Steve Hoffmann

Expression trajectories in the aging male mouse colon transcriptome

This study identifies nonlinear gene-expression trajectories in the aging male mouse colon, revealing midlife transitions and a transcriptomic clock based on three genes.

An improved epigenetic age estimation with TFMethyl Clock reveals DNA methylation changes during aging in transcription factor binding sites

The paper improves epigenetic age estimation by developing a TFMethyl Clock model that incorporates transcription factor binding sites, revealing DNA methylation changes linked to aging.

Distinct Effects of Aging and Klotho Deletion on the Choroid Plexus

This study examines how aging and Klotho deletion affect choroid plexus structure and function, finding that Klotho deficiency increases age-related calcification in specific regions.

Aging reprograms the response to chronic stress

This study shows that chronic stress accelerates brain aging in young mice but activates age-specific anti-aging programs in old mice.

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold-standard

The paper benchmarks DNA methylation sequencing workflows against an experimental gold-standard, identifying superior workflows and developing a sustainable benchmarking platform.

Multi-omics analysis highlights the link of aging-related cognitive decline with systemic inflammation and alterations of tissue-maintenance

The paper integrates multi-omics data from mice to identify molecular features linked to aging-related cognitive decline, highlighting systemic inflammation and microbiome-driven gut-brain axis dysfunction.

The Aging Synapse: An Integrated Proteomic And Transcriptomic Analysis

This study investigates changes in the synaptic proteome and transcriptome during aging, revealing decoupling between transcripts and proteins and altered ribosomal gene distribution.

The Greenland shark (Somniosus microcephalus) genome provides insights into extremelongevity

The paper presents a chromosome-level genome assembly of the Greenland shark and identifies genomic features associated with its extreme longevity.

Transthyretin orchestrates vitamin B12-induced stress resilience

This study identifies Transthyretin as a sex-specific target of vitamin B12 that influences stress resilience through DNA methylation changes in the prefrontal cortex.

Inactivation of the DREAM complex mimics the molecular benefits of sleep.

This study identifies the DREAM complex as a mediator of sleep and circadian benefits, showing that inhibiting DREAM can mimic sleep's cellular repair effects in sleep-deprived organisms.

Npbwr1 signaling mediates fast antidepressant action

This study identifies Npbwr1 as a key regulator of depressive-like symptoms and shows that its antagonist CYM50769 rapidly alleviates these symptoms in mice.

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

The paper benchmarks 16 circRNA detection tools across three human cell types, finding large differences in sensitivity but consistent precision, and recommends tool combinations for improved detection.

Multi-omics analysis identifies RFX7 targets involved in tumor suppression and neuronal processes

The paper identifies RFX7 target genes through multi-omics analysis, revealing their role in tumor suppression and neuronal processes.

Age-associated changes in endothelial transcriptome and chromatin landscape correlate with elevated risk of hemorrhage

The paper investigates age-related changes in endothelial cells of mice, identifying gene and chromatin alterations linked to increased intracerebral hemorrhage risk.

TargetGeneReg 2.0: a comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation

TargetGeneReg 2.0 expands its database to include non-coding genes and new transcription factors, enabling analysis of gene regulation by p53, ΔNp63, and cell cycle signaling.

Transcription factor RFX7 governs a tumor suppressor network in response to p53 and stress

This study identifies RFX7 as a p53-regulated tumor suppressor that activates key genes involved in cell differentiation and apoptosis in response to stress.

The HPA stress axis shapes aging rates in long-lived, social mole-rats

The paper investigates how the HPA stress axis influences aging in long-lived mole-rats, finding that reproductive status affects stress regulation and lifespan.

Dissecting the DNA binding landscape and gene regulatory network of p63 and p53

The paper identifies p63 binding sites and predicts its gene regulatory network using ChIP-seq data and motif analysis, highlighting potential therapeutic targets in SCC.

Bashing irreproducibility with shournal

The paper introduces shournal, a tool that automatically records Linux shell activity to improve reproducibility of computational workflows.

Higher transcriptome stability during aging in long-lived giant mole-rats compared to short-lived rats

This study compares transcriptome stability during aging between long-lived giant mole-rats and short-lived rats, finding greater stability in mole-rats.

Disturbance of poised chromatin coincides with increased expression of developmental genes in cancer

The paper shows that hypermethylation of poised chromatin and up-regulation of corresponding developmental genes is a common feature in cancer, using large-scale expression and methylation data.