The trRosettaRNA server for RNA structure prediction

Thu, 09 Apr 2026 11:19:11 +0000

Deep learning combined with RNA sequencing enables rapid prediction of RNA 3D structures, helping researchers understand RNA function and accelerate therapeutic development...

Who Is Missing Out on Next-Generation Sequencing in Cancer?

Thu, 09 Apr 2026 11:18:56 +0000

RNA sequencing and genomic profiling adoption is rising across cancers, yet disparities in access and delayed testing continue to limit timely precision oncology treatment decisions...

Caris Life Sciences announces launch of Caris ChromoSeq, the world’s first whole genome and whole transcriptome tumor profiling assay for myeloid malignancies

Thu, 09 Apr 2026 11:18:49 +0000

Integrating RNA sequencing with whole genome analysis, Caris ChromoSeq delivers...

New sequencing method exposes hidden gaps in immune signaling

Wed, 08 Apr 2026 11:19:05 +0000

A new single-cell technology is giving scientists their clearest view yet of immune cell behavior—capturing not just genetic intent but real-time activity. By measuring RNA and proteins simultaneously

Unraveling hair aging: a molecular atlas of human hair follicle senescence drawn by single-cell and spatiotemporal sequencing

Wed, 08 Apr 2026 11:18:49 +0000

Hair loss and graying, the earliest visible signs of skin aging, are fundamentally driven by the functional decline of the hair follicle stem cells (HFSCs) and their surrounding niche. The research, l

I Built a Personal AI Assistant on a Mac Mini

Mon, 06 Apr 2026 00:00:00 +0000

My first blog post in a long time!

I wanted an AI assistant that knew me. Knew my research. Knew my content calendar. Knew that when I say “write a thread about batch effects,”

What’s changed?

Sun, 05 Apr 2026 00:45:52 +0000

Andy Saunders writes: A couple of things come to mind. The planet on the right contains, on average, around 70% fewer animals than the planet on the left. The atmosphere of the planet on the right als

AI-Assisted Customer Screening for DNA Synthesis Orders

Thu, 02 Apr 2026 11:28:45 GMT

A new preprint shows AI can handle legitimacy verification at a fraction of the cost.

Weekly Recap (April 2, 2026)

Thu, 02 Apr 2026 08:25:58 GMT

AI automating AI research, AI + being PI, DL course, Neion Bio, NIH highlighted topics, TIP, Python type checking in Positron, R updates, biosecurity, NIH forecast graveyard, serendipity, new papers.

A Wish For Snail-Inspired Tulips

2026-03-31T20:45:00.006-04:00

About a year ago we took a family vacation to the Netherlands with a prime goal to see tulips - and tulips we did see! Even a rainy day (what are the odds of that in Holland?) couldn't steal the

Creating Enforceable Biosecurity Standards for Nucleic Acid Providers

Mon, 30 Mar 2026 13:31:54 GMT

A new paper from Raytheon BBN and IBBIS: Sometimes “good enough” consensus today beats waiting for perfect clarity that may never come.

icon16: Precise Amplification for All!

2026-03-30T09:22:00.001-04:00

I've loved the n6tec icon96 instrument since they first tipped me about it several years back. The idea of running 96 independent PCRs in parallel was just too attractive; the instrument I'd alw

Who's Going to Buy Roche Axelios?

2026-03-29T22:50:00.001-04:00

After Roche's AGBT presentation, a key question for many is "who is going to buy an Axelios?". Below are some thoughts on the topic, based around general classes of sequencing labs tha

Updated genomic analysis of the 2026 menB outbreak in Kent, UK

Mon, 30 Mar 2026 00:00:00 +0000

This is a brief update to the previous menB analysis we’d posted here.

UKHSA have released a

Importance of Data in Al-Enabled Biological Models

Sun, 29 Mar 2026 10:55:00 GMT

Chapter 5 of the National Academies report on AIxBio: Biological Data as Strategic Infrastructure

LinkedIn Laments 1 of N: Where's the API?

2026-03-27T22:17:00.000-04:00

In my current role I spend a lot of time on LinkedIn. A core task is to identify possible customers, and LinkedIn is rich hunting ground. I'm still sending each reach-out message individually (th

Weekly Recap (March 27, 2026)

Fri, 27 Mar 2026 08:41:13 GMT

NSF AI readiness, AGI forecasts, White House AI policy framework, NIH genomics technology, statistical rethinking, context anchoring, R+Quarto, NOFO graveyard & grant terminations, organ sacks, YYiki.

Life at the freezing edge

Wed, 25 Mar 2026 21:42:01 GMT

The fact that any small, cold blooded animal such as the insects can sustain temperatures below the freezing point of water has to be one of the most remarkable features of animal evolution. Even more

ElysION Fields

2026-03-23T10:23:00.002-04:00

Initial genomic analysis of the 2026 menB outbreak in Kent, UK

Mon, 23 Mar 2026 00:00:00 +0000

We’ve done a quick analysis on the meningitis outbreak genome to try and answer whether there is anything obviously genetically unusual about the publicly available outbreak strain.

Tips for managing code as a researcher in life sciences

2026-03-20T11:47:00.003+11:00

The molecular biology lab is becoming increasingly data driven and as a researcher or manager we need to make sure we're recording our

menB outbreak in Kent -- first genome

Fri, 20 Mar 2026 00:00:00 +0000

Previous posts on menB:

First thoughts and summary
menB outbreak in Kent -- more thoughts

Thu, 19 Mar 2026 00:00:00 +0000

Posted some thoughts on the menB outbreak yesterday. Now nine more cases, total at 27.

A few more thoughts today, also after dis

menB outbreak in Kent -- initial thoughts

Wed, 18 Mar 2026 00:00:00 +0000

A cluster of meningitis cases is currently dom

Making a bubble plot to show frequencies

2026-03-17T08:48:00.000-07:00

I've been using ggplot2 in R to make a bubbleplot, to show frequencies. This is an alternative to a histogram. Here's a little example:
I have a file year_data_file_example.txt with col

Furtress of solitude

Tue, 03 Mar 2026 15:46:29 GMT
In the Pilbara region of Western Australia lives the western pebble mouse ( Pseudomys chapmani ), a rarely seen rodent that excavates a complex subterranean burrow system in the rocky substrate. These

The Mentorship Index

2026-03-01T00:00:00+00:00
Background

Vibe coding with SEraster and STcompare to compare spatial transcriptomics technologies

2026-02-22T00:00:00+00:00
Introduction

Using MOB-suite to predict plasmids in bacterial genome assemblies

2026-02-20T07:07:00.000-08:00

Today I wanted to predict plasmids in a bacterial genome assembly, and used the MOB-suite tool.
Here's how I ran it on the Sanger

The Quickening

Thu, 19 Feb 2026 16:59:52 +0000
In a paper titled “THEOREMS FOR A PRICE: Tomorrow’s Semi-Rigorous Mathematics Culture” published in 1993, mathematician Doron Zeilberger wrote: There are writings on the wall that, n

Creating custom (non-Font Awesome) icons for a Jekyll-based website

Sun, 15 Feb 2026 10:40:38 +0000
This one is pretty niche even by my standards. Notes largely for my own benefit, but they may be useful if you: I’ll assume that you have git-cloned jekyll-theme-chirpy, run bundle and are able

State of the Blog

Thu, 05 Feb 2026 18:01:06 +0000

ChatGPT came out in November 2022 and it has completely changed the Internet. In my post Learning about ChatGPT via ChatGPT I had prompted: "Will ChatGPT replace Google?" to which the model back th

Using enadownloader to download fastqs from the ENA

2026-02-05T02:43:00.000-08:00

I wanted to download fastq files for a long list of SRR accessions from the ENA today.
I realised I could use the

Making assemblies for Oxford Nanopore sequence data using Dragonflye

2026-02-05T02:05:00.000-08:00

I've been making genome assemblies for some Oxford Nanopore Technology (ONT) sequencing data using the Dragonflye package by Rober

ONT read QC strategies for assembly

2026-02-05T00:00:00+00:00

P2 Solo announcement and the trade-offs of a more stable ONT

2026-01-21T00:00:00+00:00

Scale-able defense

Wed, 14 Jan 2026 21:11:17 GMT
Fish-scale geckos, Geckolepis spp., are small and arboreal lizards endemic to Madagascar and the Comoro Islands. The base coloration of the fish-scaled gecko is generally chestnut-cream with darker/b

Evaluating ONT barcode combinations

Wed, 14 Jan 2026 09:00:00 +0000

When using native barcoding kits from ONT we have noticed some low frequency miss-assignments between barcodes/samples. Now we don’t know if this is an issue from the wet lab side (cross cont

Directional markers in R/leaflet

Wed, 07 Jan 2026 22:25:16 +0000
So you have used the excellent exiftool to extract all of the GPS-related information from a directory of photos in JPG format and write to a CSV file: You’ve used R/leaflet to plot coordinates

Yes, you can use a single stick of DDR5 for bioinformatics and data analysis

2026-01-03T14:08:00.003+11:00

INTRO
DRAM prices skyrocketed 171% in 2025 [

How to fix a broken towel radiator

Fri, 02 Jan 2026 00:00:00 +0000

In a first for this blog – as a lame attempt to counter the increasing amount of dross when you google simple household tasks, and for my own reference – here’s a post with some D

Video games in 2025: puzzles galore

Tue, 30 Dec 2025 00:00:00 +0000

I played more games this year, particularly puzzle games. I also just bought a Switch 2, which seems good so far (nice screen).

Puzzle games

Brief thoughts on: iNaturalist

Fri, 05 Dec 2025 02:22:20 +0000
Let me say first: I was wrong! My profile shows that I created my account at iNaturalist in August 2008, the year that the site was launched. I created a lot of accounts in those days. At the time, th

We predict that the transcript abundance from the gene we are knocking down will (checks notes) decrease

2025-12-05T00:00:00+00:00
The problem with gene-wise characterization of genetic interventions

Mean squared error for estimates of differential expression

2025-12-01T00:00:00+00:00
Bias-variance tradeoffs for virtual cell evals are weird

Thoughts on generative AI contributions as an Open Source project maintainer

2025-11-24T09:26:00.004+00:00

To be clear up front, these are my personal opinions right now, and while they will influence any future policy I have a hand in writing, they are not the position of the Biopython Project or the O

Making a map of the locations where bacterial isolates were collected

2025-11-17T04:35:00.000-08:00

I wanted to make a map of the locations in the world were some bacterial isolates were collected. I found a nice website&

Using R/anomalize to identify delays in games of Australian Rules football

Wed, 12 Nov 2025 03:48:21 +0000
In which we generate a dataset of game durations, do a little exploratory data analysis and then try to identify unusual instances and their causes. In my Twitter-whinge-post, I mentioned that one of

Reviving BETA for Python 3: Integrating ChIP-seq and RNA-seq to Predict TF Targets

Sun, 09 Nov 2025 00:00:00 +0000

I started to learn bioinformatics because I needed to analyze public ChIP-seq data in 2012. That’s how I got to know Shirley Liu&rsquo

Review of Cold Spring Harbor Laboratory’s Obituary for Dr. James Watson

Sat, 08 Nov 2025 21:57:05 +0000
James Watson, who described himself as “not a racist in a conventional way”, has died at the age of 97. Below is a review of an obituary for Dr. James Watson published by Cold Spring Harbo

Bioinformatics Blogs

The trRosettaRNA server for RNA structure prediction

Who Is Missing Out on Next-Generation Sequencing in Cancer?

Caris Life Sciences announces launch of Caris ChromoSeq, the world’s first whole genome and whole transcriptome tumor profiling assay for myeloid malignancies

New sequencing method exposes hidden gaps in immune signaling

Unraveling hair aging: a molecular atlas of human hair follicle senescence drawn by single-cell and spatiotemporal sequencing

I Built a Personal AI Assistant on a Mac Mini

What’s changed?

AI-Assisted Customer Screening for DNA Synthesis Orders

Weekly Recap (April 2, 2026)

A Wish For Snail-Inspired Tulips

Creating Enforceable Biosecurity Standards for Nucleic Acid Providers

icon16: Precise Amplification for All!

Who's Going to Buy Roche Axelios?

Updated genomic analysis of the 2026 menB outbreak in Kent, UK

Importance of Data in Al-Enabled Biological Models

LinkedIn Laments 1 of N: Where's the API?

Weekly Recap (March 27, 2026)

Life at the freezing edge

ElysION Fields

Initial genomic analysis of the 2026 menB outbreak in Kent, UK

Tips for managing code as a researcher in life sciences

menB outbreak in Kent -- first genome

menB outbreak in Kent -- more thoughts

menB outbreak in Kent -- initial thoughts

Making a bubble plot to show frequencies

Furtress of solitude

The Mentorship Index

Vibe coding with SEraster and STcompare to compare spatial transcriptomics technologies

Using MOB-suite to predict plasmids in bacterial genome assemblies

The Quickening

Creating custom (non-Font Awesome) icons for a Jekyll-based website

State of the Blog

Using enadownloader to download fastqs from the ENA

Making assemblies for Oxford Nanopore sequence data using Dragonflye

ONT read QC strategies for assembly

P2 Solo announcement and the trade-offs of a more stable ONT

Scale-able defense

Evaluating ONT barcode combinations

Directional markers in R/leaflet

Yes, you can use a single stick of DDR5 for bioinformatics and data analysis

INTRO

How to fix a broken towel radiator

Video games in 2025: puzzles galore

Puzzle games

Brief thoughts on: iNaturalist

We predict that the transcript abundance from the gene we are knocking down will (checks notes) decrease

Mean squared error for estimates of differential expression

Thoughts on generative AI contributions as an Open Source project maintainer

Making a map of the locations where bacterial isolates were collected

Using R/anomalize to identify delays in games of Australian Rules football

Reviving BETA for Python 3: Integrating ChIP-seq and RNA-seq to Predict TF Targets

Review of Cold Spring Harbor Laboratory’s Obituary for Dr. James Watson