Steven Salzberg

my co-author pointed out that our new Perspective piece in Cancer Research has 4 generations of mentorship for the 4 authors: Chia - Nagarajan - Pop - Salzberg (youngest to oldest) ;) brnw.ch/21wWgEi

Academic freedom and freedom of speech are under assault, from both the left and the right Everyone is afraid to speak right now.

it's been a while since I wrote a blog, but I had some thoughts: stevensalzberg.substack.com/p/academic-f...

Congratulations to Dr. Lucy Shapiro for winning one of the Lasker Prizes this year! I was a co-author with her on a paper 25 years ago, on Caulobacter crescentus, the species she has studied for >50 years pubmed.ncbi.nlm.nih.gov/11259647/

this is hilarious. AI fails again 🤣

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project An analysis of TCGA whole-genome sequencing samples yields a comprehensive resource for investigating the role of microbes in cancer.

We're still not finding any good evidence for a microbiome in any cancer type: see our new paper in @ScienceTM led by PhD student Yuchen (Peter) Ge www.science.org/doi/10.1126/... and the accompanying news piece, www.science.org/content/arti...

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project An analysis of TCGA whole-genome sequencing samples yields a comprehensive resource for investigating the role of microbes in cancer.

We also see the same patterns in other datasets:
📊 PCAWG
📊 TCGA - Cleaner signals produced by a fantastic paper today from Peter Ge, @stevensalzberg.bsky.social & team)

www.science.org/doi/10.1126/...

Congrats @kuanhaochao.bsky.social ! It's been great having you in the lab, and I can't wait to see what you do next!

A study of gene expression in the living human brain - Molecular Psychiatry Molecular Psychiatry - A study of gene expression in the living human brain

fascinating article describing RNA sequencing results from living human brain tissue. Quite extraordinary how they were able to get the tissue ethically www.nature.com/articles/s41...

Former CDC Director William Foege: How public health can fight back in a time of dangerous nonsense “Kennedy would be less hazardous if he decided to do cardiac surgery. Then he would kill people only one at a time,” writes former CDC Director William Foege.

A former CDC director on RFK Jr: "Kennedy would be less hazardous if he decided to do cardiac surgery. Then he would kill people only one at a time rather than his current ability to kill by the thousands...

Opinion | Jay Bhattacharya: Why the NIH is pivoting away from mRNA vaccines As a vaccine for broad public use, mRNA technology has failed to earn the public’s trust.

really, Jay Bhattacharya? Now you are writing an apologia for the anti-vax, anti-science policies of your boss, RFK Jr.? Have you no principles? wapo.st/41B0qCx

I agree that it's clearly illegal to put all grant funding under the absolute control of OMB and Russell Vought. But did anyone notice that NIH has not issued a single new R01 award (or competing renewal) since Aug 1? So the halt last week, which was supposedly overruled, seems to have happened?

Truly awful behavior by OMB and Vought. And in case no one has noticed, NIH has issued zero new R01s or competing renewal R01s since August 1. So it seems they did in fact pause all funding last week, despite reports to the contrary.

Every Scientific Empire Comes to an End America’s run as the premier techno-superpower may be over.

Excellent but sad piece in @theatlantic.com by Ross Anderson, about the wholesale destruction of US science being executed by Trump and his followers, and how it echoes what Stalin and Hitler did to science in the USSR and Nazi Germany, causing scientists to flee www.theatlantic.com/science/arch...

I guess you've been reading the latest papers on deep learning models such as AlphaGenome and Evo2? 🤣

I listened to the clip. Vought is telling outrageous lies that he knows to be false. He is just an evil guy, there's no other way to interpret it.

I don't understand how you get to 5/8. If you fully fund a 4-year grant, doesn't that cost 4 times as much as funding just the first year? And what if a grant is in year 1 out of 4 - does this mean they fund the remaining 3 years now? How much of each year's budget goes to new grants on average?

check out the new paper led by @kuanhaochao.bsky.social In @elife.bsky.social: OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species doi.org/10.7554/eLif...

well, if you delete it, then you've lost your 23andMe account. If you signed up in the first place, you presumably found some usefulness in that. I'm saying that the upside (whatever subjective value that is) outweighs the downside for me, and for me the downside is very small.

I meant to write "it's really NOT that much of a risk" 🤣

I know genomes. Don't delete your DNA Too many people are panicking about 23andMe.

A little note of calm to reply to the WashPost and others who are worried about DNA data privacy: it's really that much of a risk: stevensalzberg.substack.com/p/i-know-gen...

Phenotype to genotype: A new and rapid approach using whole-genome sequencing Author summary Forward genetic mutagenesis screening is an unbiased approach for the identification of mutations linked to a phenotype of interest. While this approach can be a powerful tool for uncov...

Cool new paper out by @mfeltes.bsky.social and @stefarber.bsky.social, collaborating with my colleague Aleksey Zimin (and me). We used WGS to discover and map genes causing dark yolk mutations in zebrafish. Great combo of computational + wet bench science!
journals.plos.org/plosgenetics...

Stephen Colbert’s ‘Late Show’ canceled by CBS, to end in May 2026 The announcement came days after Colbert spoke out against the $16 million settlement paid by CBS News parent Paramount to settle a lawsuit filed by Donald Trump.

Sad: The @colbertlateshow is cancelled - this is just ridiculous. What depths will the media (and @ParamountPics) fall to? www.washingtonpost.com/style/2025/0...

Pitt BGSA on X: "we are thrilled to announce the 30th SOM Grad Symposium 2025 Distinguished Speaker: Dr. Steven Salzberg, Bloomberg Distinguished Professor, Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University Join us on 1st Oct 2025! https://t.co/ynkL7ByQBr" / X we are thrilled to announce the 30th SOM Grad Symposium 2025 Distinguished Speaker: Dr. Steven Salzberg, Bloomberg Distinguished Professor, Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University Join us on 1st Oct 2025! https://t.co/ynkL7ByQBr

Looking forward to visiting and speaking to the grad students at U. Pittsburgh medical school in a couple of months! x.com/BGSA_pitt/st...

Another consequence of the disastrous attack on NIH by Trump, Musk, and their followers

The world needs more scientists Trump and Musk's attacks on scientific research hurt everyone, including their own followers.

My latest take on the damage that the Trump administration is doing to science and medicine, and to the US reputation in research
open.substack.com/pub/stevensa...

sure but as far as we can tell, no intron looks like a HERV

Introns have to come from somewhere, right? @celineh2ooo.bsky.social and I looked at multiple genome alignments with 1000s of genomes and found 342 cases where humans (and our relatives) had gained a new intron. Still not sure where these come from, but it's a fascinating question

All of NIH funding to Northwestern University is frozen. This pause includes noncompeting approved funding, new and competing grants with fundable scores. No reimbursements for money already spent have been received since March. This situation is rarely reported so please Please get the word out!

I'm done with USOpen tennis events after this "innovation" that basically destroys the mixed doubles event. The new format is 2 4-game sets, no-ad scoring, and a tiebreak if the mini-sets are split. The whole match might last 30 min! Ridiculous www.usopen.org/en_US/news/a...

no but we'd love to add that. Agree that using existing repeat tools makes the most sense here