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BIOL L504 Fall 2013

Genome Biology for Physical Scientists

BIOL L504 Fall 2013

Course description


Lecture times and locations

Tues, Thur 9:30p-10:45a, Myers Hall (MY) 209

Tentative schedule (class notes can be viewed with Adobe Acrobat Reader)

btn_printerFriendly.gif version of this schedule

Tues Aug 27 0.1 Orientation
Introduction: Scope of class and resources

National Center for Biotechnology Information (NCBI), a great starting point for "anything" genomics

Current Topics in Genome Analysis 2012, a National Human Genome Research Institute lecture series:

The Genomic Landscape (Lecturer: Dr. Andy Green)
Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis)
Volker Brendel, Chun-Yuan Huang
Thur Aug 29 0.2 Proteins, DNA, and the flow of biological information Volker Brendel
Tues Sept 3 0.3 Biological Sequence Analysis II (Lecturer: Dr. Andy Baxevanis) Volker Brendel
Thur Sept 5 0.4 Chun-Yuan Huang
Tues Sept 10 1.1 Topic I: Gene structure and expression
MIT video 1
MIT video 2
MIT video 3
MIT video 4
MIT video 5
MIT video 6
Volker Brendel
Thur Sept 12 1.2 Volker Brendel
Tues Sept 17 1.3 The ENCODE project:ENCyclopedia Of DNA Elements
Nature ENCODE Explorer
A critique ...
... commented on
... and going on
Volker Brendel
Thur Sept 19 1.4 Quiz I
Tues Sept 24 2.1 Topic II: Genome content and organization
Genome Browsers (Lecturer: Dr. Tyra Wolfsberg)
Volker Brendel
Thur Sept 26 2.2 Volker Brendel
Tues Oct 1 2.3 Student presentations:

UCSC Genome Browser
Ensembl Genome Browser
NCBI MapViewer
Thur Oct 3 2.4 Quiz II
Tues Oct 8 3.1 Topic III: RNA structure and function
non-coding RNA
16S RNA Analysis
small RNA
Volker Brendel
Thur Oct 10 3.2 Volker Brendel
Tues Oct 15 3.4 Gene Silencing by Double Stranded RNA
Return to the RNAi World: Rethinking Gene Expression and Evolution
Volker Brendel
Thur Oct 17 3.4 Quiz III
Tues Oct 22 4.1 Topic IV: Protein structure and function
Overview - the protein folding problem
(lecture by Steven Skiena)
Volker Brendel
Thur Oct 24 4.2 RCSB PDB
PDB-101   - a number of wonderful tutorials!
SWISS-MODEL   - what to do if my protein is not in PDB!?
    (start here)
Volker Brendel
Tues Oct 29 DNA Sequencing James Ford
Thur Oct 31 Ecological Genomics Melissa Pespeni
Tues Nov 5 4.3 Protein structure: various topics continued Volker Brendel
Thur Nov 7 4.4 Quiz IV
Tues Nov 12 5.1 Topic V: Gene Expression Studies
NHI-NHGRI Current Topics in Genome Analysis 2012 - Paul Meltzer lecture
Volker Brendel
Thur Nov 14 5.2 iPlant Tuxedo Protocol RNA-Seq 1/2
iPlant Tuxedo Protocol RNA-Seq 2/2

Volker Brendel
Tues Nov 19 5.3 Volker Brendel
Thur Nov 21 5.4 Quiz V
Tues Dec 3 6.3 Topic VI: Molecular Evolution
BIS2C FALL2012 Lecture 4 - Parsimony Character Reconstruction and Tree Inference (Lecture by Dr. Jonathan Eisen, UC Davis)
BIS2C FALL2012 Lecture 5 - Parsimony Tree Inference (Lecture by Dr. Jonathan Eisen, UC Davis)
Volker Brendel
Thur Dec 5 6.4 Review article Volker Brendel
Tues Dec 10 7.1 Quiz VI
Thur Dec 12 7.2 Review Volker Brendel
Tues Dec 17 10:15am - 12:15pm Final Exam Students