Albin Sandelin

The paper introduces nucCAGE and PRIME to identify active cis-regulatory elements with high sensitivity and applies them to create a cell-type-resolved CRE atlas.

The paper develops SurpHer, a genetically encoded ratiometric pH sensor, and demonstrates its use in imaging extracellular pH dynamics in human cells and tumor microenvironments.

This paper introduces a microfluidic device that creates oxygen and pH gradients to study their effects on cancer and stromal cells in the tumor microenvironment.

This study identifies LINC00673, a long noncoding RNA from a Sox9-associated super-enhancer, as critical for pancreatic regeneration and PDAC initiation by regulating cell-autonomous and non-cell-autonomous processes.

This study shows that acidic tumor environments enhance pancreatic cancer stem cell properties and metastasis in mice.

The paper examines the temporal response to maternal pulmonary immune activation across maternal and fetal organs using multi-omics, finding that the placenta protects the fetus through metabolic adaptations rather than immune responses.

TranscriptomeReconstructoR provides a pipeline for accurate de novo transcriptome annotation using integrated RNA-seq and 5/3 tag sequencing data, improving gene model quality in Arabidopsis thaliana.

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

The paper reassesses the existence of PROMPTs and eRNAs in Arabidopsis thaliana using RNA sequencing in nuclear decay mutants, identifying exosome-sensitive transcripts and antisense RNAs.

CAGEfightR is an R/Bioconductor package for analyzing CAGE data, enabling TSS and enhancer identification, annotation, quantification, and visualization.

The paper extends IsoformSwitchAnalyzeR to enable genome-wide analysis of alternative splicing changes and their functional consequences using RNA-seq data from The Cancer Genome Atlas.

This study provides a comprehensive TSS map for fission yeast under various stress and media conditions using CAGE, revealing new insights into gene regulation and promoter diversity.

The paper identifies shared expression patterns of genetic variants across tissues and cell types, enabling fine mapping of disease-associated variants and revealing key cell types involved in disease pathogenesis.

The paper investigates how promoter spacing influences PROMPT expression, stability, and length, revealing a mechanism for generating alternative TSSs in mammalian transcriptomes.

This paper proposes a unified model of promoters and enhancers as a single class of transcriptional regulatory elements with shared architectural features.

The paper develops a method to classify human RNAs based on exosome sensitivity and transcription initiation, identifying functional lncRNAs and distinguishing them from unstable transcripts.