Justin English
@justingenglish.bsky.social
Scientist in love with molecular biology, pharmacology, evolution, and technology of all kinds.
Cornell 🎓, UNC CH 🥼, University of Utah 💼
Cornell 🎓, UNC CH 🥼, University of Utah 💼
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).
April 8, 2025 at 3:05 PM
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.
April 8, 2025 at 3:05 PM
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.
QC your viral preps to detect random-break packaging issues not observable in Illumina sequencing.
April 8, 2025 at 3:05 PM
So what can you do with something like this?
QC your viral preps to detect random-break packaging issues not observable in Illumina sequencing.
QC your viral preps to detect random-break packaging issues not observable in Illumina sequencing.
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.
April 8, 2025 at 3:05 PM
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.
April 8, 2025 at 3:05 PM
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.
April 8, 2025 at 3:05 PM
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.
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...
www.biorxiv.org/content/10.1...
April 8, 2025 at 3:05 PM
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...
www.biorxiv.org/content/10.1...
GPCR allosterism, a popular #ASPET2025 session chaired by @laurenslosky.bsky.social & Laura Wingler.
April 4, 2025 at 5:51 PM
GPCR allosterism, a popular #ASPET2025 session chaired by @laurenslosky.bsky.social & Laura Wingler.
An oldie but a goodie.
March 4, 2025 at 6:01 PM
An oldie but a goodie.
Well, that went about as well as expected.
March 3, 2025 at 8:22 PM
Well, that went about as well as expected.
I look at this certificate from my postdoctoral training everyday in my office and consider how to achieve it today.
February 28, 2025 at 6:51 PM
I look at this certificate from my postdoctoral training everyday in my office and consider how to achieve it today.
Not that illegality is stopping anyone right now, but I believe this text from 2024 would preclude just uh.. deciding indirects are different.
But in case it doesn't, I declare my tax rate is 2%
But in case it doesn't, I declare my tax rate is 2%
February 8, 2025 at 1:49 AM
Not that illegality is stopping anyone right now, but I believe this text from 2024 would preclude just uh.. deciding indirects are different.
But in case it doesn't, I declare my tax rate is 2%
But in case it doesn't, I declare my tax rate is 2%
Samgyetang for Christmas Eve dinner! First time makin' it, came out well.
December 25, 2024 at 12:50 AM
Samgyetang for Christmas Eve dinner! First time makin' it, came out well.
Some awesome science goin' on inside here I bet!
@drannecarpenter.bsky.social
@drannecarpenter.bsky.social
January 20, 2024 at 7:05 PM
Some awesome science goin' on inside here I bet!
@drannecarpenter.bsky.social
@drannecarpenter.bsky.social
Followed some great Chinese recipes yesterday and enjoyed them.
November 23, 2023 at 10:27 PM
Followed some great Chinese recipes yesterday and enjoyed them.
Lord of the Rings and cheese boards, my favorite Thanksgiving traditions!
November 23, 2023 at 8:15 PM
Lord of the Rings and cheese boards, my favorite Thanksgiving traditions!
The lettering for the introductory credits of "The Addams Family" is outstanding.
October 28, 2023 at 11:55 PM
The lettering for the introductory credits of "The Addams Family" is outstanding.
Nice fall wander about today. Great dynamic lighting from the clouds made for some good shots.
October 2, 2023 at 2:13 AM
Nice fall wander about today. Great dynamic lighting from the clouds made for some good shots.
rescue hounds are special creatures.
September 25, 2023 at 2:20 AM
rescue hounds are special creatures.
Just Roman Empire things.
September 13, 2023 at 2:11 AM
Just Roman Empire things.
Peter says "Hi."
September 9, 2023 at 3:30 AM
Peter says "Hi."
I woke up today to announcements of an election in Utah. Perplexed, I went to see why I hadn't received a ballot. People in my city were voting. I looked up the district..
Ah, I see. Gerrymandering.
Ah, I see. Gerrymandering.
September 5, 2023 at 2:51 PM
I woke up today to announcements of an election in Utah. Perplexed, I went to see why I hadn't received a ballot. People in my city were voting. I looked up the district..
Ah, I see. Gerrymandering.
Ah, I see. Gerrymandering.
Excited for our upcoming PostDoc Rising Stars event this month!
September 5, 2023 at 2:35 PM
Excited for our upcoming PostDoc Rising Stars event this month!