GENOMICS

BMGN 7620 (also CPBS & HMGP 7620), in Spring 2011, will introduce graduate students (and interested postdocs and faculty) to the field of genomics. An optional computer workshop will provide students with the minimal skills necessary to access databases, download and manipulate large datasets, and to visualize and interpret results.

The lecture course is designed and directed by Profs. Pollock, Johnston, and Sikela, with guest lectures by Hunter, Martin, Shaikh, Castoe, Kechris, Hansen, Davis, Spritz, Taylor, Harris, and Hesselberth.

Computational Section Director is Jason de Koning, and Assistant Director are Michael Dickens and Ken Yokoyama.

First class is January 25. Lectures (2 units) are TuTh 10:45-11:45 RC1N Rm 6107 (aim for 1 hour, time for post-lecture discussions afterwards).

Optional workshop (1 unit) is W 3-5, Ed II North, room 2201 AB. See FAQ for more info.

NEW

Final exam is now available (Friday, May 13).

New recordings are up on the abstract page (and some old ones are now fixed).

MIDTERM. Please find the Midterm here. (pdf version).

Midterm is coming up Thursday March 24. Will be available online at 10:45 am. Please follow normal take-home test guidelines and do not discuss the test with anyone else until after you (and they, if in class) have completed and it is returned to me. It is due back by email to David dot Pollock at the usual by 12:00 pm (noon) the following Monday.

In March, many of the lecture links got messed up. I am trying to fix them. Please let me know asap if something you need is still missing.

Lectures are supposed to be up through March 22.

Jason's lectures are also linked on his blog.

Thanks to Seth Welsh for a bunch of lecture recordings that are now up on the abstract page.

Put up substitute lecture notes for cancelled Feb 10 lecture.

The site has been revised for Spring 2011. If you see anything that is out of date please let DP know.

Jason is running a blog for the course.

NOTICES

A requirement of the workshop is commitment to the entire semester, and priority focus is on graduate students and people who do not necessarily know anything about programming. Thanks, David, Mark, Jim, Jason, Ken, and Michael.

MATERIALS AND LINKS

Genomics Flyer (pdf)

Course Syllabus (pdf)

Genomics FAQ (pdf)

Lecture Schedule

Lecture Abstracts and Materials

Workshop Schedule, Abstracts and Materials

Course Blog

Recommended Reading

A Primer of Population Genetics (Hartl).

Introduction to Genomics (Lesk), A Primer of Genome Science (Gibson and Muse), Genomes (Brown), Genomes (TA Brown).

Other Related Reading

Books:Modern Genetic Analysis (Griffiths, Gelbart, Lewontin, Miller), Discovering Genomics, Proteomics and Bioinformatics (Campbell, Heyer), Bioinformatics and Functional Genomics (Pevsner), Introduction to Computational Genomics (Cristiani, Hahn), Inferring Phylogenies (Felsenstein), Genetics: Analysis of Genes and Genomes (Hartl, Jones).

NIH Online Books: Computational Approaches in Comparative Genomics (Koonin & Galperin), Comparative Genomics (Bergman), Modern Genetic Analysis (Griffiths, Gelbart, Lewontin, Miller), The NCBI Handbook (McEntyre & Ostell), Genetics for Surgeons (Morrison, Spence), Diffusion and use of Genomic Innovations in Health and Medicine (Hernandez et al).

Light Reading: Genome, the Autobiography of a Species in 23 Chapters (Ridley); Bioinformatics for Dummies (Claverie), Welcome to the Genome (DeSalle, Yudell); Genomes and What to Make of Them (Barnes, Dupre), The Genome War (Shreeve).

Note: many of these items have not been checked for quality and relevance. Please contact us with opinions on/reviews of these materials if you check them out. Also, please provide other suggestions and we will put them up.