University of Oregon

John S. Conery

Professor Emeritus

Department of Biology

Institute of Ecology and Evolution


Selected papers from bioinformatics and computational biology projects are listed below. Additional links can be found on my publications page.

Sequence alignment using information theory

Workflow management

Conserved synteny (with Julian Catchen and John Postlethwait)

Neural network models of chemotaxis (with Nathan Dunn and Shawn Lockery)

A "datamart" for tRNA sequences (with Peggy Saks)

Gene duplication (with Mike Lynch)


Explorations in Computing (Taylor & Francis / CRC Press, 2011) is a textbook for CS0 or advanced high school courses on "computational thinking." Instead of teaching students how to write programs, the approach here is to have students develop a basic "literacy" so they can work on projects using software already written in Ruby.

Explorations in Computing: An Introduction to Computer Science and Python Programming (Taylor & Francis / CRC Press, 2014) features new projects and includes an introduction to programming concepts. This version was written for CS1 courses that want to introduce students to "big ideas" in computer science as part of their first-year curriculum.


The 16S rRNA analysis pipeline developed for the META Center uses a MySQL database to store results of each stage of the analysis, taking advantage of normalized tables to reduce space and optimize I/O patterns when running on a compute server.

nbscan is a command line script for working with Jupyter notebooks, especially those managed by nbgrader.


Bi 410 is an introduction to computer programming for Biology majors. Students learn basic programming concepts, how to write scripts to implement their own analysis pipelines, and Python libraries for data analysis and visualization.

CIS 211 is the second course in a year-long introduction to computer science for CS majors. Jupyter notebooks were used for lecture notes and projects in Spring 2017.