Congratulations to my colleagues in Biostatistics, @jhubiostat.bsky.social, for once again being ranked #1 in the nation, and to the Bloomberg School of Public Health, @johnshopkinssph.bsky.social, for also being ranked #1: www.usnews.com/best-graduat...

In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...

we just published (in G3, doi.org/10.1093/g3jo...) the genome of the oldest living thing on Earth: the bristlecone pine, which can live 5,000 years or more. Do we know yet what allows it to live so long? No, but the genome is a great place to start www.ucdavis.edu/climate/news...

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...

#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...

🎆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

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

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

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

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

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...

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...

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.

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...

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

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

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

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

In @elife.bsky.social, our OpenSpliceAI paper, led by @kuanhaochao.bsky.social, is now 'official' though it's been online since July. If you want to enjoy the reviewers' comments and our responses, check it out at: doi.org/10.7554/eLif...

My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...

Wow indeed. This is a disaster for U.S. science in so many ways. We're losing the future.

If you're anywhere near @cornelluniversity.bsky.social this Saturday, Oct 18, don't miss #Insectapalooza, the annual one-day insect festival! It's organized by @cornellcals.bsky.social Dept of Entomology cals.cornell.edu/entomology/r...

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

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/

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...

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/...

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...

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...

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

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...

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...

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...

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...

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

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

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...

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...

Bioinformatics folks: check out our @biorxivpreprint on a new, very efficient and accurate system for automated genome annotation, EviAnn, led by my colleague Aleksey Zimin: www.biorxiv.org/content/10.1...

can we all agree to stop using the phrase "very unique"? I know the world has bigger problems, but it's the weekend 😂

Looking forward to visiting the @donnellycentre.bsky.social at the Univ. of Toronto in 2 weeks!

My latest take on #covid19 and the role that gain-of-function research might have played–and how NIH ignored the alarm bells from many scientists: stevensalzberg.substack.com/p/we-warned-...

holy cow! This is a spark of amazing science news: www.washingtonpost.com/science/2025...

Congrats to my colleague and collaborator @benlangmead.bsky.social! Our 2012 paper on Bowtie2 (www.nature.com/articles/nme...), ranks 29th on the most-cited papers of the 21st century www.nature.com/articles/d41...