相关论文: Analysis of correlation structures in the Synechoc…

The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…

Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…

Breakage-Fusion-Bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then `unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the…

Dedicated hardware implementations of spiking neural networks that combine the advantages of mixed-signal neuromorphic circuits with those of emerging memory technologies have the potential of enabling ultra-low power pervasive sensory…

In this thesis, we consider some spin effects in QCD and recurrence lattices with multi-site exchanges. Main topic of our manuscript are critical phenomena in spin systems defined on the recurrence lattices. Main tool of our approach is the…

Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In…

Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…

The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…

We put forward a phenomenological theory for entanglement dynamics in monitored quantum many-body systems with well-defined quasiparticles. Within this theory entanglement is carried by ballistically propagating non-Hermitian quasiparticles…

The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…

Quantum algorithms have the potential to revolutionize our understanding of open quantum systems in chemistry. In this work, we demonstrate that a repeated interaction model, which could serve as the foundation for a digital quantum…

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…

Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…

We demonstrate that models of resonant cyclotron radiation transfer in a strong field (i.e. cyclotron scattering) can account for spectral lines seen at two epochs, denoted S1 and S2, in the Ginga data for GRB870303. Using a generalized…

This paper studies reconstruction of strings based upon their substrings spectrum. Under this paradigm, it is assumed that all substrings of some fixed length are received and the goal is to reconstruct the string. While many existing works…

Many complex systems involve interactions between more than two agents. Hypergraphs capture these higher-order interactions through hyperedges that may link more than two nodes. We consider the problem of embedding a hypergraph into…

Synchronized bursts (SBs) with complex structures are common in neuronal cultures. Although the origin of SBs is still unclear, they have been studied for their information processing capabilities. Here, we investigate the properties of…

Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…

Transcription is one of the essential processes for cells to read genetic information encoded in genes, which is initiated by the binding of RNA polymerase to related promoter. Experiments have found that the nucleotide sequence of promoter…

The cyanobacterium Synechococcus elongatus uses both a protein phosphorylation cycle and a transcription-translation cycle to generate circadian rhythms that are highly robust against biochemical noise. We use stochastic simulations to…