date_range Starts on March 15, 2016
event_note End date December 31, 2016
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assignment Level : Introductive
chat_bubble_outline Language : English
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About the content

We begin with an introduction to the biology, explaining what we measure and why. Then we focus on the two main measurement technologies: next generation sequencing and microarrays. We then move on to describing how raw data and experimental information are imported into R and how we use Bioconductor classes to organize these data, whether generated locally, or harvested from public repositories or institutional archives. Genomic features are generally identified using intervals in genomic coordinates, and highly efficient algorithms for computing with genomic intervals will be examined in detail. Statistical methods for testing gene-centric or pathway-centric hypotheses with genome-scale data are found in packages such as limma, some of these techniques will be illustrated in lectures and labs.

Given the diversity in educational background of our students we have divided the series into seven parts. You can take the entire series or individual courses that interest you. If you are a statistician you should consider skipping the first two or three courses, similarly, if you are biologists you should consider skipping some of the introductory biology lectures. Note that the statistics and programming aspects of the class ramp up in difficulty relatively quickly across the first three courses. By the third course will be teaching advanced statistical concepts such as hierarchical models and by the fourth advanced software engineering skills, such as parallel computing and reproducible research concepts.

These courses make up 2 XSeries and are self-paced:

PH525.1x: Statistics and R for the Life Sciences

PH525.2x: Introduction to Linear Models and Matrix Algebra

PH525.3x: Statistical Inference and Modeling for High-throughput Experiments

PH525.4x: High-Dimensional Data Analysis

PH525.5x: Introduction to Bioconductor: annotation and analysis of genomes and genomic assays 

PH525.6x: High-performance computing for reproducible genomics

PH525.7x: Case studies in functional genomics


This class was supported in part by NIH grant R25GM114818.

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Syllabus

  • Introduction to high-throughput technologies
    • Next Generation Sequencing
    • Microarrays
  • What we measure with high-throughput technologies and why
  • Preprocessing and Normalization
  • The Bioconductor Genomic Ranges Utilities
  • Genomic Annotation
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Intructors

  • Rafael Irizarry
  • Michael Love
  • Vincent Carey
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Harvard University is a private Ivy League research university in Cambridge, Massachusetts. Established in 1636 and named for its first benefactor clergyman John Harvard, Harvard is the United States' oldest institution of higher learning, and its history, influence, and wealth have made it one of the world's most prestigious universities. The Harvard Corporation is its first chartered corporation. Although never formally affiliated with any denomination, the early College primarily trained Congregational and Unitarian clergy. Its curriculum and student body were gradually secularized during the 18th century, and by the 19th century, Harvard had emerged as the central cultural establishment among Boston elites. Following the American Civil War, President Charles W. Eliot's long tenure (1869–1909) transformed the college and affiliated professional schools into a modern research university; Harvard was a founding member of the Association of American Universities in 1900. A. Lawrence Lowell, who followed Eliot, further reformed the undergraduate curriculum and undertook aggressive expansion of Harvard's land holdings and physical plant. James Bryant Conant led the university through the Great Depression and World War II and began to reform the curriculum and liberalize admissions after the war. The undergraduate college became coeducational after its 1977 merger with Radcliffe College.

The university is organized into eleven separate academic units—ten faculties and the Radcliffe Institute for Advanced Study—with campuses throughout the Boston metropolitan area: its 209-acre (85 ha) main campus is centered on Harvard Yard in Cambridge, approximately 3 miles (5 km) northwest of Boston; the business school and athletics facilities, including Harvard Stadium, are located across the Charles River in the Allston neighborhood of Boston and the medical, dental, and public health schools are in the Longwood Medical Area. The endowment of Harvard's is worth $37.1 billion, making it the largest of any academic institution.

Harvard is a large, highly residential research university. The nominal cost of attendance is high, but the university's large endowment allows it to offer generous financial aid packages. The Harvard Library is the world's largest academic and private library system, comprising 79 individual libraries holding over 18 million items. The University is cited as one of the world's top tertiary institutions by various organizations.

Harvard's alumni include eight U.S. presidents, several foreign heads of state, 62 living billionaires, 359 Rhodes Scholars, and 242 Marshall Scholars. To date, some 157 Nobel laureates, 18 Fields Medalists, and 14 Turing Award winners have been affiliated as students, faculty, or staff. In addition, Harvard students and alumni have won 10 Academy Awards, 48 Pulitzer Prizes, and 108 Olympic medals (46 gold, 41 silver and 21 bronze).

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