Tommy Kaplan

Ultrasensitive detection of neuronal DNA using genome-wide non-CG methylation patterns

This paper detects neuronal DNA in cfDNA using non-CpG methylation patterns, finding elevated levels in neurological conditions and brain-dead donors.

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.

Cell-to-cell variability and gain of methylation at polycomb CpG islands as a hallmark of aging

The paper identifies average polycomb CpG methylation as a hallmark of cellular aging using single-cell whole-genome methylation data, showing cell-to-cell variability and accelerated aging in faster proliferating cells.

Enriched Methylomes of Low-input and Fragmented DNA Using Fragment Ligation EXclusive Methylation Sequencing (FLEXseq)

The paper introduces FLEXseq, a methylation sequencing method that enriches and sequences DNA fragments flanking the CCGG motif, showing strong correlation with WGBS and potential for diagnostic applications.

The genetic basis for DNA methylation variation across tissues and development

The paper identifies genetic variants influencing DNA methylation across tissues and development in mice and humans, revealing two distinct epigenetic programming periods and linking methylation to regulatory elements and disease variants.

Functional characterization of bat limb regulatory elements

The paper identifies key regulatory elements in bat limb development by comparing bat and mouse genomic datasets and swapping enhancer sequences to observe phenotypic changes.

Systematic errors in enzymatic conversion limit cell-free DNA methylation specificity

The paper identifies a systematic over-conversion error in EM-seq that introduces false-positive methylation signals in cfDNA analysis.

Loss of Brain Structural qMRI Signatures in Aging

This study examines age-related changes in brain microstructure using qMRI, finding increased regional similarity and individual variability in older adults.

Time is encoded by methylation changes at clustered CpG sites

The paper shows that DNA methylation changes at clustered CpG sites encode chronological age with high accuracy using deep learning on blood samples.

Atlas of imprinted and allele-specific DNA methylation in the human body

The paper creates a comprehensive atlas of allele-specific DNA methylation across 39 human cell types, identifying 325k genomic regions and 460 novel imprinted loci with cell-type-specific patterns.

wgbstools: A computational suite for DNA methylation sequencing data representation, visualization, and analysis

wgbstools provides a computational suite for DNA methylation sequencing data representation, visualization, and analysis, enabling fragment-level analysis and integration with genetic data.

Accurate age prediction from blood using of small set of DNA methylation sites and a cohort-based machine learning algorithm

The paper introduces GP-age, a DNA methylation-based age prediction model using 30 CpG sites and a cohort-based machine learning approach, achieving high accuracy on both array and sequencing data.

A human DNA methylation atlas reveals principles of cell type-specific methylation and identifies thousands of cell type-specific regulatory elements

The paper constructs a human DNA methylation atlas using whole-genome bisulfite sequencing of 39 cell types, revealing cell type-specific methylation patterns and regulatory elements.

Comparative Parallel Multi-Omics Analysis During the Induction of Pluripotent and Trophectoderm States

This study compares the reprogramming dynamics of pluripotent and trophoblast stem cell states using multi-omics analysis, revealing distinct trajectories and reprogramming markers.

The H3K27me3 epigenetic mark is crucial for callus cell identity and for the acquisition of new fate during root and shoot regeneration

The paper investigates the role of H3K27me3 in maintaining chromatin accessibility of developmental genes in Arabidopsis callus cells, showing its necessity for regeneration and fate acquisition.

Remote immune processes revealed by immune-derived circulating cell-free DNA

The paper uses immune cell type-specific methylation patterns in circulating cell-free DNA to monitor immune dynamics and find that immune-derived cfDNA levels reflect immune homeostasis and predict immune responses to perturbations.

ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs

The paper introduces cfChIP-seq to analyze cell-free nucleosomes and shows it can detect disease-related transcriptional changes and patient-specific features in cancer.

Gene Activation and repression by the glucocorticoid receptor are mediated by sequestering Ep300 and two modes of chromatin binding

This study identifies how the glucocorticoid receptor (GR) activates or represses genes by sequestering Ep300 and interacting with other transcription factors in 3D chromatin structures.

Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease

The paper develops a method to determine the tissue origins of circulating cell-free DNA using a methylation atlas and validates it in healthy and disease states.

Enhancer Identification using Transfer and Adversarial Deep Learning of DNA Sequences

This paper trains deep CNNs to identify enhancer sequences across species using transfer learning and adversarial training, finding shared regulatory motifs and improved classification accuracy.

GEM: A manifold learning based framework for reconstructing spatial organizations of chromosomes

GEM reconstructs 3D chromatin structures from Hi-C data using manifold learning and conformational energy, outperforming existing methods and recovering long-range interactions.

Promoter-Enhancer Interactions Identified from Hi-C Data using Probabilistic Models and Hierarchical Topological Domains

The paper introduces PSYCHIC, a method to identify promoter-enhancer interactions from Hi-C data, revealing extensive gene regulation catalogs in human and mouse.

Genome-wide Search for Zelda-like Chromatin Signatures Identifies GAF as a Pioneer Factor in Early Fly Development

The paper identifies GAF as a pioneer factor in early Drosophila development by analyzing chromatin signatures around Zelda peaks and finding Zelda-independent enhancers.