Jess Smith

Jess Smith

@nanojess.io

I do bioinformatics stuff with @fulcrumgenomics.com. I do garden stuff at home in Somerville, MA.

146 followers428 following97 posts

Pinned

Jess Smith
@nanojess.io

Forget "geriatric millennial," I'll be introducing my generational status as the last person to be trained in mouth pipetting

Jeff Gentry@geoffjentry.bsky.social

I do recall seeing "Don't pipette with your mouth" in my onboarding training at one of the hospitals I worked at. So I at least know that much.

Jess Smith
@nanojess.io

Interesting biology and also the kind of study where you want to DOUBLE TRIPLE SUPER CHECK your methods because this is the sort of thing that could easily be an artifact. I think they did a good job in this paper, but similar studies beware!

European Virus Bioinformatics Center@evbc.bsky.social

Herpesvirus mRNAs consistently carry longer poly(A) tails than host and other virus transcripts, suggesting a widespread strategy that may enhance virus gene expression 🧬🦠 #Herpesvirus #RNA #MolecularVirology 📄 https://doi.org/10.1371/journal.ppat.1014341 👤 EVBC member: Daniel Depledge

doi.orgExtended poly(A) tails are a shared feature of herpesvirus mRNAsAuthor summary Poly(A) tails are found on almost all cellular mRNAs and many viral mRNAs, serving as binding platforms for proteins that enhance translation and regulate mRNA stability. In this study, we used a new RNA sequencing approach, nanopore direct RNA sequencing, that allows us to measure poly(A) tails on individual mRNAs during infections by herpesviruses and other DNA and RNA viruses. We found that herpesvirus mRNAs consistently possess longer poly(A) tails than both host and other viral mRNAs, suggesting a widespread and previously unrecognized strategy to enhance viral gene expression. By contrast, coronavirus and poxvirus mRNAs exhibit poly(A) tail lengths comparable to host mRNAs. While non-As are present within some herpesviral poly(A) tails, which could potentially slow poly(A) tail degradation, this “mixed tailing” occurs too infrequently to account for the broadly extended tails observed.
Jess Smith
@nanojess.io

Just going to put this here

Jamila Michener@povertyscholar.bsky.social

My research over the last several years has convinced me that organized tenants can transform our broken politics. But some folks don't yet discern the possibilities of tenant power. This piece offers insights on the real possibilities of power from the margins. www.marketplace.org/story/2026/0...

marketplace.orgWhy more tenants are forming unionsTenant unions are becoming more common across the country as tenants struggle to afford rent.
Jess Smith
@nanojess.io

Wind power seems fine. Cats on the other hand.......

Dr Paul Dorfman@drpauldorfman.bsky.social

Domestic cats kill at least 400 to 2,000 times more birds than wind turbines — between 100 and 200 million in Germany, to be exact. Wind farms pose a threat to only 0.05% of the total population of avians. www.bgr.com/2243676/wind...

bgr.comWind Turbines Cause Fewer Bird Deaths Each Year Than This Common Culprit - BGRCritics cite bird deaths as a major problem with wind power, but they often omit a comparison that changes the scale of the issue.
Jess Smith
@nanojess.io

Every time I read a paper like this I just think about what a PITA it's going to be to design off-target NGS assays that are suitable for regulatory review.

Nature Biotechnology@natbiotech.nature.com

Donor-complementary prime editing enables precise kilobase and library-compatible DNA insertions - @fudanuniversity.bsky.social www.nature.com/articles/s41...

nature.comDonor-complementary prime editing enables precise kilobase and library-compatible DNA insertions - Nature BiotechnologyModular, library-compatible DNA insertions are facilitated with complementary prime editing donors.
Jess Smith
@nanojess.io

Uhhhhhh

Science Magazine@science.org

A humanoid robot can perform aerial cartwheels on uneven ground and land smoothly, thanks to a new framework called BeyondMimic. Learn more in #ScienceRobotics: https://scim.ag/4gYIZ72

Jess Smith
@nanojess.io

This is fun to watch and it does make intuitive sense!

Matt Henderson@matthen.com

To tell if a maze is solvable, just hang it by its corners If it tears into pieces, you’ve found a solution

Jess Smith
@nanojess.io

> with AlphaFold3 performing best overall and for the third complementarity-determining region of the heavy chain I mean, that's the ball game, and we basically already knew this but it's always good to check! academic.oup.com/bioinformati...

academic.oup.comBenchmarking Antibody Modeling Tools across Structure Prediction, Docking, and Paratope–Epitope Interface AnalysisAbstractMotivation. Computational antibody engineering requires reliable prediction of antibody variable-fragment structures, antigen–antibody complexes, a
Jess Smith
@nanojess.io

> RNA-targeting CRISPR systems are commonly evaluated by RT-qPCR, but guide RNA binding can confound these measurements. We show that crRNA alone produces apparent knockdown without reducing target RNA abundance, whereas RNA sequencing remains unbiased...

bioRxiv Genomics@biorxiv-genomic.bsky.social

Guide RNA binding induces reverse transcription bias during RT-qPCR analysis of RNA-targeting CRISPR/Cas systems https://www.biorxiv.org/content/10.64898/2026.08.16.745121v1

Jess Smith
@nanojess.io

> We don’t know how to clean this stuff up and categorize it for real ML/AI, and honestly, we don’t even know if it can be.

Jess Smith reposted

Admirable Women
@admirablewomen.bsky.social

Computer scientist Margaret Hamilton coined the term “software engineer.” She directed the Software Engineering Division at MIT’s Instrumentation Lab & led development of the on-board flight software for NASA’s Apollo Guidance Computer. She was born #OTD in 1936 & turns 90 today! #WomenInSTEM

Jess Smith
@nanojess.io

👀

Albert Vilella, PhD.@albertvilella.bsky.social

I had firsthand exposure to the data coming out of Epinoma's EpiAmp technology, which can amplify cfDNA molecules whilst preserving the 5mC methylation marks, and wrote a post with the findings and what it means for Early Cancer detection assays. albertvilella.substack.com/p/methylatio...

albertvilella.substack.comMethylation liquid biopsy reaches a new level of sensitivity with Epinoma's EpiAmp technologyOvercoming the limitations of blood-based cfDNA Liquid Biopsy with EpiAmp
Jess Smith
@nanojess.io

What? What does this even mean! I have mad respect for plant people - so much more complicated than mammals

Jeff Groh@jeffgroh.bsky.social

Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...

pnas.orgBalanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNASIn avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...
Jess Smith
@nanojess.io

BUT HOW DO I PICK

Tom & Lorenzo@tomandlorenzo.bsky.social

People on Bluesky sigh and talk about The Discourse as if it were something required of them instead of something they opt to partake in, day in and day out. You really don't have to. Post about your favorite cheese

Jess Smith
@nanojess.io

Good news! It's important to sometimes read the good news and be happy

Nicolas Fulghum@nicolasfulghum.bsky.social

NEW | California just reached a world-first solar milestone Over HALF (51%) of electricity generation across the whole month of May came from solar power. Battery storage is the big difference maker, enabling California to push the share of solar generation to this level.

Jess Smith reposted

Lyndie Chiou
@lyndie.bsky.social

I interviewed 99-year old Joan Birman who must be the oldest author on a major breakthrough paper. As an added bonus: her team beat the guys trying to use AI! Please read and share about this human triumph: www.scientificamerican.com/article/how-... #science #math 👩‍🔬

scientificamerican.comHow a 99-year-old mathematician unraveled a century-old braid mysteryJoan Birman popularized the Burau representation problem decades ago. Now she and two colleagues have a proof that reveals brand new insights into the geometry of braids
Jess Smith
@nanojess.io

We definitely need to be able to measure LLM performance, but that will inevitably cause some "teaching to the test." I'm not sure how big of a problem this is though? Clearly the technology continues to improve, at least in my hands. dylancastillo.co/posts/pelica...

dylancastillo.coAre AI labs pelicanmaxxing? – Dylan CastilloI generated 1,000+ SVGs across 7 frontier models to test whether AI labs are training on Simon Willison’s pelican-riding-a-bicycle benchmark.
Jess Smith
@nanojess.io

Damn, this is how I learn the Earth's core is waaaayyyyyy hotter than I thought. What's going on in there?

Science Magazine@science.org

Earth’s core may be as much as 1000°C cooler than previously thought, according to a new technique for measuring the temperature of molten iron under extreme pressures. Learn more: https://scim.ag/4yIOLkf