Andreas Beyer

Gene expression adaptation of metastases to their host tissue

This study identifies gene expression adaptations of metastases to host tissue using single-cell RNA-sequencing and a novel computational approach, revealing liver-specific expression signatures in colorectal cancer metastases.

Rare genetic variants in the IIS/mTOR signalling pathway identified in exceptionally long-lived individuals show shared in vitro effects associated with lifespan across species

This study identifies rare genetic variants in the IIS/mTOR pathway in long-lived humans and shows they have shared functional effects on lifespan-related traits in mice.

Modulation of the RNAse P/MRP complex and mitochondrial ribosome enhances cytosolic ribosome coordination and sustains longevity

This study shows that restoring ribosomal homeostasis by targeting RNAse P/MRP or mitochondrial ribosome extends lifespan in C. elegans by improving proteostasis and ribosome assembly.

Estimating changes in RNA Polymerase II elongation and intron splicing speeds from total RNA-seq data

A combination of the geroprotectors trametinib and rapamycin is more effective than either drug alone

This study shows that combining trametinib and rapamycin extends mouse lifespan more than either drug alone and improves health markers in older age.

Single-Cell Resolution of Cellular Damage Illuminates Disease Progression

The paper develops single-cell damage scores to quantify cellular deterioration in degenerative diseases and applies them to murine and human datasets to identify molecular trajectories of damage.

Esophageal adenocarcinoma relapse after chemoradiation is dominated by a basal-like subtype

The paper identifies a basal-like subtype in esophageal adenocarcinoma associated with relapse after chemoradiation and poor survival.

Enhancing the biological insight from limited proteolysis-coupled mass spectrometry

The paper introduces a framework to deconvolve LiP-MS signals and infer protein structural changes using data from three species.

A VHL-1/HIF-1/SQRD1/COL-88 axis links extracellular matrix formation with longevity in Caenorhabditis elegans

This paper identifies a VHL-1/HIF-1/SQRD-1/COL-88 axis linking extracellular matrix formation with longevity in C. elegans, showing that loss of VHL-1 increases lifespan and alters collagen expression.

Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor

This study uses a small molecule inhibitor to rapidly and synchronously induce senescence-like features in human cells, enabling analysis of its core regulatory program without paracrine effects.

No evidence that synonymous mutations in yeast genes are mostly deleterious

The paper reanalyzes data from Shen et al. to argue that most synonymous mutations in yeast genes are not deleterious, challenging their original conclusions about fitness effects.

Aging-associated changes in transcriptional elongation influence metazoan longevity.

This study identifies aging-associated increases in transcriptional elongation speed across multiple species and shows that reducing this speed extends lifespan.

Large-scale changes of molecular network states explain complex traits

The paper identifies a central state transition in yeast molecular networks linked to PKA and TOR signaling, showing how genetic variants can cause global or local molecular changes affecting multiple cellular traits.

Predicting murine age across tissues and cell types using single cell transcriptome data

This paper trains single-cell RNA-seq-based aging clocks to predict mouse age across tissues and cell types, achieving over 90% accuracy in independent tests.

Regulatory network-based imputation of dropouts in single-cell RNA sequencing data

The paper introduces a network-based method for dropout imputation in scRNA-seq data, showing that different genes benefit from different imputation strategies and introducing the ADImpute R-package.

Optimizing Network Propagation for Multi-Omics Data Integration

This paper compares network propagation algorithms for multi-omics data integration and identifies optimal parameter settings for different research questions.

HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence

This study identifies HMGB1 as an RNA-binding protein that coordinates chromatin folding and RNA homeostasis in senescence through interactions with other RBPs and regulation of SASP-related transcripts.

Biological mechanisms of aging predict age-related disease multimorbidities in patients

The paper identifies aging mechanisms that predict age-related disease multimorbidities in humans using literature analysis and clinical data integration.

Deciphering the Signaling Network Landscape of Breast Cancer Improves Drug Sensitivity Prediction

The paper uses single-cell proteomics and perturbation experiments to improve drug sensitivity predictions in breast cancer and identify genomic features associated with treatment response.

Convergent network effects along the axis of gene expression during prostate cancer progression

The paper investigates how genomic alterations affect molecular networks in prostate cancer by integrating genomic, transcriptomic, and proteomic data from 105 samples, identifying a sub-network predictive of tumor aggressiveness and recurrence.

Novel imprints in mouse blastocysts are predominantly DNA methylation independent

The paper identifies novel imprinted genes in mouse blastocysts and shows that their expression is mostly independent of DNA methylation but associated with H3K27me3 marks.

The proteome of small urinary extracellular vesicles after kidney transplantation as an indicator of renal cellular biology and a source for markers predicting outcome

This study identifies PCK2 as a biomarker for renal function 12 months after living donor kidney transplantation using proteomic analysis of urinary extracellular vesicles.

A natural variant of the sole pyruvate kinase of fission yeast lowers glycolytic flux triggering increased respiration and oxidative-stress resistance but decreased growth

The paper identifies a natural variant in fission yeast Pyk1 that reduces glycolytic flux, increases respiration, and enhances oxidative-stress resistance but decreases growth.

Cooperative molecular networks drive a mammalian cell state transition

The paper identifies molecular networks driving the transition from naive to formative pluripotency in mammalian cells using genetic and transcriptomic analyses.

Integration of transcriptome, proteome and phosphoproteome data elucidates the genetic control of molecular networks

This study integrates transcriptome, proteome, and phosphoproteome data from yeast to show how genetic variation affects molecular networks and cellular growth traits, with phosphorylation playing a key role.

Detection of epistatic interactions with Random Forest

This paper develops three methods to detect epistasis using Random Forest, outperforming existing approaches in simulated and real yeast datasets.

Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers

This study quantifies spatial proteome heterogeneity in prostate tissues using multi-region analysis and identifies biomarker variability across benign and malignant tissues.

Individual nephron proteomes connect morphology and function in proteinuric kidney disease

The paper develops a method to analyze individual nephron proteomes in kidney disease, identifying lysosomal protein overexpression as a key mechanism in proteinuric diseases.

Conservation of expression regulation throughout the animal kingdom

The paper develops a method to map tissue-specific gene expression across species without homologous tissue definitions, finding conserved expression programs across diverse taxa.