Related papers: genomepy: genes and genomes at your fingertips

Access to genomic data is highly regulated due to its sensitive nature. While safeguards are essential, cumbersome data access processes pose a significant barrier to the development of AI methods for genomics. Synthetic data generation can…

To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a…

Genome annotation is essential for understanding the functional elements within genomes. While automated methods are indispensable for processing large-scale genomic data, they often face challenges in accurately predicting gene structures…

In this article, we present Gammapy, an open-source Python package for the analysis of astronomical $\gamma$-ray data, and illustrate the functionalities of its first long-term-support release, version 1.0. Built on the modern Python…

Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…

Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…

A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…

The human voice effectively communicates a range of emotions with nuanced variations in acoustics. Existing emotional speech corpora are limited in that they are either (a) highly curated to induce specific emotions with predefined…

Motivation: Accurate data analysis and quality control is critical for metagenomic studies. Though many tools exist to analyze metagenomic data there is no consistent framework to integrate and run these tools across projects. Currently,…

Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…

Existing Python libraries and tools lack the ability to efficiently compute statistical test results for large datasets in the presence of missing values. This presents an issue as soon as constraints on runtime and memory availability…

Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…

In this paper, we present MusPy, an open source Python library for symbolic music generation. MusPy provides easy-to-use tools for essential components in a music generation system, including dataset management, data I/O, data preprocessing…

DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…

Reference population databases are an essential tool in variant and gene interpretation. Their use guides the identification of pathogenic variants amidst the sea of benign variation present in every human genome, and supports the discovery…

Fast evolution of Internet technologies has led to an explosive growth of video data available in the public domain and created unprecedented challenges in the analysis, organization, management, and control of such content. The problems…

Genomic approaches have revolutionized medical research, providing valuable insights into human physiology and disease. Despite major benefits from large collections of genomes, the lack of diversity in genomic data represents a significant…

The ominous warnings of a `data deluge' in the life sciences from high-throughput DNA sequencing data are being supplanted by a second deluge, of cliches bemoaning our collective scientific fate unless we address the genomic data `tsunami'.…

Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed…

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…