Tessera
Folgen

Keith Robison

@omicsomics.bsky.social

Computational biologist & blogger

456 Posts3483 Follower389 Folgt
Stirling Churchman@stirlingchurchman.bsky.social · last wk.

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

Analog intrinsic recoding measures RNA dynamics without chemical conversion

Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...

biorxiv.org

Emily Lakdawalla 🏳️‍⚧️ Uranus Expert@elakdawalla.bsky.social · last wk.

A fun image processing distraction today -- how to clean up the noisy background of a photo of a microfilm of a medieval manuscript? Thread, in which I use Photoshop, but similar tools are available in GIMP and other image processing software.

Photo of a microfilm of a medieval manuscript, with a dark grey backgroundPhoto of a microfilm of a medieval manuscript, rendered more visible by removal of the background
Dr. Erika Graham-Goering@jeanneologist.bsky.social · last wk.

Got a bit of a range in quality, though much of the same type—the first picture is more or less usable, the second is tough going (especially because a lot of the words are abbreviated, so it's important to see details).

Photo of a microfilm of a medieval manuscript, with a greyish background
Keith Robison@omicsomics.bsky.social · 4mo ago

$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?

@hoffsbeefs.bsky.social · 4mo ago

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.

Jeff Gentry@geoffjentry.bsky.social · 4mo ago

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

Igor Martayan@imartayan.bsky.social · 4mo ago

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.

Matthew Cobb@matthewcobb.bsky.social · 4mo ago

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.

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.
Lee Katz@lskatz.github.io · 4mo ago

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...

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

soundcloud.com