iiinova — where your digital self keeps evolving

Reposted by Eric Talevich

DNAnexus, Inc. @dnanexus.bsky.social · 20/04/2026

This week: accelerate your drug discovery with AI-driven workflows for protein structure prediction: hubs.ly/Q04cxxTV0 #AI #DrugDiscovery #Pharma #ProteinPrediction #PrecisionMedicine #AlphaFold #Nextflow

Live Webinar: April 24, 9 AM PST | 12 PM EST. Accelerating Protein Structure Prediction and Visualization: Scalable Workflows with Nextflow. Speakers: Darren Ames, Head of Solution Science DNAnexus, and Eric Talevich, VP of Bioinformatics DataXight

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Eric Talevich @etalevich.bsky.social · 09/04/2026

I'll give a webinar talk April 24th, covering: - nf-core/proteinfold (AlphaFold2, ESMFold, etc.) - Molstar/Mol* - what comes before and after them This kicks off a series on molecular modeling using open-source tools on DNAnexus.

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Eric Talevich @etalevich.bsky.social · 09/04/2026

I wrote about how I write code for clinical use, as of 2026: etal.github.io/2026/03/30/v... Briefly: - Claude Code in one terminal, zsh in another - Papers and docs in a browser - Plugins: feature-dev, serena, python-lsp, explanatory-output-style - Lots of deterministic tools.

etal.github.io

Are you really vibe-coding CNVkit?

Clinical considerations for bioinformatics development with AI coding agents.

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Reposted by Eric Talevich

Hunter Shain @shainlab.bsky.social · 10/06/2025

I have been listening to the Hubermann-JB podcast. It is 4 hours, so it will take some time to finish, but here are some thoughts...

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Eric Talevich @etalevich.bsky.social · 21/05/2025

Regeneron picks up the 23andMe dataset -- one of the best possible outcomes, I think. REGN has a stellar track record of handling patient data responsibly and effectively, e.g. UK Biobank, Geisinger Health. www.biopharmatrend.com/post/1252-re...

biopharmatrend.com

Regeneron Acquires 23andMe Assets for $256M to Expand Consumer Genomics and Data-Driven Drug Discovery

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Reposted by Eric Talevich

Andrey Kislyuk @kislyuk.bsky.social · 10/05/2025

www.savensf.com/take-action

savensf.com

Take Action | Save NSF

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Reposted by Eric Talevich

Rohit Singh @rohitsingh8080.bsky.social · 05/04/2025

Bio foundation models are great design and engg tools. But can they help decode the fundamental principles of life? We harnessed a single-cell FM for decoding the long-debated relationship between genome arch. and gene coregulation. 1/ Preprint here: www.biorxiv.org/content/10.1...

biorxiv.org

Tracing the Shared Foundations of Gene Expression and Chromatin Structure

The three-dimensional organization of chromatin into topologically associating domains (TADs) may impact gene regulation by bringing distant genes into contact. However, many questions about TADs' fun...

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Eric Talevich @etalevich.bsky.social · 31/03/2025

A district court has struck down the FDA's Final LDT rule, which would have required clinical test developers to navigate full FDA IVD approval to bring new products to market -- a much tougher bar to clear. Tl;dr: Diagnostics biz isn't dead. Source: www.courtlistener.com/docket/68802...

courtlistener.com

American Clinical Laboratory Association v. U.S. Food and Drug Administration, 4:24-cv-00479 - CourtListener.com

Docket for American Clinical Laboratory Association v. U.S. Food and Drug Administration, 4:24-cv-00479 — Brought to you by Free Law Project, a non-profit dedicated to creating high quality open legal...

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Eric Talevich @etalevich.bsky.social · 20/03/2025

Element Bio says this on-instrument hybrid capture approach can bring total library prep time down from 12-24 hours to as little as 5 hours (before sequencing). That faster TAT should be great for NGS diagnostics.

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Reposted by Eric Talevich

Galaxy Project @galaxyproject.bsky.social · 17/03/2025

The GBCC2025 Scholarships are here! Thanks to the JXTX Foundation and Galaxy Project, 4 genomics and data science graduate students will receive scholarships to attend GBCC2025 in person. 📅 Apply by April 1, 2025 👉 jxtxfoundation.org/news/2025-2-...

jxtxfoundation.org

JXTX + GBCC 2025 Scholarships

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Eric Talevich @etalevich.bsky.social · 17/03/2025

Roche deems Spark Therapeutics, a flagship gene therapy company, has fizzled with a US$2.4bn write-off. Luxturna didn't sell well, surprisingly. I hadn't thought gene therapies were in a bubble but it seems like a broader correction is happening. www.fiercepharma.com/pharma/roche...

fiercepharma.com

Roche overhauls Spark gene therapy unit, recording $2.4B in full impairment

Roche has recently launched a “fundamental reorganization” of Spark Therapeutics, the gene therapy unit the Swiss pharma bought for $4.3 billion in 2019. | Roche has recently launched a “fundamental r...

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Reposted by Eric Talevich

Daniel MacArthur @dgmacarthur.bsky.social · 15/03/2025

New preprint! We worked with @msftresearch.bsky.social and @broadinstitute.org to see whether large language models (LLMs) can be useful to variant scientists in deciding whether genetic variants seen in a patient are responsible for their disease. tl;dr yes they can: www.biorxiv.org/content/10.1...

biorxiv.org

Evidence Aggregator: AI reasoning applied to rare disease diagnostics

Retrieving, reviewing, and synthesizing technical information can be time-consuming and challenging, particularly when requiring specialized expertise, as is the case of variant assessment for rare di...

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Eric Talevich @etalevich.bsky.social · 13/03/2025

What a great resource! Python developer tooling has matured a lot over the past decade.

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Eric Talevich @etalevich.bsky.social · 12/03/2025

LAAVA 4.0 is out! Get the latest on GitHub: github.com/formbio/laav... Long-read AAV Analysis (LAAVA) is an open-source bioinformatics pipeline that reports on AAV vector genome integrity using a standardized, published nomenclature and read classification scheme. 🧵

github.com

Release v4.0.0 · formbio/laava

What's Changed Functional changes: Handle mITR/wtITR directionality for scAAV classification via new input "mitr_label" (#70) Output aggregate summary tables for reporting (#67) Add version number...

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Reposted by Eric Talevich

Richard Sever @richardsever.bsky.social · 11/03/2025

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

openrxiv.org

Homepage - openRxiv

openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.

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Eric Talevich @etalevich.bsky.social · 06/03/2025

How I pick a bioinformatics tool to start: - Check nf-core -- is there a pipeline I can use as-is? If not, what tools are used inside other relevant pipelines? - Check the methods of studies similar to what you're trying to do -- not searching methods papers themselves initially, but who used them

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Reposted by Eric Talevich

Catharine.Aquino @catharineaquino.bsky.social · 15/02/2025

Because a lot of people had problems registering for the @RocheSequencing seminar about their new SBX sequencer , they made it easier to join . Here is the link : streamingmedia.roche.com/id/1_arrcrfhm

streamingmedia.roche.com

Introducing Sequencing By Expansion (SBX) - 20 Feb 2025 - Webcast&Video Portal

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Eric Talevich @etalevich.bsky.social · 09/02/2025

Agentic AI coding is leading to some new software development best practices: Keep projects small and modular to fit within the context window. Start with a good PRD. If the initial architecture is wrong, just start over. Use distinct, unambiguous names or the AI will get confused.

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Eric Talevich @etalevich.bsky.social · 09/02/2025

Cline.bot and Replit are not really like a senior dev or a team of junior devs. They're amazing and a good fit for the needs of one-off web app development. They struggle with legacy and maintenance, as we all do, and they have their own unique quirks.

cline.bot

Cline - Autonomous Coding Agent for VSCode

Cline is an AI-powered coding assistant for Visual Studio Code.

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Eric Talevich @etalevich.bsky.social · 27/01/2025

Eleven years after Roche acquired Genia's nanopore sequencing tech, we see what they're up to: short-read sequencing competitive with Illumina and Ultima on price, throughput, and quality.

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