Related papers: Tangle analysis of difference topology experiments…
Anomaly detection algorithms have been proved to be useful in the search of new physics beyond the Standard Model. However, a prerequisite for using an anomaly detection algorithm is that the signal to be sought is indeed anomalous. This…
We introduce topological differential testing (TDT), an approach to extracting the consensus behavior of a set of programs on a corpus of inputs. TDT uses the topological notion of a simplicial complex (and implicitly draws on richer…
Machine learning models for repeated measurements are limited. Using topological data analysis (TDA), we present a classifier for repeated measurements which samples from the data space and builds a network graph based on the data topology.…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…
Knots are fascinating topological structures that have been observed in various contexts, ranging from micro-worlds to macro-systems, and are conjectured to play a fundamental role in their respective fields. In order to characterize their…
The natural world is full of complex systems characterized by intricate relations between their components: from social interactions between individuals in a social network to electrostatic interactions between atoms in a protein.…
Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are preventing the transition from a purely-experimental to a…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby…
Protein structure prediction is one of the most important problems in computational biology. The most successful computational approach, also called template-based modeling, identifies templates with solved crystal structures for the query…
We consider the problem of developing interpretable and computationally efficient matrix decomposition methods for matrices whose entries have bounded support. Such matrices are found in large-scale DNA methylation studies and many other…
It is well-known that intrinsically disordered proteins (IDP) are highly dynamic, which is related to their functionality in various biological processes. However, the characterization of the intricate structures of IDP has been a…
Accurate prediction of protein-ligand binding affinity is critical for drug discovery. While recent deep learning approaches have demonstrated promising results, they often rely solely on structural features of proteins and ligands,…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity…
Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice…
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)…
Developing reliable methods to discriminate different transient brain states that change over time is a key neuroscientific challenge in brain imaging studies. Topological data analysis (TDA), a novel framework based on algebraic topology,…
Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…