Steven Salzberg

An Embarrassing Scandal for AI Research AI scientists' trust in their own inventions is naïve

Deep learning researchers created fake citations to support their claims in 51 papers at the latest @neuripsconf.bsky.social conference. I have concerns: stevensalzberg.substack.com/p/an-embarra...

AI is helping individual scientists, study suggests — but not science Artificial intelligence is helping researchers advance their careers and drill deeper into specific questions, but it is not necessarily benefiting science on the whole.

#ShortWave #Podcast on @npr.org | AI is helping individual scientists, study suggests -- but not science | #Bioinformatics #Proteomics #Genomics #Science #AI 🧬 🖥️ 🧪 CC/ @stevensalzberg.bsky.social
⬇️
www.npr.org/2026/02/17/n...

While leading the team sequencing the bacterium, B. anthracis, from the 2001 anthrax attacks, we had the rare opportunity to re-sequence and re-assemble an entire genome of the same strain of anthrax. All 5.3 million bases were identical to our original assembly. It was remarkable.

Setting higher standards for reports of microbial species in human cancers Nature Cancer - Nagarajan and colleagues overview the current challenges in microbiome analyses from human cancer samples and discuss the optimal practices for improving the standards of reporting...

🎆Very excited to share our perspective piece calling for higher standards in reports on microbial detection in cancers! It was great to put this together with some of the leaders in the field including @stevensalzberg.bsky.social @rafalab.bsky.social Barry Marshall and Eske Willerslev: rdcu.be/e4IaU

Setting higher standards for reports of microbial species in human cancers Nature Cancer - Nagarajan and colleagues overview the current challenges in microbiome analyses from human cancer samples and discuss the optimal practices for improving the standards of reporting...

Happy to share this free link to our new paper on the perils of trying to find microbes in human cancers, which appeared today in NatureCancer. Co-authors include Nobel laureate
Barry Marshall, ancient DNA Eske Willerslev, @niranjantw.bsky.social, Jacques Neefjes, @rafalab.bsky.social: rdcu.be/e4IaU

Annotating genomes at increased scale and resolution Nature Reviews Genetics - In this Review, Ji et al. overview how rapidly advancing experimental and computational methods are enabling improved and automated annotation of gene structure and...

Our new review on genome annotation just appeared in @naturerevgenet.bsky.social, with a particular focus on the human genome, with Hayden Ji and Mihaela Pertea: rdcu.be/e4mI1

ICE plans to spend $38.3 billion turning warehouses into detention centers ICE plans to spend $38.3 billion converting warehouses into detention centers, according to planning documents, more than the annual budgets of 22 states.

So now the US is spending the enormous sum of $38 billion to build concentration camps? ICE is calling them "detention centers" but we know what they really are. I cannot believe my country would do this. Everyone should speak out against it wapo.st/3OfarSk

time to shut it down permanently

Making America Weak The biggest own goal in modern history

US science is in trouble, and it doesn't have to be
stevensalzberg.substack.com/p/making-ame...

3000 users doesn't mean it works. It just means people were curious to try it, which isn't surprising given that it's the AlphaFold people 😅

yeah but I don't believe its predictions are any good, as I explained in detail to @carlzimmer.com. See the (brief) quotes of mine in his @nytimes.com piece, although naturally we had a much longer conversation

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...

Chinese Universities Surge in Global Rankings as U.S. Schools Slip

I strongly suspect this ranking system is driven by massive numbers of papers, not by quality. This has been widely reported over the past decade or more www.nytimes.com/2026/01/15/u...

Functional Medicine Can Treat Almost Anything Is it real or is it nonsense?

should you see a Functional Medicine doc? Hmm... stevensalzberg.substack.com/p/functional...

if you're interested, note that the time is UK time. In the US, that will be 9:00am.

I watched them, and it seems that Marty Makary actually believes the crazy claims he's making. Or maybe he's a very good actor, but either way, it's not a good look for him.

Zach, it's easy for you to throw out unsubstantiated claims, but I did nothing of the sort. I have published multiple papers on viruses (mostly influenza but also SARS-CoV-2) and related topics, and I didn't write any Forbes columns "based on stuff from conspiracy theorists." I stand by what I wrote

also my name should be spelled with the final "n", as in Steven not Steve.

really? Marty Makary really thinks Lyme disease is "an escape biowarfare agent"? He can't truly believe that - he's smart enough to know that's ridiculous. So he's just posturing?

Trump envoys press plan with Ukraine as sanctions eased on Russia President Donald Trump's envoys were to meet Thursday with Ukrainian negotiators for the third time in two weeks to press his plan to end the war as his administration eased economic pressure on Russi...

Two days after Witkoff and Kushner met Putin, the Treasury Department partially suspended sanctions on Russia announced last October
www.france24.com/en/live-news...

it's not just that they have a record of publishing GoF - twice now they have published editorials, signed by a large group of virologists including their EiC, that defended GoF as critical work that has led to all sorts of breakthroughs. In other words, they doubled down on GoF

Don't trust the CDC while RFK Jr. is in charge The HHS secretary, a notorious anti-vaxxer, is now posting his crank views on CDC's website

I can't stay quiet about what RFK jr is doing to the CDC and FDA:
stevensalzberg.substack.com/p/dont-trust...

yes, this looks like straight-up gain-of-function research in bat coronaviruses. Creating new recombinant viruses with potentially greater pathogenicity, and doing this under BSL-2 conditions which are not at all strict. And the Journal of Virology published it, unsurprising given their record

How interesting that my 2016 invited talk on Open Science now has a DOI and a link to the talk (on YouTube) where anyone can watch it. If you or your students are interested, check it out - and thanks to F1000Research for making this accessible f1000research.com/slides/5-1701

no, go ahead and call him an idiot, it's well-deserved 😆

thanks @arking.bsky.social - did you have direct experience with this? I know the rules are still in place, but I'm wondering if anyone has experienced it for their own grants

does anyone have experience yet of whether NIH is permitting the standard 25% carry-over on grants from one year to the next? (Eg if <25% of budget is unspent in year N, this automatically gets carried over to year N+1.) Or do we need to spend 100% of our budget each year to avoid losing it?

Very pleased to see that 4 faculty from our Center for Computational Biology (incl 2 @jhu-bdps.bsky.social) are listed in @clarivateag.bsky.social 2025 #HighlyCitedResearchers: Mihaela Pertea, @mikeschatz.bsky.social, @timp0.bsky.social, and me clarivate.com/highly-cited...

great thread on Jim Watson from @jeremymberg.bsky.social, an insightful perspective

Dis-Functional Medicine in the Surgeon General's office What the heck is Functional Medicine anyway?

Our soon-to-be Surgeon General has some unscientific views. I have some thoughts about that... open.substack.com/pub/stevensa...