Daniel L. Vera

Multiomic clocks to predict phenotypic age in mice

This paper develops a multi-omic model to predict phenotypic age in mice, showing it can predict remaining lifespan even among same-aged mice.

Measuring technical variability in Illumina DNA methylation microarrays

This study measures technical variability in Illumina DNA methylation microarrays, identifying positional biases and outliers that affect differential methylation testing and predictive modeling.

Novel feature selection methods for construction of accurate epigenetic clocks

This paper develops novel feature selection methods to construct epigenetic clocks with high accuracy using fewer CpG sites, outperforming existing models.

TIME-Seq Enables Scalable and Inexpensive Epigenetic Age Predictions

The paper introduces TIME-Seq, a low-cost method for epigenetic age prediction, and validates it on mouse and human samples, showing improved scalability and accuracy.

DNA Break-Induced Epigenetic Drift as a Cause of Mammalian Aging

The paper shows that DNA double-strand breaks induce epigenomic changes that accelerate the aging clock in mammals.

Erosion of the Epigenetic Landscape and Loss of Cellular Identity as a Cause of Aging in Mammals

The paper shows that inducing DNA breaks accelerates aging-related chromatin changes and loss of cell identity in mammals.

Reversal of ageing- and injury-induced vision loss by Tet-dependent epigenetic reprogramming

This paper demonstrates that epigenetic reprogramming using OSK genes can reverse age-related and injury-induced vision loss in mice by resetting DNA methylation patterns and promoting axon regeneration.

iSeg: an efficient algorithm for segmentation of genomic and epigenomic data

iSeg is an efficient algorithm for genomic and epigenomic segmentation that uses dynamic programming and a novel data structure to identify and refine segments with statistical significance.

Repli-seq: genome-wide analysis of replication timing by next-generation sequencing

This paper introduces a protocol and computational tools for genome-wide replication timing analysis using next-generation sequencing.

SRSF shape analysis for sequencing data reveal newdifferentiating patterns

The paper introduces SRSFseq, a new framework for analyzing sequencing data using shape analysis, which detects differences in read distribution patterns between experimental conditions.