Related papers: Experimental Analysis of XPCR-based protocols
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
We introduce a simple model for DNA evolution. Using the method of Peng et al.$^1$, we investigate the fractal properties of the system. For small chains and chains of intermediate size we find a fractal exponent that indicates the…
Background: High-throughput techniques bring novel tools but also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved…
Despite efforts to better understand the constraints that operate on single-step parallel (aka "package", "multiple") revision, very little work has been carried out on how to extend the model to the iterated case. A recent paper by…
In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…
The constrained linear representability problem (CLRP) for polymatroids determines whether there exists a polymatroid that is linear over a specified field while satisfying a collection of constraints on the rank function. Using a computer…
X-ray phase contrast tomography (XPCT) is widely used for 3D imaging of objects with weak contrast in X-ray absorption index but strong contrast in refractive index decrement. To reconstruct an object imaged using XPCT, phase retrieval…
In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to…
Background With microarray technology becoming mature and popular, the selection and use of a small number of relevant genes for accurate classification of samples is a hot topic in the circles of biostatistics and bioinformatics. However,…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
We describe a method of model checking called Computing Range Reduction (CRR). The CRR method is based on derivation of clauses that reduce the set of traces of reachable states in such a way that at least one counterexample remains (if…
Modifications to test-time sampling have emerged as an important extension to diffusion algorithms, with the goal of biasing the generative process to achieve a given objective without having to retrain the entire diffusion model. However,…
In many scenarios such as genome-wide association studies where dependences between variables commonly exist, it is often of interest to infer the interaction effects in the model. However, testing pairwise interactions among millions of…
RNA-seq allows detection and precise quantification of transcripts, provides comprehensive understanding of exon/intron boundaries, aids discovery of alternatively spliced isoforms and fusion transcripts along with measurement of…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model…
In microbiome studies, one of the ways of studying bacterial abundances is to estimate bacterial composition based on the sequencing read counts. Various transformations are then applied to such compositional data for downstream statistical…