Ram

BIOMAN 2023 | microbiology | Academic Tweets | xiaoxiao loves tangtang | MS Microbiology Student | Assistant to Microbiology Consortium of the Philippines

[Lior Pachter @lpachter]

Arguably the most boring step in genomics is the first one: normalization. Settled science. Scale + log. Move on.

Except that here's been a huge blind spot in the field. And it matters for AIxBio. A 🧵about what I think may be one of the most important papers I've written. 1/

[Kazuaki Amikura @amikura1986]

Generating E. coli 0.5 controlled by a half-sized genome https://t.co/UBk0y1r9mD

[GimR (Go watch SASSY!) @VGBC_GimR]

I have a theory the One Piece was gonna be something like this and Oda was PISSED when Kungfu Panda dropped

[Tominaga K. (tomiken) @pacyc1841]

Bacterial extracellular vesicles as recyclable nutrient reservoirs | Nature Communications https://t.co/YFJjptQpS0

[Olga Khazan ME, BUT BETTER @olgakhazan]

We saw an eccentric allergist with my son when he was 3 months old, and he recommended that we immediately start throwing as many allergens at him as possible, as often as possible. We did and now he's not allergic to anything 👐

[オーキド博士, Ph.D. @DrOak_PhD]

←理想の大学生活
→絶望のサンガーシークエンス

[Waggoner Lab @LabWaggoner]

Specific DNA sequence features encode the persistence of epigenetic memory of inflammation @ScienceMagazine @ElaineFuchsLab @RockefellerUniv Pe’er @MSKCancerCenter
https://t.co/A0mzL1v7pl

[Zenom @TheZenomHayab]

Student to student: Your lock-in during exams period should NEVER include being away from your class WhatsApp group for more than 3 hours.

[dille @flurryfrenzy]

i do not "organize my files", i do not "put things in separate folders", i PUT EVERYTHING IN DOWNLOADS! and if i can't find it, i LOST IT!

[Nature Microbiology @NatureMicrobiol]

Drought drives elevated antibiotic resistance across soils https://t.co/RrXCTgJ00i #MicroSky

[𝓒𝓸𝓶𝓶𝓪𝓷𝓭𝓮𝓻 🏴‍☠️ @c0mmandderr]

These still exist. You're just not invited to them, like how you wouldn't have been back then 😭

[Adam @_adamnoonan]

@paularambles real walkers close the app after checking once and only reopen after they’ve got real lost

[“paula” @paularambles]

real walkers never press “start” when using google maps

[Bo Wang @BoWang87]

Happy to see the work, GigaTIME, from my close friend, Hoifung Poon, highlighted by @satyanadella !

This is the @CellCellPress paper from Dec 2025 (paper: https://t.co/4fW1PFBam3). It's now open source on Hugging Face + Azure Foundry Labs!

A bit more technical background for GigaTIME:

Spatial proteomics tells you which proteins are active, where, at single-cell resolution. It's the closest thing we have to reading the immune "grammar" of a tumor. It also costs thousands of dollars per sample and takes days to run.

GigaTIME just broke that constraint.

Input: a routine H&E pathology slide. ~$5. Every hospital has millions of them.
Output: a full 21-channel spatial proteomics map. In seconds.

How it works:
— Trained on 40 million cells with paired H&E + mIF images (Providence health system)
— Learns cross-modal translation: cell morphology → cell state, at single-cell spatial resolution
— Not CycleGAN — beat prior SOTA by a wide margin on both Dice score and Pearson correlation

What they did with it:
— Applied to 14,256 cancer patients across 51 hospitals
— Generated ~300,000 virtual mIF images spanning 24 cancer types, 306 subtypes
— Discovered 1,234 statistically significant protein-biomarker associations (novel ones: KMT2D, KRAS pan-cancer links)
— Validated externally on 10,200 TCGA patients: Spearman r = 0.88 across subtypes

The real unlock: population-scale tumor immune microenvironment (TIME) analysis was previously infeasible. mIF data is too scarce and expensive to collect at scale. GigaTIME generates a virtual population — validated against real mIF — from what every clinic already has.

One modality (cheap morphology) implies another (expensive cell state). The model learns the grammar connecting them.

Next step they hint at: integrating with LLaVA-Med so you can literally query the spatial proteomics map conversationally. "Talk to the tumor."

[David Powell @thedavidpowell]

“I can change him.”

Please don’t. He’s in my data and I’m relying heavily on fixed effects.

[Jordan Holliday @MrJHolliday]

@ArbeePoo My biggest worry is that I'm lying to myself. Did A really look sharper than B?

[dee 🧚🏾 @deabo20]

naomi i need you to lock tf in

[PhD_Genie @PhD_Genie]

Using another paper only for its references

[꧁✿Nessa✿꧂ @Softnessa_]

Dad: *offers me a hand full of walnuts*

8 year old me: I can’t have those, I’m allergic.

Dad: What will happen?

Me: They make my mouth itch.

Dad: That’s just what walnuts do.

And that’s when my dad learned that he’s also allergic to walnuts.

[Ke Cheng, Ph.D. @KeChengLab]

Congratulations to Kaiyue Zhang on the publication @ScienceMagazine. In the paper, we built an “RNA factory” on muscle for heart repair. https://t.co/DRDhOLKbLl