John Doench
@johndoench.bsky.social
Functional genomics @ Broad Institute. Screen all the things!
Pinned
John Doench
@johndoench.bsky.social
· Sep 7
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 ...
www.biorxiv.org
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...
Reposted by John Doench
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/
www.fpbase.org/spectra/
FPbase Fluorescence Spectra Viewer
An interactive fluorescence spectra viewer to evaluate the spectral properties of fluorescent proteins, organic dyes, filters, and detectors.
www.fpbase.org
November 4, 2025 at 3:03 PM
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/
www.fpbase.org/spectra/
Reposted by John Doench
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!
Host cyclophilin-mediated maturation of an obligate intracellular bacterial surface virulence factor https://www.biorxiv.org/content/10.1101/2025.10.28.684717v1
November 3, 2025 at 7:03 PM
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!
Reposted by John Doench
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:
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:
November 3, 2025 at 1:55 PM
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:
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:
Reposted by John Doench
ICE Agent, 7-Year-Old Both Wearing Same ‘Military Commando’ Halloween Costume
October 31, 2025 at 9:00 PM
ICE Agent, 7-Year-Old Both Wearing Same ‘Military Commando’ Halloween Costume
Reposted by John Doench
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.
Feel free to sit on your ass! Just don't pretend that your lazy apathy is somehow going to advance your agenda.
October 29, 2025 at 9:21 PM
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.
Feel free to sit on your ass! Just don't pretend that your lazy apathy is somehow going to advance your agenda.
Reposted by John Doench
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
📍 : 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
October 28, 2025 at 7:32 PM
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
📍 : 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
Reposted by John Doench
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.
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.
October 19, 2025 at 10:31 AM
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.
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.
Reposted by John Doench
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.
October 15, 2025 at 11:21 PM
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.
Reposted by John Doench
New CRISPR libraries from the @johndoench.bsky.social and Root labs — Jacquere (human) and Julianna (mouse).
A perfect pairing for your next screen. 🍷🧀
https://twp.ai/9PX2kT
https://twp.ai/4irnYP
A perfect pairing for your next screen. 🍷🧀
https://twp.ai/9PX2kT
https://twp.ai/4irnYP
October 6, 2025 at 1:30 PM
New CRISPR libraries from the @johndoench.bsky.social and Root labs — Jacquere (human) and Julianna (mouse).
A perfect pairing for your next screen. 🍷🧀
https://twp.ai/9PX2kT
https://twp.ai/4irnYP
A perfect pairing for your next screen. 🍷🧀
https://twp.ai/9PX2kT
https://twp.ai/4irnYP
Reposted by John Doench
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.
September 28, 2025 at 8:26 PM
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.
Reposted by John Doench
79. American citizen.
September 28, 2025 at 5:07 PM
79. American citizen.
Reposted by John Doench
I'm sorry, what?
Breaking news from Des Moines: ICE has detained Dr. Ian Roberts, the superintendent of Iowa's largest school district.
The Des Moines Public Schools said "We have no confirmed information as to why Dr. Roberts is being detained or the next potential steps."
www.bleedingheartland.com/2025/09/26/i...
The Des Moines Public Schools said "We have no confirmed information as to why Dr. Roberts is being detained or the next potential steps."
www.bleedingheartland.com/2025/09/26/i...
ICE detains Des Moines Superintendent Dr. Ian Roberts
Iowa's largest school district had "no confirmed information" on why ICE detained Dr. Ian Roberts, the superintendent since 2023.
www.bleedingheartland.com
September 26, 2025 at 7:11 PM
I'm sorry, what?
Reposted by John Doench
Now with comments... Lots of comments
(A long thread)
1/n
(A long thread)
1/n
September 22, 2025 at 3:30 PM
Now with comments... Lots of comments
(A long thread)
1/n
(A long thread)
1/n
Reposted by John Doench
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.
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.
September 22, 2025 at 12:20 PM
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.
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.
Reposted by John Doench
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.
Let’s be clear about what happened to Jimmy Kimmel
Trump’s most brazen attack on free speech yet.
www.yahoo.com
September 18, 2025 at 2:10 PM
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.
Reposted by John Doench
Reposted by John Doench
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
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.
on.nbcboston.com
September 15, 2025 at 10:50 PM
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
Reposted by John Doench
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
September 14, 2025 at 2:44 PM
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
Reposted by John Doench
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...
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...
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 ...
www.nature.com
September 12, 2025 at 2:00 AM
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...
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...
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...
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 ...
www.biorxiv.org
September 7, 2025 at 5:02 PM
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...
Reposted by John Doench
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...
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...
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.
www.benrothenberg.com
September 6, 2025 at 6:01 PM
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...
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...
Reposted by John Doench
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.
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.
September 6, 2025 at 4:37 PM
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.
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.
Reposted by John Doench
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
If only someone could do something about it
It’s a real quandary
September 4, 2025 at 11:13 PM
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
If only someone could do something about it
It’s a real quandary
Reposted by John Doench
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.: “….”😬 🤷🏻♂️
RFK JR.: “Absolutely.”
SEN. CASSIDY: “But you just told Senator Bennet the COVID vaccine killed more people than COVID.”
RFK JR.: “….”😬 🤷🏻♂️
September 4, 2025 at 3:27 PM
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.: “….”😬 🤷🏻♂️
RFK JR.: “Absolutely.”
SEN. CASSIDY: “But you just told Senator Bennet the COVID vaccine killed more people than COVID.”
RFK JR.: “….”😬 🤷🏻♂️
Reposted by John Doench
September 4, 2025 at 12:04 AM