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Posts by Keith Robison

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

2 weeks ago 211 113 6 7

cloud.ginkgo.bio

2 weeks ago 0 0 0 0

That's Ginkgo Cloud Labs' newest offering, combining our Cell Free Protein Synthesis with Echo-MS to detect substrate depletion or product formation

2 weeks ago 1 0 1 0

$44/gene enzymatic function test with just $799 assay configuration!!!

~$5K & we will boot your assay & run full 96 well plate experiment!

How many enzymatic reactions does this entice you to deorphan?

2 weeks ago 0 0 1 0
Photo of the snowpack measurement team, with a five foot long tube to measure snow depth and water content, but it's resting on grass, with just sprinkles of white snow around the field.

Photo of the snowpack measurement team, with a five foot long tube to measure snow depth and water content, but it's resting on grass, with just sprinkles of white snow around the field.

When you go up to the Sierra Nevada to do the last seasonal snowpack depth measurement and there isn't any snow.
#climate
#climatechange
#water

2 weeks ago 158 49 13 9
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A Wish For Snail-Inspired Tulips 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 (wh...

A Wish For Snail-Inspired Tulips

My latest post: can a childhood fright inspire floral beauty?

Also some name-dropping of my favorite leading edge floral genetic engineers

omicsomics.blogspot.com/2026/03/a-wi...

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AGBT Agriculture logo rendered by depositing fluorescent bacterial strains on an agar growth plate

AGBT Agriculture logo rendered by depositing fluorescent bacterial strains on an agar growth plate

Less than two weeks until #AGBTAg26 !

Looking forward to planting @Ginkgo flag there - may many productive discussions bloom around autonomous laboratories and cloud lab services!

3 weeks ago 3 0 0 0
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icon16: Precise Amplification for All! 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 p...

icon16: Precise Amplification for All!

🧬🖥️

omicsomics.blogspot.com/2026/03/icon...

3 weeks ago 3 0 0 0

a lot depends on the complexity of the flow cell algebra but if it truly makes service lab workflows fast fast that is worth a lot. just makes planning easier.

3 weeks ago 1 1 0 0

They had one a long time ago. About 15 years or so ago I played around with something in R to pull down data via API. It was half baked even then, guess they decided ti unbake it altogether

3 weeks ago 2 1 0 0
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will I be able to run 5000 low pass libraries on it faster than on a nova? what about amplicons?

3 weeks ago 2 1 1 0

2. I don't mind if people don't want to use Rust but instead of rewriting it from scratch every single time, why don't you write bindings and make them available for everyone? This is both easier and more maintainable, and would actually be helpful for the community.

3 weeks ago 38 3 1 1
Who's Going to Buy Roche Axelios? 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 ...

Who’s Going To But Roche Axelios?

🖥️🧬

omicsomics.blogspot.com/2026/03/whos...

3 weeks ago 1 0 1 0
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LinkedIn Laments 1 of N: Where's the API? 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'...

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

omicsomics.blogspot.com/2026/03/link...

3 weeks ago 0 0 1 0
We’re updating how GitHub uses data to improve AI-powered coding tools. From April 24 onward, your interactions with GitHub Copilot—including inputs, outputs, code snippets, and associated context—may be used to train and enhance AI models unless you opt out.

If you previously opted out of the setting allowing GitHub to collect this data for product improvements, your preference has been retained— your choice is preserved, and your data will not be used for training unless you opt in.

This approach aligns with established industry practices and will enable our models to deliver more context-aware AI coding assistance. We have tested this with Microsoft interaction data and have seen meaningful improvements, including increased acceptance rates in multiple languages.

Please review your settings and choose whether your interactions with Copilot can be leveraged for training AI models before this update goes into effect on April 24. To opt out or adjust your settings:

Go to GitHub Account Settings
Select Copilot
Choose whether to allow your data to be used for AI model training

We’re updating how GitHub uses data to improve AI-powered coding tools. From April 24 onward, your interactions with GitHub Copilot—including inputs, outputs, code snippets, and associated context—may be used to train and enhance AI models unless you opt out. If you previously opted out of the setting allowing GitHub to collect this data for product improvements, your preference has been retained— your choice is preserved, and your data will not be used for training unless you opt in. This approach aligns with established industry practices and will enable our models to deliver more context-aware AI coding assistance. We have tested this with Microsoft interaction data and have seen meaningful improvements, including increased acceptance rates in multiple languages. Please review your settings and choose whether your interactions with Copilot can be leveraged for training AI models before this update goes into effect on April 24. To opt out or adjust your settings: Go to GitHub Account Settings Select Copilot Choose whether to allow your data to be used for AI model training

GitHub will be allowing Copilot to use your code for training its models, unless you opt out.

Seems like the sort of thing some people might want to opt out of…

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Screenshot from p 214 of Digby's book TWO TREATISES. It reads: And an other particular that I saw when I was att Argiers, maketh to this purpose, which was, of a woman that hauing two thumbes vpon the left hand; foure daugthers that she had, did all resemble her in the same accident, and so did a litle child, a girle of her eldest daugthers; but none of her sonnes. Whiles I was there I had a particular curiosity to see them all: and though it be not easily permitted vnto Christians to speake familiarly with Mahometan women; yet the condition I was in there, and the ciuility of the Bassha, gaue me the opportunity of full view and discourse with them: and the old woman told me, that her mother and Grandmother had beene in the same manner. But for them, it resteth vpon her creditt: the others I saw my self.

Screenshot from p 214 of Digby's book TWO TREATISES. It reads: And an other particular that I saw when I was att Argiers, maketh to this purpose, which was, of a woman that hauing two thumbes vpon the left hand; foure daugthers that she had, did all resemble her in the same accident, and so did a litle child, a girle of her eldest daugthers; but none of her sonnes. Whiles I was there I had a particular curiosity to see them all: and though it be not easily permitted vnto Christians to speake familiarly with Mahometan women; yet the condition I was in there, and the ciuility of the Bassha, gaue me the opportunity of full view and discourse with them: and the old woman told me, that her mother and Grandmother had beene in the same manner. But for them, it resteth vpon her creditt: the others I saw my self.

Same evidence can mean different things at different times. In 1644 Sir Kenelm Digby tells of a woman in Algiers with two thumbs on one hand. All her female ancestors and descendants had the same condition, but not her sons. He draws no conclusion about heredity. A century later, Maupertuis would.

3 weeks ago 12 1 0 2
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151 - Deacon part 1 In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads from metagenomic datasets. We discuss why host read

Host read removal sounds simple. It's not. 🧫

Ep. 151 of #microbinfie: we talk with @bede.im about Deacon — why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2.

#metagenomics
on.soundcloud.com/gEm7QyaTauvd...

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What's the current best strategy to sequence complete transcripts in the ~20kb range? Should we attempt generating full length cDNA, or go for direct RNA on ONT? I suppose it will be a challenge in any case..

4 weeks ago 1 1 3 0
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Dogs were widely distributed across western Eurasia during the Palaeolithic - Nature Analysis of nuclear and mitochondrial genomes from archaeological canid remains found across Europe and Anatolia shows that a genetically homogeneous dog population was already widely distributed acro...

Dogs were widely distributed across western Eurasia during the Palaeolithic

🧬🖥️

www.nature.com/articles/s41...

3 weeks ago 1 0 0 0
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Genomic history of early dogs in Europe - Nature Genome-wide analysis shows European dogs existed by 14,200 years ago, were already genetically distinct, received less Neolithic Southwest Asian admixture than humans did and contr...

Genomic history of early dogs in Europe

🖥️🧬

www.nature.com/articles/s41...

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Market research question

If you were building a course where each student gets to create their own GFP designs

How many designs per student would be minimum to be interesting?

What is ceiling on per student cost for experimental validation?

3 weeks ago 0 1 0 0
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ElysION Fields Even before new CEO Francis Van Parys took the reins at Oxford Nanopore with the start of the month, the company had made yet another primin...

ElysION Fields

omicsomics.blogspot.com/2026/03/elys...

🧬🖥️

4 weeks ago 5 1 0 0

What protocol(s) would you like us to add?

1 month ago 0 0 0 0
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Ginkgo Cloud Lab — Run Autonomous Lab Protocols On Demand Run biotech protocols on Ginkgo Bioworks' autonomous cloud laboratory. Cell-free protein expression and more — order on demand.

Another week, another protocol added to Ginkgo Cloud Lab menu

Strep tag purification w A280 quant

Last week it was HiBiT quant

Stay tuned for next week’s release

cloud.ginkgo.bio

1 month ago 0 0 1 0
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Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila - Nature Genetics Pico-C, a low-input Micro-C approach, reveals that dynamic three-dimensional genome folding precedes zygotic genome activation in Drosophila.

Excited to share my PhD work!

The question: How is genome organization established? Here, we developed a low-input Micro-C method, Pico-C, and used it to map chromatin architecture across early stages of fly development.

Here’s a quick Blue-torial 🙂 (1/n)

www.nature.com/articles/s41...

1 month ago 68 24 1 1
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Video

Frogfish vid by Natalie Bondarenko.

1 month ago 56 20 2 1
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How Genomics-saturated is Boston?

We put Circos plots on our trains!

1 month ago 10 0 0 0

This is so cool:

www.biorxiv.org/content/10.6...

Discovery of a Genetic Toxin-Antidote System in Vertebrates

hat tip to @asaflevylab.bsky.social

1 month ago 27 11 2 0
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Roche Axelios1 Run Pricing: Not A Knockout - Yet? By far the most awaited news at AGBT was Roche's reveal of the pricing scheme for Axelios 1 consumables: what would be the structure and how...

Roche Axelios1 Run Pricing: Not A Knockout - Yet?

#AGBTGM26

🧬💻

omicsomics.blogspot.com/2026/03/roch...

1 month ago 5 1 0 0
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Ginkgo Cloud Lab — Autonomous Lab Protocols Run protocols on Ginkgo's autonomous cloud lab. Cell-free protein expression and more.

Ginkgo Cloud Labs aims to democratize protein design validation

No lab skills required!

Use our EstiMate chatbot to explore protocols not yet supported.

Please contact me to inquire about early access to unreleased protocols

cloud.ginkgo.bio/protocols

1 month ago 1 0 0 0