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Jess Smith

@nanojess.io
135 followers 427 following 96 posts

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

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Jess Smith @nanojess.io · 11/09/2026
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!
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Jess Smith @nanojess.io · 11/09/2026
Just going to put this here
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Reposted by Jess Smith
Chanda Prescod-Weinstein 🌌 @chanda.blacksky.app · 01/09/2026
Three thoughts on this news item: 1. It's just one data point and not at a level of statistical significance for certainty. 2. Octavia Butler said count on the surprises, and this may turn out to be one of them! 3. Made possible by a global team using funding infrastructure that Trump is destroying.
sciencenews.org
Have scientists glimpsed the first dark matter particle?
Shadowy dark matter has eluded scientists for decades. The LZ experiment may have spotted one particle, called a WIMP, but more data is needed to check.
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Jess Smith @nanojess.io · 01/09/2026
This rules
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Jess Smith @nanojess.io · 31/08/2026
Wind power seems fine. Cats on the other hand.......
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Jess Smith @nanojess.io · 31/08/2026
This is intriguing. I also liked this quote: > There's a radical amount of divergence in the experiences, needs, and tooling of "software engineers". Sadly, it's easy to forget this, and end up in silly arguments. sketch.dev/blog/lightwe...
sketch.dev
A Lightweight Merge Queue using GitHub Actions
How to implement a simple merge queue using GitHub Actions
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Jess Smith @nanojess.io · 31/08/2026
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.
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Jess Smith @nanojess.io · 31/08/2026
Uhhhhhh
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Jess Smith @nanojess.io · 27/08/2026
This is fun to watch and it does make intuitive sense!
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Jess Smith @nanojess.io · 20/08/2026
> 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.com
Benchmarking Antibody Modeling Tools across Structure Prediction, Docking, and Paratope–Epitope Interface Analysis
AbstractMotivation. Computational antibody engineering requires reliable prediction of antibody variable-fragment structures, antigen–antibody complexes, a
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Jess Smith @nanojess.io · 20/08/2026
Damn, this is more dramatic that I would have expected! www.washingtonpost.com/climate-solu...
washingtonpost.com
Paris said au revoir to cars. Air pollution maps reveal a dramatic change.
Air pollution fell substantially as the city restricted car traffic and made way for parks and bike lanes.
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Jess Smith @nanojess.io · 20/08/2026
The headline is a little over-the-top, but this part is really worth considering: They typically cite no papers published between the mid-'90s and early 2020s at all...Why does this happen? Because GenAI models cannot get behind publishers’ firewalls... www.chronicle.com/article/ai-i...
chronicle.com
AI Is Ruining Scholarship
When we outsource literature review to algorithms, we lose entire sectors of knowledge.
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Jess Smith @nanojess.io · 19/08/2026
I'm looking, and I can't look away!
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Jess Smith @nanojess.io · 19/08/2026
We sure have been talking about these working for a while.... www.statnews.com/2026/08/19/m...
statnews.com
Moderna and Merck say mRNA cancer vaccine succeeded in late-stage melanoma trial
A personalized mRNA cancer vaccine succeeded in a late-stage melanoma study, results that could herald a new, powerful approach in oncology.
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Jess Smith @nanojess.io · 18/08/2026
Not my normal beat, but my friend wrote this interesting article about intra-party gerrymandering. Important to consider for those of us who live in deep-blue or deep-red cities/states. papers.ssrn.com/sol3/papers....
papers.ssrn.com
Intra-Partisan Gerrymandering
<div> <i>Partisan</i> gerrymandering is a familiar practice. But <i>intra-partisan</i> gerrymandering—one faction within a party designing districts to handica
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Jess Smith @nanojess.io · 18/08/2026
> 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...
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Jess Smith @nanojess.io · 17/08/2026
> But machine-learning your way to happiness with those numbers is very likely impossible, due to the huge numbers of variables in the assay conditions and indeed, in biological systems themselves. www.science.org/content/blog...
science.org
So How Is AI Drug Discovery Doing, Really?
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Reposted by Jess Smith
Admirable Women @admirablewomen.bsky.social · 17/08/2026
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
Two side-by-side black-and-white photographs of pioneering computer scientist Margaret Hamilton (born August 17, 1936). The left panel features a mature, close-up portrait where Hamilton gazes directly at the viewer with a serene, confident, and reflective expression, framed by her long, dark, slightly silvering hair. The right panel is a famous archival photograph showing a younger Hamilton standing indoors next to a towering stack of bound paper binders containing the Apollo Guidance Computer source code, which she led the development of at MIT. She is smiling broadly and wears a striped, long-sleeved mini dress with dark Mary Jane shoes and glasses, resting her hand proudly on top of the massive column of printed code. The overall composition contrasts her youthful triumph with her enduring legacy, capturing an optimistic, intellectually rigorous mood that highlights her monumental contributions to space exploration.
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Jess Smith @nanojess.io · 17/08/2026
👀
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Jess Smith @nanojess.io · 13/08/2026
This paper is over a year old but it's so cool. I love when people use DNA-mediated technology to get a more complete biological picture. www.nature.com/articles/s41...
nature.com
Quantifying metabolites using structure-switching aptamers coupled to DNA sequencing
Nature Biotechnology - Metabolites can be quantified using a combination of aptamers and DNA barcodes.
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Jess Smith @nanojess.io · 12/08/2026
Partial eclipse today, apparently!
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Reposted by Jess Smith
Alison Meynert @ameynert.bsky.social · 05/08/2026
DivRef is a resource for including common human variants and haplotypes in CRISPR off-target searches. I rebuilt the generation workflow to make its inputs, assumptions and population choices easier to inspect and change. blog.fulcrumgenomics.com/p/a-crispr-o...
blog.fulcrumgenomics.com
A CRISPR off-target search is only as good as the sequences it searches
Rebuilding DivRef so CRISPR off-target searches can account for human variation
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Jess Smith @nanojess.io · 03/08/2026
I've been using Typer more lately and I'm liking it. That's it! That's the post. Not every post can be 🔥🔥🔥🔥 typer.tiangolo.com
typer.tiangolo.com
Typer
Typer, build great CLIs. Easy to code. Based on Python type hints.
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Reposted by Jess Smith
Gravel Influencer @gravelinfluencer.bsky.social · 02/08/2026
Spotted in the bike shop parking lot
A bumper sticker that says, "No one is treading on you sweetie" with a silly looking Gadsden snake
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Jess Smith @nanojess.io · 02/08/2026
🫠
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Jess Smith @nanojess.io · 01/08/2026
We cannot let China bet us in button-having. I want buttons back!!
autobuzz.my
China says enough with touchscreens, mandates physical buttons from 2027
Whether you love or hate it, the trend of ultra-minimalist interior design in cars from China is now numbered. This shift comes as the Chinese government
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Jess Smith @nanojess.io · 31/07/2026
Rules 'n' gates blog.fsck.com/2026/04/07/r...
blog.fsck.com
Rules and Gates
I'm Jesse. I make stuff. Software, hardware. Very occasionally, trouble.
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Reposted by Jess Smith
Edd Coates | Game UI Database @eddcoates.bsky.social · 30/07/2026
LinkedIn added an "AI slop" button. The U-Turn is happening, expect to see a lot more of this from other tech companies.
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Jess Smith @nanojess.io · 30/07/2026
This is cool! I love techniques that can give us insight beyond identifying bases. Nucleic acids deserve better than their reduced representation
biorxiv.org
Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches
Progress has been made in identifying G-quadruplexes (G4s) and other non-canonical (non-B) DNA structures in live cells. However, these experiments have been limited by methodological constraints,…
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Jess Smith @nanojess.io · 30/07/2026
"There's no such thing as a free lunch"
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Jess Smith @nanojess.io · 29/07/2026
What? What does this even mean! I have mad respect for plant people - so much more complicated than mammals
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Jess Smith @nanojess.io · 29/07/2026
BUT HOW DO I PICK
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Jess Smith @nanojess.io · 29/07/2026
Haunting
science.org
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Jess Smith @nanojess.io · 28/07/2026
The rabbits ate it. They ate it all.
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Jess Smith @nanojess.io · 28/07/2026
This doesn't totally surprise me - US education system isn't great at training this kind of skilled labor
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Jess Smith @nanojess.io · 28/07/2026
More good news!
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Jess Smith @nanojess.io · 28/07/2026
Good news! It's important to sometimes read the good news and be happy
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Jess Smith @nanojess.io · 28/07/2026
Okay this is so cool. File under: yet another thing I pessimistically thought would never work
nature.com
Precise DNA base editing using AlphaFold3-based contact modelling - Nature
ContactSeek is an AlphaFold3-driven model that can improve the precision of genome-editing tools.
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Reposted by Jess Smith
Lyndie Chiou @lyndie.bsky.social · 24/07/2026
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.com
How a 99-year-old mathematician unraveled a century-old braid mystery
Joan 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
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Jess Smith @nanojess.io · 27/07/2026
I like this take because it implies I get to keep my job! > AI is an extraordinarily powerful accelerant whose value scales directly with the expertise brought to bear on it. It is a springboard, not a replacement. www.nature.com/articles/s41...
nature.com
Rethinking bioinformatics expertise in the era of artificial intelligence - npj Digital Medicine
npj Digital Medicine - Rethinking bioinformatics expertise in the era of artificial intelligence
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Reposted by Jess Smith
Universal Hub @universalhub.com · 27/07/2026
That magical time of year when the cones burst into full bloom www.universalhub.com/2026/magical... #Boston #Allston #CommAve
Three traffic cones, one in full bloom with yellow flowers
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Jess Smith @nanojess.io · 26/07/2026
You know, we could have just not had measles
wired.com
‘The Child Is Terrified’: Measles Doctors Speak Out
Hear from six pediatricians in measles hot spot Utah, as the US faces infection levels not seen in over three decades and prepares to lose its status as a country that eliminated the dangerous…
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Jess Smith @nanojess.io · 26/07/2026
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.co
Are AI labs pelicanmaxxing? – Dylan Castillo
I generated 1,000+ SVGs across 7 frontier models to test whether AI labs are training on Simon Willison’s pelican-riding-a-bicycle benchmark.
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Jess Smith @nanojess.io · 24/07/2026
Damn, this is how I learn the Earth's core is waaaayyyyyy hotter than I thought. What's going on in there?
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Jess Smith @nanojess.io · 24/07/2026
Me too!
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Jess Smith @nanojess.io · 24/07/2026
Good work, guys*! www.broadinstitute.org/news/low-cos... * guys in the gender-neutral way
broadinstitute.org
Low-cost genome sequencing approach is powering genetics research on mental illness and many other studies
The Blended Genome Exome approach delivers high-quality, unbiased genetic data at a quarter of the cost of the leading sequencing method.
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Jess Smith @nanojess.io · 23/07/2026
This seems like it can't possibly be true! Six foot wide heart! My word
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Jess Smith @nanojess.io · 23/07/2026
Hard to argue with this, she's got receipts
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Jess Smith @nanojess.io · 23/07/2026
Watch out CEOs, the bots are coming for you, lol
overpaid.lol
OverpAId — Fire Your CEO. Hire The Future.
OverpAId is the AI Executive Platform that replaces your nine-figure leadership team with something that actually works. (Satire.)
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Jess Smith @nanojess.io · 23/07/2026
Turns out we need boring government agencies to do boring regulatory things or else bad, sometimes non-boring things happen
wired.com
Taylor Farms Spent Big on MAGA and Anti-Regulatory Lobbying Before Diarrhea Outbreak
The company donated more than $3.6 million to conservative groups between 2020 and 2025, including $1 million to the MAGA Inc. super PAC.
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