blackboxpi
@blackboxpi.bsky.social
Transcription factors | ML models | cis-regulatory elements | motifs | gene regulation
Los Angeles, CA
Los Angeles, CA
Reposted by blackboxpi
Excited to see scPRINT published in @natcomms.nature.com ! scPRINT is a large cell model for the inference of gene networks pre-trained on 50Mcells with innovative pretraining tasks inspired from biology. Work led by @jkobject.com
I am super happy to annonce that after 9 months under review the first paper of my PhD: scPRINT is finally available on Nature Comms! 🎉🧬
www.nature.com/artic...
www.nature.com/artic...
scPRINT: pre-training on 50 million cells allows robust gene network predictions
Nature Communications - Authors present a state-of-the-art cell foundation model trained on 50 million cells. They show that the model generates a meaningful gene network and has zero-shot...
www.nature.com
April 16, 2025 at 1:16 PM
Excited to see scPRINT published in @natcomms.nature.com ! scPRINT is a large cell model for the inference of gene networks pre-trained on 50Mcells with innovative pretraining tasks inspired from biology. Work led by @jkobject.com
Reposted by blackboxpi
Genome architecture folks, this perspective is really worth your time www.cell.com/molecular-ce...
Cohesin as an essential disruptor of chromosome organization
Chromosomes are long strings of DNA carrying multiple genes. A chromosomal factor
called cohesin creates loops of DNA proposed to be functional units of the genome.
By contrast, it is proposed here th...
www.cell.com
February 6, 2025 at 11:31 AM
Genome architecture folks, this perspective is really worth your time www.cell.com/molecular-ce...
Reposted by blackboxpi
Happy to share this concise review and outlook for single-cell sequencing methods to unravel cell biology of the nucleus! Big shoutout to my friend and former colleague Peter Zeller for sharing the work!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Shining a light on cell biology of the nucleus with single-cell sequencing
From the preservation of genomic integrity to the regulation of RNA translation, nearly all cellular processes are regulated in a cell context-depende…
www.sciencedirect.com
February 4, 2025 at 7:27 AM
Happy to share this concise review and outlook for single-cell sequencing methods to unravel cell biology of the nucleus! Big shoutout to my friend and former colleague Peter Zeller for sharing the work!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by blackboxpi
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
January 26, 2025 at 12:13 AM
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
Reposted by blackboxpi
Exploring the gap between what LLMs really know vs what people think they know
www.nature.com/articles/s42...
www.nature.com/articles/s42...
What large language models know and what people think they know - Nature Machine Intelligence
Understanding how people perceive and interpret uncertainty from large language models (LLMs) is crucial, as users often overestimate LLM accuracy, especially with default explanations. Steyvers et al...
www.nature.com
January 21, 2025 at 4:08 PM
Exploring the gap between what LLMs really know vs what people think they know
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Reposted by blackboxpi
UCLA scientists led by Dr. Hilary Coller have found that quiescent cells express transcription factors that act as "master switches" to regulate genes that suppress cell cycle progression, prevent the adoption of irreversible fates and reorganize their metabolism. www.nature.com/articles/s41...
Transcription factor networks in cellular quiescence - Nature Cell Biology
Recent developments in single-cell technologies have increased our understanding of how the coordinated activities of transcription factors in different quiescent cells and differentiated cells mainta...
www.nature.com
January 24, 2025 at 12:09 AM
UCLA scientists led by Dr. Hilary Coller have found that quiescent cells express transcription factors that act as "master switches" to regulate genes that suppress cell cycle progression, prevent the adoption of irreversible fates and reorganize their metabolism. www.nature.com/articles/s41...
Reposted by blackboxpi
Nature research paper: Mapping cells through time and space with moscot
https://go.nature.com/40pqpvw
https://go.nature.com/40pqpvw
Mapping cells through time and space with moscot - Nature
Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal dimensions.
go.nature.com
January 23, 2025 at 5:08 PM
Nature research paper: Mapping cells through time and space with moscot
https://go.nature.com/40pqpvw
https://go.nature.com/40pqpvw
Reposted by blackboxpi
Our paper on Self-Supervised Learning in Single-Cell Genomics is out in Nature Portfolio Machine Intelligence! 🙌 🧬🤖
Big thank you to my co-authors Mojtaba Bahrami, Yufan Xia, @davidsebfischer.bsky.social, and @fabiantheis.bsky.social . 👏
nature.com/articles/s42...
Big thank you to my co-authors Mojtaba Bahrami, Yufan Xia, @davidsebfischer.bsky.social, and @fabiantheis.bsky.social . 👏
nature.com/articles/s42...
Delineating the effective use of self-supervised learning in single-cell genomics - Nature Machine Intelligence
Self-supervised learning techniques are powerful assets for enabling deep insights into complex, unlabelled single-cell genomic data. Richter et al. here benchmark the applicability of self-supervised...
nature.com
January 7, 2025 at 10:00 AM
Our paper on Self-Supervised Learning in Single-Cell Genomics is out in Nature Portfolio Machine Intelligence! 🙌 🧬🤖
Big thank you to my co-authors Mojtaba Bahrami, Yufan Xia, @davidsebfischer.bsky.social, and @fabiantheis.bsky.social . 👏
nature.com/articles/s42...
Big thank you to my co-authors Mojtaba Bahrami, Yufan Xia, @davidsebfischer.bsky.social, and @fabiantheis.bsky.social . 👏
nature.com/articles/s42...
Reposted by blackboxpi
Multiscale footprints reveal the organization of cis-regulatory elements
www.nature.com/articles/s41...
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 22, 2025 at 8:21 PM
Multiscale footprints reveal the organization of cis-regulatory elements
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by blackboxpi
Identifying transcription factors driving cell differentiation https://www.biorxiv.org/content/10.1101/2025.01.20.633856v1
January 22, 2025 at 10:47 PM
Identifying transcription factors driving cell differentiation https://www.biorxiv.org/content/10.1101/2025.01.20.633856v1
Reposted by blackboxpi
Excited to see this (cover) article on condensates come out in Scientific American. Nice quotes from me and many folks in the field. www.scientificamerican.com/article/myst...
Mysterious Blobs in Cells Are Changing the Way We Understand Life
Tiny specks called biomolecular condensates are leading to a new understanding of the cell
www.scientificamerican.com
January 22, 2025 at 1:41 AM
Excited to see this (cover) article on condensates come out in Scientific American. Nice quotes from me and many folks in the field. www.scientificamerican.com/article/myst...
Reposted by blackboxpi
We often speak about chromatin as being accessible or inaccessible, but what does it mean? We wrote a short review on this, 🔬 focused:
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.
December 20, 2024 at 3:46 PM
We often speak about chromatin as being accessible or inaccessible, but what does it mean? We wrote a short review on this, 🔬 focused:
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.