cellNexus: Quality control, annotation, aggregation and analytical layers for the Human Cell Atlas data #SingleCell 🧪🧬🖥️
www.biorxiv.org/content/10.64898/2026.04...

Single-Cell and Tissue-Specific CRISPR Editing Analyses Unveil New Insights to Off-Targets and Translocations www.biorxiv.org/content/10.64898/2026.04...

An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis Nature Communications - Primary sclerosing cholangitis (PSC) is an autoimmune condition affecting the liver. Here, the authors generate an immunobiliary transcriptomic atlas and show that dendritic...

Our study on rare immune cell networks governing liver cholangitis is now online! Using multiplexed single-cell and spatial omics, we discovered a triad of cholangiocytes, dendritic cells and gdT cells regulating the inflammatory and fibrotic tissue response. Rare immune cells matter!
rdcu.be/fc60M

We GoT a Filling…uuuuhoooo

𝗧𝗮𝗿𝗴𝗲𝘁𝗲𝗱 𝘀𝗲𝗾𝘂𝗲𝗻𝗰𝗶𝗻𝗴 𝗼𝗳 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻𝘀 𝘃𝗶𝗮 𝗥𝗡𝗔-𝘁𝗲𝗺𝗽𝗹𝗮𝘁𝗲𝗱 𝗴𝗮𝗽 𝗳𝗶𝗹𝗹𝗶𝗻𝗴 𝗼𝗳 𝗼𝗹𝗶𝗴𝗼𝗻𝘂𝗰𝗹𝗲𝗼𝘁𝗶𝗱𝗲𝘀 𝗳𝗼𝗿 𝘀𝗶𝗻𝗴𝗹𝗲-𝗰𝗲𝗹𝗹 𝗥𝗡𝗔-𝘀𝗲𝗾

www.biorxiv.org/content/10.6...

Super Bloom: Fast and precise filter for streaming k-mer queries www.biorxiv.org/content/10.64898/2026.03...

PerturbAI out of stealth paper:

Genome-scale functional mapping of the mammalian whole brain with in vivo Perturb-seq www.biorxiv.org/content/10.64898/2026.03...

CellVoyager: AI CompBio agent generates new insights by autonomously analyzing biological data - Nature Methods CellVoyager is an artificial intelligence agent capable of exploring new biological hypotheses by autonomously analyzing single-cell RNA sequencing datasets and accounting for background information a...

CellVoyager: an AI agent that explores new biological hypotheses by autonomously analyzing scRNA-seq datasets.

www.nature.com/articles/s41...

Just the beginning of what we have been building and working towards at Gordian: www.businesswire.com/news/home/20...

DINOcell: Learning Generalizable Perturbation Effects through Self-Distillation #SingleCell 🧪🧬🖥️
www.biorxiv.org/content/10.64898/2025.12...

Reconstructing developmental and disease progression with sample-level embeddings www.biorxiv.org/content/10.64898/2025.12...

Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!

We have thought about it, I did a lot of lung organoid work in my postdoc, just not convinced, for the disease we work on, that you can measure properties relevant enough to clinical outcomes in organoids

Gordian Biotechnology Discovering new therapies for complex age-related disease.

Pretty much what we do at Gordian Biotechnology, except we focus mostly on in vivo animal models. www.gordian.bio

Tahoe-x1: Scaling Perturbation-Trained Single-CellFoundation Models to 3 Billion Parameters www.biorxiv.org/content/10.1101/2025.10....

Perturbation-aware representation learning for in vivo genetic screens www.biorxiv.org/content/10.1101/2025.10....

FUSED: CROSS-DOMAIN INTEGRATION OF FOUNDATION MODELS FOR CANCER DRUG RESPONSE PREDICTION www.biorxiv.org/content/10.1101/2025.09....

Aberrant intermediate alveolar epithelial cells promote pathogenic activation of lung fibroblasts in preclinical fibrosis models - Nature Communications The direct contribution of aberrant epithelial cells to lung fibrosis is largely unknown. The authors use murine and human systems to identify how these cells activate fibroblasts, and how reciprocal signals cause them to enter a profibrotic state.

Announcing our latest publication, just out today
@NatureComms, advancing our understanding of interstitial lung disease. Congrats to co-senior authors Drs. Jeremy Katzen and Kostas Alysandratos and their teams @Penn @CReM_Boston. Check it out here: www.nature.com/articles/s41...

Domain-Invariant Feature Learning for Patient-Level Phenotype Prediction from Single-Cell Data www.biorxiv.org/content/10.1101/2025.09....

Single Cell Foundation Models Evaluation (scFME) for In-Silico Perturbation www.biorxiv.org/content/10.1101/2025.09....

Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance.

The regulation of most proteins is dominated by different regulatory mechanisms across cell types.

Gratifyingly, this complex regulation defines simple rules ⬇️

www.biorxiv.org/content/10.1...

@biorxivpreprint.bsky.social Bispecific Targeting of CHI3L1 and PD-1/PD-L1 Axis as a Novel Therapeutic Strategy for Idiopathic Pulmonary Fibrosis
www.biorxiv.org/content/10.1...

Inflammation-inducible IL-1-targeted therapy using an rAAV vector as a long-lasting, pathophysiologic treatment for chronic inflammatory diseases @moltherapy.bsky.social @umasschan.bsky.social
www.cell.com/molecular-th...

Metabolomic, Lipidomic, and Enterohormone Changes in the Progression from MASLD to MASH www.biorxiv.org/content/10.1101/2025.09....

Nutrient-Sensing Nuclear Receptor PPARα Controls Liver Proteostasis www.biorxiv.org/content/10.1101/2025.09....

PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia @nature.com
www.nature.com/articles/s41...

scAgeClock: a single-cell transcriptome based human aging clock model using gated multi-head attention neural networks www.biorxiv.org/content/10.1101/2025.08....

Single-cell atlas of human liver and blood immune cells across fatty liver disease stages reveals distinct signatures linked to liver dysfunction and fibrogenesis @natimmunol.nature.com
www.nature.com/articles/s41...

Targeting acid ceramidase enhances collagen degradation by hepatic stellate cells via PKCα and MMP-1, uncovering a pathway to reverse liver fibrosis
www.science.org/doi/10.1126/...

anndataR improves interoperability between R and Python in single-cell transcriptomics Many single-cell transcriptomics datasets are stored in the HDF5-backed AnnData (H5AD) file format, as popularised by the Python scverse ecosystem. However, accessing these datasets from R, allowing u...

www.biorxiv.org/content/10.1...