Algorithms in Bioinformatics
8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings
Chapter and Conference Paper
Clonal tree inference brings crucial insights to the analysis of tumor heterogeneity and cancer evolution. Recent progress in single cell sequencing has prompted a demand for more advanced probabilistic models...
Article
Spatial transcriptomics maps gene expression across tissues, posing the challenge of determining the spatial arrangement of different cell types. However, spatial transcriptomics spots contain multiple cells. ...
Article
Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer’s proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for underst...
Chapter and Conference Paper
Mixtures of Hidden Markov Models (MHMM) are widely used for clustering of sequential data, by letting each cluster correspond to a Hidden Markov Model (HMM). Expectation Maximization (EM) is the standard appro...
Article
Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial tra...
Article
Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the m...
Article
Over the last decade, methods have been developed for the reconstruction of gene trees that take into account the species tree. Many of these methods have been based on the probabilistic duplication-loss model...
Article
Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computat...
Article
Gene duplication is considered to be a major driving force in evolution that enables the genome of a species to acquire new functions. A reconciliation - a mapping of gene tree vertices to the edges or vertice...
Article
PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and—pe...
Article
Several bioinformatic approaches have previously been used to find novel sites of ADAR mediated A-to-I RNA editing in human. These studies have discovered thousands of genes that are hyper-edited in their non-...
Article
In recent years there has been a trend of leaving the strict molecular clock in order to infer dating of speciations and other evolutionary events. Explicit modeling of substitution rates and divergence times ...
Book and Conference Proceedings
8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings
Article
Evolutionary processes, such as gene family evolution or parasite-host co-speciation, can often be viewed as a tree evolving inside another tree. Relating two given trees under such a constraint is known as re...
Article
Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise dista...
Chapter and Conference Paper
In phylogenetic foot-printing, putative regulatory elements are found in upstream regions of orthologous genes by searching for common motifs. Motifs in different upstream sequences are subject to mutations al...
Book and Conference Proceedings
RECOMB 2004 International Workshop, RCG 2004, Bertinoro, Italy, October 16-19, 2004, Revised Selected Papers
Chapter and Conference Paper
Reconstructing the evolutionary history of a set of species is a fundamental problem in biology and methods for solving this problem are gaged based on two characteristics: accuracy and efficiency. Neighbor Jo...
Chapter and Conference Paper
Maximum likelihood (ML) (Felsenstein, 1981) is an increasingly popular optimality criterion for selecting evolutionary trees. Finding optimal ML trees appears to be a very hard computational task – in particul...
Chapter and Conference Paper
Evidence indicates that members of many gene families in the genome of an organism tend to have homologues both within their own genome and in the genomes of other organisms. Amongst these homologues, typicall...