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Moving from biotech to academia
Thoughts and advice on transitioning from a career in industry biotech to academia. 1.4k words, 6 minute reading time.
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Stephen Turner
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Weekly Recap (Aug 2025, part 2)
Metagenome assembly from nanopore reads, AI for single-cell analysis, GxE + epistasis in a vertebrate model, estimating GxE for polygenic traits…
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Stephen Turner
Ollama now has a GUI
Ollama's new app has a built-in user interface. It has a model selector, you can drop in files, and it supports multimodal and vision models like Gemma3…
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Stephen Turner
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Vibe code is legacy code
Quoting Steve Krouse
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Stephen Turner
Weekly Recap (Aug 2025, Part 1)
Rewriting regulatory DNA, zero-shot evaluation of scRNAseq foundation models, predicting gene function with coevolutionary signals, errors in long-read…
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Stephen Turner

July 2025

Autocycler: long read consensus assembly
Demo: Autocycler is fast, easy, and accurate for producing consensus bacterial genome assemblies by combining multiple long read assemblies of the same…
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Stephen Turner
Weekly Recap (July 2025, part 3)
Long-read consensus assembly with Autocycler, Progen3 for generation and functional understanding of proteins, CarpeDeam for ancient metagenome…
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Returning to Academia: UVA Data Science
Some personal news: I'm joining the University of Virginia as Associate Professor of Data Science and Assistant Dean of Research in UVA's new School of…
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Stephen Turner
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Genome engineering in biodiversity conservation and restoration
Our new perspective paper in Nature Reviews Biodiversity describes how modern gene editing technology can serve as a crucial "second aid" approach to…
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Stephen Turner
Positron Assistant: GitHub Copilot and Claude-Powered Agentic Coding in R
Positron Assistant provides inline completions with GitHub Copilot and chat using Claude 4 Sonnet. Demonstration: using agent mode to create an R…
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Stephen Turner
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Tidy RAG in R with ragnar
Retrieval augmented generation in R using the ragnar package. Demonstration: scraping text from relevant links on a website and using RAG to ask about a…
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Stephen Turner
Weekly Recap (July 2025, part 2)
Deep ancestral structure shared by humans, a genomic language model for enhancer prediction, enzyme active site scaffolding using RFdiffusion2…
© 2025 Stephen Turner
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