Related papers: Inferring clonal composition from multiple tumor b…
Clonal interference, competition between multiple co-occurring beneficial mutations, has a major role in adaptation of asexual populations. We provide a simple individual based stochastic model of clonal interference taking into account a…
One of the key phenomena in the adaptive immune response to infection and immunization is affinity maturation, during which antibody genes are mutated and selected, typically resulting in a substantial increase in binding affinity to the…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
One of many important features of the tumour microenvironment is that it is a place of active Darwinian selection where different tumour clones become adapted to the variety of ecological niches that make up the microenvironment. These…
Lung cancer has a high rate of recurrence in early-stage patients. Predicting the post-surgical recurrence in lung cancer patients has traditionally been approached using single modality information of genomics or radiology images. We…
This work aims at improving the quality of structural variant prediction from the mapped reads of a sequenced genome. We suggest a new model based on cluster editing in weighted graphs and introduce a new heuristic algorithm that allows to…
A number of statistical models have been successfully developed for the analysis of high-throughput data from a single source, but few methods are available for integrating data from different sources. Here we focus on integrating gene…
Holographic microscopy combined with forward modeling and inference allows colloidal particles to be characterized and tracked in three dimensions with high precision. However, current models ignore the effects of optical aberrations on…
Mutational signatures are patterns of somatic mutations in tumor genomes that provide insights into underlying mutagenic processes and cancer origin. Developing reliable methods for their estimation is of growing importance in cancer…
Given any two sequences of complex numbers, we establish simple relations between their binomial convolution and the binomial convolution of their individual binomial transforms. We employ these relations to derive new identities involving…
Mutational signatures describe the pattern of mutations over the different mutation types. Each mutation type is determined by a base substitution and the flanking nucleotides to the left and right of that base substitution. Due to the…
Mutational signatures connect characteristic mutational patterns in the genome with biological or chemical processes that take place in cancers. Analysis of mutational signatures can help elucidate tumor evolution, prognosis, and…
We propose a new approach for clustering DNA features using array CGH data from multiple tumor samples. We distinguish data-collapsing: joining contiguous DNA clones or probes with extremely similar data into regions, from clustering:…
We discuss the usefulness of quantum cloning and present examples of quantum computation tasks for which cloning offers an advantage which cannot be matched by any approach that does not resort to it. In these quantum computations, we need…
Reversibility of state transitions is intensively studied topic in many scientific disciplines over many years. In cell biology, it plays an important role in epigenetic variation of phenotypes, known as phenotypic plasticity. More…
First, we revisit the stochastic Luria-Delbr\"uck model: a classic two-type branching process which describes cell proliferation and mutation. We prove limit theorems and exact results for the mutation times, clone sizes, and number of…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
Cancer prognosis is a critical task that involves predicting patient outcomes and survival rates. To enhance prediction accuracy, previous studies have integrated diverse data modalities, such as clinical notes, medical images, and genomic…