Related papers: genomepy: genes and genomes at your fingertips
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
Increasingly used high throughput experimental techniques, like DNA or protein microarrays give as a result groups of interesting, e.g. differentially regulated genes which require further biological interpretation. With the systematic…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
Rapid advancements in technology have led to an increased use of artificial intelligence (AI) technologies in medicine and bioinformatics research. In anticipation of this, the National Institutes of Health (NIH) assembled the Bridge to…
While artificial intelligence (AI) has become widespread, many commercial AI systems are not yet accessible to individual researchers nor the general public due to the deep knowledge of the systems required to use them. We believe that AI…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
We introduce GraSPy, a Python library devoted to statistical inference, machine learning, and visualization of random graphs and graph populations. This package provides flexible and easy-to-use algorithms for analyzing and understanding…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
QuaPy is an open-source framework for performing quantification (a.k.a. supervised prevalence estimation), written in Python. Quantification is the task of training quantifiers via supervised learning, where a quantifier is a predictor that…
Novel technologies in genomics allow creating data in exascale dimension with relatively minor effort of human and laboratory and thus monetary resources compared to capabilities only a decade ago. While the availability of this data…
Background: Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely used technique to investigate the function of chromatin-related proteins in a genome-wide manner. ChIP-Seq generates large quantities of…
Behavioral studies using personal digital devices typically produce rich longitudinal datasets of mixed data types. These data provide information about the behavior of users of these devices in real-time and in the users' natural…
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…
Nowadays, due to the increasing amount of experimental data obtained by sequencing, the most interest is focused on determining the functions and characteristics of its individual parts of the genome instead of determining the nucleotide…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all the functional elements in the human and mouse genomes. To best serve the scientific community, all data…