Related papers: Reducibility of Gene Patterns in Ciliates using th…
Previous divide-and-conquer segmentation analyses of DNA sequences do not provide a satisfactory stopping criterion for the recursion. This paper proposes that segmentation be considered as a model selection process. Using the tools in…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
Motivation: Microarray data has been recently been shown to be efficacious in distinguishing closely related cell types that often appear in the diagnosis of cancer. It is useful to determine the minimum number of genes needed to do such a…
Choosing the most adequate kernel is crucial in many Machine Learning applications. Gaussian Process is a state-of-the-art technique for regression and classification that heavily relies on a kernel function. However, in the Gaussian…
Recent studies reveal even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce…
Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental…
Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
With conventional silicon-based computing approaching its physical and efficiency limits, biocomputing emerges as a promising alternative. This approach utilises biomaterials such as DNA and neurons as an interesting alternative to data…
Microarray data analysis is one of the major area of research in the field computational biology. Numerous techniques like clustering, biclustering are often applied to microarray data to extract meaningful outcomes which play key roles in…
Excitement at the prospect of using data-driven generative models to sample configurational ensembles of biomolecular systems stems from the extraordinary success of these models on a diverse set of high-dimensional sampling tasks. Unlike…
Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of…
The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…
We present a novel coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster the other, stable and significant…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Current biocomputing approaches predominantly rely on engineered circuits with fixed logic, offering limited stability and reliability under diverse environmental conditions. Here, we use the GRNN framework introduced in our previous work…
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of…