ECOL 346 - Bioinformatics

TENTATIVE SCHEDULE

Date

Topic

Lecturer

Readings/HomeWork

Slides

1/11

Introduction to the Course & The Unix Command Line

Barker

None

Introduction

1/18

Working on the Unix Command Line

Barker

None

Unix Introduction

1/23

Introduction to Perl

Barker

seqsHW01.txt, HW01.pdf, Learning Perl Chapters 1 & 5

Perl Introduction

1/25

Basics of Perl Scripting

Barker

est_cluster.txt, HW02.pdf, Learning Perl Chapters 2 & 3

Scalars & Arrays

1/30

Perl Scripting Continued

Barker

HW03.pdf, Ceratopteris1.fasta, Ceratopteris2.fasta, Learning Perl Chapters 6, 7, 8, 9, and 10

More Perl

2/1

Wrapping up Perl Intro

Barker

Blast Search Introduction PDF or Link Example Solutions to Previous HW: Mike_HW03.zip

2/6

Introduction to Biological Databases, Search Algorithms, and Clustering Sequences

Barker

HW04.pdf

Genomic Databases & BLAST Intro

2/8

Advanced BLAST Searching

Barker

HW05.pdf, Readings: Genome Sequence Assembly Primer and Assembly of Large Genomes using Second-Generation Sequencing

Advanced BLAST Searching

2/13

Shotgun Sequencing

Barker

Shotgun Sequencing

2/15

Assembling Genomic Data

Barker

Genome Assembly

2/20

Data Assembly Cont.

Barker

HW06.pdf Example BLAST Parsing Scripts blast_parsers.zip

Data Assembly Cont

2/22

Circumscribing Gene Families

Barker

HW07.pdf, Step by Step Guide to Building a Phylogeny Harrison & Langdale 2006

Gene Families

2/27

Building Gene Trees

2/29

Orthologs, Paralogs, and Species Trees

3/5

Midterm 1

3/7

Gene Ontology and Annotation

3/19

Comparative Genomics and Synteny Evolution

3/21

Ancestral Genome Reconstruction

3/26

Natural Variation in Genomic Data I: SNPs & CNVs

3/28

Natural Variation in Genomic Data II: Selection and Demographic History

4/2

Genome Wide Association Studies

4/4

Variation in Gene Expression I: Quantifying gene expression

4/9

Variation in Gene Expression II: Cis vs trans divergence

4/11

Networks of Genes

4/16

Taxonomic and Phenotypic Databases

4/18

Midterm 2

4/23

Biogeographic Data and Niche Modeling

4/25

Group Presentations

4/30

Group Presentations

5/2

Group Presentations