Gianluca Pegoraro
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Gianluca Pegoraro
@glpego.bsky.social
47 followers 260 following 5 posts
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Reposted by Gianluca Pegoraro
traver.bsky.social
Merry Christmas, genetic interaction nerds:

www.biorxiv.org/content/10.6...
Functional modules predict cancer-relevant genetic interactions in mammalian cells
Genetic interactions can reveal gene function and identify cancer-relevant synthetic lethals, but systematic mapping in human cells is constrained by inefficient reagents, vast combinatorial search sp...
www.biorxiv.org
December 21, 2025 at 8:42 PM
Reposted by Gianluca Pegoraro
andrew.heiss.phd
Some closing thoughts for my students this semester on LLMs and learning #rstats datavizf25.classes.andrewheiss.com/news/2025-12...
Will you incorporate LLMs and AI prompting into the course in the future? No. Why won’t you incorporate LLMs and AI prompting into the course? These tools are useful for coding (see this for my personal take on this). However, they’re only useful if you know what you’re doing first. If you skip the learning-the-process-of-writing-code step and just copy/paste output from ChatGPT, you will not learn. You cannot learn. You cannot improve. You will not understand the code. In that post, it warns that you cannot use it as a beginner: …to use Databot effectively and safely, you still need the skills of a data scientist: background and domain knowledge, data analysis expertise, and coding ability. There is no LLM-based shortcut to those skills. You cannot LLM your way into domain knowledge, data analysis expertise, or coding ability. The only way to gain domain knowledge, data analysis expertise, and coding ability is to struggle. To get errors. To google those errors. To look over the documentation. To copy/paste your own code and adapt it for different purposes. To explore messy datasets. To struggle to clean those datasets. To spend an hour looking for a missing comma. This isn’t a form of programming hazing, like “I had to walk to school uphill both ways in the snow and now you must too.” It’s the actual process of learning and growing and developing and improving. You’ve gotta struggle. This Tumblr post puts it well (it’s about art specifically, but it applies to coding and data analysis too): Contrary to popular belief the biggest beginner’s roadblock to art isn’t even technical skill it’s frustration tolerance, especially in the age of social media. It hurts and the frustration is endless but you must build the frustration tolerance equivalent to a roach’s capacity to survive a nuclear explosion. That’s how you build on the technical skill. Throw that “won’t even start because I’m afraid it won’t be perfect” shit out the window. Just do it. Just start. Good luck. (The original post has disappeared, but here’s a reblog.) It’s hard, but struggling is the only way to learn anything. You might not enjoy code as much as Williams does (or I do), but there’s still value in maintaining codings skills as you improve and learn more. You don’t want your skills to atrophy. As I discuss here, when I do use LLMs for coding-related tasks, I purposely throw as much friction into the process as possible: To avoid falling into over-reliance on LLM-assisted code help, I add as much friction into my workflow as possible. I only use GitHub Copilot and Claude in the browser, not through the chat sidebar in Positron or Visual Studio Code. I treat the code it generates like random answers from StackOverflow or blog posts and generally rewrite it completely. I disable the inline LLM-based auto complete in text editors. For routine tasks like generating {roxygen2} documentation scaffolding for functions, I use the {chores} package, which requires a bunch of pointing and clicking to use. Even though I use Positron, I purposely do not use either Positron Assistant or Databot. I have them disabled. So in the end, for pedagogical reasons, I don’t foresee me incorporating LLMs into this class. I’m pedagogically opposed to it. I’m facing all sorts of external pressure to do it, but I’m resisting. You’ve got to learn first.
December 9, 2025 at 8:17 PM
Reposted by Gianluca Pegoraro
cbartman.bsky.social
some people have security blankets

i have the 40 hidden slides in my presentation just in case i get asked specific obscure questions
December 8, 2025 at 9:58 PM
Reposted by Gianluca Pegoraro
yalesph.bsky.social
Why do babies need the hepatitis B vaccine if they aren’t high-risk?

Short answer: Because hepatitis B is a tricky virus.

Longer answer: Continue reading ⬇️

🧵1/9 @kkjetelina.bsky.social @meganranney.bsky.social @jasonlschwartz.bsky.social @enirenberg.bsky.social
February 19, 2025 at 2:46 PM
Reposted by Gianluca Pegoraro
cellmorphosero.bsky.social
If you or your trainees are just getting started with image analysis of cells & are #CellProfiler -curious, here is a fairly thorough walk-through demo I did recently. Loading files, extracting metadata (fun with Regex!), identifying objects, measuring, filtering, QC, exporting:
youtu.be/fO5nJdhj_7I
Introduction to CellProfiler - by a biologist, for biologists!
YouTube video by CellMorphoJSero
youtu.be
December 4, 2025 at 12:37 PM
Reposted by Gianluca Pegoraro
drmowinckels.io
🎄 ANNOUNCEMENT: R Package Development Advent Calendar 2025! 🎄

Starting December 1st, I'm launching a 25-day journey through modern R package development. here's why you should follow along 🧵

#rstats #RPackageAdvent2025 #OpenSource
A festive digital illustration features the blue R logo wearing a red Santa hat with white trim on the left. To its right stands a green Christmas tree made entirely of curly braces arranged in a triangular shape. White and light-blue %>% pipe symbols float across a dark blue, starry background like snowflakes. A speech bubble above the R logo says “Ho Ho Ho! 📦” in red text. At the bottom, white text reads: “R Package Development Advent Calendar 2025” and below it, “25 Days of Coding Magic • Dec 1–25.”
November 30, 2025 at 10:03 AM
Reposted by Gianluca Pegoraro
arjunraj.bsky.social
So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)!

www.cell.com/cell/fulltex...
Single-cell susceptibility to viral infection is driven by variable cell states
Not all cells that can be infected by a virus become infected with that virus. Single-cell clone tracing reveals intrinsic cell states with variable expression patterns that increase susceptibility to...
www.cell.com
November 14, 2025 at 4:47 PM
Reposted by Gianluca Pegoraro
mannlab.bsky.social
Our preprint on scPortrait is out! We built a framework + format to turn microscopy into standardized single-cell image datasets. #scPortrait scales >100M cells, integrates with @scverse.bsky.social, & enables cross-modality modeling from morphology to transcriptomics
doi.org/10.1101/2025...
scPortrait integrates single-cell images into multimodal modeling
Machine learning increasingly uncovers rules of biology directly from data, enabled by large, standardized datasets. Microscopy images provide rich information on cellular architecture and are accessi...
doi.org
September 24, 2025 at 12:22 PM
Reposted by Gianluca Pegoraro
cellpress.bsky.social
DNA from Napoleon’s 1812 army identifies the pathogens likely responsible for the army’s demise during their Russian retreat. www.cell.com/current-biol...

Nicolás Rascovan & colleagues
@currentbiology.bsky.social
Napoleon's retreat from Moscow CREDIT Barbieri et al., Current Biology
October 24, 2025 at 3:00 PM
Reposted by Gianluca Pegoraro
drannecarpenter.bsky.social
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
mitochondria from bipolar patients are closer to the nucleus in these images; control patients' are spread out further
October 10, 2025 at 4:47 PM
relay.experience.stjude.org
Relay for St. Jude - St. Jude Children's Research Hospital
Join the Relay community to support the lifesaving mission of St. Jude Children's Research Hospital: Finding cures. Saving children. (registered mark)
relay.experience.stjude.org
September 29, 2025 at 11:34 PM
Reposted by Gianluca Pegoraro
relay.fm
Y'ALLLLLLL we got $50k to go to meet our goal! 📈 📈 📈 stjude.org/relay
Relay for St. Jude - St. Jude Children's Research Hospital
Join the Relay community to support the lifesaving mission of St. Jude Children's Research Hospital: Finding cures. Saving children. (registered mark)
stjude.org
September 29, 2025 at 10:40 PM
Reposted by Gianluca Pegoraro
leahpetersen.bsky.social
You made me buy it, Darth.

Here's a puppy picture as revenge. Her name is Lily Bug.
Black puppy on brown couch with her head on a yellow pillow.
August 22, 2025 at 10:04 PM
Reposted by Gianluca Pegoraro
doc-jlmeier.bsky.social
Great news: NIH postbac program is recruiting again! If your grad school plans were affected by program cutbacks or admissions freezes this year I highly encourage you to apply, this could be a perfect opportunity. Please repost.

www.training.nih.gov/research-tra...
www.training.nih.gov
April 10, 2025 at 1:22 AM
Reposted by Gianluca Pegoraro
philromero.bsky.social
🎉Congrats to Chase on her new preprint! She developed OMEGA--a simple method for assembling custom gene panels for as little as $1.50 per gene. Big step forward protein engineering and design!🧬
www.biorxiv.org/content/10.1...
Scalable and cost-efficient custom gene library assembly from oligopools
Advances in metagenomics, deep learning, and generative protein design have enabled broad in silico exploration of sequence space, but experimental characterization is still constrained by the cost an...
www.biorxiv.org
March 24, 2025 at 4:50 PM
Reposted by Gianluca Pegoraro
mims.bsky.social
Thanks to Steve Jobs and Gorilla Glass, factories in America are now ramping up to make affordable windows, made from panes thinner than a credit card, that can:

* save Americans $25 billion / year

* withstand a 2x4 shot out of a cannon

(gift link)

www.wsj.com/business/cor...
A Piece of Glass Thinner Than a Credit Card Could Solve America’s $25 Billion Energy Problem
New windows can insulate better than most walls, and some can even survive being hit with a two-by-four shot from a cannon.
www.wsj.com
March 22, 2025 at 2:35 PM
Reposted by Gianluca Pegoraro
altnih4science.bsky.social
One of the remarkable things about #NIH is how rigorously its grants, research, and employees are reviewed. NIH science and scientists are held to a high standard by external reviewers — via study sections and councils, or BSC/site visit reviewers. And the reviews have teeth. 🧪
gdenisboston.bsky.social Gerald Denis @gdenisboston.bsky.social · Feb 25
I’ve served as one of several invited external reviewers for evaluation of an intramural division. The process was rigorous, detailed, and we external reviewers were not afraid to give sharp feedback. Program leadership heard it earnestly; the quality of the intramural science was extraordinary.
February 25, 2025 at 12:26 PM
Reposted by Gianluca Pegoraro
weratedogs.com
An orphaned wolf pup named Amora has been paired with a rescue puppy named Slinky. Amora needs socialization to develop properly and Slinky is happy to provide it. Sedgwick County Zoo shared that "Slinky’s playful nature is helping her grow into the wolf she is meant to be." 13/10 for both
a brown and black brindle puppy and a small grey wolf pup stand nose to nose in a room full of straw. they curiously sniff each other. an inset photo of the fuzzy grey wolf pup sitting up and looking over to her left.
February 6, 2025 at 12:45 AM
Reposted by Gianluca Pegoraro
cellbiol-mrclmb.bsky.social
40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.
December 29, 2024 at 9:50 AM
Reposted by Gianluca Pegoraro
mfgrp.bsky.social
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55
December 11, 2024 at 4:29 PM
Reposted by Gianluca Pegoraro
johndoench.bsky.social
A little fun with numbers on this Sunday, showing just how successful DNA really is. First, here's what DNA looks like. I'll draw your attention to the "rise" in DNA, that is, the distance between two basepairs, which is 3.4 Angstroms, also known as 3.4x10^-10 meters...
December 8, 2024 at 9:52 PM