Olivier Rivoire

Learn More
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure, and sectors, which are larger groups of structurally connected amino acids that underlie the biochemical properties of(More)
The multi-index matching is an NP-hard combinatorial optimization problem; for two indices it reduces to the well understood bipartite matching problem that belongs to the polynomial complexity class. We use the cavity method to solve the thermodynamics of the multi-index system with random costs. The phase diagram is much richer than for the case of the(More)
The multi-index matching problem generalizes the well known matching problem by going from pairs to d-uplets. We use the cavity method from statistical physics to analyse its properties when the costs of the d-uplets are random. At low temperatures we find for d ≥ 3 a frozen glassy phase with vanishing entropy. We also investigate some properties of small(More)
We consider " lattice glass models " in which each site can be occupied by at most one particle, and any particle may have at most ℓ occupied nearest neighbors. Using the cavity method for locally tree-like lattices, we derive the phase diagram, with a particular focus on the vitreous phase and the highest packing limit. We also study the energy landscape(More)
Genome-wide measurements of transcriptional activity in bacteria indicate that the transcription of successive genes is strongly correlated beyond the scale of operons. Here, we analyze hundreds of bacterial genomes to identify supra-operonic segments of genes that are proximal in a large number of genomes. We show that these synteny segments correspond to(More)
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized genes from multiple genomes, describe their organization , and study their evolutionary history. In bacterial genomes,(More)
Genome-wide measurements of transcriptional activity in bacteria indicate that the transcription of successive genes is strongly correlated beyond the scale of operons. However, the underlying mechanisms are poorly characterized and a systematic method for identifying local groups of co-transcribed genes is lacking. Here, we identify supra-operonic segments(More)
  • 1