Michael Geuenich

PhD student @UofT building ML tools to better understand immune escape in PDAC with @kieranrcampbell.

[alex rubinsteyn @iskander]

Brutal

[Michael Geuenich @MichaelGeuenich]

@iskander There is some evidence that gdT cells may be the effectors in this scenario, e.g: https://t.co/mnsUyptXow

[Michael Geuenich @MichaelGeuenich]

@kieranrcampbell @RGeigerlab has nice data on this in T-cells. See e.g. figure 6 in https://t.co/6xx3V2krpY

[Michael Geuenich @MichaelGeuenich]

@simocristea There is this resource form @AI4Pathology . Not sure to what extent clinical metadata is available though: https://t.co/DgEjt4Pqjg

[Kieran Campbell @kieranrcampbell]

How can active and self-supervised learning methods improve the efficiency of human annotation of single-cell data?

Our paper exploring this (& more!) is now out ➡️ https://t.co/M3PgVxTPx7

[Michael Geuenich @MichaelGeuenich]

@AdrianoAguzzi What about showing the predicted effect of improving AUC? So something like x = AUC (at different thresholds, e.g. from 0.9 to 0.99) and y = # of false positives or $ saved at constant screen size?

[DrNicoleCampbell.bsky.social @nk_campbell]

This macrophage tattoo is made of macrophages! Have you ever wondered why tattoos are permanent? In tattooing, ink is injected into the skin. Some of this ink is expelled with the epidermis o, but the rest remains in the dermis for life. 🧵1/10

[Michael Geuenich @MichaelGeuenich]

@marinaelpiniki @marathonofhope @tfri_research Thanks Marina! :)

[Michael Geuenich @MichaelGeuenich]

I'm trilled to share that I have been selected as one of the @marathonofhope @tfri_research Health Informatics & Data Science Award recipients. Stay tuned for details on the project 🙂

[Marathon of Hope Cancer Centres Network @marathonofhope]

8⃣ @MichaelGeuenich (@UHN – @pmcancercentre) for: Characterizing antigen presentation associated immune escape mechanisms in pancreatic adenocarcinoma using integrative computational approaches

🧬 More ▶️ https://t.co/VewXYMy1RG

[Michael Geuenich @MichaelGeuenich]

@findycang 😱 I thought you graduated from graphic design?

[Kieran Campbell @kieranrcampbell]

Interested in using scRNA-seq to help design antibody panels for e.g. highly multiplexed imaging experiments?

Introducing cytomarker, a web-app for iterative panel design, including metrics and link out to antibody catalogues

App ➡️ https://t.co/npumte7m4S

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[Shai Carmi @ShaiCarmi]

A long magazine article by @ToddLencz and myself covering the current state + pros and cons of embryo screening for adult diseases.

We worked hard to make this complex and multidisciplinary subject accessible to all audiences. Enjoy the read!

https://t.co/ZZS6dhbLXx

[Johannes Köster (@johanneskoester.bsky.social) @johanneskoester]

Does anybody know a good properly and transparently validated benchmark dataset for HLA typing? The ones we found so far (1000G, GIAB based) seem to be pretty intransparent regarding used allele database, inclusion criteria and validation approaches.

[Kieran Campbell @kieranrcampbell]

Has anyone encountered rmarkdown::render overwriting intermediate files when used in parallel on compute clusters with e.g. Snakemake? Leads to wrong output files/results, but very hard to spot. We have a fix but keen to know if it's common knowledge

[Michael Geuenich @MichaelGeuenich]

I'm helping put on an event with @biotechTO on November 10th. If you're in Toronto and want to join DM me for a promo code to register for free.

[BiotechTO @biotechTO]

Get excited for our next event on Nov 10th focussed on building synergies between academia and industry! We will be joined by Stephen Miller, policy fellow @MitacsCanada, J. Paul Santerre from @UHN and @TheHarryGandhi, Director of the Innovation Boost Zone
https://t.co/0LDYZVAn4q

[Michael Geuenich @MichaelGeuenich]

@soph_liu @z_chiang Can recommend https://t.co/8wj6hcW7D6 to create highly overfit abbreviations!

[Sophia Liu @immunoliugy]

Presenting Slide-TCR-seq: our method for measuring the transcriptomes of cells & T cell receptor (TCR) sequences in situ!

This collaboration w/ Bryan Iorgulescu, Shuqiang Li, Catherine Wu, and @insitubiology led to some cool findings...

https://t.co/bamg5yCToX
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[Daniel Schramek @DanielSchramek]

Happy to share that our new study describing how the inherited non-coding single-nucleotide polymorphism rs55705857 drives IDH-mutant glioma is (finally) published. This was a close collaboration @MayoCancerCare

https://t.co/LDqx8uTo7q

[David Keyes @dgkeyes]

Wait, hold up, you can add an arrow at the end of an axis line like this? @W_R_Chase blowing my mind!

[Michael Geuenich @MichaelGeuenich]

@tangming2005 The importance of controls, unit tests and how to design them to detect bugs early