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Mark

@mkeller7.bsky.social
866 followers 1.4K following 60 posts

Researcher in bioinformatics working on single-cell data visualization markk.co

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Reposted by Mark
Virginie Uhlmann @virginieuhlmann.bsky.social · 05/10/2026
Are you a biologist working with microscopy images? A computer scientist wanting to work with microscopy data? Their boss??? None of these, but curious how AI has transformed microscopy image analysis? 🔬🤖 This one's for you: 📄 doi.org/10.1146/annu... More in the thread! 🧵
doi.org
From Pixels to Discovery: Microscopy Image Analysis in the Age of Artificial Intelligence
Modern microscopy generates data volumes that far exceed human analytical capacity. Over the past decade, artificial intelligence (AI) has transformed microscopy image analysis into an engine for quan...
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Michael Clemens @mclem.org · 12/09/2026
The US President's new proposal to tax international students has been approved by the White House for release this week. It's an unprecedented $100,000 tax on int'l grads who stay to work after graduation on Optional Practical Training (most grads do), a crucial bridge to remaining by any channel.
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Matt Henderson @matthen.com · 03/10/2026
Visualising the distribution of substrings in the genomes of different organisms. Going up to depth eight by recursively splitting into quadrants, we get these fractal-like pictures.
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Mark @mkeller7.bsky.social · 17/09/2026
Understood, thank you!
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Mark @mkeller7.bsky.social · 17/09/2026
I love react-query, but was just trying to find a list of the options for useQuery, and the new pages are borderline un-readable for a human. The v4 pages are significantly easier to read. Are there plans to "unroll" the typescript types? Otherwise I need to click onto many typescript interfaces
API docs webpage for useQuery function for v4 on left and v5 on right. V4 lists the query options in human-readable form, while V5 lists a bunch of typescript type definition implementation details.
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Emma Dann @emmamarydann.bsky.social · 28/08/2026
Our work on systematic perturb-seq of primary human T cells is now out in Cell 🎉 www.cell.com/cell/fulltex... It's been a privilege to work with @ronghuizhu.bsky.social between @jkpritch.bsky.social @marsonlab.bsky.social labs, with a dream-team of co-authors ❤️ Highlights in preprint thread👇
cell.com
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
A dynamic atlas of gene regulation was generated by perturbing every expressed gene across 22 million primary human CD4+ T cells under resting conditions and following re-stimulation. The resulting ma...
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Kari Lavikka @karilavikka.fi · 26/08/2026
I made an R package that creates oncoplots, lollipop plots, rainfall plots, and GISTIC plots with basic interactivity such as tooltips and zooming. It's almost a drop-in replacement for the corresponding maftools' plotting functions.
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Dani León-Periñán @danilexn.bsky.social · 26/08/2026
Malva out in Nature! 🚀 RNA sequences make cells different from each other. Single-cell data captures much of this, but most stays in the dark because we reduce it to gene counts. We introduce Malva to make the world's single-cell data searchable. What took days is now one query in seconds.
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Christian Alder @hejchristian.com · 21/08/2026
I'm gonna do a quad-state theme toggle just you wait
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Nicolas Fernandez @cornhundred.bsky.social · 19/08/2026
We're excited to share our new preprint, Celldega: Integrated Toolkit for Visualization and Analysis of Spatial Data! Celldega is an open-source framework that tightly couples scalable, interactive visualization (>1M cells and >1B transcripts) with spatial-omics analysis #Xenium #StrataMap #Atera
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Mark @mkeller7.bsky.social · 24/07/2026
The Pluot docs site now supports "full window" mode and render-to-script. Find something interesting via the interactive plot? Ask the rust core for a Python or R script that reproduces it, including the current camera state and other parameters.
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Alexander Lex @alex-lex.bsky.social · 20/07/2026
I wrote a blog post, “Beyond the Demo: Building Visualization Research Software That Lasts”, based on a keynote I gave at VisGap at EuroVis in Nottingham last month. It reflects on what it takes to build visualization software that survives beyond the paper. www.visdesignlab.net/blog/2026/07...
Illustration splitting projects into successes - datavisyn, reVISit, and UpSet; and failures - Caleydo and Multinet.
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Chris Geidner @chrisgeidner.bsky.social · 03/06/2026
Sotomayor, joined by Kagan and Jackson, issues a 17-page dissent to the 4-page order: "[J]ust as Alabama doubled down on racial discrimination, the Court today doubles down on chaos."
JUSTICE SOTOMAYOR, with whom JUSTICE KAGAN and
JUSTICE JACKSON join, dissenting.
Before the Court are two paths. Down one lies an orderly election, held under a tried-and-tested congressional map that protects Black Alabamians' right to vote and with which all voters, elections officials, and candidates alike are familiar. Down the other lies a chaotic election, held under a never-before-used congressional map that intentionally discriminates against Black Alabamians, that Alabama adopted in unashamed defiance of a prior court order directly affirmed by this Court, and that will require officials to change the voter registrations of hundreds of thousands of voters in just days at best, a task that Alabama previously represented would take months.
The majority chooses the second path and disregards both democratic values and the rule of law. I respectfully dissent.Weeks ago, I warned that vacating the District Court’s
injunction in these cases would “unleash chaos and . . . con-
fuse voters.” Caster, 608 U. S., at ___ (dissenting opinion)
(slip op., at 4). Nevertheless, the Court forged ahead. Now
the Court is squarely faced with a record of the turmoil it
has caused and the harm it has wrought. Yet just as Ala-
bama doubled down on racial discrimination, the Court to-
day doubles down on chaos. Because I choose to defend the
rule of law and the right of all Alabamians to participate
equally in democracy, I respectfully dissent.
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 11/05/2026
InterScale reveals multi-scale cellular interaction programs in spatial transcriptomics www.biorxiv.org/content/10.64898/20…
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David Farrier @davidfarrier.com · 11/05/2026
new zealander everlee wihongi was due to meet with her lawyer yesterday. then ICE moved her to their most notorious tent facility in texas: 3000 people, highest death rate, most sexual assaults. and today, she disappeared off the system. please RT: www.webworm.co/everleehasdi...
webworm.co
Everlee Has Disappeared
Everlee Wihongi was transferred by ICE to the notorious "Camp East Montana" at Fort Bliss, Texas. Then she disappeared.
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BK. Titanji @boghuma.bsky.social · 06/05/2026
The CDC is really is no where to be found because of its deliberate destruction. You CDC cruise ship inspectors were laid off in April 2025. No surprise it has been crickets from HHS and CDC leadership on the situation with the Hanta virus cruise ship situation. www.cbsnews.com/news/cdc-cru...
cbsnews.com
CDC's cruise ship inspectors laid off amid bad year for outbreaks
The steep cuts to the cruise ship inspection team baffled officials in the program, which is not paid for by taxpayer dollars.
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Mark @mkeller7.bsky.social · 24/04/2026
context: markk.co/blog/2026-04...
markk.co
Why implement a data visualization toolkit in Rust?
Personal website.
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Simon Hammann @simonhammann.bsky.social · 20/04/2026
Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.
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Carl T. Bergstrom @carlbergstrom.com · 09/04/2026
Our PhD student Kennedy Orwa, who studies applications of AI to health care, was hastily deported today to Kenya along with his 13-year-old son without opportunity to speak to legal counsel. King 5 reports that he held a valid visa that was rescinded without explanation.
king5.com
UW graduate student deported through SEA as protesters demand answers
A union representing University of Washington graduate student workers says Kennedy Orwa’s student visa was rescinded without explanation.
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Senator Ed Markey @markey.senate.gov · 07/04/2026
Completely unstable and perilous. The House must bring up impeachment articles, and the Senate needs to remove a president who wants to commit war crimes. We cannot sit idly by as Donald Trump threatens to end an entire civilization.
Washington Post
Trump warns ‘a whole civilization will die’ if Iran doesn’t make a deal
The president had issued a deadline of 8 p.m. Eastern time for Iran to open up the Strait of Hormuz, pledging destruction by midnight if leaders don’t comply.

April 7, 2026 at 9:22 a.m. EDT26 minutes ago
2 min
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Mark @mkeller7.bsky.social · 04/04/2026
If you have ever been confused about these terms/concepts, @dvdkouril.xyz digs into their origins and provides a helpful survey!
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allen institute @alleninstitute.org · 01/04/2026
The Orange Cat Brain Atlas is here. 🧠🐈 Today, we published the first comprehensive cellular map of the orange cat brain. The new atlas reveals a single, specialized neuron responsible for behaviors like staring at walls, knocking objects off tables, and the 3am "zoomies."
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Harry Stevens @handle.invalid · 18/03/2026
It's not just in New Albany. More than half of the gas plants being built to serve data centers will be off grid, according to data from @globalenergymon.bsky.social. Gift link: www.nytimes.com/interactive/...
A map of the United States showing natural gas plants that have been announced or are under construction. Plants that will not be connected to the grid are highlighted in blue, and grid-connected plants are in gray.
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Max Heiman @heiman.bsky.social · 13/03/2026
NYT feature on their website's front page about our local C. elegans colleague Will Mair and NIH funding www.nytimes.com/2026/03/13/u...
nytimes.com
His Harvard Lab Was Thriving. Then Came the Cuts.
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Observable @observablehq.com · 27/02/2026
When D3 was released in February 2011, it transformed how we build data visualizations for the web and ushered in a new age of unbridled creativity in information design, data journalism, and beyond. Today, it remains the backbone of modern, interactive data viz. Happy 15th birthday, D3 🎂 d3js.org
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Mark @mkeller7.bsky.social · 24/02/2026
now with fixed pixel size physical scaling
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Mark @mkeller7.bsky.social · 23/02/2026
No context side project 👀
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Mark @mkeller7.bsky.social · 22/02/2026
Zarr ZipStore with the JSON as its .attrs
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Senator Chris Van Hollen @vanhollen.senate.gov · 18/02/2026
DHS is holding a 2-month-old BABY at a detention facility in Texas. Last night, Juan Nicolás was rushed to the hospital after choking on his own vomit & being unable to breathe. This demands accountability — not a blank check for more cruelty.
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CNN @cnn.com · 10/02/2026
The FDA has refused to accept an application from Moderna to review its first mRNA seasonal flu vaccine, the company said, in another setback for the technology that’s been a target of some Trump administration health officials. cnn.it/4kt8iyn
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Bluesky @bsky.app · 09/02/2026
v1.116 is rolling out now! For all the overthinkers and perfectionists out there, we're launching Drafts.
A demonstration of where you can find the drafts feature in the top right corner of the post composer on Bluesky.
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Aaron Reichlin-Melnick @reichlinmelnick.bsky.social · 09/02/2026
ICE has now spent over half a BILLION dollars just on purchasing warehouses around the country to convert into detention camps. If these mega-camps are utilized to the full capacity ICE intends, they'll be the largest prisons in the country, with little real oversight. www.ajc.com/politics/202...
ajc.com
ICE to begin detaining immigrants inside Social Circle warehouse in April
Homeland Security plans to build warehouse detention facilities in other cities being met with opposition.
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Mark @mkeller7.bsky.social · 06/02/2026
marimo
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MPR News @mprnews.org · 06/02/2026
A man taken into custody in Rochester Thursday by federal immigration agents and now held at the Whipple Federal Building in the Twin Cities is a recent organ transplant recipient who is without his needed anti-rejection medication, state Rep. Kim Hicks tells MPR News.
mprnews.org
Transplant recipient arrested by federal agents in Rochester needs medicine, state representative says
State Rep. Kim Hicks told MPR News she drove to the Whipple Federal Building near Ft. Snelling Thursday night to give the man his medication but authorities wouldn't take it without a doctor's note. S...
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Zeitlinger Lab @zeitlingerlab.bsky.social · 05/02/2026
The new updates for Charles McAnany’s preprint “Positional Interpretation of Cis-Regulatory Code and Nucleosome Organization with Deep Learning Models” (www.biorxiv.org/content/10.1...) are up! We introduce PISA, a tool to visualize the cis-regulatory code. See a recap below:
biorxiv.org
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Mark @mkeller7.bsky.social · 04/02/2026
First ai ruined dashes, now it has also ruined UIs with gradients and rectangular divs with lots of padding and large corner radii
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Mark @mkeller7.bsky.social · 04/02/2026
Been calling senators/reps offices a lot lately but just had a real human staffer pick up for the first time to listen to my comment. This tells me their lines are not busy enough! Fill up their voicemails!
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max nesterak @maxnesterak.bsky.social · 23/01/2026
It’s -9 degrees. Downtown Minneapolis is packed for the anti-ICE rally and the crowd keeps growing
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Katie Mack @astrokatie.com · 19/01/2026
Any one of these daily atrocities should result in a full congressional investigation and a disbanding of the agency. The fact that it’s all just shrugged off by those with the power to stop it is a national disgrace.
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Jessica Hullman @jessicahullman.bsky.social · 09/01/2026
Wrote a summary of a great keynote by @zey.bsky.social at NeurIPS, arguing that we’re having the wrong nightmares about AI: not AGI or superhuman benchmarks, but good-enough genAI at scale threatens "load bearing frictions" society relies on to signal effort, authenticity, sincerity, credibility.
open.substack.com
Zeynep Tufecki on having the wrong nightmares about generative AI
I was writing a blog post where I was going to reference Zeynep Tufecki’s 2025 NeurIPS keynote, and realized there isn’t a solid synopsis online.
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Jen Bendery @jbendery.bsky.social · 14/01/2026
The Congressional Progressive Caucus, a group of nearly 100 House Democrats, will announce later today that it's formally endorsing legislation to strip $175 billion from ICE and put it toward affordable housing. www.huffpost.com/entry/doj-fe...
huffpost.com
Progressive Caucus Backs Bill To Redirect ICE Money To Affordable Housing
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amanda moore 🐢 @noturtlesoup17.bsky.social · 13/01/2026
Today at 34 & Park in Minneapolis, a woman tried to drive down the street where a protest had broken out in front of a home ICE was raiding, saying she had a doctor apt to get to. ICE agents busted out her windows, cut off her seatbelt, and pulled her out before arresting her.
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Agustin Capeletto @lowpoly.gg · 02/12/2025
Introducing VoxCSS: a DOM based voxel engine github.com/LayoutitStud...
github.com
GitHub - LayoutitStudio/voxcss: A DOM based voxel engine. Renders HTML cuboids by stacking CSS grid layers and applying 3D transforms.
A DOM based voxel engine. Renders HTML cuboids by stacking CSS grid layers and applying 3D transforms. - LayoutitStudio/voxcss
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Dom Ervolina @dominicervolina.com · 12/01/2026
A video of ICE agents conducting door-to-door searches today in Minneapolis The homeowner requests a warrant repeatedly, is told they don't require one, then is told they're getting it, then the agents storm in anyway They also point a taser at her to try and disrupt filming
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Mark @mkeller7.bsky.social · 10/01/2026
libertypuzzles.com these are very nice
libertypuzzles.com
Liberty Puzzles | Wooden Jigsaw Puzzles
The original wooden jigsaw puzzle maker. Established in 2005, all of our 1000+ puzzles are handmade in Boulder, CO with exquisite quality & craftsmanship. Full of odd-shaped "whimsy" pieces, our woode...
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Fabian Theis @fabiantheis.bsky.social · 08/01/2026
🔬 pertpy: a unified, scalable framework for single-cell perturbation analysis, now out in Nature Methods Designed for modern perturbation data - CRISPR, drug screens, patient treatments - scaling to millions of cells and 1000s of conditions. 👉 www.nature.com/articles/s41...
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Ed Newton-Rex @ednewtonrex.bsky.social · 08/01/2026
A new paper from Stanford adds further, incontrovertible evidence that LLMs memorize training data. The authors showed that copyrighted works can be extracted from every LLM they tried: GPT-4.1, Gemini 2.5 Pro, Grok 3, and Claude 3.7 Sonnet. 🧵 1/3 arxiv.org/pdf/2601.026...
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Mark @mkeller7.bsky.social · 07/01/2026
Great points! I created dynamic-importmap in response to some of the challenges that you also note in "Improving import maps" github.com/keller-mark/... A version of this is now being used by Wordpress github.com/WordPress/gu...
github.com
GitHub - keller-mark/dynamic-importmap: Rewrite bare import specifiers at runtime in the browser
Rewrite bare import specifiers at runtime in the browser - keller-mark/dynamic-importmap
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