Element's Curious Patentsieg

Last week news broke that Element Biosciences had won a patent lawsuit against Illumina, and that it affected MiSeq.  MiSeq???? How did a patent battle in 2026 affect a platform launched nearly a decade and a half ago?  And which had been launched about five years before Element incorporated.  Which is being put out to pasture, though the MiSeqDx version What witchcraft is this?  I've done limited digging - I really dislike trying to dig through patents - and it is a strange case.

Fiber-Seq: Plasmids Model Chromosomes Well

A recent publication in Molecular Cell involving Fiber-Seq caught my attention, though I've since discovered this preprinted over a year ago.  One of the challenges in exploring the effects of genetic variations is the cost & effort to generate collections of variation which can be profiled by available methods.  This paper explores using Fiber-Seq on transfected plasmids and finds that, with important caveats, transfected plasmids evoke the same patterns of chromatin protection as the corresponding nuclear DNA.  This opens up the possibility of exploring large sets of variants for their effect on chromatin structure and either feeding that data into models or using it to understand clinical non-coding variation.  Or why not both?

The Simulator That Isn't There

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 to do that?  My title, according to me, is "Automation Visioneer", so that gives me the right - though again, self-given title, self-given right.  But I hope you'll bear with me, because I think (there again, me! me! me!) it is an interesting observation on a curious gap in the software world - one that could make a very interesting project for someone so inclined. Oh, and this is one of the "a bit of promoting the product" entries - which means I get to blog on company time.

Countable Labs Raises Funds, Heads to Clinic

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 Prout's vision to turn that money into products.  And how will Countable balance building molecular tools vs. applying those tools to clinical problems?

Alex Hastie Returns to BioNano, Takes CSO Reins

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 scientific face of BioNano's development.  .  But in February 2025 he left BioNano and headed to Arima Genomics.  But after a bit over a year at Arima and then a short stint at Inocras, Hastie has returned to the fold.

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

Another interesting preprint that fits several recent themes - genome minimization, discontinuation of products - comes from a Japanese group that reports on significantly reducing the genome of E.coli.  They tried for 1.7Mb but ended up settling - for now - with a 2.3Mb genome.  That's only about half the size of the strain they started with, but not at all a small genome.  

Shredding Genomes: Establishing Plausible Deletability

There's an interesting new preprint from Jay Shendure's lab which introduces the technique of Shred-Seq, which is a Cas3-driven approach to generating large deletions across a large eukaryotic genome.  By creating diverse collections of deletions, Shred-Seq enables identifying hidden non-coding sequences of functional importance.