Every single regulatory grade monitor in the Chicago area is recording over 400 µg/m³ of PM2.5 smoke pollution. This is so far beyond anything in the historical record it’s difficult to communicate how extreme this event really is
Helena Reyes Gopar
@hamarillo.bsky.social
Researching human endogenous retroviruses using sc sequencing data 🏊🏼♀️ 👩🏻💻 🇲🇽 LCG UNAM alumna 🧬
"I first heard the term open science in the early 2000s, but it was really something many of us were doing well before that. When you work on methods, they're only really successful if someone else uses them” ---Steven Henikoff
I used a spaghetti and glue to represent this for a high school assignment once. Truly iconic.
Helen Branswell 🇨🇦@helenbranswell.bsky.social · last mo.Have you ever seen this iconic image of the Ebola virus, from the first known outbreak in DRC in 1976? An electron microscopic image, it was captured by #CDC 's Fred Murphy, a virological giant and a very kind interviewee. He died yesterday. He will be missed, but his scientific legacy lives on.
The MOSAIC paper is out in Nature Methods. For the record I went after this paper for *years* and was so happy when they sent it to me/us. www.nature.com/articles/s41...
A multimodal adaptive optical microscope for in vivo imaging from molecules to organisms - Nature Methods
MOSAIC is a versatile multimodal microscope that allows seamless transition between various light-sheet, two-photon, label-free and super-resolution modalities. It is demonstrated in various systems r...
nature.com
Reptiles with longer Wikipedia pages tend to be bigger. The relationship is a power law with exponent = 0.85. I guess humans really like writing about big lizards? The longest article is the Komodo Dragon.
Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇
The old internet still exists y'all neocities.org
Neocities
Create and surf awesome websites for free.
neocities.org
before the internet was a corporate hellscape it was built by ordinary people! the slop was wacky and homemade just like mom (and David) used to make. alas the good old days are over but I can't believe how lucky we are to have @archive.org to remember them :') web.archive.org/web/20080803...
Hello all, our lab is recruiting a PhD candidate to study how 3D genome folding impacts gene regulation in development. We're located at the Center for Integrative Genomics department of the University of Lausanne, Switzerland. Please email me if interested. #PhDPosition, #PhDOpportunity
This is great. I've given an example in class showing how priors can make some unidentified problems identifiable: a+b=6, solve for b. Prior: a=0~4
Dr Mircea Zloteanu 🌺🌞🍃@mzloteanu.bsky.social · 5mo ago#statstab #495 Unsure Calculator Thoughts: Nifty way to incorporate your uncertainty when making some calculations and decisions. #uncertainty #calculator #unsure #chance #sensitivity filiph.github.io/unsure/
There's been endless talk about an AI bubble, but less about exactly how, why, and how much it's a bubble. So I turned to the framework put forward by scholars Brent Goldfarb and David A. Kirsch, authors of "Bubbles and Crashes," for assessing tech bubbles. Spoiler: On a scale of 1 to 8, AI is an 8
AI Is the Bubble to Burst Them All
I talked to the scholars who literally wrote the book on tech bubbles—and applied their test.
wired.com
Why aren’t language models acting/interacting like a graph? (Or are they? Idk). It seems so obvious that while human conversations are iterative, they’re nonlinear and that’s how you get to the point/good stuff
The strongest argument I keep hearing for AI is that it makes many admin tasks and paperwork easy. This basically rephrases what many have been saying for decades - there is a vast and unnecessary administrative bloat mandated by “business best practice” that needs to vanish.
Yesterday I attended Harin’s excellent defense where he talked about this study, which is a great reason to give it another shoutout. Does population size affect the diversity of the music that people listen to? Really nice example how to make use of a DAG in practice!
Harin Lee@harinlee.info · last yr.Big cities are vibrant hubs of culture, but why exactly is that? Now out in @natcomms.nature.com, we analysed music listening patterns of over 2.5 million people and demographics to examine mechanisms driving cultural diversity. With @researchdeezer.bsky.social @norijacoby.bsky.social Highlights ⬇
Are housekeeping genes now the ones we see expressed in every single single-cell cell?
We just launched Foursquare Spatial Desktop – a geospatial analysis tool powered by embedded DuckDB and built on sqlrooms.org. Everything runs locally: your data stays on your machine, no cloud needed. A modern reimagining of Kepler.gl. Mac only for now. More coming. foursquare.com/products/spa...
A single-cell transposable element atlas of human cell identity
A single-cell transposable element atlas of human cell identity
Reyes-Gopar et al. introduce Stellarscope, a computational approach for quantifying locus-specific transposable element expression in single-cell RNA sequencing data. The authors profile human PBMCs and reveal transposable elements marking specific cell subtypes. Stellarscope is available as an open-source package and promises to enable continued study of “genomic dark matter.”
dlvr.it
Thrilled to share this work! I am honored to learn from @mlbendall.bsky.social and so grateful for his guidance and mentorship. Stellarscope is just the beginning! There is so much to learn about TEs and now we can all explore the uncharted territory of single cell retro-genomics 🧬🔭
matthew.bendall@mlbendall.bsky.social · last yr.🧵1/ Introducing Stellarscope: an EM-based tool for quantifying locus-specific transposable element expression in single cells. A single-cell transposable element atlas of human cell identity: Cell Reports Methods www.cell.com/cell-reports... @hamarillo.bsky.social #TEHub #singlecell #genomics
do you ever stare at the ceiling and think about how the worldwide scientific establishment did the impossible and created a COVID vaccine in under a year and the response of the general public has been to go on an unstoppable rampage to destroy science and scientists
I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms www.nature.com/articles/s41...
Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications
Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...
nature.com
Sad news: The dataset behind this famous chart on the decline in costs of genome sequencing has had its NIH funding cut. I loved this chart because it was the first that made me appreciate the impact of dataviz. But it also tracked progress towards an ambitious goal ($1000 genome) that succeeded.
![The "$1,000 genome" catchphrase was first publicly recorded in December 2001 at a scientific retreat to discuss the future of biomedical research following publication of the first draft of the Human Genome Project (HGP), convened by the National Human Genome Research Institute at Airlie House in Virginia.[5] The phrase neatly highlighted the chasm between the actual cost of the Human Genome Project, estimated at $2.7 billion over a decade, and the benchmark for routine, affordable personal genome sequencing.
On 2 October 2002, Craig Venter introduced the opening session of GSAC (The Genome Sequencing and Analysis Conference) at the Hynes Convention Center in Boston: "The Future of Sequencing: Advancing Towards the $1,000 Genome." Speakers included George M. Church and executives from 454 Life Sciences, Solexa, U.S. Genomics, VisiGen and Amersham plc.[6][7] In 2003, Venter announced that his foundation would earmark $500,000 for a breakthrough leading to the $1,000 genome.[8] That sum was subsequently rolled into the Archon X Prize.
In October 2004, NHGRI introduced the first in a series of '$1,000 Genome' grants designed to advance "the development of breakthrough technologies that will enable a human-sized genome to be sequenced for $1,000 or less."[9]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:73aicoale2mqwrap63rdzwep/bafkreigcypk33xduk2wsfjyvwbnfzzb76p5m6jl3owhbb3ft32clwov37i)
Thanks @lecteroide.bsky.social for the opportunity to share the efforts developed in MexOmics www.the-scientist.com/mexomics-map...
MexOMICs Maps the Genetic and Social Landscape of Disease in Mexico
By focusing on twins and patients with lupus and Parkinson’s disease, a Mexican consortium is generating critical data to understand health and disease in the country.
the-scientist.com
One old fish needed to sense its environment and now I have to floss every night (Isn’t evolution the coolest thing ever?! 👹🌀🧬🤗)
Neil Shubin@neilshubin.bsky.social · last yr.New paper from the lab: Our teeth arose as sensory organs on the outside of the body of ancient jawless fish.!! Congrats to Yara Haridy and the team! Background and video: phys.org/news/2025-05... Open Access Paper: www.nature.com/articles/s41... News and Views: www.nature.com/articles/d41...
I wonder if easy-to-remember memories that are accompanied by ‘negative’ strong emotion (i.e. the opposite of insight?) follow the same or a different pathway in the brain activity
Nature@nature.com · last yr.Neuroscientists have revealed which regions of the brain are active and how they interact when discovery strikes https://go.nature.com/4k7wpkd
Been horrifying teammates by referring to undocumented information that's held only in people's heads as "locked in meat storage". Please use this with your teams/projects and report back on how they like it?
