Courses

CSCI 136(F, S) LEC Data Structures and Advanced Programming

This course builds on the programming skills acquired in Computer Science 134. It couples work on program design, analysis, and verification with an introduction to the study of data structures. Data structures capture common ways in which to store and manipulate data, and they are important in the construction of sophisticated computer programs. Students are introduced to some of the most important and frequently used data structures: lists, stacks, queues, trees, hash tables, graphs, and files. Students will be expected to write several programs, ranging from very short programs to more elaborate systems. Emphasis will be placed on the development of clear, modular programs that are easy to read, debug, verify, analyze, and modify. [ more ]

BIOL 202(F) LEC Genetics

Genetics, classically defined as the study of heredity, is today a multidisciplinary field whose principles provide critical insight and tools to most areas of biology and medicine. This course covers the experimental basis for our current understanding of the inheritance, structures, and functions of genes. It introduces approaches used by contemporary geneticists and molecular biologists to explore questions in areas of biology ranging from evolution to medicine. A primary focus of the course is on students developing familiarity with problem solving, the logic and quantitative reasoning required to understand how genetic mechanisms lead to biological patterns. The laboratory part of the course provides an experimental introduction to modern genetic analysis as well as introductions to interpreting genetic reasoning in the primary research literature. Laboratory experiments include investigating chromosome structure using microscopy, integrating multiple streams of evidence to map a mutation to the genome, determining the structure of a DNA plasmid using molecular tools. [ more ]

BIOL 305(S) LEC Evolution

This course offers a critical analysis of contemporary concepts in biological evolution. We focus on the relation of evolutionary mechanisms (e.g., selection, drift, and migration) to long term evolutionary patterns (e.g., evolutionary innovations, origin of major groups, and adaptation). Topics include micro-evolutionary models, natural and sexual selection, speciation, the inference of evolutionary history, evolutionary medicine among others. [ more ]

PSYC 312 / NSCI 322(F) SEM From Order to Disorder(s): The Role of Genes & the Environment in Psychopathology

This course examines how experimental methods in neuroscience can be used to understand the role of nature (genes) and nurture (the environment) in shaping the brain and behavior. In particular, we will explore how neuroscience informs our understanding of psychiatric disorders such as anxiety, depression, and schizophrenia. We will investigate the biological underpinning of these disorders as well as their treatments. Readings will include human studies as well as work based on animal models. Topics will include: the ways in which environmental and genetic factors shape risk and resiliency in the context of psychiatric disease, the neural circuits and peripheral systems that contribute to psychopathology, and the mechanisms through which interventions may act. In the laboratory component of the course, students will gain hands-on experience in using animal models to study complex behavior and their associated neural mechanisms. [ more ]

PHYS 315 / CSCI 315(S) LEC Computational Biology

This course will provide an overview of Computational Biology, the application of computational, mathematical, statistical, and physical problem-solving techniques to interpret the rapidly expanding amount of biological data. Topics covered will include database searching, DNA sequence alignment, clustering, RNA structure prediction, protein structural alignment, methods of analyzing gene expression, networks, and genome assembly using techniques such as string matching, dynamic programming, hidden Markov models, and statistics. [ more ]

BIOL 319 / CHEM 319 / CSCI 319 / MATH 319 / PHYS 319(S) SEM Integrative Bioinformatics, Genomics, and Proteomics Lab

What can computational biology teach us about cancer? In this lab-intensive experience for the Genomics, Proteomics, and Bioinformatics program, computational analysis and wet-lab investigations will inform each other, as students majoring in biology, chemistry, computer science, mathematics/statistics, and physics contribute their own expertise to explore how ever-growing gene and protein data-sets can provide key insights into human disease. In this course, we will take advantage of one well-studied system, the highly conserved Ras-related family of proteins, which play a central role in numerous fundamental processes within the cell. The course will integrate bioinformatics and molecular biology, using database searching, alignments and pattern matching, and phylogenetics to reconstruct the evolution of gene families by focusing on the gene duplication events and gene rearrangements that have occurred over the course of eukaryotic speciation. By utilizing high through-put approaches to investigate genes involved in the inflammatory and MAPK signal transduction pathways in human colon cancer cell lines, students will uncover regulatory mechanisms that are aberrantly altered by siRNA knockdown of putative regulatory components. This functional genomic strategy will be coupled with independent projects using phosphorylation-state specific antisera to test our hypotheses. Proteomic analysis will introduce the students to de novo structural prediction and threading algorithms, as well as data-mining approaches and Bayesian modeling of protein network dynamics in single cells. Flow cytometry and mass spectrometry may also be used to study networks of interacting proteins in colon tumor cells. [ more ]

BIMO 321 / BIOL 321 / CHEM 321(F) LEC Biochemistry I: Structure and Function of Biological Molecules

This course introduces the foundational concepts of biochemistry with an emphasis on the structure and function of biological macromolecules. Specifically, the structure of proteins and nucleic acids are examined in detail in order to determine how their chemical properties and their biological behavior result from those structures. Other topics covered include catalysis, enzyme kinetics, mechanism and regulation; the molecular organization of biomembranes; and the flow of information from nucleic acids to proteins. In addition, the principles and applications of the methods used to characterize macromolecules in solution and the interactions between macromolecules are discussed. The laboratory provides a hands-on opportunity to study macromolecules and to learn the fundamental experimental techniques of biochemistry including electrophoresis, chromatography, and principles of enzymatic assays. [ more ]

BIMO 322 / BIOL 322 / CHEM 322(S) LEC Biochemistry II: Metabolism

This lecture course provides an in-depth presentation of the complex metabolic reactions that are central to life. Emphasis is placed on the biological flow of energy including alternative modes of energy generation (aerobic, anaerobic, photosynthetic); the regulation and integration of the metabolic pathways including compartmentalization and the transport of metabolites; and biochemical reaction mechanisms including the structures and mechanisms of coenzymes. This comprehensive study also includes the biosynthesis and catabolism of small molecules (carbohydrates, lipids, amino acids, and nucleotides). Laboratory experiments introduce the principles and procedures used to study enzymatic reactions, bioenergetics, and metabolic pathways. [ more ]

BIOL 330(S) LEC Genomes: Structure, Function, Evolution

Genome sequencing technologies have opened the "book of life" to biologists. But making sense of genomes is still a work in progress. This course will examine central features of genomes, their evolution, and their contribution to human diseases such as cancer. Genome biology is a new field, and this presents the opportunity to learn science as it is being done. Biologists working today started out knowing nothing about core features of genomes, such as why most of the DNA is repetitive, or why segments of genes get removed in the RNA, or why silenced genes wake up in cancer cells. They began to find meaning by adopting dual perspectives of function and neutral evolution. Students will learn to walk these same paths and learn to evaluate for themselves what genome complexity means. In lab, students will develop hands-on and computational skills for investigating genome structural variation, then apply them in the second half of the semester in independent lab investigations. [ more ]

STAT 410 LEC Statistical Genetics

Last offered Fall 2019

Genetic studies explore patterns of genetic variation in populations and the effect of genes on diseases or traits. This course provides an introduction to statistical and computational methods for genetic studies. Topics will include Mendelian traits (such as single nucleotide polymorphisms), genome-wide association studies, pathway-based analysis, and methods for population genetics. Students will be introduced to some of the major computational tools for genetic analysis, including PLINK and R/Bioconductor. The necessary background in genetics and biology will be provided alongside the statistical and computational methods. [ more ]

BIOL 430 TUT Genome Sciences: At the Cutting Edge

Last offered Spring 2020

Research in genomics has integrated and revolutionized the field of biology, including areas of medicine, plant biology, microbiology, and evolutionary biology. Moreover, recent developments in "metagenomics" (genomic studies of entire communities of microorganisms in natural environments, such as the mammalian gut and the deep sea) and "metatranscriptomics" (studies of genome wide changes in expression and mRNA levels in natural communities of organisms) have generated unprecedented knowledge about the genomic potential of a community and the in situ biological activity of different ecological niches. In this course we will explore how research in these and related areas, including proteomics, have advanced our fundamental understanding of (1) organisms in the three domains of life, and their interactions and evolutionary relationships; (2) biological systems and environments, such as the human body, extreme environments, and the oceans; (3) strategies for solving global challenges in medicine, agriculture, energy resources, and environmental sciences. During the course, students will meet each week for one hour with a tutorial partner and the instructor. Every other week, students will present a written and oral critical analysis of the assigned research articles. On alternate weeks, students will question/critique the work of their colleague. [ more ]