Sign in

Mark

@mkeller7.bsky.social
861 followers 1.3K following 60 posts

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

PostsRepliesMedia
Reposted by Mark
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...
14620
Reposted by Mark
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.
141
Reposted by Mark
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.
1207
Reposted by Mark
Christian Alder @hejchristian.com · 21/08/2026
I'm gonna do a quad-state theme toggle just you wait
5313
Reposted by Mark
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
1183
Reposted by Mark
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.
1143
Reposted by Mark
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.
121685482
Reposted by Mark
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…
012
Reposted by Mark
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.
11752593810
Reposted by Mark
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.
11334154
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.
110
Reposted by Mark
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.
191957537
Reposted by Mark
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.
8541372247
Reposted by Mark
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
46563361706
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!
030
Reposted by Mark
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."
10379126
Reposted by Mark
Harry Stevens @harrystevens.bsky.social · 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.
131
Reposted by Mark
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.
15421
Reposted by Mark
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
016838
Mark @mkeller7.bsky.social · 23/02/2026
No context side project 👀
130
Reposted by Mark
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.
20668402493
Reposted by Mark
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
72441250
Reposted by Mark
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.
897155813357
Reposted by Mark
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.
1263127447408
Reposted by Mark
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...
11527881676
Reposted by Mark
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
1123
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
040
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!
010
Reposted by Mark
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
7913709210806
Reposted by Mark
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.
3139831073
Reposted by Mark
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.
28027
Reposted by Mark
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
9771211743
Reposted by Mark
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.
140111656313
Reposted by Mark
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
095
Reposted by Mark
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
76582414527
Reposted by Mark
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...
12811
Reposted by Mark
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...
36028
Reposted by Mark
Helena Klara Jambor @helenajambor.bsky.social · 06/01/2026
Too lazy for 2 clicks, here you go: tonsky.me/blog/tahoe-i...
tonsky.me
It’s hard to justify Tahoe icons
Looking at the first principles of icon design—and how Apple failed to apply all of them in macOS Tahoe
073
Reposted by Mark
Everyone's least favorite lab mate @kepatitis-c.bsky.social · 06/01/2026
🎉 New year, NEW PREPRINT! Bacteria exhibit astonishing genetic diversity, but where do new genes come from? My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:
14930
Reposted by Mark
Your Local Epidemiologist @ylepidemiologist.bsky.social · 05/01/2026
7/ Here's the bottom line: This is an unprecedented shift that risks weakening protection against preventable diseases at a time when outbreaks are rising and children are already being hospitalized. Vaccines don’t work without strong supporting systems...and the U.S. doesn’t have Denmark’s.
311318
Reposted by Mark
Anisota @anisota.net · 27/11/2025
Hello moths, The harvest has arrived: anisota.net/harvest It's like Spotify Wrapped, but for Bluesky and the ATmosphere. 🌾 See your most-used words, discover who you interact with most, explore your posting patterns, and find all sorts of fun insights.
anisota.net
Anisota's Annual Bluesky Harvest 2025
A recap of your year on Bluesky. Discover patterns, connections, and insights from your journey in the ATmosphere.
821439416
Reposted by Mark
evacide @evacide.bsky.social · 02/01/2026
If you are a resident of California, the state now has a portal where you can demand deletion of your personal data from 500+ registered data brokers with a single request form, for free. consumer.drop.privacy.ca.gov
consumer.drop.privacy.ca.gov
274116475134
Reposted by Mark
Becky Dale @beckydale.bsky.social · 02/01/2026
New record year for renewable electricity in Britain - thanks especially to strong solar output. Read our analysis of 2025 here www.bbc.co.uk/news/article...
Two part graphic showing the daily contribution of solar in Great Britain’s electricity. The top half is a single tile chart arranged in 30-minute blocks from midnight on left to 23:59 on right with each row representing one day and ordered top-to-bottom from 1 January to 31 December 2025. Blocks are shaded by strength of generation share. In 2025, more than a dozen blocks are dark orange to show share above 40 percent. Contribution in summer days is longer and generally stronger than in winter. The second part of the graphic repeats the format as a small multiple with one fart for each year from 2013 to 2024. Each year increases in strength over that period but 2025 is the greatest contributor overall.
36318
Reposted by Mark
David A Knowles @davidaknowles.bsky.social · 31/12/2025
#MLCB2025 proceedings are up at proceedings.mlr.press/v311/ !
proceedings.mlr.press
Proceedings of Machine Learning Research
Proceedings of the 20th Machine Learning in Computational Biology meeting Held in New York, NY, USA on 10-11 September 2025 Published as Volume 311 by the Proceedings of Machine Learning Research on 3...
072
Mark @mkeller7.bsky.social · 26/12/2025
This exists 😁
Dubai chocolate panettone
010
Mark @mkeller7.bsky.social · 17/12/2025
App idea: rover, but for sourdough starters and leivito madre. it will be called doughver
000
Reposted by Mark
Saez-Rodriguez Group @saezlab.bsky.social · 17/12/2025
See 👇 our new manuscript introducing SpaCEy, an explainable method for predicting clinical outcomes from spatial omics data 🧬 📄 Paper: www.biorxiv.org/content/10.6... 💻 Code repo: github.com/saezlab/SpaCEy
11410
Reposted by Mark
Science Magazine @science.org · 14/12/2025
The structure of the bacterial genotoxin colibactin bound to DNA shows how it might contribute to cancer risk. Learn more in a new #SciencePerspective: scim.ag/4iJPFVS
scim.ag
Molecular basis of DNA cross-linking by bacteria
The structure of the bacterial genotoxin colibactin bound to DNA shows how it might contribute to cancer risk
0366