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It is of great interest to quantify the contributions of genetic variation to brain structure and function, which are usually measured by high-dimensional imaging data (e.g., magnetic resonance imaging). In addition to the variance, the…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
We have analyzed gene expression data from 3 different kinds of samples: normal human tissues, human cancer cell lines and leukemic cells from lymphoid and myeloid leukemia pediatric patients. We have searched for genes that are over…
Tumour heterogeneity in breast cancer poses challenges in predicting outcome and response to therapy. Spatial transcriptomics technologies may address these challenges, as they provide a wealth of information about gene expression at the…
With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However,…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euchromatin predominantly occupies the…
To understand the nature of a cell, one needs to understand the structure of its genome. For this purpose, experimental techniques such as Hi-C detecting chromosomal contacts are used to probe the three-dimensional genomic structure. These…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here we capture the…
Complex gene interactions play a significant role in cancer progression, driving cellular behaviors that contribute to tumor growth, invasion, and metastasis. Gene co-expression networks model the functional connectivity between genes under…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
Cells adapt to different conditions by altering a vast number of components, which is measurable using transcriptome analysis. Given that a cell undergoing steady growth is constrained to sustain each of its internal components, the…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…