A Functional Genomics Blog

Welcome to Functional Genomics BMB550

functionalgenomics — Fri, 01 Jan 2010 23:00:23 +0000

Welcome to the web site for the University of Maine Functional Genomics graduate course (BMB550).

The course syllabus for Winter/Spring 2012 is here (pdf).

Update: January 24, 2012: The revised course syllabus for Winter/Spring 2012 is here . (pdf)

Key Dates:
February 23: Interim project presentations
February 28- March 13: Spring Break
April 19: Final project presentations
April 24: Final project presentations
April 26: Final report due

Updated January 29, 2012

Lecture 1: Course introduction (Carol Bult)

functionalgenomics — Fri, 01 Jan 2010 22:59:12 +0000

This lecture introduced the course structure and expectations.

Lecture 1 slides are here (ppt)

Lecture 2: Genome Structure and Variation (Keith Hutchison)

functionalgenomics — Fri, 01 Jan 2010 22:58:29 +0000

January 12, 2012
Lecture 2 covered the topic of genome structure and variation.

Lecture 2 can be found here (ppt).

For a recent article on this topic, see Rohs et al. The role of DNA shape in protein-DNA recognition. Nature 461:1248

Material updated January 29 2012

Lecture 3: Epigenetics (Keith Hutchison)

functionalgenomics — Fri, 01 Jan 2010 22:27:00 +0000

17 January 2012
In lecture 3 the topic of epigenetics was covered.

Lecture 3 notes for 2012 are here (ppt).

Lecture 3 manuscript (Law and Jacobsen. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics. 2010) is here (pdf).

Material updated January 29 2012

Lecture 4: Transcriptomics using Next Gen Sequencing (Doug Hinerfeld)

functionalgenomics — Fri, 01 Jan 2010 22:26:52 +0000

19 January 2012

Lecture 4 will cover the topic of using Next Generation Sequencing technology for transcriptomics.

Lecture 4 materials are here (pdf).

Updated January 2012.

Lectures 5 and 6: Gene Expression Technology and Resources (Carol Bult)

functionalgenomics — Fri, 01 Jan 2010 22:25:16 +0000

24 and 26 January 2012

Introductory slides about the Maine Innovation Cloud and Linux are here (pptx)

Video clips on Linux commands:

logging in to your linux account (avi)
ls and man commands (avi)
various commands (mkdir, rm, cp, pwd) (avi)

These lectures will cover microarray technology as well as gene expression data resources.

Slides about microarray technology are here (ppt)

Slides about the GEO gene expression resource are here (ppt)

Resources:
Visit the Gene Expression Omnibus (GEO) archive at NCBI.

Reading materials for Lecture 5:

About the Gene Expression Omnibus Resource

About NCBI resources

Materials updated January 26 2012.

Lecture 7 and 8: Introduction to R (Carol Bult)

functionalgenomics — Fri, 01 Jan 2010 22:24:49 +0000

January 31, 2012
February 3, 2012

Lectures 7 and 8 will focus on an introduction to the R statistical programming environment. We will also review how to get R started on the Maine Innovation Cloud.

Slides for lecture 7 are here (ppt)

Here is a useful resource describing bioinformatic analysis of microarray data here (pdf).

Lecture 9: Experimental Design (Gary Churchill)

functionalgenomics — Fri, 01 Jan 2010 22:24:00 +0000

February 7, 2012

Lecture 9 will focus on experimental design for microarray experiments.

Slides for lecture 9 are here (pdf)

Papers to read for lecture 6 background:

Lectures10 and 11: Normalization (Matt Hibbs)

functionalgenomics — Fri, 01 Jan 2010 22:20:11 +0000

February 9, 2012
February 14, 2012

These lectures will cover the topic of microarray data normalization.

Here is an article by John Quackenbush normalization

Here is an article on RMA normalization

Lecture 12 -15: Gene Expression Analysis (Carol Bult)

functionalgenomics — Fri, 01 Jan 2010 22:18:52 +0000

February 16, 2012
February 21, 2012
March 15, 2012
March 20, 2012

The lecture slides are here