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<h4>Summary</h4>We assess batch correction methods for MALDI mass spectrometry imaging experiments. ComBAT reduced batch-related technical variance, maintained biological variation, and improved the overall score by 19.4%.<h4>Availability and implementation</h4>Methods are available in R. comBAT is used …
Read PDF<h4>Motivation</h4>A Multiple Sequence Alignment (MSA) contains fundamental evolutionary information that is useful in the prediction of structure and function of proteins and nucleic acids. The "Number of Effective Sequences" (NEFF) quantifies the diversity of sequences …
Read PDF<h4>Motivation</h4>Phylogenetic networks represent complex biological scenarios that are overlooked in trees, such as hybridization and horizontal gene transfer. Although numerous methods have been developed for phylogenetic network inference, their scalability is severely limited by the …
Read PDF<h4>Motivation</h4>Polygenic embryo screening (PES) is a new, controversial technology, whereby human in vitro fertilization embryos are screened for their genetic risk of complex, polygenic diseases. PES aims to reduce the disease burden in offspring by …
Read PDF<h4>Motivation</h4>With the advancement of cryo-electron microscopy (cryo-EM) into the atomic resolution era, accurate Cα atom modeling has become essential for macromolecular structure determination. However, existing evaluation systems overly rely on full-atom metrics and lack a …
Read PDF<h4>Motivation</h4>Predicting protein function is a fundamental and challenging task that requires integrating diverse biological data modalities to capture complex functional relationships. Traditional machine learning methods often rely on single modalities or combine only a limited …
Read PDFThe lack of user-centered design principles in the current landscape of commonly-used bioinformatics software tools poses challenges for novice genomics researchers (NGRs) entering the modern genomics ecosystem. Comparing the usability of one analysis software to …
Read PDF<h4>Summary</h4>Public repositories such as NCBI's Gene Expression Omnibus (GEO) contain large numbers of ChIP-seq experiments, but their reuse is limited by heterogeneous free-text metadata describing target proteins, histone marks, cell lines, tissues, and disease states. …
Read PDF<h4>Background</h4>One pillar of FAIR principles adoption is Reusability by machines to enable for example more efficient data analytics in fields such as Bioinformatics. However, it is not clear to what extent current metadata exposed by …
Read PDF<h4>Summary</h4>SEMPLR is an R package that predicts transcription factor binding and variant effects using SNP Effect Matrices (SEMs), providing efficient, genome-wide scoring, enrichment testing, and visualization tools for comprehensive analysis of regulatory sequences.<h4>Availability</h4>Available on GitHub …
Read PDF<h4>Motivation</h4>Trimmomatic is a widely adopted tool for preprocessing high-throughput sequencing data, particularly from Illumina platforms. Since its original publication in 2014, the volume and complexity of sequencing data have increased dramatically, necessitating continuous tool evolution.<h4>Results</h4>We …
Read PDF[This corrects the article DOI: 10.1093/nargab/lqaf175.].
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Read PDFThe majority of SARS-CoV-2 genomes obtained during the pandemic were derived by amplifying overlapping windows of the genome ('tiled amplicons'), reconstructing their sequences and fitting them together. This leads to systematic errors in genomes unless …
Read PDFAquatic, aerial, and terrestrial habitats exist along a continuum, with biomass and energy flows transporting genetic material across environmental boundaries. Here, we use environmental DNA (eDNA) metabarcoding to characterize genetic information exchange between water and …
Read PDFHigh-throughput sequencing datasets frequently exhibit extreme read depth variation, biasing downstream analysis. Normalising coverage to a specific depth cap is important, yet existing tools rely on computationally expensive fetch-based or non-deterministic greedy algorithms. Here, we …
Read PDFWe report the complete genome of <i>Cedecea davisae</i> 739Q obtained from the ulcer secretions of a clinical patient. The genome has one circular chromosome (4.95 Mb) and one circular plasmid (76.9 Kb). These sequencing data …
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