Related papers: Mod/Resc Parsimony Inference
Bipartition cover probabilities quantify whether a collection of gene trees contains every bipartition of the underlying species tree, a condition that underlies finite-sample guarantees for summary methods such as ASTRAL. We study this…
Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
Addressing the interpretability problem of NMF on Boolean data, Boolean Matrix Factorization (BMF) uses Boolean algebra to decompose the input into low-rank Boolean factor matrices. These matrices are highly interpretable and very useful in…
We study two simple mathematical models of the epidemic. At first, we study the repetitive infection spreading in a simplified SIRS model including the effect of the decay of the acquired immune. The model is an intermediate model of the…
Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci collected across the genome. Among insects, an increasingly common approach to collecting this class of data involves…
We introduce a new algorithm called {\sc Rec-Gen} for reconstructing the genealogy or \textit{pedigree} of an extant population purely from its genetic data. We justify our approach by giving a mathematical proof of the effectiveness of…
Mobile genetic elements like conjugative plasmids play a crucial role in shaping the genetic content and population dynamics of bacterial species. Bacterial populations often contain not one, but multiple co-circulating MGEs, which modify…
Vector control plays a central role in the fight against vector-borne diseases and, in particular, arboviruses. The use of the endosymbiotic bacterium Wolbachia has proven effective in preventing the transmission of some of these viruses…
This paper proposes a novel solution to spam detection inspired by a model of the adaptive immune system known as the crossregulation model. We report on the testing of a preliminary algorithm on six e-mail corpora. We also compare our…
Several imaging applications (vessels, retina, plant roots, road networks from satellites) require the accurate segmentation of thin structures for subsequent analysis. Discontinuities (gaps) in the extracted foreground may hinder…
Sterile insect technique has been successfully applied in the control of agricultural pests, however, it has a limited ability to control mosquitoes. A promising alternative approach is Trojan Y Chromosome strategy, which works by…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…
The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing…
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such…
Given a social network $G$ and an integer $k$, the influence maximization (IM) problem asks for a seed set $S$ of $k$ nodes from $G$ to maximize the expected number of nodes influenced via a propagation model. The majority of the existing…
Pests and diseases are relevant factors for production losses in agriculture and, therefore, promote a huge investment in the prevention and detection of its causative agents. In many countries, Integrated Pest Management is the most widely…
We provide a mathematical formulation and develop a computational framework for identifying multiple strains of microorganisms from mixed samples of DNA. Our method is applicable in public health domains where efficient identification of…
This paper deals with the control of parasitism in variational integrators for degenerate Lagrangian systems by writing them as general linear methods. This enables us to calculate their parasitic growth parameters which are responsible for…
Intestinal parasitic infection leads to several morbidities to humans worldwide, especially in tropical countries. The traditional diagnosis usually relies on manual analysis from microscopic images which is prone to human error due to…