Related papers: CruzDB: software for annotation of genomic interva…
We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…
The UCSC Genome Browser is a popular tool for the exploration and analysis of reference genomes. Mirrors of the UCSC Genome Browser and its contents exist at multiple geographic locations, and this mirror procedure has been modified to…
Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data…
Curated databases have become important sources of information across scientific disciplines, and due to the manual work of experts, often become important reference works. Features such as provenance tracking, archiving, and data citation…
Genetic interactions and protein co-dependencies shape cellular fitness, buffering capacity, and disease vulnerability. However, systematic integration of co-dependency relationships across heterogeneous datasets remains limited. Here, we…
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…
Gradient-based data influence approximation has been leveraged to select useful data samples in the supervised fine-tuning of large language models. However, the computation of gradients throughout the fine-tuning process requires too many…
Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic…
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…
This paper describes a prototype of extended XDB. XDB is an open-source and extensible database architecture developed by National Aeronautics and Space Administration (NASA) to provide integration of heterogeneous and distributed…
DNA-binding proteins (DBPs) are integral to gene regulation and cellular processes, making their accurate identification essential for understanding biological functions and disease mechanisms. Experimental methods for DBP identification…
Over the past years, substantial numbers of microbial species' genomes have been deposited outside of conventional INSDC databases. The GlobDB aggregates 14 independent genomic catalogues to provide a comprehensive database of…
Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a…
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…
DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between…
Single-cell RNA sequencing (scRNA-seq) data analysis is pivotal for understanding cellular heterogeneity. However, the high sparsity and complex noise patterns inherent in scRNA-seq data present significant challenges for traditional…
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic…
The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic…
Comparative genomics methods are widely used to aid the functional annotation of non coding DNA regions. However, aligning non coding sequences requires new algorithms and strategies, in order to take into account extensive rearrangements…
Essential protein plays a crucial role in the process of cell life. The identification of essential proteins can not only promote the development of drug target technology, but also contribute to the mechanism of biological evolution. There…