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This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
Is the dire wolf back from the dead? Not exactly (www.science.org)
The bold claim was immediately met with skepticism and outrage from scientists on social media. “Colossal Bioscience[s] did not revive dire wolves,” University of Maine paleoecologist Jacquelyn Gill writes in a series of posts on Bluesky. “To see this work being done with such a casual disregard not only for the truth but for life itself is genuinely abhorrent to me.”
submitted by: Istvan Albert
The Return of the Dire Wolf | TIME (time.com)
Relying on deft genetic engineering and ancient, preserved DNA, Colossal scientists deciphered the dire wolf genome, rewrote the genetic code of the common gray wolf to match it, and, using domestic dogs as surrogate mothers, brought Romulus, Remus, and their sister, 2-month-old Khaleesi, into the world during three separate births last fall and this winter—effectively for the first time de-extincting a line of beasts whose live gene pool long ago vanished.
submitted by: Istvan Albert
Dire wolves were the last of an ancient New World canid lineage | Nature (www.nature.com)
... to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago.
submitted by: Istvan Albert
GitHub - Maggi-Chen/Inspector: A tool for evaluating long-read de novo assembly results (github.com)
Inspector is a tool for assembly evaluation with long read data. The input includes a contig file, long reads (PacBio CLR, PacBio HiFi, Oxford Nanopore, or mixed platform), and a reference genome (optional). The output includes A summary report, read-to-contig alignment file, a list of structrual errors and small-scale errors.
submitted by: Istvan Albert
Integrating electronic health records and GWAS summary statistics to predict the progression of autoimmune diseases from preclinical stages | Nature Communications (www.nature.com)
We propose a novel method Genetic Progression Score (GPS) that integrates biobank and case-control study to predict the disease progression risk. Via penalized regression, GPS incorporates PRS weights for case-control studies as prior and forces model parameters to be similar to the prior if the prior improves prediction accuracy. In simulations, GPS consistently yields better prediction accuracy than alternative strategies relying on biobank or case-control samples only and those combining biobank and case-control samples. The improvement is particularly evident when biobank sample is smaller or the genetic correlation is lower.
submitted by: Istvan Albert
@jef.works on Bluesky (bsky.app)
Related thread:
We identify evidence of off-target probe binding in the 10x Genomics #Xenium v1 Human Breast Gene Expression Panel, compromising the accuracy of resulting #singlecell #spatialtranscriptomics profiles
submitted by: Istvan Albert
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling | bioRxiv (www.biorxiv.org)
The accuracy of spatial gene expression profiles generated by probe-based in situ spatially-resolved transcriptomic technologies depends on the specificity with which probes bind to their intended target gene. Off-target binding, defined as a probe binding to something other than the target gene, can distort a gene's true expression profile, making probe specificity essential for reliable transcriptomics. Here, we investigate off-target binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel. We developed a software tool, Off-target Probe Tracker (OPT), to identify putative off-target binding via alignment of probe sequences and found at least 21 out of the 280 genes in the panel impacted by off-target binding to protein-coding genes. Our findings indicate that for some genes, the expression patterns detected by Xenium demonstrably reflect the aggregate expression of the target and predicted off-target genes based on Visium and single-cell RNA-seq rather than the target gene alone.
submitted by: Istvan Albert
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