iiinova — where your digital self keeps evolving

Denis Wirtz @deniswirtz.bsky.social · 08/09/2026

Using the new assay VITAL3D, we observe fundamental differences in the drug responsiveness of breast cancer cells for preclinical drug evaluation in 2D vs. 3D settings. More details here: www.biorxiv.org/content/10.6...

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Pedro Beltrao @pedrobeltrao.bsky.social · 03/09/2026

8.8% success rate for the ERC Starting Grant is not acceptable. It is a lottery at this point with so many great scientists and ideas left to be funded. We keep talking about the competitiveness of Europe and we can't agree to properly fund our best instrument for scientific innovation.

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Richard Sever @richardsever.bsky.social · 03/09/2026

You can now update bioRxiv/medRxiv preprints with funding information after the fact. Authors often omit/don't have all funding info when submitting, but funders understandably want it there. This solves the problem without requiring you to submit a whole new paper. openrxiv.org/updating-fun...

openrxiv.org

Updating funder information on preprints - openRxiv

For the past year, bioRxiv and medRxiv authors have been able to include funder information with their preprints. This can be entered in a dedicated field during the submission process, using Research...

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Eric Schares @eschares.bsky.social · 31/08/2026

🚨Update: Our analysis of global APC expenditure has now been expanded to cover more publishers (7 -> 14) and more years (2019-2025). We estimate $15B in APCs paid over seven years, $3.7B in 2025 alone. Elsevier crosses the $1B threshold by itself in 2025. arxiv.org/abs/2608.16322 #ScholComm

Line chart showing 5 biggest publishers from 2019-2025

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Richard Sever @richardsever.bsky.social · 27/08/2026

$3.7 billion spent on APCs in 2025. That's ~1000X more than it costs to run bioRxiv/medRxiv. Worth thinking about as we consider how to fund infrastructure... arxiv.org/pdf/2608.16322

arxiv.org

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Jason Moore @moorejh.bsky.social · 18/08/2026

NIH review

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Adam Phillippy @aphillippy.bsky.social · 06/08/2026

For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]

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Denis Wirtz @deniswirtz.bsky.social · 18/07/2026

3D multi-omics tumour atlases: from technology to biology and clinical translation Read this Nature Reviews Cancer paper here:https://www.nature.com/articles/s41568-026-00940-0

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Prasad Jallepalli, MD, PhD @prasad.bsky.social · 18/07/2026

98% of all FDA-approved drugs originate from NIH-funded studies in universities, academic medical centers, and research institutes without that investment, there would be no commercial drug or device development to speak of

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Denis Wirtz @deniswirtz.bsky.social · 09/07/2026

A detailed protocol for CODA to segment tissue components in histological sections for 3D reconstructions. Led by Johns Hopkins U. colleague Prof. Kiemen. Use this protocol here: www.nature.com/articles/s41...

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Denis Wirtz @deniswirtz.bsky.social · 07/07/2026

That was a demolition. No cinema, no drama, just goal after goal.

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Denis Wirtz @deniswirtz.bsky.social · 07/07/2026

I repeat «Ceci n’est pas un goal »

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Denis Wirtz @deniswirtz.bsky.social · 07/07/2026

« Cecí n’est pas un goal »

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Prasad Jallepalli, MD, PhD @prasad.bsky.social · 06/07/2026

www.nytimes.com/2026/07/06/u... an ominous trend: graduate admissions are down 15 percent from last year, on top of an 11 percent decrease from the previous year we are destroying our seed corn

nytimes.com

Research Universities Are Admitting Fewer Ph.D.s, a Bad Sign for Science

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Eric Topol @erictopol.bsky.social · 04/07/2026

On our 250th birthday, celebrating the contribution of immigrants and international collaboration —46% of people with doctoral-level degrees working in US science and engineering fields are foreign-born

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Ari B Friedman @abfriedman.com · 02/07/2026

"Most important, the system would be deliberately designed to insulate the selection of scientific projects from political influence[...]. Its lodestar would be scientific merit as determined by the views of thousands of established scientists who would volunteer their time [...]."

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Prasad Jallepalli, MD, PhD @prasad.bsky.social · 02/07/2026

special issue of @science.org on American science at 250 www.science.org/toc/science/...

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Denis Wirtz @deniswirtz.bsky.social · 02/07/2026

Article by Johns Hopkins President Ron Daniels about the value of academic research and the highly productive partnership between academic institutions and the federal government. Read it here: www.science.org/eprint/VXUK8...

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Denis Wirtz @deniswirtz.bsky.social · 01/07/2026

Come back from the dead 🇧🇪

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Jeff Coller @jmcoller.bsky.social · 24/06/2026

Ten months ago I had never written an op-ed. I believed the work spoke for itself. It doesn't. When the government calls a lifesaving technology unsafe and scientists stay silent, the silence becomes the story. A new @jhu.edu profile on why I stopped staying quiet: hub.jhu.edu/2026/06/24/j...

hub.jhu.edu

A staunch voice in support of science

Jeff Coller, a pioneering RNA biologist, has spent the past year vehemently advocating for the lifesaving promise of research in the face of federal cuts

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Denis Wirtz @deniswirtz.bsky.social · 22/06/2026

3D reconstruction reveals highly conserved vascular network architecture despite phylogenetic diversity spanning >300M years of evolution. Moer here: www.biorxiv.org/content/10.6...

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Denis Wirtz @deniswirtz.bsky.social · 19/06/2026

The great colleague Rong Fan led a team of experts at Yale, Hopkins, and UCSD to write a review on 3D multi-comics of tissues and tumors. Check it out: www.nature.com/articles/s41...

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Denis Wirtz @deniswirtz.bsky.social · 18/06/2026

Immune remodeling during early pancreatic cancer progression. Individual immunes cells around PanIN lesions are mapped using CODA More here: www.sciencedirect.com/science/arti...

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Denis Wirtz @deniswirtz.bsky.social · 18/06/2026

A 3D morphogenetic blueprint for metastatic outgrowth in breast cancer 3D reconstructions of mets were done using our CODA workflow More here: www.cell.com/cell/fulltex...

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Adam Phillippy @aphillippy.bsky.social · 13/06/2026

T2T roadshow this week! ✈️ Monday, ESHG talk on personalized genomes and Robertsonians ✈️ Wednesday, Sanger ToL talk on great ape acrocentric chromosomes 🚂 Thursday, QMUL talk on a little bit of both 🚇 Friday, London reunion with T2T legend @sergeynurk.bsky.social 🎉

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Denis Wirtz @deniswirtz.bsky.social · 12/06/2026

ICYMI, Hopkins will provide $280M in mid-size and large grants to support faculty for 2 years (1) $160M for all life scientists (from basic to bioengineering, from policy to translation) (2) $120M for all science and engineering. This cannot replace federal funding, not even close, but it helps.

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Denis Wirtz @deniswirtz.bsky.social · 10/06/2026

ncredibly exciting announcement. Johns Hopkins University will provide $80M per year for the next two years to support large Life Sciences projects. (1) Transformational Science Teams awards: >$10M each, $40M/year. (2) High-impact individual awards: $200-500K each, $40M/year

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Denis Wirtz @deniswirtz.bsky.social · 07/06/2026

Visiting Duke University’s VP for Research Office

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Denis Wirtz @deniswirtz.bsky.social · 05/06/2026

Columns at Homewood Johns Hopkins University

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Denis Wirtz @deniswirtz.bsky.social · 28/05/2026

Early morning at Homewood campus

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Denis Wirtz @deniswirtz.bsky.social · 25/05/2026

Spatial Regulation of CAR Signaling Enables Logic-Gated Activity Amazing paper led by PhD student Tushar Nichakawade in the Vogelstein/Kinzler group at Hopkins. More here: www.biorxiv.org/content/10.6...

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Denis Wirtz @deniswirtz.bsky.social · 24/05/2026

It’s that time of the day…

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Denis Wirtz @deniswirtz.bsky.social · 23/05/2026

A very Warholian 3D reconstruction of a developing embryo. We used CODA. More here: www.biorxiv.org/content/10.6...

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Lisa Fazio @lkfazio.bsky.social · 21/05/2026

Glad to see this from the president of Johns Hopkins and the chancellor of U Kansas A rare public acknowledgement from university leaders that the current NIH and NSF funding delays are not okay and are a violation of Congressional intent. www.wsj.com/opinion/get-...

wsj.com

Opinion | Get the Federal Science Money Flowing

The NIH has been holding back grants from funds Congress has already approved.

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Denis Wirtz @deniswirtz.bsky.social · 20/05/2026

Mapping of immune cells in 3D in the vicinity of precancers of the human pancreas (PanIN) at single-cell resolution. We used CODA. Read about it here:https://www.cell.com/cell-press-blue/fulltext/S3051-3839(26)00006-X

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Denis Wirtz @deniswirtz.bsky.social · 20/05/2026

Mapping of immune cells in 3D in the vicinity of precancers of the human pancreas (PanIN) at single-cell resolution. We used CODA. Read about it here: www.cell.com/cell-press-b...

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Denis Wirtz @deniswirtz.bsky.social · 17/05/2026

Surprisingly (to me, at least), CODA 3D mapping shows that the density of cells in a pancreatic tumor is massively lower than in healthy tissues. Tumors are first and foremost WMDs: they destroy acini and ducts.

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Denis Wirtz @deniswirtz.bsky.social · 16/05/2026

Bagels here, bagels there, bagels everywhere

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Denis Wirtz @deniswirtz.bsky.social · 09/05/2026

Download our updated database of postdoc fellowships from different foundations and agencies. We identified 275 fellowships. For each entry, we provide description of the fellowship, focus, amount, deadline, eligibility, etc. Download this database here: research.jhu.edu/rdt/funding-...

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Denis Wirtz @deniswirtz.bsky.social · 07/05/2026

Today I’m giving the introduction lecture at the neurosurgery research day at the Johns Hopkins School of Medicine They started their day at 4 am this morning

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Denis Wirtz @deniswirtz.bsky.social · 03/05/2026

Big paper coming out soon. Using AI, we mapped embryos of mice, alligators, turtles, rhesus macaques, and chickens in 3D and single-cell resolution. We discovered something truly remarkable...stay tuned!

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Denis Wirtz @deniswirtz.bsky.social · 02/05/2026

3D multi-omic single-cell maps of responsive vs. non-responsive regions of PDAC tumors to chemotherapy. Maps generated using CODA by PhD student Andre Forjaz. Follow his work here: scholar.google.com/citations?hl... More here: www.biorxiv.org/content/10.6...

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Denis Wirtz @deniswirtz.bsky.social · 30/04/2026

View from the Johns Hopkins Bloomberg Center in DC

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Denis Wirtz @deniswirtz.bsky.social · 30/04/2026

Visiting congress today to advocate for research

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