Genome-wide mapping of RNA-protein associations through sequencing
PRIM-seq combines barcoding and RNA sequencing to map over 350,000 RNA-protein interactions, offering new insight into gene regulation and disease-related molecular......
Bayesian inference for copy number intra-tumoral heterogeneity from single-cell RNA-sequencing data
Chloris uses single-cell RNA sequencing to identify tumor clones and their copy number alterations, revealing functional differences and improving understanding of tumor heterogeneity.......
Single-cell analysis and infectious disease forecasting: Google's new AI scientist
In Google's new paper, "An AI system to help scientists write expert-level empirical software" an AI supposedly "invents" new methods in bioinformatics and infectious disease modeling & forecasting....
Tiny fish open new horizons for autism research
Researchers at Niigata University used zebrafish models to show how environment shapes social behavior in autism, with RNA sequencing revealing changes in sensory pathways linked to anxiety and intera...
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing
Poly(A) tails are stretches of adenine nucleotides added to the end of messenger RNA (mRNA) molecules. These tails play a crucial role in determining how long RNA molecules survive in the cell, how ef...
Make your development environment portable and reproducible
Dotfiles, VM setup scripts, R "verse" packages, and dev containers...
New method calculates rate of gene expression to understand cell fate
Essentially all cells in an organism’s body have the same genetic blueprint, or genome, but the set of genes that are actively expressed at any given time in a cell determines what type of cell it wil...
Closing my tabs (Sep 5 2025)
NIH budget, AI, R, Bluesky & Science, state of biotech, AI in higher ed, R packages Top 40, structural variation, statistical power, Python documentary, Manhattan Project, tidymodels, ......
Cross-sample homopolymer polishing with Pypolca
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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, cross-species filtering for comparative genomics, ......