Frank M. Johannes

vafSOMA: Detecting cell-layer-fixed somatic mutations in plants

vafSOMA detects cell-layer-fixed somatic mutations in plants using tissue composition, improving mutation detection and rate estimation in bulk sequencing data.

The alpine Edelweiss genome reveals a recent allotetraploid origin and localized subgenome dominance

This study presents a chromosome-scale genome assembly of Edelweiss, revealing its recent allotetraploid origin and localized subgenome dominance.

simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants

simSOMA links plant branching topology to meristem cell-lineage dynamics; in simulations, niche size and turnover drive fixation, while terminal organ growth produces most private low-frequency variants.

DNA methylome responses to biotic and abiotic stress in Arabidopsis thaliana: A multi-study analysis

This study integrates 16 Arabidopsis thaliana DNA methylome datasets to identify common and stress-specific methylation responses across biotic and abiotic stress conditions.

Brassinosteroid-regulated transcription factors confer epigenetic changes that repress plant immunity

This study shows brassinosteroids repress plant immunity by inducing DNA methylation and altering splicing of immune receptor genes through bHLH transcription factors.

Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the 1950s

This study analyzes genetic and epigenetic divergence in Arabidopsis thaliana Col-0 laboratory lineages over decades, revealing substantial divergence and functional consequences.

GSNOR-dependent nitric oxide homeostasis promotes recovery from repeated climate stress across generations in Arabidopsis thaliana

This study shows that GSNOR-dependent nitric oxide homeostasis aids recovery from repeated climate stress in Arabidopsis across generations, while its impairment leads to persistent stress responses.

Centromeres are hotspots of cytosine methylation epimutations in a filamentous fungus

The paper identifies centromeres as hotspots for spontaneous DNA methylation epimutations in Neurospora crassa, showing these changes are mitotically stable and occur much more frequently than genetic mutations.

Somatic DNA methylation heterogeneity predicts extreme transgenerational epimutation hotspots in Arabidopsis

The paper identifies somatic DNA methylation heterogeneity in Arabidopsis leaves and links it to transgenerational epimutation hotspots.

Threshold-like transcriptomic responses of European beech to simulated future climates

This study examines the transcriptomic responses of European beech to simulated future climate scenarios, finding stronger responses under the high-emission RCP8.5 scenario compared to the mitigation-focused RCP2.6.

Accelerated growth increases the somatic epimutation rate in trees

This study shows that faster tree growth increases the annual rate of somatic epimutations at CG dinucleotides, likely due to higher cell division rates.

A multi-component power-law penalty corrects distance bias in single-cell co-accessibility and deep-learning chromatin interaction predictions

The paper corrects distance bias in single-cell co-accessibility and deep-learning chromatin interaction predictions using multi-component power-law penalties informed by Gaussian mixture modeling and polymer-physics scaling.

Somatic evolution of stem cell mutations in long-lived plants

The paper estimates parameters of somatic mutation evolution in long-lived plants using cell-layer-enriched DNA sequencing data.

Mapping genetic modifiers of epimutation rates reveals a punctuated-equilibrium model of CG methylome evolution

The paper tracks DNA methylation across generations in Arabidopsis lineages to identify a genetic modifier that increases epimutation rates and supports a punctuated-equilibrium model of methylation evolution.

The genetic architecture of cell-type-specific cis-regulation in maize

The paper identifies cell-type-specific cis-regulatory variants in maize using single-cell genomics and population genetics, revealing their role in local adaptation and flowering.

Branching architecture constrains the accumulation of somatic mutations in trees

The paper shows branching architecture in trees suppresses somatic mutation accumulation, reducing mutation burden as effectively as lowering mutation rates.

Allometric scaling of somatic mutation and epimutation rates in trees

The paper shows that the yearly rate of somatic mutations and epimutations in trees scales inversely with generation time, following the same allometric power law as in mammals.

Multi-generational biotic stress increases the rate of spontaneous epimutations in a ROS1-dependent manner

The paper shows that multi-generational exposure to biotic stress increases epimutation rates in Arabidopsis, mediated by ROS1, affecting low-methylation genes.

Somatic epigenetic drift during shoot branching: a cell lineage-based model

The paper models somatic epigenetic drift during shoot branching, showing that cell lineage independence leads to DNA methylation heterogeneity in the shoot apical meristem.

GenomicLinks: Deep learning predictions of 3Dchromatin loops in the maize genome

GenomicLinks predicts 3D chromatin loops in maize by identifying sequence features associated with transcription factor binding motifs, validated using single-cell co-accessibility data.

Parental pericentromeric methylation status drives methylome remodelling and heterosis in epigenetic hybrids

This study shows that parental pericentromeric methylation patterns drive methylome and transcriptome changes in hybrids, contributing to heterosis in Arabidopsis.

Recursive Convolutional Neural Networks for Epigenomics

This paper introduces a Recursive Convolutional Neural Network for predicting gene expression from histone modification intensity, achieving better performance with fewer parameters.

AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

AlphaBeta estimates epimutation rates and spectra from DNA methylation data in plants, showing conserved epimutation landscapes and providing a molecular clock for tree age-dating.

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

MethylStar is a pre-processing pipeline for WGBS data that improves speed and memory efficiency compared to existing tools.

The somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

The paper quantifies age-related somatic mutations and epimutations in a wild Populus trichocarpa tree over 330 years, showing lower mutation rates than annuals and distinct epimutation origins.

METHimpute: Imputation-guided construction of complete methylomes from WGBS data

METHimpute constructs complete methylomes from low-coverage WGBS data using a Hidden Markov Model, achieving high accuracy at 6X coverage compared to 60X.

Learning sequence patterns of AGO-sRNA affinity from high-throughput sequencing libraries to improve in silico functional small RNA detection and classification in plants

The paper trains SVM models on sRNA sequencing data to identify sequence features determining AGO affinity, leading to a tool for classifying sRNA function in plants.

Small RNAs reflect grandparental environments in apomictic dandelion

The paper shows that small RNAs in apomictic dandelion lineages reflect drought stress and salicylic acid treatment from two generations ago, indicating transgenerational epigenetic effects.