Efficient Two-Stage Group Testing Algorithms for Genetic Screening

Efficient two-stage group testing algorithms that are particularly suited for rapid and less-expensive DNA library screening and other large scale biological group testing efforts are investigated in this paper. The main focus is on novel combinatorial constructions in order to minimize the number of individual tests at the second stage of a two-stage disjunctive testing procedure. Building on recent work by Levenshtein (2003) and Tonchev (2008), several new infinite classes of such combinatorial designs are presented.Comment: 14 pages; to appear in "Algorithmica". Part of this work has been presented at the ICALP 2011 Group Testing Workshop; arXiv:1106.368

Phylogenetic information complexity: Is testing a tree easier than finding it?

Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following question: is the amount of sequence data required to accurately reconstruct a tree significantly more than the amount required to test whether or not a candidate tree was the `true' tree? By `significantly', we mean that the two quantities behave the same way as a function of the number of species being considered. We prove that, for a certain type of model, the amount of information required is not significantly different; while for another type of model, the information required to test a tree is independent of the number of leaves, while that required to reconstruct it grows with this number. Our results combine probabilistic and combinatorial arguments.Comment: 15 pages, 3 figure

Isomorph-free generation of 2-connected graphs with applications

Many interesting graph families contain only 2-connected graphs, which have ear decompositions. We develop a technique to generate families of unlabeled 2-connected graphs using ear augmentations and apply this technique to two problems. In the first application, we search for uniquely K_r-saturated graphs and find the list of uniquely K_4-saturated graphs on at most 12 vertices, supporting current conjectures for this problem. In the second application, we verifying the Edge Reconstruction Conjecture for all 2-connected graphs on at most 12 vertices. This technique can be easily extended to more problems concerning 2-connected graphs.Comment: 15 pages, 3 figures, 4 table

Implementing Brouwer's database of strongly regular graphs

Andries Brouwer maintains a public database of existence results for strongly regular graphs on $n\leq 1300$ vertices. We implemented most of the infinite families of graphs listed there in the open-source software Sagemath, as well as provided constructions of the "sporadic" cases, to obtain a graph for each set of parameters with known examples. Besides providing a convenient way to verify these existence results from the actual graphs, it also extends the database to higher values of $n$.Comment: 18 pages, LaTe