Lightnews — Scholar-powered news

Steven Salzberg @stevensalzberg.bsky.social · 6d

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

2

Steven Salzberg @stevensalzberg.bsky.social · 8d

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

2 3

Steven Salzberg @stevensalzberg.bsky.social · 22d

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/

Albert and Mary Lasker Foundation @laskerfdn.bsky.social · 22d

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

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

1 5

Steven Salzberg @stevensalzberg.bsky.social · 29d

this is hilarious. AI fails again 🤣

1

Steven Salzberg @stevensalzberg.bsky.social · Sep 3

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

7 18

Reposted by Steven Salzberg

Abraham Gihawi @abrahamgihawi.bsky.social · Sep 3

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/...

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

1 2 2

Steven Salzberg @stevensalzberg.bsky.social · Aug 27

Congrats @kuanhaochao.bsky.social ! It's been great having you in the lab, and I can't wait to see what you do next!

1

Steven Salzberg @stevensalzberg.bsky.social · Aug 25

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

1 7

Reposted by Steven Salzberg

Ron Chusid @rchusid.bsky.social · Aug 18

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

5 110 290

Steven Salzberg @stevensalzberg.bsky.social · Aug 13

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

2 10

Steven Salzberg @stevensalzberg.bsky.social · Aug 8

I agree that it's clearly illegal to put all grant funding under the absolute control of OMB and Russell Vought. But did anyone notice that NIH has not issued a single new R01 award (or competing renewal) since Aug 1? So the halt last week, which was supposedly overruled, seems to have happened?

2 2

Steven Salzberg @stevensalzberg.bsky.social · Aug 8

Truly awful behavior by OMB and Vought. And in case no one has noticed, NIH has issued zero new R01s or competing renewal R01s since August 1. So it seems they did in fact pause all funding last week, despite reports to the contrary.

3 3

Steven Salzberg @stevensalzberg.bsky.social · Aug 3

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

2

Steven Salzberg @stevensalzberg.bsky.social · Jul 27

I guess you've been reading the latest papers on deep learning models such as AlphaGenome and Evo2? 🤣

3

Steven Salzberg @stevensalzberg.bsky.social · Jul 27

I listened to the clip. Vought is telling outrageous lies that he knows to be false. He is just an evil guy, there's no other way to interpret it.

Steven Salzberg @stevensalzberg.bsky.social · Jul 23

I don't understand how you get to 5/8. If you fully fund a 4-year grant, doesn't that cost 4 times as much as funding just the first year? And what if a grant is in year 1 out of 4 - does this mean they fund the remaining 3 years now? How much of each year's budget goes to new grants on average?

1

Steven Salzberg @stevensalzberg.bsky.social · Jul 23

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

1 7

Steven Salzberg @stevensalzberg.bsky.social · Jul 20

well, if you delete it, then you've lost your 23andMe account. If you signed up in the first place, you presumably found some usefulness in that. I'm saying that the upside (whatever subjective value that is) outweighs the downside for me, and for me the downside is very small.

Steven Salzberg @stevensalzberg.bsky.social · Jul 19

I meant to write "it's really NOT that much of a risk" 🤣

1

Steven Salzberg @stevensalzberg.bsky.social · Jul 19

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

3 1 5

Steven Salzberg @stevensalzberg.bsky.social · Jul 18

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...

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

2 7

Steven Salzberg @stevensalzberg.bsky.social · Jul 18

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

Steven Salzberg @stevensalzberg.bsky.social · Jul 10

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

2 5

Steven Salzberg @stevensalzberg.bsky.social · Jul 3

Another consequence of the disastrous attack on NIH by Trump, Musk, and their followers

Nikolai Slavov @slavov-n.bsky.social · Jul 3

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...

1 3

Steven Salzberg @stevensalzberg.bsky.social · Jun 7

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...

The world needs more scientists

Trump and Musk's attacks on scientific research hurt everyone, including their own followers.

open.substack.com

1 6