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Only 26 days from submission to publication! The genome of the American groundhog, Marmota monax Daniela Puiu et al., published by F1000Research f1000research.com/articles/9-113…

Congratulations Dr. Alaina Shumate, PhD on successfully defending your Ph.D. thesis today! Outstanding work on Liftoff, StringTie, and other novel computational methods. H/T to committee members Mihaela Pertea Winston Timp

I’M WONDERING WHEN WE WILL STOP SEEING OURSELVES AS HAVING JUST ONE COMPLETE GENOME, BUT INSTEAD HAVING A COLLECTION OF GENOMES WHERE EVERYONE’S DIFFERENCES ARE REPRESENTED.

We've learned a lot from the ChatGPT research preview and have been making important updates based on user feedback. ChatGPT will be coming to our API and Microsoft's Azure OpenAI Service soon. Sign up for updates here: share.hsforms.com/1u4goaXwDRKC9-…

A re-analysis of multiple studies that asserted the role of bacteria in cancer raises questions at to the veracity of the findings and the link biorxiv.org/content/10.110… Steven Salzberg 💙💛 Abraham Yuchen Ge and colleagues

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One of the most informative, eye-opening, well-written papers I've read in a while. I learned a ton! Abraham Yuchen Ge Steven Salzberg 💙💛 & others biorxiv.org/content/10.110…

Eric Topol Steven Salzberg 💙💛 Abraham Yuchen Ge News from Science has our story up on this dispute science.org/content/articl…

Anshul Kundaje (anshulkundaje@bluesky) @tkorem Steven Salzberg 💙💛 Jonathan Eisen For those interested I forked the rebuttal to the rebuttal and added the lines of code that look at feature importance. Its here github.com/travisgibson/t… and shout out to Greg Sepich-Poore (Greg Sepich-Poore) for making the rebuttal^2 open source cc Jack A Gilbert (he/him/his)

I think we need to talk about how devastating this cancer microbiome refutation paper from Steven Salzberg 💙💛 and colleagues is. It really speaks to how devoid of critical thinking and intellectual depth our glam publishing ecosystem has become. 1/n biorxiv.org/content/10.110…

Many of you would have seen that since releasing this and sending the pre-print to prospective journals, we have been collaborating with Steven Salzberg 💙💛 Mihaela Pertea Yuchen Ge Jen Lu and others to take this analysis one step further. doi.org/10.1101/2023.0… 5/7

Our paper debunking the 2020 cancer microbiome results is now published, in mBio. We'll see if @nature (or the authors) will retract these deeply flawed results. h/t Professor Booty PhD Eric Topol journals.asm.org/doi/10.1128/mb…

Our paper examining critical errors in a cancer metagenomics study is now live in mBio. Work carried out with Steven Salzberg 💙💛 Daniel Brewer Mihaela Pertea Yuchen Ge Jen Lu and others. Errors in bioinformatics can be subtle but important! doi.org/10.1128/mbio.0…

Our paper on the human gene annotation catalog CHESS, which now includes all of MANE and a more rigorous definition of genes of all types. With Mihaela Pertea Ales Varabyou @thesteinegger Markus Sommer Beril Erdogdu @IliaMinkin and others: genomebiology.biomedcentral.com/articles/10.11…

.Steven Salzberg 💙💛 kicking off the opening session of Genome Informatics on Major data analysis errors invalidate cancer microbiome findings. #gi2023 Cold Spring Harbor Laboratory

Apparently @nature has a serious concern that we were correct–that the cancer microbiome is just not there, as we described in our paper now published in mBio. The Nature paper now has an Editor's Note:

Wow, @nature has retracted the 2020 Poore et al. cancer microbiome paper that we showed (journals.asm.org/doi/10.1128/mb…) was deeply flawed. The retraction date is tomorrow so I can't yet read the official notice, but I'll update when I can Retraction Watch Professor Booty PhD

Looking forward to talking about the cancer microbiome (or lack thereof!) to Broad Institute and Massachusetts Institute of Technology (MIT) tomorrow, with my colleague Abraham. I'll be virtual and Abe will be in Cambridge; we're co-authors but have never met in person!