CITE-seq

Markov Field network integration of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques

The paper uses Markov Fields to integrate multi-modal immune data from vaccinated macaques, identifying critical immune interactions and predicting perturbation effects.

Linking myelin and Epstein-Barr virus specific immune responses in multiple sclerosis: insights from integrated public T cell receptor repertoires

This study analyzes T cell receptor repertoires in MS patients and controls to explore the relationship between EBV-specific and myelin-specific immune responses, finding distinct patterns associated with MS.

Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes

The paper introduces EuPRI, a resource of RNA motifs for 34,736 RBPs across 690 eukaryotes, expanding motif knowledge and enabling functional and evolutionary insights.

Characterizing human CMV-specific CD8+ T cells using multi-layer single-cell omics

The paper characterizes human CMV-specific CD8+ T cells using a five-layer multi-omics approach and identifies novel T cell receptor sequences for CMV epitopes.

scConfluence : single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features

scConfluence improves single-cell diagonal integration by combining autoencoders with regularized Inverse Optimal Transport, outperforming existing methods in three biological applications.

The Observed T cell receptor Space database enables paired-chain repertoire mining, coherence analysis and language modelling

The paper introduces the OTS database, a curated resource of paired-chain TCR sequences, and develops a language model for analyzing TCR pairings and coherence.

Exploring the Transcriptomic Profile of Human Monkeypox Virus via CAGE and Native RNA Sequencing Approaches

This study uses CAGE and long-read RNA sequencing to analyze the transcriptional architecture of human monkeypox virus, identifying alternative TSSs, TESs, promoter elements, and novel genes.

Oncolytic vaccinia virus expression of a defined peptide-MHCI complex as a precision cancer immunotherapy platform

This study shows that oncolytic vaccinia virus expressing peptide-MHC-I complexes can effectively stimulate CD8+ T cell responses and enhance tumor clearance in cancer models.

Identification of a novel myosin antigen activating CD8+ T cells in C57BL/6 mice

The paper identifies a novel myosin antigen and specific CD8+ T cell receptors in C57BL/6 mice, expanding tools for studying heart-directed immune responses.

Accurate, fast and memory efficient quantification of immune cell phenotypes in cytometry using machine learning

The paper benchmarks machine learning algorithms for cytometry data analysis, finding decision trees provide high accuracy, speed, and memory efficiency for immune cell phenotype quantification.

FlowAtlas.jl: an interactive tool bridging FlowJo with computational tools in Julia

FlowAtlas.jl connects FlowJo with Julia-based computational tools for cytometry data analysis, demonstrating its capabilities on a human immune cell dataset.

Integrating T-cell receptor and transcriptome for large-scale single-cell immune profiling analysis

The paper introduces mvTCR, a multimodal generative model for integrating TCR and transcriptome data to improve analysis of single-cell immune profiling data.

De Novo Atomic Protein Structure Modeling for Cryo-EMDensity Maps Using 3D Transformer and Hidden MarkovModel

Cryo2Struct improves de novo atomic protein structure modeling from cryo-EM density maps using a 3D transformer and HMM, outperforming Phenix on multiple metrics.

Single-cell transcriptome and T cell receptor profiling of the tuberculin skin test

The paper profiles single-cell transcriptomes and T cell receptors in human tuberculin skin tests to characterize the immune response to Mycobacterium tuberculosis.

Perinatal brain group 3 innate lymphoid cells are involved in the formation of murine dural lymphatics

This study shows that perinatal RORγt+ ILC3s are essential for dural lymphatic vessel development in mice.

Liam tackles complex multimodal single-cell data integration challenges

Liam integrates multimodal single-cell data by learning a joint low-dimensional representation, outperforming existing methods on Multiome and CITE-seq datasets.

A Catalog of the Public T-cell Response to Cytomegalovirus

The paper provides a catalog of public T-cell receptors specific to cytomegalovirus (CMV) and explores their antigen specificity and subgroup variations.

Circulating tumor cell characterization and classification by novel combinatorial dual-color (CoDuCo) in situ hybridization and supervised machine learning

The paper develops a novel CoDuCo in situ hybridization method combined with machine learning to classify and characterize circulating tumor cells in prostate cancer, identifying resistance mechanisms and therapeutic targets.

Explainable models using transcription factor binding and epigenome patterns at promoters reveal disease-associated genes and their regulators in the context of cell-types

The paper uses epigenetic features to predict disease-associated genes and their regulators, emphasizing cell-type context and validating findings with genomic data.

Natural Killer Cell Dysfunction In Human Bladder Cancer Is Caused By Tissue-Specific Suppression of SLAMF6 Signaling

This study identifies SLAMF6 signaling suppression in bladder cancer tumor microenvironment as a cause of NK cell dysfunction, showing restoration of function under normoxic conditions.

Loss of circulating CD8α+ NK cells during human Mycobacterium tuberculosis infection

The paper identifies CD8+ NK cells as a Mtb-responsive population with enhanced maturity and cytotoxicity in human TB infection, correlating with disease resistance.

Single-cell multimodal profiling of atherosclerosis identifies CD200 as a lineage marker of vascular smooth muscle cells and their derived cells

The paper identifies CD200 as a specific marker for vascular smooth muscle cells and their derived cells in atherosclerosis using CITE-seq and validates it across multiple techniques.

SuperCellCyto: enabling efficient analysis of large scale cytometry datasets

SuperCellCyto efficiently analyzes large cytometry datasets by grouping similar cells into supercells, avoiding the need for random subsampling.

Pooled screening for CAR function identifies novel IL13Rα2-targeted CARs for treatment of glioblastoma

The paper identifies novel IL13Rα2-targeted CARs with improved anti-glioblastoma efficacy using a pooled screening platform.

TET2 regulates early and late transitions in exhausted CD8+ T-cell differentiation and limits CAR T-cell function

This study shows that targeting TET2 in CAR T-cells improves their anti-tumor responses by limiting terminal exhaustion and enhancing therapeutic potential.

Immune signatures of common exposures through co-occurrence of T-cell receptors in tens of thousands of donors

The paper identifies immune exposure signatures by clustering T-cell receptors co-occurring across donors, linking them to specific pathogens and HLA alleles.

Advancing CAR T-Cell Therapy: Simultaneously Attack Tumor and Immunosuppressive Cells in the Tumor Microenvironment

This paper develops a PD-L1-targeting CAR T-cell therapy (MC9999) that effectively attacks both tumor and immunosuppressive cells in solid tumors.

CITE-seq analysis reveals human cytomegalovirus and diabetes-associated adaptive NK cell alterations in cardiovascular disease.

The paper uses CITE-seq to analyze NK cell alterations in CAD patients, finding SPON2/IFNG ratio and adaptive NK cell signatures correlate with disease severity and inflammation.

Engineering One-Signal Activated TILs with CD3ζ-CD28 Chimeras Optimizes the Antitumor Efficacy of TIL-Based Immunotherapy

This paper engineers one-signal-activated TILs with CD3ζ-CD28 chimeras to enhance antitumor efficacy in immunotherapy.

Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infection.

This study uses single-cell lineage tracing to show that CD8 T-cell clones exhibit differential fate commitment during acute infection, with some clones adopting memory or effector biases over time.