iiinova — where your digital self keeps evolving

Reposted by Ben Berman

Lior Pachter @lpachter.bsky.social · 19/02/2026

I used Claude Opus 4.5/4.6 (and a bit of Codex GPT-5.3) to port edgeR to Python. See edgePython github.com/pachterlab/e... This allowed me to develop a single-cell DE method that extends NEBULA with edgeR Empirical Bayes. All in one week. Details in doi.org/10.64898/202...

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Ben Berman @benbfly.bsky.social · 04/12/2024

There are few perfect things in life. the @vscode.dev differ is one of them.

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Ben Berman @benbfly.bsky.social · 06/05/2024

Our latest Nanopore 🧬 liquid biopsy paper! The first long-read survey of circulating DNA in a diverse set of cancer types. We discovered 3 distinct fragmentomic subtypes, including a new hypofragmented class with fragments longer than those captured by Illumina. 👇 www.biorxiv.org/content/10.1...

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Ben Berman @benbfly.bsky.social · 22/12/2023

Excited about this important new study to investigate use of circulating chromatin /DNA as a biomarker for sepsis in the critical care environment. This is a new world of opportunity to save lives. www.guysandstthomas.nhs.uk/news/revolut...

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Ben Berman @benbfly.bsky.social · 20/12/2023

this looks like a major advancement for ChIP-seq! Query up to hundreds of antibodies in a single experiment. From Mitchell Guttman and colleagues.

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Ben Berman @benbfly.bsky.social · 11/10/2023

CNS tumor classification during surgery using rapid Oxford Nanopore sequencing. This technology is so promising for real-time, near-patient genomic analysis, not least because of direct DNA methylation detection. Very exciting paper - congrats! www.nature.com/articles/s41...

nature.com

Ultra-fast deep-learned CNS tumour classification during surgery - Nature

Sturgeon is a pretrained neural network that uses incremental results from nanopore sequencing to rapidly classify central nervous system tumours and can be used to aid critical decision-making during...

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Reposted by Ben Berman

Oded Rechavi @odedrechavi.bsky.social · 09/10/2023

Yesterday evening I found out my friend got murdered in his house together with his wife and all his kids. He was a very good man who helped anybody as a principle, even if you weren't close with whatever you might need. A real Kibbutznik. I am broken. Everybody around me getting similar news.

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Ben Berman @benbfly.bsky.social · 01/10/2023

I doubt Elon will notice the entire biosciences crowd leaving. But who is the @odedrechavi.bsky.social of the Machine Learning and Aerospace academic communities? He will notice when they leave.

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