John Doench @johndoench.bsky.social · 18/09/2026She was the editor for my first paper. Definitely a force. 030
John Doench @johndoench.bsky.social · 06/07/2026New preprint from the group, comparing CRISPRko and CRISPRi via a Perturb-seq readout: www.biorxiv.org/content/10.6...biorxiv.orgDirect comparison of CRISPR knockout and interference with Perturb-seqCRISPR 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 ... 14117
Reposted by John DoenchThe Onion @theonion.com · 03/04/2026Pete Hegseth Replaces Top General With Horse That Drinks Beer theonion.com/pete-hegseth-replaces-… 1105102838
Reposted by John Doenchandy™ @andylevy.net · 03/04/2026you, a naive fool: i do believe there are some things the nytimes won’t both sides the nytimes: 134135453108
Reposted by John DoenchRob DenBleyker @robdenbleyker.com · 27/03/2026looking good Mr President 121219250
Reposted by John DoenchColette Delawalla, PhD @cdelawalla.bsky.social · 16/03/2026Breast 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.comSusie Wiles, Trump’s White House Chief of Staff, Has Breast Cancer 23456502554
John Doench @johndoench.bsky.social · 15/03/2026I 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.orgNitrogen, Ammonia, and the Strait of Hormuz 142
Reposted by John DoenchKevin M. Kruse @kevinmkruse.bsky.social · 14/03/2026They 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. 34088054754
Reposted by John DoenchNews Eye @newseye.bsky.social · 03/03/2026Holy 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 1632896810
Reposted by John DoenchThe Red Terra @theredterra.bsky.social · 16/02/2026I’ve been to Busytown. I’ve seen these things in action. 0243
Reposted by John DoenchBen Collins @bencollins.bsky.social · 16/02/2026Incredible. We got to "Is a pedophile island really all that bad?" five times faster than I thought. 27878451676
John Doench @johndoench.bsky.social · 12/02/2026On the unintentional comedy scale, this was 10 of 10 for me. 4164
Reposted by John DoenchPareto Optimizer @paretooptimizer.bsky.social · 27/01/2026This 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. 2762080
John Doench @johndoench.bsky.social · 23/01/2026Gonna be a while until I can bike to work again... grr... 120
Reposted by John DoenchBen Collins @bencollins.bsky.social · 15/01/2026He really is doing all of it. 14864251967
Reposted by John DoenchNessa Carson @supersciencegrl.co.uk · 30/12/2025Nothing prepares you for how rapidly you accelerate between these three states #chemchat 415327
Reposted by John Doenchc0nc0rdance @c0nc0rdance.bsky.social · 22/12/2025Mary and Joseph praying over Jesus in the manger, or TWO T. REXES FIGHTING OVER A TABLE SAW? Once seen, cannot be unseen. 15413123
Reposted by John DoenchScience in Boston @scienceinboston.com · 03/12/2025Drs. 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 042
Reposted by John DoenchNY Times Pitchbot @nytpitchbot.bsky.social · 22/11/2025Magnolia'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. 1029717
Reposted by John DoenchAddgene @addgene.bsky.social · 20/11/2025Thank the @johndoench.bsky.social and Root labs for depositing these deliciously named libraries, and check out our blog post for more:twp.aiblog.addgene.orgA Tour of Addgene's Most Popular Pooled Libraries 082
Reposted by John DoenchFPbase @fpbase.org · 04/11/2025The 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.orgFPbase Fluorescence Spectra ViewerAn interactive fluorescence spectra viewer to evaluate the spectral properties of fluorescent proteins, organic dyes, filters, and detectors. 511336
Reposted by John DoenchBrandon Sit @sitbrandon.bsky.social · 03/11/2025First 🟦 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! 1145
Reposted by John DoenchTomer Ullman @tomerullman.bsky.social · 03/11/2025Nature 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: 35869252
Reposted by John DoenchThe Onion @theonion.com · 31/10/2025ICE Agent, 7-Year-Old Both Wearing Same ‘Military Commando’ Halloween Costume 307124172705
Reposted by John DoenchKevin M. Kruse @kevinmkruse.bsky.social · 29/10/2025When 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. 28968611285
Reposted by John DoenchCity of Boston @boston.gov · 28/10/2025Enjoy 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 12414
Reposted by John DoenchLarry Glickman @larryglickman.bsky.social · 19/10/2025This 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. 893011792
Reposted by John DoenchJulian Sanchez @normative.bsky.social · 16/10/2025Remember, brown 13-year-olds are hardened menaces to society, but 30-something Republican Hitler afficionados in positions of power are just li’l guys. 1437731093
Reposted by John DoenchAddgene @addgene.bsky.social · 06/10/2025New 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 045
Reposted by John DoenchPeter Sagal @petersagal.bsky.social · 28/09/2025I 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. 338120942652
Reposted by John DoenchThe Tennessee Holler @thetnholler.bsky.social · 28/09/202579. American citizen. 19442367511580
Reposted by John DoenchKevin M. Kruse @kevinmkruse.bsky.social · 26/09/2025I'm sorry, what? 871995614
Reposted by John DoenchJeremy Berg @jeremymberg.bsky.social · 22/09/2025Now with comments... Lots of comments (A long thread) 1/n 38836
Reposted by John DoenchMark Histed @markhisted.org · 22/09/2025The 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. 24907223
John Doench @johndoench.bsky.social · 20/09/2025this is the exact first thing that popped into my head as well :) 010
Reposted by John DoenchBarack Obama @barackobama.bsky.social · 18/09/2025After 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.comLet’s be clear about what happened to Jimmy KimmelTrump’s most brazen attack on free speech yet. 19826136619519
Reposted by John DoenchBarred and Boujee aka Madiba Dennie @audrelawdamercy.blacksky.app · 16/09/2025 441618303
Reposted by John DoenchNBC10 Boston @nbcboston.com · 15/09/2025After 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/JlG99keon.nbcboston.comFox News' Brian Kilmeade apologizes for saying mentally ill homeless people should be executedBrian Kilmeade suggested to "just kill" mentally ill homeless people who don't accept services offered to them. 141
Reposted by John DoenchCarl Zimmer @carlzimmer.com · 14/09/2025A 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/48iH3Crnyti.ms 12392219
Reposted by John DoenchBen Kleinstiver @bkleinstiver.bsky.social · 12/09/2025Optimization 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.comTreatment of a severe vascular disease using a bespoke CRISPR–Cas9 base editor in mice - Nature Biomedical EngineeringEngineering 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 ... 4378
John Doench @johndoench.bsky.social · 08/09/2025Hmm, not sure how to achieve (1) without just not targeting genes in those region of the genome that are prone to low-level chromosomal loss. In other words, seems unlikely that *some* successful guides targeting gene X would lead to this while others would not, right? 000
John Doench @johndoench.bsky.social · 07/09/2025Yup, chromatin can inhibit Cas protein access. But when a gene is transcribed, or DNA is replicated, chromatin is removed, so Cas proteins have a chance to find their target site. And, if your gene of interest is never accessible (on) in a cell model, no particular reason to need to knock it out! 010
John Doench @johndoench.bsky.social · 07/09/2025Best for last, the project was led by the incomparable Laura Drepanos, a computationalist in GPP (who, fun fact, will be applying to grad school this fall). I've not seen a more methodical and comprehensive analysis, or read a better first-draft of a manuscript. I ❤️ this paper. Happy screening! 120
John Doench @johndoench.bsky.social · 07/09/2025A more points to wrap things up: • We also provide the designs for a new mouse library, Julianna • This new guide selection screen is implemented in CRISPick for Cas9 knockout (off-target for CRISPRi is a another story, stay tuned!) • Libraries are on their way to @addgene.bsky.social 220
John Doench @johndoench.bsky.social · 07/09/2025We conclude with a comparison of analysis methods, including a cautionary tale of false positives arising from the use of MAGeCK RRA. We provide suggestions to "mitigate the reporting of false discoveries that, if left unchecked, would undermine confidence in large-scale perturbational screens." 100
John Doench @johndoench.bsky.social · 07/09/2025We next screened this library and assessed performance via separation of essential and non-essential genes - we see much greater depletion of the former while the distribution of the latter barely budges. So we accomplished our goal: smarter picking of guides increased on-target activity. 100
John Doench @johndoench.bsky.social · 07/09/2025Essentially, by worrying less about off-target activity (because we actually do a pretty good job of predicting it) we're able to design a library with a *much* higher distribution of on-target scores, as assessed by Rule Set 3. 100
John Doench @johndoench.bsky.social · 07/09/2025A lot of details I won't cover here, but essentially we filter out all guides with a CRISPick Aggregate CFD score > 4.8 and then select the 3 guides with the best Rule Set 3 score. This new picking scheme leads to a substantial difference between Jacquere and our prior Brunello+Gattinara libraries 100
