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Evolution in its course found a variety of solutions to the same optimisation problem. The advent of high-throughput genomic sequencing has made available extensive data from which, in principle, one can infer the underlying structure on…

This paper describes the systematic application of local topological methods for detecting interfaces and related anomalies in complicated high-dimensional data. By examining the topology of small regions around each point, one can…

Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…

Deciphering how genes interpret information from the concentration of transcription factors (TFs) within the cell nucleus remains a fundamental question in gene regulation. Recent advancements have unveiled the heterogeneous distribution of…

In this study, we propose a hidden Markov mixture model for the analysis of gene expression measurements mapped to chromosome locations. These expression values represent preprocessed light intensities observed in each probe of Affymetrix…

We present an experimental approach to detect the saturated absorption spectroscopy different from conventional scheme. Using this approach, crossovers are removed to avoid their overlap with other peaks in the spectrum and sensitivity of…

Gene expression profiles are essential in identifying different cancer phenotypes. Clustering gene expression datasets can provide accurate identification of cancerous cell lines, but this task is challenging due to the small sample size…

Background: Current research suggests that a small set of "driver" mutations are responsible for tumorigenesis while a larger body of "passenger" mutations occurs in the tumor but does not progress the disease. Due to recent pharmacological…

Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming…

Most single-molecule transport experiments produce large and stochastic datasets containing a wide range of behaviors, presenting both a challenge to their analysis, but also an opportunity for discovering new physical insights. Recently,…

The ever-increasing number of genome sequencing and resequencing projects is a central source of insights into the ecology and evolution of non-model organisms. An important aspect of genomics is the elucidation of sex determination systems…

Essential protein plays a crucial role in the process of cell life. The identification of essential proteins can not only promote the development of drug target technology, but also contribute to the mechanism of biological evolution. There…

Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the…

Cancer is a genetic disorder whose clonal evolution can be monitored by tracking noisy genome-wide copy number variants. We introduce the Copy Number Stochastic Block Model (CN-SBM), a probabilistic framework that jointly clusters samples…

Anomaly detection in random fields is an important problem in many applications including the detection of cancerous cells in medicine, obstacles in autonomous driving and cracks in the construction material of buildings. Such anomalies are…

The analysis of contagion-diffusion processes in metapopulations is a powerful theoretical tool to study how mobility influences the spread of communicable diseases. Nevertheless, many metapopulation approaches use indistinguishable agents…

The detection of change-points in heterogeneous sequences is a statistical challenge with many applications in fields such as finance, signal analysis and biology. A wide variety of literature exists for finding an ideal set of…

Cancer subtyping plays a crucial role in informing prognosis and guiding personalized treatment strategies. However, conventional subtyping approaches often rely on static, biopsy-derived scores that hardly capture the biological…

Recent advances in biological research have seen the emergence of high-throughput technologies with numerous applications that allow the study of biological mechanisms at an unprecedented depth and scale. A large amount of genomic data is…

Histopathology imaging is crucial for the diagnosis and treatment of skin diseases. For this reason, computer-assisted approaches have gained popularity and shown promising results in tasks such as segmentation and classification of skin…