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Steven Ge

@stevenge.bsky.social
73 followers 83 following 81 posts

Professor, founder of Orditus. AI, genomics, bioinformatics

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Steven Ge @stevenge.bsky.social · 28/09/2026
- The greatest waste isn’t lack of ability, but waiting for a future self. - The brain favors comfort now over rewards later. - Tiny actions break the cycle and build self-trust. I learned these from a video titled "How 90% of People Waste Their Lives", .... while doomscrolling in bed.
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Ming Tommy Tang @tommytang.bsky.social · 12/09/2026
News! My next book is coming. For 3 years I posted daily on the bioinformatics few teach you — the judgment, the traps, the sanity checks.
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Michael Love @mikelove.bsky.social · 12/09/2026
I wrote a post about how slice_sample() and other slice_* functions work in #tidyomics #Bioconductor tidyomics.github.io/tidyomicsBlo...
tidyomics.github.io
Slicing in tidyomics – tidyomicsBlog
How to use dplyr-style slice operations on omics data objects in the tidyomics project.
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Steven Ge @stevenge.bsky.social · 09/09/2026
I just received 4 free Claude subscriptions for my students via Claude Science. I paid $15 for a premium seat with 5x usage for myself. Must be a PI. Maybe they will be harvesting our data for their own science projects? You can't really trust these guys. www.anthropic.com/news/expandi...
anthropic.com
Expanding our support for scientists
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
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Steven Ge @stevenge.bsky.social · 21/07/2026
For bioinformatics coding, use Codex with gpt-5.6-sol. Beats Claude Code with Opus 4.8 by a long shot. Fable 5 won't even look at anything remotely related to biology.
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Steven Ge @stevenge.bsky.social · 13/07/2026
My 5 strategies for saving tokens—especially with Claude Fable 5: - Use Claude.ai for bounded tasks. Use Claude Code only when it needs to inspect files, edit a repo, run commands, or test its work. - Control the context. Start a new chat when switching tasks. Edit a prompt instead of piling on.
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Steven Ge @stevenge.bsky.social · 12/07/2026
Fable 5 extended again to 7/19. Thank you, Anthropic, for motivating me! I needed deadlines in the summer! 😀
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Steven Ge @stevenge.bsky.social · 09/07/2026
“Explain briefly in plain language, using bullet points.” I’ve been saying this to LLMs a lot recently. These models have become incredibly powerful. But their answers are often long, technical, and overly detailed. Sometimes I simply don’t have the time, patience, or knowledge to read.
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Steven Ge @stevenge.bsky.social · 09/07/2026
I still upload key files to the Claude or ChatGPT websites to get a fresh perspective. Claude Code or Codex can be influenced by what's in the local project folder. CLAUDE.md, AGENTS.md, and project memory files are helpful but could also prime AI. The web offer a fresh, controlled context.
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Ariaa® @ariaa.bsky.social · 05/07/2026
Supposedly the most intelligent of all species...humans.
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Steven Ge @stevenge.bsky.social · 24/06/2026
Don't worry about not keeping up with AI. Nobody is. Identify and solve a problem! Even last year's AI is underutilized! For scientists, discover something new. Or create a tool that helps others.
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Leo Hickman @leohickman.carbonbrief.org · 22/06/2026
After 18 months of R&D with a team of specialist academics, I'm VERY excited to say that @carbonbrief.org has just launched 'Project Cosmos'... ...the world's largest database of climate research Our hope is this becomes a major new resource interactive.carbonbrief.org/cosmos/index...
interactive.carbonbrief.org
Project Cosmos – the world’s largest database of climate change research
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Aalia Mauro @aaliamauro.bsky.social · 22/06/2026
On June 5th Israel attacked the home of Lebanese sea turtle conservationist Mona Khalil. Mona was hospitalized with burns and injuries to over 70% of her body. Yesterday, June 19th, Mona died from her injuries. This wasn’t an accident.
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davidegardner.bsky.social @davidegardner.bsky.social · 21/06/2026
Today's "From the Files" 06-21-26: Mountain Shack. Silverton, CO. 2025 #davidgardnerphotography #liightight #landscape #vertical #grandturkpeak #fall #mountain #structure #shack #fallcolor #aspen
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Ming Tommy Tang @tommytang.bsky.social · 20/06/2026
1/ Many genomics mistakes are hard to catch in the code. They’re in the data you never looked at. Genome browsers can change that. Here’s how.
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Steven Ge @stevenge.bsky.social · 21/06/2026
Anyone can create data dashboards with AI. Following this tutorial, you can use ChatGPT, React, and VS Code to turn a data file into a simple, interactive dashboard. You do not need to know how to code or understand HTML or JavaScript to get started.
gexijin.github.io
vibe
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Steven Ge @stevenge.bsky.social · 21/06/2026
More biologists are coding their own analyses. Next: version control. Following this 30-min tutorial, you can learn how to use ChatGPT and GitHub Desktop to build a simple data dashboard. GitHub helps you track changes, collaborate, and share your work. Tutorial: gexijin.github.io/vibe/Git_Bra...
gexijin.github.io
vibe
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Timothy Caulfield @caulfieldtim.bsky.social · 30/05/2026
I've been following & researching "precision" medicine / genomics for decades... So much hype. So much underwhelming or narrow applications. This seems genuinely exciting! 👇 Groundbreaking genomic test could spare millions of breast cancer patients chemotherapy www.theguardian.com/society/2026...
theguardian.com
Groundbreaking genomic test could spare millions of breast cancer patients chemotherapy
Trial suggests patients with a low test score could be treated with hormone therapy alone with near-identical outcomes
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 28/05/2026
Ratio Percentile Deviation (RPD): A nonparametric, compositionally robust method for measuring the divergence of a microbial sample from a reference dataset www.biorxiv.org/content/10.64898/20…
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Dr. Mar @boldnewme.bsky.social · 16/05/2026
I love and respect this scientist. Carl Sagan answers a question about creation vs evolution.
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Ming Tommy Tang @tommytang.bsky.social · 10/05/2026
Claude Code shipped /ultrareview and almost nobody is talking about what's actually new about it. It's not "AI reviews your code." We had that.
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Steven Ge @stevenge.bsky.social · 08/05/2026
Confession: I trusted Claude Code too much and moved too fast in my bioinformatics research. AI's execution outpaced my ability to understand. I was prompting & accepting without reading the full responses. The result? Cognitive debt that compounds over time.
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Ming Tommy Tang @tommytang.bsky.social · 21/04/2026
OmicClaw: executable and reproducible natural-language multi-omics analysis over the unified OmicVerse ecosystem www.biorxiv.org/content/10....
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Stephen Turner @stephenturner.us · 14/04/2026
2 years ago I went to bed feeling great, woke up next morning with a painful ear and hearing loss (which became permanent). Because of a shingles infection in my auditory nerve. Get the vaccine if you're eligible www.wired.com/story/shingl...
wired.com
You Should Be More Freaked Out by Shingles
The viral infection leaves millions with chronic pain, increased stroke risk, and lifelong nerve damage—yet vaccination rates remain dangerously low.
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Steven Ge @stevenge.bsky.social · 09/04/2026
Codex CLI is fast. Claude Code is thoughtful. Codex wins on speed and cost. Claude wins on judgment. What stood out to me is that Claude Code better understands the project as a whole: the files, the context, and what I actually want done.
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Simon Smart @simonsmart.bsky.social · 26/03/2026
I’m giving a seminar on 20th April about refactoring crsu.shinyapps.io/MetaInsight/ to use {shinyscholar}, producing crsu.shinyapps.io/MetaInsight_... Details and sign up: www.eventbrite.co.uk/e/crsu-webin... A shorter version is also coming to R/Medicine in May #rstats #metaanalysis #openscience
Poster for the seminar: MetaInsight v7: Making a comprehensive app for network meta analysis reproducible
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Steven Ge @stevenge.bsky.social · 22/03/2026
Vibe Writing: how I co-write with Claude Code, one sentence at a time. It’s not “AI, write my paper.” It’s me thinking out loud while AI handles the mechanics. I direct. AI drafts. I said, “move this to methods” → Claude saw it was already covered there and cut the redundancy.
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Stephen Turner @stephenturner.us · 18/03/2026
OmicClaw: executable and reproducible natural-language multi-omics analysis over the unified OmicVerse ecosystem. www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/Starlitnight...
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Steven Ge @stevenge.bsky.social · 19/03/2026
The new GPT-5.4 Mini is slightly less intelligent but faster and costs only 30% of GPT-5.4 and 15% of Opus 4.6. It would be great for many applications. This also makes running local models hard to justify solely on economic grounds. openai.com/index/introd...
openai.com
Introducing GPT-5.4 mini and nano
GPT-5.4 mini and nano are smaller, faster versions of GPT-5.4 optimized for coding, tool use, multimodal reasoning, and high-volume API and sub-agent workloads.
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Steven Ge @stevenge.bsky.social · 19/03/2026
OpenClaw is impressive, but you can build a more transparent AI agent with just Claude Code and Bash. Roman's video shows how to create custom agents for real-world workflows, like getting an email summary at 9 a.m. or managing email via Telegram. What clicked for me:
youtu.be
I Replaced OpenClaw with Claude Code (It's Not Even Close)
YouTube video by Agentic Lab
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Steven Ge @stevenge.bsky.social · 17/03/2026
--dangerously-skip-permissions in Claude Code worked fine for months — until today. Claude wiped all the scripts in one of my subfolders, and I hadn’t committed several hours of work yet. Lessons: Commit often. Use YOLO mode with caution.
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Steven Ge @stevenge.bsky.social · 16/03/2026
Good news: Claude Code can run complex data analyses on its own for hours. Bad news: it makes many decisions quietly along the way. Hard-coded parameters, filtering choices, and assumptions. Most are fine, but a single bad parameter can derail the entire workflow.
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Clément Canonne @ccanonne.github.io · 09/03/2026
I'm wondering if the reason many people are so keen on this "science through repeated prompts" idea is because that's already how they operate with their students (or, outside of academia, their team). Try this vague idea. Try again. Come back next week after trying more. Make this into a paper.
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Simon P. Couch @simonpcouch.com · 05/03/2026
Today we're releasing AI for RStudio. It's really, really good—I'd encourage you to point it at the messiest data sources you have and see what it can do. www.simonpcouch.com/blog/2026-03...
A screenshot of an RStudio window. On the left-hand side is a new pain called Posit Assistant. The Posit Assistant had recently run code making a lat-lon plot of Washington state, colored by whether the point had been marked as forested or not.
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Stephen Turner @stephenturner.us · 25/02/2026
Agentic AI and the rise of in silico team science in biomedical research www.nature.com/articles/s41... 🧬💻🧪 rdcu.be/e5HDu Looking forward to reading this one from @moorejh.bsky.social lab and colleagues 👀
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Ming Tommy Tang @tommytang.bsky.social · 22/02/2026
The best AI coding tool in the world now has a free course. Not $500. Not $99. Free. Resources have never been more abundant. It's the will to learn that has never been more rare. Stop scrolling. Start building → anthropic.skilljar.com/claude-code...
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Ming Tommy Tang @tommytang.bsky.social · 21/02/2026
1/ RNA‑seq batch effects are one of the easiest ways to fool yourself in genomics. They can create beautiful, completely wrong biology if you’re not careful.
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Rami Krispin @ramikrispin.bsky.social · 21/02/2026
My weekly newsletter is out! This week's agenda: 🔹 Open Source of the Week - The DuckLack R project by Travis Gerke, ScD 🔹 New learning resources 🔹Book of the week - Time Series Forecasting in Python by Marco Peixeiro ramikrispin.substack.com/p/time-serie... #rstats #python #ai #datascience
ramikrispin.substack.com
Time Series Forecasting in Python, the DuckLack R Library, New Tutorials| Issue 76
A weekly curated update on data science and engineering topics and resources.
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 14/02/2026
In many R courses, data are clean & everything just works. But real life is messy—and that’s where problems start 👉 Our course with @cecibaldoni.bsky.social -Dealing with Messy Data in R in April: clean, join & visualise real datasets with tidyverse & ggplot2 💻📊 shorturl.at/zdmht #Rstats #MessyData
physalia-courses.org
Dealing with messy data in R: data cleaning and visualisation
8-10 April 2026
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Ming Tommy Tang @tommytang.bsky.social · 09/02/2026
A human pan-disease blood atlas of the circulating proteome | Science www.science.org/doi/10.1126...
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Tomasz Kalinowski @t-kalinowski.bsky.social · 27/01/2026
ragnar 0.3.0 is now on CRAN! 🚀 An R toolkit for RAG from your docs: faster ingestion, better retrieval, Azure OpenAI + Snowflake embeddings, and MCP serving. tidyverse.org/blog/2026/01... #rstats #rag #ai
tidyverse.org
ragnar 0.3.0
The new release of ragnar adds faster ingestion, new embedding providers, improved retrieval, and new integrations for using ragnar stores from tools.
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deedotkurses @deedotk.bsky.social · 30/12/2025
TIL: Before Hans Asperger or Leo Kanner, a Jewish-Ukrainian psychiatrist named Grunya Sukhareva defined autism in 1925. Both men did not cite her work. She also had documented how it affected women and girls, where the men did not. en.wikipedia.org/wiki/Grunya_...
en.wikipedia.org
Grunya Sukhareva - Wikipedia
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Rami Krispin @ramikrispin.bsky.social · 20/12/2025
My weekly newsletter is out! ramikrispin.substack.com/p/issue-67-t... #python #ai #llm
ramikrispin.substack.com
Issue 67: The PyDMD Project, Build a Text-to-Image Generator, New Tutorials
A weekly curated update on data science and engineering topics and resources.
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Steven Ge @stevenge.bsky.social · 16/12/2025
Excited to share "Claude Code for Everyone"—a set of step-by-step, hands-on tutorials to help you put AI to work on your laptop. It isn’t just an AI coding tool for developers; it is a powerful local AI agent to support research, writing, editing, and more. Check it out: gexijin.github.io/vibe/
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Rami Krispin @ramikrispin.bsky.social · 17/12/2025
Claude Code for Everyone The following tutorial by Prof. Steven Ge (@stevenge.bsky.social ) provides a step-by-step guide for setting up and working with Claude Code. This includes different routes by OS (Mac and Windows) and programming languages ( #Rstats and #Python). gexijin.github.io/vibe/
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Hao Yin @haoyin.bsky.social · 16/12/2025
80-mer DNA aptamer as a selective marker for #Senescence Targeting EDA-Fibronectin Kd 500~1000 pM Label senescent cells in naturally aged🐭🫁 Aptamer binding ⬇️in 21-mo INK-ATTAC🐭 with p16 cells eliminated #Aging_Cell 2025 onlinelibrary.wiley.com/doi/10.1111/...
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Steven Ge @stevenge.bsky.social · 16/12/2025
Excited to share "Claude Code for Everyone"—a set of step-by-step, hands-on tutorials to help you put AI to work on your laptop. It isn’t just an AI coding tool for developers; it is a powerful local AI agent to support research, writing, editing, and more. Check it out: gexijin.github.io/vibe/
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Steven Ge @stevenge.bsky.social · 16/12/2025
Claude Code is more than coding. To prove it: here’s how I built ~100 tutorials in about a week by packaging my workflow into slash commands (reusable prompts)—write, review, and translate. It automates workflows. How I did it: gexijin.github.io/vibe/Buildin... Tutorials: gexijin.github.io/vibe/
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Simon P. Couch @simonpcouch.com · 13/11/2025
To be effective, data science agents need to be able to read plots reliably. @sara-altman.bsky.social and I wrote about some concerning findings on LLMs' ability to interpret plots when the content contradicts their expectations on the @posit.co blog. posit.co/blog/introdu...
posit.co
When plotting, LLMs see what they expect to see - Posit
Data science agents need to accurately read plots even when the content contradicts their expectations. Our testing shows today's LLMs still struggle here.
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Steven Ge @stevenge.bsky.social · 10/11/2025
This is my R development setup — built on VS Code and running both Claude Code and OpenAI’s Codex inside a Docker container. It also supports Shiny apps and has been working great for me. I am on Windows. These coding agents were initially designed for Linux, I think. github.com/gexijin/vibe
github.com
GitHub - gexijin/vibe: Vibe coding via Claude Code & Codex
Vibe coding via Claude Code & Codex. Contribute to gexijin/vibe development by creating an account on GitHub.
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