloud based) platform on which to do all programming and assignments.

Introduction to basic theoretical tools to study the evolutionary and ecological dynamics of populations. Topics to be discussed include: basic population dynamics and population genetics theory, evolutionary game theory/adaptive dynamics, social evolution (kin selection/multilevel selection), life-history evolution, and stochastic models. Other topics may be added based on the specific interests of students in the class.

This course will focus on fundamental topics related to the ecological and evolutionary processes driving the transmission of pathogenic microbes among hosts including life-history strategies; evolution of pathogenic traits; the impacts of temporal, spatial and host-trait heterogeneity; and factors causing the emergence of an infectious pathogen. Examples will be drawn from human, wildlife, and plant pathogens to illustrate these ecological and evolutionary topics. Students will learn to develop and apply current ecological and evolutionary theory to infectious microbe research and gain practical experience accessing, interpreting and synthesizing the peer-reviewed scientific literature through a combination of popular and scientific readings, discussion, and lecture.

This course is designed for advanced undergraduate and graduate students who are interested in molecular physiology of sensory signal transduction. The major topics to cover will be signal transduction mechanisms used by membrane ion channels and receptors that detect the sensory stimuli (light, sound, temperature, smell and taste, for example) and transmit the signals to the nervous system. Modern molecular, genetic and structural techniques (electrophysiology, protein structural determination/analysis, animal genetics, and human disease, for example) will be introduced along with each topic. References will be primary research articles. Students will critically evaluate research discoveries through analysis of research papers. Each student will deliver two presentations and write a 10-page research proposal.

This course will focus on the molecular basis of neurological diseases, exploring in detail key papers that cover topics including defining the disease genes, development of animal models that provide mechanistic insight, and seminal findings that reveal molecular understanding. Diseases covered will include neurological diseases of great focus today such as Alzheimer's, Fragile-X and autism, dementia, motor neuron degeneration, and microsatellite repeat expansion disorders. The course will provide a perspective from initial molecular determination through current status. Students will gain an understanding of how the molecular basis of a disease is discovered (from classical genetics to modern genomics) and how such diseases can be modeled in simple genetic systems for mechanistic insight. The course will be comprised of lectures with detailed analysis of primary literature and in-class activities. Grading will be based on class participation, exams, and written papers. Biology 2210 is a pre-requisite. Seniors are prioritized for the course

This course focuses on the current state of our knowledge about the neurobiological basis of learning and memory. A combination of lectures and student seminars will explore the molecular and cellular basis of learning in invertebrates and vertebrates from a behavioral and neural perspective.

Cytoskeleton and cell motility plays a crucial role in many aspects of normal and pathological physiology of individual cells, tissues, and whole organisms, including morphogenesis, immune response, wound healing, oncogenesis, and infection. This course will cover current topics in cell biology with emphasis on cytoskeleton and cell motility and their roles in these processes. Lectures, student presentations, and discussions in the class will be based on primary scientific literature.

This course will focus on the molecular mechanisms by which fundamental cellular processes are disrupted in the development of cancer.

Early development of microbiology, pathology, and immunobiology; molecular and cellular bases of immune phenomena including: immunity to pathogens, immune diseases, autoimmunity, and hypersensitivity. This course is open to students in the College of Liberal and Professional Studies only.

This course will focus on plants and climate change in the urban setting, specifically the city of Philadelphia. We will examine the role of plants in urban food, ancestral traditions, community, health & wellbeing, also the ecosystems benefits of plants. We will explore challenges faced by plants and ecosystems due to environmental changes, land use change, and differential access to green spaces. We will discuss plant biological, genetic, breeding, and ecological solutions for enhancing plant resilience. Students will gain hands-on experience, engage in dialog with farm, garden and ecosystem practitioners, as well as city officials and other support systems, NGOs and small businesses. Dialog will occur both on visits to local gardens, farms, or parks with representatives and stakeholders or on campus with guest speakers and each other. Students will develop project ideas, educational materials, plans, or designs that detail possible solutions to problems identified during their investigations. Activities will intersect with to those of PlantARC https://web.sas.upenn.edu/plantarc/