Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA
E. Freyhult, J.P. Bollback, P. Gardner, Genome Research 17 (2007) 117–25.

Clonal interference is alleviated by high mutation rates in large populations
J.P. Bollback, J. Huelsenbeck, Molecular Biology and Evolution 24 (2007) 1397–1406.

Genes under positive selection in Escherichia coli
L. Petersen, J.P. Bollback, M. Dimmic, M. Hubisz, R. Nielsen, Genome Research 17 (2007) 1336–1343.

AMT: A property-based monitoring tool for analog systems
D. Nickovic, O. Maler, in:, 5th International Conference on Formal Modeling and Analysis of Timed Systems, Springer, 2007, pp. 304–319.

On synthesizing controllers from bounded-response properties
O. Maler, D. Nickovic, A. Pnueli, in:, 19th International Conference on Computer Aided Verification, Springer, 2007, pp. 95–107.

Using first-order theorem provers in the Jahob data structure verification system
C. Bouillaguet, V. Kuncak, T. Wies, K. Zee, M. Rinard, in:, 8th International Conference on Verification, Model Checking, and Abstract Interpretation, Springer, 2007, pp. 74–88.

Shape analysis for composite data structures
J. Berdine, C. Calcagno, B. Cook, D. Distefano, P. O’Hearn, T. Wies, H. Yang, in:, 19th International Conference on Computer Aided Verification, Springer, 2007, pp. 178–192.

Algorithms for interface synthesis
D. Beyer, T.A. Henzinger, V. Singh, in:, Springer, 2007, pp. 4–19.

Model checking on trees with path equivalences
R. Alur, P. Cerny, S. Chaudhuri, in:, 13th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2007, pp. 664–678.

Qualitative networks: A symbolic approach to analyze biological signaling networks
M. Schaub, T.A. Henzinger, J. Fisher, BMC Systems Biology 1 (2007).

Abstract counterexample-based refinement for powerset domains
R. Manevich, J. Field, T.A. Henzinger, G. Ramalingam, M. Sagiv, in:, Program Analysis and Compilation, Theory and Practice: Essays Dedicated to Reinhard Wilhelm on the Occasion of His 60th Birthday, Springer, 2007, pp. 273–292.

The embedded machine: Predictable, portable real-time code
T.A. Henzinger, C. Kirsch, ACM Transactions on Programming Languages and Systems (TOPLAS) 29 (2007).

Quantitative generalizations of languages
T.A. Henzinger, in:, Springer, 2007, pp. 20–22.

Games, time, and probability: Graph models for system design and analysis
T.A. Henzinger, in:, Springer, 2007, pp. 103–110.

Executable cell biology
J. Fisher, T.A. Henzinger, Nature Biotechnology 25 (2007) 1239–1249.

CSL: Computer Science Logic 
J. Duparc, T.A. Henzinger, CSL: Computer Science Logic , Springer, 2007.

Predictive modeling of signaling crosstalk during C. elegans vulval development
J. Fisher, N. Piterman, A. Hajnal, T.A. Henzinger, PLoS Computational Biology 3(5):e92 (2007).

Assume-guarantee synthesis
K. Chatterjee, T.A. Henzinger, in:, Springer, 2007, pp. 261–275.

Algorithms for omega-regular games with imperfect information
K. Chatterjee, L. Doyen, T.A. Henzinger, J. Raskin, Logical Methods in Computer Science 3 (2007) 1–23.

Stochastic <9-Regular Games
K. Chatterjee, Stochastic <9-Regular Games, University of California, Berkeley, 2007.