Related papers: Inferring DNA sequences from mechanical unzipping:…
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
Many statistical models can be simulated forwards but have intractable likelihoods. Approximate Bayesian Computation (ABC) methods are used to infer properties of these models from data. Traditionally these methods approximate the posterior…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
The most famous error-decoding algorithm for convolutional codes is the Viterbi algorithm. In this paper, we present a new reduced complexity version of this algorithm which can be applied to a class of binary convolutional codes with…
Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed…
Designing DNA and protein sequences with improved function has the potential to greatly accelerate synthetic biology. Machine learning models that accurately predict biological fitness from sequence are becoming a powerful tool for…
Inferring the causal structure of a system typically requires interventional data, rather than just observational data. Since interventional experiments can be costly, it is preferable to select interventions that yield the maximum amount…
A Viterbi-like decoding algorithm is proposed in this paper for generalized convolutional network error correction coding. Different from classical Viterbi algorithm, our decoding algorithm is based on minimum error weight rather than the…
Recent advances in molecular biology allow the quantification of the transcriptome and scoring transcripts as differentially or equally expressed between two biological conditions. Although these two tasks are closely linked, the available…
This paper introduces a Bayesian framework for image inversion by deriving a probabilistic counterpart to the regularization-by-denoising (RED) paradigm. It additionally implements a Monte Carlo algorithm specifically tailored for sampling…
Recent sequential pattern mining methods have used the minimum description length (MDL) principle to define an encoding scheme which describes an algorithm for mining the most compressing patterns in a database. We present a novel…
During the past few years the development of experimental techniques has allowed the quantitative analysis of biological systems ranging from neurobiology and molecular biology. This work focuses on the quantitative description of these…
In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…
We present a novel, general-purpose method for deconvolving and denoising images from gridded radio interferometric visibilities using Bayesian inference based on a Gaussian process model. The method automatically takes into account…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
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…