Joined October 2015
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Pinned Tweet
4 Jan 2025
Spatial MOtif REcognition (SMORE) is now peer-reviewed and out at @GenomeBiology Updates include analysis of sequencing-based spatial transcriptomics (Slide-Seq) and a whole brain
dataset with ~4 million cells, showing versatility and scalability of SMORE. genomebiology.biomedcentral.…
13 Apr 2024
Have you used spatial genomics to map cell types in your favorite tissue? Are you interested in finding patterns in your results? We’ve developed a method just for you. The first paper from our lab is now on bioRxiv!
biorxiv.org/content/10.1101/…
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Amjad Askary retweeted
16 Jun 2025
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On behalf of the amazing team in @JswLab, we’re excited to share PEtracer (biorxiv.org/content/10.1101/…) a prime editing-based evolving lineage recorder compatible with both scRNA-seq and high-resolution imaging readouts in intact tissue. By applying PEtracer in a syngeneic mouse model of lung metastasis, we dissect how cell-intrinsic and environmental factors coordinately shape tumor evolution in vivo.
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Amjad Askary retweeted
8 May 2025
Kai Hoa from Amjad Askary's lab @AskaryLab on recording signaling histories in single cells via INSCRIBE
Check out their bioRxiv:
biorxiv.org/content/10.1101/…
#SysBioSC2025
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Amjad Askary retweeted
17 Mar 2025
Spatial proteomics is here, but spatial functional proteomics?
Here is our Nature BME paper on spatial protein interactomics (nature.com/articles/s41551-0…) illuminating how 47 proteins co-localize/ interact within 20 nm and their function in tissues.
@naturemethods @rita_strack
6 Dec 2024
The wait is over!! We are thrilled to announce that we have chosen Spatial Proteomics as 2024’s Method of the Year! 🥳
For more on Spatial Proteomics and a road map to this special issue, please see this month’s Editorial or read on in this thread.
nature.com/articles/s41592-0…
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Amjad Askary retweeted
1 Mar 2025
So we beat on. Gene/cell therapies often use proteins that could be recognized/rejected as non-self by our immune system. We combine algorithms to build proteins that are therapeutically relevant and can masquerade as our own parts doi.org/10.1101/2025.02.24.6…
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Nice article in Scientific American about our work on outer ear evolution and a complimentary study from the lab of Maksim Plikus on role of unique lipids in mammalian ear cartilage. @MathiThiru95 @USCStemCell @KECKSchool_USC
scientificamerican.com/artic…
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Amjad Askary retweeted
15 Jan 2025
How does one (signaling) arm know what the other is doing in the cell? Through a network of bHLH transcription factors obviously! Our work showing how neural stem cells integrate signals to coordinate a fate response is now out: cell.com/cell-reports/fullte…
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Amjad Askary retweeted
15 Jan 2025
It's published! rdcu.be/d6kVt
23 Jan 2024
When we talk about viral protease-based circuits, people wonder: "if it's meant as therapeutics, are you concerned about immunogenicity"? Now, in hDIRECT, we established control of cytokines using a human protease and its FDA-approved inhibitor: doi.org/10.1101/2024.01.18.5…
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Amjad Askary retweeted
13 Jan 2025
A month ago we @vevo_ai announced that we have generated the largest single-cell perturbation atlas in history, Tahoe-100M. Today, we announce that we will fully open-source Tahoe-100M in Feb, as part of a collaboration with @NVIDIAHealth to train cell state models.
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4 Jan 2025
Spatial MOtif REcognition (SMORE) is now peer-reviewed and out at @GenomeBiology Updates include analysis of sequencing-based spatial transcriptomics (Slide-Seq) and a whole brain
dataset with ~4 million cells, showing versatility and scalability of SMORE. genomebiology.biomedcentral.…
13 Apr 2024
Have you used spatial genomics to map cell types in your favorite tissue? Are you interested in finding patterns in your results? We’ve developed a method just for you. The first paper from our lab is now on bioRxiv!
biorxiv.org/content/10.1101/…
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4 Jan 2025
Special congratulations to @SamadiZain who developed a simple idea into a powerful algorithm.
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Amjad Askary retweeted
23 Nov 2024
A dream come true: in 2004 I started thinking about counting microstates to predict gene expression with @JKondev Rob Phillips @HernanGGarcia. 20 years later we can measure them: nature.com/articles/s41586-0… Thank you @WJGreenleaf @bgrdoughty @MichaelaThinks Julia and all co-authors!
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Amjad Askary retweeted
26 Nov 2024
New Publication Alert!
our perspective of "Aging on a chip" and "Spatial Omics" in aging single cells.
Decoding senescence of aging single cells at the nexus of biomaterials, microfluidics, and spatial omics
npj Aging10, 57 (2024)
Link: lnkd.in/ef7-ad7Q
@CoulterBME
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25 Nov 2024
Check out our new review of molecular recording, exploring cutting-edge technologies and their transformative potential for biology. A collaborative effort across multiple labs—proud to have been part of this amazing team! 🌟
25 Nov 2024
The lives of cells, recorded go.nature.com/4g2gRwG #Perspective by @AskaryLab, Wei Chen, @_Choi_Junhong, Lucia Y. Du, @ElowitzLab, @james_gagnon, @schierlab, @sophieseid, @JShendure, @TanjaStadler_CH & @tranmartink
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Amjad Askary retweeted
20 Nov 2024
Incredibly excited that our paper linking single molecule states of TF binding to gene expression using quantitative thermodynamic models is out in Nature today. An amazing collaboration with the Bintu Lab. Congrats to Ben, Michaela, and Julia! nature.com/articles/s41586-0…
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Amjad Askary retweeted
14 Nov 2024
Our work describing molecular recording of sequential information by directing a chain of insertions with prime editor in mammalian cells is now published in @nchembio here - nature.com/articles/s41589-0…. Congratulations to Theresa Loveless, @CourtneyCarls_n, and the whole team!
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Amjad Askary retweeted
29 Oct 2024
Check out this amazing resource! High quality illustrations for free!
bioart.niaid.nih.gov/
HT @LuciaScience
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Amjad Askary retweeted
21 Oct 2024
We are excited to introduce LoRNA-SH, a frontier RNA foundation model that leverages long-read transcriptomics and long-context inputs to learn and predict the transcriptome architecture with base-pair resolution: biorxiv.org/content/10.1101/…
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12 Oct 2024
What if you could find out the history of signaling activity in each cell with a single round of imaging? Wouldn't that be incredible? Well, we thought so too. And that's what we set out to achieve with INSCRIBE in our new preprint. Let’s dive in! 🚀🔬
biorxiv.org/content/10.1101/…
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12 Oct 2024
We're excited about the future applications of INSCRIBE: its simple and fast readout strategy makes it ideal for large scale tissue-level analyses of development, regeneration, cancer, and more, helping to unravel how cells 'remember' past events.
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12 Oct 2024
We’d love to hear your thoughts, ideas, and questions! Curious how molecular histories of the cells shape their behavior in your system? No need for a time machine—just a regular fluorescence microscope will do the trick.
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