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John Doench

@johndoench.bsky.social
2.9K followers 781 following 241 posts

Functional genomics @ Broad Institute. Screen all the things!

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John Doench @johndoench.bsky.social · 06/07/2026
New preprint from the group, comparing CRISPRko and CRISPRi via a Perturb-seq readout: www.biorxiv.org/content/10.6...
biorxiv.org
Direct comparison of CRISPR knockout and interference with Perturb-seq
CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) are two workhorse technologies for loss-of-function studies, yet direct comparisons between the two are scant relative to their widespread ...
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The Onion @theonion.com · 03/04/2026
Pete Hegseth Replaces Top General With Horse That Drinks Beer theonion.com/pete-hegseth-replaces-…
Pete Hegseth Replaces Top General With Horse That Drinks Beer
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andy™ @andylevy.net · 03/04/2026
you, a naive fool: i do believe there are some things the nytimes won’t both sides the nytimes:
actual nytimes headline 

FEMA Official Says He Teleported to Waffle House. Experts Are Dubious.
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Rob DenBleyker @robdenbleyker.com · 27/03/2026
looking good Mr President
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Colette Delawalla, PhD @cdelawalla.bsky.social · 16/03/2026
Breast cancer mortality dropped 58% from 1975 to 2019. Localized, early detected breast cancer has a 99% 5 year survival rate. Modern mammogram tech was developed by NASA for telescopes. Last year, RFK Jr. cancelled 87 research grants on breast cancer. www.nytimes.com/2026/03/16/u...
nytimes.com
Susie Wiles, Trump’s White House Chief of Staff, Has Breast Cancer
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John Doench @johndoench.bsky.social · 15/03/2026
I mean, these are always good. But this is So Good. Nitrogen, Ammonia, and the Strait of Hormuz | Science | AAAS www.science.org/content/blog...
science.org
Nitrogen, Ammonia, and the Strait of Hormuz
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Kevin M. Kruse @kevinmkruse.bsky.social · 14/03/2026
They made them take down the videos because they would cause "reputational damage" to people like this young man, Nathan Cavanuagh, so definitely don't post this all over the internet with the name Nathan Cavanaugh attached, or this guy might suffer reputational damage. This guy, Nathan Cavanaugh.
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News Eye @newseye.bsky.social · 03/03/2026
Holy shit. These people shouldn’t be near sharp cutlery, let alone seats of power. Mullin: “This is war.” Raju: “You concede this is war?” Mullin: “We haven’t declared war.” Reporter: “You just said it’s a war.” Mullin: *stammer
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The Red Terra @theredterra.bsky.social · 16/02/2026
I’ve been to Busytown. I’ve seen these things in action.
Lowly Worm applecar
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Ben Collins @bencollins.bsky.social · 16/02/2026
Incredible. We got to "Is a pedophile island really all that bad?" five times faster than I thought.
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John Doench @johndoench.bsky.social · 12/02/2026
On the unintentional comedy scale, this was 10 of 10 for me.
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Pareto Optimizer @paretooptimizer.bsky.social · 27/01/2026
This style of post is literally every second thing I see on here and it’s utterly absurd. Van Hollen in particular could not be a worse target.
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Ben Collins @bencollins.bsky.social · 15/01/2026
He really is doing all of it.
He has made Judges dependent on his Will alone, for the tenure of their offices, and the amount and payment of their salaries.

He has erected a multitude of New Offices, and sent hither swarms of Officers to harrass our people, and eat out their substance.

He has kept among us, in times of peace, Standing Armies without the Consent of our legislatures.

He has affected to render the Military independent of and superior to the Civil power.

He has combined with others to subject us to a jurisdiction foreign to our constitution, and unacknowledged by our laws; giving his Assent to their Acts of pretended Legislation:

For Quartering large bodies of armed troops among us:

For protecting them, by a mock Trial, from punishment for any Murders which they should commit on the Inhabitants of these States:

For cutting off our Trade with all parts of the world:

For imposing Taxes on us without our Consent:

For depriving us in many cases, of the benefits of Trial by Jury:

For transporting us beyond Seas to be tried for pretended offences:

For abolishing the free System of English Laws in a neighbouring Province, establishing therein an Arbitrary government, and enlarging its Boundaries so as to render it at once an example and fit instrument for introducing the same absolute rule into these Colonies:

For taking away our Charters, abolishing our most valuable Laws, and altering fundamentally the Forms of our Governments:

For suspending our own Legislatures, and declaring themselves invested with power to legislate for us in all cases whatsoever.

He has abdicated Government here, by declaring us out of his Protection and waging War against us.

He has plundered our seas, ravaged our Coasts, burnt our towns, and destroyed the lives of our people.
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Nessa Carson @supersciencegrl.co.uk · 30/12/2025
Nothing prepares you for how rapidly you accelerate between these three states #chemchat
Screenshot of a tweet from @MichaelCarusi
The three stages of career development: 
1. I can't wait until I'm important enough to be included in meetings. 
2. I feel so important being in these meetings! 
3. I will do anything legal and several illegal things to avoid these meetings.
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c0nc0rdance @c0nc0rdance.bsky.social · 22/12/2025
Mary and Joseph praying over Jesus in the manger, or TWO T. REXES FIGHTING OVER A TABLE SAW? Once seen, cannot be unseen.
It's one of those white cutouts that people put up in their yards that is supposed to show Joseph and Mary praying over a baby Jesus with a round halo above his head, and a star just behind the structure.
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Science in Boston @scienceinboston.com · 03/12/2025
Drs. Matthew Meyerson and Heidi Greulich from the @broadinstitute.org sit down and discuss how they and Bayer scientists developed the first FDA-approved #CancerDrug to come from a Broad scientific discovery. 🤝 Learn more about their academic-industry alliance: bit.ly/4ruQNRl
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NY Times Pitchbot @nytpitchbot.bsky.social · 22/11/2025
Magnolia's Cafe on Rochester's deep blue Park Ave might seem like a strange place to meet Trump supporters. But over the clank of metal spoons against bowls of tomato soup, you can hear whispers that the president's friendly meeting with Mamdani may be the beginning of a pivot to the center.
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Addgene @addgene.bsky.social · 20/11/2025
Thank the @johndoench.bsky.social and Root labs for depositing these deliciously named libraries, and check out our blog post for more:
twp.ai
blog.addgene.org
A Tour of Addgene's Most Popular Pooled Libraries
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FPbase @fpbase.org · 04/11/2025
The FPbase spectra viewer just had it's biggest software refactor in 6 years. It *should* be largely invisible to the end user (hopefully just faster and less buggy). Please let me know if you find any issues as you use it! www.fpbase.org/spectra/
fpbase.org
FPbase Fluorescence Spectra Viewer
An interactive fluorescence spectra viewer to evaluate the spectral properties of fluorescent proteins, organic dyes, filters, and detectors.
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Brandon Sit @sitbrandon.bsky.social · 03/11/2025
First 🟦 post - my main postdoc work is out in the world! We designed a Cas12a-based genetic screen to identify host factors that contribute to infection by the tickborne pathogen Rickettsia parkeri, and stumbled across a really exciting direct interaction between host and bacterium🦠. Check it out!
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Tomer Ullman @tomerullman.bsky.social · 03/11/2025
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
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The Onion @theonion.com · 31/10/2025
ICE Agent, 7-Year-Old Both Wearing Same ‘Military Commando’ Halloween Costume
ICE Agent, 7-Year-Old Both Wearing Same ‘Military Commando’ Halloween Costume
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Kevin M. Kruse @kevinmkruse.bsky.social · 29/10/2025
When I explain that boycotting an election over an issue has never once forced a politician to embrace that issue, I'm not "scolding people to vote." I'm explaining reality. Feel free to sit on your ass! Just don't pretend that your lazy apathy is somehow going to advance your agenda.
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City of Boston @boston.gov · 28/10/2025
Enjoy car-free small business shopping, music, games, bicycling, community tabling, and more in Jamaica Plain this weekend! 📍 : Centre Street from Lamartine St. to South St. in JP ⏰: This Sunday, November 2 from 10:30 a.m. to 3 p.m. More info: boston.gov/open-streets
An illustrated map of Jamaica Plain Open Streets on Centre Street from Lamartine St. to South St from 10:30 a.m. - 3 p.m.
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Larry Glickman @larryglickman.bsky.social · 19/10/2025
This is quite a hed/subhed. 1) Start with Vance. Use strong action verb. Accept the autocratic premise that the “Marines’ Might” are Vance’s to flex. 2) Mention the protest second and absurdly describe them as in the thousands 3) Treat Trump’s strong man use of the military as a partisan scuffle.
Vance Flexes the Marines’ Might as Thousand Protest Trump’s Agenda
VP JD Vance’s trips o a military base in California illustrated rising tensions between the federal government and Democratic leaders
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Julian Sanchez @normative.bsky.social · 16/10/2025
Remember, brown 13-year-olds are hardened menaces to society, but 30-something Republican Hitler afficionados in positions of power are just li’l guys.
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Addgene @addgene.bsky.social · 06/10/2025
New CRISPR libraries from the @johndoench.bsky.social and Root labs — Jacquere (human) and Julianna (mouse). A perfect pairing for your next screen. 🍷🧀 twp.ai/9PX2kT twp.ai/4irnYP
new at addgene
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Peter Sagal @petersagal.bsky.social · 28/09/2025
I have lived and worked in and around Chicago for 27 years and I have been assaulted less often than Sen Paul has been in his own back yard.
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The Tennessee Holler @thetnholler.bsky.social · 28/09/2025
79. American citizen.
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Kevin M. Kruse @kevinmkruse.bsky.social · 26/09/2025
I'm sorry, what?
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Jeremy Berg @jeremymberg.bsky.social · 22/09/2025
Now with comments... Lots of comments (A long thread) 1/n
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Mark Histed @markhisted.org · 22/09/2025
The New York Times piece today about US science is terrible and wrong—in many ways. I could write a whole article about this, but as one example: “To close observers, the original crisis began well before any of this…” No. I’m a close observer of science, and this is incorrect.
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Barack Obama @barackobama.bsky.social · 18/09/2025
After years of complaining about cancel culture, the current administration has taken it to a new and dangerous level by routinely threatening regulatory action against media companies unless they muzzle or fire reporters and commentators it doesn’t like.
yahoo.com
Let’s be clear about what happened to Jimmy Kimmel
Trump’s most brazen attack on free speech yet.
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Barred and Boujee aka Madiba Dennie @audrelawdamercy.blacksky.app · 16/09/2025
screencap from The Office where Michael Scott says 'I am a victim of a hate crime.' Stanley, exhausted, replies 'That's not what a hate crime is.' Michael then says 'Well, I hated it a lot, okay?'
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NBC10 Boston @nbcboston.com · 15/09/2025
After a co-host suggested that mentally ill homeless people who don't accept services offered to them should be jailed, Brian Kilmeade replied, "Or involuntary lethal injection, or something. Just kill 'em." on.nbcboston.com/JlG99ke
on.nbcboston.com
Fox News' Brian Kilmeade apologizes for saying mentally ill homeless people should be executed
Brian Kilmeade suggested to "just kill" mentally ill homeless people who don't accept services offered to them.
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Carl Zimmer @carlzimmer.com · 14/09/2025
A deep dive into the destruction of US cancer research by @jonathanmahler.bsky.social “It’s an absolutely unmitigated disaster,” a former top official at NIH told him. “It will take decades to recover from this, if we ever do.” Gift link: nyti.ms/48iH3Cr
nyti.ms
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Ben Kleinstiver @bkleinstiver.bsky.social · 12/09/2025
Optimization of a bespoke base editor to treat a severe pediatric vascular disease! 🫀🧬 Our manuscript describes: 1️⃣ Engineering a target-specific BE🧬 2⃣ A *must avoid* bystander edit that occurs with WT SpCas9 BEs! 🙅‍♂️ 3⃣ Extension of lifespan after in vivo editing! 🐁✅ www.nature.com/articles/s41...
nature.com
Treatment of a severe vascular disease using a bespoke CRISPR–Cas9 base editor in mice - Nature Biomedical Engineering
Engineering a mutant-specific customized base editor precisely corrects a mutation while minimizing bystander edits, leading to substantial phenotypic recovery in mouse models of multisystemic smooth ...
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John Doench @johndoench.bsky.social · 07/09/2025
Doomscrolling pause to chat CRISPR libraries! Preprint describes our new, data-driven approach to combine on-target and off-target predictions much more intelligently for *selecting* guides, which we use to develop our newest Cas9 knockout library, Jacquere. Thread: www.biorxiv.org/content/10.1...
biorxiv.org
Balancing off-target and on-target considerations for optimized Cas9 CRISPR knockout library design
The continued development of high-dimensional CRISPR screen readouts, such as single-cell RNA sequencing and high-content imaging, necessitates compact libraries to enable functional interrogation at ...
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Ben Rothenberg @benrothenberg.bsky.social · 06/09/2025
More news breaking at Bounces about Donald Trump's visit to the US Open men's final. The US Open has sent an email to broadcasters, obtained by Bounces, ordering them to censor any reactions or protests from the crowd to Trump's appearance. Read more here: www.benrothenberg.com/p/us-open-do...
benrothenberg.com
U.S. Open Orders Broadcasters to Censor Reactions to Trump
An email obtained by Bounces includes instructions from the U.S. Open on supporting Trump's planned stagecraft during the National Anthem.
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Governor JB Pritzker @govpritzker.illinois.gov · 06/09/2025
The President of the United States is threatening to go to war with an American city. This is not a joke. This is not normal. Donald Trump isn't a strongman, he's a scared man. Illinois won’t be intimidated by a wannabe dictator.
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Gabriel Bosslet @gbosslet.bsky.social · 05/09/2025
Lot of senators today expressing deep concern about the state of vaccine policy at HHS If only someone could do something about it It’s a real quandary
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The Tennessee Holler @thetnholler.bsky.social · 04/09/2025
SEN. CASSIDY (R) : “Do you agree Trump deserves the Nobel Prize for Operation Warp speed?” RFK JR.: “Absolutely.” SEN. CASSIDY: “But you just told Senator Bennet the COVID vaccine killed more people than COVID.” RFK JR.: “….”😬 🤷🏻‍♂️
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Universal Hub @universalhub.com · 04/09/2025
#Massachusetts authorizes pharmacies to give #Covid19 shots www.universalhub.com/2025/massach...
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Rob Reiner Fan @rob-reiner-fan.bsky.social · 01/09/2025
JFC, Atlantic Monthly. Michelle Obama wanted kids to eat healthy and exercise. She wasn't bent on destroying our federal health agencies.
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Science and Freedom Alliance - SAFA @safa-science.bsky.social · 02/09/2025
This is very good news. BUT, as we saw this year when NIH was operating under a flat budget, Trump and Russell Vought can effectively destroy NIH even if Congress holds the budget flat. To stop Vought and make sure NIH can function, Congress must go much further than “no cuts to budget.” 1/
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Emily Hahn, MD @ehahnmd.bsky.social · 31/08/2025
These are my patients. Kids dying of brain cancer. Kids and families desperate for treatment and hoping to find a cure through experimental therapies. Trump is dismantling science and children with brain tumor are the victims. www.nytimes.com/2025/08/28/w...
nytimes.com
Pediatric Brain Cancer Group to Lose Federal Funding
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Michael Clemens @mclem.org · 30/08/2025
The US Administration has decided to destroy a top network for clinical trials to test new treatments for children with brain cancer. This is another atrocity that will harm Conservative and Liberal Americans, long after the politicians responsible are gone.
nytimes.com
Pediatric Brain Cancer Group to Lose Federal Funding
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Dennis Goris | Cartoons @dennisgoris.bsky.social · 28/08/2025
I miss the old brand #CDC
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Karen Gregory @karengregory.bsky.social · 28/08/2025
Oregon Trail image with text "You have listened to RFK JR"
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