Alex K. Shalek

The paper develops scalable cell-free protein synthesis platforms to generate single-cell RNA-sequencing data on immune cell responses to cytokines and other signals, enabling functional discovery and drug target prioritization.

The paper identifies two distinct CD8 T cell gene expression programs in HBV infection that correlate with viral control and functional cure.

This study uses spatial transcriptomics to show that aging disrupts spatial and temporal coordination of folliculogenesis in mouse ovaries, leading to tissue disorganization and reproductive decline.

This study maps virus-specific nasal cell states in children using single-cell RNA sequencing and links them to disease severity and asthma risk.

This study uses spatial multi-omics to compare EBV-positive and EBV-negative cHL, identifying distinct TME features and immunological signatures linked to EBV.

The paper identifies early immune responses preceding HIV rebound and links them to viral control outcomes in individuals discontinuing antiretroviral treatment.

COSIE is a computational framework that integrates multiple spatial omics modalities to generate high-resolution molecular landscapes, outperforming existing methods across diverse datasets.

This paper introduces NCLUSION, a nonparametric clustering method for scRNA-seq that identifies marker genes and clusters simultaneously, showing improved performance and reduced runtime.

The paper introduces two methods to profile functional glycan-lectin interactions in tissues using single-cell and spatial multiomic approaches, revealing stimulus-specific glycan remodeling and spatial glycan programs in immune cells and follicular lymphoma.

The paper shows chronic metabolic stress in liver cells drives developmental programs and functional loss, mirroring tumor states and predicting poor cancer survival.

This study uses single-cell RNA-sequencing and other omics data to analyze the molecular features of pleural mesothelioma subtypes and identify potential drivers of tumor cell states.

This study shows that PPARγ downregulation in colonic CD8+ T cells of people with HIV on ART leads to epithelial barrier disruption by promoting lipid uptake and apoptosis.

This study uses scRNA-seq to analyze immune changes in SIV-infected rhesus macaques over time, revealing immune shifts during infection and ART, and identifying transcriptional signatures linked to immune dysregulation and treatment outcomes.

This study maps the spatiotemporal profile of ovulation in mice using single-cell RNA-seq and spatial transcriptomics, identifying cell state markers and interactions involved in the process.

This study uses single follicle RNA-seq to identify transcriptional signatures of ovarian follicles in mice, revealing stage-specific gene pathways involved in folliculogenesis.

This study creates a single-nucleus and spatial transcriptomic atlas of the COVID-19 liver, revealing cellular and functional disruptions associated with organ damage.

This paper introduces a method to prevent over-clustering in scRNA-seq by controlling double-dipping, improving differential expression analysis accuracy.

The paper identifies four immunomodulatory programs in glioma-associated myeloid cells using scRNA-seq and shows they are driven by microenvironmental cues and therapies, not cell type or mutation status.

This study introduces MicroCart, a framework for spatial multi-omics analysis of host-microbiome interactions in colitis, revealing tissue-level immune responses and microbial shifts.

This study examines how SARS-CoV-2 variants and vaccination affect nasal immunity across three waves, identifying changes in cellular states and immune responses.

This paper introduces IN-DEPTH and SGCC for spatial multi-omics analysis, revealing EBV-related immunomodulatory differences in DLBCL.

Congenital T cell activation in CTLA4-deficient patients impairs transitional to follicular B cell maturation and can be rescued by CTLA4 replacement therapy in vivo.

This study develops glycan-costumed virus-like particles that activate dendritic cells and induce type 1 anti-tumor immunity in a murine model.

The paper shows that CD4+ T cells reduce inflammation and disease severity during Mtb reinfection by reprogramming CD8+ T cells and innate immune cells.

The paper investigates how sequence variations in LAT affect T cell activation pathways and identifies conserved motifs critical for function.

This study identifies mutation and transcriptional state compatibility in Ph+ ALL MRD, showing that targeting these interactions can overcome BCR::ABL1 independence and improve MRD monitoring.

This study uses multi-omics approaches to analyze myeloid cell diversity in TB granulomas and identifies IFN-γ, TGF-β, and time as factors driving macrophage diversity.

This paper introduces CellSNAP, a self-supervised method that integrates spatial, transcriptomic, and proteomic data to improve cell population delineation in spatial-omics datasets.

The paper identifies a novel mechanism where CAR-T cell therapy activates CD8+ cytotoxic bystander T cells in non-human primates and patients, showing they can kill leukemic cells independently of TCR.

The paper introduces a method to prioritize causal genes for complex traits by integrating GWAS data with gene expression and biological data, achieving high precision in gene-trait pair identification.