John S. Conery

Professor Emeritus

Department of Biology

Institute of Ecology and Evolution

conery@uoregon.edu

Research

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

Conery, J. S. Aligning sequences by minimum description length. EURASIP Journal on Bioinformatics and Systems Biology. doi:10.1155/2007/72936, 2007.

Workflow management

Conery, J.S., Catchen, J.M., and Lynch, M. Rule-based workflow management for bioinformatics. VLDB Journal 14(3): 318-329, 2005.

Conserved synteny (with Julian Catchen and John Postlethwait)

Catchen, J. M., Conery, J. S., and Postlethwait, J. H. Automated identification of conserved synteny after whole-genome duplication. Genome Res 19(8):1497–1505, 2009.
Catchen, J., Conery, J. S., and Postlethwait, J. H. Inferring ancestral gene order. Methods in Molecular Biology 452 (3), 365-383, 2008

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

Dunn, N. A., Conery, J. S., and Lockery, S. R. Circuit motifs for spatial orientation behaviors identified by neural network optimization. J Neurophysiol 98(2):888–897, 2007.
Dunn, N. A., Pierce-Shimomura, J. T., Conery, J. S., and Lockery, S. R. Clustered neural dynamics identify motifs for chemotaxis in Caenorhabditis elegans. International Joint Conference on Neural Networks, pp. 547–554, 2006.

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

Saks, M. E. and Conery, J. S. Anticodon-dependent conservation of bacterial tRNA gene sequences. RNA 13(5):651–660, 2007.

Gene duplication (with Mike Lynch)

Lynch, M. and Conery, J.S. The origins of genome complexity. Science 302 (5649), 2003, pp. 1401-04.
Lynch, M. and Conery, J.S. The evolutionary fate and consequences of duplicate genes. Science 290 (5494), 2000, pp. 1151-55.

Textbooks

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.

Software for interactive tutorials: rubylabs-0.9.8.gem

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.

Software for programming projects and interactive tutorials: PythonLabs-1.0.2.tar.gz
Jupyter notebooks

Software

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.

https://github.com/conery/META-16S-pipeline

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

https://github.com/conery/nbscan

Courses

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.