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Kamil Slowikowski

@slowkow.com
655 followers 2.2K following 41 posts

Computational biologist 🧬🖥️ at Mass General Brigham and Broad Institute, PhD at Harvard. Bioinformatics, transcriptomics, COVID, genomics, immunology, genetics, statistics, and web development. I made #ggrepel and I blog at slowkow.com

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Kamil Slowikowski @slowkow.com · 15/08/2026
Maryland Crashes from 2018-2026 Data from mdsp.maryland.gov run.cosmograph.app/public/e09a3...
Visualization of Maryland State Police crash data from 2018–2026 on a dark background. Thousands of color-coded points form dense, interconnected road networks across Maryland, with the greatest concentration in the Baltimore–Washington corridor. Labels identify prominent crash locations and roads.
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Nikolai Slavov @slavov-n.bsky.social · 24/06/2026
Since the 1960s, the genetic code has been used to predict protein sequences from DNA and mRNA sequences. Our @nature.com article demonstrates that these predictions miss thousands of protein sequences present in human tissues. www.nature.com/articles/s41... 1/
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Reese Richardson @reeserichardson.bsky.social · 28/05/2026
TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
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Colette Delawalla, PhD @cdelawalla.bsky.social · 27/04/2026
The past 15 months have marked a dark chapter in US science; one that will require significant effort to repair. But I'm not interested in duct tape and bandaid solutions. Our system had problems before Jan 20th, 2025. So, @standupforscience.net is doing what we do best: TAKING ACTION. 1/7
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Mark Histed @markhisted.org · 04/04/2026
An example of the perils of presidential control over science agencies. This Budget Request is dictated by the White House, Vought, and the P2025 OMB, not NSF. We have an imperial presidency, the dream of John Roberts and Charles Koch since the 80s. And it is incompatible with successful science.
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JAMA @jama.com · 29/03/2026
#HepatitisB virus newborn vaccination rates in the US peaked at 83% in early 2023 but dropped to 73% by August 2025, coinciding with increased public discourse regarding childhood vaccination. ja.ma/47rCO6p
Line graph shows US newborn Hepatitis B virus vaccination rates, forecasting the ratio of HBV vaccinations within 30 days of birth to live births in the US. Actual, ARIMA forecast, and training data are plotted from 2017-2026.
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Roby Bhattacharyya @roby-b.bsky.social · 22/02/2026
The last part abt how measles disrupts immunity vs other infections is, imo, underappreciated (& mechanism was recently clarified). It's part of why measles vaccination was seen to help beyond just reducing measles complications - not getting measles reduces severity of subsequent infections too.
science.org
Measles virus infection diminishes preexisting antibodies that offer protection from other pathogens
Measles virus infection can cause long-term damage to the immune system.
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Joe Sabatino @jsabatino37.bsky.social · 05/02/2026
Overjoyed to share our new work exploring the antigen specificity of CSF-expanded CD8+ T cells in #multiplesclerosis #EBV in @natimmunol.nature.com #immunology 🧪🧵1/ www.nature.com/articles/s41...
nature.com
Antigen specificity of clonally enriched CD8+ T cells in multiple sclerosis - Nature Immunology
Sabatino and colleagues examine expanded CD8+ T cell clonotypes from a small cohort of multiple sclerosis patients. They identified several cognate peptide epitopes that derive from Epstein–Barr virus...
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JAMA @jama.com · 16/12/2025
The incidence and prevalence of #melanoma, the fifth most common cancer in the US, have increased over the last 5 decades. This Review summarizes the epidemiology, pathophysiology, diagnosis, and treatment of cutaneous melanoma. ja.ma/4j1AhEC
Diagram of melanoma cell immunotherapy, detailing mechanisms of action of drugs like Ipilimumab, Nivolumab, and Vemurafenib. Highlights interactions between immune cells (T cells) and melanoma cells, targeting pathways like CTLA-4, PD-1, and MAPK signaling.
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Caleb Lareau @caleblareau.bsky.social · 14/12/2025
We are very excited to share the first preprint of a new direction for our group. Led by the fearless duo of @arthurwchow.bsky.social and @hoyinchu.bsky.social, our foray into computational protein design—
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James McInerney @jomcinerney.bsky.social · 10/12/2025
This is shocking stuff. John Quackenbush has been brilliant since forever. www.statnews.com/2025/12/05/r...
statnews.com
His lab was humming with discovery. After one year under Trump, it’s almost silent
John Quackenbush built a lab that is at the forefront of human genetics research and bioinformatics. Trump administration cuts have put it in danger of collapse.
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Kamil Slowikowski @slowkow.com · 04/12/2025
You run a new command in #rlang #python #bash, and you don’t really know how long it should take. Will it be done in 30 seconds? 5 minutes? 45 minutes? Longer? 😫 An automatic notification might help to stay focused on #programming Let me introduce you to ntfy.sh slowkow.com/notes/ntfy/
slowkow.com
Get notifications on desktop and mobile from long-running jobs in your terminal sessions
If you’re like me, you get tired of waiting for long-running jobs in the terminal. You run a new command, and you don’t really know how long it should take to finish. Will it be done in 30 seconds? 5 ...
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Kamil Slowikowski @slowkow.com · 01/12/2025
Cruz Godar shares stunning Javascript and webGL applets that demonstrate the beauty of mathematics. cruzgodar.com
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Mark Histed @markhisted.org · 13/11/2025
A bad thing is unfolding at NIH this week: It looks like the Trump administration is trying to replace key civil servant scientific leaders, the Institute Directors, with political hires. These directors control the NIH budget, tens of billions. A bit of a video explainer here: 1/ 🧪
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Nicole E. Basta @nicolebasta.bsky.social · 31/10/2025
Check out our new paper @nejm.org. RSV, COVID-19 & Influenza vaccines continue to show consistent effectiveness & safety based on a review & synthesis of 500+ research studies👇! We worked hard to evaluate the evidence so you can be confident about getting vaccinated this fall!
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ProPublica @propublica.org · 26/10/2025
South Carolina schools recently sent home unvaccinated kids to stem a growing measles outbreak. It turned out 5 of them were infected and, if they'd been at school, could've unwittingly spread it to their classmates for days. That kind of precaution is now illegal in Idaho.
propublica.org
Idaho Banned Vaccine Mandates. Activists Want to Make It a Model for the Country.
The Idaho Medical Freedom Act makes it illegal to require anyone to take a vaccine or receive “medical intervention.” Leslie Manookian, the activist behind the law, hopes to make it a “societal norm” ...
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Kristoffer Magnusson @rpsychologist.com · 28/10/2025
New release of PowerLMM.js! Browser-based power analysis for longitudinal models with dropout. Now includes: - Power analysis summary report - Reproducible & shareable configs (URL/JSON) - Calculations validated against R - Hypothesis region visualization powerlmmjs.rpsychologist.com
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Rolling Stone @rollingstone.com · 16/10/2025
Long Covid Is Real — And It’s Changing an Entire Generation Hundreds of thousands of kids in America are struggling with an illness that many doctors and schools refuse to recognize.e Feature: www.rollingstone.com/culture/cult...
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Kamil Slowikowski @slowkow.com · 02/10/2025
A visualization of average resting heart rate in Germany from 2020 through 2022. Link: corona-datenspende.github.io/en/vitaldata... Data: zenodo.org/records/8229...
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Kamil Slowikowski @slowkow.com · 23/09/2025
I'd like to announce the medRxiv preprint of our latest work: A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity. www.medrxiv.org/content/10.1...
Overview of a research study about COVID-19. The study includes three cohorts: (1) 351 acute COVID-19 patients across 5 severity levels and 3 time points profiled by multiple modalities, (2) 4 acute COVID-19 patients treated with tocilizumab, (3) 73 patients, 43 of whom were previously infected with SARS-CoV-2 3 months ago. The overview shows the general study design and visualizations of the single-cell RNA sequencing data analyzed in this study.
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Kamil Slowikowski @slowkow.com · 13/09/2025
Search #Pubmed and view the results on a 2D embedding. Each point represents a paper, and similar papers are near each other. Colors indicate clusters of similar papers. By Viktor Petukhov github.com/multicore-ca...
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Iris van Rooij 💭 @irisvanrooij.bsky.social · 12/08/2025
AI slop and the destruction of knowledge irisvanrooijcogsci.com/2025/08/12/a...
irisvanrooijcogsci.com
AI slop and the destruction of knowledge
This week I was looking for info on what cognitive scientists mean when they speak of ‘domain-general’ cognition. I was curious, because the nuances are relevant for something I am researching at t…
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Kamil Slowikowski @slowkow.com · 08/08/2025
1. Make an Excel file with your author information 2. Drag and drop 3. Copy a nicely formatted author list into Word 🐶 slowkow.com/authorbud
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Kamil Slowikowski @slowkow.com · 16/07/2025
Convert Markdown to C++, Python, MATLAB, and LaTeX iheartla.github.io by Yong Li
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Stand Up for Science! @standupforscience.net · 14/05/2025
☀️THE SUMMER FIGHT FOR SCIENCE☀️ 🫵 WHO: You + all our friends 🧪 WHAT: Share science with your neighbors and tell them about the impact of proposed budget cuts. 🇺🇸 WHERE: Your local community 🏖️ WHEN: Now to Sept 30th 🔬 WHY: The 9/30 budget vote will determine the future of science in America.
The summer fight for science. The time is now. Join the fight at standupforscience.net.
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Alex Rubinsteyn @alexr.bsky.social · 04/06/2025
5 pages of this in the HHS Terminated Grants document Link: taggs.hhs.gov/Content/Data...
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BK. Titanji @boghuma.bsky.social · 04/06/2025
The destruction of the medical research enterprise in the U.S. will go down in history as one of the most damaging choices a government has made in setting its population backwards www.nytimes.com/interactive/...
nytimes.com
Here Are the Nearly 2,500 Medical Research Grants Canceled or Delayed by Trump (Gift Article)
Some cuts have been starkly visible, but the country’s medical grant-making machinery has also radically transformed outside the public eye.
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Michael Baym @baym.lol · 14/05/2025
Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab
A screenshot of the termination notice showing "Outstanding Investigator Grants"A screenshot of the termination notice with "This award is terminated effective the date of this award, due to unsafe antisemitic actions that suggest the institution lacks concern for the safety and wellbeing of Jewish students." highlighted
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Senator Bernie Sanders @sanders.senate.gov · 30/04/2025
Illegal arrests made by the Trump administration are intended to spread fear and silence dissent. We cannot allow Trump and his cronies to turn the United States of America into an authoritarian society in which people can be disappeared for their political beliefs.
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Representative Becca Balint @balint.house.gov · 16/04/2025
My colleagues and I demand answers from Kristi Noem and Marco Rubio about the illegal and inhumane abduction of Mohsen Mahdawi, a permanent legal resident of the United States. The Constitution guarantees people within our borders basic rights, including due process and free speech.
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Representative Becca Balint @balint.house.gov · 16/04/2025
Kilmar Abrego Garcia must be released and brought home to Maryland. He is innocent. No government can snatch people off the street and ship them to prison without due process. It should terrify us all. I'm thankful @vanhollen.senate.gov is headed there to demand his release.
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Democracy Now! @democracynow.org · 16/04/2025
"It is critically important that we as Americans, regardless of party, stand up for all of these students who are being detained," says Vermont's @balint.house.gov. "This has got to stop. This is Trump creating his own army of brownshirts right here in our country."
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Kamil Slowikowski @slowkow.com · 10/04/2025
Today, I watch with deep sadness as the United States’ remarkable scientific enterprise, which took generations of hard work and national investment to build, faces a concerted dismantling by the current administration.

American science is the envy of the world, but this global leadership is now threatened by draconian cuts to federal support of biomedical research through the defunding of grants and drastic reductions in funding for essential research costs and infrastructure.

This will have catastrophic consequences for the US biomedical research and medical sector, choking off the next generation of medical advances and undermining our global competitiveness at a time when other countries are working hard to overtake us.

— Ardem Patapoutian, Nobel laureate
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Keenan Crane @keenancrane.bsky.social · 07/04/2025
We often use discretization to approximate continuous laws of physics, but it also goes the other way: You can use continuous equations to approximate the behavior of discrete systems! Here we'll see how electrical circuits can be modeled using the Laplace equation Δφ=0. [1/n]
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Andy Pekosz @andrewpekosz.bsky.social · 25/03/2025
I got the news this morning on two COVID related grants that were being terminated because its no longer seen as a research priority by Health and Human Services. My people have been given their notice. I have no words to express my feelings. www.nbcnews.com/health/healt...
nbcnews.com
CDC is pulling back $11B in Covid funding sent to health departments across the U.S.
“Now that the pandemic is over, the grants and cooperative agreements are no longer necessary," federal health authorities wrote to funding recipients this week.
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BK. Titanji @boghuma.bsky.social · 16/03/2025
I am so grateful for the reporters who are doing the work on telling the story of the incredible negative impact of the cessation of US aid. The human toll is hard to wrap one's head around. This article is a must read. www.nytimes.com/interactive/...
nytimes.com
Opinion | Musk Said No One Has Died Since Aid Was Cut. That Isn’t True. (Gift Article)
A journey through the front lines of global poverty shows that when the world’s richest men slash aid for the world’s poorest children, the result is sickness, starvation and death.
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Larry Hunter @proflhunter.bsky.social · 09/03/2025
Measles, one of the most contagious diseases, was at Dulles airport last week. Get vaccinated/boosted or at least check your titers. This is serious, and, alas, the CDC is increasingly incapacitated. health.maryland.gov/newsroom/Pag...
health.maryland.gov
Pages - Release: One Case of Measles Confirmed in Maryland Resident with Recent International Travel
An official website of the State of Maryland.
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Senator Bernie Sanders @sanders.senate.gov · 07/03/2025
Trump and Musk are going after Social Security, Medicaid, the VA, and public education. In what universe, in what world, in what religion is it morally acceptable to cut programs for hungry children in order to reward the wealthy?
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Kamil Slowikowski @slowkow.com · 06/03/2025
Airborne Infection Prevention Using Germicidal UV-C: Training and Certification Program August 2025 in College Park, Maryland Developed by Dr. Rolf Bergman, Dr. Paul Jensen, Dr. David Sliney Funded by Balvi Filantropic Fund (@vitalik.ca) Sign up at: docs.google.com/forms/d/e/1F...
Airborne Infection Prevention Using Germicidal UV-C: Training and Certification Program. August 2025 in College Park, Maryland. Designed by Dr. Rolf Bergman, Dr. Paul Jensen, and Dr. David Sliney. In an era of resurgent measles, TB, and emerging pathogens, we offer a first of its kind training program for implementing Germicidal UV-C (GUV) in public settings. You will learn the fundamentals of GUV, how to design an installation, and safely install and maintain UV-C luminaires. Funded by Balvi Philanthropic Fund. Sign up at: https://docs.google.com/forms/d/e/1FAIpQLSeb_ycH_6TNdUe-nIg06R1H1ruA7dCEZMDTmr2A2e48dwJeGQ/viewform
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David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 03/03/2025
Today, a broad coalition of scientific professional societies who represent over 92,000 scientists are speaking out against the politicization and demonization of Federally funded science and government scientist jobs. It was an honor to help the Union of Concerned Scientists with this! 🧪🌎
ucsusa.org
48 Scientific Societies Representing Almost 100,000 Scientists Ask Congress to Protect the Future of Science
48 scientific societies representing almost 100,000 scientists signed on to a letter asking Congress to protect the future of science
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Stand Up for Science! @standupforscience.net · 12/02/2025
Welcome to the Bluesky account for Stand Up for Science 2025! Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide! #scienceforall #sciencenotsilence
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BWJones @bwjones.bsky.social · 27/02/2025
By @katherinejwu.com "The NIH... supported 99 percent of the drugs approved in the U.S. from 2010 to 2019. The agency has had a hand in “nearly all of our major medical breakthroughs over the past several decades,” The NIH is in a struggle for its (and our) lives. This is existential to America:
theatlantic.com
Inside the Collapse at NIH
Administration officials pressured NIH to avoid clear advice from the agency’s own lawyers to restart grant funding now.
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Herman Wong @hermanywong.bsky.social · 11/02/2025
Johns Hopkins officials said the NIH funding cut puts at risk approximately 600 current and ongoing clinical trials at Hopkins, including open clinical trials in cancer, pediatrics and children’s health, heart and vascular studies and the aging brain. www.thebaltimorebanner.com/education/hi...
thebaltimorebanner.com
Johns Hopkins sues federal government over NIH funds
Johns Hopkins University joined several universities in a lawsuit on Monday evening suing the federal government over NIH funding.
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Pete Buttigieg @petebuttigieg.bsky.social · 11/02/2025
The CFPB is one of the American people’s best defenses against waste, fraud, and abuse. Demolishing it will, of course, lead to more waste, fraud, and abuse.
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Eric Topol @erictopol.bsky.social · 11/02/2025
A Direct Hit, by @holdenthorp.bsky.social @science.org www.science.org/doi/full/10.... "This is a moment to unite."
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Amy Maxmen, PhD @amymaxmen.bsky.social · 11/02/2025
Update: 15 confirmed cases. Health officials are racing to offer vaccines to unvaccinated children, they're operating a mobile unit to screen for cases, pre-treating exposed infants. Schools & hospitals are on alert. Measles outbreaks are v hard to contain. A totally preventable situation.
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BK. Titanji @boghuma.bsky.social · 08/02/2025
Will universities finally speak up now? Or are they still "working behind the scenes" Texted with many academic colleagues last night, the consensus is, if these cuts hold, many of us can no longer have a career in academia. This will spur mass exodus. www.science.org/content/arti...
science.org
NIH slashes overhead payments for research, sparking outrage
Move to cut indirect cost rate to 15% could cost universities billions of dollars
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Kamil Slowikowski @slowkow.com · 07/02/2025
"Health institutions may be hesitant to criticise the new administration publicly, but this timidity is a mistake. Trump's actions must be called out for the damage they are doing."
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Philip Ball @philipcball.bsky.social · 07/02/2025
I have run out of patience with the apparent silence of most US science institutions (and not just US) in the face of Trump & Musk's rampage. There are of so many facets of that, but in this column for @chemistryworld.com I talk about the assaults on inclusion. www.chemistryworld.com/opinion/scie...
chemistryworld.com
Scientific institutions have a long history of anticipatory obedience
Societies should learn from this and speak up to support inclusion
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