Nature Reviews Methods Primers: Uniform manifold approximation and projection (UMAP) www.nature.com/articles/s43... 🧬🖥️🧪 read free: rdcu.be/d0YZT

Can we rename it to the Wayne Gretzky Border Crossing?

Massively parallel characterization of transcriptional regulatory elements - Nature Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.

Published in today's issue! OPEN ACCESS article, FREE massive dataset, FREE code, FREE pre-trained AI/ML model. #OpenScience was a mountain of work to make this happen: check it out if you haven't already 😉

Can't wait to see Bradford get destroyed in the next election.

Can we look at ways to make the road network profitable? How about turning every road into a toll road for drivers?

1. Imagine we land a space probe on one of Jupiters’ moons, take up a sample of material, and find it is full of organic molecules. How can we tell whether those molecules are just randomly assembled goo or the outcome of some evolutionary process taking place there? 🧪

Shame on you, Stantec

Hey #BikeTO! @cycletoronto.bsky.social has launched a campaign shaming Stantec Consulting Ltd for being retained to do work associated with Doug Ford's bike lane removal efforts. Please sign & spread the word. #TOpoli #ONpoli #VoteFordOut www.cycleto.ca/shame_on_you...

I wanted to write briefly about a very pleasant experience we recently had coordinating and collaborating closely on competing publications with 2 other teams. 1/

As someone who has been working extensively with PyTorch Ledidi: this effort is noticed and very much appreciated. I hope to have the ability eventually to contribute improvements back to the community.

Some thoughts about what I am looking forward this year from my vantage point of computational molecular biology. One mega-trend for me; we will definitely see more AI methods of all sorts emerge.

This looks like a wonderful gift to start 2025 off right 🤗

If we could put cycling in a pill, it would be the blockbuster drug to end all blockbuster drugs. (I'm also surprised that the mortality improvements for pedestrians seem much smaller than for cyclists.)

A Scottish study of 83k individuals over 17 years found commuting by bike halves the risk of early death: bmjpublichealth.bmj.com/content/2/1/.... The one outlier hazard ratio for people on bikes casts a harsh light on the Ford government's quest to destroy safe infrastructure in Toronto. #BikeTO

EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication Precise control of gene expression is essential for cellular function, but the mechanisms by which enhancers communicate with promoters to coordinate this process are not fully understood. While seque...

Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale!
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation

DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...

(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430

What's gayer than spandex? #bicycling #PattieGonia

So excited for this! The fight will be waged on all fronts.

Support @cycletoronto:

www.cycleto.ca/donate?utm_c...

Premier Ford: Stay In Your Lane MPP / Député, Ottawa Centre

In response to last Monday's passing of Bill 212, @joelharden.bsky.social launched a new petition to repeal the legislation and "immediately stop the government’s attack against life-saving active transportation infrastructure." #BikeTO #ottbike #TOpoli #ONpoli www.joelhardenmpp.ca/stay_in_your...

This is going into my list of "word usage that will earn you five lashings," to be deployed when I found my own venture. Already on the list are "learnings" and "overindex."

GitHub - atongen/yolo: A git alias A git alias. Contribute to atongen/yolo development by creating an account on GitHub.

This led me to github.com/atongen/yolo, which seems magical. I expect my colleagues to be deeply appreciative when I integrate this into my workflow.

Thank you for hosting! Caroline's talk is super cool.

Yes -- I think this is just a temporary issue caused by their server infrastructure being overloaded. The developers have done an impressive job of scaling up with the massive influx of new users, so this will probably be resolved soon.

Dougie set back Ontario by ten years. Impressive that we have managed to keep re-electing our own Mini Trump.

Following the 2013 floods that destroyed parts of that system, I had to move the first few km of that trip to suburban roads. A couple months later, while riding that part, a driver hit me intentionally with his truck. I've been radicalized ever since.

I grew up in Calgary. I became passionate about cycling when I started commuting to U of C on a Raleigh Record I got for $15 on Craiglist. It was a 58 km round trip with only 500 m not on the pathway system, and significantly faster than Calgary Transit.

The rhetoric around "we're destroying cycling infrastructure so you can get home to your family faster" is a wonderful reminder that people on bikes don't have families, and that your life stops mattering as soon as you get on a bike.

A pair of graphs I think about a lot. On the topic of pooled CRISPR screens, the left is "replicate correlation" when simply examining the abundance of guide RNAs, i.e. log-normalized read counts. On the right is taking those same data and subtracting from a common starting point, i.e. pDNA.