- 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
- 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
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