Related papers: Intra-Chromosomal Potentials from Nucleosomal Posi…
Chromosome analysis is vital for diagnosing genetic disorders and guiding cancer therapy decisions through the identification of somatic clonal aberrations. However, developing an AI model are hindered by the overwhelming complexity and…
We introduce a graph-theoretic approach to extract clusters and hierarchies in complex data-sets in an unsupervised and deterministic manner, without the use of any prior information. This is achieved by building topologically embedded…
Cancer is a number of related yet highly heterogeneous diseases. Correct identification of cancer subtypes is critical for clinical decisions. The advance in sequencing technologies has made it possible to study cancer based on abundant…
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which…
One of the major challenges arising from single-cell transcriptomics experiments is the question of how to annotate the associated single-cell transcriptomic profiles. Because of the large size and the high dimensionality of the data,…
Different numerical mappings of the DNA sequences have been studied using a new cluster-scaling method and the well known spectral methods. It is shown, in particular, that the nucleotide sequences in DNA molecules have robust…
The goal of this paper is to propose and analyze a differentially private randomized mechanism for the $K$-means query. The goal is to ensure that the information received about the cluster-centroids is differentially private. The method…
Chromosome classification is an important but difficult and tedious task in karyotyping. Previous methods only classify manually segmented single chromosome, which is far from clinical practice. In this work, we propose a detection based…
We present an investigation into data selection methods for the efficient sampling of configuration space as applied to the development of inter-atomic potentials for scale bridging in molecular dynamics (MD) simulations. This investigation…
Pathogenic chromosome abnormalities are very common among the general population. While numerical chromosome abnormalities can be quickly and precisely detected, structural chromosome abnormalities are far more complex and typically require…
The spatial positioning of chromosomes relative to functional nuclear bodies is intertwined with genome functions such as transcription. However, the sequence patterns and epigenomic features that collectively influence chromatin spatial…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
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…
Understanding chromatin dynamics across multiple spatiotemporal scales requires models that reconcile biological specificity with physics-based interactions and computational tractability. We present a modular, recognition-enabled…
Combining genome-wide structural models with phenomenological data is at the forefront of efforts to understand the organizational principles regulating the human genome. Here, we use chromosome-chromosome contact data as knowledge-based…
We present a statistical-mechanical analysis of the positioning of nucleosomes along one of the chromosomes of yeast DNA as a function of the strength of the binding potential and of the chemical potential of the nucleosomes. We find a…
Taxonomic classification in biodiversity research involves organizing biological specimens into structured hierarchies based on evidence, which can come from multiple modalities such as images and genetic information. We investigate whether…
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…
We numerically study the expansion dynamics of ultracold atoms in a one-dimensional disordered potential in the presence of a weak position measurement of the atoms. We specifically consider this position measurement to be realized by a…
We explore the potential of large-scale noisily labeled data to enhance feature learning by pretraining semantic segmentation models within a multi-modal framework for geospatial applications. We propose a novel Cross-modal Sample Selection…