Publications
Software
HYPERSPACE: [Link] A matlab package to sample high-dimensional parameter spaces in dynamical systems models of regulatory circuits in cell and developmental biology.
Zamora-Sillero, E., Hafner, M., Ibig, A., Stelling, J., Wagner, A. Efficient characterization of high-dimensional parameter spaces for systems biology. BMC Systems Biology 2011.
'Glocal' Robustness Analysis : [Link] A matlab toolbox to determine the robustness of cellular circuits through global sampling of high-dimensional parameter spaces combined with local parameter perturbations.
Hafner, M., Koeppl, H., Hasler, M., Wagner, A.,(2009) “Glocal” robustness analysis and model discrimination for circadian oscillators. PloS Computational Biology 5(10): e1000534. [reprint request] 
The Systems Biology Research Tool: [Link] An easy-to-use open source software package and API for systems biologists. It perfoms multiple analyses on stoichiometric reaction networks and other biological networks, and can be easily extended via a number of plugins.
Wright, J., Wagner, A.
(2008) The systems biology research tool: Evolvable open-source software. BMC Systems Biology 2:55. [PDF] 
Neutral Network Size Estimation: [Link] A program to estimate the size of the neutral set or neutral network associated with RNA secondary structures.
Jörg, T., Martin, OC, Wagner, A., Neutral network sizes of biological RNA molecules can be computed and are atypically large. (in press)
IScan: [Link] A package to identify insertion sequences and similar transposable elements, their inverted repeats, and the direct target repeats they generate in entire genomes.
Wagner, A., Lewis, C., Bichsel, M. (2007) A survey of transposable elements using IScan. Nucleic Acids Research 35, 5284-5293. [PDF]
Varclus: [Link] A perl utility to identify clusters of amino acid or nucleotide changes in a sequence that are too tightly spaced to have occurred by chance alone.
Wagner, A. (2007) Rapid detection of positive selection in genes and genomes through variation clusters. Genetics 176: 2451–2463. [PDF]
DatasetAssess: [Link] A tool to estimate error rates in high-throughput protein interaction datasets and other functional genomic data.
Gilchrist, M.A., Salter, L.A., Wagner, A.
(2004) A statistical framework for combining and interpreting proteomic
datasets. Bioinformatics20,
689-700. [PDF]
FindMaxCover. [Link] This tool can align DNA sequences that may have undergone changes in orientation of some parts, for example through inversions. It will find the combination of local alignments that covers the maximum number of residues in a query sequence.
Conant, G.C., Wagner, A.(2004) A
fast algorithm for determining the longest combination of local alignments
to a query sequence. BMC Bioinformatics5, 62 [PDF]
Genome History: [Link] A tool to extract duplicate genes and their amino acid and synonymous divergence from completely sequenced genomes.
Conant, G.C., Wagner, A. (2002) GenomeHistory: a software tool and its application to fully sequenced genomes. Nucleic Acids Research 30, 1-10. [PDF] [Supplement]