BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

Chromatin-level regulation of biosynthetic gene clusters.

Loss-of-function Aspergillus nidulans CclA, a Bre2 ortholog involved in histone H3 lysine 4 methylation, activated the expression of cryptic secondary metabolite clusters in A. nidulans. One new cluster generated monodictyphenone, emodin and emodin derivatives, whereas a second encoded two anti-osteoporosis polyketides, F9775A and F9775B. Modification of the chromatin landscape in fungal second...

Reconstructing Undirected Graphs from Eigenspaces

In this paper, we aim at recovering an undirected weighted graph of N vertices from the knowledge of a perturbed version of the eigenspaces of its adjacency matrix W. Our approach is based on minimizing a cost function given by the Frobenius norm of the commutator AB−BA between symmetric matrices A and B. In the Erdős-Rényi model with no self-loops, we show that identifiability (i.e., the abili...

Reconstructing Control Flow from Predicated Assembly Code

Reconstructing graphs from their odd vertex subsets

Let G = (V; E) be a simple, undirected graph. A subset U V is odd if the subgraph of G induced by U has an odd number of edges. For a xed integer k, when does the knowledge of the family of odd subsets of V having cardinality k allow the reconstruction of G? The answer is: whenever k jV j?2 and k 2 mod 4. The proof proceeds via the vector space homomorphism k : (?(n);) ?! (? k (n);), where ?(n)...

A Reconstructing Graphs from Neighborhood Data

Consider a social network and suppose that we are only given the number of common friends between each pair of users. Can we reconstruct the underlying network? Similarly, consider a set of documents and the words that appear in them. If we only know the number of common words for every pair of documents, as well as the number of common documents for every pair of words, can we infer which word...