iiinova — where your digital self keeps evolving

mdmanurung.bsky.social @mdmanurung.bsky.social · 06/08/2025

New post! Here, I highlighted a recent review article on lactate to "fuel" my growing interests in immunometabolism. mikhaeldm.substack.com/p/lactate-fr... A very interesting review to read, which highlight the journey of lactate as metabolic waste to master immune regulator!

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mdmanurung.bsky.social @mdmanurung.bsky.social · 15/07/2025

The mechanism by which CD8T exhaustion (Tex) was regulated remain unclear. In this paper, Dahabieh and colleagues showed how NRF2 involved in promoting CD8 Tex by regulating expression of the prostacyclin receptor PTGIR. Link to my summary: mikhaeldm.substack.com/p/30mpr-ptgi... #immunosky

mikhaeldm.substack.com

30MPR: PTGIR, a novel CD8+T cell immune checkpoint

How metabolic rewiring by prostacyclin receptor signalling limits the immune system's ability to control cancer

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Reposted by @mdmanurung.bsky.social

Yogesh Goyal @goyallab.bsky.social · 06/07/2025

Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications shorturl.at/2LHbw

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/07/2025

Thanks for sharing this great resource!

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/07/2025

Please note that this summary is not doing justice to this excellent paper--I am merely sharing what I manage to read in a 30-minute reading session. I highly recommend reading the paper for more cool tricks/ideas on using publicly available data to test your hypotheses.

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/07/2025

The authors showed that the 42-gene SoM scores was, to some extent, correlated with Tsang's lab 150-gene Immune Health Metric (IHM) (Fig. S5). Considering that IHM was derived using monogenic immune disorders, the authors proposed that the IHM reflects genetic factors while SoM lifestyle factors.

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/07/2025

Using publicly available single-cell data, the authors showed that the scores were associated with certain immune cell types (Figs. 2D-E). Detrimental scores were associated with neutrophils, protective scores with T/NK cells and monocytes.

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/07/2025

SoM scores, or specifically its protective module scores, were associated with favourable response to hydrocortisone in burn injury patients (Figs. 1F-G)

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/07/2025

How's the SoM score calculated in the first place? SoM score = detrimental - protective scores. Each of the detrimental/protective score was computed as the sum of scores of a few gene modules. In turn, the gene modules were scored by taking the geometric mean of their respective genes.

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/07/2025

The SoM score was identified using dataset of individuals with respiratory viral infections. By computing the score in bacterial infection datasets, the authors showed that the score was correlated with severe infection, irrespective of bacterial/viral etiology. The score has numerous applications!

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/07/2025

I'd like to try something new: sharing the summary of my 30-minute paper reading session--whether I am finished or not! Today I read a paper from Purvesh Khatri's lab on a conserved immune signature that they called as Severe-or-Mild (SoM) score. www.cell.com/immunity/ful...

cell.com

A conserved immune dysregulation signature is associated with infection severity, risk factors prior to infection, and treatment response

The impact of risk factors for severe infections (being old, male, obese, and having comorbidities) on immune dysregulation prior to infection remains understudied. Using 12,026 blood samples, Ganesan...

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/12/2023

Thanks for taking the time to write the steps!

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/12/2023

Oooh, how was the syncing? Do you have to manually export your annotations back to your computer?

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mdmanurung.bsky.social @mdmanurung.bsky.social · 14/12/2023

Yes, in my experience, most figures are unreadable when printed in B/W :(

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mdmanurung.bsky.social @mdmanurung.bsky.social · 13/09/2023

Any single-cell aficionados around here?

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mdmanurung.bsky.social @mdmanurung.bsky.social · 09/09/2023

Oh I've been wrong many times, but the overwhelming majority was in private.

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mdmanurung.bsky.social @mdmanurung.bsky.social · 09/09/2023

Absolutely not. But I think that is a skill that can only be acquired through such experience.

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Reposted by @mdmanurung.bsky.social

Thomas Lumley @tslumley.bsky.social · 08/09/2023

The amazing Di Cook and the presumptively amazing Ursula Laa have an online book on high-dimensional data visualisation

dicook.github.io

Interactively exploring high-dimensional data and models in R

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mdmanurung.bsky.social @mdmanurung.bsky.social · 09/09/2023

I have a naive question. What is the limit of data object size that can be tracked?

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mdmanurung.bsky.social @mdmanurung.bsky.social · 09/09/2023

The community taught most of what I know and I feel compelled to give back. But when a senior researcher responded with a snarking remark, I could not help but feel terrible. A year has passed and I want to start anew on this platform. Does anyone have tips to handle such a situation?

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mdmanurung.bsky.social @mdmanurung.bsky.social · 09/09/2023

A year ago, I used to enjoy sharing my learning progress via tweets and blog posts, until I got criticized for sharing something wrong but commonly done in the field (e.g. scRNA-Seq marker gene analysis using t-tests). I cannot control how others should respond, but still, it was disheartening.

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