Annika K K Weimer

Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

Polyclonal origins of human premalignant colorectal lesions

This study shows that many premalignant colorectal polyps contain multiple genetic lineages, indicating polyclonal origins rather than single-cell expansion.

The nascent transcriptome delineates the regulatory landscape in human health and disease

The paper presents a high-resolution atlas of transcriptional regulatory elements in human tissues and disease states using PRO-cap and deep learning models to prioritize noncoding variants.

Comparative atlas of genome-wide chromatin-associated protein co-occupancy

The paper identifies cell type-specific and shared chromatin-associated protein co-association modules using ChIP-Seq and machine learning in K562 and HepG2 cells.

Single-cell spatial mapping reveals alteration of tissue microenvironment during early colorectal cancer

The paper uses spatial CODEX experiments to show early colorectal cancer microenvironment changes in FAP, including CAFs, immune suppression, and beta-catenin nuclear translocation.

Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis

This study shows that early colorectal cancer loses promoter-enhancer connectivity, leading to gene expression changes and a two-phase model of transcriptional regulation.

The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states

The paper identifies regulatory programs in postnatal mouse development using single-nucleus data, revealing cell-type-specific and common regulatory topics across multiple tissues.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

Common and rare variant analyses combined with single-cell multiomics reveal cell-type-specific molecular mechanisms of COVID-19 severity

This study combines common and rare variant analyses with single-cell multiomics to identify cell-type-specific genetic risk factors for severe COVID-19, revealing molecular mechanisms and potential therapeutic targets.

Ultra high-throughput whole-genome methylation sequencing reveals trajectories in precancerous polyps to early colorectal adenocarcinoma

The paper uses ultra high-throughput methylation sequencing to study DNA methylation changes during colorectal cancer progression from normal tissue to adenocarcinoma.

Genome-wide Identification of the Genetic Basis of Amyotrophic Lateral Sclerosis

This study identifies 690 candidate ALS genes using a hierarchical Bayesian model, highlighting genetic convergence on the distal axon and functional significance in motor neurons.

High Resolution Single Cell Maps Reveals Distinct Cell Organization and Function Across Different Regions of the Human Intestine

The paper maps cell organization and function across human intestine regions using single nuclear RNA and open chromatin assays, revealing distinct cell neighborhoods and regulatory differences.