BCB-Related Spring Courses

November 6, 2015

Spring 2016 Courses to Consider


EEOB 590B-TH Macroevolution & Lineage Diversification, 2 credit seminar

Instructor: Tracy Heath, EEOB, 243 Bessey Hall; email: phylo@iastate.edu

The time will be determined based on those registered.


A graduate seminar on phylogenetic methods for understanding rates of diversification. Find the below info at: http://phyloworks.org/courses/macrodiv.html

This seminar course will focus on methods for understanding patterns of biodiversity in the Tree of Life. We will review current phylogenetic approaches for estimating rates of speciation and extinction through some lectures, studying recent papers applying these methods (such as Jetz et al. 2012 The global diversity of birds in space and time. Nature), and mini workshops. Also note that this course is an approved EEB 698 course.

Phylogenetic methods for diversification include:

  •     topological tests of variable rates of diversification
  •     speciation-extinction models
  •     methods for detecting shifts in diversification over time
  •     lineages through time plots
  •     state-dependent diversification
  •     understanding the diversification of rapidly evolving infectious diseases

Familiarity with phylogenetic trees and evolutionary biology will be assumed.

Com S 551: Parallel Computational Techniques for Analyzing Huge Genome Sequence Data

Instructor: Xiaoqiu Huang at xqhuang@iastate.edu, Time:  T R 2:10PM--3:30PM, Location:  Atanasoff 213


This course will give an introduction to the hot Big Data research area in bioinformatics. An organism's genome carries most of the genetic instructions for its development, functioning and reproduction. This course will focus on applying parallel computational techniques to huge genomic sequence data to find genome variation between individuals of an organism.

These techniques include finding an optimal sequence alignment by dynamic programming, parallel programming with MPI, using a Linux cluster with distributed memory, performing a genome assembly, and mapping DNA sequences onto a genome assembly. These techniques can be used to find single-nucleotide variants (SNVs) and copy-number variants (CNVs) in 100-Gb of compressed human sequence data in a day on a single compute node of a cluster.

Students with different backgrounds are encouraged to team up in groups to work on a research project in Genomics.

Prerequisites: Graduate standing in Computer Science or Biology/Genetics/Evolution.

About the Professor: Xiaoqiu Huang has developed several versions of a genome assembly program for next-generation sequencing data. His current research is focused on understanding genome evolution and function by using genome sequence data.

GDCB576X, Comparative Genomics and Phenomics

Tuesday and Thursday, 11 am-12:20 noon (3 cr., location TBD)

Instructor: Prof. Xun Gu, 536 Science II, 4-8075, xgu@iastate.edu


Phenomics is the systematic study of phenotypes, and the use of high-throughput data to refine models for how genetic information is translated to phenotypic traits.  The emergence of phenomics is a paradigm-shifting advance in the genome sciences.  Young scientists will have tremendous opportunities in this field, including interdisciplinary research initiatives on the ISU campus.  This course will provide students with foundational knowledge and skills to make advances in comparative genomics and phenomics.

In this course, students will address:

  1. How are genomic differences related to organismal differences in morphology or fitness?  What is known?  What is unknown?
  2. Why are scientists excited about the potential of high-throughput phenomics?  What knowledge or skills do we need to succeed in this field?

Learning Outcomes:  

  • Students will improve their understanding of current theory and practice in comparative genomics and phenomics.
  • Students will learn current methods for mapping phenotypes to genomic locations.
  • Students will be able to describe representative genomic changes that underlie the evolution of traits.
  • Students will learn methods for comparative transcriptome analysis.
  • Students will synthesize information in the production of publication-ready reviews.

Course structure and prerequisites:  The 3-cr course is lecture and discussion‐based. The prerequisite is an introductory course in genomics such as BCBio322, BCBio444, Gen349 or similar. Emphasis will be given on student participation in literature reviews, discussions and written reports as a group. Individual students will be required to write term papers on special topics for class discussions and presentations.

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