Related papers: Machine learning for plant microRNA prediction: A …
Machine Learning algorithms are good tools for both classification and prediction purposes. These algorithms can further be used for scientific discoveries from the enormous data being collected in our era. We present ways of discovering…
In recent years, several machine learning approaches have been proposed to predict gene expression and epigenetic signals from the DNA sequence alone. These models are often used to deduce, and, to some extent, assess putative new…
We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and…
One of the main goals of developmental biology is to reveal the gene regulatory networks (GRNs) underlying the robust differentiation of multipotent progenitors into precisely specified cell types. Most existing methods to infer GRNs from…
Agriculture is vital for human survival and remains a major driver of several economies around the world; more so in underdeveloped and developing economies. With increasing demand for food and cash crops, due to a growing global population…
Microstructural evolution is a key aspect of understanding and exploiting the structure-property-performance relation of materials. Modeling microstructure evolution usually relies on coarse-grained simulations with evolution principles…
Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential…
Machine Science, or Data-driven Research, is a new and interesting scientific methodology that uses advanced computational techniques to identify, retrieve, classify and analyse data in order to generate hypotheses and develop models. In…
There is a warning light for the loss of plant habitats worldwide that entails concerted efforts to conserve plant biodiversity. Thus, plant species classification is of crucial importance to address this environmental challenge. In recent…
Identification of nonlinear systems is a challenging problem. Physical knowledge of the system can be used in the identification process to significantly improve the predictive performance by restricting the space of possible mappings from…
Background: MicroRNAs (miRNAs) play multiple roles in tumor biology [1]. Interestingly, reports from multiple groups suggest that miRNA targets may be coupled through competitive stoichiometric sequestration [2]. Specifically, computational…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate…
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction…
Machine Learning is a powerful tool to reveal and exploit correlations in a multi-dimensional parameter space. Making predictions from such correlations is a highly non-trivial task, in particular when the details of the underlying dynamics…
Biological cells, by definition, are the basic units which contain the fundamental molecules of life of which all living things are composed. Understanding how they function and differentiating cells from one another therefore is of…
Single-particle traces of the diffusive motion of molecules, cells, or animals are by-now routinely measured, similar to stochastic records of stock prices or weather data. Deciphering the stochastic mechanism behind the recorded dynamics…
RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly…
Motivation: Prediction of phenotypes from high-dimensional data is a crucial task in precision biology and medicine. Many technologies employ genomic biomarkers to characterize phenotypes. However, such elements are not sufficient to…
Lung transplantation remains the only viable treatment option for the majority of patients with advanced lung diseases. However, 5-year post-transplant survival rates remain low primarily secondary to chronic rejection. Novel insights from…