Abstract Synchronization (insertions–deletions) errors are still a major challenge for reliable information retrieval in DNA storage. Unlike traditional error correction codes (ECC) that add redundancy the stored information, multiple sequence alignment (MSA) solves this problem by searching conserved subsequences. In paper, we conduct comprehensive simulation study on capability of typical MSA algorithm, MAFFT. Our results reveal its exhibits phase transition when there around 20% errors....

Synthetic DNA has been widely considered an attractive medium for digital data storage. However, the random insertion–deletion–substitution (IDS) errors in sequenced reads still remain a critical challenge to reliable recovery. Motivated by modulation technique communication field, we propose new storage architecture solve this problem. The main idea is that all binary are modulated into sequences with same AT/GC patterns, which facilitate detection of indels noisy reads. signal could not...

Abstract DNA, or deoxyribonucleic acid, is a powerful molecule that plays fundamental role in storing and processing genetic information of all living organisms. In recent years, scientists have harnessed hybridization powers between DNA molecules to perform various computing tasks storage. Unlike specific hybridization, non-specific provides natural way measure similarity the objects represented by different sequences. We utilize such property build an instance-based learning model which...

Signalling pathway analysis is a popular approach that used to identify significant cancer‐related pathways based on differentially expressed genes (DEGs) from biological experiments. The main advantage of signalling lies in the fact it assesses both number DEGs and propagation signal perturbation pathways. However, this method simplifies interactions between by categorising them only as activation (+1) suppression (−1), which does not encompass range real pathways, where interaction...

Contrastive learning has achieved remarkable success in computer vision, however it is built on instance-level discrimination which leaves the valuable intra-class correlation dataset unexploited. Current semantic clustering methods are proven to be helpful but they would suffer from error accumulated iteration process without ground-truth guidance. In an attempt remedy accumulation when utilizing for contrastive learning, we propose online Visual Clustering (CVC) method with two actions:...

Abstract Boolean networks are widely used to model gene regulatory and design therapeutic intervention strategies affect the long-term behavior of systems. In this paper, we investigate less-studied one-bit perturbation, which falls under category structural intervention. Previous works focused on finding optimal perturbation maximally alter steady-state distribution (SSD) undesirable states through matrix theory. However, application SSD is limited with about ten genes. 2007, Xiao et al....

Numerous computational drug repurposing methods have emerged as efficient alternatives to costly and time-consuming traditional discovery approaches. Some of these are based on the assumption that candidate should a reversal effect disease-associated genes. However, such not applicable in case there is limited overlap between disease-related genes drug-perturbed In this study, we proposed novel Drug Repurposing method Inhibition Effect gene regulatory network (DRIE) identify potential drugs...

Rapid development in synthetic technologies has boosted DNA as a potential medium for large-scale data storage. Meanwhile, how to implement security the storage system is still an unsolved problem.

MicroRNAs (miRNAs) are a class of small endogenous non-coding genes that play important roles in post-transcriptional regulation as well other biological processes. Accumulating evidence indicated miRNAs were extensively involved the pathology cancer. However, determining which related to specific cancer is problematic because one miRNA may target multiple and gene be targeted by miRNAs. The authors proposed new approach, named miR_SubPath, identify cancer-associated three steps. determined...

Densely connected patterns in biological networks can help biologists to elucidate meaningful insights. How detect dense subgraphs effectively and quickly has been an urgent challenge recent years. In this paper, we proposed a local measure named the edge density coefficient, which could indicate whether locates subgraph or not. Simulation results showed that improve both accuracy speed detecting subgraphs. Thus, G-N algorithm be extended large by measure.

Abstract Thanks to its high density and long durability, synthetic DNA has been widely considered as a promising solution the data explosion problem. However, due large amount of random base insertion-deletion-substitution (IDSs) errors from sequencing, reliable recovery remains critical challenge, which hinders large-scale application. Here, we propose modulation-based storage architecture. Experiments on simulation real datasets demonstrate that it two distinct advantages. First,...

Drug repurposing is a promising approach to find new therapeutic indications for approved drugs. Many computational approaches have been proposed prioritize candidate anticancer drugs by gene or pathway level. However, these methods neglect the changes in interactions at edge To address limitation, we develop drug method (iEdgePathDDA) based on information and topology. First, identify drug-induced disease-related edges (the interactions) within pathways using Pearson correlation...

To prevent disease, it is of great importance to detect the critical point (pre-disease state) when biological system abruptly transforms from normal disease state. However, rapid and accurate pre-disease state detection still a challenge there only single sample available. The transition driven by variation in regulations between genes.

Abstract Thanks to its high density and long durability, synthetic DNA has been widely considered as a promising solution the data explosion problem. However, due large amount of random base insertion-deletion-substitution (IDSs) errors from sequencing, reliable recovery remains critical challenge, which hinders large-scale application. Here, we propose modulation-based storage architecture. Experiments on simulation real datasets demonstrate that it two distinct advantages. First,...

Abstract With the rapid development of DNA (Deoxyribonucleic Acid) storage technologies, storing digital images in is feasible. Meanwhile, information security system still a problem to solve. Therefore, this paper, we propose storage-oriented image encryption algorithm utilizing processing mechanisms molecule biology. The basic idea perform pixel replacement by gene hybridization, and implement dual diffusion mutation. ciphertext can be synthesized stored after encryption. Experimental...

Based on the photonic bandgap-photonic crystal fibers( PBG-PCF) fiber core fills namitic liquid crystal. By readjusting temperature to change refractive index, constitute new fiber-optic sensor. In this paper, we use finite element COMSOL software simulate and analyze optical sensitive properties. The research show that after PBG – PCF filling crystal, its mode field distribution, effective waveguide dispersion etc changing with is so big. Therefore, properties index of CF medium, provides...

A salient problem in translational genomics is the use of gene regulatory networks to determine therapeutic intervention strategies.Theoretically, a complete network, optimal policy performs better than suboptimal policy.However, this theory may not hold if we intervene system based on control derived from imprecise inferred networks, especially small-sample scenario.In paper, compare performance unconstrained (UC) with that mean-first-passage-time (MFPT) terms quality determined and...

Abstract DNA, or deoxyribonucleic acid, is a powerful molecule that plays fundamental role in the storing and processing genetic information of all living organisms. In recent years, scientists over world have devoted to taking advantage its high density, energy efficiency long durability solve challenges technology. Here, we propose build an instance-based learning model by DNA molecules. The handwriting digit images MNIST dataset are encoded sequences using deep encoder. And reversal...

A function plays a pivotal role when it comes to the improvement of system task information. It is basis for guarantee effectiveness and performance system. However, this implies that health be fully effective its resources need also up par. An antagonistic relationship between resource health, wherein are low standard only brings about downgrade in function. In paper, we aim showcase study on relation functions from data functions' matrix how can excavate functions. previous studies, most...

Boolean networks are widely used to model gene regulatory and design therapeutic intervention strategies affect the long-term behavior of systems. Here, authors investigate 1 bit perturbation, which falls under category structural intervention. The authors' idea is that, if only a perturbed state evolves from desirable attractor an undesirable or attractor, then size basin may decrease increase. In this case, obtain net BOS states, they can quickly optimal perturbation by finding maximum...