Steven Salzberg

Maryland

Professor and Contributor at Forbes

Bloomberg Distinguished Professor of BME, CS, and Biostats at Johns Hopkins Univ., tennis player, https://t.co/xwqVB2TYkL, @stevensalzberg.bsky.social

Articles

Science and skepticism

2 weeks ago | stevensalzberg.substack.com | Steven Salzberg

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The world needs more scientists

3 weeks ago | stevensalzberg.substack.com | Steven Salzberg

Most people alive today don’t realize how much science has improved their lives. Indeed, most people alive today wouldn’t even be here if not for the scientific and medical advances of the past 150 years. And for the billions of people alive today, most have much better lives than our recent ancestors did. Thanks for reading Science and skepticism! Subscribe for free to receive new posts and support my work. You don’t have to look back very far to learn how difficult life was for humans in the past.
We warned about dangerous gain-of-function work years ago.

2 months ago | stevensalzberg.substack.com | Steven Salzberg

I’ve been re-reading some things that I and others wrote about the dangers of creating deadly new viruses in the lab, “super bugs” as some have called them. Today I’m sharing some of my earlier commentary along with a fresh perspective, in light of the pandemic that the world suffered starting in 2020. Here’s what I wrote in late 2017. Thanks for reading Science and skepticism! Subscribe for free to receive new posts and support my work.
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling

2 months ago | biorxiv.org | Caleb Hallinan |Hyun Ji |Steven Salzberg |Jean Fan

AbstractThe accuracy of spatial gene expression profiles generated by probe-based in situ spatially-resolved transcriptomic technologies depends on the specificity with which probes bind to their intended target gene. Off-target binding, defined as a probe binding to something other than the target gene, can distort a gene's true expression profile, making probe specificity essential for reliable transcriptomics.
OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species

Mar 23, 2025 | biorxiv.org | Kuan-Hao Chao |Alan Mao |Anqi Liu |Steven Salzberg

AbstractThe SpliceAI deep learning system is currently one of the most accurate methods for identifying splicing signals directly from DNA sequences. However, its utility is limited by its reliance on older software frameworks and human-centric training data. Here we introduce OpenSpliceAI, a trainable, open-source version of SpliceAI implemented in PyTorch to address these challenges.
Virologists are still bringing dangerous, novel pathogens in from the wild

Mar 10, 2025 | stevensalzberg.substack.com | Steven Salzberg

So here’s what’s going on. A team of scientists in Wuhan, China collected viruses from bats in remote caves, brought the viruses back to Wuhan, and started doing experiments. They discovered that one of the viruses, which they called HKU5-CoV-2, seems to be really good at infecting human cells. How exciting, they thought! After more experimentation to confirm how dangerous this virus was, they published their results in a prestigious scientific journal, Cell, just a couple of weeks ago.
Conservation assessment of human splice site annotation based on a 470-genome alignment

Feb 20, 2025 | biorxiv.org | Ilia Minkin |Steven Salzberg |Johns Hopkins

AbstractDespite many improvements over the years, the annotation of the human genome remains imperfect. The use of evolutionarily conserved sequences provides a strategy for selecting a high-confidence subset of the annotation. Using the latest whole genome alignment, we found that splice sites from protein-coding genes in the high-quality MANE annotation are consistently conserved across more than 350 species.
The pointless destruction of the world's leading scientific and medical research system

Feb 16, 2025 | stevensalzberg.substack.com | Steven Salzberg

For 75 years, the U.S. has led the world in scientific research, most of it centered in our universities. Beginning in 1945 with a famous report by Vannevar Bush, the President’s science advisor, the U.S. has invested in science as a strategic effort to compete with its rivals and to build a better future.
RFK Jr. is not a serious person. Don't take him seriously.

Nov 29, 2024 | stevensalzberg.substack.com | Steven Salzberg

Well, president-elect Trump has announced that he will nominate Robert F. Kennedy Jr. to be the Secretary of Health and Human Services (HHS), putting him in charge of most of the nation's public health and medical research. I can't say strongly enough how unqualified RFK Jr. is for this job. He isn't qualified to come anywhere within a thousand miles of any medical or science-related issue, much less to be in charge of health policy for the whole country.
RFK Jr. is not a serious person. Don't take him seriously.

Nov 29, 2024 | genome.fieldofscience.com | Steven Salzberg

I can't say strongly enough how unqualified RFK Jr. is for this job. He isn't qualified to come anywhere within a thousand miles of any medical or science-related issue, much less to be in charge of health policy for the whole country. Virtually everything RFK says about science is wrong–actually, it's worse than that, because he speaks with such absolutely certainty, despite being wrong, that he convinces people to take actions that end up hurting themselves.