Sun, Ruping

PI @umnmedschool. Dynamics of cancer in light of genomic heterogeneity.
🖥️🧬🦀 🎼🏊

[Sun, Ruping @Sun_Ruping]

📣 RECOMB-CCB 2026 is now accepting submissions in Computational Cancer Biology!
📍 Thessaloniki, Greece | 📅 May 24–25, 2026
💡 Share your latest research in computational cancer science.
🔗 https://t.co/S7HWVVe00l
#ComputationalBiology #CancerResearch #CFP #RECOMBCCB2026

[Keyon Vafa @keyonV]

Can an AI model predict perfectly and still have a terrible world model?

What would that even mean?

Our new ICML paper formalizes these questions

One result tells the story: A transformer trained on 10M solar systems nails planetary orbits. But it botches gravitational laws 🧵

[Sean Pitroda, M.D. @SeanPitroda]

🧵1/
Tumor aneuploidy—long viewed as a hallmark of cancer—is emerging as a key biomarker of immune resistance.
In our latest @NatureGenet Perspective, we explore how aneuploidy can guide immunotherapy decisions and shape future treatment strategies.
🔗 https://t.co/2U0vAhnkQG

[Andrea Sottoriva @AndreaSottoriva]

Can we discover the rules of morphogenesis, tissue formation and tumour growth from spatial biology data using AI? We designed *stochastic* Neural Cellular Automata to model the temporal dynamics of biological tissues, from development to cancer. https://t.co/H1qxvT7jkO

[Andrew Ng @AndrewYNg]

One of the most effective things the U.S. or any other nation can do to ensure its competitiveness in AI is to welcome high-skilled immigration and international students who have the potential to become high-skilled. For centuries, the U.S. has welcomed immigrants, and this helped make it a worldwide leader in technology. Letting immigrants and native-born Americans collaborate makes everyone better off. Reversing this stance would have a huge negative impact on U.S. technology development.

I was born in the UK and came to the U.S. on an F-1 student visa as a relatively unskilled and clueless teenager to attend college. Fortunately I gained skills and became less clueless over time. After completing my graduate studies, I started working at Stanford under the OPT (Optional Practical Training) program, and later an H-1B visa, and ended up staying here. Many other immigrants have followed similar paths to contribute to the U.S.

I am very concerned that making visas harder to obtain for students and high-skilled workers, such as the pause in new visa interviews that started last month and a newly chaotic process of visa cancellations, will hurt our ability to attract great students and workers. In addition, many international students without substantial means count on being able to work under OPT to pay off the high cost of a U.S. college degree. Gutting the OPT program, as has been proposed, would both hurt many international students’ ability to study here and deprive U.S. businesses of great talent. (This won’t stop students from wealthy families. But the U.S. should try to attract the best talent without regard to wealth.)

Failure to attract promising students and high-skilled workers would have a huge negative impact on American competitiveness in AI. Indeed, a recent report by the National Security Commission on Artificial Intelligence exhorts the government to “strengthen AI talent through immigration.”

If talented people do not come to the U.S., will they have an equal impact on global AI development just working somewhere else? Unfortunately, the net impact will be negative. The U.S. has a number of tech hubs including Silicon Valley, Seattle, New York, Boston/Cambridge, Los Angeles, Pittsburgh and Austin, and these hubs concentrate talent and foster innovation. (This is why cities, where people can more easily find each other and collaborate, promote innovation.) Making it harder for AI talent to find each other and collaborate will slow down innovation, and it will take time for new hubs to become as advanced.

Nonetheless, other nations are working hard to attract immigrants who can drive innovation — a good move for them! Many have thoughtful programs to attract AI and other talent. There are the UK’s Global Talent Visa, France’s French Tech Visa, Australia’s Global Talent Visa, the UAE’s Golden Visa, Taiwan’s Employment Gold Card, China’s Thousand Talents Plan, and many more. The U.S. is fortunate that many people already want to come here to study and work. Squandering that advantage would be a huge unforced error.

Beyond the matter of national competitiveness, there is the even more important ethical matter of making sure people are treated decently. I have spoken with international students who are terrified that their visas may be canceled arbitrarily. One recently agonized about whether to attend an international conference to present a research paper, because they were worried about being unable to return. In the end, with great sadness, they cancelled their trip. I also spoke with a highly skilled technologist who is in the U.S. on an H-1B visa. Their company shut down, leading them — after over a decade in this country, and with few ties to their nation of origin — scrambling to find alternative employment that would enable them to stay.

These stories, and many far worse, are heartbreaking. While I do what I can to help individuals I know personally, it is tragic that we are creating such an uncertain environment for immigrants, that many people who have extraordinary skills and talents will no longer want to come here.

To every immigrant or migrant in the U.S. who is concerned about the current national environment: I see you and empathize with your worries. As an immigrant myself, I will be fighting to protect everyone’s dignity and right to due process, and to encourage legal immigration, which makes both the U.S. and individuals much better off.

[Full text, with links: https://t.co/6JNJz88Qyq ]

[Jason Sheltzer @JSheltzer]

Many incredible biomedical scientists have left academia for biotech/pharma.

While also noting many caveats, I want to share the observation that among top scientists who left academia for industry, their biggest new discoveries almost always happened in academia:

[Steven Salzberg 💙💛 @StevenSalzberg1]

Major, fatal errors found in the data and methods of a 2020 paper in @Nature, including millions of reads mis-identified as bacteria. The "cancer microbiome" in this study was simply not there. @abrahamgihawi @elapertea @YuchenGe1 @JenniferLu717 https://t.co/z5Aja84kiR

[Joao Ascensao @jaascensao]

Do you enjoy mysterious population stochasticity, chaotic dynamics, and/or popgen? Then this preprint might be for you!

Super excited to share a project that has been an exciting journey, and a fun blend of theory and experiment! @ohallats

https://t.co/df08f55E7H

[Patrick Hsu @pdhsu]

Is DNA all you need?

In new work, we report Evo, a genomic foundation model that learns across the fundamental languages of biology: DNA, RNA, and proteins. Evo is capable of both prediction tasks and generative design, from molecular to whole genome scale.

[Ivana Bozic @IBozic_]

We think we found something cool about cell-free DNA, would love to hear your thoughts/comments.
https://t.co/zfDzvUtAg0 1/n

[Emma V. Watson @game_of_chroms]

1/
Today I'm happy to share our work on tumor karyotype selection, explored experimentally in @elledge_stephen's lab!

https://t.co/S78qPawn3P

[Sun, Ruping @Sun_Ruping]

@ewa_szczurek @HelmholtzMunich Wow! Congratulations 👏

[Jason Sheltzer @JSheltzer]

Check out our new study in @ScienceMagazine, where we take on a 100-year-old debate: what’s the role of aneuploidy in cancer?

We discovered that genetically removing extra chromosomes blocks cancer growth - a phenomenon we call “aneuploidy addiction”. https://t.co/K5ny7Ureph

[Magnus Haughey @magnushaughey]

Do spatial patterns of tumour cells hold clues about sub-clonal evolution? We developed a random walk-based method to describe the dynamics of mutant sub-clones in human colorectal cancer using only their spatial arrangement. 🧵

https://t.co/VtGSlq4weI

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[Jeffrey West @mathoncbro]

This week in #MathOnco 240
-cell shape
-optimal control
-evolutionary tumor boards
-agent-based models

Art: @oceanlee2008, @huang_weini

Sign up here:
https://t.co/RASvJNhauC

[Jason Sheltzer @JSheltzer]

In my view, the most exciting papers about aneuploidy/chromosome engineering are on bioRxiv:

https://t.co/XyuWEF7p08 (@McclellandLab)
https://t.co/uddx6whCkT (@TeresaDavoli3)
https://t.co/wpNPHqZNRp (@Sun_Ruping)

And our work on "aneuploidy addictions":
https://t.co/cqHctKBorR

[Jason Sheltzer @JSheltzer]

Out now in @genomeresearch - our comprehensive analysis of the effects of aneuploidy on protein expression. Changes in gene dosage trigger complex compensatory mechanisms that are conserved from yeast to cancer! Great work led by @DrKlaske.

https://t.co/D3G6GlNIhA

[Jeffrey West @mathoncbro]

Just sent out #MathOnco newsletter issue 216:

-evolutionary game theory
-continuum resistance
-reaction-diffusion
-stochastic control
-clinical translation

Artwork: @TuratiVirginia 💯

[Genetics Society of America @GeneticsGSA]

Guo and Amir find that the change in the form of fitness trajectory due to clonal interference arises only through changes in the supply of beneficial mutations, independent of any changes in the average fitness effect of beneficial mutations. #GENETICS | https://t.co/Oov7ugrSYI

[Alex Xu @alexxubyte]

Great resource for visual learners: https://t.co/V7Cb1RkGGR is a site developed by the National University of Singapore. It visualizes data structures through animation.

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