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CHEM 319
Integrative Bioinformatics, Genomics, and Proteomics Lab Spring 2021
Division III Quantative/Formal Reasoning
Cross-listed MATH 319 / CHEM 319 / BIOL 319 / PHYS 319 / CSCI 319

Class Details

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.
The Class: Format: seminar/laboratory; two afternoons of lab, with one hour of lecture, per week. In most weeks, we will meet one day for lecture discussions.
Limit: 12
Expected: 12
Class#: 4796
Grading: yes pass/fail option, yes fifth course option
Requirements/Evaluation: lab participation, several short homework assignments, one lab report, a programming project, and a grant proposal
Prerequisites: BIOL 202; students who have not taken BIOL 202 but have taken BIOL 101 and a CSCI course, or CSCI/PHYS 315, may enroll with permission of instructor. No prior computer programming experience is required.
Enrollment Preferences: seniors, then juniors, then sophomores
Unit Notes: does not satisfy the distribution requirement for the Biology major
Distributions: Division III Quantative/Formal Reasoning
Notes: This course is cross-listed and the prefixes carry the following divisional credit:
MATH 319 Division III CHEM 319 Division III BIOL 319 Division III PHYS 319 Division III CSCI 319 Division III
QFR Notes: Through lab work, homework sets and a major project, students will learn or further develop their skills in programming in Python, and about the basis of Bayesian approaches to phylogenetic tree estimation.
Attributes: BIGP Courses
BIMO Interdepartmental Electives

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