A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
I wish to highlight an interesting new preprint from a group at Danish Technical University which explores the schmutz in PCR reactions, demonstrates some surprising conclusions, shows how their results might be very relevant to a common use of amplicon sequencing, and demonstrate a specific utility running PCR on in cases where typical PCR absolutely can't succeed. Put another way, how often do…
My father was a very methodical person, and that particularly applied when he decided to purchase the second IBM PC clone to appear on the market. A whole host of manuals appeared on his desk and when I started skimming them it was clear he had been there first. Sentences highlighted, marginal notes and of course editing marks to suit his sense of grammar and style. The hardware, operating system,…
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…
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…
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…
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? Read more »
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…
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. Read more »
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. Read more »
Last week brought news that Standard Biotools, which is what Fluidigm morphed into, is being acquired by Treeline Biosciences, a drug developer. The deal values Standard at about its cash position - and Treeline made it immediately clear this is a reverse merger to grab the cash and in effect go public by also grabbing Standard's stock listing. What Treeline has made very clear is that they have…
Alexander Hoischen and colleagues have a brief piece in New England Journal of Medicine that published early this morning , in conjunction with the European Society of Human Genomics (ESHG) meeting. I'm now in the thrall of ESHG FOMO - I attended last year in part because it was immediately after London Calling and it seemed silly not to extend my trip (plus Alex had asked me personally to go),…
The last bit of Craig Venter's career a followed, often a bit green with envy, was his work to build genomes. This all revolved around the Mycoplasma genitalium they had knocked out a genome as a victory lap after completing the first bacterial genome. This bug is held up as the bacterium with the smallest genome which can be grown in a defined medium. To first reconstruct an entire genome, with…
Few bombshells have hit genomics like the day in May 1998 when Craig Venter and Applied Biosystems announced he would be launching Celera Genomics to sequence the human genome by a complete shotgun approach. A couple of colleagues at Millennium had just announced they were leaving to form a contract research organization which would perform high throughput sequencing on demand - they were…
In the early 1990s, Craig Venter left the NIH over disputes around the patenting of ESTs. Investors backed him, but then William Haseltine basically pushed him out of direct operation of Human Genome Sciences (HGS) and Venter went to start The Institute for Genome Research, far better known as TIGR. TIGR would attract an amazing array of talent both wet lab and dry lab - a pattern that Venter had…
I am overdue in getting back to my very personal review of how the recently passed J. Craig Venter made a huge impact on genomics science. But especially after being at London Calling, I worry that many in genomics today just won't have the context to grasp how unusual his approaches were. I met some amazing graduate students there - and most likely they were born after the joint announcement by…
The Festival of Genomics, Biodata and AI - thankfully known as FoG and not FogBA or FogBDA - will be at the Boston convention center this Wednesday and Thursday. It's an interesting conference that typically has two editions each year, one in London and one here in Boston. I'll be wandering around the floor part of both days - my beacon/hat to be announced on LinkedIn and Twitter that day (leaning…
Now to run through the long term technical projections from Oxford Nanopore's Tech Talk. Well, projection is probably not the correct word - hints and teasers might be closer to the mark. None of these pronouncements came with any hint of timing for when the community might be able to access them - indeed, CSO Lakmal Jayasinghe made it very clear that this section would have no timing information.…
I returned from London Calling 2026 much as I usually have - exhausted, more than a little hoarse, happy for discussions had and ruing connections missed. The meeting felt much like prior ones, except in all the ways it was a little different. The company continues its trajectory towards restraint and corporate maturity, with new CEO Francis Van Parys for the first time exhibiting his "evolution…
My series on Craig Venter is on a small pause since I didn't get it out before I arrived here in London for Oxford Nanopore's annual shindig at Old Billingsgate. On the plus side (well, I hope my readers find it a plus), I've sketched out an additional piece - I realized that our world of fast whole genome sequencing powered by long read technologies such as Oxford Nanopore may make it challenging…
Venter's big Expressed Sequence Tag - soon known as ESTs - paper came out in June during my final summer as an intern; I photocopied it at my internship. I looked it up, and it had only a bit over 600 sequences - a small beginning to what would become an industry-wide exercise. That was a momentous time for me, as only the past December had I pivoted from thinking I would get a degree in…
Craig Venter's sudden passing has triggered many writings about his life and work. I'm overdue on my own personal reflections, and am breaking them into three thematic pieces. While I only met him a few times and never one-on-one, his career had an enormous impact on mine. So I am going to write a series of posts this week reviewing, in a very personal way, Venter's enormous impact on genomics and…
Another edition of my dabbling with AI. Somewhat like what I reported before - a customer asked if Ginkgo Cloud Lab's Echo-MS option could configure an assay to replicate the analytical results in a published paper, so I'm using Claude to do the heavy lifting. Plus part of what I described earlier showed some issues on review. But the big thing I'm keying into this morning is Claude is having…
Vibe coding - solving problems by extended conversation with a machine learning program rather than writing the code yourself - is all the rage. But I hadn't really been partaking, finding one excuse after another. I don't have time. It's a lazy approach to the craft I've honed. Abandonment of my skills. But I've also taken to referring to myself as a "lapsed computational biologist", as I was…
The liquid biopsy space continues to grow and heat up - just this week Roche's Foundation Medicine unit announced the acquisition of Minimal Residual Disease (MRD) test developer Saga Diagnostics for just over a half billion dollars. Numerous MRD and Multi-Cancer Early Detection (MCED) companies continue to spring up, with even more analyte types - first it was cell-free DNA, but now cell-free RNA…
AGBT Agriculture was a really nice meeting - lovely venue in the Arizona desert, a meeting size that you felt you could (but weren't compelled to) introduce yourself to everyone, good food, great scientific content, and everyone super-friendly. I came for the workshops on Sunday, and there were two on graph genomes / pangenomes. Which was a theme throughout the meeting - not every talk or paper…