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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…
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
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Stephen Turner
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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…
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Stephen Turner
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…
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Stephen Turner
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…
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Stephen Turner
Weekly Recap (July 2025, part 3)
Long-read consensus assembly with Autocycler, Progen3 for generation and functional understanding of proteins, CarpeDeam for ancient metagenome…
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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…
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Stephen Turner
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…
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…
Weekly Recap (June 2025, part 2)
Interactive visualization of tabular data, shared foundations of gene expression and chromatin structure, fast protein structure searching with graph…
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Stephen Turner
Weekly Recap (June 2025, part 1)
PhyloSketch for drawing phylogenies, Uncalled4 for DNA/RNA modification detection, Severus for long read SV calling, CREsted for synthetic enhancer…
Weekly Recap (May 2025, part 3)
Polars-bio, LiftOn, feature selection for scRNA-seq, STRkit for genotyping STRs with long reads, nf-core/detaxizer, Uncalled4, RegionScan, CREsted…
© 2025 Stephen Turner
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