Bioinformatics, computational biology, and data science updates from the field. Occasional posts on programming.

This week’s recap highlights pangenome graph construction with nf-core/pangenome, building pangenome graphs with PGGB, benchmarking algorithms for single-cell multi-omics prediction and integration, RNA foundation models, and a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted bulk RNA-seq data.

Stephen Turner

Pangenome graph construction with nf-core/pangenome, pangenome graphs, single cell multi-omics, RNA foundation models, Nextflow for B-cell receptor sequencing from nontargeted bulk RNA-seq, ...

Weekly Recap (Nov 2024, part 3)

I just returned from a week in Barcelona where I attended the Nextflow Summit and nf-core hackathon, and I can hardly contain my excitement for the near term future of bioinformatics, computational biology, and open science in general.

Highlights from the 2024 Nextflow Summit and nf-core hackathon in Barcelona

Nextflow Summit Barcelona 2024

This week’s recap highlights protein design with RoseTTAFold, surveillance with wastewater sequencing, T2T human genomes, Vitessce for visualization of multimodal spatial single-cell data, and Taxometer for taxonomic classification of metagenomics contigs.

Protein design with RoseTTAFold, wastewater sequencing T2T human genomes, single-cell spatial transcriptomics, taxonomic classification, ...

Weekly Recap (Oct 2024, part 4)

I am in the middle of writing a review / perspectives paper. One that I’m confident will be exciting once we get it published. Some sections of the review cover subject matter at the outer periphery of my expertise.

Listen now | Inciteful with the Zotero plugin is the perfect combo for filling in gaps in your knowledge of the literature in a particular field. BioloGPT and Semantic Scholar are useful too.

Inciteful+Zotero to find relevant literature

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

What I'm reading this week on multispecies codon optimization, personalized pangenome references, spike-in normalization, automating polygenic scoring, transformers vs linear models, bactoneurons, ...

Weekly Recap (Oct 2024, part 1)

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

Regulatory element mapping, phylogenetic tree analysis+viz, mapping cellular interactions with scRNA-seq, bioprospecting, transformers in single-cell omics, nf-core/omicsgenetraitassociation, ...

Weekly Recap (Sep 2024, part 4)

This week’s recap highlights an AI agent for automated multi-omic analysis (AutoBA), rapid species-level metagenome profiling and containment (sylph), a review on genome-wide association analysis beyond SNPs, private information leakage from scRNA-seq count matrices, and a method to “unlearn” viral knowledge in protein language models as a means to develop safe PLM-based variant effect analysis (PROEDIT).  Others that caught my attention include

What I'm reading in agentic multiomic analysis, metagenome profiling, GWAS beyond SNPs, private information leakage from scRNA-seq, unlearning viral knowledge for safe protein language models, ...

Weekly Recap (Nov 2024, part 2)

I recently stumbled across Phil Ewels’s ~18 minute nf-core/bytesize talk on Excalidraw: For years I’ve been using draw.io for making flowcharts and diagrams for documentation, papers, presentations, and for general brainstorming and communication with my team, clients, and collaborators.1 Excalidraw (excalidraw.com) looks like an attractive alternative.

Excalidraw might be my new go-to open-source tool over draw.io for creating and sharing workflow diagrams. It's simple, fast, aesthetically pleasing, and has amazing VS Code integration.

Excalidraw: create and share workflow diagrams with end-to-end encryption

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.

What I'm reading this week in structural variant analysis, population/medical genetics, infectious disease modeling+forecasting, ML in single cell omics, paleogenetics, pangenomes, cancer genomics ...

What I'm reading (Aug 2024, part 3)

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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

What I'm reading this week in alignment and indexing millions of genomes at scale, gene age and family analysis and visualization, synthetic enhancers and cell fate programming, single cell omics, ...

Weekly Recap (Sep 2024, part 3)

This week’s recap highlights a new Nextflow workflow for calculating polygenic scores with adjustments for genetic ancestry, a paper demonstrating that whole exome plus imputation on more samples is more powerful than whole genome sequencing for finding more trait associated variants, a new deep-learning-based splice site predictor that improves spliced alignments, a new method for accurate community profiling of large metagenomic datasets, and

Nextflow workflow for polygenic scoring, WES+imputation &gt; WGS, DL method for splice site prediction, metagenomics profiling, and a new NIST/GIAB matched tumor-normal with 13 sequencing modalities

Weekly Recap (Oct 2024, part 3)

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 &gt;4B years old!).  Others that caught my attention include a new

What I'm reading this week in protein design with AlphaProteo, biases in polygenic risk scores, scRNA-seq HVG selection, reconstruction of a 4.2 billion year old last universal common ancestor, ...

Weekly Recap (Sep 2024, part 2)

What I'm reading this week in genomics, bioinformatics, cancer biology, epigenome editing, biosecurity, synthetic biology, single-cell omics, population genetics, microbial genomics, ...

What I'm reading (Aug 2024, part 2)

This week’s recap highlights a new method for gene-level alignment of single-cell trajectories, an R package for integrating gene and protein identifiers across biological sequence databases, characterization of SVs across humans and apes, universal prediction of cellular phenotypes, a method to quantify cell state heritability versus plasticity and infer cell state transition with single cell data, and a new AI-driven, natural language-oriented

Gene-level alignment of scRNA-seq trajectories, integrating identifiers across databases, SVs in humans and apes, universal prediction of cellular phenotypes, and a bioinformatics analysis chatbot

Weekly Recap (Oct 2024, part 2)

Google has a new experimental1 tool called Illuminate (

 illuminate.google.com

) that takes a link to a preprint2 and creates a podcast discussing the paper. When I tested this with a few preprints, the podcasts it generated are about 6-8 minutes long, featuring a male and female voice discussing the key points of the paper in a conversational style. There are some obvious shortcomings.

Listen now | Google's new Illuminate tool takes a PDF from arXiv and generates a short podcast discussion on the paper's key points

Illuminate preprints with an AI-generated podcast discussion

This week’s recap highlights a new way to turn Nextflow pipelines into web apps, DRAGEN for fast and accurate variant calling, machine-guided design of cell-type-targeting cis-regulatory elements, a Nextflow pipeline for identifying and classifying protein kinases, a new language model for single cell perturbations that integrates knowledge from literature, GeneCards, etc., and a new method for scalable protein design in a relaxed sequence

Nextflow to web apps, variant analysis with DRAGEN, synthetic cis-regulatory elements, Nextflow for kinase ID+characterization, language model for single cell analysis, scalable protein design, ...

Weekly Recap (Dec 2024, part 2)

This week’s recap highlights the WorkflowHub registry for computational workflows, building a virtual cell with AI, a review on bioinformatics methods for prioritizing causal genetic variants in candidate regions, a benchmarking study showing deep learning methods are best for variant calling in bacterial nanopore sequencing, and a new ML model from researchers at Genentech for predicting cell-type- and condition-specific gene expression across

WorkflowHub computational workflow registry, building a virtual cell with AI, bioinformatics for prioritizing causal variants, DL methods for nanopore variant calling, predicting gene expression, ...

Weekly Recap (Dec 2024, part 1)

This post expands on a few of the papers I posted in this 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 to Paired Ends to get summaries like this in your e-mail as soon as I write them.

What I’m reading this week in synthetic biology, population genetics, AI in genomics/bioinformatics, microbial genomics, and more

What I'm reading (July 2024)

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.

What I'm reading this week in de-extinction and patent law, ATAC-seq benchmarking, large animal genomes, SV genotyping with long reads, cell type-specific enhancer prediction, AI in biosecurity, ...

Weekly Recap (Sep 2024, part 1)

What I'm reading this week in single cell omics, spatial transcriptomics, kinship and selection inference in archaeogenomics, population and medical genetics, ...

What I'm reading (Aug 2024, part 4)

This post expands on a few of the papers I posted in this 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 to Paired Ends to get summaries like this delivered to your e-mail as soon as I write them. Subscribe now You might remember me from Getting Genetics Done where I blogged about genetics, statistics, and bioinformatics from 2008-2017.

What I’m reading this week in synthetic biology, population genetics, AI in genomics/bioinformatics, pangenomes, and more

What I'm reading (July 2024, part 2)

This week's recap highlights a new pipeline for metagenome quality assessment and taxonomic annotation (MAGFlow &amp;

Nextflow for metagenomics QA &amp; taxonomic classification, SNP/SV benchmarking, SNV calling with nanopore data, assembly polishing with transformers, Nextflow for variant simulation &amp; evaluation, ...

Weekly Recap (Nov 2024, part 1)

In the spirit of Learning in Public, I wanted an excuse to explore (1)

 click

for creating command line interfaces, (2)

 Cookiecutter

project templates, and (3) modern tools in the Python packaging ecosystem. If you’re primarily an R developer like me, I recently wrote about resources for getting better at Python for R users.

Demonstration for how to build a Python command line utility with Click using a Cookiecutter project template, and how to publish to PyPI and Docker Hub

Build a Python CLI with Click+Cookiecutter

I wrote my first public blog post in 2009. I started Getting Genetics Done to share what I was learning at the end of my PhD/postdoc through my first few years as faculty. Some of the earliest posts were simple, such as how to write and run a simple Perl script, to bigger topics like why it’s usually a bad idea to categorize continuous variables in a linear model.

A short essay on writing about what you're learning

Learning in Public

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.

A new eQTL Nextflow workflow, spatial transcriptomics / scRNA-seq, guide assignment in CRISPR screens, on-/off-target analysis after CRISPR editing experiments, digital microbes, paleogenomics, ...

Weekly Recap (Sep 2024, part 5)

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.

What I'm reading this week in SV analysis with long reads, spatial transcriptomics, gene prediction and annotation, synthetic biology, AI in genomics &amp;

What I'm reading (Aug 2024, part 1)

Last week I posted about a web app that turns a GitHub repo into a single text file for LLM-friendly input. This is great for capturing LLM-friendly text from a GitHub repo, but what about any other arbitrary website or PDF? I was catching up on Simon Willison’s newsletter reading about an app he made with Claude artifacts that uses the Jina Reader API to generate Markdown from a website. You don’t need to use the API to do this.

Add r.jina.ai/ in front of any URL to turn the entire page into Markdown for LLM-friendly input. Works on PDFs too.

Turn any webpage into markdown for LLM-friendly input

A few days ago I wrote about translating R package help documentation using a local LLM (e.g. llama3.x)… …when Mick Watson commented: I was already thinking of wiring up something like this using local AI models — something to summarize podcasts, conference recordings, etc. The relatively new (as of this writing) Gemini 2.0 Flash model will do this for you for YouTube videos. But what if you wanted to do this offline using a local LLM?

Using local LLMs to extract and summarize audio transcripts from YouTube and podcasts. Examples: DESeq2 tutorial from YouTube, and the Nextflow Podcast.

Video to audio to transcript to summary using local AI: whisperfile and llama3.3

This week’s recap highlights the Evo model for sequence modeling and design, biomedical discovery with AI agents, improving bioinformatics software quality through teamwork, a new tool from Brent Pedersen and Aaron Quinlan (vcfexpress) for filtering and formatting VCFs with Lua expressions, a new paper about the NHGRI-EBI GWAS Catalog, and a review paper on designing and engineering synthetic genomes.

The Evo model for sequence modeling and design, AI agents in biomedical research, improving bioinfo software with teamwork, VCF manipulation, GWAS Catalog, designing+engineering synthetic genomes...

Weekly Recap (Dec 2024, part 3)

The Baader–Meinhof phenomenon (aka the frequency illusion) is the name for that thing that happens when you buy a new car, and suddenly you notice that same model car everywhere you drive.

Something a little different this week: book recommendations! De-extinction is a common theme across a few of the fiction and nonfiction books I read this year.