Related papers: Pattern Analysis of Tandem Repeats in Nlrp1
Identification of causal genes and pathways is a critical step for understanding the genetic underpinnings of rare diseases. We propose novel approaches to gene prioritization and pathway identification using DNA language model, graph…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
There are several approaches to study occurrences of consecutive patterns in permutations such as the inclusion-exclusion method, the tree representations of permutations, the spectral approach and others. We propose yet another approach to…
In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…
With the widespread application of efficient pattern mining algorithms, sequential patterns that allow gap constraints have become a valuable tool to discover knowledge from biological data such as DNA and protein sequences. Among all kinds…
In this paper we present a neural network-based method for the automatic detection of phase transitions and classification of hidden percolation patterns in a (1+1)-dimensional replication process. The proposed network model is based on the…
The pathogenesis of cancer in human is still poorly understood. With the rapid development of high-throughput sequencing technologies, huge volumes of cancer genomics data have been generated. Deciphering those data poses great…
We propose a method for gene expression based analysis of cancer phenotypes incorporating network biology knowledge through unsupervised construction of computational graphs. The structural construction of the computational graphs is driven…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
Irreducible frequent patters (IFPs) are introduced for transactional databases. An IFP is such a frequent pattern (FP),(x1,x2,...xn), the probability of which, P(x1,x2,...xn), cannot be represented as a product of the probabilities of two…
Recurrent neural networks (RNNs) have been applied to a broad range of applications, including natural language processing, drug discovery, and video recognition. Their vulnerability to input perturbation is also known. Aligning with a view…
Detecting the interactions of genetic compounds like genes, SNPs, proteins, metabolites, etc. can potentially unravel the mechanisms behind complex traits and common genetic disorders. Several methods have been taken into consideration for…
Stochastic rearrangement of germline DNA by VDJ recombination is at the origin of immune system diversity. This process is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions…
Proteins encoded by genes containing regions of variable number tandem repeats (VNTRs) are known to be polymorphic within species but the influence of their instability in molecular interactions remains unclear. VNTRs are overrepresented in…
The V(D)J recombination forms the immunoglobulin genes by joining the variable (V), diversity (D), and joining (J) germline genes. Since variations in germline genes have been linked to various diseases, personalized immunogenomics aims at…
The decreasing costs and increasing speed and accuracy of DNA sample collection, preparation, and sequencing has rapidly produced an enormous volume of genetic data. However, fast and accurate analysis of the samples remains a bottleneck.…
Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes…
Research on long non-coding RNAs (lncRNAs) has garnered significant attention due to their critical roles in gene regulation and disease mechanisms. However, the complexity and diversity of lncRNA sequences, along with the limited knowledge…