Mod/Resc Parsimony Inference

We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by \textsc{Mod/Resc Parsimony Inference}, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the \textsc{Bipartite Biclique Edge Cover} problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the \textsc{Bipartite Biclique Edge Cover}. Finally, we present experimental results where we applied some of our techniques to a real-life data set.Comment: 11 pages, 3 figure

Minimal unsatisfiable formulas with bounded clause-variable difference are fixed-parameter tractable

Recognition of minimal unsatisfiable CNF formulas (unsatisfiable CNF formulas which become satisfiable if any clause is removed) is a classical DP-complete problem. It was shown recently that minimal unsatisfiable formulas with n variables and n+k clauses can be recognized in time . We improve this result and present an algorithm with time complexity ; hence the problem turns out to be fixed-parameter tractable (FTP) in the sense of Downey and Fellows (Parameterized Complexity, 1999). Our algorithm gives rise to a fixed-parameter tractable parameterization of the satisfiability problem: If for a given set of clauses F, the number of clauses in each of its subsets exceeds the number of variables occurring in the subset at most by k, then we can decide in time whether F is satisfiable; k is called the maximum deficiency of F and can be efficiently computed by means of graph matching algorithms. Known parameters for fixed-parameter tractable satisfiability decision are tree-width or related to tree-width. Tree-width and maximum deficiency are incomparable in the sense that we can find formulas with constant maximum deficiency and arbitrarily high tree-width, and formulas where the converse prevails

Sibling Rivalry among Paralogs Promotes Evolution of the Human Brain

Geneticists have long sought to identify the genetic changes that made us human, but pinpointing the functionally relevant changes has been challenging. Two papers in this issue suggest that partial duplication of SRGAP2, producing an incomplete protein that antagonizes the original, contributed to human brain evolution

Detecting cycles through three fixed vertices in a graph

We present a simple linear time algorithm for finding a cycle through three fixed vertices in an undirected graph. The algorithm is based on decompositions into triconnected components and on a combinatorial result of Lovász