Archibald Enninful

Determining cellular phylogeny and migration at high resolution in spatial genomics

StarTrak infers cellular migration and phylogeny by integrating somatic variants, spatial data, and transcriptomics at single-pixel resolution in spatial genomics.

Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights

A free Meta Quest virtual reality app harmonizes CODEX, Visium, Xenium, volumetric immunofluorescence and electron microscopy data from 5 organs into 4 scale levels using the Human Reference Atlas.

All-Optical Multimodal Mapping of Single Cell Type-Specific Metabolic Activities via REDCAT

REDCAT maps single-cell type-specific metabolic activities in tissues using multimodal all-optical imaging, revealing metabolic specialization and reprogramming in immune and liver tissues.

SenNet Portal: Build, Optimization and Usage

The paper introduces the SenNet Portal, a resource for senescent cell data and tools, and discusses its usage and future developments.

Human Lymph Node Cellular Senescence Atlas Reveals Age-Dependent Alteration in Germinal Center B Cell Function and Niches

This study maps age-related cellular senescence in human lymph nodes, identifying senescence markers and spatial shifts in germinal center B cells.

Single-cell spatial multi-omics molecular pathology enabled by SuperFocus

SuperFocus integrates histopathology with single-cell spatial multi-omics data from spot-based measurements, improving accuracy by 28-73% over existing methods.

Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

Thermostable RNaseH release of barcoded cDNA keeps sections intact for CODEX imaging, yielding same-section whole-transcriptome and protein maps plus CODEX-guided spot deconvolution in FFPE tissues.

Exploring endothelial cell environments across organs in spatially resolved omics data

The paper analyzes endothelial cell environments across organs using spatially resolved omics data and provides an interactive tool for visualizing cell distances and neighborhoods.

Spatial epigenomic niches underlie glioblastoma cell state plasticity

This study identifies two epigenetically-defined spatial niches in glioblastoma that influence cell state plasticity through local and long-range molecular signals.

Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT

Perturb-DBiT co-sequences spatial transcriptomes and gRNAs on one tissue section, supporting genome-wide in vivo CRISPR screens in FFPE and fresh-frozen tumors across three cancer models.

Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues

This paper introduces Patho-DBiT, a method for spatial transcriptomics in FFPE tissues, enabling RNA biology analysis including splicing, variants, and regulatory networks in clinical samples.

Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping

Spatial-CITE-seq profiles proteins and transcriptomes in tissues, revealing spatially distinct immune responses in mouse and human tissues.

Spatial Epigenome Sequencing at Tissue Scale and Cellular Level

This paper presents spatial epigenome profiling using CUT&Tag and microfluidic barcoding to map histone modifications at tissue scale and single-cell level in mouse embryos and olfactory bulbs.

High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue

DBiT-seq enables high-spatial-resolution multi-omics mapping of mouse embryos by deterministic barcoding, revealing tissue types and fine features like retinal pigmented epithelium and microvasculature.

Spatial transcriptome sequencing of FFPE tissues at cellular level

The paper develops DBiT-seq for spatial transcriptome sequencing of FFPE tissues at the cellular level, demonstrating its application in mouse embryos and adult tissues.

High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue

The paper was withdrawn due to a duplicate posting and directs readers to the current version on bioRxiv.