Arnav

Soft money is great. Until there’s no money left. Academics are about to learn the hard way that we are nothing but independent contractors who can be terminated pretty darn easily. “Tenure” be damned. (Many of us knew this already, of course…)

6 months as a developmental biologist. Merry Christmas!

Super-enhancers imply the existence of super-duper-enhancers.

Has anyone managed to get higlass running on a cluster using Singularity?

The data were generated globally but I'm only interested in a few local views. Coverage is relatively even across timepoints.

In the era of enhancer RNAs and other transcribed cis-regulatory elements, do we have an updated definition of "gene"?

Genome scientists: Let's say I have 10 timepoints of CTCF ChIP-seq data. I want to see both the magnitude of signal as well as time-dependent changes. How should I visualize this? Stacked/overlapping lines? Heatmap? Something else? Definitely want to prioritize interpretability!

GitHub - COMBINE-lab/simpleaf: A rust framework to make using alevin-fry even simpler A rust framework to make using alevin-fry even simpler - GitHub - COMBINE-lab/simpleaf: A rust framework to make using alevin-fry even simpler

10X Genomics just made the source for CellRanger available (but not open source); github.com/10XGenomics/...! While I strongly advocate for using truly open tools for sc preprocessing e.g. github.com/COMBINE-lab/..., this is still a huge win for computational transparency in single cell analysis! 🖥️🧬

Perfect sentence, 10/10 no notes

AGBT had Flo Rida
ASHG had Macklemore
Which artist will appear at AAO?

My vote is for Billie 👁️ Eilish

Falling behind: postdocs in their thirties tire of putting life on hold Temporary contracts, low salaries and cost-of-living hikes force many researchers to put off parenthood and other big decisions. Temporary contracts, low salaries and cost-of-living hikes force many r...

So much to relate to in this article, and I think older medical residents and fellow will find kinship here. But nothing beats this quote:

“Doing science is still so rewarding. But the personal costs are many. It’s like eating caviar off a paper plate.”

Dressed in fog

Fall, in your face

(Late) night science thoughts: Is a fossil a model? In the sense that is not the actual biological object of study, but rather a representation with strengths and flaws from which we make conjectures and draw conclusions.

We really need a tool where you can feed a GEO accession number into a browser and visualize the data. Bonus points for automatically incorporating liftOver to account for differences in genome builds.

An arrangement of fall leaves arranged in a color gradient

Every color of the season

Who’s got the best prices for Cy3B (not Cy3!) modified oligos? Is it me or is this mod more commonly available in Europe?

"We believe that people who have had nonlinear career trajectories bring unique and beneficial qualities to academia." 🔥 100% agree! I'm always inspired by those who've taken the long road to science/medicine.

Question for the FISH crowd: is there a relationship between number of probes to target mRNA and expected brightness of the corresponding spot? If so, what is the shape of that curve?

You've officially left your PhD lab when you've been kicked off the lab Slack 😂

Not yet on What’s Science so if someone can tag it that would be great!

Q for biochem Bluesky: what is the most disfavorable chemical reaction (largest activation energy) for which there is an enzyme catalyzing said reaction?

Hogfish ‘See’ With Their Skin, Even When They’re Dead The camouflaging talents of this fish are driven by a mysterious new type of cell, setting it apart from other animals that know how to blend in.

Nbd just fishes that can see the color of their own skin from the inside 🧪🦑😱

Amazing, thanks!

Gonna start a genomics-themed feed, tag = skyseq

I'm a simple scientist with simple needs, like DOIs at the top of a webpage and a PDF that automatically includes methods and supplemental data.

Bartman lab is seeking a postdoc!
We use metabolic tracing and mass spec to measure metabolism in immune cells and inflamed tissues. As a PI, my goal is to support trainees to reach their career and scientific goals. https://bartmanlabpenn.squarespace.com/ for contact info. (pls rt!)

Really enjoyed this review of optical super-resolution microscopy, relatively quick way to get up to speed on the field: https://iopscience.iop.org/article/10.1088/2050-6120/aaae0c/meta

Picasso’s napkin is an almost-certainly apocryphal story of the value of “quick” work. This site dives into its potential origins; https://quoteinvestigator.com/2018/01/14/time-art/

MD/PhD career path:

25 started med school
27 started grad school
32 first kid
32 defended
34 graduated med school
35 second kid
35 finished intern year
35 started postdoc
39 anticipated residency graduation
40-41 finish fellowship, get “real” job
?? K08
?? R01, “independence”