ECOL-346 Bioinformatics, Spring 2019

Meets:

Lectures 12:30–1:45 PM, Tue Thu, ENR2 N250

Labs 9:00–10:50 AM, Thu, ENR2 N250

Instructors:

Dr. Mike Barker; BioSciences West 321E; 520-621-2213; msbarker@email.arizona.edu

TA: Joe Braasch; BioSciences West ; jbraasch@email.arizona.edu 

Office Hours:

Barker: 2:00–3:00 PM, Monday, BioSciences West 321E

Braasch: 2:30–3:30 PM, Tuesday, BioSciences West 333

Full Syllabus

Mid-Term Exam: Thursday, February 28

Final Exam: Wednesday, May 8, 1:00 - 3:00 PM

Summer Internships & Positions:

https://cepceb.ucr.edu/reu/

http://careers.cbd.cmu.edu/

Tensor Flow at Google Summer of Code: https://summerofcode.withgoogle.com/organizations/?sp-search=tensor#6137730124218368

Rise program in Germany: https://www.daad.de/deutschland/stipendium/datenbank/en/21148-scholarship-database/?detail=50020910

http://stemdiv.ucsc.edu/prep/ 


COURSE SCHEDULE (Updated Weekly)

Labs are Highlighted in Orange

Date

Topic

HW/Lab Assignment

Readings

1/10

Introduction

Reading Responses: Questions and Answers

Reading Responses: Questions Only

1/15

Genomic Big Data

Reading Assignment Instructions

Goodwin et al. 2016 “Coming of Age: Ten years of next-generation sequencing technologies” 

&

Stephens et al. 2015 “Big Data: Astronomical or Genomical?”

1/17

Group Project Proposal Pitches

Idea Board!

1/17

Genomic Databases

HW 1

1/22

Pairwise Alignment & Dynamic Programming

Reading Assignment Instructions

&

HW 2

Alignment Introduction & Wiki

1/24

Group Project Organization

Project Proposal

1/24

Pairwise Alignment & Dynamic Programming

1/29

BLAST

Reading Assignment Instructions

HPC Account Signup Directions

Having a BLAST with Bioinformatics

1/31

Lab: HPC Tour & Job Submission

(Location: Computer Center Lab 130A)

BLAST Lab Exercise

Unix/Linux Tutorial, Unix/Linux Cheat Sheet

1/31

BLAST

2/5

NO CLASS

2/7

Complete last week’s BLAST lab and this week’s assignment.

BLAST Lab 2

2/7

Substitution Matrices

Pearson 2014

&

Dayhoff Biography; Strasser 2006 

2/12

Genome Assembly

Readings for Discussion and Questions:

Richards 2018: Genome assembly is still hard

Tan et al. 2018: Finding Nemo: Hybrid Illumina and Nanopore Assembly of clownfish

Jain et al. 2018: Nanopore sequencing and assembly of a human genome

Background Reading:

Genome Assembly Primer: http://www.cbcb.umd.edu/research/assembly_primer

DeBruijn Graph Assembly

& Flicek and Birney 2009

2/14

Group Projects

2/14

Genome Assembly

Example Graphs

2/19

Genome Assembly Continued

No New Readings for 2/19

2/21

Project Proposal Checkpoint Talks

2/21

Genome Annotation

2/26

Assembly Exercise

2/28

Exam Study Time

2/28

MID-TERM EXAM

SPRING BREAK

3/12

Gene Families & Orthology

Between a chicken and a grape

3/14

Group Projects

3/14

Ortholog Conjecture Discussion

Of mice and men: or revisiting the ortholog conjecture

Nehrt et al. 2011

Sonnhammer et al. 2014

3/19

Populations (Andrea & Chad)

Andrews and Luikart 2014

Gamble 2016

3/21

Group Projects

3/21

Kyle

3/26

Minhao & Drake

McDonald & Kreitman 1991

Arensburger et al. 2005

3/28

Group Project Checkpoint Presentations

3/28

Michael & Alex

4/2

Brandon & Samantha

4/4

Group Projects

4/4

Andrew & Ryan

4/9

Ash

4/11

Group Projects

4/11

Yandi

4/16

Rick & Emily

4/18

Group Projects

4/18

Machine Learning

4/23

Bioinformatics Wrap-Up

4/25

Group Projects

4/25

Final Project Presentations (Part 1)

Final Project Papers Due

4/30

Final Project Presentations (Part 2)

5/8

Final Exam

1 - 3 PM


Please send questions or comments about website to Mike Barker