Related papers: From In Silico to In Vitro: A Comprehensive Guide …
In biomedical research, validation of a new scientific discovery is tied to the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility still remain imprecise. Here, we argue…
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…
Different research communities have developed various approaches to assess the credibility of predictive models. Each approach usually works well for a specific type of model, and under some epistemic conditions that are normally satisfied…
Software is a great enabler for a number of projects that otherwise would be impossible to perform. Such projects include Space Exploration, Weather Modeling, Genome Projects, and many others. It is critical that software aiding these…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…
Many bioinformatics problems, such as sequence alignment, gene prediction, phylogenetic tree estimation and RNA secondary structure prediction, are often affected by the "uncertainty" of a solution; that is, the probability of the solution…
Scientific machine learning (SciML) models are transforming many scientific disciplines. However, the development of good modeling practices to increase the trustworthiness of SciML has lagged behind its application, limiting its potential…
Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…
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…
In vitro cellular experimentation with genetic interventions, using for example CRISPR technologies, is an essential step in early-stage drug discovery and target validation that serves to assess initial hypotheses about causal associations…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Bioinformatics is a new discipline that addresses the need to manage and interpret the data that in the past decade was massively generated by genomic research. This discipline represents the convergence of genomics, biotechnology and…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
A biological experiment is the most reliable way of assigning function to a protein. However, in the era of high-throughput sequencing, scientists are unable to carry out experiments to determine the function of every single gene product.…
The vast amount of sequencing data presently available allow the scientific community to explore a range of genetic variables that may drive and progress cancer. A myriad of predictive tools has been proposed, allowing researchers and…
Proteomics will celebrate its 20th year in 2014. In this relatively short period of time, it has invaded most areas of biology and its use will probably continue to spread in the future. These two decades have seen a considerable increase…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…