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...

Very pleased to see that the BME and Biostatistics Departments at Hopkins, both of which I hold appointments in, are both ranked #1 in the US (@jhubiostat.bsky.social): www.usnews.com/best-graduat... and www.usnews.com/best-graduat...

We identify evidence of off-target probe binding in the 10x Genomics #Xenium v1 Human Breast Gene Expression Panel, compromising the accuracy of resulting #singlecell #spatialtranscriptomics profiles See our preprint for more details: www.biorxiv.org/content/10.1... #AcademicSky 🧵👇 1/n

By shedding light on off-target probe binding + providing a tool to enable prediction, we hope this work will enhance the quality of #spatialtranscriptomics data + improve reproducibility in #spatialtranscriptomics research (13/13) 🎉 Team Caleb Hallinan, Hayden Ji, and @stevensalzberg.bsky.social

@kuanhaochao.bsky.social and Alan Mao built an open-source version of SpliceAI, a deep learning model for predicting human splice sites, and it turned into quite a project! Many new features including training modules, check out the whole thread below

Check out our new paper in @narjournal.bsky.social on discovering extensive conservation of human introns across hundreds of other mammals, with Ilia Minkin academic.oup.com/nar/article/...

looks like Meta/Facebook pirated millions of books and papers to train its AI, as reported by @theatlantic.com: www.theatlantic.com/technology/a.... I searched the dataset and found that Meta stole 30 of my papers too - maybe I should sue 🤣

interesting: @zey.bsky.social wrote a piece for the @nytimes that makes several of the same points I just made in Substack. Her piece: nytimes.com/2025/03/16/o... and mine: stevensalzberg.substack.com/p/virologist.... I assume this is just 'great minds think alike' and that she didn't read my piece

fantastic thread to remind us of what science can do and is still doing, in this case led by government scientists at NASA

Virologists continue to bring dangerous bat viruses back into the middle of cities–and journals like @cellpress.bsky.social reward them with publications. My take: stevensalzberg.substack.com/p/virologist...

Holy cow. This appears to be blatantly illegal but that's how our gov't is operating now.

How can the Utah legislature be so stupid? This move will harm children, and it's based on a belief in conspiracy theories www.nytimes.com/2025/02/26/w...

Friends, LiftOn is now published in @genomeresearch.bsky.social! LiftOn maps genes across genomes using a protein-centric, homology-based approach with both DNA & protein alignments @stevensalzberg.bsky.social Mihaela Pertea, Jakob Heinz, Alaina Shumate, Celine Hoh, Alan Mao doi.org/10.1101/gr.2...

Holy s***. Virologists in China are still going out in the wild to find new viruses in bats, bringing them back to Wuhan, and running dangerous experiments. Haven't they learned anything? www.nytimes.com/2025/03/03/o...

I talked to NIH officials, current and former, about what's been happening inside the agency since the Trump administration shut down their grantmaking pipeline in January. Their stories showed just how willing our new leaders are to break the law: www.theatlantic.com/health/archi...

@nytimes.com reveals the tech bros and others who form Elon Musk's DOGE staffers. These are the faces of modern-day cruelty. Maybe they are not sociopaths, but their boss is, and they are enabling him www.nytimes.com/interactive/...

@jeffbezos has decided the @washingtonpost.com editorial pages will now be the Jeff Bezos editorial pages. And he says that newspapers don't need broad-based, thoughtful opinion sections because "the internet does that job." Could he be any more dishonest? No, I didn't think so x.com/jeffbezos/st...

“Totalitarianism in power invariably replaces all first-rate talents, regardless of their sympathies, with those crackpots and fools whose lack of intelligence and creativity is still the best guarantee of their loyalty.” -Hannah Arendt, “The Origins of Totalitarianism,” 1951. It's happening now 😰

my thoughts on the destructive chaos targeting university research right now. Btw I've left @forbes and moved to @SubstackInc, where all my content is free: stevensalzberg.substack.com/p/the-pointl...