James M. Ward
@jmw86069.bsky.social
he/him, bioinformatics research scientist, fellow respectful human, dataviz enthusiast, discovering knowledge one slow mental click at a time.
Always innovating.
No cap. lol
No cap. lol
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 7, 2025 at 8:00 AM
Always innovating.
No cap. lol
No cap. lol
Reposted by James M. Ward
If you are 25 years old, you have never known a moment where humans have not been in space. To celebrate the ISS's 25 years of permanent human presence in space, you can relive those moments thanks to Ben Fiest, who created ISS in Real Time. Visit here --- > issinrealtime.org #ISSInRealTime
ISS in Real Time
Explore 25 years onboard the International Space Station.
issinrealtime.org
November 2, 2025 at 3:34 PM
If you are 25 years old, you have never known a moment where humans have not been in space. To celebrate the ISS's 25 years of permanent human presence in space, you can relive those moments thanks to Ben Fiest, who created ISS in Real Time. Visit here --- > issinrealtime.org #ISSInRealTime
From the first sentence of the Intro 🔥 and throughout,
great paper and tool. Even the population PCA plot made a statement,
really nice work.
great paper and tool. Even the population PCA plot made a statement,
really nice work.
A new paper from the lab! Work led by
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."
The Great Genotyper: a graph-based method for population genotyping of small and structural variants
Long-read sequencing (LRS) enables high-quality structural variant (SV) discovery. SV genotypers utilize these precise call sets to improve the recall and precision of genotyping in short-read sequenc...
pmc.ncbi.nlm.nih.gov
October 8, 2025 at 3:34 AM
From the first sentence of the Intro 🔥 and throughout,
great paper and tool. Even the population PCA plot made a statement,
really nice work.
great paper and tool. Even the population PCA plot made a statement,
really nice work.
Exciting work!
And one more important pathway to add to the enrichment tests.
And one more important pathway to add to the enrichment tests.
I’m excited to highlight our latest paper, just published in Cell 🎉
We report the existence of a previously uncharacterized signaling pathway that is responsible for activating cell death upon loss of gene expression.
1/n 🧪
www.cell.com/cell/fulltex...
We report the existence of a previously uncharacterized signaling pathway that is responsible for activating cell death upon loss of gene expression.
1/n 🧪
www.cell.com/cell/fulltex...
RNA Pol II inhibition activates cell death independently from the loss of transcription
When RNA polymerase II (RNA Pol II) is inhibited, the inhibition is sensed and signaled
to mitochondria, leading to programmed cell death independently of the loss of RNA
Pol II transcription activity...
www.cell.com
August 16, 2025 at 12:56 AM
Exciting work!
And one more important pathway to add to the enrichment tests.
And one more important pathway to add to the enrichment tests.
On urging an evidence-based approach to COVID origin.
Reasonable review of the underlying logic.
Reasonable review of the underlying logic.
Another email to Bhattacharya about his interview and his continued statements that NIH's gain of function research caused the COVID pandemic and killed millions of people.
1/8
1/8
August 3, 2025 at 2:56 PM
On urging an evidence-based approach to COVID origin.
Reasonable review of the underlying logic.
Reasonable review of the underlying logic.
The only opportunity here is finally to force Congress address it directly. They’ve been talking about it, with nothing definitive to address. Now, if nothing else (and it’s as close to nothing as it can be) there’s no more denying it.
Congress passed flat budget, OMB acts as if they had cuts.
Congress passed flat budget, OMB acts as if they had cuts.
July 30, 2025 at 2:15 AM
The only opportunity here is finally to force Congress address it directly. They’ve been talking about it, with nothing definitive to address. Now, if nothing else (and it’s as close to nothing as it can be) there’s no more denying it.
Congress passed flat budget, OMB acts as if they had cuts.
Congress passed flat budget, OMB acts as if they had cuts.
Best thread about the best boys and girls.
One like, one opinion about dogs.
(Will stop if I run out of good opinions.)
(Will stop if I run out of good opinions.)
Okay, lets do this.
One like, one opinion that's not on politics.
One like, one opinion that's not on politics.
July 26, 2025 at 4:07 PM
Best thread about the best boys and girls.
Reposted by James M. Ward
I recently ran a session at CSAMA with Laurent Gatto and this is the way. "Good enough" with knowledge of the tools that can help you get there. Here's some of the recs from the paper.
July 13, 2025 at 5:13 AM
I recently ran a session at CSAMA with Laurent Gatto and this is the way. "Good enough" with knowledge of the tools that can help you get there. Here's some of the recs from the paper.
Amazing paper, exactly what spatial transcriptomics is made for, and look at this system! Each hippocampus region lit up, it’s stunning.
I was thrilled to play a part!
#keepCA2weird
I was thrilled to play a part!
#keepCA2weird
Now officially out! What do CA2 neurons become in an Nr3c2 KO? We used spatial transcriptomics to find out.
With @neuroerin.bsky.social and @jmw86069.bsky.social
Lots in the suppl data rdcu.be/evGGh
With @neuroerin.bsky.social and @jmw86069.bsky.social
Lots in the suppl data rdcu.be/evGGh
Mineralocorticoid receptor knockout alters hippocampal CA2 neurons to become like those in CA1
Communications Biology - Spatial transcriptomics reveals that the molecular phenotype of hippocampal area CA2, which is critical for many social behaviors, is profoundly altered upon knock-out of...
rdcu.be
July 11, 2025 at 3:54 AM
Amazing paper, exactly what spatial transcriptomics is made for, and look at this system! Each hippocampus region lit up, it’s stunning.
I was thrilled to play a part!
#keepCA2weird
I was thrilled to play a part!
#keepCA2weird
Reposted by James M. Ward
Researchers learned a function of enzyme MORC2, that helps organise DNA and turn off genes when not needed. Mutations in MORC2 cause Charcot-Marie-Tooth disease, a rare condition that weakens muscles. These findings could lead to new treatments.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
July 2, 2025 at 4:49 AM
Researchers learned a function of enzyme MORC2, that helps organise DNA and turn off genes when not needed. Mutations in MORC2 cause Charcot-Marie-Tooth disease, a rare condition that weakens muscles. These findings could lead to new treatments.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Relevant to projects focusing on effects of long term elevated heat.
As the world warms, plants in natural ecosystems and agricultural settings find ways to respond to the heat.
In a new special issue of Science, researchers examine how heat affects plants at multiple scales, from the molecular level to the biosphere. (THREAD 🧵) scim.ag/44cSw3Z
In a new special issue of Science, researchers examine how heat affects plants at multiple scales, from the molecular level to the biosphere. (THREAD 🧵) scim.ag/44cSw3Z
June 17, 2025 at 4:01 PM
Relevant to projects focusing on effects of long term elevated heat.
Apologies in advance…
June 17, 2025 at 2:39 AM
Apologies in advance…
Reposted by James M. Ward
For those of you who may not have known him, Dr. Atul Butte, a pioneer in informatics, was the winner of the 2024 Morris F. Collen award, a pinnacle achievement in our field, as part of his storied career.
His passing is a major loss to us all.
RIP Dr. Butte
#MedSky
His passing is a major loss to us all.
RIP Dr. Butte
#MedSky
2024 Morris F. Collen Award Winner - Atul Butte, MD, PhD, FACMI
This is "2024 Morris F. Collen Award Winner - Atul Butte, MD, PhD, FACMI" by AMIA on Vimeo, the home for high quality videos and the people who love them.
vimeo.com
June 14, 2025 at 1:59 PM
For those of you who may not have known him, Dr. Atul Butte, a pioneer in informatics, was the winner of the 2024 Morris F. Collen award, a pinnacle achievement in our field, as part of his storied career.
His passing is a major loss to us all.
RIP Dr. Butte
#MedSky
His passing is a major loss to us all.
RIP Dr. Butte
#MedSky
Care it. ?
carrot = 🥕
carat =💎
karat = 🥇
caret = ^
carat =💎
karat = 🥇
caret = ^
June 7, 2025 at 2:25 AM
Care it. ?
Random Reddit post whereupon J learned
(1) click lighters generate a tiny EMP that can turn off a computer monitor, and
(2) desk chair pistons can do the same 🤯
Will this become a feature of desk chairs? “Certified EMP-free”
www.reddit.com/r/pcmasterra...
(1) click lighters generate a tiny EMP that can turn off a computer monitor, and
(2) desk chair pistons can do the same 🤯
Will this become a feature of desk chairs? “Certified EMP-free”
www.reddit.com/r/pcmasterra...
From the pcmasterrace community on Reddit: My monitor turns off when I light this lighter at this exact angle. What is happening?
Explore this post and more from the pcmasterrace community
www.reddit.com
June 5, 2025 at 4:24 PM
Random Reddit post whereupon J learned
(1) click lighters generate a tiny EMP that can turn off a computer monitor, and
(2) desk chair pistons can do the same 🤯
Will this become a feature of desk chairs? “Certified EMP-free”
www.reddit.com/r/pcmasterra...
(1) click lighters generate a tiny EMP that can turn off a computer monitor, and
(2) desk chair pistons can do the same 🤯
Will this become a feature of desk chairs? “Certified EMP-free”
www.reddit.com/r/pcmasterra...
Again, reminder for American policymakers that return on investment is 2.5x for NIH funded research.
Includes many short term benefits to cancer patients, and many medium term benefits broadly to health and quality of life.
This research is not wasteful spending.
Includes many short term benefits to cancer patients, and many medium term benefits broadly to health and quality of life.
This research is not wasteful spending.
This is when the depression starts to creep in. What good am I... what good are any of us if we can't even get 1 out of every 10 cancer proposals funded?
May 24, 2025 at 6:14 PM
Again, reminder for American policymakers that return on investment is 2.5x for NIH funded research.
Includes many short term benefits to cancer patients, and many medium term benefits broadly to health and quality of life.
This research is not wasteful spending.
Includes many short term benefits to cancer patients, and many medium term benefits broadly to health and quality of life.
This research is not wasteful spending.
Reposted by James M. Ward
Senator Durbin noted that some (I believe Republican Senators) had indicated the US had been doing more than its share of biomedical research and it was time for other countries take a turn.
I felt I had to interrupt to respond...
I felt I had to interrupt to respond...
May 23, 2025 at 8:53 PM
Senator Durbin noted that some (I believe Republican Senators) had indicated the US had been doing more than its share of biomedical research and it was time for other countries take a turn.
I felt I had to interrupt to respond...
I felt I had to interrupt to respond...
Random post, the comments are gold.
I’m the guy who invents new bathroom faucet designs for every hotel. You might know me from Knob That Goes The Other Way and Joystick That’s Hard To Turn Off. Lately I’ve been lacking inspiration, even thinking about hanging it up. I’ve had a good run, but — wait, never mind: Ball You Turn Diagonal
May 24, 2025 at 5:35 PM
Random post, the comments are gold.
My
“Step 2. Draw the rest of the owl” jokes might lose their edge if I could actually draw the rest of the owl like this! Very nice.
“Step 2. Draw the rest of the owl” jokes might lose their edge if I could actually draw the rest of the owl like this! Very nice.
May 22, 2025 at 5:24 PM
My
“Step 2. Draw the rest of the owl” jokes might lose their edge if I could actually draw the rest of the owl like this! Very nice.
“Step 2. Draw the rest of the owl” jokes might lose their edge if I could actually draw the rest of the owl like this! Very nice.
Reposted by James M. Ward
Thanks to everybody who chimed in!
I arrived at the conclusion that (1) there's a lot of interesting stuff about interactions and (2) the figure I was looking for does not exist.
So, I made it myself! Here's a simple illustration of how to control for confounding in interactions:>
I arrived at the conclusion that (1) there's a lot of interesting stuff about interactions and (2) the figure I was looking for does not exist.
So, I made it myself! Here's a simple illustration of how to control for confounding in interactions:>
May 11, 2025 at 5:34 AM
Thanks to everybody who chimed in!
I arrived at the conclusion that (1) there's a lot of interesting stuff about interactions and (2) the figure I was looking for does not exist.
So, I made it myself! Here's a simple illustration of how to control for confounding in interactions:>
I arrived at the conclusion that (1) there's a lot of interesting stuff about interactions and (2) the figure I was looking for does not exist.
So, I made it myself! Here's a simple illustration of how to control for confounding in interactions:>
Sweet!
Okay that's a good title
"Our results reveal the structural basis for sweet detection, provide insights into how a single receptor mediates all our responses to such a wide range of sweet-tasting compounds, and open up unique possibilities for designing a generation of taste modulators"🧪
"Our results reveal the structural basis for sweet detection, provide insights into how a single receptor mediates all our responses to such a wide range of sweet-tasting compounds, and open up unique possibilities for designing a generation of taste modulators"🧪
The structure of human sweetness
A single taste receptor initiates our reactions to both sugars and artificial sweeteners,
triggering a signaling process that drives our intense attraction to sweet foods.
Single-particle cryo-EM reve...
www.cell.com
May 9, 2025 at 11:56 PM
Sweet!
Reposted by James M. Ward
I am excited to share a new version of svglite for #rstats with the world. It includes support for all the new features in the graphics engine as well as providing a more powerful and polished experience for embedding web fonts in the file.
Read all about it her:
Read all about it her:
svglite 2.2.0
A new release of svglite has arrived, and with it full support for all the latest capabilities of the R Graphics Engine. Further, it finalizes the new approach to handling web fonts and font embedding...
www.tidyverse.org
May 7, 2025 at 12:27 PM
I am excited to share a new version of svglite for #rstats with the world. It includes support for all the new features in the graphics engine as well as providing a more powerful and polished experience for embedding web fonts in the file.
Read all about it her:
Read all about it her:
Reposted by James M. Ward
Another win for Justice Allison Riggs, this time in US District Court!
Let’s hope Jefferson Griffin finally accepts his loss. (He has one week to appeal.)
Source: bit.ly/4iRIqK5
Let’s hope Jefferson Griffin finally accepts his loss. (He has one week to appeal.)
Source: bit.ly/4iRIqK5
May 6, 2025 at 2:33 AM
Another win for Justice Allison Riggs, this time in US District Court!
Let’s hope Jefferson Griffin finally accepts his loss. (He has one week to appeal.)
Source: bit.ly/4iRIqK5
Let’s hope Jefferson Griffin finally accepts his loss. (He has one week to appeal.)
Source: bit.ly/4iRIqK5
A new R-4.5.0 function “grepv()” mimics a function I’ve used for years in jamba:
vgrep(): value-returning grep
and moreso
vigrep(): case-insensitive value
Okay I’m not the only one. 👀
Next up, version-type sorting?
To order chromosomes
chr1, chr2, … chr9, chr10
vgrep(): value-returning grep
and moreso
vigrep(): case-insensitive value
Okay I’m not the only one. 👀
Next up, version-type sorting?
To order chromosomes
chr1, chr2, … chr9, chr10
New version of R is out!
Our Data Scientist, Russ Hyde, has put together a quick review of the key features and changes in R 4.5 — from new language features to graphics updates and more.
📝 Read the full blog post here: www.jumpingrivers.com/blog/whats-n...
#rstats #Rprogramming #opensource
Our Data Scientist, Russ Hyde, has put together a quick review of the key features and changes in R 4.5 — from new language features to graphics updates and more.
📝 Read the full blog post here: www.jumpingrivers.com/blog/whats-n...
#rstats #Rprogramming #opensource
What's new in R 4.5.0?
Here we summarise some of the more interesting changes that have been introduced in R 4.5.0.
www.jumpingrivers.com
April 11, 2025 at 1:39 PM
A new R-4.5.0 function “grepv()” mimics a function I’ve used for years in jamba:
vgrep(): value-returning grep
and moreso
vigrep(): case-insensitive value
Okay I’m not the only one. 👀
Next up, version-type sorting?
To order chromosomes
chr1, chr2, … chr9, chr10
vgrep(): value-returning grep
and moreso
vigrep(): case-insensitive value
Okay I’m not the only one. 👀
Next up, version-type sorting?
To order chromosomes
chr1, chr2, … chr9, chr10
Well said.
All ballot applications so far (30,000+) have had valid license or SSN on their application, not one has lacked info.
The core issue is a coding glitch that “didn’t match” DMV/ID records, and simply stored “unverified.”
Headlines calling it “a twist” are wildly misrepresenting the story.
All ballot applications so far (30,000+) have had valid license or SSN on their application, not one has lacked info.
The core issue is a coding glitch that “didn’t match” DMV/ID records, and simply stored “unverified.”
Headlines calling it “a twist” are wildly misrepresenting the story.
Horrifying. Allison Riggs won by 734 votes but Judge Griffin has tried to throw out 65,000+ ballots from voters who all showed valid ID. Now the court has sided with him, giving those voters just 15 days to cure their ballots. This is a direct attack on the will of the people.
April 5, 2025 at 2:54 PM
Well said.
All ballot applications so far (30,000+) have had valid license or SSN on their application, not one has lacked info.
The core issue is a coding glitch that “didn’t match” DMV/ID records, and simply stored “unverified.”
Headlines calling it “a twist” are wildly misrepresenting the story.
All ballot applications so far (30,000+) have had valid license or SSN on their application, not one has lacked info.
The core issue is a coding glitch that “didn’t match” DMV/ID records, and simply stored “unverified.”
Headlines calling it “a twist” are wildly misrepresenting the story.