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Chromosome analysis and identification from metaphase images is a critical part of cytogenetics based medical diagnosis. It is mainly used for identifying constitutional, prenatal and acquired abnormalities in the diagnosis of genetic…
Many types of tumors exhibit chromosomal losses or gains, as well as local amplifications and deletions. Within any given tumor type, sample specific amplifications and deletionsare also observed. Typically, a region that is aberrant in…
We propose a novel computational framework leveraging hypergraph theory to analyse cancer stem cell markers (CSCMs) across multiple organs. Hypergraphs provide a robust representation of CSCM co-expression patterns, capturing their complex…
We propose a novel approach for estimating the location of block boundaries (change-points) in a random matrix consisting of a block wise constant matrix observed in white noise. Our method consists in rephrasing this task as a variable…
Unsupervised learning on high-dimensional RNA-seq data can reveal molecular subtypes beyond standard labels. We combine an autoencoder-based representation with clustering and stability analysis to search for rare but reproducible genomic…
In this paper, we develop and analyze a nonparametric procedure for detecting a single change point in sequences of independent observations using energy distance. The asymptotic properties of the test statistic are derived under both null…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
We intend to identify relationships between cancer cases and pollutant emissions and attempt to understand whether cancer in children is typically located together with some specific chemical combinations or is independent. Co-location…
Methods to effectively detect multi-locus genetic association are becoming increasingly relevant in the genetic dissection of complex trait in humans. Current approaches typically consider a limited number of hypotheses, most of which are…
We propose a novel nonparametric approach for estimating the location of block boundaries (change-points) of non-overlapping blocks in a random symmetric matrix which consists of random variables having their distribution changing from one…
Mapper algorithm can be used to build graph-based representations of high-dimensional data capturing structurally interesting features such as loops, flares or clusters. The graph can be further annotated with additional colouring of…
The problem of change-point estimation is considered under a general framework where the data are generated by unknown stationary ergodic process distributions. In this context, the consistent estimation of the number of change-points is…
The ability to detect change-points in a dynamic network or a time series of graphs is an increasingly important task in many applications of the emerging discipline of graph signal processing. This paper formulates change-point detection…
Exchange type chromosome aberrations (ETCAs) are rearrangements of the genome that occur when chromosomes break and the resulting fragments rejoin with other fragments from other chromosomes. ETCAs are commonly observed in cancer cells and…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Meta-analysis of multiple genome-wide association studies (GWAS) is effective for detecting single or multi marker associations with complex traits. We develop a flexible procedure ("STAMP") based on mixture models to perform region based…
Genomic aberrations, such as somatic copy number alterations, are frequently observed in tumor tissue. Recurrent aberrations, occurring in the same region across multiple subjects, are of interest because they may highlight genes associated…
Change point detection has become an important part of the analysis of the single-particle tracking data, as it allows one to identify moments, in which the motion patterns of observed particles undergo significant changes. The segmentation…
Astrocytes are critical glial cells whose altered morphology and density are hallmarks of many neurological disorders. However, their intricate branching and stain dependent variability make automated detection of histological images a…
We define several new models for how to define anomalous regions among enormous sets of trajectories. These are based on spatial scan statistics, and identify a geometric region which captures a subset of trajectories which are…