Justin English

Nobel laureate: I owe America my success. Today, its scientific future is in danger | CNN Dr. Ardem Patapoutian says he watches “with deep sadness as the United States’ remarkable scientific enterprise, which took generations of hard work and national investment to build, faces a concerted...

Published an op-ed for @cnn.com: “Nobel laureate: I owe America my success. Today, its scientific future is in danger.”
A personal reflection on what’s at stake as science funding gets slashed. I’d be grateful if you could amplify both in and beyond the science world.
www.cnn.com/2025/04/09/h...

A multi-institutional investigation of psilocybin's effects on mouse behavior Studies reporting novel therapeutic effects of psychedelic drugs are rapidly emerging. However, the reproducibility and reliability of these findings could remain uncertain for years. Here, we impleme...

A much-needed joint effort from five labs to see which behavioral effects of psilocybin in mice are reliable, and which may be spurious 🐁🍄

@theborislab.bsky.social @mazenkheirbek.bsky.social @indigenerd.bsky.social Vikaas Sohal and Stephan Lammel 👏

www.biorxiv.org/content/10.1...

Yeah, this was a real headache, and was the impetus for writing the pairwise program. Alignment success rates also varied based on chemistry (see v9 vs. v10 in supplement). Maybe because some of our reads were shorter than medaka was intended for?

DOGE cuts shut down San Diego County’s wastewater testing system Other alternatives are available, but none show coronavirus subtypes like San Diego’s SEARCH

Very thankful to @sandiegouniontribune.com for covering the termination of our wastewater surveillance in San Diego.

If we don't want to lose sight of infectious diseases in our community, we need new funding - please reach out: searchcovid.info

www.sandiegouniontribune.com/2025/04/07/d...

We are satisfied with the results and will use this pipeline until such a time that 100% accurate single molecule Nanopore is achieved. We are now using this in many of our synthetic biology pipelines -- directed evolution, MPRAs, DMS libraries. Hit me up with questions or for help.

Grab serum from virally infected (here, COVID) patients to map and monitor single molecule quasi-species distributions of the circulating genomes (would suggest deeper than MinIon reads, we repeat sample preparation multiple times. GridIon probably best).

Accurately quantify edit distributions from CRISPR/Cas9 genome KO pools.

So what can you do with something like this?

QC your viral preps to detect random-break packaging issues not observable in Illumina sequencing.

GitHub - JGEnglishLab/ConSeqUMI: Bioinformatics software package for increasing the accuracy of nanopore sequencing data. Bioinformatics software package for increasing the accuracy of nanopore sequencing data. - JGEnglishLab/ConSeqUMI

We develop:
1. Bootstrap algorithm to benchmark # of clusters needed to give accurate sequences on a per run basis.
2. Our own aligner to overcome tandem repeat issues
3. A Docker-based GUI wrapper for the program.

Get it here:
github.com/JGEnglishLab...

Issue #3, Origin of Mismatches. We see rare mutations in our sequences. Are they real? Yes, we develop a method to PCR the samples directly and confirm by Sanger. Where are they from, bacterial passaging or PCR? Ran LTE of bacteria and repeated PCR -- both contribute, PCR orders of magnitude more.

Issue #2, Abundance Reproducibility. Is the content of a sample accurately reproduced in the data output? We mixed plasmids of known sequence together in a logarithmic range of concentrations and repeatedly measured the sample demonstrating reproducible, accurate readout of abundances.

Issue #1, Chimeric Molecules. Inevitable oligo contamination between tagging and amplification rounds creates hybrid pairs. How to accurately discard them computationally? Using a deep barcoded template as an internal barcode we observed chimera formation patterns and programmed to filter them out.

This work was led by Adam Zahm and Caleb Cranney in our group. There are lots of unique molecular index (UMI) strategies out there, but both the software packages and ground-truth sequence accuracy validations were severely lacking. So we decided to tackle this problem and deliver a unified solution

Want to Nanopore sequence complex nucleotide populations accurately, at low cost, with QC standards, using a plug-and-play informatics GUI, where you can PCR observed sequences out from your sample and not synthesize them? See our new pre-print!

www.biorxiv.org/content/10.1...

I’m Trying a Wild Experimental Diet Where I Restrict My Working Hours to Certain Times of the Day I never thought I’d follow a dieting fad. I always prided myself on being the type of laid-back person who worked as much as I wanted, whenever I w...

"Within a week, I was already experiencing the benefits of intermittent working. My bloodshot eyes faded from red to dark pink, and my back hunch started to unfurl. I found myself forming new thoughts that had nothing to do with performing wage labor."

Exclusive | Ousted Vaccine Chief Says RFK Jr.’s Team Sought Data to Justify Anti-Science Stance Peter Marks says the new health secretary’s team wants to show vaccines aren’t safe while promoting dangerous and unproven treatments.

More from Peter Marks on RFK Jr and the FDA
This extends beyond anti-vax to unproven use of stem cells
Gift link
www.wsj.com/health/healt...

The Humanities as Canary: Understanding this Crisis Now - The Scholarly Kitchen The Humanities have always been the canary in the coal mine of the full knowledge industry. What information can help us understand this crisis and its implications?

"It has come for science because it was never just about the Humanities, but about how we assess American progress through infrastructures of new knowledge and its application." scholarlykitchen.sspnet.org/2025/04/02/t...

GPCR allosterism, a popular #ASPET2025 session chaired by @laurenslosky.bsky.social & Laura Wingler.

Encrypted Messaging Is Essential—But It Isn’t Magic As recent events have shown, using an encrypted messaging app like WhatsApp or Signal is no privacy panacea.

Signal is a great privacy tool, but it isn’t magic. And even if you’re not discussing war plans in your group chat, it’s a good idea to know the limits of encryption.

Read our piece on what Signal can—and can’t—do for you here: www.wired.com/story/encryp...

Review: Ripoll, von Zastrow and @emilyblythe.bsky.social discuss the evolving understanding of cellular #GPCR signaling, highlighting recent advances and noting caveats and open questions. rupress.org/jcb/article/...

#CellSignaling #Physiology

That’s right, I’m the worst kind of super villain in this country… I’m a *checks notes* NIH trainee 😂

so you're saying American financial policy decisions should be made to appease and court our least responsible voters? Or that we should pump and dump them like our current President and make them poorer?

The job of Democrats is so clear right now: It's to do everything possible in the next 48 hours to keep the Atlantic story front-burner and make people understand the issues and the stakes. It couldn't be a simpler test of who gets it and who doesn't.

Fast & Fair peer review: a pilot study demonstrating feasibility of rapid, high-quality peer review in a biology journal Traditional peer review is slow, often delayed by the time-consuming process of identifying reviewers and lengthy review turnaround times. This study tests the feasibility of the Fast & Fair peer revi...

New preprint, very proud of this one www.biorxiv.org/content/10.1...

"GOP warms to idea children should live" just to keep it wholesome.

In another instance, the Social Security Administration briefly ended a contract that had allowed parents of newborn babies in Maine to sign their children up for a Social Security number at the hospital, instead requiring them to do so in person at an office. Mr. Dudek said he had ordered the move after watching Janet Mills, Maine’s Democratic governor, clash with Mr. Trump at the White House. He quickly reversed that decision, as well as another to end electronic death reporting in the state.

Holy shit: the weirdo running Social Security added administrative burdens to service delivery in Maine after its Governor disagreed with Trump over trans athletes. The idea that public services should be provided consistently and honestly seems beyond them.
www.nytimes.com/2025/03/24/u...

The Chaos of NIH Cuts Has Left Early-Career Scientists Scrambling As graduate programs lose spots and labs face shutdowns following Trump administration cuts to science funding, the path to a science career for students and researchers just got a whole lot harder.

This is what breaks my heart. These young people who are so eager and full of promise and who are the next generation of Nobel Prize winners, scientists inventors, teachers. #Trump and #Musk have destroyed it all. www.wired.com/story/the-ch...

The publicly tweeted flights, a state secret. War plans, shared by text!

The “state secrets” doctrine applies to things that are generally more sensitive than *classified* information. And here, the government hasn’t alleged any of this is classified. In fact, it involves conduct that the government itself splashed across the media in an orchestrated PR campaign!

Pm Private GIF ALT: Pm Private GIF

I would like to nominate Maxwell Smart for national security advisor.