Related papers: genomepy: genes and genomes at your fingertips
Gene studies are crucial for fields such as protein structure prediction, drug discovery, and cancer genomics, yet they face challenges in fully utilizing the vast and diverse information available. Gene studies require clean, factual…
A recent study showed that more than 70% of researchers fail to reproduce their peers's experiments and more than half fail to reproduce their own experiments. Obviously, from a perspective of scientific quality this is a more than…
Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of…
The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…
Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization, and sharing of biomedical…
Public omics databases like the Gene Expression Omnibus and the Sequence Read Archive offer substantial opportunities for data reuse to address novel biomedical questions. However, it is still difficult to find samples and studies of…
This paper provides a global picture about the deployment of networked processing services for genomic data sets. Many current research make an extensive use genomic data, which are massive and rapidly increasing over time. They are…
RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet…
GCsnap2 Cluster is a scalable, high performance tool for genomic context analysis, developed to overcome the limitations of its predecessor, GCsnap1 Desktop. Leveraging distributed computing with mpi4py[.]futures, GCsnap2 Cluster achieved a…
Software Testing is a process to identify the quality and reliability of software, which can be achieved through the help of proper test data. However, doing this manually is a difficult task due to the presence of number of predicate nodes…
The cost of DNA sequencing has resulted in a surge of genetic data being utilised to improve scientific research, clinical procedures, and healthcare delivery in recent years. Since the human genome can uniquely identify an individual, this…
With the boom in modern software development, open-source software has become an integral part of various industries, driving progress in computer science. However, the immense complexity and diversity of the open-source ecosystem also pose…
Addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological…
Trajectories, sequentially measured quantities that form a path, are an important presence in many different fields, from hadronic beams in physics to electrocardiograms in medicine. Trajectory anal-ysis requires the quantification and…
In this manuscript, we introduce a semi-automatic scene graph annotation tool for images, the GeneAnnotator. This software allows human annotators to describe the existing relationships between participators in the visual scene in the form…
The study of DNA charge dynamics is a highly interdisciplinary field that bridges physics, chemistry, biology, and medicine, and plays a critical role in processes such as DNA damage detection, protein-DNA interactions, and DNA-based…
Over the last 20 years, there has been an explosion of genomic data collected for disease association, functional analyses, and other large-scale discoveries. At the same time, there have been revolutions in cloud computing that enable…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Background: To understand individual genomes it is necessary to look at the variations that lead to changes in phenotype and possibly to disease. However, genotype information alone is often not sufficient and additional knowledge regarding…
Combinatorial group testing reduces screening costs and turnaround time but remains challenging to apply due to design complexity, varying applicability, and lack of implementation tools. Here we present PoolPy, a unified end-to-end…