Related papers: Modeling of two-dimensional DNA display
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as an image, (ii) computes distances between these images, and (iii) uses these distances to output a map wherein each sequence is a…
Modelling deformation of anatomical objects observed in medical images can help describe disease progression patterns and variations in anatomy across populations. We apply a stochastic generalisation of the Large Deformation Diffeomorphic…
In segmentation problems, inference on change-point position and model selection are two difficult issues due to the discrete nature of change-points. In a Bayesian context, we derive exact, non-asymptotic, explicit and tractable formulae…
The accurate prediction and characterization of DNA melting domains by computational tools could facilitate a broad range of biological applications. However, no algorithm for melting domain prediction has been available until now. The main…
Visual object tracking is a significant computer vision task which can be applied to many domains such as visual surveillance, human computer interaction, and video compression. In the literature, researchers have proposed a variety of 2D…
Standard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting…
3D scatterplots are a well-established plotting technique that can be used to represent data with three or more dimensions. On paper and computer monitors they are essentially two-dimensional projections of the three-dimensional Cartesian…
We present a computational method for real-time, patient-specific simulation of 2D ultrasound (US) images. The method uses a large number of tracked ultrasound images to learn a function that maps position and orientation of the transducer…
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription,…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
This work concerns formal descriptions of DNA code properties, and builds on previous work on transducer descriptions of classic code properties and on trajectory descriptions of DNA code properties. This line of research allows us to give…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Anderson localisation -- the inhibition of wave propagation in disordered media -- is a surprising interference phenomenon which is particularly intriguing in two-dimensional (2D) systems. While an ideal, non-interacting 2D system of…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Surviving in a diverse environment requires corresponding organism responses. At the cellular level, such adjustment relies on the transcription factors (TFs) which must rapidly find their target sequences amidst a vast amount of…
Eye image segmentation is a critical step in eye tracking that has great influence over the final gaze estimate. Segmentation models trained using supervised machine learning can excel at this task, their effectiveness is determined by the…