Genome Biology for Computational and Physical Scientists

BIOL L504 Fall 2014


Course description

BIOL L504 GBPS

Lecture times and locations

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

Tentative schedule

HTML version of this schedule

DAYDATELECTURETOPICLECTURER
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
Students
Thur Oct 3 2.4 Quiz II
Tues Oct 8 3.1 Topic III: RNA structure and function
non-coding RNA
16S RNA Analysis
siRNA
small RNA
Eterna
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

NCBI GEO
Volker Brendel
Tues Nov 19 5.3 Volker Brendel
Thur Nov 21 5.4 Quiz V
Tues Nov 26 THANKSGIVING BREAK n/a
Thur Nov 28 THANKSGIVING BREAK n/a
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