iiinova — where your digital self keeps evolving

Reposted by Ryan Z Friedman, PhD

Maitreya Dunham @maitreya.bsky.social · 06/10/2026

Here's the ad for the Genome Sciences faculty positions ap.washington.edu/ahr/position...

ap.washington.edu

Position Details - Academic Personnel & Faculty

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Reposted by Ryan Z Friedman, PhD

Jay Shendure @jshendure.bsky.social · 30/07/2026

New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 30/06/2026

Syd’s work is so cool and has wowed me since the day I first saw it. Check out her amazing preprint!!!

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 12/06/2026

Hello! I am honored to say that I won a departmental Outstanding Service Award!

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 12/06/2026

Yes, that is me!! Thanks for the kind words Michael!

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 20/05/2026

Do you work at a public university? Does it offer retirement benefits to postdocs? Does it matter whether or not postdocs have a fellowship? Let me know!

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 20/02/2026

Thanks for putting into words what I’ve struggled to articulate cogently and convincingly. The struggle, the time it takes, the critical thinking required to identify gaps — that’s the point of the creative process. Too many folks treat the AI takeover as a forgone conclusion, when it’s clearly not

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Reposted by Ryan Z Friedman, PhD

Liz Haswell @ehaswell.bsky.social · 20/02/2026

New post on Unprofessoring. Is there really "No Other Choice" or are we giving in to "narratives of inevitability"? Thanks to a post by @docfreeride.bsky.social for the framing.

A stack of old books and the title "Narratives of AI inevitability"

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 19/02/2026

Are grad students students or trainees or employees or some yet-to-be-discovered word?

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 08/09/2025

I decided to try out blogging! My first post is a reflection of my time on science Twitter and why I decided to start blogging. I'm going to give Bluesky a second chance, but It's nice to have a space for casual long-form writing ryanzfriedman.com/2025/09/06/s...

ryanzfriedman.com

Reflections of an ex-Twitter user

I’ve had this website for almost 5 years. In that time, it’s been pretty bare-bones, primarily serving as a landing page for me to share my general scientific interests with the world. I built a blog ...

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 08/01/2025

I first had this idea 6.5 years ago, early on in grad school. This journey has been a long one. I couldn't have done it without the support and guidance from @genologos.bsky.social and Barak Cohen, our collaboration with @corbolab.bsky.social, or help with the modeling and analysis from my coauthors

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 08/01/2025

Our solution is to let your model guide you. By focusing on uncertain sequences and testing them functional genomic assays, you can *iteratively* train a model. We applied this to understand why the same DNA sequence motif has radically different effects in different contexts.

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 08/01/2025

My thesis work on active machine learning to model regulatory DNA is now out in Cell Systems! We answer the question: When you can synthesize any DNA sequence you want, how do you decide which ones are worth testing? www.sciencedirect.com/science/arti...

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Reposted by Ryan Z Friedman, PhD

Holden Thorp @holdenthorp.bsky.social · 26/04/2024

I posted an editorial yesterday on the need for neurodiversity in science where I also disclosed my own diagnosis as autistic. I also wrote a substack on my journey to the disclosure also in this thread. #actuallyautistic www.science.org/doi/10.1126/...

science.org

Science needs neurodiversity

All brains work differently. Individuals process information and engage with the world in ways that are influenced by a multitude of biological, cultural, and social factors. In the world of science, ...

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 20/02/2024

Many thanks to Yawei Wu, Lloyd Tripp, and Daniel Lyon for their help with these analyses! The manuscript itself is also restructured. Figs 2 and 4 are swapped, there's a 5th fig for the K562 analysis, and we reworked the Discussion. Apologies if threading isn't the way to go on Bsky. 🧬🔄 8/8

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 20/02/2024

We analyzed a second pair of sequences with similar motif content. The model correctly predicts that the RORB motif must be 3' of the CRX motif. These results show our model learns the context that distinguishes functionally non-equivalent motifs. 7/

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 20/02/2024

RORB motifs have a wide range of effects when mutated. Our model predicts this correctly & these effects are correlated with motif affinity. Along with our other results, this shows active learning generates the data needed to learn regulatory grammars. 6/

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 20/02/2024

We have a new result showing that our model accurately predicts when CRX motifs increase vs. decrease expression. This is crucial because nc variants can change activity in unexpected directions, so it's important to have data that can tell when a motif has a positive vs negative effect. 5/

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 20/02/2024

Our experiments suggest that inactive sequences are low-information training examples. This is important because large libraries derived from random DNA are mostly inactive seqs. We think iteratively training models on smaller but more informative training data is more effective 4/

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 20/02/2024

When we did many rounds, active learning was more efficient, approached the upper bound with less data, and enriched for positive examples! This demonstrates that active learning is broadly effective and illustrate that enriching for active sequences is more informative 3/

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 20/02/2024

We tested active learning in a second system using Nadav Ahituv and @jshendure.bsky.social's genome-wide MPRA in K562s. We downsampled the data, trained a CNN, then sampled from the remaining data. Active learning consistently outperformed random sampling across many starting conditions. 2/

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 20/02/2024

We substantially revised our active learning manuscript. A brief summary of what's new. TLDR: several new analyses, benchmarking w a 2nd MPRA dataset, and a refocused argument on active learning to leverage the capacity of MPRAs to generate large datasets. www.biorxiv.org/content/10.1... 1/8 🧬🔄

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 17/01/2024

A project I contributed to during grad school is now up at PLoS Comp Bio! We used the MAVE-NN package by @jbkinney.bsky.social's group to learn about the behavior of synthetic regulatory elements 🧬🔄 Keep an eye on @genologos.bsky.social's Twitter for more details. journals.plos.org/ploscompbiol...

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 17/01/2024

I should note that I set up my folders somewhere around my third year of grad school and haven't meaningfully reorganized it since then, so I'm open to a complete overhaul.

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 17/01/2024

I want to reorganize my @paperpile.bsky.social. I have folders covering broad topics with very few subfolders. Tags are for different manuscripts. Is there anyone in genomics 🖥️🧬 who wants to share how they organize their reference managers? I'm looking for more meaningful and detailed categories.

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 05/12/2023

Next time I meet a techie asking how to move into compbio I’ll connect them with you!

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 05/12/2023

Yeah, I struggle with finding a polite way to say “go learn a bunch of biology or take a huge pay cut to be an entry level bioinformatician for a few years” but there is definitely a mode of thought among some techies that they can watch 20 hours of YouTube videos and call it good

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Reposted by Ryan Z Friedman, PhD

Peter Koo @pkoo562.bsky.social · 05/12/2023

🤗

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 04/12/2023

I've had several software engineers ask me recently about transitioning into genomics/comp bio from tech. I never know what to say -- everyone I know in the field in industry went to school for biology/comp bio. Anyone have any suggestions, either of what to say or concrete resources to provide? 🧬🖥️

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 11/10/2023

Agreed that there is strong cell to cell variability. But changes in e.g. the ZRS enhancer of Shh can cause loss of limbs or gain of extra digits. Some of that is due to changes in Shh in space/time, but some is also due to how *much* Shh is produced

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 11/10/2023

hmm...A difference in 2 vs 3 fold change can definitely matter! Over/underactive CREs can cause developmental defects and disease. Agreed that cell culture won't tell you space+time, but they can tell you information about how sequence features encode activity.

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 11/10/2023

My expertise is also in distal elements, but I think that diffs in DBDs reflects different points in evolution. TFIIB and the sigma factors are homologous. But most DBD families in euks are totally absent from proks and vice versa! Suggests txn initiation is more conserved than specifying space-time

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 11/10/2023

I'm not entirely sure, but my sense is that GTFs have structural classes of DBDs you don't see binding to distal regions

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 11/10/2023

I think that enhancers+silencers control space and time as well as expression levels 😊

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 11/10/2023

I think of promoters as regions where transcription is initiated, while enhancers (and silencers!) are regions that dictate how much RNA is produced.

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 11/10/2023

I think it depends what counts as a promoter. If you think that the promoter is only the ~100 bp core promoter near the TSS, then there is a difference because the core is bound by GTFs. If you consider the ~1kb upstream of the promoter as the promoter, more overlap.

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Reposted by Ryan Z Friedman, PhD

Dr. Stephanie @punkrockscience.bsky.social · 06/10/2023

“The initial data leak was… 1 million lines of data for Ashkenazi people.” “The information… includes full names, usernames, profile photos, sex, date of birth, genetic ancestry results, and geographical location.” Well, that’s surely not going to be a fucking problem. (sarcastically) 🧪

bleepingcomputer.com

Genetics firm 23andMe says user data stolen in credential stuffing attack

23andMe has confirmed to BleepingComputer that it is aware of user data from its platform circulating on hacker forums and attributes the leak to a credential-stuffing attack.

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Reposted by Ryan Z Friedman, PhD

Jonathan Pritchard @jkpritch.bsky.social · 01/10/2023

I'm delighted to release the first half of my new textbook in human genetics: web.stanford.edu/group/pritch... "An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"

web.stanford.edu

An Owner's Guide to the Human Genome

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Ryan Z Friedman, PhD @rfriedman22.bsky.social · 27/09/2023

Hello, world! I'm a computational biology postdoc at UW in Seattle interested in genomics 🖥️ 🧬, gene regulation 🧬 🔄, machine learning, data viz, and zebrafish 🐟 #DevBio. Also enjoy emo/punk music, sci-fi books, cooking, and gaming! #LGBTQSTEM 🏳️‍🌈 #HiSciSky

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