Paired Ends Podcast

Moving from biotech to academia I recently wrote a piece about leaving academia for biotech. I left academia for industry in 2019. I spent four years at a consulting firm before joining Colossal Biosciences . This week I’m returning to the University of Virginia School of Data Science as a tenured associate professor and dean of research. The transition from academia to industry can be tricky, but...

https://blog.stephenturner.us/p/ai-in-data-science-education Something a little different for this week’s recap. I’ve been thinking a lot lately about the practice of data science education in this era of widely available (and really good!) LLMs for code. I provide some commentary at the top based on my own data science teaching experience, with a deep dive into a few recent papers below. Audio ge...

https://blog.stephenturner.us/p/enlightenment-conservatory I had good intentions to give NaNoWriMo a try this year but didn’t get very far. Instead I gave OpenAI’s Creative Writing Coach GPT a try for a (very) short story I had in mind, inspired by my frustration trying to access closed-access research articles for a review article I’m preparing. I found it to be an excellent writing coach with sp...

https://blog.stephenturner.us/p/weekly-recap-dec-2024-part-3 This week’s recap highlights the Evo model for sequence modeling and design, biomedical discovery with AI agents, improving bioinformatics software quality through teamwork, a new tool from Brent Pedersen and Aaron Quinlan (vcfexpress) for filtering and formatting VCFs with Lua expressions, a new paper about the NHGRI-EBI GWAS Catalog, a...

https://blog.stephenturner.us/p/weekly-recap-dec-2024-part-2 This week’s recap highlights a new way to turn Nextflow pipelines into web apps, DRAGEN for fast and accurate variant calling, machine-guided design of cell-type-targeting cis-regulatory elements, a Nextflow pipeline for identifying and classifying protein kinases, a new language model for single cell perturbations that integrates knowle...

https://blog.stephenturner.us/p/weekly-recap-dec-2024-part-1 This week’s recap highlights the WorkflowHub registry for computational workflows, building a virtual cell with AI, a review on bioinformatics methods for prioritizing causal genetic variants in candidate regions, a benchmarking study showing deep learning methods are best for variant calling in bacterial nanopore sequencing, and a new M...

Full recap: https://blog.stephenturner.us/p/weekly-recap-nov-2024-part-3 This week’s recap highlights pangenome graph construction with nf-core/pangenome, building pangenome graphs with PGGB, benchmarking algorithms for single-cell multi-omics prediction and integration, RNA foundation models, and a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted bulk RNA-seq dat...

https://blog.stephenturner.us/p/inciteful-zotero-biologpt-semantic-scholar I am in the middle of writing a review / perspectives paper. One that I’m confident will be exciting once we get it published. Some sections of the review cover subject matter at the outer periphery of my expertise. These are areas where I don’t have as strong of a command of the relevant literature as my collaborators do....

Full post at https://blog.stephenturner.us/p/illuminate-preprints-with-an-ai-generated-podcast Google has a new experimental tool called Illuminate ( illuminate.google.com ) that takes a link to a preprint and creates a podcast discussing the paper. When I tested this with a few preprints, the podcasts it generated are about 6-8 minutes long, featuring a male and female voice discussing the key po...

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