Related papers: Estimating Clonality
Partial clonality is widespread across the tree of life, but most population genetics models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary…
The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian…
In cancer research, clustering techniques are widely used for exploratory analyses and dimensionality reduction, playing a critical role in the identification of novel cancer subtypes, often with direct implications for patient management.…
A major challenge for cancer pathologists is to determine whether a new tumor in a patient with cancer is a metastasis or an independent occurrence of the disease. In recent years numerous studies have evaluated pairs of tumor specimens to…
This paper is motivated by the need to quantify human immune responses to environmental challenges. Specifically, the genome of the selected cell population from a blood sample is amplified by the well-known PCR process of successive…
In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection,…
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…
Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution…
We build networks of genetic similarity in which the nodes are organisms sampled from biological populations. The procedure is illustrated by constructing networks from genetic data of a marine clonal plant. An important feature in the…
Tumor cell populations can be thought of as being composed of homogeneous cell subpopulations, with each subpopulation being characterized by overlapping sets of single nucleotide variants (SNVs). Such subpopulations are known as subclones…
Recent progress in genetic techniques has shed light on the complex co-evolution of malignant cell clones in leukemias. However, several aspects of clonal selection still remain unclear. In this paper, we present a multi-compartmental…
Diverse T and B cell repertoires play an important role in mounting effective immune responses against a wide range of pathogens and malignant cells. The number of unique T and B cell clones is characterized by T and B cell receptors (TCRs…
Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population…
Despite initial success, cancer therapies often fail due to the emergence of drug-resistant cells. In this study, we use a mathematical model to investigate how cancer evolves over time, specifically focusing on the state of the tumor when…
Cluster analysis of biological samples using gene expression measurements is a common task which aids the discovery of heterogeneous biological sub-populations having distinct mRNA profiles. Several model-based clustering algorithms have…
The task of clustering a set of objects based on multiple sources of data arises in several modern applications. We propose an integrative statistical model that permits a separate clustering of the objects for each data source. These…
Genetic data are frequently categorical and have complex dependence structures that are not always well understood. For this reason, clustering and classification based on genetic data, while highly relevant, are challenging statistical…
Objectives: In this study, we quantify the growth variability of tumour cell clones from a human leukemia cell line. Materials and methods: We have used microplate spectrophotometry to measure the growth kinetics of hundreds of individual…
A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor reoccurs. Genome sequencing and…
A measure called Physical Complexity is established and calculated for a population of sequences, based on statistical physics, automata theory, and information theory. It is a measure of the quantity of information in an organism's genome.…