This week’s recap highlights a new multispecies codon optimization method, personalized pangenome references with vg, a commentary on the wild west of spike-in normalization, a new pipeline for comprehensive and scalable polygenic scoring across ancestrally diverse populations, a paper showing deep learning / transformer-based methods don’t outperform simple linear models for predicting gene expression after genetic perturbations, and finally, a

This week’s recap highlights a Nextflow pipeline for eQTL detection, an end-to-end pipeline for spatial transcriptomics (visium) data analysis, a method for identification of perturbed cell types in single cell RNA-seq data, a method for guide assignment in single-cell CRISPR screens, a tool for on-target/off-target analysis of gene editing outcomes, and “digital microbes” for collaborative team science on emerging microbes.

This week’s recap highlights a new nf-core workflow for multi-omics trait association studies, a new tool for linking genotype to phenotype (G2P) by directly sequencing alleles from CRISPR base editing experiments, the SplitsTree app for interactive analysis and visualization using phylogenetic trees and networks, mapping cellular interactions from spatially resolved transcriptomics data, a study of marine microbial diversity and bioprospecting

This week’s recap highlights a new tool from Wei Shen and Zamin Iqbal for efficient sequence alignment against millions of prokaryotic genomes (LexicMap), a new tool from Heng Li for efficiently constructing and querying a sequence index at scale, an R/Bioconductor package for detecting and correcting DNA contamination in RNA-seq data, a method for dating gene age using synteny, how AlphaFold predictions for some types of conformations are

This week’s recap highlights Google/Deepmind’s new AlphaProteo tool for protein design, tools for protein structure alignment and analysis, biases in polygenic risk scores due to overlap and kinship, highly variable gene selection in single cell RNA-seq, and reconstruction of a 4.2 billion year old last universal common ancestor of life on Earth (spoiler alert: CRISPR-Cas is >4B years old!). Others that caught my attention include a new

This week’s recap highlights perspectives in de-extinction and patent law, systematic benchmarking of scATAC-seq methods, a 91 gigabase (!) animal genome, structural variant genotyping with long reads, cell type-specific enhancer prediction, and a perspective piece in AI in biosecurity.

Here are a few papers that caught my attention recently. I summarize a few in the deep dive at the top, then link to a few other papers of note later on. Subscribe to Paired Ends to get periodic summaries like this delivered to your e-mail.

Here are a few papers that caught my attention recently. I summarize a few in the deep dive at the top, then link to a few other papers of note later on. Subscribe to Paired Ends to get periodic summaries like this delivered to your e-mail.

Here are a few papers that caught my attention recently. I summarize a few in the deep dive at the top, then link to a few other papers of note later on. Subscribe to Paired Ends to get periodic summaries like this delivered to your e-mail.

It’s been a big week in the genomics+bioinformatics space. This post expands on a few of the recent papers I posted in a Twitter thread. I highlight a few in the deep dive at the top, then link to a few other papers of note later on. Subscribe (free!) to Paired Ends to get summaries like this delivered to your e-mail as soon as I write them.