@bioalgorithmist

Scientist, ML at Tessera | Algorithms for Gene Writing™ | PhD from Salis Lab at Penn State | threads/X/bsky @bioalgorithmist | Opinions are Mine Only

 Boston, MA
github.com/ayaanhossain/
Joined April 2017
  • Tweets552
  • Following263
  • Followers284
Ayaan Hossain retweeted
BURKOV
@burkovFeb 12
Human coders know they lost, but they keep fighting with windmills because they aren't ready to accept it.
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Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @NatureBiotech
Nature Biotechnology
@NatureBiotech11 Nov 2025
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording go.nature.com/49eTPCu
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A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording go.nature.com/49eTPCu
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🧠 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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Ayaan Hossain retweeted
Nic Fishman@njwfish26 May 2025
🚨 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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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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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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Ayaan Hossain retweeted
Asimov
@AsimovBio13 Nov 2024
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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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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Ayaan Hossain retweeted
Akos Nyerges@AkosNyerges15 Jul 2024
Thanks for the highlight @doescience! Read more about our research: nature.com/articles/s41586-0… biorxiv.org/content/10.1101/…

A swapped genetic code prevents viral infections and gene transfer

Nature - A study details the creation of an Escherichia coli genetically recoded organism that is resistant to viral infection, and describes a further modification that keeps the organism and its...

nature.com
DOE Office of Science@doescience14 Jul 2024
Engineered bacteria are great for making biofuels and other bioproducts, but you don’t want those changes escaping to the wild. Scientists @Harvard & @WUSTLmed engineered the E. coli genome to keep useful edits from spreading in an uncontrolled way: energy.gov/science/ber/artic…
A bacterial virus inserting genetic material inside a bacterial cell during infection. Image courtesy of Behnoush Hajian.

ALT A bacterial virus inserting genetic material inside a bacterial cell during infection. Image courtesy of Behnoush Hajian.

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Ayaan Hossain retweeted
Akos Nyerges@AkosNyerges17 Jun 2024
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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Ayaan Hossain retweeted
Akos Nyerges@AkosNyerges17 Jun 2024
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/s41587-0…
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Ayaan Hossain retweeted
Alex Reis@alexcampreis28 Feb 2024
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@hsalis28 Feb 2024
Replying to @anshulkundaje
Our bacterial Promoter Calculator model has 348 parameters and predicts cont-val TX rates with R^2=0.80 (other factors constant). Our bacterial RBS Calculator has 12 free parameters and predicts cont-val TL rates with R^2=0.75. The bar is pretty high, but they don’t compare.
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Ayaan Hossain retweeted
David Ding@ding_david23 Feb 2024
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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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 retweeted
Chappell Lab@ChappellLab30 Aug 2023
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/s41467-0…

A portable regulatory RNA array design enables tunable and complex regulation across diverse...

Nature Communications - A lack of composable and tunable gene regulators has hindered efforts to engineer nonmodel bacteria and consortia. Here the authors deliver a tunable gene regulatory...

nature.com
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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-steer…

A Steering Council notice about PEP 703 (Making the Global Interpreter Lock Optional in CPython)

Posting for the whole Steering Council, on the subject of @colesbury’s PEP 703 (Making the Global Interpreter Lock Optional in CPython). Thank you, everyone, for responding to the poll on the no-GIL...

discuss.python.org
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Ayaan Hossain retweeted
Feng Zhang
@zhangf28 Jun 2023
Since the discovery of CRISPR-Cas systems, people have wondered if a similar type of system exists in eukaryotes. Today, we report in @Nature the characterization of Fanzor, a eukaryotic RNA-guided system that can be reprogrammed for human genome editing. nature.com/articles/s41586-0…

Fanzor is a eukaryotic programmable RNA-guided endonuclease

Nature - Fanzor is shown to be an RNA-guided DNA endonuclease, demonstrating that such endonucleases are found in all domains of life and indicating a potential new tool for genome engineering...

nature.com
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Biotechnology has entered a period of rapid growth, where cellular engineering will touch every aspect of society. I look forward to working with my colleagues to lead MIT BE through this era. @MIT @MITdeptofBE
MIT Dept of BE@MITdeptofBE20 Jun 2023
Prof Christopher A. Voigt will be the next head of the MIT Department of Biological Engineering. Learn more about Prof Voigt at ow.ly/ZkVT50OSVBp @Geneticdesigner
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Researchers @Penn_State @PennStateChE have developed a low-cost RNA-based sensor that detects protein biomarkers >>> bit.ly/3J64r8Z @grace_vezeau @hsalis
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