Papers

Weekly recap (Sep 19, 2025)

AI-generated genomes, R news for my posit::conf() FOMO, biosecurity, mirror life, teaching and AI, ELSI for AI, in defense of CRAN, Anthropic Economy…

Sep 19 •

Closing my tabs (Sep 12, 2025)

AI in academia, $1B NSF cut, AI+biosecurity, bacterial DNA from mammoth bones, understanding LLMs and their math, bioacoustics for conservation…

Sep 12 •

Weekly Recap (Sep 2025 part 1)

Biobank-scale relatedness estimation, SNP calling and phasing with long RNA-seq reads, predicting expression-altering promoter mutations with DL…

Sep 2 •

Weekly Recap (Aug 2025, part 4)

Genome annotation, viral genome clustering, metagenomic diagnostics, SV analysis on ONT reads, functional prediction, gene loss, DNA damage/repair…

Aug 21

Closing My Tabs: Aug 15 2025

Closing my browser tabs: papers, blogs, news stories, YouTube videos, tutorials, etc. from the world of data science + biotech

Aug 15 •

Weekly Recap (Aug 2025, part 3)

De novo mutation rates from a 4-gen pedigree, how LLMs internalize scientific literature, pedigree and genetic data simulations, a review on predicting…

Aug 13 •

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…

Aug 8 •

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…

Aug 1 •

Weekly Recap (July 2025, part 3)

Long-read consensus assembly with Autocycler, Progen3 for generation and functional understanding of proteins, CarpeDeam for ancient metagenome…

Jul 24

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…

Jul 18 •

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…

Jul 11

Weekly Recap (July 2025, part 1)

Rust-based wgatools for alignment manipulation & analysis, Nextflow nf-core/scnanoseq for ONT scRNA-seq, Sawfish for long-read SV analysis, BINSEQ…

Jul 3

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