Excited to share our new paper out in @natcomms.nature.com ! We introduce ArchVelo, a new computational framework for RNA velocity and trajectory inference from single-cell multi-omic (scATAC+RNA-seq) data: doi.org/10.1038/s414...

ArchVelo: archetypal velocity modeling for single-cell multi-omic trajectories - Nature Communications

Mapping cell dynamics from static data is a challenge in genomics. Here, authors introduce ArchVelo, a computational method for modeling transcription dynamics and trajectory inference using chromatin...

doi.org

Excited to share our new paper at Cell Reports @cp-cellreports.bsky.social led by fantastic Gabe Dolsten! We characterized multi-megabase and interchromosomal chromatin interactions in primary T cells, revealing a previously underappreciated layer of genome organization: doi.org/10.1016/j.ce...

Wang et al. in @yuripritykin.bsky.social's lab at Princeton University present Domino, a deep learning framework that maps genomic sequences to insulation scores, revealing a comprehensive insulation grammar defined by 24 motifs that account for 59% of Drosophila chromatin boundaries.

bioRxiv (Genomics)

biorxiv.org

Sequence-to-function modeling uncovers the context-specific grammar of Drosophila chromatin insulation https://www.biorxiv.org/content/10.64898/2026.06.15.732488v1

Excited to share our new paper at Cell Reports @cp-cellreports.bsky.social led by fantastic Gabe Dolsten! We characterized multi-megabase and interchromosomal chromatin interactions in primary T cells, revealing a previously underappreciated layer of genome organization: doi.org/10.1016/j.ce...

Happy to present Gloss, our new computational method for the analysis of multi-modal LIPSTIC + scRNA-seq data coupling cell-cell interaction measurements with intracellular transcriptomes. Paper: doi.org/10.1016/j.cr... Led by an amazing PhD student Tamjeed Azad, with @victora.bsky.social

Predictive modeling of molecular activity underlying physical cell-cell interactions

Predictive modeling of molecular activity underlying physical cell-cell interactions

Azad et al. introduce Gloss, a computational framework that links intracellular gene programs measured with scRNA-seq to physical cell-cell interactions measured by LIPSTIC. Using a group lasso approach, Gloss robustly identifies the molecular drivers of immune communication in models of cancer and viral infection.

dlvr.it

Benchmarking cell type deconvolution in spatial transcriptomics and application to cancer immunotherapy https://www.biorxiv.org/content/10.64898/2026.01.13.699379v1

Thrilled to announce a new PhD from the lab, Dr. Sarah Walker! A well-deserved congratulations on a successful defense last week! The amazing work speaks for itself: doi.org/10.1101/2025... doi.org/10.1038/s415... doi.org/10.1038/s415... and more coming soon Excited to follow her future success!

Huge congrats to Gabe Dolsten on a fantastic PhD defense last week!!! The 1st PhD from the lab! So proud of his many research achievements e.g.: doi.org/10.1038/s415... doi.org/10.1101/2025... doi.org/10.1016/j.xg... He's bound to do amazing things ahead!

Happy to present today at AAI Introduction to Computational Immunology Course today at UPenn

Temporal and context-dependent requirements for the transcription factor Foxp3 expression in regulatory T cells @natimmunol.nature.com @yuripritykin.bsky.social Rudensky @princetonupress.bsky.social @mskcancercenter.bsky.social www.nature.com/articles/s41...

Our paper is out today at @natimmunol.nature.com! Very timely! We performed extensive exploration of Foxp3 in Treg cells, using inducible protein degradation in vivo. Wonderful collaboration led by Sasha Rudensky and Wei Hu, computation led by talented Gabe Dolsten. Read it here: rdcu.be/eJ0hH

Temporal and context-dependent requirements for the transcription factor Foxp3 expression in regulatory T cells - Nature Immunology

Rudensky and colleagues demonstrate a context-dependent differential requirement for Foxp3 for Treg cell transcriptional and functional programs.

nature.com

Extremely happy about the Nobel prize recognizing regulatory T cells! A fascinating concept with so many potential clinical applications. Very lucky to have been working on the genomics of Treg cells in collaboration with the giant in the field, Sasha Rudensky @mskcc.bsky.social !

Excited to share our new study: Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection bioRxiv: doi.org/10.1101/2025... 🧵 Key findings below 👇

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection

T cells protect against pathogens and tumors and can differentiate into various functionally distinct subsets. While each subset exhibits a characteristic epigenomic and transcriptional profile, essen...

doi.org

bioRxiv Immunology@biorxiv-immuno.bsky.social · last yr.

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection https://www.biorxiv.org/content/10.1101/2025.09.08.675014v1

Metadomain and metaloop genome interactions in mammalian T cells https://www.biorxiv.org/content/10.1101/2025.09.19.677419v1

Excited to share our new study: Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection bioRxiv: doi.org/10.1101/2025... 🧵 Key findings below 👇

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection

T cells protect against pathogens and tumors and can differentiate into various functionally distinct subsets. While each subset exhibits a characteristic epigenomic and transcriptional profile, essen...

doi.org

bioRxiv Immunology@biorxiv-immuno.bsky.social · last yr.

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection https://www.biorxiv.org/content/10.1101/2025.09.08.675014v1

ArchVelo: Archetypal Velocity Modeling for Single-cell Multi-omic Trajectories https://www.biorxiv.org/content/10.1101/2025.09.14.676182v1

Happy to share our new paper! We present high-resolution Micro-C maps across Drosophila embryogenesis, integrated with 149 ChIP-seq datasets. This systematic analysis enabled clustering of loops & boundaries into 4 distinct classes with distinct regulatory roles. www.cell.com/cell-genomic...

3D chromatin structures precede genome activation in Drosophila embryogenesis

Dolsten et al. map the 3D chromatin architecture across early Drosophila development using high-resolution Micro-C, and, by integrative analysis with 149 public ChIP-seq datasets, identify four classe...

cell.com

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection https://www.biorxiv.org/content/10.1101/2025.09.08.675014v1

Comp bio postdoc positions available! Come work with us at Princeton University on computational method development and applications in regulatory genomics, genome editing, immunology and cancer, in mouse and human: pritykinlab.github.io#jobs Please share among all those who may be interested!

Pritykin Lab

Pritykin Lab at the Lewis-Sigler Institute for Integrative Genomics and the Department of Computer Science at Princeton University.

pritykinlab.github.io

After a long trip and a long sleep, i am ready to enjoy the rich scientific program at #ISMBECCB2025 in Liverpool. This is also the first year of our new COSI in Computational and System Immunology (CSI) happening on Tuesday. And of course looking forward RegSys, as usual with fantastic organizers

For CSI COSI, I am very thankful to my co-chair Jishnu Das and steering committee @yuripritykin.bsky.social, Hatice Ulku Osmanbeyoglu, Aly Azeem Khan. And everyone who submitted their for consideration for this session www.iscb.org/ismbeccb2025...

A belated announcement about our GuideScan2 paper finally out in Genome Biology: doi.org/10.1186/s130... GuideScan2 is a new flexible and efficient CRISPR gRNA design and analysis tool with command line and web interfaces. Please let us know what you think!

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2 - Genome Biology

We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA librari...

doi.org

A belated announcement about our GuideScan2 paper finally out in Genome Biology: doi.org/10.1186/s130... GuideScan2 is a new flexible and efficient CRISPR gRNA design and analysis tool with command line and web interfaces. Please let us know what you think!

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2 - Genome Biology

We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA librari...

doi.org

Memory efficient and scalable gRNA design with GuideScan2 genomebiology.biomedcentral.com/articles/10....

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2 - Genome Biology

We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA librari...

genomebiology.biomedcentral.com

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2 genomebiology.biomedcentral.com/articles/10.... 🧬🖥️🧪 CLI github.com/pritykinlab/... Web app guidescan.com

Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants

Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...

biorxiv.org

Anshul Kundaje@anshulkundaje.bsky.social · 2y ago

Aiming to release our long awaited ChromBPNet preprint by early next week as well. I'm recovering from back to back infections for the past 6 weeks. But we're almost there. We have some solid variant prediction benchmarks in there against large supervised models and lots more. Stay tuned.

Excited to host @jianma.bsky.social today at Princeton CS and looking forward to his talk: cs.princeton.edu/events/26752 Come to CS 105 at 12:30 today if you are around!