Alexis J. Combes

This study identifies RasGRP1 as a regulator of tuft cell differentiation in the intestine, showing it restricts progenitor proliferation and enhances IL-13-driven responses.

SNUPR enables single-cell UPR profiling and reveals the role of IRE-1 axis in predicting bortezomib resistance in multiple myeloma.

The paper identifies CD8+ T cells as key drivers of fibrosis in morphea-spectrum diseases through fibroblast IFN-γ signaling using spatial transcriptomics.

This study develops an iSCST framework for FFPE biopsies, identifying colitis-associated cell networks and VDZ response signatures in IBD patients.

The paper compares mouse and human tumor microenvironments, identifying conserved and species-specific features in immune composition and gene expression programs.

The paper introduces a temporal AI model, MaxToki, trained on extensive gene data to predict cell state changes across human aging and identifies age-modulating targets.

The paper profiles myeloid cells in breast cancer primary tumors and metastases to show how tumor heterogeneity drives shifts in myeloid cell phenotypes from anti- to pro-metastatic.

The paper uses local gene editing in mouse tumor models to discover a novel fibroblast state and its impact on the tumor microenvironment.

The paper identifies coordinated variation between immune systems and microbiomes in healthy humans, linking it to tonic interferon states.

This study shows neonatal human naive CD4+ T cells have higher CD38 expression, linking it to glycolytic metabolism and tolerogenic function compared to adult cells.

This study uses spatial transcriptomics to identify CXCL12+ fibroblasts as central immune organizers in AAA through CXCR4 signaling, revealing stromal-immune interactions that drive disease progression.

The paper shows congenital CMV infection leads to oligoclonal expansion of cytotoxic γδ T cells with fetal-like TCR features in neonates.

This study shows that activating the STING pathway in osteosarcoma leads to tumor regression and immune memory, suggesting it as a therapeutic target.

The paper identifies shared mechanisms of HBsAg seroclearance using a mouse model and longitudinal PBMCs from CHB patients, showing CD4+ T cell activation is essential for clinical cure.

The paper introduces anticlustering to balance batches and minimize batch effects in high-throughput sequencing, showing improved balance compared to existing methods.

The paper uses single-cell proteomics and metabolomics to study how Ras pathway mutations affect hematopoiesis, finding distinct impacts on HSC compartments and metabolism.

The paper uses single-cell transcriptomics to analyze endometrial cells from endometriosis patients, revealing altered cellular features and immune communication networks across the menstrual cycle.

This study shows that a short-term high-fat diet during the onset of psoriasis worsens disease severity through immune system changes, even after returning to a normal diet.

This study identifies a biomarker, {beta}Alt, that predicts immune checkpoint blockade response in cold tumors by integrating TGF{beta} signaling, DNA repair, and immune context signatures.

The paper identifies two immunological subtypes of Sjögren's disease using single-cell RNA sequencing, highlighting distinct IFN-I signatures and transitional B cell characteristics.

This study shows that CD206+ macrophages support an anti-tumor network involving cDC1, NK cells, and CD8 T cells, and their depletion impairs tumor control in mice and correlates with poor survival in humans.

This study creates a comprehensive single-cell atlas of the maternal-fetal interface, identifying cell-type-specific dysregulation in pregnancy complications.

The paper identifies space-time gene expression patterns in healing wounds and finds their conservation in tumors, revealing multicellular coordination and gene program activation.

This study identifies ethnicity-specific transcriptomic subgroups in SLE patients using RNA-seq data and correlates them with disease activity.