david van ijzendoorn

Pathology resident | Former Stanford Postdoc | Developer of and

[david van ijzendoorn @vanijzen]

Prefer to listen? Audio version of the paper, via Paper2Pod:
https://t.co/ITnuYKftA0

[david van ijzendoorn @vanijzen]

Atera whole-transcriptome profiling maps immune responses across tumor clones in DCIS. We reconstruct clonal architecture in situ, validate it with DNA sequencing and track how immunity adapts as tumors evolve. First independent evaluation of the platform
https://t.co/eFQT4TRHtR

[david van ijzendoorn @vanijzen]

Mapping fine-grained immune annotations onto reconstructed clonal architecture shows how the microenvironment changes as individual clones expand - a framework for tumor-immune coevolution in archival patient tissue.
Very proud of this work, led by @Matusiak

[david van ijzendoorn @vanijzen]

We laser-microdissected 16 tumor regions and sequenced them to confirm copy-number alterations inferred from transcriptomics. First time single-cell spatial WTA copy-number calls have been validated against direct DNA measurement. The inferred clones are real.

[david van ijzendoorn @vanijzen]

Atera captures what targeted panels miss: rare cell states and functional populations invisible to fixed gene panels. 18,000 genes vs 280-5,000 on Xenium - whole-transcriptome at single-cell resolution, tumor architecture preserved, genome-scale inference enabled. @10xGenomics

[Magdalena Matusiak @MagdaMatusiak]

Wanna learn abt spatial #macrophage niches in human? Listen to our paper in a form of #AI generated podcast #Paper2pod by @vanijzen. Link below

[david van ijzendoorn @vanijzen]

@Ozerddd @MushtaqBilalPhD There shouldn't be a real page limit, it should cut off after 15k words. However, I'm seeing that large documents cause the @supabase edge function to give a "cpu time exceeded" error. Another bug to add to the list.

[david van ijzendoorn @vanijzen]

@Ozerddd @MushtaqBilalPhD Ah I see, yes this is meant for research papers. You are trying to run an almost 500 page book ;)

[david van ijzendoorn @vanijzen]

@Ozerddd @MushtaqBilalPhD A quick look in the database - seems to generate successfully: https://t.co/lZ5L5uBnyy
seems that sometimes the app does not receive the task completed message from the API. I'm guessing it will show up if you press the refresh icon. Will work on a fix asap!

[david van ijzendoorn @vanijzen]

@Ozerddd @MushtaqBilalPhD Sorry to hear! From the logs it looks like the traffic from the post caused some requests to fail, I've added some more compute. If you are still having issues, please mail me the pdf ([email protected]) so i can find out what's happening!

[Magdalena Matusiak @MagdaMatusiak]

Tired of reading your papers? Transform them into a podcast with #Paper2Pod. Great idea @vanijzen

[AI Research Tools 👨‍🎓 🧬🧪 🐬 🔬 @airesearchtools]

It seems I also have to try Paper2Pod

Paper2Pod is a free iPhone app that turns research papers into audio podcasts 👇

NotebookLM app also coming!😊

[david van ijzendoorn @vanijzen]

@MushtaqBilalPhD Thanks for the share @MushtaqBilalPhD. I love building tools to make academic work easier.
Let me know if anyone has any suggestions for additional features!

[Mushtaq Bilal, PhD @MushtaqBilalPhD]

NotebookLM generates AI podcasts but you can't use it on the phone.

Paper2Pod is a free iPhone app that turns research papers into audio podcasts, so you can listen to them on the go.

Here's how to use it:

[david van ijzendoorn @vanijzen]

@MushtaqBilalPhD Agree, great paper, give it a listen if you are interested: https://t.co/tYX6gvFNrs

[david van ijzendoorn @vanijzen]

@LiorOnAI Or listen to the paper: https://t.co/IKeywA2jys

[Magdalena Matusiak @MagdaMatusiak]

The Spatial Human #Macrophage Map is finally online in @CD_AACR! We show how phenotypically distinct macrophage populations occupy spatially segregated tissue #niches, with #IL4I1 and #SPP1 TAMs predicting opposite outcomes in colon cancer!

[Mushtaq Bilal, PhD @MushtaqBilalPhD]

✅Instead of ChatGPT, use apps like Scite(dot)ai, Consensus(dot)app, EvidenceHunt(dot)com, and The-Literature(dot)com.

These apps will answer your questions with references to published papers.

See how Scite answers my question and cites real articles👇

[Ash Paul @pash22]

Evidence Hunt
https://t.co/KYhlW9MHRG via @vanijzen et al