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This edition of the Herald was brought to you by contribution from Jeremy Leipzig, GenoMax, n.s.j.vandervelden, Rob, and was edited by GenoMax, Istvan Albert,
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UK Biobank suspends all downloading of data, instead directing all users to migrate to the Research Analysis Platform (UKB-RAP) hosted by DNAnexus.
submitted by: Jeremy Leipzig
Bridge RNAs direct programmable recombination of target and donor DNA | Nature (www.nature.com)
Also: https://www.nature.com/articles/s41586-024-07570-2
Non-CRISPR guided recombination. DNA-based parasite that moves itself around bacterial genomes through a mechanism that hasn't been previously described.
submitted by: GenoMax
x.com (x.com)
After considerably controversy, the publication of a “rebuttal” paper](https://journals.asm.org/doi/10.1128/mbio.01607-23), and a ‘follow-up study, Nature has decided to retract the original article Microbiome analyses of blood and tissues suggest cancer diagnostic approach.
submitted by: Rob
https://academic.oup.com/jamia/advance-article/doi/10.1093/jamia/ocae128/7693164
Comparison of ChatGPT v.3.5 and 4.0 for selected genetics related questions
submitted by: GenoMax
Gene Cluster Visualizations in R • geneviewer (nvelden.github.io)
geneviewer is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more.
submitted by: n.s.j.vandervelden
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When I read the piece by Salzberg, it seemed very convincing that the results of the original paper were a consequence of two fundamental mistakes and required both to occur.
I felt that the rebuttal failed to plainly acknowledge either mistake - instead, I argued that the signal is still there and with that, invited the readers to verify themselves.
It took four years to retract this paper, and from my reading between the lines, it seems that Nature themselves did so, and the authors grudgingly went along with it rather than admitting to their errors.
My problem is there's no way to retract the paper without also retracting the finding.
In this case, the finding (microbial population shifts between tumors) appears to be valid on re-analysis, while the original paper was deeply flawed. Because of this, there should be a mechanism to re-publish corrected analysis. Otherwise anyone interested in the topic will see "retraction" and think the whole idea lacks merit.
In my opinion, when scientists publish a finding with a fundamentally wrong analysis, they need to retract the paper.
It is immaterial whether the actual finding happens to be true later and when done correctly.
If the finding is true, then someone else discovering it in a valid manner should get all the credit. It is not realistic to assume that scientists would be discouraged from the field because someone did an analysis in a completely wrong way.
FWIW, whether or not there is such a thing as tumor microbiome seems far from being settled.
Steven Salzberg seems to believe that ALL papers in this field are complete nonsense. Prof. Salzberg is, in my opinion, one of the greatest, if not the greatest, data science-oriented bioinformaticians of all time. So his words carry a lot of weight for me.
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Very well articulated.