CITE-seq

Cleanet: robust doublet detection in cytometry data based on protein expression patterns

Cleanet detects and classifies doublets in cytometry data using protein expression patterns, improving accuracy over traditional bivariate gating methods.

BCG Vaccination at Birth Shapes the TCR Usage and Functional Profile of MR1T Cells at 9 Weeks of Age

This study examines how BCG vaccination at birth affects MR1T cell TCR usage and function in infants, finding increased type I interferon response and a TCR cluster enriched in vaccinated infants.

SCREAM: Single-cell Clustering using Representation Autoencoder of Multiomics

SCREAM is a deep learning framework for integrating and clustering multi-omics single-cell data, showing superior performance in benchmarking with high ARI and NMI scores.

Discovering Condition-specific Cell Populations via Integrative Clustering of Single-cell Data

INCLOSE identifies condition-specific cell populations by integrating single-cell omics data and metadata, revealing immune suppression in acute myeloid leukemia.

Base edited "universal" donor CAR T cell strategies for acute myeloid leukaemia

This study shows that base edited universal donor CAR T cells targeting multiple antigens can inhibit AML in mice, with combination therapies needed for heterogeneous disease.

Delineating inter- and intra-antibody repertoire evolution with AntibodyForests

AntibodyForests quantifies inter- and intra-antibody repertoire evolution using protein language models and structure analysis.

Integrate and generate single-cell proteomics from transcriptomics with cross-attention

This paper introduces scProca, a deep generative model that integrates and generates single-cell proteomics data from transcriptomics using cross-attention mechanisms.

A rare HSC-derived megakaryocyte progenitor accumulates via enhanced survival and contributes to exacerbated thrombopoiesis upon aging

The paper identifies a rare HSC-derived megakaryocyte progenitor that accumulates with age, contributing to exaggerated thrombopoiesis and age-related platelet-mediated morbidities.

CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data

CLUEY improves cell type detection and clustering in single-cell omics by integrating biological knowledge to guide clustering and enhance interpretability.

Single-cell proteomics of pancreatic islet cells reveals type 1 diabetes and donor-specific features

The paper performs single-cell proteomics on pancreatic islets from healthy and T1DM donors, identifying cell type-specific differences and donor-specific features.

LieOTMap: A Differentiable Approach to Cryo-EM Fitting via Lie-Theoretic Optimal Transport

LieOTMap fits high-resolution atomic models into cryo-EM maps using a differentiable framework based on Lie algebra and optimal transport, achieving accurate alignment of E. coli GroEL.

LieMap: A Fast and Transparent Gradient-Based Method for Cryo-EM Structure Fitting

LieMap fits high-resolution atomic models into cryo-EM maps using gradient-based optimization, achieving a low RMSD for E. coli GroEL structure fitting.

CytoVI: Deep generative modeling of antibody-based single cell technologies

CytoVI is a deep generative model for antibody-based single cell technologies that improves integration, imputation, and analysis across different platforms and antibody panels.

IL-25-induced memory ILC2s mediate long-term small intestinal adaptation

This study shows that IL-25 induces memory ILC2s in the small intestine that provide long-term protection against barrier pathogens.

Simultaneous Profiling of the Blood and Gut T and B Cell Repertoires in Crohn's Disease and Symptomatic Controls Illustrates Tissue-specific Alterations in the Immune Repertoire of Crohn's Disease Patients

Antigen stimulation drives clonal expansion of latent CD4+ T cells using a full-length HIV latency reporter

This study shows antigen stimulation drives clonal expansion of latent HIV-infected CD4+ T cells through TCR and co-stimulatory signals, with IL-7 and CD28 playing key roles.

Immune interaction signatures in adipose tissue fibroblasts in obesity-associated atherosclerosis

The paper identifies immune-related transcriptional changes in adipose-derived fibroblasts in obesity-associated atherosclerosis using single-cell RNA sequencing and spatial transcriptomics.

CD33KO-CD33-mesothelin loop CAR design avoids fratricide and improves efficacy of iNK cells against acute myeloid leukemia

This study designs a CD33-mesothelin loop CAR to enhance iNK cell efficacy against AML by avoiding fratricide and improving cytotoxicity.

Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling

Clonotrace integrates gene expression and clonotype data to infer cell state transitions and fate biases, improving understanding of lineage dynamics in various biological systems.

Chronic Infection Perturbs the Affinity Hierarchy of Antiviral B Cells

This study shows that chronic viral infection disrupts B cell affinity hierarchies by preferentially causing attrition of high-affinity B cells due to excessive antigen stimulation.

Monocyte Dysregulation Defines an MDD-Specific Transcriptional Signature Closely Linked to Clinical MDD Traits

The paper identifies a monocyte dysregulation signature in MDD linked to clinical symptoms using CITE-Seq data from PBMCs.

Accurate and scalable multi-disease classification from adaptive immune repertoires

This paper introduces FACTS, a scalable machine learning framework for multi-disease classification using TCR repertoires, achieving high accuracy and preserving biological signals.

The quest continues: Human CD4+ CD16+ CD56+ "exTreg" resemble NKT cells instead

The paper re-evaluates the identity of CD4+ CD56+ CD16+ cells in human PBMC, finding they resemble NKT cells rather than exTreg, and explores Treg stability and Tr17 induction for therapeutic applications.

IL-7 armed binary CAR T cell strategy to augment potency against solid tumors

This study develops a binary CAR T cell strategy targeting PSCA and MUC1 with IL-7 expression to improve antitumor potency and persistence in pancreatic tumors.

Superior batch alignment and hyper-dimensional cytometry representations allow ultra-sensitive classification of disease phenotypes

This paper introduces a neural network-based batch alignment method for cytometry data that preserves biological signals and enables hyperdimensional representation for improved disease phenotype classification.

Single-Cell Antigen Receptor Sequencing in Pigs with Influenza

This study uses single-cell receptor sequencing to analyze T and B cell repertoires in pigs infected with influenza, finding expanded T cell clonotypes after re-exposure to antigens.

Conserved heavy/light contacts and germline preferences revealed by a large-scale analysis of natively paired human antibody sequences and structural data.

PairedAbNGS pools 58 single-cell bioprojects of natural paired human and mouse antibodies, revealing heavy/light V gene pairing biases beyond usage frequencies and conserved CDR3-FWR2 inter-chain contacts.

Analyzing the T cell receptor repertoire of 2,804 individuals with inflammatory bowel disease identifies public T cell responses involved in the pathogenesis

The paper identifies and validates T cell receptor clonotypes associated with Crohn's disease and ulcerative colitis, suggesting they are potential therapeutic targets.

Cutting Edge: An mRNA Platform to Create Isolated, Monospecific Th1 Responses

This paper develops an mRNA platform to generate monospecific Th1 responses in mice by encoding epitopes linked to MHCII, demonstrating efficacy against Salmonella infection.

A new double reporter strategy reveals a subset of non-migratory hematopoietic stem cells localized in a dynamic bone marrow niche.

This paper introduces a double reporter strategy to identify a non-migratory subset of hematopoietic stem cells in the bone marrow niche and shows their dynamic interactions during stress and aging.