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Luca Pinello @lucapinello.bsky.social · 3h

@zainmunirpatel.bsky.social will also present this afternoon 2.30 to 4.30
Poster 4022W. Systematic benchmarking of computational methods for SVG detection. #spatial #ASHG2025

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Luca Pinello @lucapinello.bsky.social · 6h

📅OCT 17 | 2:30-4:30 PM | Poster 5057F
Jayoung Ryu ( @jykr.bsky.social ) presents "SIMBA+: Dissecting genetic variant function through single-cell multiomics integration"
Exciting multiomics integration work! #SingleCell #Multiomics #VariantInterpretation #ASHG2025

Luca Pinello @lucapinello.bsky.social · 6h

📅 OCT 16 | 2:30-4:30 PM | Poster 6020T
I'll be at my poster: "CRISPRlungo: Accurate Quantification of Genome Editing Events from Long Reads"
Come chat about long-read sequencing & CRISPR! #GenomeEditing #LongReads #ASHG2025

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Luca Pinello @lucapinello.bsky.social · 6h

📅 OCT 16 | 10:45-11:00 AM | Room 205ABC
Basheer Becerra presents "Multi-modal functional mapping of non-coding sequences regulating fetal hemoglobin"
Exciting work on therapeutic targets! #FetalHemoglobin #ASHG2025

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Luca Pinello @lucapinello.bsky.social · 6h

Zhijian Li ( @zhijianli.bsky.social )presents "Cell2net: A Deep Learning Framework to Decode Genotype-Specific Gene Regulatory Networks from Single-Cell Multi-Omics"
#DeepLearning #GeneRegulation #ASHG2025

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Luca Pinello @lucapinello.bsky.social · 6h

📅 OCT 15 | 11:00-11:15 AM | Room 258ABC
Logan Blaine presents "PerTurbo: A scalable Bayesian framework for whole-transcriptome differential expression analysis & optimal design of single-cell CRISPR screens"
#CRISPRscreen #SingleCell #ASHG2025

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Luca Pinello @lucapinello.bsky.social · 6h

🧬Excited to be at #ASHG2025! My lab is presenting 5 studies this week. Join us for talks and posters on #SingleCell #CRISPR, #DeepLearning & more! Thread below with all presentation details 👇

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Reposted by Luca Pinello

Anne Carpenter @drannecarpenter.bsky.social · 5d

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

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Reposted by Luca Pinello

Sasha Gusev @sashagusevposts.bsky.social · Aug 27

I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:

Beneath the surface of the sum

When genetic interactions matter and when they don't

open.substack.com

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Luca Pinello @lucapinello.bsky.social · Jul 25

It was indeed fantastic! Thank you so much to all the organizers for supporting this community. 🙏

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Reposted by Luca Pinello

Saez-Rodriguez Group @saezlab.bsky.social · Jul 22

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form
🔗 Paper: www.nature.com/articles/s42...
📖 News & Views: www.nature.com/articles/s42...
💻 Code: corneto.org
🧵 Thread 👇

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Reposted by Luca Pinello

Doug Fowler @dougfowler.bsky.social · Jul 21

Interested in using functional data to understand clinical variants? Been hunting for a good review of the topic? We just wrote one! rdcu.be/exaEU

Multiplexed assays of variant effect for clinical variant interpretation

Nature Reviews Genetics - Multiplexed assays of variant effect (MAVEs) are highly scalable experimental approaches used to generate functional data for genetic variants. In this Review, McEwen et...

www.nature.com

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Luca Pinello @lucapinello.bsky.social · Jul 20

Excited to be at #ISMBECCB2025! I'll be presenting at RegSys on "Learning the Regulatory Genome by Destruction and Creation" (Thursday 3:15PM in Room 11BC). I'm looking forward to connecting with both new and old friends throughout the conference! 🧬 #CRISPR #Genomics #Diffusion

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Luca Pinello @lucapinello.bsky.social · Jun 8

This changed how I write. No context switching, no copying - just select, shortcut, done!
👉 github.com/lucapinello/claude-text-editor
Feedback welcome! Thanks @anthropic.com for MCP, Claude Code and Claude Desktop!

What will you build on your next rainy afternoon? 🌧️✨

GitHub - lucapinello/claude-text-editor: MCP-powered text editing system that integrates Claude

MCP-powered text editing system that integrates Claude - lucapinello/claude-text-editor

github.com

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Luca Pinello @lucapinello.bsky.social · Jun 8

Why it rocks:

File-based (no timeouts!)
Desktop notifications
Auto-clipboard magic
Works with Claude Desktop
Open source (MIT)

Built for macOS 14+ 🍎

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Luca Pinello @lucapinello.bsky.social · Jun 8

Want Claude to channel Hemingway? Add emojis? Write formally?
Edit ~/.claude_text_editor/claude_prompt.txt
Make Claude YOUR personalized writing assistant! ✍️
The possibilities are endless...

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Luca Pinello @lucapinello.bsky.social · Jun 8

Love the terminal? Add this to ~/.zshrc:
ce() {
if [ $# -eq 0 ]; then
pbpaste | ~/claude-text-editor/claude_text_client.py
else
printf '%s\n' "$*" | ~/claude-text-editor/claude_text_client.py
fi
}
Now: ce Fix this sentence that have bad grammer ✨

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Luca Pinello @lucapinello.bsky.social · Jun 8

Here's the killer feature...
No text selected? It auto-grabs your clipboard!
Already copied something? Just hit the shortcut. Claude polishes it instantly.
Smart defaults FTW! 🧠

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Luca Pinello @lucapinello.bsky.social · Jun 8

Quick setup:
git clone github.com/lucapinello/...
cd claude-text-editor
./install.sh
Import shortcut → Assign ⌥⌘. in System Settings → Done! 🎯

GitHub - lucapinello/claude-text-editor: MCP-powered text editing system that integrates Claude

MCP-powered text editing system that integrates Claude - lucapinello/claude-text-editor

github.com

1

Luca Pinello @lucapinello.bsky.social · Jun 8

The magic? Select text → Hit ⌥⌘. → Claude edits it → Auto-copies to clipboard! 📋
Works in Gmail, Slack, VS Code, Terminal - literally ANY app. It's like having Claude as your co-pilot, always ready.
Built with @anthropic.com's MCP protocol 🔧

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Luca Pinello @lucapinello.bsky.social · Jun 8

🧵 It's raining outside, perfect for some vibe coding... ☔
So I built something cool with @anthropic.com's Claude Desktop!
Introducing Claude Text Editor - edit ANY text, ANYWHERE on macOS with Claude's help. No more copy-paste gymnastics! 🚀

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Luca Pinello @lucapinello.bsky.social · Apr 24

Great to see it finally out —such a fantastic collaboration with @bkleinstiver.bsky.social , @rachelsilverstein9.bsky.social and team!

Ben Kleinstiver @bkleinstiver.bsky.social · Apr 22

In @nature.com we describe the use of scalable #proteinengineering & #machinelearning to predict millions of bespoke CRISPR enzymes, offering safer & more efficient genome editing tools 🧬🖥️ @rachelsilverstein9.bsky.social @mgbresearch.bsky.social @harvardmed.bsky.social
www.nature.com/articles/s41...

Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning - Nature

Nature - Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning

www.nature.com

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Reposted by Luca Pinello

Anders Sejr Hansen @andersshansen.bsky.social · Jan 16

Excited to share James Jusuf's preprint:

By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)

We quantify mESC 36k loops: are generally rare (2.3%)

www.biorxiv.org/content/10.1...

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Reposted by Luca Pinello

Caleb Lareau @caleblareau.bsky.social · Jan 8

Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...

Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics

Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...

www.nature.com

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Luca Pinello @lucapinello.bsky.social · Dec 23

😂