Random Introduction to Bioinformatics

I was asked recently to recommend some introductory reading material about bioinformatics, which made me realize I haven't read enough myself. Here's what I came up with plus a few additions.

• An Introduction to Bioinformatics Algorithms, Jones and Pevzner: a fun and easy read, if you already have a CS background.
• Genetics: From Genes to Genomes
• Algorithms on Strings, Trees and Sequences, by Daniel Gusfield: Who doesn't love string algorithms?

If you're into stats, both of these are highly regarded, but miles over my head.

• Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids by Durbin and Eddy
• Statistical Methods in Bioinformatics: An Introduction by Warren J. Ewens and Gregory Grant

Papers

• Uri Alon's Network motifs: theory and experimental approaches
• Creating a bioinformatics nation by Lincoln Stein is entertaining reading and may let you know the kind of morass you're getting yourself into.
• Integrating biological databases, also by Lincoln Stein
• An overview of sequence comparison algorithms in molecular biology, Tech. Rep. TR-91-29, Dept. of Computer Science, Univ. of Arizona. Eugene Myers
• SR Eddy, "What is Bayesian statistics?" Nat. Biotechnol., 22, #9 (2004) 1177-8.
• SR Eddy, "What is a hidden Markov model?" Nat. Biotechnol., 22, #10 (2004) 1315-6.
• Foundations for engineering biology, Drew Endy
• Engineering life: Building a fab for biology, from Scientific American, 2006
• Tangentially related and well worth reading is: Software Design Patterns for Information Visualization by Jeffrey Heer
• Executable Cell Biology

Dr. Larry Ruzzo at UW teaches a Computational Biology course. Some of the links above are from his reading list, particularly the Sean Eddy Primer articles from Nature Biotechnology.

In winter of 2008, some UW CS grad students held a seminar course on data management issues in life sciences. In case that link doesn't stay up forever, here's some of the reading list:

Intro to Biology

• Bioinformatics - An Introduction for Computer Scientists
• Life and Its Molecules: A Brief Introduction

Overview on biological data integration

• Data integration and genomic medicine
• Addressing the problems with life-science databases for traditional uses and systems biology
• Integration of biological sources: current systems and challenges ahead

Specific tools and techniques

• BioGuideSRS: Querying Multiple Sources with a user-centric perspective
• Path-based systems to guide life scientists in the maze of biological data sources
• (Almost) Hands-Off Information Integration for the Life Sciences
• Gaggle: (cheers to us!) Gaggle paper and Firegoose paper.
• Bioverse: functional, structural and contextual annotation of proteins and proteomes
• Computational representation of biological systems
• The BioMediator system as a tool for integrating biologic databases on the Web

Also on the subject of data: Dynamic Fusion of Web Data.

Books I wanna read

Finally, here are some books that I haven't read, will probably never get the time to read, but I wish I would read.

• An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon
• Systems Biology: Properties of Reconstructed Networks by Bernhard O. Palsson
• Dynamic Models in Biology by Stephen P. Ellner, John Guckenheimer
• Evolutionary Dynamics: Exploring the Equations of Life by Martin A. Nowak
• System Modeling in Cellular Biology: From Concepts to Nuts and Bolts by Zoltan Szallasi
• The Music of Life: Biology beyond the Genome by Denis Noble
• Bioinformatics and Functional Genomics By Jonathan Pevsner