Steven Salzberg
@stevensalzberg.bsky.social
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
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
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.
f1000research.com
November 21, 2025 at 4:05 PM
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?
November 19, 2025 at 5:49 PM
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...
November 12, 2025 at 5:04 PM
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
Bluetorial-Jim Watson
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
November 8, 2025 at 3:07 PM
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...
Dis-Functional Medicine in the Surgeon General's office
What the heck is Functional Medicine anyway?
open.substack.com
November 2, 2025 at 3:30 PM
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...
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.
doi.org
October 31, 2025 at 11:44 AM
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...
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...
www.jcvi.org
October 29, 2025 at 11:26 PM
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.
Wow. Harvard nuking its PhD programs
- Science PhD admissions reduced by more than 75%
- Arts & Humanities reduced by about 60%
- Social Sciences by 50–70%
- History by 60%
- Biology by 75%
- The German department will lose all PhD seats
- Sociology from six PhD students to zero
- Science PhD admissions reduced by more than 75%
- Arts & Humanities reduced by about 60%
- Social Sciences by 50–70%
- History by 60%
- Biology by 75%
- The German department will lose all PhD seats
- Sociology from six PhD students to zero
Harvard FAS Cuts Ph.D. Seats By More Than Half Across Next Two Admissions Cycles | News | The Harvard Crimson
The Faculty of Arts and Sciences slashed the number of Ph.D. student admissions slots for the Science division by more than 75 percent and for the Arts & Humanities division by about 60 percent for th...
www.thecrimson.com
October 22, 2025 at 2:50 PM
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...
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.
cals.cornell.edu
October 14, 2025 at 3:09 PM
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
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...
brnw.ch
October 1, 2025 at 10:14 PM
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...
Academic freedom and freedom of speech are under assault, from both the left and the right
Everyone is afraid to speak right now.
stevensalzberg.substack.com
September 29, 2025 at 8:16 PM
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/
2025 #LaskerAward winner Lucy Shapiro asked: How do living organisms translate information from a linear genetic code into three-dimensional structures?
And with that, she broke open a new field. 🧪
@pnas.org
#Lasker2025 #systemsbiology
And with that, she broke open a new field. 🧪
@pnas.org
#Lasker2025 #systemsbiology
The Lasker~Koshland Special Achievement Award in Medical Science awarded to Lucy Shapiro | PNAS
Scientists can contribute to society in numerous ways. Some scientists discover new biological principles and found entirely new fields. Some scien...
www.pnas.org
September 15, 2025 at 11:34 PM
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...
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.
www.science.org
September 3, 2025 at 8:45 PM
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...
Reposted by Steven Salzberg
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/...
📊 PCAWG
📊 TCGA - Cleaner signals produced by a fantastic paper today from Peter Ge, @stevensalzberg.bsky.social & team)
www.science.org/doi/10.1126/...
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.
www.science.org
September 3, 2025 at 7:00 PM
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/...
📊 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 study of gene expression in the living human brain - Molecular Psychiatry
Molecular Psychiatry - A study of gene expression in the living human brain
www.nature.com
August 25, 2025 at 12:27 PM
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...
Reposted by Steven Salzberg
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...
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.
www.statnews.com
August 18, 2025 at 2:03 PM
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
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.
wapo.st
August 13, 2025 at 11:19 AM
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...
Every Scientific Empire Comes to an End
America’s run as the premier techno-superpower may be over.
www.theatlantic.com
August 3, 2025 at 9:05 PM
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...
OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species
doi.org
July 23, 2025 at 1:44 AM
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...
I know genomes. Don't delete your DNA
Too many people are panicking about 23andMe.
stevensalzberg.substack.com
July 19, 2025 at 8:18 PM
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...
journals.plos.org/plosgenetics...
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...
journals.plos.org
July 18, 2025 at 5:29 PM
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...
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...
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.
www.washingtonpost.com
July 18, 2025 at 11:44 AM
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...
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
x.com
July 10, 2025 at 4:50 PM
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 3-decade-old competition that enabled the emergence and evaluate of AlphaFold has run out of NIH funding.
The program will be terminated in weeks.
This is terminating success.
www.science.org/content/arti...
The program will be terminated in weeks.
This is terminating success.
www.science.org/content/arti...
July 3, 2025 at 2:09 PM
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...
open.substack.com/pub/stevensa...
The world needs more scientists
Trump and Musk's attacks on scientific research hurt everyone, including their own followers.
open.substack.com
June 7, 2025 at 3:02 PM
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...
open.substack.com/pub/stevensa...