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A probabilistic clustering algorithm is proposed for the analysis of forensic DNA mixtures in which individual cells are isolated and short tandem repeats are amplified using the polymerase chain reaction to generate single cell…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
An efficient MCMC algorithm is presented to cluster the nodes of a network such that nodes with similar role in the network are clustered together. This is known as block-modelling or block-clustering. The model is the stochastic blockmodel…
Identifying the complete set of functional elements within the human genome would be a windfall for multiple areas of biological research including medicine, molecular biology, and evolution. Complete knowledge of function would aid in the…
Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed…
A model based clustering procedure for data of mixed type, clustMD, is developed using a latent variable model. It is proposed that a latent variable, following a mixture of Gaussian distributions, generates the observed data of mixed type.…
Inherent stochasticity in gene expression leads to distributions of mRNA copy numbers in a population of identical cells. These distributions are determined primarily by the multitude of states of a gene promoter, each driving transcription…
Genetic mutations are footprints of tumour growth. While mutation data in bulk samples has been used to infer evolutionary parameters hard to measure in vivo, the advent of single-cell data has led to strong interest in the mutational…
Non-synonymous single nucleotide polymorphisms (nsSNPs) are single nucleotide substitution occurring in the coding region of a gene and leads to a change in amino-acid sequence of protein. The studies have shown these variations may be…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
In this paper, we discuss the construction of a multivariate generalisation of the Dirichlet-multinomial distribution. An example from forensic genetics in the statistical analysis of DNA mixtures motivates the study of this multivariate…
Migration is a key mechanism for expansion of communities. In spatially heterogeneous environments, rapidly gaining knowledge about the local environment is key to the evolutionary success of a migrating population. For historical human…
The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely…
Clustering algorithms are pivotal in data analysis, enabling the organization of data into meaningful groups. However, individual clustering methods often exhibit inherent limitations and biases, preventing the development of a universal…
Symmetry in biological and physical systems is a product of self organization driven by evolutionary processes, or mechanical systems under constraints. Symmetry based feature extrac-tion or representation by neural networks may unravel the…
Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate…
In this paper, we review recent results of ours concerning branching processes with general lifetimes and neutral mutations, under the infinitely many alleles model, where mutations can occur either at birth of individuals or at a constant…