Bioinformatics Blogs

Closing my tabs, July 10, 2026

Fri, 10 Jul 2026 20:38:33 GMT

Off switches for dual-use knowledge, the PhD admissions drop, a Brown cheating mess, the end of reading, AI labs at the bench, and planning for a "Bio Mythos" moment. 1.7k words, 8 min reading time.

The Simulator That Isn't There

2026-07-10T09:14:08.954-04:00

Okay, this is one of those cases where I kvetch about other people not having built the tools I want to use - perhaps a bit of a insufferably egotistical position. I mean, what gives me the chutzpah

Dorado v2.0.0 part 3: methylation

2026-07-08T00:00:00+00:00

Countable Labs Raises Funds, Heads to Clinic

2026-07-07T11:44:18.444-04:00

I caught up by teleconference recently with Countable Labs CEO Giovanna Prout, fresh off Countable Labs' $26M equity fundraising - a round which was oversubscribed. Top on my agenda: what is Pro

My Comment on OMB-2026-0034

Tue, 07 Jul 2026 09:45:57 GMT

...

Fewer Rungs on the Ladder

Mon, 06 Jul 2026 20:18:17 GMT

Automating the analyst's work doesn't turn analysts into principal scientists

Minibwa is the new bwa-mem

2026-07-04T00:00:00+00:00

Preprinted in 2013, bwa-mem is a popular mapper for 100+ bp short reads. It is often the first choice in varia

Five things (July 2, 2026): AIxBio, NIH, QED

Thu, 02 Jul 2026 09:00:05 GMT

GeneBench-Pro, LLM agents and biological tools, the volition premium, NIH’s 235 flagged words, QED’s top 1%

Test Driving Claude Science

Tue, 30 Jun 2026 21:06:43 GMT

Anthropic released Claude Science today. I tried it out for an AIxBio literature review and for an analysis using the IUCN Red List API with R.

Alex Hastie Returns to BioNano, Takes CSO Reins

2026-06-28T08:54:17.899-04:00

An interesting news item this week is that BioNano Genomics has appointed Alex Hastie as Chief Scientific Officer. Hastie is an obvious choice for CSO, as for many years he was very much the public s

trout: finding tandem repeat outliers in a cohort

Fri, 26 Jun 2026 09:00:00 +0200

Getting locked in

Thu, 25 Jun 2026 13:37:52 +0000

Like many people who work in bioinformatics, my background was in biology and had nothing to do with computers. As I worked longer in this field, my responsibilities grew from writing code and perf

aSTRonaut, now in Rust

Thu, 25 Jun 2026 09:00:00 +0200

E.coli Doesn't Like Diets Either, At Least Genomic Ones

2026-06-24T23:19:01.344-04:00

Another interesting preprint that fits several recent themes - genome minimization, discontinuation of products - comes from a Ja

Shredding Genomes: Establishing Plausible Deletability

2026-06-23T10:43:39.133-04:00

There's an interesting new preprint from Jay Shendure's lab which introduces the technique of Shred-Seq, which is a Cas3-driv

Dorado v2.0.0 part 2: assembly polishing

2026-06-19T00:00:00+00:00

Dorado v2.0.0: no more sup?

2026-06-11T00:00:00+00:00

Is Truth Absolutely Necessary for Science?

Wed, 27 May 2026 00:00:00 -0700

These days, corporate entities are increasingly dominating research in basic science. This essay looks into how this will change the most cherised convention of science.

Resear

Batch Effect: To Correct or Not for Bulk RNA-seq Data

Fri, 22 May 2026 00:00:00 +0000

A colleague sent me a PCA plot last week. Three replicates per condition, control vs KO of a gene. PC1 cleanly separated replicate 1 from replicate 2 from replicate 3. PC2 separated control vs KO.

Pawsitively prehistoric

Thu, 21 May 2026 12:21:04 GMT

First described from Laos in 2005, the Laotian rock rat Laonastes aenigmamus quickly gained fame as one of the most remarkable “living fossil” discoveries in modern mammalogy. A. Abramov (Zoological I

Biology is Messy, Because Physicists Failed

Thu, 21 May 2026 00:00:00 -0700

I came across an interesting blog post titled Biology is Messy. The main argument is that biology is not built on top of reduction

Mathematical Side of AI and Its Applications in Biology

Wed, 20 May 2026 00:00:00 -0700

Right now everyone is either enamored of or is completely turned off by AI. Speaking of being fed up, please check the students at University of Florida booing

Gene Regulatory Network Reconstruction with Single-cell Data

Thu, 14 May 2026 00:00:00 -0700

On the subject of reconstructing gene regulatory networks (GRNs) from RNAseq and scRNAseq data, I am working through a number of review papers and the techniques described therein.

Scientific Questions (and Maybe Answers) for 2021-2038

Mon, 11 May 2026 00:00:00 -0700

In an earlier post, I divided the modern era of genetics into 18-year periods (eras). The discoveries of each

Organic

Fri, 08 May 2026 19:15:12 +0000

When I hear the word organic, two thoughts immediately come up: organic search and organic chemistry. The latter comes up because it is ingrained in me that organic chemistry is one of the hardest

The Perceptron - classifying items into two classes based on numerical input variables

2026-05-06T01:51:00.000-07:00

I've been reading Sebastian Raschka's excellent book Machine Learning with PyTorch and Scikit-Learn

Benchmarking R based bioinformatics speed across different computer types

2026-05-06T15:06:00.002+10:00

As a bioinformatician, or other type of data analyst, we should be using the right tool for the job. There are many types of compute we can use from laptops, desktops, pro workstations, on prem-ser

AI-guided data visualization of gas prices in different geographical locations across the US over time

2026-05-04T00:00:00+00:00

In this blog post, I will walk through how I went from a question regarding gas prices in different geographical locations across the US over time, to using AI to help me find the relevant data for my

In Data Analysis We Trust

Wed, 29 Apr 2026 09:00:00 +0000

Installing Python libraries within virtualenv

2026-04-28T01:47:00.000-07:00

Today I learnt how to install Python libraries in a virtual environment (in my case, on the Sanger compute farm), using virtualenv.

Has AI Changed the Course of Drug Development? Three Years Later

Fri, 24 Apr 2026 00:00:00 +0000

Almost three years ago I wrote Has AI Changed the Course of Drug Development?. The post w

Now published: Ten common mistakes that could ruin your enrichment analysis

2026-04-23T11:47:00.005+10:00

Workshop alert! Mastering Reproducible Enrichment Analysis

2026-04-23T11:00:00.002+10:00

Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊

Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.

📅 When:

The AI Rewrite Dilemma

2026-04-17T00:00:00+00:00

There have been multiple ongoing efforts (see Appendix below), and debates, regarding porting bioinformatics tools to Rust. These include two rewrites of minimap2. Here are some of

How is the nectar of RNA-seq produced?

Thu, 16 Apr 2026 17:31:41 +0000

Hi everyone. It’s been a while since I last wrote on the blog. Unfortunately, sometimes life gets tough—you lose energy, motivation, and above all, your sense of priorities. I’m not out of this dar

Hausdorff

Tue, 14 Apr 2026 14:44:37 +0000

The philosopher Felix Hausdorff, famous for his foundational philosophical work Das Chaos in kosmischer Auslese (Chaos in Cosmic Selection) in which he rejects metaphysics, also did mathematics as a

Nowakia

Fri, 10 Apr 2026 19:50:56 +0000

Among the millions of pages in the Epstein files, there is an inconspicuous, seemingly mundane short email, EFTA00896810, dated 14th September, 2010. It is a message from Jeffrey Epstein to Martin Now

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

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

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

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

Targeting the chromatin modifying enzyme, KDM5C, enhances AKT inhibition response in ER+ breast cancer

Sun, 15 Mar 2026 00:00:00 +0000

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