Related papers: Predicting pathways for old and new metabolites th…
The structure of defect clusters formed in a displacement cascade plays a significant role in the micro-structural evolution during irradiation. Molecular dynamics simulations have been widely used to study collision cascades and subsequent…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
Accurately identifying metabolites i.e. small molecules from mass spectrometry data remains a core challenge in metabolomics, with broad applications in drug discovery, environmental analysis, and clinical research. We address the Molecule…
Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…
Genome-wide association studies (GWASs) aim to detect genetic risk factors for complex human diseases by identifying disease-associated single-nucleotide polymorphisms (SNPs). The traditional SNP-wise approach along with multiple testing…
Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…
In recent decades, traditional drug research and development have been facing challenges such as high cost, long timelines, and high risks. To address these issues, many computational approaches have been suggested for predicting the…
Rapid technological advances have allowed for molecular profiling across multiple omics domains from a single sample for clinical decision making in many diseases, especially cancer. As tumor development and progression are dynamic…
One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…
Graph clustering is a fundamental problem in unsupervised learning, with numerous applications in computer science and in analysing real-world data. In many real-world applications, we find that the clusters have a significant high-level…
There is a crescent use of enzymes in multiple industries and sciences, ranging from materials and fuel synthesis to pharmaceutical and food production. Their applicability in this variety of fields depends not only on their biochemical…
There is a wide variety of data mining methods available, and it is generally useful in exploratory data analysis to use many different methods for the same dataset. This, however, leads to the problem of whether the results found by one…
A systematic search of the 2MASS point source catalog, covering 47% of the sky, was carried out aiming to reveal any hidden globular clusters in our Galaxy. Eight new star clusters were discovered by a search algorithm based on finding…
In recent years there has been a growing interest in the role of networks and clusters in the global economy. Despite being a popular research topic in economics, sociology and urban studies, geographical clustering of human activity has…
The widening gap between known proteins and their functions has encouraged the development of methods to automatically infer annotations. Automatic functional annotation of proteins is expected to meet the conflicting requirements of…
Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form…
A hierarchical scheme for clustering data is presented which applies to spaces with a high number of dimension ($N_{_{D}}>3$). The data set is first reduced to a smaller set of partitions (multi-dimensional bins). Multiple clustering…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…