Related papers: Modeling of two-dimensional DNA display
We have deluge of data in time series format for numerous phenomena. The number of snapshots, resolution and many other factors come into play as we look to identify the dynamics in a given problem. The pre-processing and post-processing…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
Tracking single molecules is instrumental for quantifying the transport of molecules and nanoparticles in biological samples, e.g., in brain drug delivery studies. Existing intensity-based localisation methods are not developed for imaging…
Recent advances in imaging technology now provide us with 3D images of developing organs. These can be used to extract 3D geometries for simulations of organ development. To solve models on growing domains, the displacement fields between…
A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
The 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…
The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
Two-dimensional patterns are used in many research areas in computer science, ranging from image processing to specification and verification of complex software systems (via scenarios). The contribution of this paper is twofold. First, we…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
In the field of computational molecule generation, an essential task in the discovery of new chemical compounds, fragment-based deep generative models are a leading approach, consistently achieving state-of-the-art results in molecular…
DNA microarray experiments, a well-established experimental technique, aim at understanding the function of genes in some biological processes. One of the most common experiments in functional genomics research is to compare two groups of…
Motion estimation is a fundamental step in dynamic medical image processing for the assessment of target organ anatomy and function. However, existing image-based motion estimation methods, which optimize the motion field by evaluating the…
Generative models are invaluable in many fields of science because of their ability to capture high-dimensional and complicated distributions, such as photo-realistic images, protein structures, and connectomes. How do we evaluate the…
Like other applications in computer vision, medical image segmentation has been most successfully addressed using deep learning models that rely on the convolution operation as their main building block. Convolutions enjoy important…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
This work considers semi-supervised segmentation as a dense prediction problem based on prototype vector correlation and proposes a simple way to represent each segmentation class with multiple prototypes. To avoid degenerate solutions, two…