John Prensner

All- don't miss the chance to register for the European Association for Cancer Research meeting in Budapest in June.

I'll be there if you want to chat about all things microproteins!

#EACR
#CancerResearch

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now?
www.nature.com/articles/s41...

More functional data, many thousands of words removed, and a few other updates from last year's preprint.

China turns the tables in biotech For at least a century, major scientific research initiatives have reliably occurred in the United States, usually in response to geopolitical competition. This helped establish the country’s status a...

“Success in US science has come from sustained funding and welcoming the best talent from around the world, yet both of these advantages are in decline”

www.science.org/doi/10.1126/...

Check out the very important topic:
how does poverty influence childhood cancer biology and treatment response?

wonderful work from Birgit Knoechel and Kira Bona!
@huntsmancancer.bsky.social
@danafarber.bsky.social

www.biorxiv.org/content/10.6...

Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...

Hallmarks of cancer—Then and now, and beyond Hanahan revisits the evolving framework of cancer hallmarks, synthesizing 25 years of conceptual refinement into a multidimensional view of tumor biology. This review highlights how aberrant capabilit...

Today at Cell: A new #HallmarksofCancer review by Doug Hanahan: www.cell.com/cell/fulltex...
This review marks 25 years since the original seminal Cell review by Hanahan & Robert Weinberg and its impactful follow up in 2011.
@cp-cell.bsky.social @cellpress.bsky.social

From the great @xuebingwu.bsky.social and team!

Highly recommend 👀

A protest about ICE in Ann Arbor

A protest against ICE in Ann Arbor

“The power of the people is greater than the people in power”

Even at 10F.

Ann Arbor this evening.

Systematic Analysis of C-Termini of Small Open Reading Frame-Encoded Peptides in Human Cancer Cell Lines The C-termini often regulate protein biological functions through specific structures or modifications. Small open reading frame-encoded peptides (SEPs) make up a novel class of gene expression products that participate in various biological activities. Their C-termini have also been found to affect their function, but the polymorphism of SEPs’ C-termini has not yet been systematically elucidated. Using C-terminal proteomics, we identified 3636 C-terminal peptides from 2168 proteins in three human cancer cell lines, including 3364 peptides from 1901 classical proteins and 272 peptides from 267 SEPs. Approximately 20% of all of the identified C-terminal peptides had been reported in previous studies, originating from mRNA alternative splicing or protease cleavage, while more than 85% of the C-terminal peptides from SEPs were novel. Bioinformatics analysis revealed that most new SEP C-termini are likely produced by protease cleavage by the KLK, MMP, and CAT protease families. Others without accurately predicted hydrolysis sites may originate from alternative splicing or protein trimming. The intact and hydrolysis products of some SEPs were verified by immunoblotting. Some cleavage occurs in the predicted domain, which might affect SEPs’ function. This study enriches the SEP sequence information, provides experimental evidence for SEP in vivo processing, and supports the subsequent functional analysis of SEP.

Systematic analysis of C-termini of small open reading frame-encoded peptides.

#Riboseq
#proteomics
#darkproteome

pubs.acs.org/doi/10.1021/...

The inside/ outside temperature differential exceeds 75 degrees this morning in Ann Arbor!

Sausage with eggplant with tomato sauce.

Lunch at Cafe du Lys in Geneva today. Magnificent!

New preprint on technologies to scale up CRISPR screens.

We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.

We also introduce an approach for cloning lentiviral libraries with billions of elements.

Congress passes bill to fund U.S. science agencies, rebuffing Trump's requested cuts The Senate voted to provide billions more to NASA, NOAA and the National Science Foundation than the president had asked for.

Nice to see strong support in Congress: “In an 82-15 vote, the Senate approved a minibus budget bill to fund agencies involved in science and the environment, among other issues, through Sept. 30. The bill passed in the House last week by a vote of 397 to 28.” www.nbcnews.com/politics/pol...

Time for some fun!
A lovely paper on mathematical oncology.

🧪

#Math
#Cancer
#CANsky

www.biorxiv.org/content/10.6...

Bus with sign that says AAATA

Ann Arbor- where even the buses love to think about alternative polyadenylation sequences.

#RNAsky

Kids with brain cancer were already in a life and death struggle. Then came Trump The US president vowed to ‘end childhood cancer’. But his administration is dismantling the search for a cure and sending families scrambling for treatment

#ChildhoodCancer advocates-
This is a powerful piece on the negative impact of Trump administration policies on children with brain cancer, written by a spouse who lived this horror.

#DMG/DIPG
#ETMR
#Medulloblastoma
#PEDCAN

www.theguardian.com/us-news/ng-i...

Read our full statement by AAP President Dr. Andrew Racine on today’s HHS announcement about the childhood immunization schedule: www.aap.org/en/news-room...

Introducing you all to @mishamehta.bsky.social who has spent tireless hours advocating for children with brain tumors, supporting researchers doing their work, and building community for other families.

We are indebted to her: www.youtube.com/watch?v=_r_7...

#PEDCan
#CanSky
#CancerSurvivors

Humpback whale genomes reflect the increased efficiency of commercial whaling Humpback whale genomes reflect shifts in whaling practices and their potential impact on the animals’ adaptive capacity.

A new #ScienceAdvances study shows that commercial whaling in the Southern Ocean over the past century reduced the genetic diversity—and possibly the evolutionary fitness—of the region’s humpback whales. https://scim.ag/4anxPpM

My lab is hiring a postdoc (ERC funded)! If you're interested, get in touch!

Figure S7 with panels A through UU

Wow this is a seriously serious supplementary figure from @cellpress.bsky.social today. Panels A through UU.

I get that Cell likes to minimize the number of supplementary figures. But is this really what is happening here?

www.cell.com/cell/fulltex...

Whoa!

New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:

THE ELEPHANT IN THE ROOM Kay Ryan The room is almost all elephant. Almost none of it isn't. Pretty much solid elephant. So there's no room to talk about it.

The room is
almost all
elephant.
Almost none
of it isn’t.
Pretty much
solid elephant.
So there’s no
room to talk
about it.

-Kay Ryan, “The Elephant in the Room”
#everynightapoem

So honored to take this position with @wearecbtn.bsky.social and it will be delightful to work on behalf of the pediatric brain tumor community!

Battle between Trump and universities hurting scientific research in need of federal funding Federal research funding to universities has fueled breakthroughs for years. The White House is pressuring universities to align with the president's political agenda, or risk losing their funding.

Very well done story on 60 Minutes about the harms of grant terminations and freezes at Harvard with Joan Brugge, Don Engbar, David Liu, and a very compelling young cancer patient, now cured with Liu's technology.

Transcript and video here

www.cbsnews.com/news/researc...

The R2 platform : Democratizing bioinformatics through an easily accessible public online software platform for non-experts in the field of Genomics

r2platform.com

#genomics #datascience #expertise #fair #public #science #bioinformatics #nocode #tcga #gtex #depmap

JAMA viewpoint cover: "The New Clinician-Scholars—Dual Training in Medicine and Humanities Drives Health Research Innovation" by Vinayak Jain, Kayla Zamanian, and Lakshmi Krishnan. Published online September 18, 2025.

💬 Viewpoint: The evolving health care landscape necessitates a new clinician-scholar paradigm incorporating humanities and social sciences to address complex challenges and enhance scientific inquiry and health outcomes.

ja.ma/4qtBLL0

I feel like I’m going to reference this all the time. A+ meme.