The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here.
This edition of the Herald was brought to you by contribution from GenoMax, Istvan Albert, and was edited by Istvan Albert,
Rafael Irizarry on Twitter (x.com)
Biologists, stop putting UMAP plots in your papers!
UMAP is a powerful tool for exploratory data analysis, but without a clear understanding of how it works, it can easily lead to confusion and misinterpretation.
submitted by: Istvan Albert
Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation | bioRxiv (www.biorxiv.org)
Here, using a variety of bacterial and human datasets, we systematically evaluate the performance of existing methylation models for 5mC (both CpG and non-CpG contexts), 6-methyladenine, and 4-methylcytosine. We also demonstrate the effect of other parameters such as sequencing depth, read quality, basecalling mode, and more importantly, the presence of neighboring DNA modifications.
submitted by: Istvan Albert
Wei Shen on Twitter (x.com)
We're thrilled to introduce LexicMap v0.5.0🎉 It's more accurate and slightly faster!
LexicMap has helped some scientists align genes and plasmids in AllTheBacteria and GenBank, each has > 2 million prokaryotic genomes!
submitted by: Istvan Albert
Introducing the New NIH Public Access Policy – NIH Extramural Nexus (nexus.od.nih.gov)
New NIH publication access policy removes the 12-month embargo.
submitted by: GenoMax
Genomic reproducibility in the bioinformatics era | Genome Biology | Full Text (genomebiology.biomedcentral.com)
In biomedical research, validating a scientific discovery hinges on the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility remain imprecise. We argue that genomic reproducibility, defined as the ability of bioinformatics tools to maintain consistent results across technical replicates, is essential for advancing scientific knowledge and medical applications. Initially, we examine different interpretations of reproducibility in genomics to clarify terms. Subsequently, we discuss the impact of bioinformatics tools on genomic reproducibility and explore methods for evaluating these tools regarding their effectiveness in ensuring genomic reproducibility. Finally, we recommend best practices to improve genomic reproducibility.
submitted by: Istvan Albert
NCBI RefSeq: reference sequence standards through 25 years of curation and annotation (academic.oup.com)
Reference sequences and annotations serve as the foundation for many lines of research today, from organism and sequence identification to providing a core description of the genes, transcripts and proteins found in an organism's genome. Interpretation of data including transcriptomics, proteomics, sequence variation and comparative analyses based on reference gene annotations informs our understanding of gene function and possible disease mechanisms, leading to new biomedical discoveries. The Reference Sequence (RefSeq) resource created at the National Center for Biotechnology Information (NCBI) leverages both automatic processes and expert curation to create a robust set of reference sequences of genomic, transcript and protein data spanning the tree of life.
submitted by: Istvan Albert
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