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 · 04/10/2023

Maybe 3rd goes to Nanopore?

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Ben Berman @benbfly.bsky.social · 04/10/2023

I agree - flourescent DNA sequencing - without which we wouldn't have the human genome or the millions of genomes, transcriptomes, epigenomes since. So who? Lee Hood for 1st generation and Shankar Balasubramanian for 2nd generation? Who would be the 3rd?

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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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