Related papers: Identifying topologically associating domains usin…
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a…
Compound-protein pairs dominate FDA-approved drug-target pairs and the prediction of compound-protein affinity and contact (CPAC) could help accelerate drug discovery. In this study we consider proteins as multi-modal data including 1D…
We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA…
Cross-Domain Recommendation (CDR) seeks to enable effective knowledge transfer across domains. Existing works rely on either representation alignment or transformation bridges, but they struggle on identifying domain-shared from…
The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer…
With coronary artery disease (CAD) persisting to be one of the leading causes of death worldwide, interest in supporting physicians with algorithms to speed up and improve diagnosis is high. In clinical practice, the severeness of CAD is…
Cellular functions crucially depend on the precise execution of complex biochemical reactions taking place on the chromatin fiber in the tightly packed environment of the cell nucleus. Despite the availability of large data sets probing…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
Persistent homology provides information about the lifetime of homology classes along a filtration of cell complexes. Persistence barcode is a graphical representation of such information. A filtration might be determined by time in a set…
Camouflaged object detection (COD) aims to identify the objects that seamlessly blend into the surrounding backgrounds. Due to the intrinsic similarity between the camouflaged objects and the background region, it is extremely challenging…
Microscopic examination of slides prepared from tissue samples is the primary tool for detecting and classifying cancerous lesions, a process that is time-consuming and requires the expertise of experienced pathologists. Recent advances in…
In this paper, we investigate that the normalized coordinate expression is a key factor as reliance on hand-crafted components in query-based detectors for temporal action detection (TAD). Despite significant advancements towards an…
The identification of drug-target binding affinity (DTA) has attracted increasing attention in the drug discovery process due to the more specific interpretation than binary interaction prediction. Recently, numerous deep learning-based…
Topological Data Analysis (TDA) is an emergent field that aims to discover topological information hidden in a dataset. TDA tools have been commonly used to create filters and topological descriptors to improve Machine Learning (ML)…
Tree kernels have demonstrated their ability to deal with hierarchical data, as the intrinsic tree structure often plays a discriminative role. While such kernels have been successfully applied to various domains such as nature language…
Chiral perturbation theory predicts that in quantum chromodynamics (QCD), light dynamical quarks suppress the gauge-field topological susceptibility of the vacuum. The degree of suppression depends on quark multiplicity and masses. It…
We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single…
Involved in mitotic condensation, interaction of transcriptional regulatory elements or isolation of structural domains, understanding loop formation is becoming a paradigm in the deciphering of chromatin architecture and its functional…
Drug target binding affinity (DTA) is a key criterion for drug screening. Existing experimental methods are time-consuming and rely on limited structural and domain information. While learning-based methods can model sequence and structural…
It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA…