相关论文: Algebraic and Topological Indices of Molecular Pat…
Identifying altered pathways that are associated with specific cancer types can potentially bring a significant impact on cancer patient treatment. Accurate identification of such key altered pathways information can be used to develop…
Genomics, especially multi-omics, has made precision medicine feasible. The completion and publicly accessible multi-omics resource with clinical outcome, such as The Cancer Genome Atlas (TCGA) is a great test bed for developing…
The Cancer Genome Atlas (TCGA) provides researchers with clinicopathological data and genomic characterizations of various carcinomas. These data sets include expression microarrays for genes and microRNAs -- short, non-coding strands of…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
Cancers are characterized by remarkable heterogeneity and diverse prognosis. Accurate cancer classification is essential for patient stratification and clinical decision-making. Although digital pathology has been advancing cancer diagnosis…
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as…
Molecular signaling networks are believed to determine cancer robustness. Although cancer patient survivability was reported to correlate with the heterogeneous connectivity of the signaling networks inspired by theoretical studies on the…
Cocaine addiction accounts for a large portion of substance use disorders and threatens millions of lives worldwide. There is an urgent need to come up with efficient anti-cocaine addiction drugs. Unfortunately, no medications have been…
Breast cancer is the most common cancer in women worldwide, and discovering the biomarkers of this disease became so vital nowadays and Cell in Cell structure could be one of them, and it may be used as an available proxy for tumor…
Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the case of SARS-CoV-2, we performed a structural analysis of the network of protein interactions obtained from the integration of three sources:…
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…
In this paper we present the first mathematical analysis of the protein interaction network found in the yeast, S. cerevisiae. We show that, (a) the identified protein network display a characteristic scale-free topology that demonstrate…
We show that numerical approximations of Kolmogorov complexity (K) applied to graph adjacency matrices capture some group-theoretic and topological properties of graphs and empirical networks ranging from metabolic to social networks. That…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
Apart from the knots formed by the main-chain, the proteins can form numerous topological structures, when included the covalent and ion-mediated interactions. In this work, we define the protein non-trivial $\theta$-curves and identify 7…
The interactions between tumor cells and the tumor microenvironment (TME) dictate therapeutic efficacy of radiation and many systemic therapies in breast cancer. However, to date, there is not a widely available method to reproducibly…
Background. Diet and inflammation are critical factors influencing cancer risk. However, the combined impact of nutritional status and inflammatory biomarkers on cancer status and type, using machine learning (ML), remains underexplored.…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…