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Steven Salzberg

@stevensalzberg.bsky.social
1.8K followers 117 following 176 posts

Bloomberg Distinguished Professor of BME, CS, and Biostats at Johns Hopkins Univ., tennis player, @StevenSalzberg1 on Twitter, lab: salzberg-lab.org, Substack blog: stevensalzberg.substack.com

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Steven Salzberg @stevensalzberg.bsky.social · 24/09/2026
I have some thoughts about the increasing distrust of science, caused largely by misinformation spread on social media. The anti-vaxxers are particularly damaging. They are undoing decades of progress, and I fear it will take decades to recover stevensalzberg.substack.com/p/why-scienc...
stevensalzberg.substack.com
Why Science Denialism Sets Us Back
Humans don’t always act in their own best interests.
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Steven Salzberg @stevensalzberg.bsky.social · 24/09/2026
Check our new @biorxiv-genomic.bsky.social preprint on a method for masking low-complexity regions in genome databases, led by Yuchin (Peter) Ge in my lab. Also includes a new release of a very large, pre-masked microbial database: www.biorxiv.org/content/10.6...
biorxiv.org
Improving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity Regions
Abstract Accurate taxonomic classification in metagenomics is often compromised by low-complexity sequences, which lead to chance matches that in turn cause sequences to be misclassified. Here we pres...
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Steven Salzberg @stevensalzberg.bsky.social · 13/09/2026
Check out our new preprint on thousands of novel recursive exons in the human genome (if you don't know about recursive exons, they are pretty cool), led by PhD student David Bass @davidb256.bsky.social : www.biorxiv.org/content/10.6...
biorxiv.org
Large-scale analysis of transcript data reveals thousands of recursive splicing events in human introns
Recursive splicing (RS) is a process in which an intron is removed from a nascent RNA molecule in two or more splicing events rather than one. We introduce a novel approach for detecting recursive spl...
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Steven Salzberg @stevensalzberg.bsky.social · 15/08/2026
Congratulations to Beril Erdogdu on successfully defending her Ph.D. thesis in Biomedical Engineering yesterday! Very well done, Dr. Erdogdu, and good luck in your postdoc at @ucberkeleyofficial.bsky.social!
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Steven Salzberg @stevensalzberg.bsky.social · 07/08/2026
I'm very pleased to be part of this paper on the first-ever complete diploid human genome, led by my (new!) Hopkins colleague @aphillippy.bsky.social and his lab, with contributions from Hayden Ji in my lab plus many other @jhu.edu and @hopkinsengineer.bsky.social faculty and students.
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Steven Salzberg @stevensalzberg.bsky.social · 07/07/2026
Our new genome annotation method relies almost entirely on transcriptome and alignment evidence, and as a result outperforms pretty much all other de novo pipelines. Check out the just-published paper led by Aleksey Zimin: rdcu.be/frSOg
rdcu.be
Efficient evidence-based genome annotation with EviAnn
Nature Methods - EviAnn surpasses existing genome annotation methods by leveraging gene expression and protein sequence homology evidence to achieve higher accuracy and efficiency.
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Steven Salzberg @stevensalzberg.bsky.social · 14/06/2026
AlphaFold2 is great, but sometimes it creates structures that aren't real - about 1 out of 435 times for its predictions with a score>70, as we report in our new preprint. With @jhu.edu undergrad Amanda Xu www.biorxiv.org/content/10.6...
biorxiv.org
Testing the reliability of AI-generated protein structures
Although AlphaFold2 and its competitors have demonstrated remarkable abilities to predict protein structure, more work is needed to explore the limitations of these methods. Here we investigated the r...
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Steven Salzberg @stevensalzberg.bsky.social · 09/06/2026
A scary new move against science and towards autocracy: OMB wants to grab the power to approve or cancel any and all federal grants, at the whim of its Director, Russell Vought: stevensalzberg.substack.com/p/a-dangerou...
stevensalzberg.substack.com
A dangerous move towards totalitarian science
The new rules proposed by Trump's henchman Russell Vought would destroy US science
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Steven Salzberg @stevensalzberg.bsky.social · 04/06/2026
A surprising finding: nearly all of the bacterial contamination in your grocery store's fresh or frozen chicken originates in a tiny number of breeders, not at the massive chicken breeding farms. We might be able to eliminate these contaminants very cheaply www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Steven Salzberg @stevensalzberg.bsky.social · 04/06/2026
Just found this inappropriate ad hominem attack on a recent PNAS paper by David Lipman. @dutchscientist.bsky.social just says it's "bad" without saying why he thinks so, and then erroneously claims Lipman was the handling editor (he wasn't). I read the paper; it's excellent.
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Reposted by Steven Salzberg
Nature Reviews Genetics @natrevgenet.nature.com · 21/05/2026
Our featured article: Annotating genomes at increased scale and resolution go.nature.com/3RlsRSY by Hyun Joo Ji, Mihaela Pertea & @stevensalzberg.bsky.social @jhu.edu
go.nature.com
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 function, providing researchers wit...
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Steven Salzberg @stevensalzberg.bsky.social · 19/05/2026
Congratulations Dr. Chao! Although he finished his Ph.D. last August, the official "hooding" ceremony was yesterday, where Ela Pertea and I conferred the hood to Kuan-Hao. @kuanhaochao.bsky.social
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Steven Salzberg @stevensalzberg.bsky.social · 04/05/2026
stevensalzberg.substack.com/p/my-convers...
stevensalzberg.substack.com
My conversation with Craig: how we decided to sequence the human genome
It all started with a discussion in 1998
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Steven Salzberg @stevensalzberg.bsky.social · 01/05/2026
I was saddened to learn yesterday that Craig Venter, with whom I published 20 papers in the 90s and 00s, died this week. He was a difficult person, but he transformed genomics by claiming, repeatedly, that we could do things far faster and at greater scale - and he delivered on those claims.
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Steven Salzberg @stevensalzberg.bsky.social · 18/04/2026
@jhuclsp.bsky.social posted a video of a talk I gave at JHU in 2000, where I was introduced by the legendary Fred Jelinek, whose work laid the foundation for today's AI language understanding abilities. My talk is a fun look back at where #genomics was 26 years ago: www.youtube.com/watch?v=Gh-m...
youtube.com
Steve Salzberg: Computational Methods for Genome Sequence Analysis
YouTube video by Center for Language & Speech Processing(CLSP), JHU
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Steven Salzberg @stevensalzberg.bsky.social · 07/04/2026
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...
usnews.com
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Steven Salzberg @stevensalzberg.bsky.social · 30/03/2026
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...
stevensalzberg.substack.com
AI is starting to look like pseudoscience
Not all of it, but some scientists are too eager to believe their own hype
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Steven Salzberg @stevensalzberg.bsky.social · 23/03/2026
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...
ucdavis.edu
Unlocking Longevity Insights From Ancient Bristlecone Pine
Scientists have sequenced the bristlecone pine genome, which could help unlock the secrets of this tree's exceptionally long life.
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Steven Salzberg @stevensalzberg.bsky.social · 04/03/2026
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...
stevensalzberg.substack.com
An Embarrassing Scandal for AI Research
AI scientists' trust in their own inventions is naïve
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Reposted by Steven Salzberg
BF Francis Ouellette @bffo.bsky.social · 23/02/2026
#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...
npr.org
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.
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Reposted by Steven Salzberg
Niranjan Nagarajan @niranjantw.bsky.social · 21/02/2026
🎆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
rdcu.be
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...
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Steven Salzberg @stevensalzberg.bsky.social · 19/02/2026
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
rdcu.be
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...
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Steven Salzberg @stevensalzberg.bsky.social · 17/02/2026
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
rdcu.be
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...
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Steven Salzberg @stevensalzberg.bsky.social · 14/02/2026
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
wapo.st
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.
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Steven Salzberg @stevensalzberg.bsky.social · 08/02/2026
US science is in trouble, and it doesn't have to be stevensalzberg.substack.com/p/making-ame...
stevensalzberg.substack.com
Making America Weak
The biggest own goal in modern history
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Steven Salzberg @stevensalzberg.bsky.social · 16/01/2026
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...
embl.org
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.
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Steven Salzberg @stevensalzberg.bsky.social · 15/01/2026
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...
nytimes.com
Chinese Universities Surge in Global Rankings as U.S. Schools Slip
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Steven Salzberg @stevensalzberg.bsky.social · 11/01/2026
should you see a Functional Medicine doc? Hmm... stevensalzberg.substack.com/p/functional...
stevensalzberg.substack.com
Functional Medicine Can Treat Almost Anything
Is it real or is it nonsense?
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Steven Salzberg @stevensalzberg.bsky.social · 07/01/2026
if you're interested, note that the time is UK time. In the US, that will be 9:00am.
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Reposted by Steven Salzberg
Anne Applebaum @anneapplebaum.wsocial.eu · 04/12/2025
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...
france24.com
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...
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Steven Salzberg @stevensalzberg.bsky.social · 29/11/2025
I can't stay quiet about what RFK jr is doing to the CDC and FDA: stevensalzberg.substack.com/p/dont-trust...
stevensalzberg.substack.com
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
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Steven Salzberg @stevensalzberg.bsky.social · 21/11/2025
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
f1000research.com
Slide: Open source, open access, and open data: why science moves faster in an open world has been published by F1000Research.
Read this work by Salzberg SL, at F1000Research.
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Steven Salzberg @stevensalzberg.bsky.social · 19/11/2025
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?
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Steven Salzberg @stevensalzberg.bsky.social · 12/11/2025
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...
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Steven Salzberg @stevensalzberg.bsky.social · 08/11/2025
great thread on Jim Watson from @jeremymberg.bsky.social, an insightful perspective
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Steven Salzberg @stevensalzberg.bsky.social · 02/11/2025
Our soon-to-be Surgeon General has some unscientific views. I have some thoughts about that... open.substack.com/pub/stevensa...
open.substack.com
Dis-Functional Medicine in the Surgeon General's office
What the heck is Functional Medicine anyway?
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Steven Salzberg @stevensalzberg.bsky.social · 31/10/2025
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...
doi.org
OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman species
OpenSpliceAI is an open, retrainable framework for splice site prediction that enables rapid, memory-efficient, cross-species analyses at scale with accuracy comparable to SpliceAI.
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Steven Salzberg @stevensalzberg.bsky.social · 29/10/2025
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...
jcvi.org
Remembering Hamilton O. Smith
Hamilton O. Smith August 31, 1931 – October 25, 2025 It is with profound sorrow that we announce the loss of Hamilton O. Smith, M.D., a...
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Steven Salzberg @stevensalzberg.bsky.social · 22/10/2025
Wow indeed. This is a disaster for U.S. science in so many ways. We're losing the future.
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Steven Salzberg @stevensalzberg.bsky.social · 14/10/2025
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...
cals.cornell.edu
Insectapalooza
Come see the bizarre, bad, and beneficial of the insect world.2025 date will be Saturday, October 18th from 9am to 3pm. Stocking Hall.
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Steven Salzberg @stevensalzberg.bsky.social · 01/10/2025
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
brnw.ch
Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes
Abstract. The study of cancer-associated microbiomes has gained significant attention in recent years, spurred by advances in high-throughput sequencing and metagenomic analysis. Microbiome research h...
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Steven Salzberg @stevensalzberg.bsky.social · 29/09/2025
it's been a while since I wrote a blog, but I had some thoughts: stevensalzberg.substack.com/p/academic-f...
stevensalzberg.substack.com
Academic freedom and freedom of speech are under assault, from both the left and the right
Everyone is afraid to speak right now.
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Steven Salzberg @stevensalzberg.bsky.social · 16/09/2025
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/
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Steven Salzberg @stevensalzberg.bsky.social · 03/09/2025
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...
science.org
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.
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Reposted by Steven Salzberg
Abraham Gihawi @abrahamgihawi.bsky.social · 03/09/2025
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/...
science.org
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.
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Steven Salzberg @stevensalzberg.bsky.social · 25/08/2025
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...
nature.com
A study of gene expression in the living human brain - Molecular Psychiatry
Molecular Psychiatry - A study of gene expression in the living human brain
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Reposted by Steven Salzberg
Ron Chusid @rchusid.bsky.social · 18/08/2025
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...
statnews.com
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.
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Steven Salzberg @stevensalzberg.bsky.social · 13/08/2025
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
wapo.st
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.
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Steven Salzberg @stevensalzberg.bsky.social · 03/08/2025
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...
theatlantic.com
Every Scientific Empire Comes to an End
America’s run as the premier techno-superpower may be over.
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Steven Salzberg @stevensalzberg.bsky.social · 23/07/2025
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...
doi.org
OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species
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