Arnav
@arnavm.bsky.social
SOAR resident at Stanford Ophthalmology & postdoc in Boettiger lab. MD/PhD WashU/Mitra Lab. 👨👩👧👦👨🔬👨💻🧬👨⚕️🐈🏔🏃🛶🧗♂️🥖🍕🎮📸 Opinions mine, subject to change. He/him.
Reposted by 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…)
👀
What a time to propose this policy:
"Duke University School of Medicine (SOM) plans to implement new faculty productivity guidelines that would tie tenured professors’ salaries to external research funding, according to documents reviewed by The Chronicle"
www.dukechronicle.com/article/2025...
What a time to propose this policy:
"Duke University School of Medicine (SOM) plans to implement new faculty productivity guidelines that would tie tenured professors’ salaries to external research funding, according to documents reviewed by The Chronicle"
www.dukechronicle.com/article/2025...
Duke School of Medicine plans salary cuts for tenured faculty who do not meet grant expectations
Set to go in effect in 2026, the proposed policy would apply to the School’s basic sciences units. These units rely heavily on grants from the National Institutes of Health, which have been increasing...
www.dukechronicle.com
July 19, 2025 at 3:36 PM
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!
December 26, 2023 at 2:17 AM
6 months as a developmental biologist. Merry Christmas!
Super-enhancers imply the existence of super-duper-enhancers.
November 30, 2023 at 10:20 PM
Super-enhancers imply the existence of super-duper-enhancers.
Has anyone managed to get higlass running on a cluster using Singularity?
November 15, 2023 at 7:49 PM
Has anyone managed to get higlass running on a cluster using Singularity?
In the era of enhancer RNAs and other transcribed cis-regulatory elements, do we have an updated definition of "gene"?
November 15, 2023 at 5:56 PM
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!
November 14, 2023 at 11:18 PM
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!
Reposted by Arnav
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! 🖥️🧬
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
github.com
November 10, 2023 at 8:05 PM
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
November 8, 2023 at 5:19 PM
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
ASHG had Macklemore
Which artist will appear at AAO?
My vote is for Billie 👁️ Eilish
November 4, 2023 at 1:09 AM
AGBT had Flo Rida
ASHG had Macklemore
Which artist will appear at AAO?
My vote is for Billie 👁️ Eilish
ASHG had Macklemore
Which artist will appear at AAO?
My vote is for Billie 👁️ Eilish
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.”
“Doing science is still so rewarding. But the personal costs are many. It’s like eating caviar off a paper plate.”
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...
www.nature.com
October 25, 2023 at 5:54 AM
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.”
“Doing science is still so rewarding. But the personal costs are many. It’s like eating caviar off a paper plate.”
(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.
October 7, 2023 at 9:30 AM
(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.
October 2, 2023 at 5:13 PM
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.
Every color of the season
October 1, 2023 at 7:09 AM
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?
September 21, 2023 at 7:42 PM
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.
Many people take "non-traditional" career paths in academia.
My Leading Edge colleagues and I did! We wrote for
PLOS Biology about how non-linear careers are increasingly common, but funding agencies and search committees penalize these paths. journals.plos.org/plosbiology/...
My Leading Edge colleagues and I did! We wrote for
PLOS Biology about how non-linear careers are increasingly common, but funding agencies and search committees penalize these paths. journals.plos.org/plosbiology/...
Supporting nonlinear careers to diversify science
Those who follow non-linear career trajectories often face disadvantages in academia. This Perspective looks at why individuals might choose non-linear careers and how these benefit diversity in scien...
journals.plos.org
September 15, 2023 at 7:30 PM
"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?
September 13, 2023 at 10:42 PM
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 😂
September 8, 2023 at 6:17 PM
You've officially left your PhD lab when you've been kicked off the lab Slack 😂
Q for biochem Bluesky: what is the most disfavorable chemical reaction (largest activation energy) for which there is an enzyme catalyzing said reaction?
August 27, 2023 at 4:40 AM
Q for biochem Bluesky: what is the most disfavorable chemical reaction (largest activation energy) for which there is an enzyme catalyzing said reaction?
Reposted by Arnav
Nbd just fishes that can see the color of their own skin from the inside 🧪🦑😱
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.
www.nytimes.com
August 23, 2023 at 12:50 AM
Nbd just fishes that can see the color of their own skin from the inside 🧪🦑😱
Gonna start a genomics-themed feed, tag = skyseq
August 21, 2023 at 5:39 AM
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.
August 11, 2023 at 9:22 PM
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.
Reposted by Arnav
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!)
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!)
August 9, 2023 at 3:57 PM
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!)
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
An introduction to optical super-resolution microscopy for the adventurous biologist - IOPscience
iopscience.iop.org
August 8, 2023 at 5:26 PM
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