Lightnews — Scholar-powered news

Alex Swarbrick @alexswarbrick.bsky.social · Aug 10

Felling inspired after my visit to The Broad Institute. Brilliant science in a collaborative energised environment. Thanks @azizalkhafaji.bsky.social and Gammy Al-Eryani for hosting

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Alex Swarbrick @alexswarbrick.bsky.social · Aug 1

I’m looking for a PhD student to work on an exciting new collaboration with @azizalkhafaji.bsky.social at the @broadinstitute.org. Together we are using single cell long-read sequencing to understand tumour evolution and microenvironments. Hybrid computational and molecular role. 🧬

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Alex Swarbrick @alexswarbrick.bsky.social · Aug 1

Thankyou for hosting us! We are so impressed by the quality of the science, collaboration and facilities at @pmresearch-uhn.bsky.social. Looking forward to developing exciting new projects together

Princess Margaret Cancer Centre @pmresearch-uhn.bsky.social · Jul 31

🇨🇦🇦🇺 Thank you to @garvaninstitute.bsky.social for joining us at the Allan Slaight Breakthrough Forum! Scientists were brought together to tackle tumour complexity for translational impact. Together, we’re accelerating the path toward more precise and effective cancer care.💙

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Reposted by Alex Swarbrick

PLOS Biology @plosbiology.org · Aug 1

In this #Perspective @alexswarbrick.bsky.social @jeremymedonc.bsky.social &co argue that better preclinical models and understanding of stromal cells in the tumor microenvironment are needed to improve #cancer therapies 7/9
plos.io/4of0fXe

TiME for a change: The tumor microenvironment as the missing piece in cancer therapeutics

Current anti-cancer treatments often neglect the role of the tumor microenvironment (TME) in resistance and progression. In this Perspective, the authors argue that better preclinical models, understa...

plos.io

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Alex Swarbrick @alexswarbrick.bsky.social · Jun 13

An exciting new paper on the application of federated deep learning to pan-cancer proteomic data. Congrats to the Procan team for this achievement! Very happy to have contributed our breast cancer dataset to this important work.

doi.org/10.1158/2159...
www.cmrijeansforgenes.org.au/research/res...

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Alex Swarbrick @alexswarbrick.bsky.social · Jun 13

Today is the last day in the lab for for Marion Motard, who joined the lab for her Masters then stayed on as a research assistant. She did brilliant work on GNNs to predict gene module enrichment in histology images. She is returning to Europe, quickly offer her a job in ML/computational !

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Alex Swarbrick @alexswarbrick.bsky.social · Jun 9

I had a great time at the #wehispatial25 meeting. So much excellent spatial ‘omics going on in Oz.
But weware the @wehi rubber chicken

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Alex Swarbrick @alexswarbrick.bsky.social · Apr 26

#aacr2025 Here we go…

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Alex Swarbrick @alexswarbrick.bsky.social · Mar 27

I'm chairing session ED52 "Innovative Approaches in TME Biology: From Profiling to Function" at #AACR2025. I'll present data using cellular and functional genomics to identify small molecule mediators of stromal plasticity. Also the amazing Illaria Malanchi and Nick Navin. LMK if u will be there!

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Reposted by Alex Swarbrick

Valentine Svensson @nxn.se · Mar 18

SCVI — Integrating or not? - www.nxn.se/p/scvi-integ...

SCVI — Integrating or not?

In modern single cell analysis workflows you fit a model to your data that allow you to ask questions about the data.

www.nxn.se

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Reposted by Alex Swarbrick

Itai Yanai @itaiyanai.bsky.social · Jan 2

The four basic kinds of scientific papers:
1. Noise (no claim and no evidence)
2. Resource (no claim but lots of data)
3. Conjecture (makes a claim, but no evidence)
4. Scientific advance (both makes a claim and presents evidence)

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Reposted by Alex Swarbrick

Sara Zanivan @zanivanlab.bsky.social · Dec 18

If you are interested in joining our growing Lab of CAFs enthusiasts @mdanderson.bsky.social and to understand how CAF metabolism can be harnessed to modulate the immune-TME, we are looking for talented postdocs! 👇🏻
jobs.mdanderson.org/search/jobde...

Postdoctoral Fellow - Experimental Therapeutics (Zanivan Lab) at MD Anderson

MD Anderson is Hiring! Search available jobs or submit your resume now by visiting this link. Please share with anyone you feel would be a great fit.

jobs.mdanderson.org

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Alex Swarbrick @alexswarbrick.bsky.social · Dec 16

Thanks Sandra ☺️

Alex Swarbrick @alexswarbrick.bsky.social · Dec 16

Wanted- *Bioinformatics Research Assistant*. Projects include generation of an international, large-scale, multi-omic breast cancer atlas and understanding response to immunotherapy in breast cancer, prostate cancer and melanoma. Great training opportunities 🧬💻
More info ⤵️
tinyurl.com/33wxkswz

Research Assistant - Bioinformatics

The Garvan Institute of Medical Research brings together world leading researchers and clinicians, collaborating locally and globally, to improve human health. Our mission is to harness all the inform...

tinyurl.com

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Alex Swarbrick @alexswarbrick.bsky.social · Dec 12

Jobortunities: Shortly advertising for 2 positions, both working on the Breast Cancer Atlas, in Sydney.
- Wet lab research assistant: mol bio +/- pathology desirable
- Comp. Research Assistant: scRNA-Seq, spatial transcriptomics and ML
Details to follow, DM or email if you are a great fit.

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Alex Swarbrick @alexswarbrick.bsky.social · Dec 12

🤩

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Alex Swarbrick @alexswarbrick.bsky.social · Dec 12

Im thrilled for this recogntion of Christina Curtis and Steffi Oesterreich by the @theaacr.bsky.social at @sabcs.bsky.social. I'm in awe of their achievements and impacts on breast cancer research. They are also two of the nicest people you'll ever meet !
sabcs.cmail19.com/t/d-l-smtjdd...

AACR to honor trailblazing breast cancer researchers during the 2024 SABCS® - SABCS Meeting News

Christina Curtis, PhD, MSc, left, and Steffi Oesterreich, PhD, will be recognized by the American Association for Cancer Research (AACR) for significant contributions to breast cancer research.

www.sabcsmeetingnews.org

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Reposted by Alex Swarbrick

Eric Topol @erictopol.bsky.social · Dec 4

One of the alluring and theoretical strategies for extending healthspan and longevity is to rejuvenate the thymus gland, promote an intact immune system. Now there's a way to do that in aged mice.

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

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Alex Swarbrick @alexswarbrick.bsky.social · Dec 5

Thanks to @aruthak.bsky.social and colleagues for the invitation to this fantastic, unique meeting #multi-omics2024.
Thnx for the shoutout to the awesome @martinalexsmith.bsky.social

Martin Smith @martinalexsmith.bsky.social · Dec 2

One of the Multi-Omics O.G.s, @alexswarbrick.bsky.social from @garvaninstitute.bsky.social, speaking on charting an atlas of #cancer #ecosystems with single-cell and spatial omics #multiomics2024

Finished talk with an appeal to join @bsky.app

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Reposted by Alex Swarbrick

Jasmine Plummer @jasmineplummer.bsky.social · Dec 1

When you get to be your own caricature!! Grateful to be in #oz sharing science with #friends. For those missing out #multiomics2024 is where #singlecell #spatial #omics #immunology #oncology and #precisionmedicine is where it’s at🥳

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Reposted by Alex Swarbrick

Martin Smith @martinalexsmith.bsky.social · Dec 2

Yesterday, I presented our latest results mining single molecule m6A data at #multiomics2024:
We see changes in m6A levels following CRISPR-cas13 knock-down of oncogenic lncRNAs that are independent of mRNA expression levels, revealing new dimensions of highly pertinent biological information

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Reposted by Alex Swarbrick

Garvan Institute Cancer Ecosystems Program @cancerecogarvan.bsky.social · Nov 29

A nice explanation of the space our Cancer Ecosystems Program researchers work in - its tricky! but they are applying spatial and single cell multiomics to clinical samples and taking big steps forward towards better outcomes for patients - check out our team at www.garvan.org.au/research/str...

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Reposted by Alex Swarbrick

Matt Sikora @mjsikora.bsky.social · Nov 25

Public Service Announcement: Check colorblind-compatibility in Illustrator! Under 'View', 'Proof Setup' you can selected a colorblindness type to view your image in that spectra. Click 'Proof Colors' after to remove filter. We chose pink/green, yellow/blue here for accessibility (PMID 38112643).

Screen capture of an Adobe Illustrator window in standard viewing mode (that is, without colorblind filter applied).

Screen capture of an Adobe Illustrator window with 'View' menu pulled down, showing selection of a relevant colorblindness filter being applied.

Screen capture of an Adobe Illustrator window with the previous image in a protanopia-type colorblindness mode applied.

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Reposted by Alex Swarbrick

Johanna Joyce @johannajoyce.bsky.social · Nov 23

Both #Cancer #Research starter packs are now completely full!

~300 researchers, oncologists, students, postdocs, patient advocates, and organizations supporting cancer research 🧪🔬⚕️

I hope you'll find these useful to build our community here

Pack 1: go.bsky.app/FEoaJMc
Pack 2: go.bsky.app/6EcjWNA

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Reposted by Alex Swarbrick

danapeer.bsky.social @danapeer.bsky.social · Nov 22

Truly brilliant work. Calling it a foundation model is a stretch (a mistake many people in the field make). But, the only single-cell AI model in its class that I think is worth the GPU energy expended and one that I excited to utilize. My stamp of approval. www.nature.com/articles/s41...

A cell atlas foundation model for scalable search of similar human cells - Nature

Nature - A cell atlas foundation model for scalable search of similar human cells

www.nature.com

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