Ayaan Hossain @bioalgorithmist

Scientist, ML at Tessera | Algorithms for Gene Writing™ | PhD from Salis Lab at Penn State | threads/X/bsky @bioalgorithmist | Opinions are Mine Only github.com/ayaanhossain/ Boston, MA Joined April 2017

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Jessica Sacher, PhD @JessicaSacher

3 months ago

🧠 Why do smart scientists feel stupid when reading papers? Because nobody teaches you HOW to read them efficiently. This 3-pass system will change how you approach every paper: 🧵

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Nic Fishman @njwfish

3 months ago

🚨 New preprint 🚨 We introduce Generative Distribution Embeddings (GDEs) — a framework for learning representations of distributions, not just datapoints. GDEs enable multiscale modeling and come with elegant statistical theory and some miraculous geometric results! 🧵

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Omar Abudayyeh @omarabudayyeh

3 months ago

New lab preprint! 🚀 Modeling complex data distributions is tough. We designed GDEs, a new framework that tackles this head-on! GDEs generalize across text, images & MANY bio apps (think virtual cells, spatial bio, viral genome tracking). Thread 👇

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François Chollet @fchollet

6 months ago

If you have a solid strategy and a small amount of compute, you can go pretty far. If you have huge clusters of GPUs and no strategy, your only achievement will be burning capital.

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Asimov @AsimovBio

10 months ago

This is a great paper from the @hsalis lab. - Measure the decay rates of 50,000 mRNAs in bacteria. - Use biophysical models + ML to build models of mRNA stability. - Profit. And a good reminder of what's possible when one turns a biological problem into a sequencing problem!

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Daniel Cetnar @DanielCetnar

10 months ago

I am pleased to announce our latest publication ‘Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning’ in @NatureComms

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Akos Nyerges @AkosNyerges

a year ago

Thanks for the highlight @doescience! Read more about our research: nature.com/articles/s4158… biorxiv.org/content/10.110…

DOE Office of Science @doescience

a year ago

Thanks for the highlight @doescience! Read more about our research: nature.com/articles/s4158… biorxiv.org/content/10.110…

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Ayaan Hossain @bioalgorithmist

a year ago

Supremely entertaining paper, "ChatGPT is bullshit": link.springer.com/article/10.100…

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Akos Nyerges @AkosNyerges

a year ago

In our newest preprint, • we explore the effects of synonymous genome recoding, and • construct & troubleshoot a synthetic 57-codon E. coli genome using multi-omics, editing, and laboratory evolution. 1/n

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Akos Nyerges @AkosNyerges

a year ago

After almost two years of optimization, SynOMICS's plasmid system is a fusion of @dbikard @MarraffiniLab's Cas9 & the pORTMAGE plasmids & ELSA/nonrepetitive parts by @hsalis @bioalgorithmist Alex Reis & co I highly recommend using multiplexed sgRNAs from nature.com/articles/s4158…

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Ayaan Hossain @bioalgorithmist

2 years ago

Please RT: If there's an old unmaintained software that is prohibitively slow and is only one of its kind do you not benchmark your new tool against it? How to properly address reviewers and frame this issue in paper?

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Alex Reis @alexcampreis

2 years ago

If you are using Language Models to predict gene expression, you better compare with latest state-of-the-art biophysical or ML models

Howard Salis @hsalis

2 years ago

If you are using Language Models to predict gene expression, you better compare with latest state-of-the-art biophysical or ML models

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David Ding @ding_david

2 years ago

Do you need a billion parameters and millions of sequences for #proteindesign? Maybe not! See our paper: shorturl.at/novMO We show that interpretable, non-autoregressive structure-based protein design can work! Original thread: shorturl.at/cdgCP

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Senti Biosciences @SentiBio

2 years ago

Today we announced FDA clearance of our IND application for SENTI-202, a potential first-in-class, logic-gated treatment for acute myeloid leukemia. Learn more: bit.ly/3v4IMJY $SNTI #AML #CARNK

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Ayaan Hossain @bioalgorithmist

2 years ago

This. Starting with C only makes you a strong programmer overall.

Giulio Ermanno Pibiri @giulio_pibiri

2 years ago

This. Starting with C only makes you a strong programmer overall.

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Chappell Lab @ChappellLab

2 years ago

Check out our latest paper describing a novel 'RNA array design strategy' for creating tunable RNA circuits that function across different microbes! A big congrats to Baiyang Liu who led the work and our collaborators @FrancoLabUCLA @biodesign_lab nature.com/articles/s4146…

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Soumith Chintala @soumithchintala

2 years ago

No More GIL! the Python team has officially accepted the proposal. Congrats @colesbury on his multi-year brilliant effort to remove the GIL, and a heartfelt thanks to the Python Steering Council and Core team for a thoughtful plan to make this a reality. discuss.python.org/t/a-steering-c…