Bashorlab
@bashorlab.bsky.social
Reposted by Bashorlab
Now published! Big congrats to first author @gginell.bsky.social
We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions.
www.science.org/doi/10.1126/...
We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions.
www.science.org/doi/10.1126/...
May 23, 2025 at 11:31 AM
Now published! Big congrats to first author @gginell.bsky.social
We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions.
www.science.org/doi/10.1126/...
We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions.
www.science.org/doi/10.1126/...
Reposted by Bashorlab
I'm so happy to report that our preprint on light-induced collective cell migration has now been published in Cell Systems! This project was a lot of fun and will be the basis for a lot of our ongoing & future work.
Large-scale control over collective cell migration using light-activated epidermal growth factor receptors
Programmable control over tissue movement is a fundamental challenge for tissue engineering
and wound healing. Suh, Thornton, et al. discovered that a light-controlled EGF receptor
controls long-range...
www.cell.com
March 25, 2025 at 6:29 PM
I'm so happy to report that our preprint on light-induced collective cell migration has now been published in Cell Systems! This project was a lot of fun and will be the basis for a lot of our ongoing & future work.
Reposted by Bashorlab
Excited to share our paper in @cp-cellrepphyssci.bsky.social! Building on a fundamental study of bond strength and bursting in textile-based devices, we programmed local failure in a fuse that enables selection and sequencing of tasks with one pressure input. news.rice.edu/news/2025/ha...
February 18, 2025 at 10:17 PM
Excited to share our paper in @cp-cellrepphyssci.bsky.social! Building on a fundamental study of bond strength and bursting in textile-based devices, we programmed local failure in a fuse that enables selection and sequencing of tasks with one pressure input. news.rice.edu/news/2025/ha...
Reposted by Bashorlab
🧬🧪Protein codes promote selective subcellular compartmentalization | Science www.science.org/doi/10.1126/...
Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social
Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social
Protein codes promote selective subcellular compartmentalization
Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. Here, we demonstrate that prote...
www.science.org
February 8, 2025 at 11:39 PM
🧬🧪Protein codes promote selective subcellular compartmentalization | Science www.science.org/doi/10.1126/...
Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social
Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social
Reposted by Bashorlab
SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci - @j-eyquem.bsky.social go.nature.com/4gBnaqY
SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci - Nature Biotechnology
Primary T cells with multiple genetic modifications are rapidly isolated by negative selection.
go.nature.com
February 5, 2025 at 2:42 PM
SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci - @j-eyquem.bsky.social go.nature.com/4gBnaqY
Reposted by Bashorlab
Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Multiplex generation and single-cell analysis of structural variants in mammalian genomes
Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) ...
www.science.org
January 31, 2025 at 7:41 PM
Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Bashorlab
OxLDL-targeted Chimeric Antigen Receptor T Regulatory Cells Reduce Atherosclerotic Plaque Development https://www.biorxiv.org/content/10.1101/2025.01.24.634830v1
January 28, 2025 at 2:07 PM
OxLDL-targeted Chimeric Antigen Receptor T Regulatory Cells Reduce Atherosclerotic Plaque Development https://www.biorxiv.org/content/10.1101/2025.01.24.634830v1
Reposted by Bashorlab
Fun to see it out in print! I was really lucky to have an amazing team to work with on this. If this sort of work seems interesting to you or someone you know, please feel free to reach out (planning to staff a lab later this year).
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A map of the rubisco biochemical landscape - Nature
A massively parallel assay developed to map the essential photosynthetic enzyme rubisco showed that non-trivial biochemical changes and improvements in CO2 affinity are possible, signposting further e...
www.nature.com
January 22, 2025 at 10:34 PM
Fun to see it out in print! I was really lucky to have an amazing team to work with on this. If this sort of work seems interesting to you or someone you know, please feel free to reach out (planning to staff a lab later this year).
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Bashorlab
Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning.
Paper: www.nature.com/articles/s41...
Paper: www.nature.com/articles/s41...
Multiscale footprints reveal the organization of cis-regulatory elements - Nature
We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.
www.nature.com
January 23, 2025 at 2:11 AM
Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning.
Paper: www.nature.com/articles/s41...
Paper: www.nature.com/articles/s41...
Reposted by Bashorlab
I'd like to draw your attention to this truly excellent paper from the Taraska lab on cryoET of plasma membrane associated proteins. Everyone who is thinking about probes in the cryoET space should also see what they could do with ferritag (fig 6) www.nature.com/articles/s41...
January 22, 2025 at 4:40 PM
I'd like to draw your attention to this truly excellent paper from the Taraska lab on cryoET of plasma membrane associated proteins. Everyone who is thinking about probes in the cryoET space should also see what they could do with ferritag (fig 6) www.nature.com/articles/s41...
Reposted by Bashorlab
Gene syntax defines supercoiling-mediated transcriptional feedback https://www.biorxiv.org/content/10.1101/2025.01.19.633652v1
January 20, 2025 at 7:54 AM
Gene syntax defines supercoiling-mediated transcriptional feedback https://www.biorxiv.org/content/10.1101/2025.01.19.633652v1
Reposted by Bashorlab
Reposted by Bashorlab
Our global study on the state of trust in scientists is now out in Nature Human Behaviour! 🥳
With a team of 241 researchers, we surveyed 71,922 people in 68 countries, providing the largest dataset on trust in scientists post-pandemic 👇🧵https://www.nature.com/articles/s41562-024-02090-5
With a team of 241 researchers, we surveyed 71,922 people in 68 countries, providing the largest dataset on trust in scientists post-pandemic 👇🧵https://www.nature.com/articles/s41562-024-02090-5
January 20, 2025 at 10:16 AM
Our global study on the state of trust in scientists is now out in Nature Human Behaviour! 🥳
With a team of 241 researchers, we surveyed 71,922 people in 68 countries, providing the largest dataset on trust in scientists post-pandemic 👇🧵https://www.nature.com/articles/s41562-024-02090-5
With a team of 241 researchers, we surveyed 71,922 people in 68 countries, providing the largest dataset on trust in scientists post-pandemic 👇🧵https://www.nature.com/articles/s41562-024-02090-5
Reposted by Bashorlab
New review / perspective with @albertilab-tud.bsky.social on our thoughts on condensate speciality and recruitment, focusing on interplay between site specific and chemically specific interactions
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
Molecular determinants of condensate composition
Biomolecular condensates are non-stochiometric assemblies that organize cellular matter
in space and time. Despite much work, many questions remain regarding what determines
the recruitment and exclus...
www.cell.com
January 17, 2025 at 10:23 AM
New review / perspective with @albertilab-tud.bsky.social on our thoughts on condensate speciality and recruitment, focusing on interplay between site specific and chemically specific interactions
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
Reposted by Bashorlab
Proteases might serve as versatile control knobs for gene and cell therapies, but there looms the risk of immunogenicity as we and others have been using viral proteases. We now report a control system based on a an engineered human protease and its clinically approved inhibitor. rdcu.be/d6kVt
Orthogonalized human protease control of secreted signals
Nature Chemical Biology - Engineering of a human-derived protease controlled exogenously by its FDA-approved inhibitor enables control over cytokine activity in cell-based therapies with reduced...
rdcu.be
January 15, 2025 at 7:25 PM
Proteases might serve as versatile control knobs for gene and cell therapies, but there looms the risk of immunogenicity as we and others have been using viral proteases. We now report a control system based on a an engineered human protease and its clinically approved inhibitor. rdcu.be/d6kVt
Reposted by Bashorlab
A new large language of life model (LLLM) for the transcriptome that predicts gene expression within and across human cell types www.nature.com/articles/s41... @nature.com
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
A foundation model of transcription across human cell types - Nature
A foundation model learns transcriptional regulatory syntax from chromatin accessibility and sequence data across a range of cell types to predict gene expression and transcription factor interactions...
www.nature.com
January 8, 2025 at 4:27 PM
A new large language of life model (LLLM) for the transcriptome that predicts gene expression within and across human cell types www.nature.com/articles/s41... @nature.com
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...
Reposted by Bashorlab
Congrats to Johannes Linder, David Kelley et al. on the journal publication of Borzoi - a long context sequence models of RNA-seq coverage profiles with many nice applications for transcriptional & post-transcriptional regulation & variant effect prediction.
www.nature.com/articles/s41... 1/
www.nature.com/articles/s41... 1/
Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation - Nature Genetics
Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.
www.nature.com
January 8, 2025 at 10:06 PM
Congrats to Johannes Linder, David Kelley et al. on the journal publication of Borzoi - a long context sequence models of RNA-seq coverage profiles with many nice applications for transcriptional & post-transcriptional regulation & variant effect prediction.
www.nature.com/articles/s41... 1/
www.nature.com/articles/s41... 1/
🚨NEW PUBLICATION ALERT🚨: In a paper out now in
@science.org we describe a way to build synthetic phosphorylation circuits with customizable sense-and-response functions in human cells. Check it out at science.org/doi/10.1126/....
@science.org we describe a way to build synthetic phosphorylation circuits with customizable sense-and-response functions in human cells. Check it out at science.org/doi/10.1126/....
Engineering synthetic phosphorylation signaling networks in human cells
Protein phosphorylation signaling networks have a central role in how cells sense and respond to their environment. We engineered artificial phosphorylation networks in which reversible enzymatic phos...
science.org
January 7, 2025 at 8:24 AM
🚨NEW PUBLICATION ALERT🚨: In a paper out now in
@science.org we describe a way to build synthetic phosphorylation circuits with customizable sense-and-response functions in human cells. Check it out at science.org/doi/10.1126/....
@science.org we describe a way to build synthetic phosphorylation circuits with customizable sense-and-response functions in human cells. Check it out at science.org/doi/10.1126/....