相关论文: Perfect Reconstruction of Oncogenetic Trees

Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…

We establish necessary and sufficient conditions on simultaneous symplectic spectral decomposition of a family of $2n \times 2n$ real positive semidefinite matrices with symplectic kernels. We also provide a precise algebraic condition on a…

Generating accurate digital tree models from scanned environments is invaluable for forestry, agriculture, and other outdoor industries in tasks such as identifying biomass, fall hazards and traversability, as well as digital applications…

Combinatorial trees can be used to represent genealogies of asexual individuals. These individuals can be endowed with birth and death times, to obtain a so-called `chronological tree'. In this work, we are interested in the continuum…

We construct quark mixing matrices within a group theoretic framework which is easily applicable to any number of generations. Familiar cases are retrieved and related, and it is hoped that our viewpoint may have advantages both…

Necessary and sufficient conditions for a sequence of positive integers to be the degree sequence of a k-connected simple graph are detailed. Conditions are also given under which such a sequence is necessarily k-connected.

We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…

Existing techniques to reconstruct tree models of progression for accumulative processes, such as cancer, seek to estimate causation by combining correlation and a frequentist notion of temporal priority. In this paper, we define a novel…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

We provide the necessary and sufficient conditions for the edge-binomials of the tree forming a $d$-sequence in terms of the degree sequence notion of a graph. We study the regularity of powers of the binomial edge ideals of trees generated…

For a given directed tree and weights associated with vertices from a subtree the completion problem is to determine if these weights may be completed in a way to obtain a bounded weighted shift on the whole tree, which possibly satisfies…

The paper contains a simple approach to reconstruction in Thermoacoustic and Photoacoustic Tomography. The technique works for any geometry of point detectors placement and for variable sound speed satisfying a non-trapping condition. A…

We provide sufficient criteria for explosion in Crump-Mode-Jagers branching process, via the process producing an infinite path in finite time. As an application, we deduce a curious phase-transition in the infinite tree associated with a…

We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in…

A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…

We propose an approach to 3D reconstruction via inverse procedural modeling and investigate two variants of this approach. The first option consists in the fitting set of input parameters using a genetic algorithm. We demonstrate the…

Certain families of combinatorial objects admit recursive descriptions in terms of generating trees: each node of the tree corresponds to an object, and the branch leading to the node encodes the choices made in the construction of the…

We consider matrices on infinite trees which are universal covers of Jacobi matrices on finite graphs. We are interested in the question of the existence of sequences of finite covers whose normalized eigenvalue counting measures converge…

A general model for the ontogenetic growth of living organisms has been recently proposed. Here we investigate the extension of this model to the growth of solid malignant tumors. A variety of in vitro and in vivo data are analyzed and…

More than 30 years ago, we published a paper entitled as abnormal chromatin configuration and oncogenesis, which proposed the first hypothesis that links oncogenesis to abnormal three-dimensional (3D) genome structure. Recently, many…