Shawn Liu

Our In Vivo DNA methylation editing paper is finally published. Happy to share these two transgenic mouse lines to help investigate the function of DNA methylation at gene/locus of your interest! Happy holidays! #citeas" target="_blank" rel="nofollow noopener">nature.com/articles/s4146…

I am so excited to share our new paper in @Nature: the first programmable, site-specific integration of a large DNA payload into T cells in vivo. A single IV injection results in therapeutic levels of TRAC-targeted CAR T cells in multiple models. #Ack1" target="_blank" rel="nofollow noopener">nature.com/articles/s4158… a 🧵

We are excited to announce the release of the Human Methylation Atlas Summary and Signals tracks for hg38 and hg19. The tracks display genome-wide DNA methylation profiles across 39 primary human cell types from 205 healthy tissue samples. Learn more at bit.ly/humanMethylati…

Fluorescence Amplification Tags for Single-Molecule Imaging and Tracking of Proteins, RNA, and DNA in Live Cells (Lu Wang and co-workers) onlinelibrary.wiley.com/doi/10.1002/an…

Generates publication-ready scientific illustrations from text github.com/ResearAI/AutoF…

A new long-read preprint: run PIP-seq then PCR & put the library on ONT. Sadly, no data available so comparisons to other tech impossible (& scripts missing). Requires @FluentBio kits (they tried to reverse engineer the whitelist which seems to breach the @FluentBio EULA).

openai.com/index/new-ways… "Today, we’re making learning these [math and science] concepts in ChatGPT even more interactive with new dynamic visual explanations. Starting with more than 70 core math and science concepts, ChatGPT will guide learners by showing how formulas, variables, and relationships behave in real time. These experiences will be available globally across all plans starting today."

Thanks for inviting me to ASBMB meeting @WertLaboratory I had a great time to catch up with colleagues and trainees!

Kicked off with an excellent talk on epigenome editing by @ShawnLiu_Lab

🚨 Someone just turned Claude into a full AI research scientist. This GitHub repo called claude-scientific-skills just quietly changed what's possible with AI in science. Most people are using Claude to write emails and summarize docs. These researchers are using it to run actual drug discovery pipelines, analyze single-cell RNA sequencing data, interpret clinical variants, and generate publication-ready reports all from a single prompt. Here's how it works: You install one plugin in Claude Code. Claude automatically discovers and uses 140 scientific skills across every major research domain bioinformatics, cheminformatics, proteomics, clinical research, medical imaging, materials science, quantum computing, laboratory automation. The skills connect Claude directly to the databases and tools scientists actually use: → Query ChEMBL for bioactive compounds → Annotate variants with ClinVar and Ensembl → Dock molecules with DiffDock against AlphaFold structures → Analyze 10X genomics data with Scanpy → Search ClinicalTrials. gov and match patients to trials → Generate PDF clinical reports with ReportLab One prompt. Real scientific libraries. Live database APIs. Actual results. This is what happens when someone stops treating Claude like a chatbot and starts treating it like a research platform. /plugin install scientific-skills@claude-scientific-skills 100% Opensource. MIT License. (Link in the comments)

Our most recent work on the “function and evolution” of #nuclear_speckles is now online at Cell @CellCellPress cell.com/cell/fulltext/… Read the thread 👇for the highlights of our findings.

@jrblundell This is so cool. Lineage tracing is possible by methylation!

In 1999, Tom Maniatis discovered something remarkable: neurons achieve self-avoidance via stochastic methylation of the protocadherin gene cluster. We've just discovered this locus is an evolvable in-vivo barcode across the human tissues: biorxiv.org/cgi/content/sh… 🧵

@tangming2005 I love this case study to connect biology with bioinformatics. Pleased do more 🙏

🧵 That V-plot showing transcription factor binding? It might be an artifact. New research shows chromatin fragmentation methods create patterns even on naked DNA. Here's what went wrong.

Amazing paper from @PhilHolliger science.org/doi/10.1126/sc…

Papers submitted on Tuesdays are more likely to be accepted by Nature whereas Wednesdays seem the most likely day to submit and secure acceptance to PLOS ONE. For Cell, Mondays and Tuesdays seem the best submission days in case of accepted papers. link.springer.com/article/10.100…

New Year, new paper from our lab. Emily Kramer used 3D light-sheet imaging and tissue clearing to examine the spatial architecture of mouse amygdala engram ensembles. onlinelibrary.wiley.com/doi/10.1002/hi…

@Mykalt45 Yes and can be done in a cell-type specific manner.

@ShawnLiu_Lab Could this be used to look at deamination after methylation?

Our In Vivo DNA methylation editing paper is finally published. Happy to share these two transgenic mouse lines to help investigate the function of DNA methylation at gene/locus of your interest! Happy holidays! #citeas" target="_blank" rel="nofollow noopener">nature.com/articles/s4146…

「Claude Code for Everyone」を公開しました—ノートPC上でAIを実際に使いこなすための、ステップバイステップのハンズオン教材です。開発者向けのAIコーディング支援にとどまらず、ローカルAIエージェントとして、調査・執筆・編集などもサポートできます。 内容： - Windows / Mac のセットアップガイド - 学習ロードマップ：基礎 → R / Python - VS Code、Git、WSL（Windows）、Docker を使った実践ワークフロー - 実例プロジェクト（例：Claude Codeを活用した研究論文の執筆サポート） - 英語版をAIで翻訳 ぜひご覧ください： gexijin.github.io/vibe/ja/ #AI #ClaudeCode #Python #RStats #VSCode #Git #DeveloperTools #Productivity

@taekjip Amazing story!

Check out our model of how homology search in mammalian cells may be aided by a motor protein! A link for free access to the paper can be found here. tjhalab.com/the-lab

What if we could autocomplete DNA based on function? Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes with desired functions.🧵 nature.com/articles/s4158…