scATAC-seq

Convergent Epigenetic Evolution Drives Relapse in Acute Myeloid Leukemia

This study identifies convergent epigenetic evolution in AML relapse using ATAC-seq and mtscATAC, showing that epigenetic changes drive relapse independent of genetic mutations.

HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling

HIPSD&R-seq profiles genomic copy number and transcriptomes in thousands of cells, enabling rare clone detection in human cell models and primary tissue.

Robust CNV detection using single-cell ATAC-seq

This paper introduces RIDDLER, a single-cell ATAC-seq CNV detection algorithm that outperforms existing methods in cancer cell line models and 10x multimome data.

Multimodal single-cell profiling of T cell specificity and reactivity in lung cancer

This study uses multimodal single-cell profiling to analyze T cell specificity and reactivity in lung cancer patients, identifying tumor- and virus-reactive T cells and their functional states.

Longitudinal and multimodal auditing of tumor adaptation to CDK4/6 inhibitors in HR+ metastatic breast cancers

This study creates a multimodal tumor atlas to analyze how metastatic HR+ breast cancers adapt to CDK4/6 inhibitors, revealing mechanisms like mTORC1 activation and immune microenvironment changes.

scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data

scEpiTools is a database that organizes and recommends tools for analyzing single-cell epigenomic data, including an ensemble method for chromatin accessibility analysis.

Scalable joint non-negative matrix factorisation for paired single cell gene expression and chromatin accessibility data

The paper introduces intNMF, a scalable method for integrating single cell gene expression and chromatin accessibility data, showing improved efficiency and interpretability in analyzing biological systems.

Single-cell multi-omics map of human foetal blood in Down's Syndrome

This study integrates single-cell multi-omics data from human foetal blood to show that trisomy restructures enhancer-gene maps, leading to dysregulated erythroid differentiation and haematological abnormalities in Down's Syndrome.

Regulatory Mechanisms Orchestrating Cellular Diversity in Cd36+ Olfactory Sensory Neurons Revealed by Single-Cell Multi-omics Analysis.

Discovering chromatin dysregulation induced by protein-coding perturbations at scale

The paper introduces PROD-ATAC, a method to study chromatin effects of protein-coding variants, revealing common dysregulation mechanisms across oncofusions and cancers.

Pathological beige remodeling induced by cancer cachexia depends on the disease severity and involves mainly the trans-differentiation of mature white adipocytes

This study investigates beige remodeling in cancer cachexia, showing it depends on disease severity and involves transdifferentiation of mature white adipocytes.

Metabolic adaptation pilots the differentiation of human hematopoietic cells

The paper investigates how metabolic perturbations affect chromatin structure and gene expression during human hematopoietic cell differentiation.

Universal preprocessing of single-cell genomics data

The paper describes a universal preprocessing workflow for single-cell genomics data using the cellatlas package.

SnapATAC2: a fast, scalable and versatile tool for single-cell omics analysis

SnapATAC2 is a fast, scalable dimensionality reduction tool for single-cell omics data that improves accuracy and efficiency in capturing cellular heterogeneity across multiple modalities.

KaryoTap Enables Cost-Effective High-Throughput Single-Cell Aneuploidy Profiling and Reveals How Positive and Negative Selection Shapes Cancer Genomes

KaryoTap enables high-throughput single-cell aneuploidy profiling, revealing that positive and negative selection shape cancer genomes by influencing chromosomal gains and losses.

Multi-dimensional profiling of hepatoblastomas and patient-derived tumor organoids uncovers tumor subpopulations with divergent WNT activation profiles and identifies pan-hepatoblastoma drug sensitivities

This study identifies two hepatoblastoma subtypes with distinct WNT activation profiles and discovers drug sensitivities in patient-derived tumor organoids.

Single-Cell Transcriptional and Epigenetic Profiles of Male Breast Cancer Nominate Salient Cancer-Specific Enhancers

This study presents single-cell transcriptional and epigenetic profiles of male breast cancer to identify cancer-specific enhancers and their regulatory roles.

Nuclear genetic control of mtDNA copy number and heteroplasmy in humans

Blood whole genomes from 274,832 people yield 92 independent nuclear signals for mtDNA copy number and 42 for inherited heteroplasmy levels, implicating mtDNA replication machinery.

Predicting the impact of sequence motifs on gene regulation using single-cell data

The paper uses a convolutional neural network to identify regulatory motifs and their cell type-specific importance from single-cell data, explaining 29% of gene expression variance in mouse tissues.

Single-cell multi-omic topic embedding reveals cell-type-specific and COVID-19 severity-related immune signatures

This study introduces moETM, a deep learning method for analyzing single-cell multi-omic data, and shows it identifies immune signatures and COVID-19 severity biomarkers.

Continuous lifelong learning for modeling of gene regulation from single cell multiome data by leveraging atlas-scale external data

LINGER improves GRN inference from single-cell multiome data by integrating atlas-scale bulk data and TF motif knowledge, achieving 2-3 fold higher accuracy.

simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data

simCAS generates high-fidelity scCAS data using embeddings, enabling benchmarking of computational methods for cell clustering, trajectory inference, and cis-regulatory interaction analysis.

Mathematical modeling of clonal interference by density-dependent selection in heterogeneous cancer cell lines

The paper models clonal interference in cancer cell lines using phenotypic data to predict growth rate and carrying capacity differences between karyotypes.

TriTan: An efficient triple non-negative matrix factorisation method for integrative analysis of single-cell multiomics data

TriTan is a triple non-negative matrix factorisation method for single-cell multiomics data integration, offering efficient computation and improved interpretability.

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

SCENIC+ infers enhancer-driven gene regulatory networks from single-cell multi-omics data, improving TF identification and enabling analysis of regulatory dynamics and perturbations.

Tutorial: guidelines for manual cell type annotation of single-cell multi-omics datasets using interactive software

The paper provides a framework and interactive software tools for manually annotating cell types in single-cell multi-omics datasets, demonstrating how different modalities can be combined to improve annotation accuracy.

CMOT: Cross Modality Optimal Transport for multimodal inference

CMOT infers missing single-cell modalities using optimal transport, outperforming existing methods and producing biologically interpretable results.

LRT: T Cell Trajectory Inference by Integrative Analysis of Single Cell TCR-seq and RNA-seq data

LRT integrates scTCR-seq and scRNA-seq data to infer T cell trajectories by combining clonal relationships with transcriptomic profiles.

CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE

The paper compares chromatin accessibility and gene regulatory networks in invasive trophoblast cells between rat and human to identify conserved regulatory mechanisms.

MultiVI: deep generative model for the integration of multi-modal data

MultiVI integrates multi-modal single-cell data by creating a joint representation and imputing missing values while correcting batch effects.